gebhart/patrepeval huggingface dataset:
Stochastic effects in 11 nm imaging of extreme ultraviolet lithography with chemically amplified resists (2014)

The resolution of extreme ultraviolet (EUV) lithography with chemically amplified resist processes has reached 16 nm (half-pitch). The development of chemically amplified resists is ongoing toward the 11 nm node. However, the stochastic effects are increasingly becoming a significant concern with the continuing shrinkage of features. In this study, the fluctuation of protected unit distribution caused by the stochastic effects during image formation was investigated assuming line-and-space patterns with 11 nm half-pitch. Contrary to expectations, the standard deviation of the number of protected units connected to a polymer after postexposure baking (PEB) did not differ from that for 16 nm half-pitch. The standard deviation after PEB increased with the effective reaction radius for deprotection and the initial standard deviation before PEB. Because of the severe requirements for resist processes, the stochastic effects in chemical reactions should be taken into account in the design of next-generation resists.
Application of an equation‐oriented framework to formulate and estimate parameters of chemical looping reaction models (2022)

Abstract Accurate, predictive reaction models are critical for the design and optimization of chemical looping combustion (CLC) reactors. The formulation and estimation of kinetic parameters for these reaction models using a first‐principles equation‐oriented (EO) approach is particularly beneficial as large amounts of experimental data spanning process‐relevant conditions can be used to estimate parameters in a computationally tractable way. This work demonstrates the application of a novel EO framework to develop reduction reaction kinetic models of an iron‐based CLC oxygen carrier (OC). An optimization problem is formulated to estimate kinetic parameters that provide the best fit to the experimental data. The model predicts the state of the OC with mean square error values of 2.5%–4.4% across the full range of validation data, including multiple reduction cycles.
Imaging Virus-Associated Cancer (2008)

Cancer remains an important and growing health problem. Researchers have made great progress in defining genetic and molecular alterations that contribute to cancer formation and progression. Molecular imaging can identify appropriate patients for targeted cancer therapy and may detect early biochemical changes in tumors during therapy, some of which may have important prognostic implications. Progress in this field continues largely due to a union between molecular genetics and advanced imaging technology. This review details uses of molecular-genetic imaging in the context of tumor-associated viruses. Under certain conditions, and particularly during pharmacologic stimulation, gammaherpesviruses will express genes that enable imaging and therapy in vivo. The techniques discussed are readily translatable to the clinic.
Virus-specific Activation of a Novel Interferon Regulatory Factor, IRF-5, Results in the Induction of Distinct Interferon α Genes (2001)

Interferon regulatory factor (IRF) genes encode DNA-binding proteins that are involved in the innate immune response to infection. Two of these proteins, IRF-3 and IRF-7, serve as direct transducers of virus-mediated signaling and play critical roles in the induction of type I interferon genes. We have now shown that another factor, IRF-5, participates in the induction of interferon A (IFNA) and IFNB genes and can replace the requirement for IRF-7 in the induction of IFNA genes. We demonstrate that, despite the functional similarity, IRF-5 possesses unique characteristics and does not have a redundant role. Thus, 1) activation of IRF-5 by phosphorylation is virus-specific, and its in vivo association with the IFNA promoter can be detected only in cells infected with NDV, not Sendai virus, while both viruses activate IRF-3 and IRF-7, and 2) NDV infection of IRF-5-overexpressing cells preferentially induced the IFNA8 subtype, while IFNA1 was primarily induced in IRF-7 expressing cells. These data indicate that multiple signaling pathways induced by infection may be differentially recognized by members of the IRF family and modulate transcription of individual IFNA genes in a virus and cell type-specific manner.
Water-Borne Transmission of Influenza A Viruses? (1979)

The isolation of influenza A viruses from unconcentrated lake water and from fecal samples on the shore of these lakes is reported for the first time. Influenza A viruses, representative of most of the major antigenic subtypes, co-circulate in ducks on the lakes.
Spatial relationship between human well-being and community capital in the Black Belt region of Alabama (2010)

This paper examines the relationship between human well-being and forms of community capital in the eight Black Belt counties in the west-central region of Alabama. This region is one of the poorest in the United States with high proportion of African-American populations. Cross-sectional spatial regression models were estimated using the data from the U.S. Population and Economic Census, Geographic Information System, and satellite imageries of 2000. The results indicate that geographic space is highly segregated in these counties and African Americans are less likely to be found in areas high in built, natural, and political capital. Service-providing entities such as financial, industrial, and social capital are located more in urbanized centers. The results suggest that social capital is strongly correlated with human well-being. The findings provide spatially-explicit empirical insights and suggest targeting rural development policies to create more social capital and address specific needs of the region, especially of African-American populations.

	 

	Key words: African Americans, census data, land cover, proximity, rural, social capital, spatial.
Histamine H3 receptor ligands with a 3-cyclobutoxy motif: a novel and versatile constraint of the classical 3-propoxy linker (2010)

Antagonists/inverse agonists for the histamine H3 receptor (H3R) are subject to intensive research. Many chemical classes contain a 3-propoxy linker to connect an aromatic moiety and a basic amine. Rigidifying this linker by several moieties has proven successful. However, so far, a 3-cyclobutoxy constraint has not been disclosed in H3R research. Here, we present novel synthetic methodology toward compounds with this functionality. A condensation between piperidine and 1,3-cyclobutanedione followed by a reduction furnishes a versatile cis-3-piperidino-cyclobutanol building block which allows ready access to constrained compounds having a 3-piperidino-cyclobutoxy moiety. Pharmacological studies reveal that this particular rigidification leads to a significant increase in H3R affinity compared to the non-constrained counterpart. In all, the constrained 3-cyclobutoxy linker emerges as a novel, versatile and attractive motif for H3R ligands.
Interpretable Approximation of a Deep Reinforcement Learning Agent as a Set of If-Then Rules (2019)

In many industrial applications, one of the major bottlenecks in using advanced learning-based methods (such as reinforcement learning) for controls is the lack of interpretability of the trained agent. In this paper, we present a methodology for translating a trained reinforcement learning agent into a set of simple and easy to interpret if-then rules by using the proven universal approximation property of the rules with fuzzy predicates. Proposed methodology combines the optimality of reinforcement learning with interpretability of the theory of approximate reasoning, thus making reinforcement learning-based solutions more accessible to industrial practitioners. The framework presented in this paper has the potential to help address the fundamental problem in widespread adoption of reinforcement learning in industrial applications.
Preview control for impulse-free continuous-time descriptor systems (2014)

This paper studies the preview control problem of impulse-free linear continuous-time descriptor systems. The system is first decomposed into a normal system (i.e., slow subsystem) and an algebraic equation set, by restricted equivalent linear transformation. Then, applying the method of preview control theory to the slow subsystem, by taking derivatives on both the error vector and the state function, and with the error vector being a part of the new state vector, the augmented system is constructed and the tracking problem is transformed into a regulation problem. According to preview control theory, the controller of the augmented system can be obtained and the control input of the original descriptor system with preview function can be acquired by integrating on the controller of the augmented system. Both the stabilisability and detectability of the augmented system are discussed. Numerical simulation verifies the presented results.
Variability of water uptake studies of biomedical polymers (2011)

Abstract Water uptake influences many properties of polymers and has been widely studied. In the context of polymeric biomaterials, several publications reported an unusual high variability of analytical results, without further investigating the cause for this phenomenon. Using selected polymers from the library of L ‐tyrosine‐derived polyarylates and poly( D , L lactic acid), we showed that nonaged and nonannealed compression molded film samples exhibit the typical large variation in water uptake observed in previous reports. The introduction of an annealing step allows accurate and reproducible water uptake measurements for these polymers. We evaluated the use of 3 H‐radiolabeled water for the determination of water uptake, finding that the use of radiolabeled water yields statistically indistinguishable measurements, compared to gravimetric methods, while providing significant advantages in throughput and sensitivity. Using the recommended methods of annealing and 3 H‐radiolabled water, the water uptake profiles of 24 polymers of the library of L ‐tyrosine‐derived polyarylates are reported. This article addresses experimental concerns related to water uptake studies and may assist other researchers in improving the accuracy of their water uptake results. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Supplementary information;Supplementary tables from A multi-sensory code for emotional arousal (2019)

People express emotion using their voice, face and movement, as well as through abstract forms as in art, architecture and music. The structure of these expressions often seems intuitively linked to its meaning: e.g. romantic poetry is written in flowery curlicues, while the logos of death metal bands use spiky script. Here, we show that these associations are universally understood because they are signalled using a multi-sensory code for emotional arousal. Specifically, variation in the central tendency of the frequency spectrum of a stimulus—its spectral centroid—is used by signal senders to express emotional arousal, and by signal receivers to make emotional arousal judgements. We show that this code is used across sounds, shapes, speech and human body movements, providing a strong multi-sensory signal that can be used to efficiently estimate an agent's level of emotional arousal.
Isolated limb perfusion with the tumor‐targeting human monoclonal antibody–cytokine fusion protein L19‐TNF plus melphalan and mild hyperthermia in patients with locally advanced extremity melanoma (2012)

ILP with L19-TNF had a favorable safety and a promising activity profile at a dose of 650 µg of L19-TNF, supporting the exploration of higher L19-TNF doses and a Phase II trial comparing L19-TNF ILP with standard melphalan-containing ILP.
Transgenic Expression of the Mitochondrial Chaperone TNFR-associated Protein 1 (TRAP1) Accelerates Prostate Cancer Development (2016)

Protein homeostasis, or proteostasis, is required for mitochondrial function, but its role in cancer is controversial. Here we show that transgenic mice expressing the mitochondrial chaperone TNFR-associated protein 1 (TRAP1) in the prostate develop epithelial hyperplasia and cellular atypia. When examined on a Pten<sup>+/-</sup> background, a common alteration in human prostate cancer, TRAP1 transgenic mice showed accelerated incidence of invasive prostatic adenocarcinoma, characterized by increased cell proliferation and reduced apoptosis, in situ Conversely, homozygous deletion of TRAP1 delays prostatic tumorigenesis in Pten<sup>+/-</sup> mice without affecting hyperplasia or prostatic intraepithelial neoplasia. Global profiling of Pten<sup>+/-</sup>-TRAP1 transgenic mice by RNA sequencing and reverse phase protein array reveals modulation of oncogenic networks of cell proliferation, apoptosis, cell motility, and DNA damage. Mechanistically, reconstitution of Pten<sup>+/-</sup> prostatic epithelial cells with TRAP1 increases cell proliferation, reduces apoptosis, and promotes cell invasion without changes in mitochondrial bioenergetics. Therefore, TRAP1 is a driver of prostate cancer in vivo and an "actionable" therapeutic target.
Visions & Reflections The SARS-CoV S glycoprotein (2004)

The severe acute respiratory syndrome-coro- navirus (SARS-CoV) spike (S) glycoprotein alone can mediate the membrane fusion required for virus entry and cell fusion. It is also a major immunogen and a target for
Utilizing field usage patterns for Java heap space optimization (2006)

This research studies the characteristics of field usage patterns in the SpecJVM98 benchmarks. It finds that multiple object instances of the same class often exhibit different field-usage patterns. Motivated by this observation, we designed a heap compression mechanism that classifies object instances at runtime based on their field-usage patterns and eliminates unused fields to save space. To achieve the maximum space savings while minimizing the space and time overhead, our design combines three interrelated techniques in a novel manner: runtime object instance classification, field virtualization, and bidirectional object layout. An experimental evaluation reveals that this mechanism can reduce the maximum heap occupancy of SpecJVM98 benchmarks by up to 18% and 14% on average while keeping the application execution overhead low.
Pollen contamination in seed mixture increases the dominance of resistance to Bt maize in Spodoptera frugiperda (Lepidoptera: Noctuidae) (2017)

The results suggest that pollen contamination in RIB could increase the dominance of resistance for ear-feeding insects by significantly reducing susceptible refuge populations and supporting higher survival of heterozygotes relative to homozygous susceptible insects. © 2017 Society of Chemical Industry.
Inter-α-inhibitor heavy chain-1 has an integrin-like 3D structure mediating immune regulatory activities and matrix stabilization during ovulation (2020)

Inter-α-inhibitor is a proteoglycan essential for mammalian reproduction and also plays a less well-characterized role in inflammation. It comprises two homologous "heavy chains" (HC1 and HC2) covalently attached to chondroitin sulfate on the bikunin core protein. Before ovulation, HCs are transferred onto the polysaccharide hyaluronan (HA) to form covalent HC·HA complexes, thereby stabilizing an extracellular matrix around the oocyte required for fertilization. Additionally, such complexes form during inflammatory processes and mediate leukocyte adhesion in the synovial fluids of arthritis patients and protect against sepsis. Here using X-ray crystallography, we show that human HC1 has a structure similar to integrin β-chains, with a von Willebrand factor A domain containing a functional metal ion-dependent adhesion site (MIDAS) and an associated hybrid domain. A comparison of the WT protein and a variant with an impaired MIDAS (but otherwise structurally identical) by small-angle X-ray scattering and analytical ultracentrifugation revealed that HC1 self-associates in a cation-dependent manner, providing a mechanism for HC·HA cross-linking and matrix stabilization. Surprisingly, unlike integrins, HC1 interacted with RGD-containing ligands, such as fibronectin, vitronectin, and the latency-associated peptides of transforming growth factor β, in a MIDAS/cation-independent manner. However, HC1 utilizes its MIDAS motif to bind to and inhibit the cleavage of complement C3, and small-angle X-ray scattering-based modeling indicates that this occurs through the inhibition of the alternative pathway C3 convertase. These findings provide detailed structural and functional insights into HC1 as a regulator of innate immunity and further elucidate the role of HC·HA complexes in inflammation and ovulation.
Plasma levels of hepatocyte growth factor and placental growth factor predict mortality in a general population: a prospective cohort study (2017)

Background

Circulating levels of growth factors involved in leucocyte production and angiogenesis could be indicative of underlying aberrations of tissue homeostasis and therefore be utilized as predictors of risk for all-cause cardiovascular disease (CVD) or cancer mortality.
Methods

Baseline plasma levels of a range of growth factors were measured in two cohorts of the population-based FINRISK study (1997 Discovery cohort, N = 8444, aged 25–74; 2002 Replication cohort, N = 2951, aged 51–74 years) using a multiplexed bead array methodology and ELISA. Participants were followed up by linking them to registry data.
Results

In the Discovery cohort (653 deaths; 216 CVD-related, 231 cancer-related), fully adjusted Cox proportional hazard regression models showed that increased plasma hepatocyte growth factor (HGF) and placental growth factor (PlGF) were associated with higher risk of 10-year mortality (HR, 1.29 [95% confidence interval (CI), 1.18–1.41] and HR, 1.23 [95% CI, 1.14–1.32], respectively). In the Replication cohort (259 deaths; 83 CVD-related, 90 cancer-related), baseline HGF levels also predicted all-cause mortality (HR, 1.2 [95% CI, 1.08–1.32]; PlGF data not available). By including HGF levels in a CVD mortality model, 9% of all CVD deaths were correctly reclassified in the Discovery cohort (categorical net reclassification improvement [NRI] for events, P = 4.0 × 10−4). Moreover, adding HGF to all-cause and CVD mortality models resulted in an overall clinical NRI of 0.10–0.18 in the Discovery cohort and meta-analyses (P < 0.05 for all tests).
Conclusion

Blood levels of HGF and PlGF may serve as new biomarkers for predicting increased risk of death in the general population.
Quantitative temporally and spatially resolved X-ray fluorescence microprobe characterization of the manganese dissolution-deposition mechanism in aqueous Zn/α-MnO2 batteries (2020)

<italic>Operando</italic>, spatiotemporal resolved synchrotron X-ray fluorescence mapping measurements on a custom aqueous Zn/α-MnO<sub>2</sub> cell provided direct, quantitative evidence of a Mn dissolution-deposition faradaic mechanism that governs the electrochemistry.
Treatment of Atopic Dermatitis Associated with Malassezia sympodialis by Green Tea Extracts Bath Therapy: A Pilot Study (2012)

Multiple treatment modalities, including topical and systemic corticosteroid and phototherapy, have been used in treatment of patients with atopic dermatitis. However, long-term corticosteroid therapy may have various adverse effects. The purpose of this study was to investigate the therapeutic efficacy and safety of bath therapy using green tea extracts for treatment of patients with atopic dermatitis. A total of four patients with atopic dermatitis were enrolled in this study. A Malassezia multiplex detection kit was used in performance of multiplex PCR on clinical isolates, which confirmed Malassezia sympodialis. Subjects underwent treatment with bath therapy using green tea extracts three times per wk for a period of 4 wk. Assessment using the scoring atopic dermatitis (SCORAD) index, the visual analogue scale for pruritus, and transepidermal water loss was performed weekly. Laboratory tests were performed before and after treatment. All patients showed marked improvement on the mean SCORAD and visual analogue scale, and a significant decrease in the mean values of serum eosinophil counts was observed after treatment. Bath therapy with green tea extract is an effective, safe, and nonsteroidal therapy for treatment of patients with atopic dermatitis associated with Malassezia sympodialis.
The Enzymatic Activity of Apoptosis-inducing Factor Supports Energy Metabolism Benefiting the Growth and Invasiveness of Advanced Prostate Cancer Cells (2012)

Apoptosis-inducing factor (AIF) promotes cell death yet also controls mitochondrial homeostasis and energy metabolism. It is unclear how these activities are coordinated, and the impact of AIF upon human disease, in particular cancer, is not well documented. In this study we have explored the contribution of AIF to the progression of prostate cancer. Analysis of archival gene expression data demonstrated that AIF transcript levels are elevated in human prostate cancer, and we found that AIF protein is increased in prostate tumors. Suppression of AIF expression in the prostate cancer cell lines LNCaP, DU145, and PC3 demonstrated that AIF does not contribute to cell toxicity via a variety of chemical death triggers, and growth under nutrient-rich conditions is largely unaffected by AIF ablation. However, under growth stress conditions, AIF depletion from DU145 and PC3 cell lines led to significant reductions in cell survival and growth that were not observed in LNCaP cells. Moreover AIF-deficient PC3 cells exhibited substantial reduction of tumorigenic growth in vivo. This reduced survival correlated with decreased expression of mitochondrial complex I protein subunits and concomitant changes in glucose metabolism. Finally, restoration of AIF-deficient PC3 cells with AIF variants demonstrated that the enzymatic activity of AIF is required for aggressive growth. Overall these studies show that AIF is an important factor for advanced prostate cancer cells and that through control of energy metabolism and redox balance, the enzymatic activity of AIF is critical for this support.
A Wireless Sensor Network for Structural Health Monitoring: Performance and Experience (2005)

While sensor network research has made significant strides in the past few years, the literature has relatively few examples of papers that have evaluated and validated a complete experimental system. In this paper, we discuss our deployment experiences and evaluate the performance of a multi-hop wireless data acquisition system (called Wisden) for structural health monitoring (SHM) on a large seismic test structure used by civil engineers. Our experiments indicate that, with the latest sensor network hardware, Wisden can reliably deliver time-synchronized tri-axial structural vibration data reliably across multiple hops with low latencies for sampling rates up to 200 Hz. This performance was achieved by iteratively refining the system design using a series of test deployments. Our experiences suggested the need for careful onset detection in order to preserve the fidelity of the structure's frequency response. Furthermore, the high damping characteristics of large structures motivated an exploration of the processing, sampling, and communication limits of current platforms.
A short synthesis of 5′‐O‐trityl‐protected threo‐ and erythro‐ 3′‐cyano‐3′‐deoxythymidine epimers using free‐radical chemistry (1992)

Abstract A reinvestigation of a synthetic route to 5′‐ O ‐trityl‐protected erythro ‐CNT that incorporates a modification of the Stork radical cyclization‐cyanation reaction generates an unexpected threo ‐epimer.
Semi-quantitative design of black phosphorous field-effect transistor sensors for heavy metal ion detection in aqueous media (2018)

A statistical thermodynamics model was developed to illuminate sensing mechanisms and guide design of field-effect transistor sensors using 2D nanomaterials.