gebhart/patrepeval huggingface dataset:
Biological Transmission of Arboviruses: Reexamination of and New Insights into Components, Mechanisms, and Unique Traits as Well as Their Evolutionary Trends (2005)

Among animal viruses, arboviruses are unique in that they depend on arthropod vectors for transmission. Field research and laboratory investigations related to the three components of this unique mode of transmission, virus, vector, and vertebrate host, have produced an enormous amount of valuable information that may be found in numerous publications. However, despite many reviews on specific viruses, diseases, or interests, a systematic approach to organizing the available information on all facets of biological transmission and then to interpret it in the context of the evolutionary process has not been attempted before. Such an attempt in this review clearly demonstrates tremendous progress made worldwide to characterize the viruses, to comprehend disease transmission and pathogenesis, and to understand the biology of vectors and their role in transmission. The rapid progress in molecular biologic techniques also helped resolve many virologic puzzles and yielded highly valuable data hitherto unavailable, such as characterization of virus receptors, the genetic basis of vertebrate resistance to viral infection, and phylogenetic evidence of the history of host range shifts in arboviruses. However, glaring gaps in knowledge of many critical subjects, such as the mechanism of viral persistence and the existence of vertebrate reservoirs, are still evident. Furthermore, with the accumulated data, new questions were raised, such as evolutionary directions of virus virulence and of host range. Although many fundamental questions on the evolution of this unique mode of transmission remained unresolved in the absence of a fossil record, available observations for arboviruses and the information derived from studies in other fields of the biological sciences suggested convergent evolution as a plausible process. Overall, discussion of the diverse range of theories proposed and observations made by many investigators was found to be highly valuable for sorting out the possible mechanism(s) of the emergence of arboviral diseases.
Chemokine Receptor-5Δ32 Mutation is No Risk Factor for Ischemic-Type Biliary Lesion in Liver Transplantation (2009)

It has been shown that certain chemokine receptor polymorphisms may correspond to certain complications after organ transplantation. Ischemic-type biliary lesion (ITBL) encounters for major morbidity and mortality in liver transplant recipients. So far, the exact cause for ITBL remains unclear. Certain risk factors for the development of ITBL like donor age and cold ischemic time are well described. In a previous study, a 32-nucleotide deletion of the chemokine receptor-5Delta32 (CCR-5Delta32) was strongly associated with the incidence of ITBL in adult liver transplantation. This study re-evaluates the association of CCR-5Delta32 gene polymorphism and the incidence of ITBL. 169 patients were included into this retrospective analysis. 134 patients were homozygous for wild-type CCR-5, 33 patients heterozygous, and 2 patients were homozygous for CCR-5Delta32 mutation. There were no major differences in donor or recipients demographics. No association was found between CCR-5Delta32 mutation and the development of ITBL. We conclude that CCR-5Delta32 is no risk factor for the development of ITBL in our patient cohort.
How small-molecule inhibitors of dengue-virus infection interfere with viral membrane fusion (2018)

Dengue virus (DV) is a compact, icosahedrally symmetric, enveloped particle, covered by 90 dimers of envelope protein (E), which mediates viral attachment and membrane fusion. Fusion requires a dimer-to-trimer transition and membrane engagement of hydrophobic 'fusion loops'. We previously characterized the steps in membrane fusion for the related West Nile virus (WNV), using recombinant, WNV virus-like particles (VLPs) for single-particle experiments (Chao et al., 2014). Trimerization and membrane engagement are rate-limiting; fusion requires at least two adjacent trimers; availability of competent monomers within the contact zone between virus and target membrane creates a trimerization bottleneck. We now report an extension of that work to dengue VLPs, from all four serotypes, finding an essentially similar mechanism. Small-molecule inhibitors of dengue virus infection that target E block its fusion-inducing conformational change. We show that ~12-14 bound molecules per particle (~20-25% occupancy) completely prevent fusion, consistent with the proposed mechanism.
Ritens aktörer : En studie över rituella utövare i Sydskandinavien under bronsåldern (2010)

Mainly focusing on the big picture regarding the research concerning the religious sphere in Bronze Age Scandinavia, the research field has been missing out on the smaller picture. The results have a tendency to produce a picture where the big landscape monuments, social structures and cosmology appear in the foreground. This essay is a comment to this phenomena and a methodological and terminological discussion regarding the way in which we as archaeologist’s works with questions about religion and rites. The main task though is to make an attempt in trying to identify the ritual performers and to answer the question whether it's possible or not to do that. This kind of work needs empirical studies with a theoretical background. The grave material can be the key to find these individuals since it's a context where the person’s belongings can be connected with the individual. The theoretical stance is that the Bronze Age research has been unable to identify these performers and that this in factcan be done. The etuis of belongings discovered for the first time in 1845 with the archaeological excavation of the Hvidegaard grave outside Copenhagen in Denmark, containing objects referred to as magical objects, can be one way to make these actors of rites come alive.The etuis of belongings and other grave material are presented in this work and a discussion about the graves material is made. The approach to study the bigger picture by studying the small empirical material is also made in this essay where a model of the ritual sphere is presented in the results with an attempt to show a none official cult existing side by side and in interaction with the official one.
ChemInform Abstract: PRODUCTION OF HYDROGEN BY ULTRAVIOLET IRRADIATION OF BINUCLEAR MOLYBDENUM(II) COMPLEXES IN ACIDIC AQUEOUS SOLUTIONS. OBSERVATION OF MOLYBDENUM HYDRIDE INTERMEDIATES IN OCTAHALODIMOLYBDATE(II) PHOTOREACTIONS (1978)

Abstract Die Photoredoxreaktionen A‐Cwerden untersucht und die Quantenausbb.
Identificación y caracterización de esterasas de Lactobacillus plantarum con interés en tecnología de alimentos (2013)

Resumen del trabajo presentado a la 7ª Reunión de la Red Tematica Bal: "Participación de las Bacterias Lácticas en la Salud Humana y en la Calidad Alimentaria" celebrado en Madrid del 4 al 5 de julio de 2013.
Downlink Transmission of Broadband OFCDM Systems—Part I: Hybrid Detection (2005)

The broadband orthogonal frequency and code division multiplexing (OFCDM) system with two-dimensional spreading (time and frequency domain spreading) is becoming a very attractive technique for high-rate data transmission in future wireless communication systems. In this paper, a quasianalytical study is presented on the downlink performance of the OFCDM system with hybrid multi-code interference (MCI) cancellation and minimum mean square error (MMSE) detection. The weights of MMSE are derived and updated stage by stage of MCI cancellation. The effects of channel estimation errors and sub-carrier correlation are also studied. It is shown that the hybrid detection scheme performs much better than pure MMSE when good channel estimation is guaranteed. The power ratio between the pilot channel and all data channels should be set to 0.25, which is a near optimum value for the two-dimensional spreading system with time domain spreading factor (N/sub T/) of 4 and 8. On the other hand, in a slow fading channel, a large value of the channel estimation window size /spl gamma/N/sub T/, where /spl gamma/ is an odd integer, is expected. However, /spl gamma/=3 is large enough for the system with N/sub T/=8 while /spl gamma/=5 is more desirable for the system with N/sub T/=4. Although performance of the hybrid detection degrades in the presence of the sub-carrier correlation, the hybrid detection still works well even the correlation coefficient is as high as 0.7. Finally, given N/sub T/, although performance improves when the frequency domain spreading factor (N/sub F/) increases, the frequency diversity gain is almost saturated for a large value of N/sub F/ (i.e., N/sub F/ /spl ges/ 32).
Average quantizer adaptation rates for stable ADPCM (2002)

This paper gives a sufficient condition on the average rate of quantizer step size adaptation rate that preserves adaptive differential pulse code modulated (ADPCM) stability under the assumption that the predictor is nonadaptive. The result appeals to some new developments in the passivity analysis of linear time varying systems.
Single Image Super-Resolution Based on Support Vector Regression (2007)

Motivated by the success of support vector regression (SVR) in blind image deconvolution, we apply SVR to single-frame super-resolution. Initial results show that even when trained on as little as a single image, SVR is able to learn a generally applicable model that can super-resolve dissimilar images.
Static Time-of-Flight Secondary Ion Mass Spectrometry of Monolayers on Scribed Silicon Derived from 1-Alkenes, 1-Alkynes, and 1-Haloalkanes (2002)

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) was performed on monolayers prepared by scribing silicon under a homologous series of 1-alkenes, 1-alkynes, and 1-haloalkanes: CH2CH(CH2)nCH3 (n = 2, 5, 9), HC⋮C(CH2)nCH3 (n = 2, 5, 9), Cl(CH2)nCH3 (n = 4, 7, 9), Br(CH2)nCH3 (n = 4, 7, 11), I(CH2)nCH3 (n = 0, 1, 2, 4, 7, 11), and I13CH3. Numerous SiCxHy+ and CxHy+ fragments and adduct ions were observed. The results support a proposed binding model that 1-haloalkanes bind to the silicon surface through one C−Si bond and that 1-alkenes and 1-alkynes generally bind through two C−Si bonds. For instance, silicon surfaces scribed under 1-haloalkanes show less carbon by X-ray photoelectron spectroscopy (XPS) than silicon scribed under 1-alkenes and 1-alkynes with the same number of carbon atoms, but they show more intense SiCxHy+ fragments by ToF-SIMS. Above a certain chain length, the relative intensities of the fragment and adduct ions for a homologous series generally increase with increasing alkyl chain length, which is in agreement with carbon surface coverages measured by XPS and the proposed binding models. Anomalously strong SiCH3+ and SiC2H5+ fragments observed in silicon scribed under CH3I and CH3CH2I suggest formation of methyl- and ethyl-terminated silicon, respectively. An isotopic study of silicon scribed under 13CH3I and CH3I provides additional evidence for formation of methyl-terminated silicon and suggests sputter-induced decomposition of the near-surface region by ToF-SIMS. Ab initio calculations of a few SiCxHy+ type fragments are shown to verify assignments of structure. We also note an alternative explanation for some of the results based on the density of alkyl chains on the surfaces.
Deep Learning in Orthopedics: How Do We Build Trust in the Machine? (2020)

The paradigm of manual radiological assessment in orthopedics is at the point of significant disruption due to major breakthroughs in deep learning algorithms and computational power. Deep learning is a subset of the broader family of artificial intelligence methods that leverages artificial neural networks to assess imaging data sets. Deep learning has already been applied for automatic assessment of plain film radiographs with high degree of success in different orthopedic applications. However, a major limitation of deep learning is that it is a “black-box” algorithm, meaning its process and how it makes decisions are not easily interpretable. Interpretability in a medical setting is of utmost importance to build trust in the machine's outcome and move toward its meaningful integration into healthcare. In this article, we first briefly explain a deep learning algorithm and how it works at a high level. Next, we implement two different methods to enhance interpretability of a deep learning algorithm applied to an orthopedic application for detecting mechanical loosening of total hip replacement implants (1) on a high level using saliency maps and (2) on a lower level using activation maximization. By combining these two visualization methods, we can get a better understanding about deep learning function and shed light on its decision-making process to build more trust in the machine.
High‐resolution Epigenome Mapping Reveals Distinct and Divergent Roles for UHRF1 in the Maintenance of DNA Methylation (2020)

The E3 ubiquitin ligase UHRF1 is an established cofactor for replication‐coupled DNA methylation inheritance. Our group and others have made recent progress dissecting biochemical mechanisms linking UHRF1 to DNA methylation control. Our current model posits a step‐wise pathway in which UHRF1 engages nucleosomes through histone and DNA binding. This multivalent nucleosome readout directs UHRF1 ubiquitin ligase activity toward the N‐terminal tail of histone H3, a binding site for DNMT1. While this elegant chromatin regulatory process is now taking shape, it remains unclear whether the reliance on UHRF1 for DNA methylation maintenance is localized or genome‐wide. Here we present comparative, high‐resolution, genome‐scale analysis of DNA methylation maintenance following acute depletion of UHRF1 and DNMT1 in a human colorectal cancer cell line. As expected, DNMT1 depletion resulted in global reduction of DNA methylation genome‐wide. However, depletion of UHRF1 revealed distinct attributes of the genome that rely on UHRF1 for DNA methylation maintenance. Significantly, these distinct genomic attributes are divergent on their dependency of ubiquitin deposition on the histone H3 tail by UHRF1 to recruit DNMT1 and maintain DNA methylation. Notably, these newly identified UHRF1‐ubiquitin dependent DNA methylation signatures are consistent with the observed loss of DNA methylation that occurs during aging and cancer progression. We propose that UHRF1 misregulation is a key contributor to DNA methylation erosion that occurs through human lifespan and cancer. Support or Funding Information This work was supported by the Van Andel Institute, and grants from the National Institutes of Health to S.B.R. (R35GM124736) and the American Cancer Society ‐ Michigan Cancer Research Fund to R.L.T. (PF‐16‐245‐01‐DMC).
Toward automatic robot instruction from perception-recognizing a grasp from observation (1993)

Deals with the programming of robots to perform grasping tasks. To do this, the assembly plan from observation (APO) paradigm is adopted, where the key idea is to enable a system to observe a human performing a grasping task, understand it, and perform the task with minimal human intervention. A grasping task is composed of three phases: pregrasp phase, static grasp phase, and manipulation phase. The first step in recognizing a grasping task is identifying the grasp itself. The proposed strategy of identifying the grasp is to map the low-level hand configuration to increasingly more abstract grasp descriptions. To achieve the mapping, a grasp representation is introduced, called the contact web, which is composed of a pattern of effective contact points between the hand and the object. A grasp taxonomy based on the contact web is also proposed as a tool to systematically identify a grasp. The grasp can be described at higher conceptual levels using a certain mapping function that results in an index called the grasp cohesive index. This index can be used to identify the grasp. Results from grasping experiments show that it is possible to distinguish between various types of grasps using the proposed contact web, grasp taxonomy and grasp cohesive index.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Lignin Distribution in Soda-Oxygen and Kraft Fibers as Determined by Conventional Electron Microscopy (1979)

The lignin distribution in loblolly pine (Pinus turdu L.) fibers produced by soda-oxygen and kraft pulping was investigated by electron microscopy of KMnO, stained ultrathin sections and direct carbon replicas.A more extensive delignification of outer layers of fibers was found in soda-oxygen pulps than in kraft pulps.However, kraft pulping is more effective than soda-oxygen pulping in removing lignin from the lumen side of fibers.These observations were in good agreement with an earlier study of the lignin distribution within pulp fibers performed with SEM-EDXA technique.
Bony Increased-Offset Reverse Shoulder Arthoplasty (BIO-RSA) With Allograft Bone Grafting of the Glenoid Surface (2018)

BACKGROUND:Bony increased-offset reverse shoulder arthroplasty (BIO-RSA) creates a long-necked scapula, providing the benefits of lateralization. Experience with allogenic bone grafting of the glen...
ChemInform Abstract: A Perovskite Oxide Optimized for Oxygen Evolution Catalysis from Molecular Orbital Principles. (2012)

Abstract Ba 0.5 Sr 0.5 Co 0.8 Fe 0.2 O 3‐δ catalyzes the oxygen evolution reaction with intrinsic activity that is at least one order of magnitude higher than that of the state‐of‐the‐art IrO 2 catalyst in alkaline media.
From receptor binding kinetics to signal transduction; a missing link in predicting in vivo drug-action (2017)

An important question in drug discovery is how to overcome the significant challenge of high drug attrition rates due to lack of efficacy and safety. A missing link in the understanding of determinants for drug efficacy is the relation between drug-target binding kinetics and signal transduction, particularly in the physiological context of (multiple) endogenous ligands. We hypothesized that the kinetic binding parameters of both drug and endogenous ligand play a crucial role in determining cellular responses, using the NK1 receptor as a model system. We demonstrated that the binding kinetics of both antagonists (DFA and aprepitant) and endogenous agonists (NKA and SP) have significantly different effects on signal transduction profiles, i.e. potency values, in vitro efficacy values and onset rate of signal transduction. The antagonistic effects were most efficacious with slowly dissociating aprepitant and slowly associating NKA while the combination of rapidly dissociating DFA and rapidly associating SP had less significant effects on the signal transduction profiles. These results were consistent throughout different kinetic assays and cellular backgrounds. We conclude that knowledge of the relationship between in vitro drug-target binding kinetics and cellular responses is important to ultimately improve the understanding of drug efficacy in vivo.
Beyond-Cu Intermediate-Length Interconnect Exploration for SRAM Application (2022)

AbstractPromising interconnect materials continue to emerge and are considered as potential replacements for Cu interconnects. In this paper, an intermediate-length interconnect technology exploration framework for SRAM array-level performance based on CACTI 7 is presented to efficiently optimize various emerging interconnect technologies. Three graphene-based interconnect materials are benchmarked against their traditional Cu counterpart for optimal SRAM array-level performance. Furthermore, we investigate the scalability of the emerging interconnect for the SRAM application under five technology nodes based on ASU Predictive Technology Model for FinFET devices and quantify the impact of different cache sizes on key performance metrics, including energy-delay product (EDP) and energy-delay-area product (EDAP). Results demonstrate that the cache using thick graphene interconnects has over 19% EDP reduction comparing the Cu counterpart. It is shown that up to 37% of the EDAP improvement can be achieved by thick graphene interconnects for 2MB cache size at 7nm.
Finding effectors in social networks (2010)

Assume a network (V,E) where a subset of the nodes in V are active. We consider the problem of selecting a set of k active nodes that best explain the observed activation state, under a given information-propagation model. We call these nodes effectors. We formally define the k-Effectors problem and study its complexity for different types of graphs. We show that for arbitrary graphs the problem is not only NP-hard to solve optimally, but also NP-hard to approximate. We also show that, for some special cases, the problem can be solved optimally in polynomial time using a dynamic-programming algorithm. To the best of our knowledge, this is the first work to consider the k-Effectors problem in networks. We experimentally evaluate our algorithms using the DBLP co-authorship graph, where we search for effectors of topics that appear in research papers.
Limitations of the tuning of interface dipoles for the reduction of the contact resistance in organic thin-film transistors (2020)

Achieving gigahertz transit frequencies in low-voltage organic thin-film transistors (TFTs) will require a contact resistance below about 1 Ohm-cm [1,2]. A general approach to reduce the contact resistance in organic devices is to modify the surface of the metal contacts with a chemisorbed interface layer, ostensibly by reducing the nominal injection barrier. Combined with a thin gate dielectric, this approach can enable contact resistances below 30 Ohm-cm and transit frequencies above 10 MHz at low voltages in coplanar organic TFTs [3,4]. However, further reduction of the contact resistance depends strongly on non-idealities of the interface other than the nominal barrier height according to the Schottky-Mott limit. We show a detailed study on the efficacy of interface layers based on various thiols to improve the contact resistance in coplanar dinaphtho[2,3-b:2′,3′-f]thieno[3,2-b]thiophene (DNTT) TFTs. We compare the contact resistance of multiple sets of TFTs to results from ultraviolet photoelectron spectroscopy measurements and find strong evidence that Fermi-level pinning prevents a significant reduction of the contact resistance below about 100 Ohm-cm in DNTT TFTs. Therefore, we conclude that this approach may not be a generally sufficient method by itself to eliminate the contact resistance in organic TFTs.