gebhart/patrepeval huggingface dataset:
Evaluating the absolute quality of a single protein model using structural features and support vector machines (2008)

Knowing the quality of a protein structure model is important for its appropriate usage. We developed a model evaluation method to assess the absolute quality of a single protein model using only structural features with support vector machine regression. The method assigns an absolute quantitative score (i.e. GDT-TS) to a model by comparing its secondary structure, relative solvent accessibility, contact map, and beta sheet structure with their counterparts predicted from its primary sequence. We trained and tested the method on the CASP6 dataset using cross-validation. The correlation between predicted and true scores is 0.82. On the independent CASP7 dataset, the correlation averaged over 95 protein targets is 0.76; the average correlation for template-based and ab initio targets is 0.82 and 0.50, respectively. Furthermore, the predicted absolute quality scores can be used to rank models effectively. The average difference (or loss) between the scores of the top-ranked models and the best models is 5.70 on the CASP7 targets. This method performs favorably when compared with the other methods used on the same dataset. Moreover, the predicted absolute quality scores are comparable across models for different proteins. These features make the method a valuable tool for model quality assurance and ranking.
MATHEMATICAL BASIS OF THE CRITICAL PATH METHOD* by (1962)

NOTICE: When government or other drawings, speci-fications or other data are used for any purpose other than in connection with a definitely related government procurement operation, the U. S. Government thereby incurs no responsibility, nor any obligation whatsoever; and the fact that the Govern-ment may have formulated, furnished, or in any way supplied the said drawings, specifications, or other data is not to be regarded by implication or other-wise as in any manner licensing the holder or any other person or corporation, or conveying any rights or permission to manufacture, use or sell any patented invention that may in any way be related thereto. oo
Clustering near-duplicate images in large collections (2007)

Near-duplicate images introduce problems of redundancy and copyright infringement in large image collections. The problem is acute on the web, where appropriation of images without acknowledgment of source is prevalent. In this paper, we present an effective clustering approach for near-duplicate images, using a combination of techniques from invariant image local descriptors and an adaptation of near-duplicate text-document clustering techniques; we extend our earlier approach of near-duplicate image pairwise identification for this clustering approach. We demonstrate that our clustering approach is highly effective for collections of up to a few hundred thousand images. We also show --- via experimentation with real examples --- that ourapproach presents a viable solution for clustering near-duplicate images on the Web.
Performance evaluation of series and parallel strategies for financial time series forecasting (2017)

Improving financial time series forecasting is one of the most challenging and vital issues facing numerous financial analysts and decision makers. Given its direct impact on related decisions, various attempts have been made to achieve more accurate and reliable forecasting results, of which the combining of individual models remains a widely applied approach. In general, individual models are combined under two main strategies: series and parallel. While it has been proven that these strategies can improve overall forecasting accuracy, the literature on time series forecasting remains vague on the choice of an appropriate strategy to generate a more accurate hybrid model. Therefore, this study’s key aim is to evaluate the performance of series and parallel strategies to determine a more accurate one. Accordingly, the predictive capabilities of five hybrid models are constructed on the basis of series and parallel strategies compared with each other and with their base models to forecast stock price. To do so, autoregressive integrated moving average (ARIMA) and multilayer perceptrons (MLPs) are used to construct two series hybrid models, ARIMA-MLP and MLP-ARIMA, and three parallel hybrid models, simple average, linear regression, and genetic algorithm models. The empirical forecasting results for two benchmark datasets, that is, the closing of the Shenzhen Integrated Index (SZII) and that of Standard and Poor’s 500 (S&P 500), indicate that although all hybrid models perform better than at least one of their individual components, the series combination strategy produces more accurate hybrid models for financial time series forecasting.
Níveis críticos e tóxicos de boro em solos de Pernambuco determinados em casa de vegetação (2007)

Pesquisas sobre a disponibilidade de B em solos são necessárias para avaliar o comportamento das culturas sob diferentes teores disponíveis desse elemento no solo. Com essa finalidade, foi realizado um experimento em casa de vegetação para avaliar a resposta de milho (Zea mays) a doses de boro (0, 2, 4, 6 e 12 mg dm-3) em dez solos de Pernambuco. O B disponível foi determinado por três extratores: água quente, ácido clorídrico 0,05 mol L-1 e Mehlich-1. Foram ainda determinados os níveis críticos (90 e 95 % da produção máxima de matéria seca) e tóxicos (equivalente à redução de 10 % da produção máxima) nos solos e na planta, além da descrição de sintomas de toxidez de B em milho. Os resultados demonstraram que os níveis críticos e tóxicos de B nos solos variaram de 0,4 a 2,3 mg kg-1 e de 1,8 a 8,3 mg kg-1, respectivamente. Em plantas de milho, os níveis críticos variaram de 13,8 a 129,6 mg kg-1, enquanto teores tóxicos foram obtidos entre 43,3 e 372,2 mg kg-1. O extrator que obteve a melhor correlação com o teor de B na planta foi o HCl 0,05 mol L-1, seguido pelo Mehlich-1 e pela água quente. A disponibilidade do B no solo pelo extrator HCl e os teores de B na folha foram afetados negativamente pelo aumento no teor de argila e matéria orgânica dos solos. Os solos que apresentaram plantas com maior teor de B no tecido vegetal mostraram sintomas mais graves de toxidez, fator associado à maior disponibilidade de boro em solos com textura mais arenosa e, ou, baixos teores de matéria orgânica.
Clinical Significance of Expression of Estrogen Receptor α and β mRNAs in Ovarian Cancers (2000)

Novel human estrogen receptor (ER)-beta was identified in cDNA libraries from human testis. ER-beta specifically expresses in testis, ovary, thymus, spleen, osteoblasts and fetus. ER-beta might not conserve the same physiological functions as does ER-alpha. Therefore, the clinical significance of the expression of ER-alpha and ER-beta mRNAs in ovarian cancers was investigated. The percentage of ER-beta mRNA to ER-alpha mRNA ranged from 1.5 to 10% in normal ovaries. On the other hand, the ratios of ER-beta mRNA to ER-alpha mRNA were in a wide range in ovarian cancers. There was no significant difference in the ratios among ovarian cancers classified according to histological types or clinical stages. In a 48-month survival rate, the patient prognosis in ovarian cancers with a low or high ratio of ER-beta mRNA to ER-alpha mRNA (<1.5 or >10% of ER-beta mRNA to ER-alpha mRNA) was significantly worse than that in ovarian cancers with a medium ratio (>==1.5 to <==10% of ER-beta mRNA to ER-alpha mRNA). In conclusion, the intact synchronized expression of ER-beta mRNA interacting with ER-alpha mRNA might be damaged in some ovarian cancers, which might lead to poor patient prognosis.
Human Adipose-Derived Mesenchymal Stem Cells Are Resistant to HBV Infection during Differentiation into Hepatocytes in Vitro (2014)

The therapeutic methods for chronic hepatitis B are limited. The shortage of organ donors and hepatitis B virus (HBV) reinfection obstruct the clinical application of orthotopic liver transplantation (OLT). In the present study, adipose-derived mesenchymal stem cells (AD-MSCs) and bone marrow-derived mesenchymal stem cells (BM-MSCs) were isolated from chronic hepatitis B patients and characterized for morphology, growth potency, surface phenotype and the differentiation potential. The results showed that both MSCs had adipogenic, osteogenic and neuron differentiation potential, and nearly all MSCs expressed CD105, CD44 and CD29. Compared with AD-MSCs, BM-MSCs of chronic hepatitis B patients proliferated defectively. In addition, the ability of AD-MSCs to differentiate into hepatocyte was evaluated and the susceptibility to HBV infection were assessed. AD-MSCs could differentiate into functional hepatocyte-like cells. These cells express the hepatic-specific markers and have glycogen production and albumin secretion function. AD-MSCs and hepatic differentiation AD-MSCs were not susceptible to infection by HBV in vitro. Compared with BM-MSCs, AD-MSCs may be alternative stem cells for chronic hepatitis B patients.
Multilevel modular converter with reduced device count for hybrid and electric vehicle (2015)

This paper presents a low cost multilevel modular switched capacitor dc-dc converter for high power and high voltage conversion ratio application with reduced device count. The switching devices number of the traditional multilevel modular switched capacitor dc-dc converter is increasing fast with the increase of conversion ratio. Large number of switching devices means more gate drive circuit, more complex and higher cost. The proposed circuit has low device number, low device voltage stress and current stress. The proposed circuit also inherits the modular structure, simple control, low conduction loss, high switching frequency operation capability, and soft switching features from the traditional multilevel modular switched capacitor dc-dc converter. Therefore, a high voltage conversion ratio switched capacitor dc-dc converter with low cost and simple structure can be built using the proposed circuit. Simulation results are provided to validate the operating principle and features of the circuit.
A role for urokinase-type plasminogen activator in human immunodeficiency virus type 1 infection of macrophages (1996)

Urokinase-type plasminogen activator (uPA), a proteinase which activates plasminogen by cleaving at -CPGR(arrow downward)V-, was shown to cleave the V3 loop in recombinant gp120 of human immunodeficiency virus type 1 (HIV-1) IIIB and MN strains, as well as a synthetic, cyclized peptide representing the clade B consensus sequence of V3. Proteolysis occurred at the homologous -GPGR(arrow downward)A-, an important neutralizing determinant of HIV-1. It required soluble CD4 and was prevented by inhibitors of uPA but not by inhibitors of likely contaminating plasma proteinases. It was accelerated by heparin, a known cofactor for plasminogen activation. In immune capture experiments, tight binding of uPA to viral particles, which did not depend on CD4, was also demonstrated. Active site-directed inhibitors or uPA diminished this binding, as did a neutralizing antibody to V3. Addition of exogenous uPA to the laboratory-adapted IIIB strain of HIV-1, the macrophage-tropic field strains JR-CSF and SF-162, or a fresh patient isolate of indeterminate tropism, followed by infection of macrophages with the various treated viruses, resulted in severalfold increases in subsequent viral replication, as judged by yields of reverse transcriptase activity and p24 antigen, as well as incorporation, as judged by PCR in situ. These responses were reversible by inhibitors or antibodies targeting the proteinase active site or the V3 loop. We propose that uPA, a transcriptionally regulated proteinase which is upregulated when macrophages are HIV infected, can be bound and utilized by the virus to aid in fusion and may be an endogenous component that is critical to the infection of macrophages by HIV-1.
Steroid-Responsive Chronic Cerebellitis With Positive Glutamate Receptor δ2 Antibody (2007)

We report the clinical course of a 4-year-old girl with chronic cerebellitis (onset 2 days after diphtheria-pertussis-tetanus vaccination at 1 year and 7 months old) associated with anti-glutamate receptor delta 2 antibody, who improved dramatically with steroid therapy (methylprednisolone pulse therapy plus oral prednisolone). Recently, it has been reported that the anti-glutamate receptor delta 2 selectively expressed at the post-synaptic site of parallel fiber-Purkinje cell synapses has an important role in cerebellar function in the developing brain. The present case suggests that anti-glutamate receptor delta 2 antibody plays a primary role in an immune-mediated process causing chronic cerebellar symptoms, and the lesion site seems to be localized to the parallel fiber-Purkinje cell synapse. Because the cerebellum is strongly involved in language acquisition as well as motor development, treatment must facilitate time for language learning while reducing the side effects of the corticosteroid therapy.
Biochemometrics for Natural Products Research: Comparison of Data Analysis Approaches and Application to Identification of Bioactive Compounds (2016)

A central challenge of natural products research is assigning bioactive compounds from complex mixtures. The gold standard approach to address this challenge, bioassay-guided fractionation, is often biased toward abundant, rather than bioactive, mixture components. This study evaluated the combination of bioassay-guided fractionation with untargeted metabolite profiling to improve active component identification early in the fractionation process. Key to this methodology was statistical modeling of the integrated biological and chemical data sets (biochemometric analysis). Three data analysis approaches for biochemometric analysis were compared, namely, partial least-squares loading vectors, S-plots, and the selectivity ratio. Extracts from the endophytic fungi Alternaria sp. and Pyrenochaeta sp. with antimicrobial activity against Staphylococcus aureus served as test cases. Biochemometric analysis incorporating the selectivity ratio performed best in identifying bioactive ions from these extracts early in the fractionation process, yielding altersetin (3, MIC 0.23 μg/mL) and macrosphelide A (4, MIC 75 μg/mL) as antibacterial constituents from Alternaria sp. and Pyrenochaeta sp., respectively. This study demonstrates the potential of biochemometrics coupled with bioassay-guided fractionation to identify bioactive mixture components. A benefit of this approach is the ability to integrate multiple stages of fractionation and bioassay data into a single analysis.
Early Detection of Steel Corrosion via “Turn-On” Fluorescence in Smart Epoxy Coatings (2009)

In the present work, we describe the successful application of spiro[1H-isoindole-1,9'-[9H]xanthen]-3(2H)-one, 3',6'-bis(diethylamino)-2-[(1-methylethylidene)amino] ("FD1") as a smart indicator in epoxy-based coatings for the early detection of steel corrosion. The FD1 indicator was used for epoxy-based coatings on steel for its desirable property of "turn-on" fluorescence upon forming a complex with ferric ions produced at the anodic site during steel corrosion and because it does not prematurely fluoresce when mixed with the coating precursors (i.e., epoxy resin and amine). This indicator, after incorporation into a filled epoxy coating at a concentration as low as 0.5 wt %, was observed to become fluorescent in areas where corrosion started before any obvious sign of metal damage was observable. FD1 fluorescence was apparent both in areas around a scribed portion of the coating where the metal was exposed and in undercoating corrosion, where the coating surface was intact. This nondestructive method of early corrosion detection can help signal when maintenance is needed before the metal suffers serious damage.
Guided search: An alternative to the feature integration model for visual search. (1989)

Subjects searched sets of items for targets defined by conjunctions of color and form, color and orientation, or color and size.Set size was varied and reaction times (RT) were measured.For many unpracticed subjects, the slopes of the resulting RT x Set Size functions are too shallow to be consistent with Treisman's feature integration model, which proposes serial, self-terminating search for conjunctions.Searches for triple conjunctions (Color x Size x Form) are easier than searches for standard conjunctions and can be independent of set size.A guided search model similar to Hoffman's (1979) two-stage model can account for these data.In the model, parallel processes use information about simple features to guide attention in the search for conjunctions.Triple conjunctions are found more efficiently than standard conjunctions because three parallel processes can guide attention more effectively than two.
A survey of physical database design methodology and techniques (1978)

The problem of physical database design has received considerable attention by researchers over the past several years. This paper provides a survey of a large number of design techniques that have resulted from this activity. More attention has been given to some of the latest work. This survey is by no means exhaustive and is intended to motivate the interested reader into a more detailed study of this area.
Arrayed waveguide grating DWDM interleaver (2002)

Arrayed waveguide grating DWDM interleavers are proposed and analyzed. With simple design rules, interleavers with low channel cross-talk and flat-top passband can be easily implemented.
New low-viscosity overlay medium for viral plaque assays. (2006)

Plaque assay under Avicel-containing overlay media is easier, faster and more sensitive than assays under agar- and methylcellulose overlays. The assay can be readily performed in a 96-well plate format and seems particularly suitable for high-throughput virus titrations, serological studies and experiments on viral drug sensitivity. It may also facilitate work with highly pathogenic agents performed under hampered conditions of bio-safety labs.
Theory of the Static Stability of Cylindrical Domains in Uniaxial Platelets (1970)

A theory of the static stability of circular cylindrical domains in uniaxial magnetic platelets has been developed. The predictions of the theory agree well with experiments and provide requirements which link material properties to domain geometry. The theory is developed by assuming a model in which the domains have cylindrical walls of zero width and by then calculating the size and stability of the domains, using a straightforward although somewhat lengthy energy method. It is found that in order for domains to exist Ku⪞2πMs2, where Ku is the uniaxial anisotropy constant and Ms is the saturation magnetization. However, the model is most accurate when Ku≫2πMs2, although in this case the domains tend to have a low mobility. A formula relating domain size to the material parameters, the plate thickness and the applied bias field is obtained. More important, static stability considerations indicate that when all parameters except the bias field are held constant the domains are stable only over a 3:1 diameter range and at best a 1.6:1 bias field range. Cylindrical domains are found to be most stable for device applications when the domain radius is equal to the plate thickness which is in turn approximately equal to σw/πMs2, where σw is the wall energy density.
The design of an RFID security protocol based on RSA signature for e-ticket (2010)

As an RFID application, e-ticket system is evolving as a ubiquitous infrastructure, commonly used for access control to some services like entrance to public transportations or some sports or cultural events. It presents lots of advantages, but brings numerous open issues that need to be addressed. Two open issues we mostly care about are security and cost issues. We propose an RFID security protocol based on RSA signature that can address these two issues. The RSA signature scheme has many blind sides, thus we improve the original RSA signature scheme with one-way Hash function and a cryptographic algorithm to resist forgery attack and other adversaries' aggressions. Then we design a lightweight RFID protocol with our improved RSA signature scheme for e-ticket systems. Finally, we analyze the performance of our proposed protocol, it guarantees the owners' digital rights written on the e-ticket are secure, and reduces the cost of e-tickets due to its basic bitwise logical or arithmetic operations executed at the e-ticket side.
Lateral organ boundaries domain transcription factors (2012)

Over the last two decades, several transcription factor gene families have been identified with some of them characterized in detail for their roles on transcriptional regulation of plant defense responses against pest or pathogen attack. We have recently added another transcription factor gene family to this list through the characterization of the LATERAL ORGAN BOUNDARIES (LOB) DOMAIN (LBD)-CONTAINING PROTEIN20 (LBD20). We showed LBD20 acts as a repressor of a subset of jasmonate mediated defenses and in susceptibility to the root-infecting fungal pathogen Fusarium oxysporum. However, possible roles for other members of this gene family in plant defense are currently unknown. Here we searched publically available microarray expression data and provide an overview of the expression patterns of selected members of the LBD gene family for their response to other fungal pathogens and soil nematodes. Distinct expression patterns of the LBD genes suggest that certain members of this gene family have previously undescribed roles in plant defense.
Candidate Serum Biomarkers for Early Intestinal Cancer Using <sup>15</sup>N Metabolic Labeling and Quantitative Proteomics in the <i>Apc</i><sup><i>Min/+</i></sup> Mouse (2013)

Current screening procedures for colorectal cancer are imperfect and highly invasive and result in increased mortality rates due to low compliance. The goal of the experiments reported herein is to identify potential blood-based biomarkers indicative of early stage intestinal cancers using the ApcMin/+ mouse model of intestinal cancer as an experimental system. Serum proteins from tumor-bearing ApcMin/+ mice were quantitatively compared to tumor-free Apc+/+ wild-type mice via in anima metabolic labeling with 14N/15N-labeled Spirulina algae and an LTQ Orbitrap mass spectrometer. Out of 1116 total serum proteins quantified, this study identified 40 that were differentially expressed and correlated with the increase in intestinal neoplasms. A subset of these differentially expressed proteins underwent a secondary quantitative screen using selected reaction monitoring-mass spectrometry with stable isotope-labeled peptides. Using both quantitative techniques, we identified MGAM and COL1A1 as downregulated and ITIH3 and F5 as upregulated in serum. All but COL1A1 were similarly differentially expressed in the mRNA of neoplastic colonic tissues of ApcMin/+ mice compared to normal wild-type tissue. These differentially expressed proteins identified in the ApcMin/+ mouse model have provided a set of candidate biomarkers for future validation screens in humans.