Miracle-dz/UniFAR-FTUs huggingface dataset:
Crystallographic and biochemical studies revealing the structural basis for antizyme inhibitor function

Antizyme inhibitor (AzI) regulates cellular polyamine homeostasis by binding to the polyamine‐induced protein, Antizyme (Az), with greater affinity than ornithine decarboxylase (ODC). AzI is highly homologous to ODC but is not enzymatically active. In order to understand these specific characteristics of AzI and its differences from ODC, we determined the 3D structure of mouse AzI to 2.05 Å resolution. Both AzI and ODC crystallize as a dimer. However, fewer interactions at the dimer interface, a smaller buried surface area, and lack of symmetry of the interactions between residues from the two monomers in the AzI structure suggest that this dimeric structure is nonphysiological. In addition, the absence of residues and interactions required for pyridoxal 5′‐phosphate (PLP) binding suggests that AzI does not bind PLP. Biochemical studies confirmed the lack of PLP binding and revealed that AzI exists as a monomer in solution while ODC is dimeric. Our findings that AzI exists as a monomer and is unable to bind PLP provide two independent explanations for its lack of enzymatic activity and suggest the basis for its enhanced affinity toward Az.
Identification of Speech Transients Using Variable Frame Rate Analysis and Wavelet Packets

Speech transients are important cues for identifying and discriminating speech sounds. Yoo et al. and Tantibundhit et al. were successful in identifying speech transients and, emphasizing them, improving the intelligibility of speech in noise. However, their methods are computationally intensive and unsuitable for real-time applications. This paper presents a method to identify and emphasize speech transients that combines subband decomposition by the wavelet packet transform with variable frame rate (VFR) analysis and unvoiced consonant detection. The VFR analysis is applied to each wavelet packet to define a transitivity function that describes the extent to which the wavelet coefficients of that packet are changing. Unvoiced consonant detection is used to identify unvoiced consonant intervals and the transitivity function is amplified during these intervals. The wavelet coefficients are multiplied by the transitivity function for that packet, amplifying the coefficients localized at times when they are changing and attenuating coefficients at times when they are steady. Inverse transform of the modified wavelet packet coefficients produces a signal corresponding to speech transients similar to the transients identified by Yoo et al. and Tantibundhit et al. A preliminary implementation of the algorithm runs more efficiently
Practical PIR for electronic commerce

We extend Goldberg's multi-server information-theoretic private information retrieval (PIR) with a suite of protocols for privacy-preserving e-commerce. Our first protocol adds support for single-payee tiered pricing, wherein users purchase database records without revealing the indices or prices of those records. Tiered pricing lets the seller set prices based on each user's status within the system; e.g., non-members may pay full price while members may receive a discounted rate. We then extend tiered pricing to support group-based access control lists with record-level granularity; this allows the servers to set access rights based on users' price tiers. Next, we show how to do some basic bookkeeping to implement a novel top-K replication strategy that enables the servers to construct bestsellers lists, which facilitate faster retrieval for these most popular records. Finally, we build on our bookkeeping functionality to support multiple payees, thus enabling several sellers to offer their digital goods through a common database while enabling the database servers to determine to what portion of revenues each seller is entitled. Our protocols maintain user anonymity in addition to query privacy; that is, queries do not leak information about the index or price of the record a user purchases, the price tier according to which the user pays, the user's remaining balance, or even whether the user has ever queried the database before. No other priced PIR or oblivious transfer protocol supports tiered pricing, access control lists, multiple payees, or top-K replication, whereas ours supports all of these features while preserving PIR's sublinear communication complexity. We have implemented our protocols as an add-on to Percy++, an open source implementation of Goldberg's PIR scheme. Measurements indicate that our protocols are practical for deployment in real-world e-commerce applications.
Towards Legal Knowledge Management Systems for Regulatory Compliance

Maintaining regulatory compliance is an increasing concern. Legal Knowledge Management systems could support the work of compliance managers. However, there are challenges to overcome, of interpreting legal knowledge and mapping it onto business processes. In this discussion paper we determine requirements for Legal Knowledge Management systems that can handle these challenges. We argue that an approach to Legal Knowledge Management should consist of four pillars: (1) a legal ontology to express the legal concepts that are central to the interpretation of rules and regulations in practice, (2) natural language processing techniques, to semi-automatically populate the ontology, (3) a systematic method for mapping the legal concepts onto the actual data and business processes of a company, and (4) a method to construct an audit trail as part of the process design, providing legally acceptable evidence of compliance. The challenges are illustrated by an example of MIFID, a set of European regulations in the financial domain.
HEMATOPOIESIS AND STEM CELLS Hif-2 a is not essential for cell-autonomous hematopoietic stem cell maintenance

Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom; Paul O’Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom; Henry Wellcome Building for Molecular Physiology, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom; and Stem Cell Laboratory, UCL Cancer Institute, University College London, London, United Kingdom
Malware detection method based on the control-flow construct feature of software

The existing anti-virus methods extract signatures of software by manual analysis. It is inefficient when they deal with a large number of malware. Meanwhile, the limitation of unknown malware detection often is found in them too. By the research on software structure, it has been found that the control flow of software can be divided into many basic blocks by the interior cross-references, and a feature-selection approach based on this phenomenon is proposed. It can extract opcode sequences from the disassembled program, and translate them into features by vector space model. The algorithms of data mining are employed to find the classify rules from the software features, and then the rules can be applied to the malware detection. Experimental results illustrate that the proposed method can achieve the 97.0% malware detection accuracy and 3.2% false positive rate with the Random Forest classifier. Furthermore, as high as 94.5% overall accuracy can be achieved when only 5% experimental data are used as training data.
Exploring interaction patterns of cohesive subgroups during organizational disintegration

We suggest that changes in the interactions patterns of communications networks have implications for exploring the phases of organisational disintegration. We develop a set of criteria for measuring the phases of organisational disintegration and apply that to Enron e-mail communications data for testing our preliminary assumptions. We explore the roles of cohesive subgroups (or cliques) and the changes in the composition of clique structure during organisational disintegration. Our preliminary assumptions that drive the work are as follows: (i) the number of cliques increase during organisational disintegration; (ii) structural changes occur in the composition of clique structure and its membership (i.e., we see more contributing actors for the disintegration state clique structure than during the normal state of an organisation).
Evaluation of Differential Pressure Setpoint of Chilled Water Pumps in Clean Room HVAC Systems for Energy Savings in High-Tech Industries

Variable-frequency speed control technologies are widely used in chilled water pumps in clean room heating, ventilation, and air-conditioning (HVAC) systems in high-tech industries to reduce energy consumption. Pumps with variable frequency drivers work based on the reading from the differential pressure sensor placed between the chilled water supply and return lines before the secondary and tertiary pumps. The determination of the differential pressure setpoint must take pipeline topology and material, chilled water flow demand, heat loading, and system equipment aging into account so as to provide operating flexibility for energy conservation while ensuring the secure operation of the clean room. To enhance clean room energy efficiency, a new methodology is proposed in this paper for determining the proper chilled piping pressure setpoint for the pumps. The mathematic model of head loss required for generic secondary and tertiary chilled networks widely used in clean rooms is derived using the Hazen-Williams formula principle. The field testing results confirm the validity of the proposed approach through a practical clean room HVAC system for electronic semiconductor manufacturing, and the energy savings and investment benefits due to the use of the proper differential pressure setpoint are determined.
Mechanisms of guanosine triphosphate hydrolysis by Ras and Ras‐GAP proteins as rationalized by ab initio QM/MM simulations

The hydrolysis reaction of guanosine triphosphate (GTP) by p21ras (Ras) has been modeled by using the ab initio type quantum mechanical–molecular mechanical simulations. Initial geometry configurations have been prompted by atomic coordinates of the crystal structure (PDBID: 1QRA) corresponding to the prehydrolysis state of Ras in complex with GTP. Multiple searches of minimum energy geometry configurations consistent with the hydrogen bond networks have been performed, resulting in a series of stationary points on the potential energy surface for reaction intermediates and transition states. It is shown that the minimum energy reaction path is consistent with an assumption of a two‐step mechanism of GTP hydrolysis. At the first stage, a unified action of the nearest residues of Ras and the nearest water molecules results in a substantial spatial separation of the γ‐phosphate group of GTP from the rest of the molecule (GDP). This phase of hydrolysis process proceeds through the low barrier (16.7 kcal/mol) transition state TS1. At the second stage, the inorganic phosphate is formed in consequence of proton transfers mediated by two water molecules and assisted by the Gln61 residue from Ras. The highest transition state at this segment, TS3, is estimated to have an energy 7.5 kcal/mol above the enzyme–substrate complex. The results of simulations are compared to the previous findings for the GTP hydrolysis in the Ras‐GAP (p21ras–p120GAP) protein complex. Conclusions of the modeling lead to a better understanding of the anticatalytic effect of cancer causing mutation of Gln61 from Ras, which has been debated in recent years. Proteins 2007. © 2006 Wiley‐Liss, Inc.
Western Mediterranean Sea Paleothermometry Over the Last Glacial Cycle Based on the Novel RI‐OH Index

RI‐OH (ring index of hydroxylated tetraethers) has recently been proposed to reconstruct paleotemperatures in middle‐ to low‐latitude marginal seas. However, RI‐OH has barely been tested in marginal seas under substantial terrigenous inputs. Here we analyze tetraether lipids in two adjacent marine cores from the Gulf of Lions. We then test for the first time the RI‐OH paleothermometer from 160 to 9 ka BP in the western Mediterranean Sea. While terrigenous inputs prevent TEX86 (TetraEther indeX of tetraethers consisting of 86 carbon atoms) from behaving as a paleothermometer, RI‐OH is generally consistent with other paleothermometric proxies. RI‐OH also responds systematically and coherently to glacial‐interglacial transitions as well as to abrupt climatic events. The average difference between RI‐OH temperatures and November–May UK′37 (C37 ketone unsaturation ratio) temperatures is −2.0 °C with a standard error of 0.4 °C based on 249 RI‐OH‐UK′37 comparisons. This systematic difference suggests that hydroxylated tetraethers and alkenones record different temperatures, for instance, winter and/or subsurface temperatures for RI‐OH. Another source of bias could be linked to the available RI‐OH‐temperature calibration, which clearly needs more work at the global and regional scales, notably for semienclosed basins such as the Mediterranean Sea. Nevertheless, our RI‐OH‐based interglacial‐glacial anomalies are of 10 °C, a value within the high end of anomalies from previously published temperature records in the western Mediterranean Sea (from 3 to 13 °C). The RI‐OH‐based temperature anomalies also confirm the regional differences and seasonal contrasts in interglacial‐glacial anomalies produced by models.
THE URBAN AND ENVIRONMENTAL PLANNING OF SMART CITIES: INNOVATION AS A SOCIAL, ECONOMIC AND SUSTAINABLE DEVELOPMENT OF AN URBAN CENTRE

The goal of transforming an urban centre into a smart city leverages on the integration of technological and social components but, above all, on an urban development model born from a vision that aspires at creating smarter, more sustainable and inclusive cities, not only with the introduction of technology, but by generating innovation as well. In order to achieve this, the smart city must adopt an urban life cycle planning and management model capable of constantly allowing the ICT components to interact with those of governance, modelling itself on the locational decisions of major urban functions. In this article, we essentially want to highlight how, for an urban centre, smart cities represent a successful business model with significant economic potential and, additionally, the development strategies necessary to enable cities to become smart.
GMM-HMM acoustic model training by a two level procedure with Gaussian components determined by automatic model selection

This paper investigates the Bayesian Ying-Yang (BYY) learning for speech recognition via Gaussian mixture models (GMMs) based Hidden Markov models (HMMs). A two level procedure is proposed with the hidden Markov level trained still under the maximum likelihood principle by the Baum-Welch algorithm but with the GMMs level trained under the BYY best harmony. We proposed a new batch way EM-like Ying-Yang alternation algorithm and used it as a plug-in block to the Baum-Welch algorithm. The advantage is that number of GMM components can be automatically determined during this BYY harmony learning and that the resulted model parameters become less affected than EM-ML training by the problem of overfitting and singular solution. In comparison with the standard EM-ML training and classical model selection criterions, including BIC and AIC, speech recognition experiments in a large vocabulary task on the Hub4 broadcast news database shown that the proposed algorithm provides an improved performance and also good convergence.
Snow cover dynamics of four lake basins over Tibetan Plateau using time series MODIS data (2001–2010)

Snow over the Tibetan Plateau (TP) is an important water source of major Asian rivers and greatly influences water availability in the downstream areas. In this study, snow cover dynamics of the four characteristic lake basins, Cedo Caka, Selin Co, Nam Co, and Yamzhog Yumco during hydrological years 2001–2010 (September through August) are examined at the basin scale using the flexible multiday combined MODIS snow cover products. The time series of multiday, seasonal, and annual snow covered area (SCA), onset/disappearance dates of snow, snow covered days (SCD), peaks of maximum SCA, and snow cover index (SCI) for each hydrological year (HY) are examined. Results show there is no obvious trend of snow cover change in the examined period, although Nam Co basin has the greatest SCA in all four basins and in all years, and Cedo Caka and Selin Co basins show the smallest SCA in most of the years. Overall, the HY2007 shows a greater snow extent and HY2010 a smaller for the region, with exceptions for the Nam Co basin where the HY2003 is the greatest and for Cedo Caka basin where the HY2004 is the smallest. Statistical analysis between lake level changes and lake basin's SCA, precipitation and pan evaporation (ETpan) changes shows that (1) Cedo Caka's water level rise was highly correlated with the basin's SCA changes (r = 0.94, p = 0.063); (2) Selin Co's water level rise was significantly correlated with the basin's SCA, precipitation and ETpan changes (r = 0.99, p = 0.029); and (3) lake level changes of Nam Co and Yamzhog Yumco were correlated with their corresponding lake basin's SCA, precipitation and ETpan changes (r = 0.87 and r = 0.86, respectively), although insignificant at the 95% level. This could have been due to precipitation and ETpan data of a distant meteorological station for Nam Co lake basin and the complex hydrological processes in the Yamzhog Yumco basin. This study suggests that the examination of time series snow cover dynamics is important to evaluate the water budget of lake basins with snow as a major component of water balance.
Mechanisms of Tolerance and High Degradation Capacity of the Herbicide Mesotrione by Escherichia coli Strain DH5-α

The intensive use of agrochemicals has played an important role in increasing agricultural production. One of the impacts of agrochemical use has been changes in population structure of soil microbiota. The aim of this work was to analyze the adaptive strategies that bacteria use to overcome oxidative stress caused by mesotrione, which inhibits 4-hydroxyphenylpyruvate dioxygenase. We also examined antioxidative stress systems, saturation changes of lipid membranes, and the capacity of bacteria to degrade mesotrione. Escherichia coli DH5-á was chosen as a non-environmental strain, which is already a model bacterium for studying metabolism and adaptation. The results showed that this bacterium was able to tolerate high doses of the herbicide (10× field rate), and completely degraded mesotrione after 3 h of exposure, as determined by a High Performance Liquid Chromatography. Growth rates in the presence of mesotrione were lower than in the control, prior to the period of degradation, showing toxic effects of this herbicide on bacterial cells. Changes in the saturation of the membrane lipids reduced the damage caused by reactive oxygen species and possibly hindered the entry of xenobiotics in the cell, while activating glutathione-S-transferase enzyme in the antioxidant system and in the metabolizing process of the herbicide. Considering that E. coli DH5-α is a non-environmental strain and it had no previous contact with mesotrione, the defense system found in this strain could be considered non-specific. This bacterium system response may be a general adaptation mechanism by which bacterial strains resist to damage from the presence of herbicides in agricultural soils.
Performance of Direct Visual Inspection of the Cervix with Acetic Acid and Magnification in a Previously Screened Population

Objective. To assess the screening performance of direct visual inspection with acetic acid and ×2 magnification (VIAM) in a previously screened population, as performed by experienced gynecologic nurses with minimal training in VIAM. Patients and Methods. Performance of VIAM was evaluated in 2,080 women from a population-based cohort in Guanacaste, Costa Rica, 5 years after they had negative enrollment results of conventional and liquid-based cytologic analysis, cervigram, and human papillomavirus DNA by Hybrid Capture Tube Test (Digene Corporation, Gaithersburg, MD). The VIAM results were compared with repeat conventional Pap smears, liquid-based cytologic examinations, and cervicography, with adjudication of differences by reference to MY09/MY11 L1 consensus primer polymerase chain reaction detection of oncogenic human papillomavirus DNA. Results. Less than 5% of women were classified as having positive results using VIAM. The VIAM positivity was also very low among women with high-grade squamous intraepithelial lesion conventional Pap smear results (8.3%), high-grade squamous intraepithelial lesion liquid-based cytologic results (6.3%), or cervigrams suggesting cervical intraepithelial neoplasia 2,3 or cancer (30%). The VIAM positivity was not associated with human papillomavirus DNA positivity. Conclusions. As we practiced it, VIAM was not sensitive for detection of possibly serious incident cervical lesions in this previously screened population where cytologic screening is in place.
Improving the characterisation of fractured hydrocarbon reservoir dolomites (Vienna Basin, Austria) by 3D and 2D micro-imaging and permeability measurements

In Kohlenwasserstoff-Lagerstatten konnen Gesteine auftreten, die naturliche Klufte aufweisen, welche die Porositats- und Permeabilitatseigenschaften deutlich beeinflussen. Bei der Untersuchung kleiner Proben (d.h. Bohrkerne und Plugs) aus solchen Lagerstatten existieren allerdings mehrere Nachteile bei der Anwendung konventioneller Methoden (z.B. Labormessungen von Porositat und Permeabilitat, Dunnschliffanalysen). Unter anderem konnen diese Methoden z.B. nicht ausreichend detailliert sein oder nur zweidimensionale oder gemittelte Informationen liefern. Mit dem Ziel diese Nachteile zu umgehen, pruft die vorliegende Arbeit die Anwendbarkeit von 3D Rontgen- Microcomputertomographie (μCT) an kleinen Bohrkernen (Plugs) aus Proben eines zerklufteten Dolomitgesteins, das aus dem pra-neogenen Untergrund des Wiener Beckens stammt. μCT ist eine nicht-destruktive Methode und erlaubt die Darstellung der internen Struktur von Gesteinsproben in 3D. Die gewonnenen Daten werden mittels einer eigens entwickelten Technik zur Filterung (Hessian Filtering) prozessiert, um das Kluftnetzwerk zu extrahieren und daraus Parameter wie Porositat, Kluftweite oder Orientierung der Klufte zu bestimmen. Weiters werden die 3D μCT Daten durch eine Reihe anderer analytischer Methoden erganzt und kalibriert. So geben Gesteinsdunnschliffe in 2D im Rasterelektronenmikroskop (SEM) mittels ruckgestrahlter Elektronen (BSE) einen detaillierteren Einblick in Mikrostruktur und Mineralbestandteile der Proben. Auserdem wurden durch Ionenstrahl-Rasterelektronen-mikroskopie (FIB-SEM) serielle Schnitte im Mikrometer-Bereich erzeugt, die ein noch detaillierteres Bild bieten und zur Bestimmung der Mikroporositat herangezogen werden. Daruber hinaus wurden Laborexperimente zur Messung der Permeabilitat unter steigendem Umgebungsdruck durchgefuhrt, die eine Annaherung an das Verhalten der Gesteine unter realistischen Bedingungen in der Lagerstatte selbst bieten konnen. In dieser Dissertation werden sowohl Moglichkeiten und Grenzen der oben genannten Methoden, als auch die effizientesten Ablaufe zur Bearbeitung und Kombination der verschiedenen Informationsquellen aufgezeigt. Die Ergebnisse und Techniken sollen folglich auch in umfassenderen Studien an geklufteten Lagerstattengesteinen angewandt und standardisiert werden.