Miracle-dz/UniFAR-FTUs huggingface dataset:
Crystal Structures of Trypanosoma brucei Sterol 14α-Demethylase and Implications for Selective Treatment of Human Infections*♦

Sterol 14α-demethylase (14DM, the CYP51 family of cytochrome P450) is an essential enzyme in sterol biosynthesis in eukaryotes. It serves as a major drug target for fungal diseases and can potentially become a target for treatment of human infections with protozoa. Here we present 1.9 Å resolution crystal structures of 14DM from the protozoan pathogen Trypanosoma brucei, ligand-free and complexed with a strong chemically selected inhibitor N-1-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl)ethyl)-4-(5-phenyl-1,3,4-oxadi-azol-2-yl)benzamide that we previously found to produce potent antiparasitic effects in Trypanosomatidae. This is the first structure of a eukaryotic microsomal 14DM that acts on sterol biosynthesis, and it differs profoundly from that of the water-soluble CYP51 family member from Mycobacterium tuberculosis, both in organization of the active site cavity and in the substrate access channel location. Inhibitor binding does not cause large scale conformational rearrangements, yet induces unanticipated local alterations in the active site, including formation of a hydrogen bond network that connects, via the inhibitor amide group fragment, two remote functionally essential protein segments and alters the heme environment. The inhibitor binding mode provides a possible explanation for both its functionally irreversible effect on the enzyme activity and its selectivity toward the 14DM from human pathogens versus the human 14DM ortholog. The structures shed new light on 14DM functional conservation and open an excellent opportunity for directed design of novel antiparasitic drugs.
Evaluating the Potential to Extract High-Resolution Paleoclimate Information from the Near-Shore New Zealand Molluscan Species Austrovenus stutchburyi

Li, B, Mg, Al, Mn, Cu, Zn, As, Sr, Ba and U/Ca ratios were measured by laser ablation inductively coupled plasma mass spectrometry for 11 modern Austrovenus stutchburyi clams to assess the potential of this molluscan species as a proxy for paleo-ocean temperature and environmental change. A. stutchburyi is an intertidal, infaunal, bivalve, widespread in New Zealand coastal regions and throughout the Quaternary-Pliocene sedimentary rock record. Five individuals from Ligar Bay and Estuary (South Island, New Zealand) were analysed to evaluate the variability between individuals calcifying in similar environmental conditions. A further six individuals were sampled from a range of latitudes (38˚ to 40˚) in the North Island, New Zealand to evaluate variability between individuals from different environments. A strong positive correlation between growth rate and Mg, Al, Mn, Sr, Ba and U/Ca ratios was observed, and a marked negative correlation was found between the same trace element/Ca ratios and ontogenetic age as growth rates slow during the molluscs' life. Thus, biological effects are the primary influence on trace element incorporation in A. stutchburyi. No clear seasonal variations were observed in the Mg and Sr/Ca ratio profiles through A. stutchburyi shells representing time periods of several years. Furthermore, for two shells for which chronologies could be reliably constructed, there were no significant correlations between Mg and Sr/Ca ratios and sea surface temperature. When Mg/Ca ratios were normalised to Sr/Ca ratios in order to eliminate the growth rate effect on trace element incorporation into the mollusc shells, some of the remaining variations appeared to visually correlate positively with sea surface temperature in several sections of a shell. However, a quantitative correlation did not confirm this (r² = 0.012). It is likely that neither Mg nor Sr incorporation into A. stutchburyi shell are primarily thermodynamically controlled. Several coincident Ba/Ca peaks in two of the Ligar Bay shells are most likely caused by environmental processes such as short periods of phytoplankton blooms or elevated seawater Ba/Ca from river flooding. Mn/Ca and U/Ca variations in A. stutchburyi from different coastal sites with different sediment characteristics appeared to be linked to the redox conditions prevailing at an open ocean sand-dominated environment (Ligar Bay) versus tidal mud flat environments (e.g. Miranda). Thus, while A. stutchburyi is unlikely to be a useful archive for past coastal ocean temperatures, it holds considerable promise for tracking past changes in coastal ocean productivity and river run-off, as well as sediment redox conditions.
3 POINT SAMPLE RENDERING

We present an algorithm suitable for real-time, high quality rendering of complex objects. Objects are represented as a dense set of surface point samples which contain colour, depth and normal information. These point samples are obtained by sampling orthographic views on an equilateral triangle lattice. They are rendered directly and independently without any knowledge of surface topology. We introduce a novel solution to the problem of surface reconstruction using a hierarchy of Z-buffers to detect tears. The algorithm is fast, easily vectorizable, and requires only modest resources. Thesis Supervisor: William J. Dally Title: Professor of Electrical Engineering and Computer Science
Serum enzymes and genetic carriers in muscular dystrophy.

STUDIES FROM THIS LABORATORY have demonstrated that muscular dystrophy in man, exclusive of myotonic, myositic, neurogenic, ocular, and distal types, can be divided by genetic and clinical criteria into four categories: the domi-nant facioscapulohumeral type, the sex-linked Duchenne type, the recessive limb-girdle type, and the sporadic limb-girdle type (Chung and Morton, 1959; Morton and Chung, 1959). The first three classes had been recognized by other workers (Stevenson, 1953; Walton, 1955), but unambiguous proof of the fourth type required methods which have only recently become available (Morton, 1959). The correctness of this classification was established by analysis not only of our Wisconsin material, but also of seven other large studies from the litera-ture which had been interpreted differently. The eight sources proved to be consistent with each other and with genetic expectation.
Shorter Telomeres May Mark Early Risk of Dementia: Preliminary Analysis of 62 Participants from the Nurses' Health Study

Background Dementia takes decades to develop, and effective prevention will likely require early intervention. Thus, it is critical to identify biomarkers of preclinical disease, allowing targeting of high-risk subjects for preventive efforts. Since telomeres shorten with age and oxidative stress, both of which are important contributors to the onset of dementia, telomere length might be a valuable biomarker. Methodology/Principal Findings Among 62 participants of the Nurses' Health Study, we conducted neurologic evaluations, including patient and caregiver interviews, physical exam, neurologic exam, and neuropsychologic testing. We also conducted magnetic resonance imaging (MRI) in a sample of 29 of these women. In these preliminary data, after adjustment for numerous health and lifestyle factors, we found that truncated telomeres in peripheral blood leukocytes segregate with preclinical dementia states, including mild cognitive impairment (MCI); the odds of MCI were 12-fold higher (odds ratio = 12.00, 95% confidence interval 1.24–116.5) for those with shorter telomere length compared to longer telomere length. In addition, decreasing telomere length was strongly related to decreasing hippocampal volume (p = 0.038). Conclusions These preliminary data suggest that telomere length may be a possible early marker of dementia risk, and merits further study in large, prospective investigations.
Energy Efficiency for Clustered Heterogeneous Multicores

Heterogeneous multicore systems clustered in multiple Voltage Frequency Islands (VFIs) are the next-generation solution for power and energy efficient computing systems. Due to the heterogeneity, the power consumption and execution time of a task changes not only with Dynamic Voltage and Frequency Scaling (DVFS), but also according to the task-to-island assignment, presenting major challenges for power management and energy minimization techniques. This paper focuses on energy minimization of periodic real-time tasks (or performance-constrained tasks) on such systems, in which the cores in an island are homogeneous and share the same voltage and frequency, but different islands have different types and numbers of cores and can be executed at other voltages and frequencies. We present an efficient algorithm to minimize the total energy consumption while satisfying the timing constraints of all tasks. Our technique consists of the coordinated selection of the voltage and frequency levels for each island, together with a task partitioning strategy that considers the energy consumption of the task executing on different islands and at different frequencies, as well as the impact of the frequency and the underlying core architecture to the resulting execution time. Every task is then mapped to the most energy efficient island for the selected voltage and frequency levels, and to a core inside the island such that the workloads of the cores in a VFI are balanced. We experimentally evaluate our technique and compare it to state-of-the-art solutions, resulting in average in 25 percent less energy consumption (and up to 87 percent for some cases), while guaranteeing that all tasks meet their deadlines.
Supporting a Flexible Parallel Programming Model on a Network of Non-Dedicated Workstations

A network of non-dedicated workstations can provide computational resources at minimal or no additional cost. If harnessed properly, the combined computational power of these otherwise “wasted” resources can outperform even mainframe computers. Performing demanding computations on a network of non-dedicated workstations efficiently has previously been studied, but inadequate handling of the unpredictable behavior of the environment and possible failures resulted in limited success only. This dissertation presents a shared memory software system for executing programs with nested parallelism and synchronization on a network of non-dedicated workstations. The programming model exhibits a very convenient and natural programming style and is especially suitable for computations whose complexity and parallelism emerges only during their execution, such as in divide and conquer problems. To both support and take advantage of the flexibility inherent in the programming model, an architecture that distributes both the shared memory management and the computation is developed. This architecture removes bottlenecks inherent in centralization, thus enhancing scalability and dependability. By adapting available resource dynamically and coping with unpredictable machine slowdowns and failures, the system also supports dynamic load balancing, and fault tolerance-both transparently to the programmer.
Element Detection in Japanese Comic Book Panels

iv ABSTRACT Element Detection in Japanese Comic Book Panels Toshihiro Kuboi Comic books are a unique and increasingly popular form of entertainment combining visual and textual elements of communication. This work pertains to making comic books more accessible. Specifically, this paper explains how we detect elements such as speech bubbles present in Japanese comic book panels. Some applications of the work presented in this paper are automatic detection of text and its transformation into audio or into other languages. Automatic detection of elements can also allow reasoning and analysis at a deeper semantic level than what's possible today. Our approach uses an expert system and a machine learning system. The expert system process information from images and inspires feature sets which help train the machine learning system. The expert system detects speech bubbles based on heuristics. The machine learning system uses machine learning algorithms. Specifically, Naive Bayes, Maximum Entropy, and support vector machine are used to detect speech bubbles. The algorithms are trained in a fully-supervised way and a semi-supervised way. Both the expert system and the machine learning system achieved high accuracy. We are able to train the machine learning algorithms to detect speech bubbles just as accurately as the expert system. We also applied the same approach to eye detection of characters in the panels, and are able to detect majority of the eyes but with low precision. However, we are able to improve the performance of our eye detection system significantly by combining the SVM and either the Naive Bayes or the AdaBoost classifiers. v ACKNOWLEDGMENTS This thesis is inspired by Eriq Augustine's original project on the machine translation of Japanese comic books. I would like to thank Eriq for his guidance and assistance on the selection of this thesis topic.
Development and applications of porous tantalum trabecular metal-enhanced titanium dental implants.

BACKGROUND Porous tantalum trabecular metal has recently been incorporated in titanium dental implants as a new form of implant surface enhancement. However, there is little information on the applications of this material in implant dentistry. PURPOSE The purpose of this article is to summarize the contemporary concept on the applications of porous tantalum trabecular metal in implant dentistry. MATERIALS AND METHODS We therefore review the current literature on the basic science and clinical uses of this material. RESULTS Porous tantalum metal is used to improve the contact between osseous structure and dental implants and therefore presumably facilitate osseointegration. Success of porous tantalum metal in orthopedic implants led to the incorporation of porous tantalum metal in the design of root-form endosseous titanium implants. The porous tantalum three-dimensional enhancement of titanium dental implant surface allows for combining bone ongrowth together with bone ingrowth, or osseoincorporation. While little is known about the biological aspect of the porous tantalum in the oral cavity, there seems to be several possible advantages of this implant design. This article reviews the biological aspects of porous tantalum-enhanced titanium dental implants, in particular the effects of anatomical consideration and oral environment to implant designs. CONCLUSIONS We propose here possible clinical situations and applications for this type of dental implant. Advantages and disadvantages of the implants as well as needed future clinical studies are discussed.
Construcción de un mercado de datos para el almacenamiento de lesiones de causa externa [Building a Data Mart for the storage of injuries from external causes]

Resumen En este articulo se presenta el resultado de la segunda fase del proyecto de investigacion que tiene como objetivo detectar patrones delictivos con tecnicas de mineria de datos en el Observatorio del Delito del municipio de Pasto (Colombia). En esta fase se construyo un mercado de datos que almacenara los datos historicos, limpios y transformados sobre las lesiones de causa externa fatal y no fatales registradas en este Observatorio en un periodo de 10 anos. Este mercado permitira realizar analisis multidimensional y soportar la deteccion de patrones delictivos que facilite a los organismos gubernamentales y de seguridad tomar decisiones eficaces en lo relacionado a la implementacion de planes de prevencion de delitos y seguridad ciudadana. Palabras Clave: Mercado de Datos, Patrones Delictivos, Analisis Multidimensional, Mineria de Datos Abstract This paper presents the results of the second phase of the research project that aims to detect crime patterns with data mining techniques in the Crime Observatory of the municipality of Pasto (Colombia). At this stage, it has been built a data mart that will store historical, clear and processed data about injuries from fatal and non-fatal external causes recorded at the Observatory over a period of 10 years. This data mart will support multidimensional analysis in order to detect crime patterns which aim to facilitate the effective decision making in relation to the implementation of crime prevention plans and public safety by the government and security agencies. Keywords: Data Mart, Criminal Patterns, Multidimensional Analysis, Data Mining.
Query rewriting using statistical machine translation

In the area of Information Retrieval, user queries often mismatch the documents users exactly want. We regard this problem as a Query Rewriting task from user queries to document space. Using query logs containing query-keywords-CTR pairs, we trained a state-of-the-art statistical machine translation model to translate the user query to keywords of a web document. Using this method we successfully built the ¿lecical gap¿ between user queries and document keywords, and got the keywords as rewritings of the queries. We separately use BLUE and CTR-Recall as optimization target to complete eight comparable experiments. CTR-Recall is presented by us as an optimization target and evaluation indicator. It shows that if forcing the same word to be aligned in word alignment and using BLEU as optimization target we get both the best CTR-Recall and BLEU. At the same time using CTR-Recall as optimization target we get both the best CTR-Recall and BLEU too.
Sentinel Asia initiative for disaster management support in the Asia-Pacific region

The 'Sentinel Asia' initiative was established by regional space agencies, to use Remote Sensing information and Web-GIS data-delivery technologies in support of disaster management in the Asia-Pacific region. Sentinel Asia is 'voluntary and best-efforts-basis initiatives' led by the Asia-Pacific Regional Space Agency Forum (APRSAF) to share the disaster information in the region using the 'Digital Asia' (Web-GIS) platform and to make the best use of earth observation satellites data for disaster management in the Asia-Pacific region. The system is to initially be an internet-based, node-distributed, information distribution backbone, eventually distributing relevant satellite and in-situ spatial information on multiple hazards in the Asia-Pacific region. The system will also be used by member countries of Sentinel Asia in the Asia-Pacific region to 'trigger' dedicated satellite-data acquisitions by regionally operated satellites through their participating and cooperating space agencies during major and minor disasters in their countries. Operations of Sentinel Asia are to be commenced in October 2006 through a dedicated web site.
Variation of the mammary glands response of inbred female mice treated with estrogen.

Variations in mammary response and corrected mammary response of inbred female mice with estrogen treatment were investigated in comparison with those of mice which were randomly and inbred for short time. All mice tested were injected with total doses of 12.5 I. U. of synthetic estrogen five times from 20 days of birth every third day. Mammary response was manifested in mammary area of mice treated with estrogen and further, corrected for body weight.It seemed to be plausible that inbred mice did not show more uniform response in respect to both mammary response and corrected mammary response than the mice which were bred randomly and inbred for short time. Therefore, it was conclued that the use of inbred mice itself might not be necessarily preferred to that of mice which have been kept without inbreeding, in respect to variation of a character chosen to be of the type measured in bio-assay.
Sparse Implementations of Revised Simplex Algorithms on Parallel Computers

Parallelizing sparse simplex algorithms is one of the most challenging problems. Because of very sparse matrices and very heavy communication, the ratio of computation to communication is extremely low. It becomes necessary to carefully select parallel algorithms , partitioning patterns, and communication optimization to achieve a speedup. Two implementations on Intel hypercubes are presented in this paper. The experimental results show that a nearly linear speedup can be obtained with the basic revised simplex algorithm. However, the basic revised simplex algorithm has many ll-ins. We also implement a revised simplex algorithm with LU decomposition. It is a very sparse algorithm, and it is very diicult to achieve a speedup with it.
Microstructured Optical Fiber Sensors Embedded in a Laminate Composite for Smart Material Applications

Fiber Bragg gratings written in highly birefringent microstructured optical fiber with a dedicated design are embedded in a composite fiber-reinforced polymer. The Bragg peak wavelength shifts are measured under controlled axial and transversal strain and during thermal cycling of the composite sample. We obtain a sensitivity to transversal strain that exceeds values reported earlier in literature by one order of magnitude. Our results evidence the relevance of using microstructured optical fibers for structural integrity monitoring of composite material structures.
Channel Characterisation for an OFDM-MISO Train Communications System

To design an OFDM train communications system it is essential to characterize and consider the channel parameters. For a high train scenario the transmission channel is frequency selective as well as time variant. Thus, delay spread and Doppler spread are investigated as crucial parameters for the OFDM system performance. Using a ray-tracing tool realistic impulse responses of the transmission channels are simulated. The investigated system includes three base stations operating in common frequency mode along a railway track and one mobile station situated on a high-speed train. Mobile station antennas with different patterns are included in the simulation model. The results are compared and assessed with respect to delay spread and Doppler spread
Population-Based Survey of Filamentous Fungi and Antifungal Resistance in Spain (FILPOP Study)

A. Alastruey-Izquierdo, E. Mellado, T. Peláez, J. Pemán, S. Zapico, M. Alvarez, J. L. Rodríguez-Tudela, M. Cuenca-Estrella, FILPOP Study Group National Center for Microbiology, Madrid, Spain; Hospital General Universitario Gregorio Marañón, Madrid, Spain; Hospital Universitario La Fe, Valencia, Spain; Hospital Universitario Donostia, Guipuzcoa, Spain; Hospital Universitario Central de Asturias, Oviedo, Spain
Methane emissions estimate from airborne measurements over a western United States natural gas field

Methane (CH4) emissions from natural gas production are not well quantified and have the potential to offset the climate benefits of natural gas over other fossil fuels. We use atmospheric measurements in a mass balance approach to estimate CH4 emissions of 55 ± 15 × 103 kg h−1 from a natural gas and oil production field in Uintah County, Utah, on 1 day: 3 February 2012. This emission rate corresponds to 6.2%–11.7% (1σ) of average hourly natural gas production in Uintah County in the month of February. This study demonstrates the mass balance technique as a valuable tool for estimating emissions from oil and gas production regions and illustrates the need for further atmospheric measurements to determine the representativeness of our single‐day estimate and to better assess inventories of CH4 emissions.
nEASE: a method for gene ontology subclassification of high-throughput gene expression data

UNLABELLED High-throughput technologies can identify genes whose expression profiles correlate with specific phenotypes; however, placing these genes into a biological context remains challenging. To help address this issue, we developed nested Expression Analysis Systematic Explorer (nEASE). nEASE complements traditional gene ontology enrichment approaches by determining statistically enriched gene ontology subterms within a list of genes based on co-annotation. Here, we overview an open-source software version of the nEASE algorithm. nEASE can be used either stand-alone or as part of a pathway discovery pipeline. AVAILABILITY nEASE is implemented within the Multiple Experiment Viewer software package available at http://www.tm4. org/mev. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.