Miracle-dz/UniFAR-FTUs huggingface dataset:
Maximizing OSD Performance with EBOFS Technical Report UCSC-SSRC-04-02 March 2004

The current and coming generations of large distributed file systems stripe data across large numbers of objectbased storage devices (OSDs). Subsequently, individual OSD workloads tend to exhibit no inter-object locality of reference. Small object sizes reduce OSD efficiency due to disk seek overheads. EBOFS, an extent and B+tree based object file system, allows arbitrarily sized objects and preserves intra-object locality of reference by allocating data contiguously on disk, and maintains high levels of contiguity even over the entire lifetime of a disk’s file system, allowing OSDs to operate more efficiently and distributed file systems to maximize performance.
Recognizing Algorithms Using Roles of Variables , Language Constructs and Software Metrics : A Machine Learning Approach

Roles of Variables (RoV) are concepts that describe the behavior and usage of variables in computer programs. RoV have originally been introduced to help novices learn programming. Algorithm Recognition (AR) is a subfield of program comprehension, where the problem is to identify algorithms from the source code. AR covers recognizing different algorithms that carry out different computational task, as well as different types of algorithms that perform the same task. The main application of AR is in automatic assessment of students' programs to verify that the program implements the required algorithm. This thesis investigates the applicability and usefulness of RoV in AR. The idea is to analyze different implementations of basic algorithms to see whether RoV appear in those algorithms is such a way that they can be distinguished on this basis. In addition to RoV, other distinctive characteristics that can be used in the recognition process are also identified from the algorithms. These characteristics are related to language constructs and various software metrics. Based on the results of these analyses, a method for AR is introduced and a tool for automatic algorithm recognition is developed. Two experiments on sorting algorithms are carried out to illustrate the feasibility of the AR method. In the first experiment, sorting algorithms are recognized using a manually constructed decision tree. The second experiment uses the C4.5 algorithm to construct the decision tree. The results of the experiments (86% and 97.1% correctly recognized algorithms respectively) show the applicability of RoV and the other characteristics in AR problem. Moreover, the performance of the automatically constructed decision tree demonstrates that machine learning techniques are also suitable for AR task. and was partially funded by the Academy of Finland. I would like to thank my supervisor, Professor Lauri Malmi, for providing me the opportunity to do this work. I highly appreciate his valuable input, feedback and suggestions during the project. I am sincerely thankful to him. I am also grateful to my instructor, Docent Ari Korhonen, for his insightful comments, helpful ideas and great discussions. Finally, I would like to express my greatest gratitude to my family; my wife, Elmira, my daughter Ava and my son Arad, for their love, understanding and encouragement, as well as my parents for their support over the years. This paper discusses roles of variables, their application to algorithm recognition and introduces a method for algorithm recognition. It also presents an extensive literature …
Genotyping of Candida orthopsilosis Clinical Isolates by Amplification Fragment Length Polymorphism Reveals Genetic Diversity among Independent Isolates and Strain Maintenance within Patients

ABSTRACT Candida parapsilosis former groups II and III have recently been established as independent species named C. orthopsilosis and C. metapsilosis, respectively. In this report, 400 isolates (290 patients) previously classified as C. parapsilosis by conventional laboratory tests were screened by BanI digestion profile analysis of the secondary alcohol dehydrogenase gene fragment and by amplification fragment length polymorphism (AFLP). Thirty-three strains collected from 13 patients were identified as C. orthopsilosis, thus giving the first retrospective evidence that C. orthopsilosis was responsible for 4.5% of the infections/colonization attributed to C. parapsilosis. AFLP was proven to unambiguously identify C. orthopsilosis at the species level and efficiently delineate intraspecific genetic relatedness. A high percentage of polymorphic AFLP bands was observed for independent isolates collected from each patient. Statistical analysis of the pairwise genetic distances and bootstrapping revealed that clonal reproduction and recombination both contribute to C. orthopsilosis genetic population structure. AFLP patterns of sequential isolates obtained from two patients demonstrated that a successful strain colonization within the same patient occurred, as revealed by strain maintenance in various body sites. No association between AFLP markers and drug resistance was observed, and none of the clinical C. orthopsilosis isolates were found to produce biofilm in vitro.
Shader-Based Stereo Matching with Local Algorithms

Modern graphic cards can perform extreme amounts of calculations. In addition, the problem within the field of computer vision is often that the algorithms are very time consuming. The objective of this thesis is to find solutions to the stereo matching problem, employing dense local two-frame stereo matching algorithms and hardware support within modern graphic cards. The performance of the implementations is measured against CPU-algorithms, to test the advantage of the shader approach. The algorithms were examined in Matlab and thereafter written in C++, using the DirectX API. Several different local area-based algorithms were tested and implemented as separate components (filters). The separate design created flexibility and testing became easy. The shader programming was done with standard DirectX assembler, for high control and efficiency. The results clearly indicate the advantage of implementing algorithms from image processing by using commodity shaders instead of the CPU.
A nearly linear time algorithm for the half integral disjoint paths packing

We consider the following problem, which is called the <i>half integral k disjoint paths packing. </i> <b>Input</b>: A graph <i>G</i>, <i>k</i> pair of vertices (<i>s</i><sub>1</sub>, <i>t</i><sub>1</sub>), (<i>s</i><sub>2</sub>, <i>t</i><sub>2</sub>),…, (<i>s<sub>k</sub></i>, <i>t<sub>k</sub></i>) in <i>G</i> (which are sometimes called <i>terminals</i>). <b>Output</b>: Paths <i>P</i><sub>1</sub>,…, <i>P<sub>k</sub></i> in <i>G</i> such that <i>P<sub>i</sub></i> joins <i>s<sub>i</sub></i> and <i>t<sub>i</sub></i> for <i>i</i> = 1,2,…, <i>k</i>, and in addition, each vertex is on at most two of these paths. We present an <i>O</i>(<i>n</i> log <i>n</i>) time algorithm for this problem for fixed <i>k. </i> This improves a result by Kleinberg [21] who gave an <i>O</i>(<i>n</i><sup>3</sup>) algorithm for this problem. In fact, we also have algorithms running in <i>O</i>(<i>n</i><sup>(1+ε)</sup>) time for any ε > 0 for these problems, if <i>k</i> is up to <i>o</i>((log log <i>n</i>)<sup>2/5</sup>) for general graphs, up to <i>o</i>((log <i>n</i>/(log log <i>n</i>))<sup>1/4</sup>) for planar graphs, and up to <i>o</i>((log <i>n/g/</i>(log log <i>n/g</i>))<sup>1/4</sup>) for graphs on the surface, where <i>g</i> is the Euler genus. Furthermore, if <i>k</i> is fixed, then we have linear time algorithms for the planar case and for the bounded genus case. We also obtain <i>O</i>(<i>n</i> log <i>n</i>) algorithms for several optimization problems related to the bounded unsplittable flow problem when the number of terminal pairs is bounded. These results can all carry over to problems involving edge capacities.
Homocysteine and cognitive function in the elderly

Background: Elevated plasma total homocysteine (tHcy) concentrations are associated with AD and vascular dementia, but the relation with cognitive performance in nondemented elderly people is not known. Objective: To examine the association of tHcy and cognitive function in the elderly, and assess whether this may be mediated by structural brain changes on MRI. Methods: The Rotterdam Scan Study is a population-based study of 1,077 nondemented elderly. Cognitive performance was assessed, and compound scores were constructed for psychomotor speed, memory function, and global cognitive function. Cerebral infarcts, white matter lesions, and generalized brain atrophy were measured on MRI. The cross-sectional relationship between tHcy levels and neuropsychological test scores was assessed by multiple regression. Results: Mean tHcy level was 11.5 μmol/L (SD 4.1). Increasing tHcy levels were associated with lower scores for psychomotor speed, memory function, and global cognitive function, and this was largely due to the association with tHcy levels in the upper quintile (>14 μmol/L). Adjusted differences between test scores of participants in the upper quintile as compared with the lower four quintiles of tHcy were −0.26 (95% CI: −0.37; −0.14) for psychomotor speed, −0.13 (95% CI: −0.27; 0.01) for memory function, and −0.20 (95% CI: −0.30; −0.11) for global cognitive function. These associations were not mediated by structural brain changes on MRI. Conclusion: Elevated tHcy levels are associated with decreased cognitive performance in nondemented elderly people, and the relation was most marked for psychomotor speed. This association was independent of structural brain changes on MRI.
Programming Strategies for Contextual Runtime Specialization

Runtime adaptability is expected to adjust the application and the mapping of computations according to usage contexts, operating environments, resources availability, etc. However, extending applications with adaptive features can be a complex task, especially due to the current lack of programming models and compiler support. One of the run-time adaptability possibilities is the use of specialized code according to data workloads and environments. Traditional approaches use multiple code versions generated offline and, during runtime, a strategy is responsible to select a code version. Moving code generation to runtime can achieve important improvements but may impose unacceptable overhead. This paper presents an aspect-oriented programming approach for runtime adaptability. We focus on a separation of concerns (strategies vs. application) promoted by a domain-specific language for programming runtime strategies. Our strategies allow runtime specialization based on contextual information. We use a template-based runtime code generation approach to achieve program specialization. We demonstrate our approach with examples from image processing, which depict the benefits of runtime specialization and illustrate how several factors need to be considered to efficiently adapt the application.
Image based vehicle type identification

Vehicle type (make and model) recognition provides high level of security to the systems that are solely based on automatic license plate detection and recognition. Most of the work in this direction has been done in controlled conditions. In this paper we evaluate in an extensive experimental setting, the strength and weakness of various global and local feature based methods on vehicle images captured under controlled as well as uncontrolled conditions. We have introduced a challenging database that has been collected in complex conditions i-e scale, rotation, illumination variation, low contrast etc. Our method achieves 65 % rank-1 recognition accuracy on vehicle images captured under uncontrolled conditions with strong background clutter and 85 % recognition accuracy on segmented vehicle images captured under controlled conditions.
A hybrid method for parameter estimation

In this paper a method is presented for plant model parameter estimation. The method combines the artificial neural networks ability for function approximation with a nonlinear least-squares regression technique using the Levenberg-Marquardt optimization method. This combination intends to overcome problems that arise when artificial neural networks or nonlinear least-squares regression are separately applied to parameter estimation, which is accomplished by means of potentiating each of the methods advantages. The estimation of atracurium effect concentration model parameters is used as a case study to show the efficiency of the proposed method.
The effect of artificially induced drought on radial increment and wood properties of Norway spruce.

We studied experimentally the effects of water availability on height and radial increment as well as wood density and tracheid properties of Norway spruce (Picea abies (L.) Karst. ). The study was carried out in two long-term N-fertilization experiments in Southern Finland (Heinola and Sahalahti). At each site, one fertilized and one control plot was covered with an under-canopy roof preventing rainwater from reaching the soil. Two uncovered plots were monitored at each site. The drought treatment was initiated in the beginning of growing season and lasted for 60-75 days each year. The treatment was repeated for four to five consecutive years depending on the site. Altogether, 40 sample trees were harvested and discs sampled at breast height. From the discs, ring width and wood density were measured by X-ray densitometry. Tracheid properties were analysed by reflected-light microscopy and image analysis. Reduced soil water potential during the growing season decreased annual radial and height increment and had a small influence on tracheid properties and wood density. No statistically significant differences were found in the average tracheid diameter between the drought-treated and control trees. The average cell wall thickness was somewhat higher (7-10%) for the drought treatment than for the control, but the difference was statistically significant only in Sahalahti. An increased cell wall thickness was found in both early- and latewood tracheids, but the increase was much greater in latewood. In drought-treated trees, cell wall proportion within an annual ring increased, consequently increasing wood density. No interaction between the N fertilization and drought treatment was found in wood density. After the termination of the drought treatment, trees rapidly recovered from the drought stress. According to our results, severe drought due to the predicted climate change may reduce Norway spruce growth but is unlikely to result in large changes in wood properties.
The retina rapidly incorporates ingested C20-D3-vitamin A in a swine model

Purpose To determine how the retina uses vitamin A for vision, we studied the flux of oral vitamin A into and out of the swine retina. Methods We administered labeled vitamin A to swine daily for 30 days and measured the percent of the labeled vitamin A to native unlabeled vitamin A in the retinal epithelium, neuroretina, plasma, liver, lung, and kidney. Results We show that during normal vitamin A homeostasis, the retina rapidly assimilates newly ingested dietary vitamin A, which replaces native vitamin A. Retinal vitamin A is turned over faster than previously thought. Provitamin A carotenoids do not significantly contribute to retinal vitamin A pools when consuming diets adequate in vitamin A. Conclusions Fast vitamin A turnover in the retina has direct implications for emerging therapies to prevent major forms of blindness based on controlling the concentrations of retinal vitamin A.
Balanced Query Methods for Improving OCR-Based Retrieval

Since many documents are available only print, improving OCR-based retrieval of scanned documents is an important problem. This paper presents a novel language independent technique for mapping queries from an error-free space to an OCR-degraded document space using a noisy channel model to produce possible degraded versions of query terms. The new technique yielded statistically significant improvements in retrieval effectiveness of as much as 39% over clean queries when tested on an Arabic document image collection.
Kinetics of Perrhenate Uptake and Comparative Biodistribution of Perrhenate, Pertechnetate, and Iodide by Nai Symporter–expressing Tissues in Vivo

Pertechnetate (as 99m TcO 4 Ϫ), 123 I Ϫ , and 131 I Ϫ have a long and successful history of use in the diagnosis and therapy of thyroid cancer, with uptake into thyroid tissue mediated by the sodium-iodide symporter (NIS). NIS has also emerged as a potential target for radiotherapy of nonthyroid malignancies that express the endogenous or transfected symporter. Perrhenates (as 188 ReO 4 Ϫ and 186 ReO 4 Ϫ) are promising therapeutic substrates of NIS, although less is known about their behavior in vivo. In this study, we endeavored to characterize the biologic behavior of perrhenate, especially in relation to iodide and pertechnetate, to better explore its possible therapeutic role. Methods: We describe the simultaneous biodistribution and uptake in vivo of iodide, pertechnetate, and perrhenate in groups of healthy CD1 mice, either with or without coadministration of perchlorate (ClO 4 Ϫ), a potent NIS inhibitor. Animals administered single ra-diopharmaceuticals were imaged as a means of illustrating these findings. Kinetic properties of perrhenate were compared with those of iodide in a stably transfected NIS-bearing Madin– Darby canine kidney (MDCK) cell line. Results: Biodistributions of iodide, pertechnetate, and perrhenate in live mice were remarkably similar. Activity in salivary gland and stomach was severalfold greater than in blood, remained elevated over the initial 2 h, and subsequently washed out. A similar pattern characterized pertechnetate and perrhenate uptake by the thyroid , in which the 2-h concentration was slightly more elevated than at the 20-min time point. However, uptake subsequently decreased by 19 h. In contrast, iodide continued to increase through the 19-h time point, presumably as a result of organi-fication. The addition of perchlorate sharply decreased uptake of all 3 radiopharmaceuticals by the stomach, salivary glands, and thyroid and resulted in their rapid clearance, paralleling blood-pool clearance. In tissues that do not express NIS (liver, muscle, spleen), uptake of all 3 radiopharmaceuticals was low and rapidly decreased over time, paralleling blood-pool clearance. Similar findings were seen in kidney, where only minimal amounts of NIS are expressed in tubular cells. In stably trans-fected MDCK cells, steady-state accumulation of iodide was approximately 4-fold higher than that of perrhenate at 30 min. No active transport was demonstrated in nontransfected MDCK cell lines or after perchlorate administration. Uptake values measured at different concentrations of substrate demonstrated saturation kinetics. Apparent maximal velocity values for perrhenate and iodide were 25.6 Ϯ 1.4 and 106 Ϯ 3.2 …
Pharmacokinetics of Anti-HBV Polyoxometalate in Rats

Polyoxometalates are non-nucleoside analogs that have been proven to exhibit broad-spectrum antiviral activity. In particular, Cs2K4Na[SiW9Nb3O40]. H2O 1 shows low toxicity and high activity against HBV. The preclinical pharmacokinetics of Compound 1 in rats were characterized by establishing and applying inductively coupled plasma-mass spectrometry method to determine the concentration of W in plasma, urine, feces, bile and organ samples. The quantitative ICP-MS method demonstrated good sensitivity and application in the pharmacokinetics study of polyoxometalates. The pharmacokinetic behavior of Compound 1 after intravenous or oral administration fit a two-compartment model. Tmax ranges from 0.1 h to 3 h and the T1/2 of Compound 1 is between 20 h and 30 h. The absolute bioavailability of Compound 1 at 45, 180 and 720 mg/kg groups were 23.68%, 14.67% and 11.93%, respectively. The rates of plasma protein binding of Compound 1 at 9, 18 and 36 mg/ml of Compound 1 are 62.13±9.41%, 71.20±24.98% and 49.00±25.59%, respectively. Compound 1 was widely distributed throughout the body, and high levels of compound 1 were found in the kidney and liver. The level of Compound 1 in excretion was lower: 30% for urine, 0.28% for feces and 0.42% for bile, respectively. For elaborate pharmacokinetic characteristics to be fully understood, the metabolism of Compound 1 needs to be studied further.
A Novel Compact Printable Dual-Polarized Chipless RFID System

A novel compact design of an ultralow-cost fully printable slot-loaded dual-polarized chipless radio frequency identication tag is presented with four near- and far-field reading techniques. The tag consists of four rectangular metallic patches loaded with multiple slot resonators. Slots with the same polarization for adjacent frequencies are placed alternately into two patches to reduce the mutual coupling between the slots. Then two similar sets are placed in horizontal and vertical polarizations to double the number of bits within the same frequency bandwidth. The tag can be detected using dual-polarized waveguide(s) or dual-polarized antennas. This single-sided compact chipless tag has higher data capacity and lower cost compared with the existing printable chipless tags and can be used in personal ID or credit cards and banknotes and can be directly printed on paper or plastic packets for item-level tagging.
Engaging employers, graduates and students to inform the future curriculum needs of soil science

This paper reports on the findings of a project to investigate the future needs of a soil science curriculum to produce work-ready graduates. Soil scientists are expected to deal with increasingly complex problems and graduates are required to have not only have well developed soil science knowledge and skills, but can also work between and across other disciplines communicate their findings appropriately. Survey results obtained from current student, graduates and employers of soil science indicated some areas of discipline knowledge that need to be addressed, as well as more emphasis on developing critical thinking and problem solving skills. Employers also expressed the desire to not only provide advice on curriculum change but a willingness to be involved in the learning environment. Using problem based learning as the scaffold an example of how industry maybe engaged is provided. Issues are raised around the need to align the graduate outcomes for soil science with Threshold Learning Outcomes for Science and Agriculture and the need for a core-body of knowledge (CBoK) that characterise graduates with soil science knowledge. As a result of widespread stakeholder consultations during the project a set of soil science teaching principles was developed (Field et al., 2011). Field, D. J., Koppi, A. J., Jarrett, L. E. , Abbott, L. K. , Cattle, S. R. , Grant, C. D. McBratney A. B. , Menzies N. W. , Weatherly A. J. (2011). Soil Science Teaching Principles. Geoderma, 167-168, 9-14.
Secure image retrieval using pyramid histogram of oriented gradient descriptor

Secure Content Based Image Retrieval (CBIR) deals with retrieving similar images from an image database without revealing the contents of the query image. In the traditional CBIR, it is not practically possible to store large volumes of image database locally. Hence, image database has to be stored in a remote server. In this paper, the images are encrypted using double key RSA algorithm and are stored in the remote servers. The pyramid histogram of oriented gradients (PHoG) descriptor is used as feature for representing the images. The PHoG descriptor is computed on the original image and are encrypted and then stored in the remote server. The double key RSA ensures security and the attacker cannot effortlessly decrypt the images stored in the public server.