Miracle-dz/UniFAR-FTUs huggingface dataset:
A new architecture for the fast Viterbi algorithm

A novel architecture design to speed up the Viterbi algorithm is proposed. By doubling the number of states in the trellis, the serial operation of a traditional add-compare-select (ACS) unit is transformed into a parallel operation, thus achieving a substantial speed increase. The use of the proposed architecture would increase the speed by 33% at the expense of a fairy modest increase in area, thus removing the Viterbi detector/decoder from the worst case speed bottleneck path in most high-speed applications. A simple example is shown to illustrate the proposed algorithm in a maximum likelihood sequence detector.
Evaluation of soybean germplasm conserved in NIAS genebank and development of mini core collections

Genetic variation and population structure among 1603 soybean accessions, consisted of 832 Japanese landraces, 109 old and 57 recent Japanese varieties, 341 landrace from 16 Asian countries and 264 wild soybean accessions, were characterized using 191 SNP markers. Although gene diversity of Japanese soybean germplasm was slight lower than that of exotic soybean germplasm, population differentiation and clustering analyses indicated clear genetic differentiation among Japanese cultivated soybeans, exotic cultivated soybeans and wild soybeans. Nine hundred ninety eight Japanese accessions were separated to a certain extent into groups corresponding to their agro-morphologic characteristics such as photosensitivity and seed characteristics rather than their geographical origin. Based on the assessment of the SNP markers and several agro-morphologic traits, accessions that retain gene diversity of the whole collection were selected to develop several soybean sets of different sizes using an heuristic approach; a minimum of 12 accessions can represent the observed gene diversity; a mini-core collection of 96 accession can represent a major proportion of both geographic origin and agro-morphologic trait variation. These selected sets of germplasm will provide an effective platform for enhancing soybean diversity studies and assist in finding novel traits for crop improvement.
A Novel Approach for Automated Analysis of Cell Attachment and Spreading Based on Backscattered Electron Imaging by Scanning Electron Microscopy

The development of new materials for biological application requires in vitro testing of cell/surface interactions. Cell adhesion and spreading are difficult to quantify as most materials are non-transparent and transmission microscopy cannot be used. Contrast in reflection microscopy is rather poor. We propose an alternative method for the automated screening of cell attachment and spreading using backscattered electron imaging of scanning electron microscopy. The enhanced cell contrast permits study of cell/material interactions by little differences between cells and material.
Soma‐germline interactions that influence germline proliferation in Caenorhabditis elegans

Caenorhabditis elegans boasts a short lifecycle and high fecundity, two features that make it an attractive and powerful genetic model organism. Several recent studies indicate that germline proliferation, a prerequisite to optimal fecundity, is tightly controlled over the course of development. Cell proliferation control includes regulation of competence to proliferate, a poorly understood aspect of cell fate specification, as well as cell‐cycle control. Furthermore, dynamic regulation of cell proliferation occurs in response to multiple external signals. The C. elegans germ line is proving a valuable model for linking genetic, developmental, systemic, and environmental control of cell proliferation. Here, we consider recent studies that contribute to our understanding of germ cell proliferation in C. elegans. We focus primarily on somatic control of germline proliferation, how it differs at different life stages, and how it can be altered in the context of the life cycle and changes in environmental status. Developmental Dynamics 239:1449–1459, 2010. © 2010 Wiley‐Liss, Inc.
Deoxynucleoside Triphosphate and Pyrophosphate Binding Sites in the Catalytically Competent Ternary Complex for the Polymerase Reaction Catalyzed by DNA Polymerase I (Klenow Fragment) (*)

We have employed site-directed mutagenesis to identify those amino acid residues that interact with the deoxynucleoside triphosphate (dNTP) and pyrophosphate in the Klenow fragment-DNA-dNTP ternary complex. Earlier structural, mutagenesis, and labeling studies have suggested that the incoming dNTP molecule contacts a region on one side of the polymerase cleft, primarily involving residues within the so-called “fingers” subdomain. We have made mutations in residues seen to be close to the dNTP in the crystal structure of the Klenow fragment-dNTP binary complex and have examined their kinetic parameters, particularly K. The results are consistent with the notion that there are significant differences between the dNTP interactions in the binary and ternary complexes, although some contacts may be present in both. When dTTP is the incoming nucleotide, the side chains of Arg and Phe make the largest contributions to binding; measurement of K suggests that Arg contacts the β- or -phosphate of the dNTP. With dGTP, the contribution of Arg remains the same, but the additional interactions are provided by both Lys and Phe, suggesting that the binding of the incoming dNTP is not identical under all circumstances. Mutations in Arg and Lys also cause a substantial decrease in the rate of polymerase-catalyzed incorporation, and sulfur elemental effect measurements indicate that loss of Arg (and perhaps also Lys) slows the rate of the chemical step of the reaction. Mutations of Arg, His, and Tyr affect the binding of DNA, suggesting that these mutations, whose effect on dNTP binding is small, may influence dNTP binding indirectly via the positioning of the DNA template-primer.
Perceptual Grouping and Visual Enumeration

We used lateralized Event-Related Potential (ERP) measures – the N2pc and CDA/SPCN components – to assess the role of grouping by target similarity during enumeration. Participants saw a variable number (0, 1, 2 or 3) of same- or differently-colored targets presented among homogeneous distracters, and performed an enumeration task. Results showed that the N2pc, but not the CDA, was larger for multiple targets of identical color relative to targets of different colors. The findings are interpreted in terms of the effects of grouping on early versus late stages of multiple object processing. Within this framework, they reveal that grouping has an effect on early individuation mechanisms, while later processing mechanisms are less prone to such an influence.
Ensemble Modeling of Biological Systems

Mathematical modeling of biological systems must cope with difficulties that are rarely present in traditional fields of applied mathematics, such as a large number of components involved, extreme complexity and variety of interactions, and the lack of reproducible and consistent data. These difficulties may be overcome by models of new type, termed ensemble models, which allow for the parameters and the model structure to vary and thereby describe a population of all models that are consistent with biological knowledge about the system. Ensemble models are identified and their parameters are estimated using Bayesian techniques, and the models are subsequently used to provide probabilistic predictions about the system behavior and and its response to changes in conditions. We here survey the basic methodology of ensemble modeling and its applications to biological systems.
Bayesian Classification

This paper describes a Bayesian technique for unsupervised classification of data and its computer implementation, Autoclass. Given real valued or discrete data, AutoClass automatically determines the most probable number of classes present in the data, the most probable descriptions of those classes, and each object's probability of membership in each class. The program performs as well as or better than existing automatic classification systems when run on the same data, and contains no ad hoc similarity measures or stopping criteria. Researchers have also applied AutoClass to several large databases where it has discovered classes corresponding to new phenomena which were previously unsuspected. ( N A S AT M1 i ) I 2 7 4 ) d A Y C 5 T AY f LA 5 S I F I C A T 1 Ci& ( N A T A ) 17 r_,
Sequencing of hsp65 Distinguishes among Subsets of the Mycobacterium avium Complex

ABSTRACT The Mycobacterium avium complex consists of epidemiologically distinct subsets. The classification of these subsets is complicated by a number of factors, including the ambiguous results obtained with phenotypic and genetic assays and the recent appreciation that human and avian strains appear to be distinct. In previous work, sequencing based on a 441-bp portion of the hsp65 gene has proven to efficiently classify isolates within the Mycobacterium genus but provides low resolution for distinguishing among members of the M. avium complex. Therefore, in this study, we have targeted the more variable 3′ region of the hsp65 gene to determine whether it can effectively discriminate M. avium complex isolates at the levels of species and subspecies. Primers designed for this target consistently generated amplicons for all organisms classified as M. avium complex. Sequences obtained indicate that M. intracellulare is genetically divergent from M. avium organisms, and distinct sequevars were obtained for M. avium subsets, including M. avium subsp. avium (bird type), M. avium subsp. hominissuis, and M. avium subsp. paratuberculosis. In addition, sequence differences served to distinguish bovine from ovine strains of M. avium subsp. paratuberculosis. A unique profile for M. avium subsp. silvaticum was not obtained. These results indicate that sequencing the 3′ region of the hsp65 gene can simply and unambiguously distinguish species and subspecies of the M. avium complex.
Splinting vs surgery in the treatment of carpal tunnel syndrome: a randomized controlled trial.

CONTEXT Carpal tunnel syndrome (CTS) can be treated with nonsurgical or surgical options. However, there is no consensus on the most effective method of treatment. OBJECTIVE To compare the short-term and long-term efficacy of splinting and surgery for relieving the symptoms of CTS. DESIGN, SETTING, AND PATIENTS A randomized controlled trial conducted from October 1998 to April 2000 at 13 neurological outpatient clinics in the Netherlands. A total of 176 patients with clinically and electrophysiologically confirmed idiopathic CTS were assigned to wrist splinting during the night for at least 6 weeks (89 patients) or open carpal tunnel release (87 patients); 147 patients (84%) completed the final follow-up assessment 18 months after randomization. MAIN OUTCOME MEASURES General improvement, number of nights waking up due to symptoms, and severity of symptoms. RESULTS In the intention-to-treat analyses, surgery was more effective than splinting on all outcome measures. The success rates (based on general improvement) after 3 months were 80% for the surgery group (62/78 patients) vs 54% for the splinting group (46/86 patients), which is a difference of 26% (95% confidence interval [CI], 12%-40%; P<.001). After 18 months, the success rates increased to 90% for the surgery group (61/68 patients) vs 75% for the splinting group (59/79 patients), which is a difference of 15% (95% CI, 3%-27%; P =.02). However, by that time 41% of patients (32/79) in the splint group had also received the surgery treatment. CONCLUSION Treatment with open carpal tunnel release surgery resulted in better outcomes than treatment with wrist splinting for patients with CTS.
Production of stem cell factor and expression of c‐kit in human rhabdomyosarcoma cells: Lack of autocrine growth modulation

Human rhabdomyosarcoma cells produce autocrine and paracrine growth factors that can sustain their growth and malignancy. Here we report constitutive production of stem cell factor (SCF) by 5 of 5 human rhabdomyosarcoma cell lines both of alveolar and embryonal histotype. SCF production, ranging from 30 to 162 pg/ml, was independent from the degree of myogenic differentiation and was not modulated by exogenous addition of retinoic acid (RA) or tumor necrosis factor‐α (TNF‐α). Four of 5 rhabdomyosarcoma cell lines expressed the mRNA for SCF receptor c‐kit, while the 5th cell line became weakly positive for c‐kit mRNA only after stimulation with retinoic acid. On the cell surface, c‐kit protein was detectable at very low levels in only 1 of 5 rhabdomyosarcoma cell lines and was not up‐regulated by RA or TNF‐α. Addition of anti‐c‐kit and anti‐SCF blocking antibodies, or of exogenous SCF did not alter the in vitro growth ability of rhabdomyosarcoma cells. In conclusion, our data show that rhabdomyosarcoma cells produce consistent amounts of SCF but did not demonstrate autocrine growth modulation. SCF secretion may thus have a paracrine, rather than an autocrine activity in this tumor. Int. J. Cancer 78:441–445, 1998. © 1998 Wiley‐Liss, Inc.
A novel 6-DoF biped active walking robot — Walking gaits, patterns and experiments

Combining the advantages of active and passive walking robots, we have developed a novel active biped walking robot with only six DoFs. The robot is built with six 1-DoF joint modules and two wheels as the feet. It achieves locomotion in special gaits different from those of traditional biped robots. In this paper, this novel biped robot is introduced, and four walking gaits, namely turning-around gait, foot-wheel hybrid gait, side-stepping gait and turning-over gait are proposed, and their walking patterns and motion planning are presented and analyzed. Walking experiments are carried out to verify the locomotion function, the effectiveness of the presented gaits and to illustrate the features of this novel biped robot. It has been shown that biped active walking may be achieved with only a few DoFs and simple kinematic configuration.
The Cost of Homelessness: A Perspective from the United States

> > _ This paper discusses how researchers and others have analyzed the services histories of persons who have experienced homelessness, as well as their imputed costs. This research has been used both to make visible the ways in which the clients of mainstream social welfare systems (health, corrections, income maintenance and child welfare) become homeless and, complementarily, the impact of people who experience homelessness on the use of these service systems. Most published work in this area has been based on the integration of administrative databases to identify cases and service utilization patterns ; some have used retrospective interviews. Results have been used to encourage agency administrators and policymakers to make investments in programs that reduce homelessness and/or the duration of homelessness periods. Quite recently, many local homeless services planning organizations in the US have used this approach to demonstrate the high costs of chronic homelessness and the potential cost offsets associated with the placement of people in supported housing. The opportunities and limitations associated with these various approaches, including their potential applicability to other countries and service sectors are discussed.
Proving NP-hardness for clique-width II: non-approximability of clique-width

Clique-width is a graph parameter that measures in a certain sense the complexity of a graph. Hard graph problems (e.g., problems expressible in Monadic Second Order Logic with second-order quantication on vertex sets, that includes NP-hard problems) can be solved ecien tly for graphs of certied small clique-width. It is widely believed that determining the clique-width of a graph is NP-hard; in spite of considerable eorts, no NP-hardness proof has been found so far. We give the rst hardness proof. We show that the clique-width of a given graph cannot be absolutely approximated in polynomial time unless P = NP. We also show that, given a graph G and an integer k, deciding whether the clique-width of G is at most k is NP-complete. This solves a problem that has been open since the introduction of clique-width in the early 1990s.
Automated Image Classification System using Color and Texture Features

With the consolidation of the Internet as a medium for information interchange, several news agencies and educational organizations have allowed on-line access to their image and video collections in digital format. Therefore, a crucial task is to organize these large volumes of pictorial data, in order to extract relevant information. It is possible to address this problem by performing an automatic classification of images. This paper is an attempt to develop an automated system for image classifications for aquamarine learning system. The proposed system will have fast & robust retrieval algorithm for contour images.
Cost-Benefit Arbitration Between Multiple Reinforcement-Learning Systems

Human behavior is sometimes determined by habit and other times by goal-directed planning. Modern reinforcement-learning theories formalize this distinction as a competition between a computationally cheap but inaccurate model-free system that gives rise to habits and a computationally expensive but accurate model-based system that implements planning. It is unclear, however, how people choose to allocate control between these systems. Here, we propose that arbitration occurs by comparing each system’s task-specific costs and benefits. To investigate this proposal, we conducted two experiments showing that people increase model-based control when it achieves greater accuracy than model-free control, and especially when the rewards of accurate performance are amplified. In contrast, they are insensitive to reward amplification when model-based and model-free control yield equivalent accuracy. This suggests that humans adaptively balance habitual and planned action through on-line cost-benefit analysis.
Uropathogen antibiotic resistance in adult women presenting to family physicians with acute uncomplicated cystitis.

BACKGROUND Increasing rates of trimethoprim-sulfamethoxazole (TMP-SMX) resistance among uropathogens have raised concerns about its continued role in empirical treatment of acute uncomplicated cystitis in adult women. OBJECTIVE To determine current rates of antibiotic resistance among uropathogens in the community. METHODS Urine culture reports from adult women with symptoms of cystitis attending the offices of family physicians from across Canada were examined. Antibiotic sensitivities and the total number of antibiotics an organism was resistant to was determined. RESULTS In 446 women, 235 (61.4%) positive urine cultures were identified. Of these, 38.2% were resistant to at least one antibiotic and 21.5% were resistant to two or more antibiotics. The rate of ampicillin resistance was 34.1%. For TMP-SMX, resistance was reported in 10.8% of samples. Antibiotic resistance was higher in British Columbia (55%) and western provinces (48%), compared with Ontario (33.3%) and the eastern provinces (26.3%, P=0.04, Fisher's exact test). Multidrug resistance was also higher in western Canada (33.9%) than in eastern Canada (16.6%, P=0.007). CONCLUSIONS TMP-SMX resistance in Canada remains within current recommended guidelines, allowing for its continued use as a first line empirical treatment for acute cystitis in adult women. The reasons for higher rates of antibiotic resistance in western Canada merit further study.
Power-Law Topology Models with Given Spatial Distribution

Many real networks have power-law topological properties as well as some spatial properties. This paper presents a set of models for such topologies. A coverage area (CA) based model (CAM) is proposed with CA of a node to associate the spatial and topological properties. A heuristic gravity algorithm (ERA) is proposed in the sense that a node with heavier mass has larger CA and with gravity to associate both properties. A probabilistic variant of ERA, PERA, is proposed to model the dynamic evolution mechanism of power law network with specific spatial properties. Analysis and simulation show that these models can generate power-law graphs with given spatial distribution and can be realized easily with good scalability
A new hash algorithm exploiting triple-state bucket directory for flash storage devices

Recently, the flash storage device becomes more important to the mobile consumer electronics that supports various functionalities because of its portability and reliability. The capacity of the flash storage device is becoming larger and its price is going down due to the mass production of the Triple-Level Cell (TLC) flash memory. Since TLC flash memories are very cheap, they are widely deployed in the mobile flash storage device although its durability is poor. In addition, it is difficult to handle the large-scale flash memories with limited memory resources in the mobile flash storage device. Therefore, TLC-based flash storage device requires to internally optimize the write and erase operations with small memory resources. This paper proposes a new hash-based mapping algorithm, which reduces the redundant write and erase operations and uses only a few memory resources, for the mobile flash storage device. The proposed hash algorithm also guarantees uniform performance regardless of various workload patterns. Through various experiments with related works, this paper shows the superiority of the proposed hash algorithm.
HIV/AIDS and Antiretroviral Treatment Knowledge, Attitudes, Beliefs, and Practices in HIV-Infected Adults in Soweto, South Africa

Summary:A cross-sectional study of knowledge, attitudes, beliefs, and practices (KABPs) toward HIV and antiretroviral therapy (ART) was conducted in Soweto, South Africa, using a standardized validated questionnaire. Of 105 HIV clinic patients evaluated, 70% of whom were not on ART, 89% had good knowledge about the cause of HIV infection and 83% knew about modes of transmission. Fifty-nine percent reported they were not worried about ART side effects. Sixty-five percent agreed that missing ART doses can lead to disease progression. Ninety percent had disclosed their HIV serostatus to 1 or more persons, but only 62% of those with a current sexual partner reported having told that partner. Approximately 80% reported that if they were taking ART, they would not be worried about family or friends finding out. Forty-nine percent believed that ART can cure HIV, a belief that was associated with a low level of education (P < 0.001). Overall, knowledge of the cause of HIV/AIDS, modes of transmission, and importance of ART adherence was good in our study population. Further research is warranted to assess the extent to which this knowledge and attendant attitudes predict ART adherence levels. The low rate of HIV serostatus disclosure to sexual partners calls for multidimensional interventions to reduce HIV-related stigma.
A simple method to assess the added value using high‐resolution climate distributions: application to the EURO‐CORDEX daily precipitation

Regional climate models (RCMs) are used with increasing resolutions seeking to represent in an improved way regional to local‐scale atmospheric phenomena. The EURO‐CORDEX simulations at 0.11° and simulations exploiting finer grid spacing approaching the convective‐permitting regimes are representative examples. These climate runs are computationally very demanding and do not always show improvements, which depend on the region, variable and object of study. The gains or losses associated with the use of higher resolution in relation to the forcing model (global climate model or reanalysis), or to different resolution RCM simulations, are widely known as added value. Its characterization is a long‐standing issue, and many different added‐value measures have been proposed.