Miracle-dz/UniFAR-FTUs huggingface dataset:
Asymptotically Optimal Sampling-Based Algorithms for Topological Motion Planning

Topological motion planning is a planning problem embedding topological concept of trajectories. In this work, we propose two asymptotically optimal sampling-based algorithms for topological motion planning: (a) a batch processing-based planner, termed Fast Marching Homology-embedded Tree star (FMHT*); and (b) an incremental anytime algorithm, termed Rapidly-exploring Random Homology-embedded Tree star (RRHT*). The methods commonly expand a graph directly in the configuration space and project the associated tree onto the topological concept-augmented space; the computational cost in edge computation and collision checking is significantly reduced by allowing trajectories with different topology to share the edge and collision information. Illustrative numerical examples are presented to demonstrate the validity and applicability of the proposed approach.
Anaerobic hydrocarbon and fatty acid metabolism by syntrophic bacteria and their impact on carbon steel corrosion

The microbial metabolism of hydrocarbons is increasingly associated with the corrosion of carbon steel in sulfate-rich marine waters. However, how such transformations influence metal biocorrosion in the absence of an electron acceptor is not fully recognized. We grew a marine alkane-utilizing, sulfate-reducing bacterium, Desulfoglaeba alkanexedens, with either sulfate or Methanospirillum hungatei as electron acceptors, and tested the ability of the cultures to catalyze metal corrosion. Axenically, D. alkanexedens had a higher instantaneous corrosion rate and produced more pits in carbon steel coupons than when the same organism was grown in syntrophic co-culture with the methanogen. Since anaerobic hydrocarbon biodegradation pathways converge on fatty acid intermediates, the corrosive ability of a known fatty acid-oxidizing syntrophic bacterium, Syntrophus aciditrophicus was compared when grown in pure culture or in co-culture with a H2-utilizing sulfate-reducing bacterium (Desulfovibrio sp., strain G11) or a methanogen (M. hungatei). The instantaneous corrosion rates in the cultures were not substantially different, but the syntrophic, sulfate-reducing co-culture produced more pits in coupons than other combinations of microorganisms. Lactate-grown cultures of strain G11 had higher instantaneous corrosion rates and coupon pitting compared to the same organism cultured with hydrogen as an electron donor. Thus, if sulfate is available as an electron acceptor, the same microbial assemblages produce sulfide and low molecular weight organic acids that exacerbated biocorrosion. Despite these trends, a surprisingly high degree of variation was encountered with the corrosion assessments. Differences in biomass, initial substrate concentration, rates of microbial activity or the degree of end product formation did not account for the variations. We are forced to ascribe such differences to the metallurgical properties of the coupons.
Learning lazy naive Bayesian classifiers for ranking

Naive Bayes (simply NB) has been well-known as an effective and efficient classification algorithm. However, it is based on the conditional independence assumption that it is often violated in applications. In addition, in many real-world data mining applications, however, an accurate ranking of instances is often required rather than an accurate classification. For example, a ranking of customers in terms of the likelihood that they buy one's products is useful in direct marketing. In this paper, we firstly investigate the ranking performance of some lazy learning algorithms for extending naive Bayes. The ranking performance is measured by Hand and Till (2001) and Bradley (1997). We observe that they can not significantly improve naive Bayes' ranking performance. Motivated by this fact and aiming at improving naive Bayes with accurate ranking, we present a new lazy learning algorithm, called lazy naive Bayes (simply LNB), to extend naive Bayes for ranking. We experimentally tested our algorithm, using the whole 36 UCI data sets (Blake and Merz, 2000) recommended by Weka, and compared it to NB and C4.4 (Provost and Domingos, 2003) measured by AUC. The experimental results show that our algorithm significantly outperforms both NB and C4.4
Karyotyping of comparative genomic hybridization human metaphases using kernel nearest-neighbor algorithm.

BACKGROUND Comparative genomic hybridization (CGH) is a relatively new molecular cytogenetic method that detects chromosomal imbalances. Automatic karyotyping is an important step in CGH analysis because the precise position of the chromosome abnormality must be located and manual karyotyping is tedious and time-consuming. In the past, computer-aided karyotyping was done by using the 4',6-diamidino-2-phenylindole, dihydrochloride (DAPI)-inverse images, which required complex image enhancement procedures. METHODS An innovative method, kernel nearest-neighbor (K-NN) algorithm, is proposed to accomplish automatic karyotyping. The algorithm is an application of the "kernel approach," which offers an alternative solution to linear learning machines by mapping data into a high dimensional feature space. By implicitly calculating Euclidean or Mahalanobis distance in a high dimensional image feature space, two kinds of K-NN algorithms are obtained. New feature extraction methods concerning multicolor information in CGH images are used for the first time. RESULTS Experiment results show that the feature extraction method of using multicolor information in CGH images improves greatly the classification success rate. A high success rate of about 91.5% has been achieved, which shows that the K-NN classifier efficiently accomplishes automatic chromosome classification from relatively few samples. CONCLUSIONS The feature extraction method proposed here and K-NN classifiers offer a promising computerized intelligent system for automatic karyotyping of CGH human chromosomes.
Genome-Wide SNP and STR Discovery in the Japanese Crested Ibis and Genetic Diversity among Founders of the Japanese Population

The Japanese crested ibis is an internationally conserved, critically threatened bird. Captive-breeding programs have been established to conserve this species in Japan. Since the current Japanese population of crested ibis originates only from 5 founders donated by the Chinese government, understanding the genetic diversity between them is critical for an effective population management. To discover genome-wide single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs) while obtaining genotype data of these polymorphic markers in each founder, reduced representation libraries were independently prepared from each of the founder genomes and sequenced on an Illumina HiSeq2000. This yielded 316 million 101-bp reads. Consensus sequences were created by clustering sequence reads, and then sequence reads from each founder were mapped to the consensus sequences, resulting in the detection of 52,512 putative SNPs and 162 putative STRs. The numbers of haplotypes and STR alleles and the investigation of genetic similarities suggested that the total genetic diversity between the founders was lower, although we could not identify a pair with closely related genome sequences. This study provided important insight into protocols for genetic management of the captive breeding population of Japanese crested ibis in Japan and towards the national project for reintroduction of captive-bred individuals into the wild. We proposed a simple, efficient, and cost-effective approach for simultaneous detection of genome-wide polymorphic markers and their genotypes for species currently lacking a reference genome sequence.
Optimized Octtree Datastructure and Access Methods for 3D Mapping

3D maps are becoming increasingly important for robots operating in real world scenarios. As occupancy grids are a popular standard in 2D mapping, it is a natural choice to extend them to spatial representation in 3D. But this approach suffers from large memory requirements that render 3D grids unfeasible for realistic mapping applications. A well-known alternative is quadtrees in 2D, respectively octtrees for 3D, where cells that contain identical information are collapsed into a single node in a tree. But octtrees only allow relative slow access to the spatial information stored in them. Here, a very efficient implementation of an octtree is presented. It is based on technical optimizations as well as newly introduced heuristics like the exploitation of typical access patterns. It is shown that the optimizations are indeed beneficial through experiments with real world 3D sensor data. In addition to basic access methods, a very fast nearest neighbor operation -as needed for example for registration in SLAM or map merging algorithms -for octtrees is presented. It is shown in experiments with real world data that this nearest neighbor operation outperforms a comparable operation on occupancy grids by far.
Identification of Retinoid-Modulated Proteins in Squamous Carcinoma Cells Using High-Throughput Immunoblotting

Retinoids have shown clinical efficacy in cancer chemoprevention and therapy presumably by modulating the growth, differentiation, and apoptosis of normal, premalignant, and malignant cells. To better understand the mechanisms by which retinoids exert their effects, we used a high-throughput Western blotting method (Becton-Dickinson PowerBlot) to evaluate changes in the levels of cellular signaling proteins in head and neck squamous cell carcinoma cells treated with the cytostatic all-trans-retinoic acid or with the proapoptotic retinoids 6-[3-(1-adamantyl)-4-hydroxyphenyl]-2-naphthalene carboxylic acid or N-(4-hydroxyphenyl)retinamide. Treatments of the head and neck squamous cell carcinoma cells with these retinoids for 24 h resulted in increased levels of 14, 22, and 22 proteins and decreased levels of 5, 10, and 7 proteins, respectively. The changes in the levels of the following proteins were confirmed by conventional western immunoblotting: all-trans-retinoic acid increased ELF3, topoisomerase II α, RB2/p130, RIG-G, and EMAPII and decreased MEF2D and cathepsin L. N-(4-Hydroxyphenyl)retinamide up-regulated ELF3, c-Jun, Rb2/p130, JAK1, p67phox, Grb2, O6-methylguanine-DNA methyltransferase, and Ercc-1. 6-[3-(1-Adamantyl)-4-hydroxyphenyl]-2-naphthalene carboxylic acid increased Rb2/p130, c-Jun, Sp1, Sin, and tomosyn and decreased cathepsin L, Mre11, and topoisomerase II α. Some of these proteins were also modulated by these retinoids in other human cancer cell lines. A subset of the proteins were modulated similarly by the different retinoids, whereas changes in other proteins were unique for each retinoid. These results suggest that the mechanisms by which these retinoids modulate proteins are distinct but may overlap. Some of the retinoid-modulated proteins identified in this study may be novel candidates for mediating different responses to retinoids.
Protein Localization with Flexible DNA or RNA

Localization of activity is ubiquitous in life, and also within sub-cellular compartments. Localization provides potential advantages as different proteins involved in the same cellular process may supplement each other on a fast timescale. It might also prevent proteins from being active in other regions of the cell. However localization is at odds with the spreading of unbound molecules by diffusion. We model the cost and gain for specific enzyme activity using localization strategies based on binding to sites of intermediate specificity. While such bindings in themselves decrease the activity of the protein on its target site, they may increase protein activity if stochastic motion allows the acting protein to touch both the intermediate binding site and the specific site simultaneously. We discuss this strategy in view of recent suggestions on long non-coding RNA as a facilitator of localized activity of chromatin modifiers.
The Illusory Diffusion of Innovation: An Examination of Assimilation Gaps

Innovation researchers have known for sometime that a new information technology maybe widely acquired, but then only sparsely deployed among acquiring firms. When this happens, the observed pattern of cumulative adoptions will vary depending on which eventin the assimilation process (i.e., acquisition or deployment) is treated as the adoption event. Instead of mirroring one another, a widening gap-termed here an assimilation gap-will existbetween the cumulative adoption curves associated with the alternatively conceived adoption events. When a pronounced assimilation gap exists, the common practice of using cumulative purchases or acquisitions as the basis for diffusion modeling can present an illusory picture of the diffusion process-leading to potentially erroneous judgments about the robustness ofthe diffusion process already observed, and of the technology's future prospects. Researchers may draw inappropriate theoretical inferences about the forces driving diffusion. Practitioners may commit to a technology based on a belief that pervasive adoption is inevitable, when it is not. This study introduces the assimilation gap concept, and develops a general operational measure derived from the difference between the cumulative acquisition and deployment patterns. It describes how two characteristics-increasing returns to adoption and knowledge barriers impeding adoption-separately and in combination may serve to predispose a technology to exhibit a pronounced gap. It develops techniques for measuring assimilation gaps, for establishing whether two gaps are significantly different from each other, and for establishing whether a particular gap is absolutely large enough to be of substantive interest. Finally, it demonstrates these techniques in an analysis of adoption data for three prominent innovations in software process technology-relational database management systems (RDBs), general purpose fourth generation languages (4GLs), and computer aided software engineering tools (CASE). The analysis confirmed that assimilation gaps can be sensibly measured, and that their measured size is largely consistent with a priori expectations and recent research results. A very pronounced gap was found for CASE, while more moderate-though still significant-gaps were found for RDBs and 4GLs. These results have the immediate implication that, where the possibility of a substantial assimilation gap exists, the time of deployment should be captured instead of, or in addition to, time of acquisition as the basis for diffusion modeling. More generally, the results suggest that observers be guarded about concluding, based on sales data, that an innovation is destined to become widely used. In addition, by providing the ability to analyze and compare assimilation gaps, this study provides an analytic foundation for future research on why assimilation gaps occur, and what might be done to reduce them.
Attitudes toward and Uptake of H1N1 Vaccine among Health Care Workers during the 2009 H1N1 Pandemic

Background Though recommended by many and mandated by some, influenza vaccination rates among health care workers, even in pandemics, remain below optimal levels. The objective of this study was to assess vaccination uptake, attitudes, and distinguishing characteristics (including doctor-nurse differences) of health care workers who did and did not receive the pandemic H1N1 influenza vaccine in late 2009. Methodology/Principal Findings In early 2010 we mailed a self-administered survey to 800 physicians and 800 nurses currently licensed and practicing in Minnesota. 1,073 individuals responded (cooperation rate: 69%). 85% and 62% of Minnesota physicians and nurses, respectively, reported being vaccinated. Accurately estimating the risk of vaccine side effects (OR 2.0; 95% CI 1.5–2.7), agreeing with a professional obligation to be vaccinated (OR 10.1; 95% CI 7.1–14.2), an ethical obligation to follow public health authorities' recommendations (OR 9.9; 95% CI 6.6–14.9), and laws mandating pandemic vaccination (OR 3.1; 95% CI 2.3–4.1) were all independently associated with receiving the H1N1 influenza vaccine. Conclusions/Significance While a majority of health care workers in one midwestern state reported receiving the pandemic H1N1 vaccine, physicians and nurses differed significantly in vaccination uptake. Several key attitudes and perceptions may influence health care workers' decisions regarding vaccination. These data inform how states might optimally enlist health care workers' support in achieving vaccination goals during a pandemic.
Matching Supply and Demand

Course Modules help faculty select and sequence HBS Publishing titles for use in segments of a course. Each module represents subject matter experts' thinking about the best materials to assign and how to organize them to facilitate learning. In making selections, we've received guidance from faculty at Harvard Business School and other major academic institutions. Each module recommends four to six items. Whenever possible at least one alternative item for each main recommendation is included. Cases form the core of many modules, but we also include readings from Harvard Business Review, HBS background notes, and other course materials. (Enspire Learning-online delivery) Hammond 6107 2003 2-4 hours 605070 4. ZARA: IT for Fast Fashion McAfee 604081 2004 23p 604104 Alternative: Rapid-Fire Fulfillment (HBR) Ferdows R0411G 2004 6p-Austin Dell & Magretta 699198 98208 1999 1998 9p 13p 601172-II. Rationale for selection and sequencing the items in this module Each of the alternatives in the opening slot provides a broad overview of basic supply-chain issues, and either will help students get their footing, especially if this module is used early in a course on SCM or if students have had no courses or professional background in operations management. The next two items form the core of this module. The Sport Obermeyer case (one of HBS's bestselling operations cases) facilitates discussion of three topics especially relevant in today's business environment: production planning for short-life-cycle fashion products, operational changes that reduce the cost of mismatched supply and demand, and coordination issues in a global supply chain. Sport Obermeyer prepares students to confront tricky supply-demand issues head-on through the online interactive product " The Global Supply Chain Management Simulation, " which casts students as the
Linking Leadership to Student Learning: The Contributions of Leader Efficacy

Purposes: This study aimed to improve our understanding of the nature, causes and consequence of school leader efficacy, including indirect influences on student learning. We asked about district contributions to school leader efficacy, whether leader self- and collective efficacy responded to the same or different district conditions and the effects of leader efficacy on conditions in the school and the learning of students. Methods: Evidence for the study was provided by 96 principal and 2,764 teacher respondents to two separate surveys, along with student achievement data in language and math averaged over 3 years. Path analytic techniques were used to address the objectives for the study. Findings: In this study, school leaders' collective efficacy was an important link between district conditions and both the conditions found in schools and their effects on student achievement. School leaders'sense of collective efficacy also had a strong, positive, relationship with leadership practices found to be effective in earlier studies. Implications: These results suggest that district leaders are most likely to build the confidence and sense of collective efficacy among principals by emphasizing the priority they attach to achievement and instruction, providing targeted and phased focus for school improvement efforts and by building cooperative working relationships with schools.
Cyclin-like accumulation and loss of the putative kinetochore motor CENP-E results from coupling continuous synthesis with specific degradation at the end of mitosis

CENP-E is a kinesin-like protein that binds to kinetochores through the early stages of mitosis, but after initiation of anaphase, it relocalizes to the overlapping microtubules in the midzone, ultimately concentration in the developing midbody. By immunoblotting of cells separated at various positions in the cell cycle using centrifugal elutriation, we show that CENP-E levels increase progressively across the cycle peaking at approximately 22,000 molecules/cell early in mitosis, followed by an abrupt (> 10 fold) loss at the end of mitosis. Pulse-labeling with [35S]methionine reveals that beyond a twofold increase in synthesis between G1 and G2, interphase accumulation results primarily from stabilization of CENP-E during S and G2. Despite localizing in the midbody during normal cell division, CENP-E loss at the end of mitosis is independent of cytokinesis, since complete blockage of division with cytochalasin has no affect on CENP-E loss at the M/G1 transition. Thus, like mitotic cyclins, CENP-E accumulation peaks before cell division, and it is specifically degraded at the end of mitosis. However, CENP-E degradation kinetically follows proteolysis of cyclin B in anaphase. Combined with cyclin A destruction before the end of metaphase, degradation of as yet unidentified components at the metaphase/anaphase transition, and cyclin B degradation at or after the anaphase transition, CENP-E destruction defines a fourth point in a mitotic cascade of timed proteolysis.
Impairs a Specific Antitumor Response Transgenic Expression of Ly49A on T Cells

Inhibitory MHC receptors determine the reactivity and speciﬁcity of NK cells. These receptors can also regulate T cells by modulating TCR-induced effector functions such as cytotoxicity, cytokine production, and proliferation. Here we have assessed the capacity of mouse T cells expressing the inhibitory MHC class I receptor Ly49A to respond to a well-deﬁned tumor Ag in vivo using Ly49A transgenic mice. We ﬁnd that the presence of Ly49A on the vast majority of lymphocytes prevents the development of a signiﬁcant Ag-speciﬁc CD8 1 T cell response and, consequently, the rejection of the tumor. Despite minor alterations in the TCR repertoire of CD8 1 T cells in the transgenic lines, precursors of functional tumor-speciﬁc CD8 1 T cells exist but could not be activated most likely due to a lack of appropriate CD4 1 T cell help. Surprisingly, all of these effects are observed in the absence of a known ligand for the Ly49A receptor as deﬁned by its ability to regulate NK cell function. Indeed, we found that the above effects on T cells may be based on a weak interaction of Ly49A with K b or D b class I molecules. Thus, our data demonstrate that enforced expression of a Ly49A receptor on conventional T cells prevents a speciﬁc immune response in vivo and suggest that the functions of T and NK cells are differentially sensitive to the presence of inhibitory MHC class I receptors. The Journal of Immunology, 2000, 165: 1871–1876.