Miracle-dz/UniFAR-FTUs huggingface dataset:
High speed 3-D registration using GPU

This paper describes high speed 3D object recognition based on DAI (depth aspect image) matching and M-ICP (modified iterative closest point). We regards GPU(graphic processing units) as coprocessor which are capable of computation for general purpose. We proposed 3D object recognition method which consists of two step pose estimation and positioning, i.e. the DAI matching for coarse step and HM-ICP (hierarchical M-ICP) for fine one Our method on GPU which has remarkable performance for parallel computation. The experimental results show the effectiveness of our method. This method can process 2 or 3 times faster than the original one, although the calculation amount of this method is at least 20 times bigger than the original one. Additionally, its processing time is more stabler than original method.
On the young age of intraspecific herbaceous taxa.

Dated phylogenies rarely include the divergence times of sister intraspecific taxa, and when they do little is said about this subject. We show that over 90% of the intraspecific plant taxa found in a literature search are estimated to be 5 million yr old or younger, with only 4% of taxa estimated to be over 10 million yr old or older. A Bayesian analysis of intraspecific taxon ages indicates that indeed these taxa are expected to be < 10 million yr old. This result for the young age of intraspecific taxa is consistent with the earlier observation that post-pollination reproductive barriers develop between 5 and 10 million yr after lineage splitting, thus leading to species formation. If lineages have not graduated to the species level of divergence by 10 million yr or so, they are likely to have gone extinct by that time as a result of narrow geographical distributions, narrow niche breadths, and relatively small numbers across populations.
Cortical folding defects as markers of poor treatment response in first-episode psychosis.

IMPORTANCE At present, no reliable predictors exist to distinguish future responders from nonresponders to treatment during the first episode of psychosis. Among potential neuroimaging predictors of treatment response, gyrification represents an important marker of the integrity of normal cortical development that may characterize, already at illness onset, a subgroup of patients with particularly poor outcome. OBJECTIVE To determine whether patients with first-episode psychosis who do not respond to 12 weeks of antipsychotic treatment already have significant gyrification defects at illness onset. DESIGN Case-control study with 12 weeks' longitudinal follow-up to determine treatment response. SETTING Secondary psychiatric services in an inner-city area (South London, England). PARTICIPANTS A total of 126 subjects, including 80 patients presenting with first-episode psychosis and 46 healthy controls. Patients were scanned at the outset and received various antipsychotic medications in a naturalistic clinical setting. They were followed up for 12 weeks and classified as responders or nonresponders if they reached criteria for symptom remission, evaluated with the Psychiatric and Personal History Schedule. OBSERVATION Patients were exposed to naturalistic antipsychotic treatment for 12 weeks following a magnetic resonance imaging scan. MAIN OUTCOMES AND MEASURES Cortical gyrification was assessed using local gyrification index in a vertexwise fashion across the entire cortical surface with correction for multiple testing using permutation analysis. Differences in local gyrification index were assessed between responders, nonresponders, and healthy controls. The effect of diagnosis (affective vs nonaffective psychosis) on the local gyrification index was also investigated in responders and nonresponders. RESULTS Patients with first-episode psychosis showed a significant reduction in gyrification (hypogyria) across multiple brain regions compared with healthy controls. Interestingly, nonresponders showed prominent hypogyria at bilateral insular, left frontal, and right temporal regions when compared with responders (all clusters significant at P < .05). These effects were present for both affective and nonaffective psychoses. CONCLUSIONS AND RELEVANCE Gyrification appears to be a useful predictor of antipsychotic treatment response. Early neurodevelopmental aberrations may predict unfavorable prognosis in psychosis, irrespective of the existing diagnostic boundaries.
Toll-Like Receptor Ligand-Based Vaccine Adjuvants Require Intact MyD88 Signaling in Antigen-Presenting Cells for Germinal Center Formation and Antibody Production

Vaccines are critical in the fight against infectious diseases, and immune-stimulating adjuvants are essential for enhancing vaccine efficacy. However, the precise mechanisms of action of most adjuvants are unknown. There is an urgent need for customized and adjuvant formulated vaccines against immune evading pathogens that remain a risk today. Understanding the specific role of various cell types in adjuvant-induced protective immune responses is vital for an effective vaccine design. We have investigated the role of cell-specific MyD88 signaling in vaccine adjuvant activity in vivo, using Neisserial porin B (PorB), a TLR2 ligand-based adjuvant, compared with an endosomal TLR9 ligand (CpG) and toll-like receptor (TLR)-independent (alum, MF59) adjuvants. We found that intact MyD88 signaling is essential, separately, in all three antigen-presenting cell types [B cells, macrophages, and dendritic cells (DCs)] for optimal TLR ligand-based adjuvant activity. The role of MyD88 signaling in B cell and DC in vaccine adjuvant has been previously investigated. In this study, we now demonstrate that the immune response was also reduced in mice with macrophage-specific MyD88 deletion (Mac-MyD88−/−). We demonstrate that TLR-dependent adjuvants are potent inducers of germinal center (GC) responses, but GCs are nearly absent in Mac-MyD88−/− mice following immunization with TLR-dependent adjuvants PorB or CpG, but not with TLR-independent adjuvants MF59 or alum. Our findings reveal a unique and here-to-for unrecognized importance of intact MyD88 signaling in macrophages, to allow for a robust vaccine-induced immune responses when TLR ligand-based adjuvants are used.
Development of ISSR‐derived SCAR marker‐targeted PCR for identification of Aspergillus section Flavi members

Aspergillus section Flavi is a heterogeneous fungal cluster including some of the most economically important Aspergillus species. The section is comprised of toxigenic and nontoxigenic aspergilli that are phenotypically undistinguishable. The aim of this study was to develop a genetic marker specific to Aspergillus section Flavi on the whole. Based on inter–simple sequence repeat (ISSR) fingerprinting profiles of major Aspergillus section Flavi members, a sequence‐characterized amplified region (SCAR) marker was identified. Primers were designed in the conserved regions of the SCAR marker and were utilized in a PCR for concurrent identification of major members of the section. The detection level of the SCAR‐PCR was found to be 0·1 ng purified DNA, and when applied to 45 naturally contaminated food samples, 28 samples were found infected with Aspergillus section Flavi members. The present SCAR‐PCR is rapid and less cumbersome unlike conventional identification techniques.
First-order causal process for causal modelling with instantaneous and cross-temporal relations

Motivated by the real damped simple harmonic oscillator (SHO) system, in this paper, we propose a process interpretation of causality and the first-order causal process (FoCP) model for temporal causal modelling. Compared with existing causal models that are able to model feedbacks, such as the structural equation model (SEM) and the structure vector autoregressive (SVAR) model, the FoCP model entails a novel 2-stage evolution semantic for instantaneous and cross-temporal causal relations existing in many real world dynamic systems. Graphical representations are developed to illustrate the causal structure compactly. Useful properties of the new model are identified and used to develop a conditional independence based algorithm for learning the causal structure from a multivariate time series dataset. Experiments on both simulated and real data validate the feasibility of the method to discover simple while meaningful causal structures of dynamic systems.
Governance of Corporate Takeovers: Time for Say-on-Takeovers?

We study the potential for digital, online information and electronic voting to improve shareholder surplus by facilitating a new governance structure, owner-governance, which shifts control of the takeover decision from the board to shareholders. We compare analytical models of owner-governance to the current practice of delegated-governance in the context of increasing availability of online information, which increases public informedness. Our analysis shows that shareholders of the target firm and the acquirer both prefer owner-governance to delegated-governance when informedness is sufficiently high. Interestingly, we find a region where owner-governance offers a higher probability of takeover but delegated-governance offers higher shareholder surplus. Under delegated-governance, the board endogenously sets an entrenchment level that is always greater than the entrenchment level preferred by the shareholders and increasing informedness reduces the probability of a takeover. Our results suggest that owner-governance should be considered because of increasing informedness.
Implications of solar energy harvesting on sensor networks design

The design of wireless sensor networks presents a host of challenges like power management, ensuring coverage of an area with sensor nodes, providing fault tolerance in case of node failures and localization of nodes. But managing the power of a sensor node given the energy constraints, such that the lifetime of the node, the network and the application’s performance are maximized, still continues to be most dominant challenge. Energy harvesting has a good potential to solve the problem of energy constraint of nodes, as nodes can harvest more energy from the environment. Specifically, harvesting solar energy is ideal for outdoor sensor networks due to the omnipresent nature of sun light. In this report, we study the various challenges involved, in the design of a sensor network that uses solar energy harvesting. Solar panels and batteries are the most important components in a sensor node that uses solar energy harvesting. A study of issues of a solar panel and the trade offs in using the various battery chemistries is discussed. Power management has both node level and network level implications. Node level power management can be done by changing the duty cycles of nodes, to match the power consumption profile to the energy harvesting profile, as a way to increase the lifetime of the node and the application performance. Two approaches in this direction are discussed along with a relative comparison of both of them. Managing power at the network level involves “effective energy”, a parameter that is indicative of both the harvesting opportunity of a node and its current battery status. Approaches to find this parameter, and use it as a cost-metric in flat-routing schemes like Bellman-Ford, and to elect nodes as cluster-heads in cluster-based routing schemes like LEACH, is discussed. Another direction is to adapt data based routing schemes like Directed Diffusion, to preferably route data via solar powered nodes when both types of nodes are present. An approach in this direction has been studied.
New results on space-time code design criteria

A sub-class of space-time codes, defined via compliance with a new criterion of optimality, is introduced. A new distance between two codewords is defined and leads to new criteria for code design. It is shown that, unlike the non-Euclidian metrics currently in use, the new distance measure is a true metric, its square has a useful additive property and, in itself, preserves the traditional form of the upper bound to the probability of mistaking two codewords, as encountered in the union bound. The resulting new criteria for space-time code design are presented.
On Implementation and Evaluation of Inverse Iteration Algorithm with compact WY Orthogonalization

A new inverse iteration algorithm that can be used to compute all the eigenvectors of a real symmetric tri-diagonal matrix on parallel computers is developed. The modified Gram-Schmidt orthogonalization is used in the classical inverse iteration. This algorithm is sequential and causes a bottleneck in parallel computing. In this paper, the use of the compact WY representation is proposed in the orthogonalization process of the inverse iteration with the Householder transformation. This change results in drastically reduced synchronization cost in parallel computing. The new algorithm is evaluated on both an 8-core and a 32-core parallel computer, and it is shown that the new algorithm is greatly faster than the classical inverse iteration algorithm in computing all the eigenvectors of matrices with several thousand dimensions.
Association analysis of polymorphisms in the mu opioid gene and heroin abuse in Chinese subjects

We examined four polymorphisms in the mu opioid receptor gene in 282 Chinese heroin addicts from Sichuan Province, Southwest China and compared the allele and genotype frequencies to those in 258 normal controls from the same geographic region. Two of these polymorphisms (Ala6Val and Ser147Cys) were not polymorphic in the Chinese, with only Ala6 and Ser147 observed. The frequencies of the two other polymorphisms were significantly different from those observed in Caucasians, African Americans and Native Americans. The Asn40Asp and IVS2 + 691G/C polymorphisms did not differ significantly for allele (p= 0.16; p = 0.21), genotype (p= 0.32; p = 0.09) or haplotype frequencies (p= 0.24) between the Chinese heroin‐addicted cases and normal controls. Similarly, we did not detect any association when the population was stratified by gender, route of administration (nasal inhalation and/or injection) and age‐at‐onset (above or below 25 years). This indicates that the mu opioid receptor is not likely to be a major genetic risk factor for heroin abuse in this population.
Semiparametric Bayesian Analysis of Case–Control Data under Conditional Gene‐Environment Independence

Summary In case–control studies of gene‐environment association with disease, when genetic and environmental exposures can be assumed to be independent in the underlying population, one may exploit the independence in order to derive more efficient estimation techniques than the traditional logistic regression analysis ( Chatterjee and Carroll, 2005 , Biometrika92, 399–418). However, covariates that stratify the population, such as age, ethnicity and alike, could potentially lead to nonindependence. In this article, we provide a novel semiparametric Bayesian approach to model stratification effects under the assumption of gene‐environment independence in the control population. We illustrate the methods by applying them to data from a population‐based case–control study on ovarian cancer conducted in Israel. A simulation study is conducted to compare our method with other popular choices. The results reflect that the semiparametric Bayesian model allows incorporation of key scientific evidence in the form of a prior and offers a flexible, robust alternative when standard parametric model assumptions do not hold.
Equivariant K-homology for hyperbolic reflection groups

We compute the equivariant K-homology of the classifying space for proper actions, for cocompact 3-dimensional hyperbolic reflection groups. This coincides with the topological K-theory of the reduced C∗-algebra associated to the group, via the Baum-Connes conjecture. We show that, for any such reflection group, the associated K-theory groups are torsion-free. As a result we can promote previous rational computations to integral computations. Our proof relies on a new efficient algebraic criterion for checking torsion-freeness of K-theory groups, which could be applied to many other classes of groups.
Treading a fine line: is diagnosing depression in young people just medicalising moodiness?

Depressed mood in young people is common, with a prevalence of up to 20% among teenagers consulting their GP.1 Depression during the teenage years is associated with functional impairment and health risk behaviours;2,3 episodes can be severe and prolonged, often not resolving over 18 months.4 Adolescent depression is a chronic and relapsing condition with a high level of continuity into adulthood,5,6 where it is associated with impaired psychosocial functioning.2 Even young people with low levels of depressive symptoms and associated impairment — so-called ‘subsyndromal depression’ — have been shown to have persistent impairment.7 There is some evidence that intervention can reduce psychological morbidity and it is therefore possible that early intervention could alter the experience of mental ill-health in later life.8 However, young people with psychological morbidity are difficult to engage in psychological therapies,9 even though such therapies appear to reduce symptoms and case prevalence.10 This reluctance to engage reduces the capacity of GPs and their practice counsellors to review depressed teenagers. The NICE guidelines on depression in children and young people11 argue for enhanced detection and risk profiling in community settings, but the precise means to achieve this remain unclear. GPs may be seen as being well placed to undertake detection and …
West Nile virus infection transmitted by blood transfusion

BACKGROUND: A patient with transfusion‐transmitted West Nile virus (WNV) infection confirmed by viral culture of a blood component is described. A 24‐year‐old female with severe postpartum hemorrhage developed fever, chills, headache, and generalized malaise after transfusion of 18 units of blood components; a serum sample and the cerebrospinal fluid tested positive for the presence of WNV IgM antibodies. An investigation was initiated to determine a possible association between transfusion and WNV infection.
Stable stylized wireframe rendering

Stylized wireframe rendering of 3D model is widely used in animation software in order to depict the configuration of deformable model in comprehensible ways. However, since some inherent flaws in traditional depth test based rendering technology, shape of lines can not been preserved as continuous movement or deformation of models. There often exists severe aliasing like flickering artifact when objects rendered in line form animate, especially rendered with thick or dashed line. To cover this artifact, unlike traditional approach, we propose a novel fast line drawing method with high visual fidelity for wireframe depiction which only depends on intrinsic topology of primitives without any preprocessing step or extra adjacent information pre‐stored. In contrast to previous widely‐used solutions, our method is advantageous in highly accurate visibility, clear and stable line appearance without flickering even for thick and dashed lines with uniform width and steady configuration as model moves or animates, so that it is strongly suitable for animation system. In addition, our approach can be easily implemented and controlled without any additional preestimate parameters supplied by users. Copyright © 2010 John Wiley & Sons, Ltd.
Enhancement of antitumor immune response in glioma models in mice by genetically modified dendritic cells pulsed with Semliki forest virus-mediated complementary DNA.

OBJECT The aim of this study was to further investigate dendritic cell (DC)-based immunotherapy for malignant glioma to improve its therapeutic efficacy. METHODS Dendritic cells were isolated from the bone marrow and pulsed with phosphate-buffered saline, tumor RNA, tumor lysate, Semliki Forest virus (SFV)-LacZ, SFV-mediated B16 complementary (c)DNA, or SFV-mediated 203 glioma cDNA, respectively, to treat mice bearing tumors of the 203 glioma cell line. The results indicated that pre-immunization with DCs pulsed with the same type of cDNA as in the tumor by a self-replicating RNA vector (that is, SFV) protected mice from tumor challenge, and that therapeutic immunization prolonged the survival of mice with established tumors. The SFV induced apoptosis in DCs and their death facilitated the uptake of apoptotic cells by other DCs, thus providing a potential mechanism for enhanced immunogenicity. CONCLUSIONS Therapy with DCs that have been pulsed with SFV-mediated tumor cDNA may be an excellent procedure for the development of new cancer vaccines.
Receptor‐mediated endocytosis of Neisseria gonorrhoeae into primary human urethral epithelial cells: the role of the asialoglycoprotein receptor

Urethral epithelial cells are invaded by Neisseria gonorrhoeae during gonococcal infection in men. To understand further the mechanisms of gonococcal entry into host cells, we used the primary human urethral epithelial cells (PHUECs) tissue culture system recently developed by our laboratory. These studies showed that human asialoglycoprotein receptor (ASGP‐R) and the terminal lactosamine of lacto‐N‐neotetraose‐expressing gonococcal lipooligosaccharide (LOS) play an important role in invasion of PHUECs. Microscopy studies showed that ASGP‐R traffics to the cell surface after gonococcal challenge. Co‐localization of ASGP‐R with gonococci was observed. As ASGP‐R‐mediated endocytosis is clathrin dependent, clathrin localization in PHUECs was examined after infection. Infected PHUECs showed increased clathrin recruitment and co‐localization of clathrin and gonococci. Preincubating PHUECs in 0.3 M sucrose or monodansylcadaverine (MDC), which both inhibit clathrin‐coated pit formation, resulted in decreased invasion. N. gonorrhoeae strain 1291 produces a single LOS glycoform that terminates with Gal(β1–4)GlcNac(β1–3)Gal(β1–4)Glc (lacto‐N‐neotetraose). Invasion assays showed that strain 1291 invades significantly more than four isogenic mutants expressing truncated LOS. Sialylation of strain 1291 LOS inhibited invasion significantly. Preincubation of PHUECs in asialofetuin (ASF), an ASGP‐R ligand, significantly reduced invasion. A dose–response reduction in invasion was observed in PHUECs preincubated with increasing concentrations of NaOH‐deacylated 1291 LOS. These studies indicated that an interaction between lacto‐N‐neotetraose‐terminal LOS and ASGP‐R allows gonococcal entry into PHUECs.
Visualization of p53264–272/HLA-A*0201 Complexes Naturally Presented on Tumor Cell Surface by a Multimeric Soluble Single-Chain T Cell Receptor1

Intracellular Ags are processed into small peptides that are presented on cell surfaces in the context of HLA class I molecules. These peptides are recognized by TCRs displayed by CD8+ T lymphocytes (T cells). To date, direct identification and quantitation of these peptides has relied primarily on mass spectrometry analysis, which is expensive and requires large quantities of diseased tissues to obtain useful results. Here we demonstrate that multimerization of a soluble single-chain TCR (scTCR), recognizing a peptide from p53 presented in the context of HLA-A2.1, could be used to directly visualize and quantitate peptide/MHC complexes on unmanipulated human tumor cells. Tumor cells displaying as few as 500 peptide/MHC complexes were readily detectable by flow cytometry. The scTCR/multimers exhibited exquisite recognition capability and could distinguish peptides differing in as little as a single amino acid. We also demonstrate that scTCR/multimers could specifically stain human tumors generated in mice, as well as tumors obtained from patient biopsies. Thus, scTCR/multimers represent a novel class of immunostaining reagents that could be used to validate, quantitate, or monitor epitope presentation by cancer cells.