Miracle-dz/UniFAR-FTUs huggingface dataset:
A Method of Automated Landmark Generation for Automated 3D PDM Construction

Abstract A previous publication has described a method of pairwise three-dimensional (3D) surface correspondence for the automated generation of landmarks on a set of examples from a class of shape (A.D. Brett, A. Hill, C.J. Taylor, A method of 3D surface correspondence for automated landmark generation, in: 8th British Machine Vision Conference, Essex, England, September 1997, pp 709–718). In this paper we describe a set of improved algorithms which give more accurate and more robust results. We show how the pairwise corresponder can be used in an extension of an existing framework for establishing dense correspondences between a set of training examples (A. Hill, A.D. Brett, C.J. Taylor, Automatic landmark identification using a new method of non-rigid correspondence, in: J. Duncan, G. Gindi, (Eds.), 15th Conference on Information Processing in Medical Imaging, Poulteney, VT, Springer, Berlin, 1997, pp. 483–488) to build a 3D Point Distribution Model. The framework relies upon additional algorithms for the production of surface paths between vertices on a polyhedral mesh, and these are described. Example statistical models are shown for both smooth synthetic data and the left lateral ventricle of the brain, a complex biological shape which demonstrates considerable variation between individuals.
Clique Cover and Graph Separation: New Incompressibility Results

The field of kernelization studies polynomial-time preprocessing routines for hard problems in the framework of parameterized complexity. In this article, we show that, unless the polynomial hierarchy collapses to its third level, the following parameterized problems do not admit a polynomial-time preprocessing algorithm that reduces the size of an instance to polynomial in the parameter: ---Edge Clique Cover, parameterized by the number of cliques, ---Directed Edge/Vertex Multiway Cut, parameterized by the size of the cutset, even in the case of two terminals, ---Edge/Vertex Multicut, parameterized by the size of the cutset, and ---k-Way Cut, parameterized by the size of the cutset.
A crucial role for β2 integrins in podosome formation, dynamics and Toll-like-receptor-signaled disassembly in dendritic cells

ABSTRACT The dynamic properties of podosomes, their ability to degrade the underlying matrix and their modulation by Toll-like receptor (TLR) signaling in dendritic cells (DCs) suggests they have an important role in migration. Integrins are thought to participate in formation and dynamics of podosomes but the multiplicity of integrins in podosomes has made this difficult to assess. We report that murine DCs that lack &bgr;2 integrins fail to form podosomes. Re-expression of &bgr;2 integrins restored podosomes but not when the membrane proximal or distal NPxF motifs, or when an intervening triplet of threonine residues were mutated. We show that &bgr;2 integrins are remarkably long-lived in podosome clusters and form a persistent framework that hosts multiple actin-core-formation events at the same or adjacent sites. When &bgr;2 integrin amino acid residues 745 or 756 were mutated from Ser to Ala, podosomes became resistant to dissolution mediated through TLR signaling. TLR signaling did not detectably modulate phosphorylation at these sites but mutation of either residue to phospho-mimetic Asp increased &bgr;2 integrin turnover in podosomes, indicating that phosphorylation at one or both sites establishes permissive conditions for TLR-signaled podosome disassembly.
Generating an LTAG out of a Principle-based Hierarchical Representation

Lexicalized Tree Adjoining Grammars have proved useful for NLP. However, numerous redundancy problems face LTAGs developers, as highlighted by Vijay-Shanker and Schabes (92). We present and a tool that automatically generates the tree families of an LTAG. It starts from a compact hierarchical organization of syntactic descriptions that is linguistically motivated and carries out all the relevant combinations of linguistic phenomena.
Myeloid Zinc Finger 1 (MZF‐1) Regulates Expression of the CCN2/CTGF and CCN3/NOV Genes in the Hematopoietic Compartment

Connective Tissue Growth Factor (CCN2/CTGF) and Nephroblastoma Overexpressed (CCN3/NOV) execute key functions within the hematopoietic compartment. Both are abundant in the bone marrow stroma, which is a niche for hematopoiesis and supports marrow function. Roles for 1,25‐dihydroxyvitamin D3 (calcitriol) and all‐trans retinoic acid in the bone marrow have also been elucidated. Interestingly, some of the annotated roles of these vitamins overlap with established functions of CCN2 and CCN3. Yet, no factor has been identified that unifies these observations. In this study, we report the regulation of the CTGF and NOV genes by Myeloid Zinc Finger‐1 (MZF‐1), a hematopoietic transcription factor. We show the interaction of MZF‐1 with the CTGF and NOV promoters in several cell types. Up‐regulation of MZF‐1 via calcitriol and vitamin A induces expression of CTGF and NOV, implicating a role for these vitamins in the functions of these two genes. Lastly, knockdown of MZF1 reduces levels of CTGF and NOV. Collectively, our results argue that MZF‐1 regulates the CTGF and NOV genes in the hematopoietic compartment, and may be involved in their respective functions in the stroma. J. Cell. Physiol. 9999: 2634–2639, 2015. © 2015 Wiley Periodicals, Inc.
Instructions for use Title Dietary fructo-oligosaccharides improve insulin sensitivity along with the suppression of adipocytokinesecretion from mesenteric fat cells in rats

Short-chain fructo-oligosaccharides (FOS) are known to have beneficial effects on health. However, the effects of FOS on insulin resistance have not been fully clarified. We observed the effects of FOS feeding on insulin sensitivity and adipocytokine release from abdominal adipocytes in weaning rats. Male Sprague–Dawley rats, 3 weeks old, were divided into three groups and fed a sucrose-based American Institute of Nutrition (AIN)-93 growth diet (control), the control diet containing 5 % FOS for 5 weeks (FOS-5wk) or the control diet for 2 weeks followed by the 5 % FOS diet for 3 weeks (FOS-3wk). Tail blood was collected after fasting for 9 h on day 33 of feeding, and glucose and insulin levels were measured. On the last day, rats were anaesthetised and killed after the collection of aortic blood. Smalland large-intestinal mesenteric fat tissues were immediately excised, and the release of adiponectin, leptin and TNF-a was evaluated from the subsequently isolated adipocytes. The weight of the large-intestinal mesenteric fat, fasting blood insulin level and homeostatic model assessment for insulin resistance decreased in a time-dependent manner, and were much lower in the FOS-5wk group than in the control group. These values were correlated with aortic blood leptin levels. The secretion rate of leptin from the isolated mesenteric adipocytes in the small intestine, but not in the large intestine, was lower in the FOS-fed groups than in the control group. In conclusion, FOS feeding improved insulin sensitivity accompanied by the reduction in large-intestinal fat mass and leptin secretion from the mesenteric adipocytes of the small intestine.
Dealing with contract violations: formalism and domain specific language

This paper presents a formal system for reasoning about violations of obligations in contracts. The system is based on the formalism for the representation of contrary-to-duty obligations. These are the obligations that take place when other obligations are violated as typically applied to penalties in contracts. The paper shows how this formalism can be mapped onto the key policy concepts of a contract specification language. This language, called Business Contract Language (BCL) was previously developed to express contract conditions of relevance for run time contract monitoring. The aim of this mapping is to establish a formal underpinning for this key subset of BCL.
Proceedings of the 5th Symposium on Operating Systems Design and Implementation Supporting Time-sensitive Applications on a Commodity Os

Commodity operating systems are increasingly being used for serving time-sensitive applications. These applications require low-latency response from the kernel and from other system-level services. In this paper, we explore various operating systems techniques needed to support time-sensitive applications and describe the design of our Time-Sensitive Linux (TSL) system. We show that the combination of a high-precision timing facility , a well-designed preemptible kernel and the use of appropriate scheduling techniques is the basis for a low-latency response system and such a system can have low overhead. We evaluate the behavior of realistic time-sensitive user-and kernel-level applications on our system and show that, in practice, it is possible to satisfy the constraints of time-sensitive applications in a commodity operating system without significantly compromising the performance of throughput-oriented applications.
Evaluating collaborative applications from a knowledge management approach

Different focuses exist to evaluate collaborative systems. Since knowledge is becoming the most important asset of enterprises, we propose evaluating collaborative tools by using a knowledge management approach. To do so, we analyze six aspects of the knowledge management process, which are: knowledge creation, knowledge accumulation, knowledge sharing, knowledge utilization, knowledge internalization and knowledge integration and then propose a model to evaluate each one.
D 6 . 1 : Improved confidence estimation and hybrid architectures for machine translation

Distribution Public Contractual date of delivery December 2007 Actual date of delivery December 2007 Deliverable number D 6.1 Deliverable title Improved confidence estimation and hybrid architectures for machine translation Type Status & version Number of pages 28 Contributing WP(s) 6 WP / Task responsible Andreas Eisele Other contributors Author(s)
Security of quantum key distribution

Quantum Information Theory is an area of physics which studies both fundamental and applied issues in quantum mechanics from an information-theoretical viewpoint. The underlying techniques are, however, often restricted to the analysis of systems which satisfy a certain independence condition. For example, it is assumed that an experiment can be repeated independently many times or that a large physical system consists of many virtually independent parts. Unfortunately, such assumptions are not always justified. This is particularly the case for practical applications — e.g. in quantum cryptography — where parts of a system might have an arbitrary and unknown behavior. We propose an approach which allows us to study general physical systems for which the above mentioned independence condition does not necessarily hold. It is based on an extension of various information-theoretical notions. For example, we introduce new uncertainty measures, called smooth min- and max-entropy, which are generalizations of .
Experimental Assessment Trigeminal Neuralgia Induced by Cobra Venom in the Rat Leads to Deficits in Abilities of Spatial Learning and Memory

Methods: Thirty adult male Sprague-Dawley rats were randomly divided into 2 groups (n = 15): NS control group and cobra venom group, 0.9% sterile saline or cobra venom solution was injected into the sheath of the infraorbital nerve (ION), respectively. The development of trigeminal neuralgia was accessed by changes in free behavioral activity 3 days before the surgery and 3, 7, 12, 20, and 30 days after the surgery to identify whether the model was successful or not. Morris water maze test determined the abilities of spatial learning and memory at the time points before the surgery, and 2 weeks and 5 weeks after the surgery. We also observed the ultrastructure of the ION and medulla oblongata of rats following 8 weeks of chronic trigeminal neuropathic pain.
Comparison of Methods to Account for Relatedness in Genome-Wide Association Studies with Family-Based Data

Approaches based on linear mixed models (LMMs) have recently gained popularity for modelling population substructure and relatedness in genome-wide association studies. In the last few years, a bewildering variety of different LMM methods/software packages have been developed, but it is not always clear how (or indeed whether) any newly-proposed method differs from previously-proposed implementations. Here we compare the performance of several LMM approaches (and software implementations, including EMMAX, GenABEL, FaST-LMM, Mendel, GEMMA and MMM) via their application to a genome-wide association study of visceral leishmaniasis in 348 Brazilian families comprising 3626 individuals (1972 genotyped). The implementations differ in precise details of methodology implemented and through various user-chosen options such as the method and number of SNPs used to estimate the kinship (relatedness) matrix. We investigate sensitivity to these choices and the success (or otherwise) of the approaches in controlling the overall genome-wide error-rate for both real and simulated phenotypes. We compare the LMM results to those obtained using traditional family-based association tests (based on transmission of alleles within pedigrees) and to alternative approaches implemented in the software packages MQLS, ROADTRIPS and MASTOR. We find strong concordance between the results from different LMM approaches, and all are successful in controlling the genome-wide error rate (except for some approaches when applied naively to longitudinal data with many repeated measures). We also find high correlation between LMMs and alternative approaches (apart from transmission-based approaches when applied to SNPs with small or non-existent effects). We conclude that LMM approaches perform well in comparison to competing approaches. Given their strong concordance, in most applications, the choice of precise LMM implementation cannot be based on power/type I error considerations but must instead be based on considerations such as speed and ease-of-use.
The Minimal Repression Domain of MBD2b Overlaps with the Methyl-CpG-binding Domain and Binds Directly to Sin3A*

Different mechanisms mediating methylation-dependent repression have been demonstrated. Two of these mechanisms play a role in the context of the granulocyte/macrophage-specific lysozyme gene: direct interference with DNA binding of the transcription factor GA-binding protein and deacetylation of histones. Besides enhancement in the unmethylated state, and transcriptional repression upon DNA methylation, the lysozyme downstream enhancer confers tissue-specific demethylation. Because both demethylation activity and repression ability have been attributed to the methyl-CpG-binding domain-containing protein MBD2, we analyzed this protein. The short form MBD2b binds to the methylated lysozyme enhancer and mediates transcriptional repression. MBD2b is capable of binding to the transcriptional repressor Sin3A. The interaction domain of Sin3A required for binding to MBD2b contains the paired amphipathic helix 3. We identified a minimal functional domain that confers both transcriptional repression as well as the interaction to Sin3A. In contrast to the functionally related proteins MeCP2 and MBD1, the repression domain of MBD2b overlaps with the methyl-CpG-binding domain.
The Effectiveness of Aromatherapy for Depressive Symptoms: A Systematic Review

Background. Depression is one of the greatest health concerns affecting 350 million people globally. Aromatherapy is a popular CAM intervention chosen by people with depression. Due to the growing popularity of aromatherapy for alleviating depressive symptoms, in-depth evaluation of the evidence-based clinical efficacy of aromatherapy is urgently needed. Purpose. This systematic review aims to provide an analysis of the clinical evidence on the efficacy of aromatherapy for depressive symptoms on any type of patients. Methods. A systematic database search was carried out using predefined search terms in 5 databases: AMED, CINHAL, CCRCT, MEDLINE, and PsycINFO. Outcome measures included scales measuring depressive symptoms levels. Results. Twelve randomized controlled trials were included and two administration methods for the aromatherapy intervention including inhaled aromatherapy (5 studies) and massage aromatherapy (7 studies) were identified. Seven studies showed improvement in depressive symptoms. Limitations. The quality of half of the studies included is low, and the administration protocols among the studies varied considerably. Different assessment tools were also employed among the studies. Conclusions. Aromatherapy showed potential to be used as an effective therapeutic option for the relief of depressive symptoms in a wide variety of subjects. Particularly, aromatherapy massage showed to have more beneficial effects than inhalation aromatherapy.
On the Use of Situational and Body Information in Goalkeeper Actions during a Soccer Penalty Kick

This study investigated the contribution of situation information about a player’s preference to kick to either side of the goal on the goalkeeper’s performance in a soccer penalty kick. Nine goalkeepers were tested under different situational information conditions: a non-probability, an equal-probability (i.e., 50% of the kicks to either side of the goal), and two high-probability conditions (i.e., 80% to the right or left side). In the high-probability conditions, the goalkeepers’ performance tended to increase and significantly improved in terms of diving to the same side as the ball was directed. In addition, goalkeepers initiated their dive earlier in the high-probability conditions. Gaze analysis in four participants suggested that goalkeepers who relied more strongly on body information profited less from situational information. In conclusion, soccer goalkeepers can benefit from situational information about a penalty taker’s preferences, but these benefits may depend on the individual goalkeeper’s information-using profile.
Molecular efficacy of radio- and chemotherapy sequences from direct DNA damage measurements

Abstract Purpose: To investigate the molecular aspects of the synergy between ionizing radiation and platinum (Pt) chemotherapeutic agents in cancer treatment with chemoradiation therapy (CRT) by measuring damages induced by low-energy electrons (LEE) to DNA bound to cisplatin. LEE are produced abundantly by any type of ionizing radiation and cisplatin represents a typical Pt-chemotherapeutic agents. Materials and methods: Our strategy involves two parallel administrations of cisplatin and irradiation with a 4.6 and 9.6 eV electron fluence of 1.1 × 1012: (1) LEE bombardment of supercoiled DNA and its subsequent reaction with cisplatin; (2) the reaction of DNA with cisplatin followed by LEE irradiation. The damage yields for the loss of supercoiled (LS), single-strand breaks (SSB) and double-strand breaks (DSB) were obtained from gel electrophoresis analysis. Base modifications were revealed by treating the samples with Escherichia coli base excision repair endonuclease (Nth and Fpg). Results: The yields were deduced from the respective time–response for the reaction of DNA with cisplatin. The results show that binding cisplatin to DNA followed by LEE irradiation, consistently yields more DNA damages than the reverse order. In comparison to non-treated DNA, administration (2) results in an increase of LS and SSB of 1.4–3.3 folds and of DSB by more than an order of magnitude. Furthermore, after enzyme treatment, the yields of DSB rise by factors of 5.3–15.4, indicating a large increase of clustered damages, which should at least partially translate into an increase of lethal damages in cancer cells during the CRT. Conclusions: Our results demonstrate that a strong synergy between radiation and cisplatin can only be achieved at the molecular level, if the drug is present at the time of irradiation. Furthermore, this work confirms the LEE mechanism previously proposed to explain the synergy between radiation and Pt drugs in CRT. It involves chemical sensitization of DNA prior to irradiation, to facilitate strand breaks and clustered damages induced by the highly reactive LEE.
Statistical query translation models for cross-language information retrieval

Query translation is an important task in cross-language information retrieval (CLIR), which aims to determine the best translation words and weights for a query. This article presents three statistical query translation models that focus on the resolution of query translation ambiguities. All the models assume that the selection of the translation of a query term depends on the translations of other terms in the query. They differ in the way linguistic structures are detected and exploited. The co-occurrence model treats a query as a bag of words and uses all the other terms in the query as the context for translation disambiguation. The other two models exploit linguistic dependencies among terms. The noun phrase (NP) translation model detects NPs in a query, and translates each NP as a unit by assuming that the translation of a term only depends on other terms within the same NP. Similarly, the dependency translation model detects and translates dependency triples, such as verb-object, as units. The evaluations show that linguistic structures always lead to more precise translations. The experiments of CLIR on TREC Chinese collections show that all three models have a positive impact on query translation and lead to significant improvements of CLIR performance over the simple dictionary-based translation method. The best results are obtained by combining the three models.
Multidrug resistance-associated protein 2 (MRP2) affects hepatobiliary elimination but not the intestinal disposition of tenofovir disoproxil fumarate and its metabolites

The role of multidrug resistance-associated protein 2 (MRP2) on the intestinal disposition and hepatobiliary elimination of tenofovir disoproxil fumarate (DF) and its metabolites [tenofovir (mono)ester and tenofovir] was studied in the Caco-2 system, Ussing chambers and rat in-situ efflux experiments. In the Caco-2 model and Ussing chambers, no statistically significant differences in transport could be observed when the MRP inhibitor probenecid was included. In Ussing chambers, transport was also similar when using intestinal tissue from MRP2-deficient rats. After intravenous administration of tenofovir DF, the excretion of tenofovir [(mono)ester] in bile was significantly decreased in MRP2-deficient rats and in rats treated with probenecid. The area under the blood concentration–time curve was increased in MRP2-deficient rats [1.0 ± 0.1 and 0.36 ± 0.03 µM. min−1 for tenofovir and tenofovir (mono)ester, respectively] and rats treated with probenecid (1.42 ± 0.04 and 0.36 ± 0.02 µM.min−1) compared with control rats (0.64 ± 0.05 and 0.15 ± 0.06 µM.min−1). The appearance of tenofovir [(mono)ester] in intestinal perfusate was similar in control rats upon co-administering probenecid or when using MRP2-deficient rats. In conclusion, MRP2 appeared to have no modulatory effect on the intestinal disposition of tenofovir and tenofovir (mono)ester. However, inhibition (probenecid) or the total absence of MRP2 (MRP2-deficient rats) significantly reduced hepatobiliary elimination, which was accompanied by increased systemic exposure.