Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of surface registration algorithms for PET motion correction

Recent advancements in high resolution Positron Emission Tomography (PET) have made it possible to study metabolic activity and the anatomy of the brain in great details. It becomes increasingly important to perform motion correction on these data. Motion tracking with a structured light system is pursued by Ph.D. student Oline V. Olesen. This thesis covers the registration (alignment) of point cloud surfaces acquired from a structured light scanner. An introduction to the concepts of rigid motion and point cloud properties is given. These include representations of rotations, surface curvature estimates and solutions to the nearest neighbor problem. The iterative closest point (ICP) algorithm is detailed with some of its most promising variants. Non linear optimization is introduced conceptually. Experimental data is used to compare these different variants in terms of convergence, accuracy, robustness and speed. It is concluded, that implementational simple variations of the ICP algorithm can yield much improved performance and reliability, and that, with the proper choice of acceleration techniques, real time performance is a realistic perspective. In the appendix derivations of the most important mathematical formulas are given.
Optimizing the IEEE 802.15.4 MAC

This paper optimally determines the IEEE 802.15. 4 medium access control (MAC) attributes macbeaconorder (BO) and macsuperframeorder (SO) (by which the periods of time that the sensor is active and non-active can be computed) such that the overall energy consumption of the network is minimized. Considering an IEEE 802.15. 4 beacon-enabled network laid out in a single-hop star topology, we evaluated the performance of the IEEE 802.15. 4 MAC through simulation. Numerical results show that the optimal solutions of BO and SO can be obtained for a range of user-specific quality of service requirements, such as proportion of successful packet transmissions and maximum delay constraint
Body fat distribution in pubertal girls quantified by magnetic resonance imaging.

We examined body fat distribution in relation to anthropometrically derived variables in 24 girls in early and late stages of puberty. The amounts of subcutaneous and intra-abdominal body fat were derived from transverse slices at the levels of the waist, hip and trochanter using magnetic resonance imaging (MRI), and were compared to the related circumferences, the circumference ratios and the trunk-to-extremity skinfold ratios. Waist, hip and trochanter circumferences were highly correlated to the respective related MRI total fat surface area both in early and late pubertal girls (r = 0.79-0.97), while waist circumference, and waist-hip, waist-thigh or skinfold ratios were not significantly correlated to intra-abdominal fat areas. Late pubertal girls (n = 11) were significantly taller, heavier and fatter compared to early pubertal girls (n = 13), yet their anthropometric waist-to-hip or waist-to-trochanter circumference ratios were significantly lower. The intra-abdominal fat area measured in a transverse MRI section at the level of the waist was 24.1 +/- 4.1 cm2 in early pubertal girls and 25.7 +/- 4.1 cm2 in late pubertal girls (mean +/- s.e.m.). As compared to early pubertal girls, the MRI derived amount of subcutaneous fat in late pubertal girls was significantly higher at the trochanter level (142.1 +/- 12.7 vs. 201.3 +/- 26.3 cm2; P less than 0.05). We conclude that circumferences at the trunk are good measures for the related amounts of fat in pubertal girls. In contrast conventional anthropometric measurements, such as trunk-to-extremity skinfold ratio or waist-to-hip circumference ratio, cannot be used to predict the amount of intra-abdominal fat in pubertal girls. (ABSTRACT TRUNCATED AT 250 WORDS)
Effect of Priming with Gibberellic Acid (GA 3 ) on Germination and Growth of Corn (Zea mays L.) under Saline Conditions

In order to study the effect of priming with Gibberellic acid (GA 3) on germination and growth of corn under saline conditions, an experiment was conducted as factorial with completely randomized design with three replications. The factors of the experiment are different levels of Gibberellic acid concentration (0, 1.5, 2.5 and 5 mgL -1 ) and salinity (0, 5, 10, 12 and 15 dsm -1 ). The results showed that increasing salinity would decrease the components of germination including germination percentage, germination rate, root and shoot length and fresh and dry weight of seedling. Priming with GA 3 had no effect on seed germination however in some concentrations GA 3 increased shoot length, root length, dry weight, fresh weight and tissue water content.
Determination of the esterification degree of the pectin of different origin and composition by the method of infrared spectroscopy

The change in infrared spectrum of the pectin films of different origin accompanying the transformation of potassium pectinate into potassium pectate was investigated. It was revealed that the intensity ratio of the bands va s(COO-) at 1608 cm"' and v(C = 0) e s t e r at 1745 cm" 1 corresponding to fully deesterified pectin and methyl pectate, respectively, is a constant independent of the kind of fruit used for the isolation of pectin as well as of the pectin composition. Thus, it has been proved that the method of the determination of the degree of esterification of the pectin by methanol based on the measure­ ment of absorbances in the maxima of these bands can be used for different kinds of pectins. The degree of esterification of pectin (E %) can be determi­ ned with absolute error ± 1.3%.
Detection of repetitions in spontaneous speech in dialogue sessions

We present a study on detecting repeated speech segments in consecutive utterances in a user session of a dialogue application. Such repetition patterns often carry important information of a user’s expectation from or frustration about the dialogue system and therefore provide a source of clues for the system to adjust its dialogue strategies when such repetitions occur in order to improve system performance. We propose a recursive dynamic-time warping based pattern comparison algorithm with no ﬁxed end-points to ﬁnd similar parts within the two utterances, called original and correction utterances. Candidate reference patterns are generated from the correction utterance by an unsupervised segmentation scheme. When no prior information about the position of the repeated parts is used, each reference pattern is compared with the original utterance from the beginning to the end. Experiments are conducted on 190 utterances of spontaneous speech from simulated dialogue sessions. The proposed algorithm achieves detection and rejection rates of 80.3% and 85.2% for the repeated and non-repeated parts, respectively. When segmentation information provided by the recognizer in the dialog system is incorporated into preparing the reference patterns, the rates are increased to 93.8% and 91.1%.
HOX genes in the sepiolid squid Euprymna scolopes: Implications for the evolution of complex body plans

Molluscs display a rich diversity of body plans ranging from the wormlike appearance of aplacophorans to the complex body plan of the cephalopods with highly developed sensory organs, a complex central nervous system, and cognitive abilities unrivaled among the invertebrates. The aim of the current study is to define molecular parameters relevant to the developmental evolution of cephalopods by using the sepiolid squid Euprymna scolopes as a model system. Using PCR-based approaches, we identified one anterior, one paralog group 3, five central, and two posterior group Hox genes. The deduced homeodomain sequences of the E. scolopes Hox cluster genes are most similar to known annelid, brachiopod, and nemertean Hox gene homeodomain sequences. Our results are consistent with the presence of a single Hox gene cluster in cephalopods. Our data also corroborate the proposed existence of a differentiated Hox gene cluster in the last common ancestor of Bilaterians. Furthermore, our phylogenetic analysis and in particular the identification of Post-1 and Post-2 homologs support the Lophotrochozoan clade.
Quantification of nanoparticle concentration in colloidal suspensions by a non-destructive optical method

The estimation of nanoparticle number concentration in colloidal suspensions is a prerequisite in many procedures, and in particular in multi-stage, low-yield reactions. Here, we describe a rapid, non-destructive method based on optical extinction and dynamic light scattering (DLS), which combines measurements using common bench-top instrumentation with a numerical algorithm to calculate the particle size distribution (PSD) and concentration. These quantities were derived from Mie theory applied to measurements of the optical extinction spectrum of homogeneous, non-absorbing nanoparticles, and the relative PSD of a colloidal suspension. The work presents an approach to account for PSDs achieved by DLS which, due to the underlying model, may not be representative of the true sample PSD. The presented approach estimates the absolute particle number concentration of samples with mono-, bi-modal and broad size distributions with <50% precision. This provides a convenient and practical solution for number concentration estimation required during many applications of colloidal nanomaterials.
Research on group POIs recommendation fusion of users' gregariousness and activity in LBSN

In the study of Location-Based Social Network (LBSN) sign-in data as the recommended point of interest for groups, there are some problems such as poor recommendation accuracy and high bias in recommendation results because of the unbalanced number and diversity of individual sign-in and the different degree of group user association. In this paper, a new group recommendation model is proposed. Firstly, the existing individual recommendation model is combined with the text retrieval idea and the threshold function to improve the user rating strategy. Secondly, the recommendation strategy is used to aggregate the individual recommendation list. Considering users' friends relationship, similarity and frequency of sign-in, lead into the user gregariousness weight and activity weight, and form a new group user preference model to make recommendation. The experimental results show that the improved scoring strategy can improve the accuracy of recommendation, and the new group weighting model which recommend the points of interest for the groups can improve the recommendation quality by reducing the recommended deviation.
CDK-Dependent Hsp 70 Phosphorylation Controls G 1 Cyclin Abundance and Cell-Cycle Progression

Andrew W. Truman,1,2 Kolbrun Kristjansdottir,1,2 Donald Wolfgeher,1,2 Naushaba Hasin,3 Sigrun Polier,4 Hong Zhang,5 Sarah Perrett,5 Chrisostomos Prodromou,4 Gary W. Jones,3 and Stephen J. Kron1,2,* 1Ludwig Center for Metastasis Research 2Department of Molecular Genetics and Cell Biology The University of Chicago, Chicago, IL 60637, USA 3Department of Biology, National University of Ireland Maynooth, Maynooth, County Kildare, Ireland 4Genome Damage and Stability Centre, Science Park Road, University of Sussex, Brighton BN1 9RQ, England 5National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China *Correspondence: skron@uchicago.edu http://dx.doi. org/10.1016/j.cell. 2012.10. 051
The Impact of Network Layer Attacks in Wireless Sensor Networks

Security threats are present in Wireless Sensor Networks and aim to destruct, manipulate the network, or eavesdrop network traffic for malicious intent. The first line of defense is to prevent attacks, usually by applying cryptography, the second line of defense is detecting the presence of the attack within the network, and the third is stopping or recovering quickly from the attack. In this work we deal with the detection phase and examine the impact of routing layer attacks in WSNs in an effort to build better intrusion detection systems (IDS). IDSs base their detection decision on the knowledge gained from known attacks. The attacks' characteristics and methods to manipulate the network are analysed and used to drive recovery mechanisms. In this paper we implemented routing-layer packet drop attacks and investigated the impact of the attacks as "seen" from the Sink node and the victim node. We show that the attacks can have an effect on all network layers of the victim node and the degree of impact depends on many factors, including the topology of WSN and the distance from the Sink.
Mining Patents with tmChem , GNormPlus and an Ensemble of Open Systems

The significant amount of medicinal chemistry information contained in patents make them an attractive target for text mining. The CHEMDNER task at BioCreative V focused on information extraction from patents. This manuscript describes our submissions to the CEMP (chemical named entity recognition) and GPRO (gene and related object identification) subtasks. Our CEMP submission is an ensemble of five open systems, including both versions of tmChem, our previous work on chemical named entity recognition. Their output is combined using a machine learning classification approach. Our CEMP system obtained 0.8752 precision and 0.9129 recall, for 0.8937 f-score. Our submission to the GPRO task is an extension of GNormPlus, our previous work for gene and protein named entity recognition. Our GPRO system obtained a performance of 0.8143 precision and 0.8141 recall for 0.8137 f-score. Both submissions achieved the highest performance in their respective tasks.
Structural mechanism of RuBisCO activation by carbamylation of the active site lysine

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is a crucial enzyme in carbon fixation and the most abundant protein on earth. It has been studied extensively by biochemical and structural methods; however, the most essential activation step has not yet been described. Here, we describe the mechanistic details of Lys carbamylation that leads to RuBisCO activation by atmospheric CO2. We report two crystal structures of nitrosylated RuBisCO from the red algae Galdieria sulphuraria with O2 and CO2 bound at the active site. G. sulphuraria RuBisCO is inhibited by cysteine nitrosylation that results in trapping of these gaseous ligands. The structure with CO2 defines an elusive, preactivation complex that contains a metal cation Mg2+ surrounded by three H2O/OH molecules. Both structures suggest the mechanism for discriminating gaseous ligands by their quadrupole electric moments. We describe conformational changes that allow for intermittent binding of the metal ion required for activation. On the basis of these structures we propose the individual steps of the activation mechanism. Knowledge of all these elements is indispensable for engineering RuBisCO into a more efficient enzyme for crop enhancement or as a remedy to global warming.
EXPLORING GENDER IDENTIFICATION EFFECTS ON STEREOTYPE THREAT 2 Acknowledgements

Stereotype threat impairs performance in situations where a stereotype holds that one’s social group will perform poorly. A study of women’s college students examined whether this effect influenced performance on spatial cognition tasks when participants were presented with threat on the basis of gender socialization. Transgender and cisgender participants, all designated female at birth, were randomly assigned to one of four stereotype threat conditions and were asked to complete two spatial cognition tasks. Three of the conditions described the task as traditionally displaying gender differences favoring males, due to differences in gender socialization of young boys and girls. Of those three, one empowered all participants through their identity as a women’s college student, and another empowered non-cisgender participants through their non-female identity. Participants also completed measures of implicit and explicit gender identity. Stereotype threat was predicted to decrease performance of cisgender and noncisgender participants in the classic threat condition, but not in the women’s college empowerment condition. Performance was expected to vary as an function of gender identity in non-cisgender empowerment condition. Implicit and explicit gender identification were also predicted to correlate. No significant effect of condition was found. The relation between implicit gender identification and different measures of explicit gender varied for cisgender and non-cisgender participants. Discussion includes consideration of framing factors that may have influenced results for the two groups.
Serological analysis of human renal cell carcinoma

Serological analysis of cDNA expression libraries (SEREX) has proven to be a useful technique in the quest to elucidate the repertoire of immunogenic gene products in human cancer. We have applied the SEREX method to human renal cell carcinoma (RCC) in order to identify associated immunogenic gene products. cDNA expression libraries were prepared from a RCC tumor, a RCC cell line and human testis. The 3 libraries were screened with sera from 35 RCC patients and 15 healthy controls. Approximately 4.5 × 106 phage plaques were screened resulting in 234 positive clones, which corresponded to 74 different gene products. The seroreactivity toward 49 of these antigens was assessed. Seroreactivity to 21 (43%) of the antigens was similar in RCC patients and healthy controls, 9 antigens (18%) elicited antibodies more frequently and 19 antigens (39%) solely in RCC patients. In the reverse setting, reactivity of RCC patients' sera was tested against a panel of 44 previously identified “tumor‐associated” antigens via the SADA (serum antibody detection array) method; 6 antigens reacted with RCC patients' and healthy donors' sera, 8 were reactive only with RCC patients' sera. From the 27 antigens identified by SEREX and SADA, which did not react with sera from healthy controls, 10 antigens reacted with a significant proportion of RCC patients' sera and 77% of RCC patients' sera reacted at least with one of these antigens. Sera from patients with non‐malignant renal diseases or an autoimmune disease did not react with these 10 antigens. © 2005 Wiley‐Liss, Inc.
Complete mitochondrial genome and phylogenetic analysis of the Asian swallowtail, Papilio xuthus

Abstract The Asian swallowtail, Papilio xuthus, a member of the Papilioniniis family, is one of the most popular swallowtail. Here, we first assembled the complete mitochondrial genome of P. xuthus. The mitogenome is 15 359 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNA genes, and 2 ribosomal RNA genes. The structure of non-coding control region was also analyzed. The gene content and the order are in accord with the common Invertebrate form. Phylogenetic tree was constructed based on the complete mitogenomes of P. xuthus and closely related nine swallowtail species to assess their phylogenic relationship and evolution. The complete mitochondrial genome data would be useful for further studies of P. xuthus.
Spontaneous physical activity and mediators of energy homeostasis in the hypothalamus of mice from 4 to 10 months of age

What is the central question of this study? Is the initial decline of spontaneous physical activity (SPA) in mice related to impaired insulin and leptin signalling or brain‐derived neurotrophic factor expression in the hypothalamus? What is the main finding and its importance? We showed that SPA started to decline at an early stage, concomitantly with an impairment of hypothalamic leptin signalling. Consequently, energy expenditure decreased and glucose tolerance worsened. Our results demonstrate the need to counteract the initial decline in SPA to avoid metabolic impairments and indicate the possible involvement of central leptin in the reduction in SPA with age.
Tunable BST capacitor loss compensation using active circuit

The compensation of the ohmic and the material dielectric losses in a barium strontium titanate (BST) capacitor using an active circuit is reported in this letter. The negative resistance (NR) circuit creates an effective conductance of -|Gn| which adds to the positive conductance of the passive BST-based tuned capacitor. As a result, the compensation of the losses is significantly improved in the hybrid circuit by more than 50%. To our knowledge, this is the first work in tunable BST capacitor loss compensation using a NR circuit ever reported
Prevalence and factors affecting breastfeeding among Aboriginal women in Northwestern Ontario.

OBJECTIVE To evaluate breastfeeding outcomes among Aboriginal women and to determine variables affecting breastfeeding in the early postpartum period. DESIGN Prospective cohort study. SETTING Two sites in Northwestern Ontario, Canada: a tertiary care center and a rural hospital. PARTICIPANTS One hundred thirty breastfeeding Aboriginal women agreed to participate in the study. METHODS All women completed a baseline survey in hospital that included questions regarding demographic, prenatal, breastfeeding, obstetric, postpartum, and neonatal characteristics. Women were then telephoned at 4 and 8 weeks postpartum to complete additional questionnaires regarding infant feeding. RESULTS Low rates of breastfeeding initiation (69%) and exclusive breastfeeding were identified at 4 (37.5%) and 8 (35.3%) weeks postpartum. Among those who initiated breastfeeding, duration rates at 4 (86%) and 8 weeks (78%) postpartum are comparable to other studies. Variables associated with any and exclusive breastfeeding at 8 weeks included the following: (a) household income, (b) intended breastfeeding duration, (c) plan to exclusively breastfeed, (d) perception of meeting their planned duration goal, and (e) higher breastfeeding self-efficacy. Partner support was associated with any breastfeeding at 8 weeks but not exclusivity. Women who were breastfeeding exclusively in hospital (prevalence ratio [PR] = .48, 95% confidence interval [CI] [0.27, 0.86]), did not smoke (PR = 2.5, 95% CI [1.4, 4.3]) and/or use substances during pregnancy (PR = 4.5, 95% CI [1.5, 14]) were more likely to be breastfeeding exclusively at 8 weeks. CONCLUSION Many of the variables may be considered modifiable and amenable to intervention. Targeted interventions should be directed toward improving breastfeeding outcomes among Aboriginal women.
Fluorescence Signal Generation Optimization by Optimal Filling of the High Numerical Aperture Objective Lens for High-Order Deep-Tissue Multiphoton Fluorescence Microscopy

Deep-tissue multiphoton microscopy (MPM) enables noninvasive optical imaging into the deep regions of the tissue in animal models in vivo. High-order MPM techniques, such as three- and four-photon fluorescence microscopy at the 1700-nm window, are emerging as promising imaging techniques for deeper penetration. Currently, signal depletion at large imaging depth sets the depth limit for these imaging techniques. As a result, how to further boost signal level is the key to achieving a larger imaging depth. Contrary to the previous thought that overfilling the back aperture of the objective yields the highest multiphoton fluorescence signal, in this paper, through numerical simulation, we show that, due to the effect of exponential decay of the excitation beam, the signal generation is maximized for certain underfilling of the back aperture of the objective lens. This will provide a simple strategy for signal generation maximization in deep-tissue MPM and potentially enables deeper imaging penetration into the tissue.
Alternative approach for modeling material interfaces in FDTD

A simple alternative way to position dielectric materials in the finite‐difference time‐domain (FDTD) Yee cell grid is proposed. Plane‐wave illuminated spheres are used as examples to study the performance of the alternative method compared to the standard FDTD method. Although the performances are generally equally good, the alternative method may sometimes give significantly improved accuracy. © 2008 Wiley Periodicals, Inc. Microwave Opt Technol Lett 50: 1211–1214, 2008; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.23309