Miracle-dz/UniFAR-FTUs huggingface dataset:
Axon guidance by growth-rate modulation

Guidance of axons by molecular gradients is crucial for wiring up the developing nervous system. It often is assumed that the unique signature of such guidance is immediate and biased turning of the axon tip toward or away from the gradient. However, here we show that such turning is not required for guidance. Rather, by a combination of experimental and computational analyses, we demonstrate that growth-rate modulation is an alternative mechanism for guidance. Furthermore we show that, although both mechanisms may operate simultaneously, biased turning dominates in steep gradients, whereas growth-rate modulation may dominate in shallow gradients. These results suggest that biased axon turning is not the only method by which guidance can occur.
Composition, Morphology, and Stratigraphy of Noachian Crust around the Isidis basin

Definitive exposures of pristine, ancient crust on Mars are rare, and the finding that much of the ancient Noachian terrain on Mars exhibits evidence of phyllosilicate alteration adds further complexity. We have analyzed high-resolution data from the Mars Reconnaissance Orbiter in the well-exposed Noachian crust surrounding the Isidis basin. We focus on data from the Compact Reconnaissance Imaging Spectrometer for Mars as well as imaging data sets from High Resolution Imagine Science Experiment and Context Imager. These data show the lowermost unit of Noachian crust in this region is a complex, brecciated unit of diverse compositions. Breccia blocks consisting of unaltered mafic rocks together with rocks showing signatures of Fe/Mg-phyllosilicates are commonly observed. In regions of good exposure, layered or banded phyllosilicate-bearing breccia rocks are observed suggestive of pre-Isidis sedimentary deposits. In places, the phyllosilicate-bearing material appears as a matrix surrounding mafic blocks, and the mafic rocks show evidence of complex folded relationships possibly formed in the turbulent flow during emplacement of basin-scale ejecta. These materials likely include both pre-Isidis basement rocks as well as the brecciated products of the Isidis basin–forming event at 3.9 Ga. A banded olivine unit capped by a mafic unit covers a large topographic and geographic range from northwest of Nili Fossae to the southern edge of the Isidis basin. This olivine-mafic cap combination superimposes the phyllosilicate-bearing basement rocks and distinctly conforms to the underlying basement topography. This may be due to draping of the topography by a fluid or tectonic deformation of a previously flatter lying morphology. We interpret the draping, superposed olivine-mafic cap combination to be impact melt from the Isidis basin–forming event. While some distinct post-Isidis alteration is evident (carbonate, kaolinite, and serpentine), the persistence of olivine from the time of Isidis basin suggests that large-scale aqueous alteration processes had ceased by the time this unit was emplaced.
Multiplex Fluorescence Melting Curve Analysis for Mutation Detection with Dual-Labeled, Self-Quenched Probes

Probe-based fluorescence melting curve analysis (FMCA) is a powerful tool for mutation detection based on melting temperature generated by thermal denaturation of the probe-target hybrid. Nevertheless, the color multiplexing, probe design, and cross-platform compatibility remain to be limited by using existing probe chemistries. We hereby explored two dual-labeled, self-quenched probes, TaqMan and shared-stem molecular beacons, in their ability to conduct FMCA. Both probes could be directly used for FMCA and readily integrated with closed-tube amplicon hybridization under asymmetric PCR conditions. Improved flexibility of FMCA by using these probes was illustrated in three representative applications of FMCA: mutation scanning, mutation identification and mutation genotyping, all of which achieved improved color-multiplexing with easy probe design and versatile probe combination and all were validated with a large number of real clinical samples. The universal cross-platform compatibility of these probes-based FMCA was also demonstrated by a 4-color mutation genotyping assay performed on five different real-time PCR instruments. The dual-labeled, self-quenched probes offered unprecedented combined advantage of enhanced multiplexing, improved flexibility in probe design, and expanded cross-platform compatibility, which would substantially improve FMCA in mutation detection of various applications.
Evaluating Glucocorticoid Administration on Biomechanical Properties of Rats’ Tibial Diaphysis

Background: Osteoporosis is a disease, which causes bone loss and fractures. Although glucocorticoids effectively suppress inflammation, their chronic use is accompanied by bone loss with a tendency toward secondary osteoporosis. Objectives: This study took into consideration the importance of cortical bone in the entire bone's mechanical competence. Hence, the aim of this study was to assess the effects of different protocols of glucocorticoid administration on the biomechanical properties of tibial bone diaphysis in rats compared to control and low-level laser-treated rats. Materials and Methods: This experimental study was conducted at Shahid Beheshti University of Medical Sciences, Tehran, Iran. We used systematic random sampling to divide 40 adult male rats into 8 groups with 5 rats in each group. Groups were as follows: 1) control, 2) dexamethasone (7 mg/week), 3) dexamethasone (0.7 mg/week), 4) methylprednisolone (7 mg/kg/week), 5) methylprednisolone (5 mg/kg twice weekly), 6) dexamethasone (7 mg/kg three times per week), 7) dexamethasone (0.7 mg/kg thrice per week), and 8) low-level laser-treated rats. The study periods were 4-7 weeks. At the end of the treatment periods, we examined the mechanical properties of tibial bone diaphysis. Data were analyzed by statistical analyses. Results: Glucocorticoid-treated rats showed weight loss and considerable mortality (21%). The biomechanical properties (maximum force) of glucocorticoid-treated rats in groups 4 (62 ± 2.9), 6 (63 ± 5.1), and 7 (60 ± 5.3) were comparable with the control (46 ± 1.5) and low-level laser-treated (57 ± 3.2) rats. Conclusions: In contrast to the findings in humans and certain other species, glucocorticoid administration caused anabolic effect on the cortical bone of tibia diaphysis bone in rats.
Continuous Postnatal Neurogenesis Contributes to Formation of the Olfactory Bulb Neural Circuits and Flexible Olfactory Associative Learning

The olfactory bulb (OB) is one of the two major loci in the mammalian brain where newborn neurons are constantly integrated into the neural circuit during postnatal life. Newborn neurons are generated from neural stem cells in the subventricular zone (SVZ) of the lateral ventricle and migrate to the OB through the rostral migratory stream. The majority of these newborn neurons differentiate into inhibitory interneurons, such as granule cells and periglomerular cells. It has been reported that prolonged supply of newborn neurons leads to continuous addition/turnover of the interneuronal populations and contributes to functional integrity of the OB circuit. However, it is not still clear how and to what extent postnatal-born neurons contribute to OB neural circuit formation, and the functional role of postnatal neurogenesis in odor-related behaviors remains elusive. To address this question, here by using genetic strategies, we first determined the unique integration mode of newly born interneurons during postnatal development of the mouse OB. We then manipulated these interneuron populations and found that continuous postnatal neurogenesis in the SVZ-OB plays pivotal roles in flexible olfactory associative learning and memory.
CHAPTER 4 Bias in Psychological Assessment An Empirical Review and Recommendations

UNDERSTANDING BIAS IN PSYCHOLOGICAL ASSESSMENT 82 MINORITY OBJECTIONS TO TESTS AND TESTING 83 ORIGINS OF THE TEST BIAS CONTROVERSY 84 EFFECTS AND IMPLICATIONS OF THE TEST BIAS CONTROVERSY 86 POSSIBLE SOURCES OF BIAS 86 WHAT TEST BIAS IS AND IS NOT 87 RELATED QUESTIONS 89 EXPLAINING GROUP DIFFERENCES 90 CULTURAL TEST BIAS AS AN EXPLANATION 91 HARRINGTON’S CONCLUSIONS 92 MEAN DIFFERENCES AS TEST BIAS 93 RESULTS OF BIAS RESEARCH 95 EXAMINER–EXAMINEE RELATIONSHIP 104 HELMS AND CULTURAL EQUIVALENCE 105 TRANSLATION AND CULTURAL TESTING 105 NATURE AND NURTURE 106 CONCLUSIONS AND RECOMMENDATIONS 107 REFERENCES 108
MicroRNA-338 Inhibits Growth, Invasion and Metastasis of Gastric Cancer by Targeting NRP1 Expression

NRP1 as multifunctional non-tyrosine-kinase receptors play critical roles in tumor progression. MicroRNAs (miRNAs) are an important class of pervasive genes that are involved in a variety of biological functions, particularly cancer. It remains unclear whether miRNAs can regulate the expression of NRP1. The goal of this study was to identify miRNAs that could inhibit the growth, invasion and metastasis of gastric cancer by targeting NRP1 expression. We found that miR-338 expression was reduced in gastric cancer cell lines and in gastric cancer tissues. Moreover, we found that miR-338 inhibited gastric cancer cell migration, invasion, proliferation and promoted apoptosis by targeting NRP1 expression. As an upstream regulator of NRP1, miR-338 directly targets NRP1. The forced expression of miR-338 inhibited the phosphorylation of Erk1/2, P38 MAPK and Akt; however, the expression of phosphorylated Erk1/2, P38 MAPK and Akt was restored by the overexpression of NRP1. In AGS cells infected with miR-338 or transfected with SiNRP1, the protein levels of fibronectin, vimentin, N-cadherin and SNAIL were decreased, but the expression of E-cadherin was increased. The expression of mesenchymal markers in miR-338-expressing cells was restored to normal levels by the restoration of NRP1 expression. In vivo, miR-338 also decreased tumor growth and suppressed D-MVA by targeting NRP1. Therefore, we conclude that miR-338 acts as a novel tumor suppressor gene in gastric cancer. miR-338 can decrease migratory, invasive, proliferative and apoptotic behaviors, as well as gastric cancer EMT, by attenuating the expression of NRP1.
Truss size and topology optimization using harmony search method

When a truss structure is to be designed two important questions should be answered. First, how should the truss that requires the minimum amount of materials look like? Second, what are the possible members' cross sectional areas that support the applied load safely? In this work these two questions are answered using a two stage optimization process. In stage one, starting with hyper-connected truss ground structures that fully encompass the design region together with specified support conditions and load cases, the discrete combinations and arrangement of truss members that will yield the lightest and stiffest structure are sought. In the second stage the minimum cross sectional areas of the members that satisfy the imposed constraints are sought. In both stages harmony search algorithms are employed. These represent one of the most recent heuristic, stochastic search optimization methods that, while relatively simple and robust, overcome some of the drawbacks of preceding search techniques such as: the ability to converge to a global optimum, and the ability to optimize non-differentiable and non-continuous functions. The viability of the proposed framework is documented on numerous benchmark problems from the literature. 2.2 Maximum, minimum, and average number of iterations to solve example problem 2. vi LIST OF FIGURES Figure 1.1 Different classes of structural optimization problems. a) Initial truss design; b) topology optimized truss; c) a design where the cross sectional areas of the members have been optimized and line weight are proportional to cross-2.7 Influence of HMCR on number of iterations required to solve example problem 2.1. The problem was solved ten times with each value of HMCR to obtain a range of iterations for convergence.
Hierarchical self-assembly of chiral fibres from achiral particles

We investigate, by molecular dynamics simulation, the behaviour of discotic particles in a solvent of Lennard-Jones spheres. When chromonic disc–sphere interactions are imposed on these systems, three regimes of self-assembly are observed. At moderate temperatures, numerous short threads of discs develop, but these threads remain isolated from one another. Quenching to low temperatures, alternatively, causes all of the discs to floc into a single extended aggregate which typically comprises several distinct sections and contains numerous packing defects. For a narrow temperature range between these regimes, however, defect-free chiral fibres are found to freely self-assemble. The spontaneous chirality of these fibres results from frustration between the hexagonal packing and interdigitation of neighbouring threads, the pitch being set by the particle shape. This demonstration of aggregate-wide chirality emerging owing to packing alone is pertinent to many biological and synthetic hierarchically self-assembling systems.
Anti-bacterial effects of enzymatically-isolated sialic acid from glycomacropeptide in a Helicobacter pylori-infected murine model

BACKGROUND/OBJECTIVES Helicobacter pylori (H. pylori) colonization of the stomach mucosa and duodenum is the major cause of acute and chronic gastroduodenal pathology in humans. Efforts to find effective anti-bacterial strategies against H. pylori for the non-antibiotic control of H. pylori infection are urgently required. In this study, we used whey to prepare glycomacropeptide (GMP), from which sialic acid (G-SA) was enzymatically isolated. We investigated the anti-bacterial effects of G-SA against H. pylori in vitro and in an H. pylori-infected murine model. MATERIALS/METHODS The anti-bacterial activity of G-SA was measured in vitro using the macrodilution method, and interleukin-8 (IL-8) production was measured in H. pylori and AGS cell co-cultures by ELISA. For in vivo study, G-SA 5 g/kg body weight (bw)/day and H. pylori were administered to mice three times over one week. After one week, G-SA 5 g/kg bw/day alone was administered every day for one week. Tumor necrosis factor-α (TNF-α), IL-1β, IL-6, and IL-10 levels were measured by ELISA to determine the anti-inflammatory effects of G-SA. In addition, real-time PCR was performed to measure the genetic expression of cytotoxin-associated gene A (cagA). RESULTS G-SA inhibited the growth of H. pylori and suppressed IL-8 production in H. pylori and in AGS cell co-cultures in vitro. In the in vivo assay, administration of G-SA reduced levels of IL-1β and IL-6 pro-inflammatory cytokines whereas IL-10 level increased. Also, G-SA suppressed the expression of cagA in the stomach of H. pylori-infected mice. CONCLUSION G-SA possesses anti-H. pylori activity as well as an anti-H. pylori-induced gastric inflammatory effect in an experimental H. pylori-infected murine model. G-SA has potential as an alternative to antibiotics for the prevention of H. pylori infection and H. pylori-induced gastric disease prevention.
Collaborative spectrum sensing for opportunistic access in fading environments

Traditionally, frequency spectrum is licensed to users by government agencies in a fixed manner where licensee has exclusive right to access the allocated band. This policy has been de jure practice to protect systems from mutual interference for many years. However, with increasing demand for the spectrum and scarcity of vacant bands, a spectrum policy reform seems inevitable. Meanwhile, recent measurements suggest the possibility of sharing spectrum among different parties subject to interference-protection constraints. In this paper we study spectrum-sharing between a primary licensee and a group of secondary users. In order to enable access to unused licensed spectrum, a secondary user has to monitor licensed bands and opportunistically transmit whenever no primary signal is detected. However, detection is compromised when a user experiences shadowing or fading effects. In such cases, user cannot distinguish between an unused band and a deep fade. Collaborative spectrum sensing is proposed and studied in this paper as a means to combat such effects. Our analysis and simulation results suggest that collaboration may improve sensing performance significantly
Towards the Mirror Symmetry for Calabi-Yau Complete intersections in Gorenstein Toric Fano Varieties

We propose a combinatorical duality for lattice polyhedra which conjecturally gives rise to the pairs of mirror symmetric families of Calabi-Yau complete intersections in toric Fano varieties with Gorenstein singularities. Our construction is a generalization of the polar duality proposed by Batyrev for the case of hypersurfaces.
A Study of Chinese Document Representation and Classification with Word2vec

Word2vec is a neural network language model which can convert words and phrases into a high-quality distributed vector (called word embedding) with semantic word relationships, so it offers a unique perspective to the text classification and other natural language processing (NLP) tasks. In this paper, we propose to combine improved tfidf algorithm and word embedding as a way to represent documents and conduct text classification experiments on the Sogou Chinese classification corpus. Our results show that the combination of word embedding and improved tf-idf algorithm can outperform either individually.
Integration of biological knowledge in the mixture-of-Gaussians analysis of genomic clustering

The analysis of biological data produced by state of the art high throughput technologies like DNA microarrays presents many challenges due both to the domain itself (e.g. high dimensionality) and the technologies themselves (e.g. noisy data). In this paper we advocate the exploitation of existing biological knowledge in order to guide the cluster analysis of gene expression data. To this end we present a biologically inspired probabilistic model and a modified Expectation-Maximization algorithm for the estimation of its parameters. Finally we perform some initial evaluation of the clustering results of the proposed model.
CIRCADIAN RHYTHMS OF PERFORMANCE: NEW TRENDS

This brief review is concerned with how human performance efficiency changes as a function of time of day. It presents an overview of some of the research paradigms and conceptual models that have been used to investigate circadian performance rhythms. The influence of homeostatic and circadian processes on performance regulation is discussed. The review also briefly presents recent mathematical models of alertness that have been used to predict cognitive performance. Related topics such as interindividual differences and the postlunch dip are presented. (Chronobiology International, 17(6), 719–732, 2000)
Estimating Respiratory and Heart Rates from the Correntropy Spectral Density of the Photoplethysmogram

The photoplethysmogram (PPG) obtained from pulse oximetry measures local variations of blood volume in tissues, reflecting the peripheral pulse modulated by heart activity, respiration and other physiological effects. We propose an algorithm based on the correntropy spectral density (CSD) as a novel way to estimate respiratory rate (RR) and heart rate (HR) from the PPG. Time-varying CSD, a technique particularly well-suited for modulated signal patterns, is applied to the PPG. The respiratory and cardiac frequency peaks detected at extended respiratory (8 to 60 breaths/min) and cardiac (30 to 180 beats/min) frequency bands provide RR and HR estimations. The CSD-based algorithm was tested against the Capnobase benchmark dataset, a dataset from 42 subjects containing PPG and capnometric signals and expert labeled reference RR and HR. The RR and HR estimation accuracy was assessed using the unnormalized root mean square (RMS) error. We investigated two window sizes (60 and 120 s) on the Capnobase calibration dataset to explore the time resolution of the CSD-based algorithm. A longer window decreases the RR error, for 120-s windows, the median RMS error (quartiles) obtained for RR was 0.95 (0.27, 6.20) breaths/min and for HR was 0.76 (0.34, 1.45) beats/min. Our experiments show that in addition to a high degree of accuracy and robustness, the CSD facilitates simultaneous and efficient estimation of RR and HR. Providing RR every minute, expands the functionality of pulse oximeters and provides additional diagnostic power to this non-invasive monitoring tool.
Electromagnetic Shielding Properties of Plain Knitted Fabrics Containing Conductive Yarns

In this study, stainless steel conductive yarns with 500 tex fineness and 14 Ω/m linear resistances were inserted into the reverse side of the knitted fabrics made from acrylic yarns. Six types of knitted fabrics with conductive yarns were produced on an E=7 gauge electronic flat bed knitting machine. Then the electromagnetic shielding efficiency (EMSE) of the sample fabrics were measured in the frequency range of 750 MHz – 3000 MHz. The EMSE variations of the sample fabrics having conductive yarns with respect to fabric structure and polarization type (vertical and horizontal) were also investigated. It was observed that the same samples showed different behaviors and have dissimilar EMSE values in different polarization conditions. When compared to horizontal polarization measurements, the vertical measurement results gave better EMSE values.
Quantitative Deficits of Preschool Children at Risk for Mathematical Learning Disability

The study tested the hypothesis that acuity of the potentially inherent approximate number system (ANS) contributes to risk of mathematical learning disability (MLD). Sixty-eight (35 boys) preschoolers at risk for school failure were assessed on a battery of quantitative tasks, and on intelligence, executive control, preliteracy skills, and parental education. Mathematics achievement scores at the end of 1 year of preschool indicated that 34 of these children were at high risk for MLD. Relative to the 34 typically achieving children, the at risk children were less accurate on the ANS task, and a one standard deviation deficit on this task resulted in a 2.4-fold increase in the odds of MLD status. The at risk children also had a poor understanding of ordinal relations, and had slower learning of Arabic numerals, number words, and their cardinal values. Poor performance on these tasks resulted in 3.6- to 4.5-fold increases in the odds of MLD status. The results provide some support for the ANS hypothesis but also suggest these deficits are not the primary source of poor mathematics learning.