Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying temporal trace of biological process during phase transition

Phase transition widely exists in the biological world, such as the transformation of cell cycle phases, cell differentiation stages, cancer development steps, and so on. These are considered as the conversions of a genetic system from one phenotype/genotype to another. In previous studies, the molecular mechanisms of biological phase transition have attracted much attention, in particular, on the different genotypes related to specific phase but less of focus on the cascade of genes' functions during the phase change. However, it is a fundamental but important mission to track the temporal characteristics of a genetic system during specific phase transition or process, which can offer clues for understanding life and advancing its quality. By overcoming the hurdles of traditional time segmentation and temporal biclustering methods, a causal process model (CPM) in the present work is proposed to study the biological phase transition in a systematic way: boundary gene estimation for gene-specific segmentation and temporal block construction for whole data division. After the computational validation on synthetic data, CPM was used to analyze the well-known Yeast cell cycle data to identify the time periods of six phases in two cell cycles, and revealed phase/cycle related biological processes. These primary results demonstrate that CPM is efficient comparing to traditional methods, and has potential to elucidate the genetic mechanism with more complicated phase transitions.
Radical scavenging activity of various fractions of Cephalotaxus sinensis (Rehd et Wile) Li

Cephalotaxus sinensis (Rehd et Wile) Li, belongs to family Cephalotaxaceae, common in China, is an indigenous medicinal plant due to its antiascariasis, antiinflammation, anticough and antidyspepsia activity. The overindulgence of free radicals has been concerned in the development of chronic diseases and play an imperative role in the development of neurodegenerative disorders, such as Alzheimer's and Parkinson's diseases. Various fractions of this plant were evaluated for their radical scavenging activity by the DPPHldr and reducing power activity assays. Also, the Folin-Ciocalteu method was used to determine the total phenolic content. The results of both methods revealed that Cephalotaxus. sinensis possesses potent antioxidant activity. The polyphenolic content and antioxidant activities of the different fractions tested decreased in the order of EaF > BtF > CfF > WtF > PtF. The radical scavenging activity of the ethyl acetate fraction higher than BHT and slightly lower than Vit-C. A positive linear correlation between antioxidant activity and contents of polyphenol was established. This information shows that ethyl acetate fraction of C. sinensis can be used as antioxidant in medicinal preparations.
Tunable Bandstop Filter with Bandwidth Compensation

─ In this paper, a tunable bandstop filter with bandwidth compensation is proposed. The equivalent circuit model of the tunable capacitor network is presented to study the tunable mechanism. The electric coupling factor of the tunable capacitor network increases while the tunable capacitor increases. This mechanism can be used to compensate the bandwidth of the tunable filter. In our work, semiconductor varactor diode loaded microstrip LC resonator is adopted to design a tunable bandstop filter. Each resonator requires only one varactor diode for both central frequency and resonator coupling coefficient control. The Sparameters and group delays of the tunable bandstop filter are presented. The measurement shows that the -30 dB absolute bandwidth varies from 371 MHz to 305 MHz, while the central frequency of the stopband varyies from 3.195 GHz to 2.285 GHz. Index Terms ─ Electric coupling, tunable bandstop filter.
Plant Communities Rather than Soil Properties Structure Arbuscular Mycorrhizal Fungal Communities along Primary Succession on a Mine Spoil

Arbuscular mycorrhizal fungal (AMF) community assembly during primary succession has so far received little attention. It remains therefore unclear, which of the factors, driving AMF community composition, are important during ecosystem development. We addressed this question on a large spoil heap, which provides a mosaic of sites in different successional stages under different managements. We selected 24 sites of c. 12, 20, 30, or 50 years in age, including sites with spontaneously developing vegetation and sites reclaimed by alder plantations. On each site, we sampled twice a year roots of the perennial rhizomatous grass Calamagrostis epigejos (Poaceae) to determine AMF root colonization and diversity (using 454-sequencing), determined the soil chemical properties and composition of plant communities. AMF taxa richness was unaffected by site age, but AMF composition variation increased along the chronosequences. AMF communities were unaffected by soil chemistry, but related to the composition of neighboring plant communities of the sampled C. epigejos plants. In contrast, the plant communities of the sites were more distinctively structured than the AMF communities along the four successional stages. We conclude that AMF and plant community successions respond to different factors. AMF communities seem to be influenced by biotic rather than by abiotic factors and to diverge with successional age.
Underwater acoustic image segmentation using neural deformable template

This paper describes a neural network architecture that has been developed to perform underwater acoustic image segmentation based on deformable template techniques. The template shift is guided by external energy from the image under consideration, which attracts them towards the target characteristics and by internal energy, which tries to maintain the smoothness of the contour curve. The resulting deformable templates are used to train and test the neural network, which is able to distinguish interest objects from other kinds of objects. We have used the neural deformable template to segment underwater acoustic images. The results show that this algorithm is efficient, precise and very immune to image deformation and noise when compared to results obtained from several other deformable template-based methods.
Influence of local government on port investment: implications of China’s decentralized port governance system

ABSTRACT The pursuit of better performance by the local government can influence the investment decision-making related to port expansion. This paper compares the ceilings at which the port enterprise and the local government would stop making investments. To achieve this, the benefits to the port enterprise and the local government are measured over a given time period. An empirical study investigating how a port would respond if a rival port uses a type of capacity investment strategy is conducted for two major ports in Liaoning. The time at which the local government and the port enterprise would stop making investments and the final equilibrium are developed using the data from 2010. From the empirical results, it was found that investment in port capacity contributes greatly to the local government’s performance. Meanwhile, different investment ceilings are discovered for the port enterprise and the local government. This research is meaningful for discussing the institutional relationship between the local government and the port enterprise in China’s current decentralized port governance system. This paper is a revised and expanded version of a paper entitled ‘Port expansion mechanism in the context of political achievement of local government: a special phenomenon in China’ presented at International Association of Maritime Economists 2012 Taipei Conference during 5th September –8th September.
Experiments and Simulations of the Colliding Pulse Injection of Electrons in Plasma Wakefields

In this paper, we report on recent experimental results on electron acceleration using two counterpropagating ultrashort and ultraintense laser pulses. We demonstrate that the use of a second laser pulse provides enhanced control over the injection and subsequent acceleration of electrons into plasma wakefields. The experimental results show that the electron beams obtained in this manner are collimated, monoenergetic, tuneable, and stable. Simulations of the process emphasize the crucial role of kinetic effects and the need for self-consistent models.
Rising car user costs: comparing aggregated and geo-spatial impacts on travel demand and air pollutant emissions

Transport is debated by many, and liberalization processes, transport policy, transport and climate change and increased competition between transport modes are the subject of heated discussion. Smart Transport Networks illustrates that whether concerning road, water, rail or air, knowledge on the structure of transport markets is crucial in order to tackle transport issues. The book therefore explores key factors concerning the structure of transport markets, their environmental impact, and questions why decision makers often fail to tackle transport-related problems.
Oxidative stress, DNA damage and apoptosis in male infertility: a clinical approach

clearly independent measures of sperm quality. Therefore, pathogenic ROS levels or poor-quality sperm chromatin structure may be considered indicative of male subfertility [1,2]. IDIOPATHIC INFERTILITYMen with idiopathic infertility generally present with signiﬁcantly higher seminal ROS levels and lower antioxidant properties than healthy controls [3]. Therefore, it appears that the presence of OS in infertile normozoospermic men may be the cause behind previously unexplained cases of infertility. Similarly, sperm DNA damage analysis may reveal hidden sperm DNA abnormalities in infertile men with normal standard sperm values who were diagnosed with idiopathic infertility. The increase in sperm DNA damage in these patients may be partly related to high levels of seminal OS.Finally and importantly, some conditions may pass unnoticed but still affect the sperm genomic integrity. In one case report [4], a fertile patient who had inﬂuenza and a 1-day fever of 39.9 ∞ C presented with a relatively high percentage of sperm with damaged DNA (36%) 18 days after the onset of his fever.GENITAL TRACT INFECTIONSGenital tract infections are usually associated with leukocytospermia and elevated ROS levels, as leukocytes represent the major source of ROS production in ejaculates. Although leukocytes are a constant component of human ejaculates and virtually no semen sample is free of them, if the prevalence of leukocytes exceeds normal values (1 ¥ 10
Expression of Telomerase Activity, Human Telomerase RNA, and Telomerase Reverse Transcriptase in Gastric Adenocarcinomas

Telomerase is an RNA-dependent DNA polymerase that synthesizes TTAGGG telomeric DNA onto chromosome ends to compensate for sequence loss during DNA replication. It has been detected in 85–90% of all primary human cancers, implicating that the telomerase seems to be reactivated in tumors and that such activity may play a role in the tumorigenic process. The purpose of this study was to evaluate telomerase activity, human telomerase RNA (hTR), and telomerase reverse transcriptase (TERT) in stomach cancer and to determine their potential relationships to clinicopathologic parameters. Frozen and corresponding methacarn-fixed paraffin-embedded tissue samples were obtained from 51 patients with gastric adenocarcinoma and analyzed for telomerase activity by using a TRAPeze ELISA kit. Tissue sections of all the samples were further investigated for hTR and TERT by in situ hybridization and a sensitive immunohistochemical technique, respectively. Telomerase activity was detected in 37 (73%) tumors. Telomerase positivity from methacarn-fixed paraffin blocks was found to be 35% of that from frozen tissues. hTR was overexpressed in 46 (90%) samples: 33/37 (89%) with and 13/14 (93%) without telomerase activation. Expression of TERT was demonstrated in 40 (78%) cases: 30/37 (81%) with and 10/14 (71%) without telomerase. Telomerase activity correlated well with depth of invasion (P = .037) and tumor differentiation (P = .022), whereas hTR significantly correlated with nodal metastasis (P = .047) and tumor size (P = .023). These data suggest that reactivated telomerase may play a significant role in the tumorigenesis of gastric cancer and may reflect, along with enhanced hTR, the malignant potential of the tumor. It is noteworthy that methacarn-fixed tissue cannot as yet substitute for the frozen section in the TRAP assay.
Seasonal variation in basal and plastic cold tolerance: Adaptation is influenced by both long‐ and short‐term phenotypic plasticity

Abstract Understanding how thermal selection affects phenotypic distributions across different time scales will allow us to predict the effect of climate change on the fitness of ectotherms. We tested how seasonal temperature variation affects basal levels of cold tolerance and two types of phenotypic plasticity in Drosophila melanogaster. Developmental acclimation occurs as developmental stages of an organism are exposed to seasonal changes in temperature and its effect is irreversible, while reversible short‐term acclimation occurs daily in response to diurnal changes in temperature. We collected wild flies from a temperate population across seasons and measured two cold tolerance metrics (chill‐coma recovery and cold stress survival) and their responses to developmental and short‐term acclimation. Chill‐coma recovery responded to seasonal shifts in temperature, and phenotypic plasticity following both short‐term and developmental acclimation improved cold tolerance. This improvement indicated that both types of plasticity are adaptive, and that plasticity can compensate for genetic variation in basal cold tolerance during warmer parts of the season when flies tend to be less cold tolerant. We also observed a significantly stronger trade‐off between basal cold tolerance and short‐term acclimation during warmer months. For the longer‐term developmental acclimation, a trade‐off persisted regardless of season. A relationship between the two types of plasticity may provide additional insight into why some measures of thermal tolerance are more sensitive to seasonal variation than others.
Regulation of Muscle Protein Synthesis in Neonatal Pigs During Prolonged Endotoxemia

In adults, protein synthesis in skeletal muscle is reduced by as much as 50% after a septic challenge, and is associated with repression of translation initiation. Neonates are highly anabolic and their muscle protein synthesis rates are elevated and uniquely sensitive to amino acid and insulin stimulation. In the present study, neonatal piglets were infused with Endotoxin (lipopolysaccharide, LPS) for 20 h at 0 (n = 6) and 13 μg/kg•h (n = 8). During the last 2 h, dextrose and an amino acid mixture were infused to attain fed plasma concentrations of amino acids, glucose, and insulin. Fractional protein synthesis rates and translational control mechanisms were examined. LPS reduced protein synthesis in glycolytic muscles by only 13% and had no significant effect in oxidative muscles. This depression was associated with reductions in the phosphorylation of 4E-BP1 (−31%) and S6 K1 (−78%), and a decrease in eIF4G binding to eIF4E (−62%), an event required for formation of the active mRNA binding complex. By comparison, LPS increased protein synthesis in the liver (+29%), spleen (+32%), and kidney (+27%), and in the liver, this increase was associated with augmented eIF4G to eIF4E binding (+88%). In muscle and liver, LPS did not alter eIF2B activity, an event that regulates initiator met-tRNAi binding to the 40S ribosomal complex. These findings suggest that during sustained endotoxemia, the high rate of neonatal muscle protein synthesis is largely maintained in the presence of substrate supply, despite profound changes in translation initiation factors that modulate the mRNA binding step in translation initiation.
Investigation on selection schemes and population sizes for genetic algorithm in unmanned aerial vehicle path planning

Genetic algorithm has been widely used in numerous fields. Recently, researchers have developed significant interest in applying GA in unmanned aerial vehicle path planning. However, experiments should be conducted to determine selection schemes and population sizes. This process is time consuming and inconvenient for users. Thus, a study is conducted on the performance of GA at various selection schemes and population sizes. Results show that large population sizes do not contribute in improving the performance of GA. Tournament selection shows the highest performance in terms of path cost, whereas the weakest performance is in terms of computational cost. Truncation selection shows the optimum performance among the selection schemes.
Multicultural Healthcare: A Transatlantic Project

Healthcare is increasingly multicultural, posing a challenge for nurse educators in both Europe and the United States. Nursing education faculties are responding to the challenge of internationalization, for instance, by participating in international student exchange projects to foster students' intercultural competence. The authors describe an educational model constructed during a transatlantic project between European and American universities. The benefits of the project from the Finnish partner's perspective are also reported.
Optimum Design of Tubular Permanent-Magnet Motors for Thrust Characteristics Improvement by Combined Taguchi–Neural Network Approach

Although tubular permanent-magnet motors have advantages such as remarkable force capability and high efficiency due to lack of end winding, they suffer from high thrust force ripple. This paper presents the use of Taguchi method and artificial neural network (ANN) for shape optimization of axially magnetized tubular linear permanent-magnet (TLPM) motors. A multiobjective design optimization is presented to improve force ripple, developed thrust, and permanent-magnet volume simultaneously. The iron pole-piece slotting technique is used and its design parameters are optimized to minimize the motor's force pulsation. To obtain optimal configuration using this technique, four design variables are selected and their approximate optimum values are determined by the Taguchi method using analysis of means (ANOM). In the next step, two more influential parameters are selected by analysis of variance (ANOVA) and their accurate optimum values are obtained by a trained ANN. Finite-element analysis (FEA) is used to appraise the performance of the motor in different experiments of the Taguchi method and for training the ANN. The results show that force pulsation of the optimized motor is greatly reduced while there is small drop in the motor thrust.
Rapid and Efficient Directed Differentiation of Human Pluripotent Stem Cells Into Retinal Pigmented Epithelium

Controlling the differentiation of human pluripotent stem cells is the goal of many laboratories, both to study normal human development and to generate cells for transplantation. One important cell type under investigation is the retinal pigmented epithelium (RPE). Age‐related macular degeneration (AMD), the leading cause of blindness in the Western world, is caused by dysfunction and death of the RPE. Currently, RPE derived from human embryonic stem cells are in clinical trials for the treatment of AMD. Although protocols to generate RPE from human pluripotent stem cells have become more efficient since the first report in 2004, they are still time‐consuming and relatively inefficient. We have found that the addition of defined factors at specific times leads to conversion of approximately 80% of the cells to an RPE phenotype in only 14 days. This protocol should be useful for rapidly generating RPE for transplantation as well as for studying RPE development in vitro.
Postnatal maturation of carotid chemoreceptor responses to O2 and CO2 in the cat.

This study aimed to characterize neural responses of the carotid chemoreceptors of the maturing cat to natural stimuli and to determine the time course of carotid chemoreceptor development from the neonatal period to adulthood. Carotid sinus nerve (CNS) responses to O2 and CO2 were studied in cats at 1, 4, and 8 wk of age and in adult cats (n = 6 at each age). Pentobarbital sodium-anesthetized cats were exposed to three levels of O2 (arterial PO2 = 40-45, 80-90, and > 300 Torr) at five levels of arterial PCO2 (22, 35, 48, 63, and 75 Torr) while the moving average of whole nerve output from the CSN was recorded. Ganglioglomerular nerves were sectioned. All cats at every age increased CSN activity during hypoxia. However, the CSN response to hypoxia was not sustained in some immature cats. Of the cats that sustained CSN activity during hypoxia, four of the six 1-wk-old cats showed a biphasic pattern of response, with an initial overshoot followed by a steady level of discharge. Older cats did not exhibit this pattern. CNS sensitivity to hypoxia was weakest in 1-wk-old kittens but increased to nearly adult levels by 4 wk of age. Carotid chemoreceptor responses to CO2 were also smallest in 1-wk-old kittens and increased with maturation. However, unlike hypoxia responses, CO2 sensitivity during hypoxia continued to develop between 8 wk and adulthood. O2-CO2 interaction did not become significant until after 4 wk of age. Thus, carotid chemoreceptor responses to both O2 and CO2 are weak in newborn cats and increase during postnatal development. (ABSTRACT TRUNCATED AT 250 WORDS)
FDTD Schemes for Wave Propagation in Davidson-Cole Dispersive Media Using Auxiliary Differential Equations

Two finite-difference time-domain (FDTD) schemes based on the use of auxiliary differential equations are proposed for modeling time-domain wave propagation in dispersive Davidson-Cole media. The main difficulty in FDTD implementations for such media is the appearance of fractional derivatives in the time-domain polarization relation. To circumvent this difficulty, the relative complex permittivity of the medium is approximated by Padé approximants resulting in auxiliary differential equations of integer order. Moreover, it is proven that under certain conditions the Padé approximation is equivalent to one given by a sum of Debye terms. Hence, an alternative set of auxiliary differential equations is derived. Over a wideband frequency domain, the comparisons between analytical and calculated values of the relative complex permittivity as well as of the transfer function inside the dispersive medium illustrate the efficiency of both FDTD schemes.
Is Fiscal Deficit Valid for Long Run Economic Growth in Nigeria? An Empirical Investigation

The Impact of fiscal deficit on long run economic growth is one of the issues in macroeconomic management that has attracted much attention over the years. Although fiscal balance is a useful indicator of macroeconomic health, developing countries, Nigeria inclusive, run persistent budget deficits as a matter of policy. This study investigated the possibility of long run relationship between fiscal deficit and long run economic growth. This study applied the Johansen cointegration test on Nigerian time series data from 1986 to 2010 and discovered that there is no long run relationship between these variables and concluded that the running of fiscal deficit is not an appropriate tool for achieving long run economic growth in Nigeria and recommended that other policy measures should be considered.