Miracle-dz/UniFAR-FTUs huggingface dataset:
The effects of different antioxidants on post-thaw microscopic and oxidative stress parameters in the cryopreservation of Brown-Swiss bull semen.

The aim of this study was to research the effects of four antioxidants that had been added to semen diluents, on spermatological parameters, anti-oxidant enzymes activities and DNA integrity after the freeze-thaw procedures in Brown-Swiss bull semen. A total of 24 ejaculates were collected from three bulls. Each ejaculate was divided into five equal parts and they diluted to the Tris + 25 mM trehalose base extender containing fetuin 1 mg/ml, dithioerithritol 1 mM, cysteamine 4 mM or linoleic acid 0.5 ml/50 ml, and no additives (control). Group dithioerithritol and linoleic acid showed the higher rates of CASA progressive motility, CASA sperm motility (P<0.05) compared with the other groups. Group linoleic acid provided the better protective effect for acrosome and total abnormalities (P<0.01, P<0.05; respectively). Also, group dithioerithritol showed the highest values for the HOS test (P<0.01). In the comet test, group dithioerithritol enhanced tail with lesser chromatin damage than the other groups (P<0.05). Supplementation of dithioerithritol significantly affected the GSH activity (P<0.01). Also groups dithioerithritol and linoleic acid gave higher CAT values than the other groups (P<0.05). Additionally, supplementation of fetuin and cysteamine showed the lowest total antioxidant activity value (P<0.05). In conclusion, we may said that, the addition of antioxidants, specially dithioerithritol and linoleic acid, to added with 25 mM trehalose Tris extender improve post-thaw sperm parameters.
Enhanced light‐vapor interactions and all optical switching in a chip scale micro‐ring resonator coupled with atomic vapor

The coupling of atomic and photonic resonances serves as an important tool for enhancing light‐matter interactions and enables the observation of multitude of fascinating and fundamental phenomena. Here, by exploiting the platform of atomic‐cladding wave guides, the resonant coupling of rubidium vapor and an atomic cladding micro ring resonator is experimentally demonstrated. Specifically, cavity‐atom coupling in the form of Fano resonances having a distinct dependency on the relative frequency detuning between the photonic and the atomic resonances is observed. Moreover, significant enhancement of the efficiency of all optical switching in the V‐type pump‐probe scheme is demonstrated. The coupled system of micro‐ring resonator and atomic vapor is a promising building block for a variety of light vapor experiments, as it offers a very small footprint, high degree of integration and extremely strong confinement of light and vapor. As such it may be used for important applications, such as all optical switching, dispersion engineering (e.g. slow and fast light) and metrology, as well as for the observation of important effects such as strong coupling, and Purcell enhancement.
Holistic 3 D Indoor Scene Parsing and Reconstruction from a Single RGB Image

We propose a computational framework to parse and reconstruct the 3D configuration of an indoor scene from a single RGB image using a stochastic grammar model. We introduce a Holistic Scene Grammar (HSG) to represent the 3D scene structure, which characterizes a joint distribution over the functional and geometric space of indoor scenes. The proposed HSG captures three essential but often latent dimensions of the indoor scenes: i) latent human context, describing the affordance and the functionality of a room arrangement, ii) geometric constraints over the scene configurations, and iii) physical constraints that guarantee physically plausible parsing and reconstruction. We solve this parsing and reconstruction problem in an analysis-bysynthesis fashion, seeking to minimize the differences between the input image and the rendered image generated by our 3D representation, over the space of depth, surface normal, and object segmentation map. The optimal configuration (i.e., parse graph) is inferred using Markov chain Monte Carlo (MCMC), which efficiently traverses through the non-differentiable solution space, jointly optimizing object localization, 3D layout, and hidden human context.
GENETIC DIVERSITY AND POPULATION STRUCTURE AMONG 98 MAIZE INBRED LINES INVESTIGATED WITH SSR MARKERS

The conversion of exotic germplasm into domestic maize breeding materials is essential to solve the narrow genetic base for maize improvement in China. The present study applied SSR markers and three complementary cluster methods (STRUCTURE, UPGMA and PCoA) to 98 foreign hybridselected lines for effective hybrid breeding. A total of 450 alleles, with an average of 3.98 alleles per locus, were detected. Among 10 chromosomes, there were 13-19 loci and 33-59 alleles with averaged alleles 2.54~3.43 per chromosome. The polymorphism information content (PIC) among 10 chromosomes ranged from 0.4504~0.5582 and 69.4% PIC variation were explained by allele number/Locus. The highest PIC was observed in chromosome 7 (0.5582) and the lowest in chromosome 8 (0.4965). The STRUCTURE clustering analysis grouped the test lines into four subpopulations (i.e. REID, Lancaster, P and Domestic) in accordance with UPGMA and PCoA clustering. The higher genetic diversity were detected among the inbred lines in P and Domestic subpopulations. The allele frequencies, gene diversity and population structure obtained in the present study lead us to conclude that the 98 inbred lines derived from foreign hybrid-selected lines contain extensive genetic variation and are a valuable resource for Chinese maize breeding. The result obtained in the present study will assist in effective utilization of the lines in Chinese hybrid maize breeding programs.
Type 1 autoimmune pancreatitis may develop in gastric-type intraductal papillary mucinous neoplasm

A subtype of autoimmune pancreatitis (AIP) is associated with increased serum IgG4, and IgE levels and steroid responsiveness, suggesting abnormal immunity, including allergy or autoimmunity. This subtype also exhibits dense infiltration of IgG4-positive plasma cells, storiform fibrosis, and obliterative phlebitis. Recognized as lymphoplasmacytic sclerosing pancreatitis (LPSP; type 1 AIP), this is a pancreatic manifestation of IgG4-related diseases (IgG4-RD). IgG4-RD can occur simultaneously with malignancies, which might also be applicable to AIP. However, the relationship between AIP and pancreatic carcinoma needs to be clarified. Recently, there are 4 reported cases of the coexistence of intraductal papillary mucinous neoplasm (IPMN) and AIP. We report another case of a 68-year-old Japanese man, where AIP developed in IPMN 4 years after the initial radiological detection of branchand gastric-type IPMN. We believe that the 4 previously reported cases also result from the coexistence of AIP and branchand gastric-type IPMN. Two cases exhibited the occurrence of AIP during IPMN follow up similar to our case. These findings suggest that IPMN, particularly the branchand gastric-type IPMN, might induce AIP. Further studies are necessary in order to conclusively define the relationship between IPMN and AIP.
Discharge of landslide-induced debris flows: case studies of Typhoon Morakot in southern Taiwan

Abstract. Three debris-flow gullies, the Hong-Shui-Xian (HSX), Sha-Xin-Kai (SXK), and Xin-Kai-Dafo (XKD) gullies, located in the Shinfa area of southern Taiwan, were selected as case studies on the discharge of landslide-induced debris flows caused by Typhoon Morakot in 2009. The inundation characteristics of the three debris flows, such as the debris-flow volume V, deposition area Ad, and maximum flow depth, were collected by field investigations and simulated using the numerical modeling software FLO-2D. The discharge coefficient cb, defined as the ratio of the debris-flow discharge Qdp to the water-flow discharge Qwp, was proposed to determine Qdp, and Qwp was estimated by a rational equation. Then, cb was calibrated by a comparison between the field investigation and the numerical simulation of the inundation characteristics of debris flows. Our results showed that the values of cb range from 6 to 18, and their values are affected by the landslide ratio RL. Empirical relationships for cb versus RL, Qdp versus Qwp, Qdp versus V, and Ad versus V are also presented.
Continuous-Flow Cell Dipping and Medium Exchange in a Microdevice using Dielectrophoresis

Medium exchange is the process of changing the suspension medium of cells/particles, and has applications in washing, surface modifications, nutrient replenishment, or simply changing the environment of the target entities. Dipping involves diverting the path of target cells in the carrying fluid to immerse them in another fluid for a short duration, and pushing them again into the original medium. In this paper, a simple microfluidic platform is introduced that employs dielectrophoresis to achieve medium exchange and dipping of micro-objects in a continuous manner. The essential feature of the platform is a microchannel that includes two arrays of microelectrodes that partly enter the bottom surface from both sides. In the first step, numerous finite element-based parametric studies are carried out to obtain the optimized geometrical and operational parameters ensuring successful dipping and medium exchange processes. The results of those studies are utilized to fabricate the platform using standard photolithography techniques. The electrodes are patterned on a glass substrate, while the channel, made out of polydimethylsiloxane, is bonded on top of the glass. Trajectories of blood cells from numerical studies and experimentations are reported, and both results exhibited close agreement.
Biclustering methods and a Bayesian approach to fitting Boltzmann machines in statistical learning

This disertation focuses on two topics in Statistical Learning. One is biclustering, and the other is deep learning. The whole dissertation has three chapters, where Chapter 1 and 2 focus on biclustering; Chapter 3 focuses on the deep learning topic. Biclustering is a Statistical Learning technique that simultaneously partitions the set of samples and the set of their attributes into homogeneous subsets. In Chapter 1, motivated by movie rating data, we firstly propose a Bayesian model and an MCMC algorithm for model estimation. Because this algorithm is too slow to be of practical use with current computation power, we next propose a simplified model and design a Genetic Algorithm for maximizing the likelihood function. This approach works well on a small data set. However, due to the NP-hard nature of the problem, both approaches fail to be practically useful with current computation power. Nonetheless, they provide principled ways of solving a biclustering problem for future use as computation power develops. Also motivated by movie rating data, where missing values need to be addressed, in Chapter 2 we propose a new Prototype-based Biclustering method. We evaluate our method on test cases with various percentages of missing values in terms of the Rand Index between our result and “true” partitions. In fact, our method has good performance on test cases even with a large missing value percentage. We further evaluate our method on a gene expression data set, that contains no missing values. Our method outperforms an existing biclustering method, i.e., Spectral Biclustering, in terms of a Mean Squared Error criterion.
Acute toxicity of the aqueous methanolic Moringa oleifera(Lam) leaf extract on female Wistar Albino rats

Background: Herbal preparations are widely assumed to be safe on oral administration and therefore the documentation of the toxic potential of some herbal concoctions used as medicine and nutrients is limited. Moringa oleifera ( MO ) is a plant that is gaining tremendous popularity in rural communities in Kenya as a means of offsetting nutritional and medicinal needs. However, very little is known about the safety of the plant on oral administration. Thus, the aim of the current study was to assess the biochemical and histological changes in the liver following the administration of an aqueous-methanolic (AQ-ME) MO leaf extract in female Wistar albino rats. Methods: Acute oral toxicity study on the AQ-ME MO leaf extract was conducted by the use of the limit test dose of the up and down procedure (OECD guideline number 425) with slight modifications. Briefly, ten (10) healthy, nulliparous, non-pregnant female Wistar strain albino rats aged 8-12 weeks and weighing 180±20 grams were used for the study. These animals were randomly selected into two groups; control and treatment group each having five (5) animals. They were then labelled to enable identification and control group animals were orally administered with physiological buffer saline once daily over a 48-hour period. The five (5) rats in the treatment group were dosed orally one at a time and once daily with a 2000 mg/kg dose of the AQ-ME MO leaf extract to determine the median lethal dose over a 48 hour period. Blood was then collected and used to prepare serum for biochemical analysis of aspartate amino transferase (AST), alanine amino transferase (ALT) and total bilirubin (TB) which are important biomarkers of liver dysfunction. Biochemical assays of these enzymes were performed using the method of the International Federation of Clinical Chemists (IFCC). Death was used as an endpoint, livers harvested and used to prepare transverse sections for histopathological examination. These sections were stained using the haematoxylin and eosin (H&E) method and observed for pathological changes using an optical microscope. Results: A 2000 mg/kg oral dose of AQ-ME MO leaf extract caused a significant (p 0.05) increase in the mean levels of total bilirubin in the treatment group relative to the control group. On the other hand, the extract caused a non-significant (p>0.05) decrease in the mean levels of ALT in the treatment group relative to the control. The post mortem analysis of the hepatic index (liver to body weight ratio) revealed that there was a non-significant increase (p>0.05) in the hepatic index of the treatment group relative to the control. However, the transverse liver sections of treatment group animals showed mild distortions in the architecture of liver cells. Conclusions: Based on these results, the LD 50 of the AQ-ME MO leaf extract was found to be >2000 mg/kg in female wistar albino rats.
Headquarters ' Involvement in Managing

Within contemporary research on the multinational corporation (MNC), the topic of headquarters' involvement has grown considerably in importance. As the central organisational unit in the MNC, headquarters has the potential to add value to the firm by performing an administrative and entrepreneurial role. While the administrative role concerns synergetic coordination and control activities, the entrepreneurial role pertains to developing and implementing new innovations such as management innovations at the corporate-wide level. Existing literature has generated valuable insights into headquarters' administrative and entrepreneurial role and the potential to create value for the MNC. However, more research is needed on how headquarters can advantageously involve itself and integrate subsidiaries to ensure that their activities are aligned with the MNC strategy without impinging upon subsidiaries' autonomy and without incurring their resistance to headquarters' coordination, control, and innovation activities. This thesis aims to advance our knowledge on headquarters' involvement in managing its subsidiaries. Within the administrative role, I examine coordination and control activities, and within the entrepreneurial role, I examine the process of developing and implementing management innovations and facilitating factors. The thesis draws on a single longitudinal case study of the development and implementation of a new performance management practice by a European MNC within the construction industry. During the fieldwork, I gathered empirical material from observations and interviews as well as secondary data. While this thesis has been carried out as a single case study, the outcome of the thesis is presented in four separate papers, exploring headquarters' involvement in coordination, control and innovation activities. This thesis contributes to the literature on headquarters' involvement in managing subsidiaries by suggesting a collaborative approach to subsidiary engagement and participation that addresses 1) the issue of subsidiary demotivation by feeling degraded to an implementer, 2) the suitability issue by reducing the risk of mismatch between new headquarters integration and innovation activities and subsidiary contexts. Combining headquarters' and subsidiaries' stocks of perspectives and knowledge helps transcend the spatial, cultural, institutional and political boundaries between headquarters and subsidiaries.
SIMULATION OF TWO-FLUID FLOWS BY THE LEAST-SQUARES FINITE ELEMENT METHOD USING A CONTINUUM SURFACE TENSION MODEL

In this paper a numerical procedure for simulating two-fluid flows is presented. This procedure is based on the Volume of Fluid (VOF) method proposed by Hirt and Nichols and the Continuum Surface Force (CSF) model developed by Brackbill et al. In the VOF method fluids of different properties are identified through the use of a continuous field variable (colour function). The colour function assigns a unique constant (colour) to each fluid. The interfaces between different fluids are distinct due to sharp gradients of the colour function. The evolution of the interfaces is captured by solving the convective equation of the colour function. The CSF model is used as a means to treat surface tension effect at the interfaces. Here a modified version of the CSF model, proposed by Jacqmin, is used to calculate the tension force. In the modified version, the force term is obtained by calculating the divergence of a stress tensor defined by the gradient of the colour function. In its analytical form, this stress formulation is equivalent to the original CSF model. Numerically, however, the use of the stress formulation has some advantages over the original CSF model, as it bypasses the difficulty in approximating the curvatures of the interfaces. The least-squares finite element method (LSFEM) is used to discretize the governing equation systems. The LSFEM has proven to be effective in solving incompressible Navier–Stokes equations and pure convection equations, making it an ideal candidate for the present applications. The LSFEM handles all the equations in a unified manner without any additional special treatment such as upwinding or artificial dissipation. Various bench mark tests have been carried out for both two-dimensional planar and axisymmetric flows, including a dam breaking, oscillating and stationary bubbles and a conical liquid sheet in a pressure swirl atomizer. © 1998 John Wiley & Sons, Ltd.
A time series analysis of household income inequality in Brazil 1977 to 2013

Abstract This paper analyses the evolution of household income inequality in Brazil from 1977 and 2013 using Brazilian National Household Survey data at aggregated and regional levels. Four income shares quantiles are analyzed: Top 1%, Top 10%, Bottom 10% and Bottom 50%. The novelty of our study is to use time series techniques to understand the phenomenon of income inequality within this period. We use Markov-Switching Regime Change Model (Hamilton (1989)) and State Space Unobservable Model (Harvey (1990)) techniques. Both strategies suggest that income concentration periods are related to low growth rates but high inflation rates as opposed to many developed countries (Piketty and Saez (2014)). Results from Markov-switching models suggest a detection of a new regime during first decade of 2000's in poorest quantiles (bottom 10% and 50%) increasing their correspondent income shares. Moreover a regime of low shares started to prevail at the same time for Top 10% whereas for those at the Top 1% had prevailed a concentrated income share regime during eighties and nineties. We argue that Brazilian macroeconomic instability helped to produce a regime of low income shares at the bottom of the distribution. Our results suggest that recent inequality reduction in the shares of top 1% quantile can be seen as a “back to normality” instead of “a new era” whereas significant changes can be seen in other quantiles. State space models results also suggests that macroeconomic of the eighties had a severe effects on Brazilian inequality whereas the dynamics of Top 1% income shares reinforce the return of 70's level considering aggregated data. Last, our estimates unveil important regional differences in many quantiles mainly on the low brackets where poorer regions seem to have persistent income-inequality that take longer to be reduced.
Leveraging intercalibration techniques to support stray-light removal from Landsat 8 Thermal Infrared Sensor data

Abstract. Since its launch in 2013, the Thermal Infrared Sensor (TIRS) onboard Landsat 8 has exhibited artifacts in its image data that can be attributed to stray-light. A 3-year effort was initiated to develop a stray-light correction algorithm to support TIRS calibration. A methodology was developed to predict the additional (stray-light) signal on each detector from an estimate of the stray-light source locations in the sensor’s out-of-field area. The initial version of the algorithm estimated the magnitude of out-of-field radiance sources through the use of geostationary wide-field thermal band imagers. However, this methodology necessitated a strong effort to cross calibrate the two sensors. Ultimately, a variation of the algorithm was implemented operationally into the United States Geological Survey ground system that utilizes image data from TIRS itself as an estimate of the out-of-field stray-light sources. This paper highlights the intercalibration techniques investigated while developing the stray-light correction algorithm. The impact of differing view-angles, spectral responses, and collection times on at-sensor radiance was considered to assess the feasibility of using data from Geostationary Operational Environmental Satellite geostationary instruments to estimate the out-of-field stray-light radiance incident on the TIRS detectors. Results of the studies presented here illustrate the complexities associated with intercalibration in the thermal and provide justification for the current form of the TIRS stray-light correction algorithm.
Investigation of deep learning approaches for overhead imagery analysis

Analysis of overhead imagery has a great potential to produce realtime data cost-effectively. This can be an important foundation for decision-making for businesses and politics. Every day a massive amount of new satellite imagery is produced. To fully take advantage of these data volumes a computationally efficient pipeline is required for the analysis. This thesis proposes a pipeline which outperforms the Segment Before you Detect network [6] and different types of fast region based convolutional neural networks [61] with a large margin in a fraction of the time. The model obtains a prediction error for counting cars of 1.67% on the Potsdam dataset and increases the vehiclewise F1 score on the VEDAI dataset from 0.305 reported by [61] to 0.542. This thesis also shows that it is possible to outperform the Segment Before you Detect network in less than 1% of the time on car counting and vehicle detection while also using less than half of the resolution. This makes the proposed model a viable solution for large scale satellite imagery analysis.