Miracle-dz/UniFAR-FTUs huggingface dataset:
Surgical Navigation System for Transsphenoidal Pituitary Surgery Applying U-Net-Based Automatic Segmentation and Bendable Devices

Conventional navigation systems used in transsphenoidal pituitary surgery have limitations that may lead to organ damage, including long image registration time, absence of alarms when approaching vital organs and lack of 3-D model information. To resolve the problems of conventional navigation systems, this study proposes a U-Net-based, automatic segmentation algorithm for optical nerves and internal carotid arteries, by training patient computed tomography angiography images. The authors have also developed a bendable endoscope and surgical tool to eliminate blind regions that occur when using straight, rigid, conventional endoscopes and surgical tools during transsphenoidal pituitary surgery. In this study, the effectiveness of a U-Net-based navigation system integrated with bendable surgical tools and a bendable endoscope has been demonstrated through phantom-based experiments. In order to measure the U-net performance, the Jaccard similarity, recall and precision were calculated. In addition, the fiducial and target registration errors of the navigation system and the accuracy of the alarm warning functions were measured in the phantom-based environment.
The Impact of Journal Writing Training on Self Efficacy and Attitude of Postgraduate Program Students in Writing Scientific Publication Articles

The purpose of this study is to determine the effect of journal writing training on the attitudes and self efficacy of Postgraduate Masters (PPs) students at Yogyakarta State University (UNY) in writing scientific publications in the form of journal articles as a graduation requirement. The method used to achieve the objectives of this research is restrospective causalcomparative design or ex-post facto research (Gay and Airasian, 2011). The population in this study were students of the UNY Postgraduate Masters program. The sampling technique used was cluster random sampling, with 304 students from 14 Study Programs. Self-efficacy instruments with reliability (0.802) and validity (0.320 0.712), while the attitude instruments with reliability (0.895) and validity (0.248 0.843). The data analysis technique uses Regression followed by Anova. The results of the study showed that: (1) participation in journal writing training significantly affected the attitudes and facilitation of the students of the Postgraduate Program of the UNY Postgraduate Program that they were able to write scientific publications in the form of Journal articles as graduation requirements. Even being able to contribute effectively reaches 35%. However, the positive attitude of the students of the Postgraduate Program at UNY did not affect their ability to write journals as a graduation requirement. Keywords— attitude, self efficacy, training in journal writing, students
Influence of soil fertility, drought, and host plant on fine root endophytes along a 2-million-year soil chronosequence

Understanding of fine root endophytes (FRE) (Planticonsortium tenue) ecology and especially the drivers of colonisation, diversity and community assemblage is limited. Field observations suggest that they are specialised to occur within extreme environmental conditions. I investigated the influences of drought (water availability), soil fertility (chronosequence stage) and host species on colonisation (abundance), diversity, and community assemblage of FRE using a glasshouse experiment. I planted seedlings of Microlaena stipoides Labill (weeping grass) and Trifolium subterraneum L. (subterranean clover) in soils collected from four soil ages of a 2-million-year soil chronosequence, which is phosphorus (P) limited and experiences lower nutrient availability in the youngest and oldest stages. I also included a drought treatment which was initiated for half of the pots from week 4; plants were harvested in week 10. Fine root endophytes showed consistent responses in relation to chronosequence stage. Root colonisation was higher within the two most P-limited stages (i.e. youngest and oldest). Community assemblage was found to change, and richness was highest in the youngest and oldest stages. Fine root endophytes were not observed to colonise M. stipoides Labill when using microscopy. However, FRE were found in the roots via DNA sequencing, suggesting some FRE might not be visible with the staining and microscopy techniques used. Other non-mycorrhizal fungi belonging within Mucoromycotina may also have been present in and around the roots and contributed to this finding. Drought was found to have no effect on FRE, potentially due to P being more limiting than water in this system. Responses of FRE differed to arbuscular mycorrhizal fungi (AMF) and colonisation and richness were consistently lower. Overall, my results show that abundance and diversity of FRE follow the opposite trend than available P across this chronosequence. This shows that FRE can potentially be suited to P limited soils. More studies are needed to understand the generality of these findings. Drought had no influence on FRE in my experiment. My data suggest FRE may have different ecological roles to AMF such as specialisation in highly P limiting soils. However, there is also potential for the co-occurring fungi to share some ecological similarities like preference for low P soils.
Topics in Group Testing with Multiple Infections

Group testing, dating back to the early 1940s, was first proposed to screen for syphilis among US inductees during World War II (Dorfman, 1943). Since then, the benefits of reducing testing costs by employing group testing have been demonstrated in many areas, such as drug discovery, genetics, and infectious disease testing. Traditionally, statistical research in group testing has largely been motivated by applications involving a single infection. With the recent development of multiplex assays that can diagnose multiple infections simultaneously, generalizing the existing group testing literature to incorporate multiple infections is a natural and necessary next step. This dissertation consists of three research projects that extend group testing to multiple infections. In Chapter 2 and Chapter 3, we propose two different testing algorithms to accommodate the use of multiplex assays. Compared to the two-stage hierarchical group testing algorithms currently employed by the Infertility Prevention Project (IPP) in Iowa, our algorithms are proven to confer significant cost savings. In Chapter 4, we propose a semi-parametric regression framework to estimate individual-level marginal probability of infection from multiple infection group testing data. The performance of our testing algorithms and estimation techniques is evaluated through numerical study, simulation, and application to chlamydia and gonorrhea data collected by five states as part of the IPP.
Sheath-less high throughput inertial separation of small microparticles in spiral microchannels with trapezoidal cross-section

Various mechanisms of different designs have emerged for the purpose of microparticle separation and cell sorting. The main goals behind such designs are to create high throughput and high purity sample isolation. In this study, high efficiency, high throughput and precise separation of microparticles under inertial lift and drag forces induced by trapezoidal curvilinear channels are reported. This work is the first to focus and recover 2 from 5 μm and 2 from 10 μm particles in spiral channels in a sheath-less flow device, which reduces the overall complexity of the system and allows for higher throughput. The new microfluidic chip design is fabricated in glass using femtosecond laser ablation. In addition, mathematical force calculations were conducted during the design phase of the microfluidic channels and compared with experiments. The results show a close prediction of the equilibrium position of the tested microparticles.
Improvement of bioavability of medicinal herbs by fermentation with Lactobacillus plantarum

Background: Medicinal and aromatic plants, which are rich sources of bioactive conpounds, have been used in traditional medicine for ancient times. Epidemiological studies have shown that bioactive compounds of medicinal plants possess antioxidant, anti-inflammatory, antiatherosclerotic, antitumor, antimutagenic, anticarcinogenic, antibacterial and antiviral activities. Intake of natural antioxidants derived from medicinal plants into body has been associated with reduced risks of cancer, cardiovascular disease, diabetes, and other diseases. It has also been demonstrated that the fermentation of plants is a versatile way for improvement of their functionality and bioavailability. The aim of this study was to determine the effect of probiotic fermentation and vacuum drying on the bioavailability of peppermint ( Mentha piperita ) and basil ( Ocimum basilicum ) exposed to in vitro digestion. Methods: Fresh basil and peppermint were divided to 3 lots, one lot of each plant was vacuum dried at 40 °C for 8 hours to obtain the dried samples while one lot was fermented with probiotic Lactobacillus plantarum for 21 days at room temperature after incorporation with sterile brine (1:20 w:v) containing 5 % of NaCl. Thereby, 3 samples were obtained: Fresh peppermint/basil, vacuum dried peppermint/basil and fermented peppermint/basil. During the in vitro digestion comprised from gastric and pancreatic digestion, bioavailability of the samples were investigated by measurement of their total phenolic contents (TPCs), total flavonoid contents (TFCs) and antiradical activity. TPC was determined using Folin-Ciocalteu method while TFC was measured aluminum chloride colorimetric assay. The antiradical activity of the samples was analyzed by determination of the DPPH radical scavenging activity. Results: The initial (undigested) TPC levels of fresh, vacuum dried and fermented mint and basils ranged from 166.24 to 295.08 mg gallic acid equivalent (GAE)/g. Drying and fermentation increased TPCs of the plants. Similarly, TFCs and antiradical activities were also increased by these treatments. When considering bioavailability of the bioactive compounds, fermentation process enabled higher recovery levels after in vitro digestion while basil exhibited higher percent recovery than mint. Conclusion: This study demonstrated that vacuum drying and fermentation of basil and mint with probiotic Lactobacillus plantarum provided much stronger antioxidant activity and bioavailability than fresh ones and increased their in vitro bioavailability.
Gender, Political Connection, and Tax Avoidance in China

This paper investigates whether female chief executive officers (CEOs) perform different level of tax avoidance behavior compared with male CEOs in China. We further examine whether female CEOs with political background/connection can transform the relation between gender and tax avoidance behavior. Using the total book-tax differences and permanent book-tax differences to measure the level of tax avoidance behavior following prior studies, we find that Chinese female CEOs perform the same level of tax avoidance behavior relative to their male counterparts. In addition, we find significant evidence that female CEOs with political background tend to conduct more tax avoidance activities relative to those female CEOs without political relation. These results are in contrast to a traditional western viewpoint that female managers have a higher risk aversion attitude.
Benign and Malignant Classification Model of Pulmonary Nodules Based on Residual Neural Network

— Computer-assisted diagnosis is of significance in the timely treatment of lung cancer with classifying benign and malignant pulmonary nodules. Aiming at improving the low accuracy rate of benign and malignant pulmonary nodules and reducing the misdiagnosis rate and wrong-diagnosis rate in computer-aided diagnosis system, a classification model of pulmonary nodules based on residual network was proposed. Firstly, selected some lung CT images from LIDC-IDRI as a data set, amplified the data by horizontal flipping, and then converted them into single channel images. After cropping and normalization, the data was finally divided into training set and test set (7:3), and used to train and test a residual network (ResNet-26). After training, test results represent that the model accuracy rate, sensitivity and specificity are 97.53%, 97.91% and 97.18%. By comparing various methods, the raised method performs better than others according to accuracy, sensitivity and specificity, which demonstrates that it has the ability to help doctors in diagnosis.
The National Foreclosure Mitigation Counseling Program (NFMC) and Spanish-Speaking Immigrants: A Case Study

ABSTRACT The National Foreclosure Mitigation Counseling Program was a consumer-level response to the 2008 foreclosure crisis. Evaluations of the NFMC argued its effectiveness across groups, yet little work has addressed its effectiveness in communities navigating structural barriers to housing market participation, such as recent immigration and language preferences. Using administrative data collected between 2007 and 2013, as well as in-depth interviews with foreclosure-mitigation counselors, this case study examines the implementation of the NFMC in a predominantly Spanish-speaking, immigrant community. Results indicate foreclosure-counseling outcomes were strongly associated with factors related to recent immigration and language preference.
Too Legit to Rage Quit: Do Social Ties Impact Staying Power in eSports?

Sim racing, a sub-genre of eSports, is an online motorsports simulation where participants from around the world use specialized hardware to compete virtually in racing vehicles around a track. While most competitors complete the races they start, some opt to disconnect following a frustrating racing event. This is considered a ”rage quit” in modern gamer slang. This research aims to identify the social factors associated with a rage quit through a binary logistic regression model populated with a unique dataset from iRacing, a major online sim racing platform, consisting of over 19,000 races over 4 racing seasons (12 months) in 2018, 300,000 individual race results, and 16,000 unique drivers. The findings suggest that social factors of past experience with competitors, racing with competitors in one’s own region, and presence of other rage quitters all influence a driver’s decision to rage quit.
A Reallocation Approach for Software Trustworthiness Based on Trustworthy Attributes

Software trustworthiness is an important research field in software engineering. In order to appropriately evaluate it, some different measurement approaches have been proposed, which have important guiding significance for improving software trustworthiness. Recently, we have investigated attributes-based approaches. That is, how to maximize trustworthy degree of some software satisfying a given threshold by adjusting every attribute value such that the cost is minimal, i.e., the sum of all attribute values is as small as possible. The work is helpful to improve the software quality under the same cost. This paper continues this work and considers a reallocation approach to dealing with the problem that the threshold and the minimal constraints of every attribute values dynamically increase. In this process, the costs of trustworthiness improvement should be ensured to be minimal. For this purpose, we firstly define a reallocation model by mathematical programming. Then we introduce the notion of growth function. Based on this, a polynomial reallocation algorithm is designed to solve the above reallocation model. Finally, we verify our work on spacecraft softwares and the results show that this work is valid.
Milk Fat Content, Vitamin D, and Andiposity in Early Childhood

Background: Vitamin D is fat soluble and cow’s milk is the main dietary source of vitamin D in North America. I hypothesized higher fat milk would be associated with higher 25hydroxyvitamin D and decreased BMI in children. Methods: Multivariable linear regression and bivariate regression models were used to test the associations between percent fat content of milk and 25(OH)D, and both 25(OH)D and BMI zscores (zBMI) in children 12-72 months. Results: Higher fat milk had a positive effect on 25(OH)D, but a negative effect on zBMI. Children who drank whole milk had 25(OH)D 5.4 nmol/L (95% CI 4.3 to 6.5) higher than children who drank 1% milk, but a 0.72 (95% CI 0.68 to 0.76) lower zBMI. Volume of milk modified the relationship between percent fat content of milk and 25(OH)D (p=0.003), but not
Financial development and agricultural performance in Nigeria: what role do institutions play?

The centrality of agricultural sector to the economy, particularly in developing countries, has drawn the attention of researchers to critically examine different factors determining the performance of the sector. Given that massive investment is required to ensure maximum productivity in the sector, one of the factors identified is the issue of financing. However, financing agricultural sector in a poor institutional environment can be depressing. In the light of this, the purpose of this paper is to examine the nexus between financial development and agricultural performance in Nigeria with a view to investigating the role of institutions. ,The study employed annual data spanning the period from 1981 to 2016. Three indicators of financial development and five institutional variables were used. Besides, for robust analysis, the study also computed an aggregate measure of financial development and institutions using principal component method. Autoregressive distributed lag method of estimation was used to examine the short-run and long-run effects of financial development on agricultural performance in Nigeria. ,The findings showed that financial development has a positive impact on agricultural performance in Nigeria. However, this positive impact is being undermined by institutional variables. ,To the best of the authors’ knowledge, this is the only study that examines the mediating role of institutional factors such as the rule of law, control of corruption, etc., in the financial development–agricultural performance nexus in Nigeria.
Unravelling electrocatalytic properties of metal porphyrin-like complexes hosted in graphene matrices

Carbon-based materials are a promising class of catalysts for oxygen and carbon dioxide reduction reactions to value-added chemicals. Here we study the electrocatalytic properties of nitrogen doped graphene structures hosting four pyrrolic rings able to coordinate metal ions in a porphyrin-like configuration. The analysis is carried out by means of density functional theory (DFT) with hybrid functionals, employed to estimate the overpotentials of oxygen reduction reaction to water and hydrogen peroxide, as well as carbon dioxide reduction to carbon monoxide and formic acid. The competing hydrogen evolution reaction is also studied. We predict that Co- and Mn-doped structures exhibit low overpotentials for oxygen reduction to water, with the concurrent suppression of hydrogen peroxide production in the Mn case. Carbon dioxide reduction to formic acid is instead favored by Ti and Mn doping with overpotentials lower than 1 V, while hydrogen evolution reaction is disfavored.
Perioperative neutrophil immune function

Within the UK severe sepsis is responsible for 29% of intensive care admissions and carries a mortality of 44.7%. Decades of research have failed to deliver a single clinically successful immune modulating therapeutic agent. These failings may be explained by fundamental methodological challenges of sepsis laboratory investigations, namely diagnostic uncertainty, an indeterminate onset and the identification of an immunologically similar control population. The underlying hypothesis for this thesis is that the translational investigation of surgical patients may overcome many of these methodological challenges, since surgical trauma generates a homogenous inflammatory insult at a planned time to a carefully phenotyped human population. The biological basis for modelling sepsis with traumatic injury is discussed. Firstly, I reviewed the current literature to demonstrate the methodological advantages of studying surgical patients as a surrogate for sepsis. Next, I performed an observational study of neutrophil immune function following major elective surgery which identified a reduced neutrophil respiratory burst and changes in cell surface immune receptor expression. This impairment of activated neutrophil immune function was associated with resting neutrophil mitochondrial dysfunction, namely a raised mitochondrial membrane potential and increased production of reactive oxygen species. Using two different models of mitochondrial dysfunction I demonstrated that neutrophil respiratory burst may be regulated by altered mitochondrial functionality. Finally, I provide evidence that the cytoplasmic target for this mitochondrial signal is the enzyme pyruvate kinase M2, which through oxidative inhibition reduces the production of the respiratory burst substrate NADPH by limiting flow of glucose through the hexose monophosphate shunt. In summary, major elective surgery provides a translational model of human sepsis. Using this model, I demonstrate impairment of the neutrophil respiratory burst, and provide evidence that this is mediated through neutrophil mitochondrial dysfunction which promotes oxidative inhibition of the glycolytic regulatory enzyme pyruvate kinase.
Defining endemism levels for biodiversity conservation: tree species in the Atlantic Forest hotspot

Endemic species are important for biodiversity conservation. Yet, quantifying endemism remains challenging because endemism concepts can be too strict (i.e., pure endemism) or too subjective (i.e., near endemism). We propose a data-driven approach to objectively estimate the proportion of records inside a given the target area (i.e., endemism level) that optimizes the separation of near-endemics from non-endemic species. We apply this approach to the Atlantic Forest tree flora using millions of herbarium records retrieved from multiple sources. We first report an updated checklist of 5044 species for the Atlantic Forest tree flora and then we compare how species-specific endemism levels obtained from herbarium data match species-specific endemism accepted by taxonomists. We show that an endemism level of 90% separates well pure and near-endemic from non-endemic species, which in the Atlantic Forest revealed an overall endemism ratio of 45% for its tree flora. We also found that the diversity of pure and near endemics and of endemics and overall species was congruent in space. Our results for the Atlantic Forest reinforce that pure and near endemic species can be combined to quantify regional endemism and therefore to set conservation priorities taking into account endemic species distribution. We provided general guidelines on how the proposed approach can be used to assess endemism levels of regional biotas in other parts of the world.