Miracle-dz/UniFAR-FTUs huggingface dataset:
Preoperatively Grading Rectal Cancer with the Combination of Intravoxel Incoherent Motions Imaging and Diffusion Kurtosis Imaging

Purpose To combine Intravoxel Incoherent Motions (IVIM) imaging and diffusion kurtosis imaging (DKI) which can aid in the quantification of different biological inspirations including cellularity, vascularity, and microstructural heterogeneity to preoperatively grade rectal cancer. Methods A total of 58 rectal patients were included into this prospective study. MRI was performed with a 3T scanner. Different combinations of IVIM-derived and DKI-derived parameters were performed to grade rectal cancer. Pearson correlation coefficients were applied to evaluate the correlations. Binary logistic regression models were established via integrating different DWI parameters for screening the most sensitive parameter. Receiver operating characteristic analysis was performed for evaluating the diagnostic performance. Results For individual DWI-derived parameters, all parameters except the pseudodiffusion coefficient displayed the capability of grading rectal cancer (p < 0.05). The better discrimination between high- and low-grade rectal cancer was achieved with the combination of different DWI-derived parameters. Similarly, ROC analysis suggested the combination of D (true diffusion coefficient), f (perfusion fraction), and Kapp (apparent kurtosis coefficient) yielded the best diagnostic performance (AUC = 0.953, p < 0.001). According to the result of binary logistic analysis, cellularity-related D was the most sensitive predictor (odds ratio: 9.350 ± 2.239) for grading rectal cancer. Conclusion The combination of IVIM and DKI holds great potential in accurately grading rectal cancer as IVIM and DKI can provide the quantification of different biological inspirations including cellularity, vascularity, and microstructural heterogeneity.
Identifying IPA humor styles

As intelligent personal assistants (IPAs) become increasingly ubiquitous in our lives, their creators invest heavily in developing unique personalities for their products. Humor is often used to deepen this experience much the same way humans use it to enhance social interactions. And just as people engage in different types of humor, so do these devices. This study attempts to determine which humor styles are most commonly employed amongst IPA responses. The findings can be used to assist the further development of IPA responses in an effort to enhance user experience and increase customer loyalty.
Assessing user reactions to intelligent personal assistants’ humorous responses

The paper reports on the study that developed a classification of humorous interactions with intelligent personal assistants (IPAs) and applied the classification to compare four IPAs, Apple Siri, Google Assistant, Amazon Alexa and Microsoft Cortana, on their humor performance. The study relied on volunteer participants recruited through traditional academic channels (e.g. mailing lists) as well as Amazon Mechanical Turk (AMT). While AMT and non‐AMT participants differed on some demographic characteristics, their overall ratings of IPA humor were not significantly different and were analyzed jointly using descriptive and inferential statistics. The results revealed that Apple Siri and Google Assistant received higher average ratings on humorous IPA responses compared to Amazon Alexa and Microsoft Cortana. IPA responses to joke requests were judged as being funnier than IPA responses to questions related to the IPA's personality, rhetorical statements and other humor types. Consistent with previous studies on humor, our findings did not demonstrate strong relationships between select user demographics (age, gender and humor style) and their ratings of humorous IPA responses.
Mechanical Turk or volunteer participant? Comparing the two samples in the study of intelligent personal assistants

A challenge in academic and practitioner research is recruiting study participants that match target demographics, possess a desired skillset, and will participate for little to no compensation. An alternative to traditional participant recruitment struggles is crowdsourcing participants through online labor markets, such as Amazon Mechanical Turk (AMT). AMT is a platform that provides the tool for finding and recruiting participants with diverse demographics, skills, and experiences. This paper aims to demystify the use of crowdsourcing, and particularly AMT, by comparing the performance of traditionally recruited volunteers and AMT participants on tasks related to the evaluation of intelligent personal assistants (IPAs such as Amazon Alexa, Google Assistant, Apple Siri, and Microsoft Cortana). The comparison of AMT and non‐AMT samples indicated that while the two samples differed on demographics, their task performance was not significantly different. The paper discusses the costs and benefits of using AMT samples and would be of particular relevance to researchers who employ questionnaires and/or task‐specific data collection methods in their work.
Mining genomic variants and causal pathways linking HDL and triglycerides to coronary disease

Blood lipids are important biomarkers of risk of coronary heart disease (CHD), the leading cause of death in the world. Myriad data support a causal role of low-density lipoprotein cholesterol (LDL-C) in increasing risk of CHD. Long-standing epidemiology suggests that high-density lipoprotein cholesterol (HDL-C) may protect from disease while high triglycerides (TGs) increase CHD risk. However, the causality of HDL-C and TG to CHD remains controversial. New genetic methodologies have allowed a better look into causal pathways underlying relationships between these traits and disease. Using a combination of approaches for interrogating rare genetic variation in humans, we investigated how HDL and TG may relate to CHD. First, through sequencing and exome-wide genotyping of subjects with extremely high HDL-C, we identified the first homozygote for a loss-of-function (LOF) variant in SCARB1, which encodes scavenger receptor class BI (SR-BI), a hepatic receptor for HDL-C. Despite markedly elevated HDL-C, carriers of this variant had an increased risk of CHD. These findings suggest that HDL functionality in driving cholesterol removal through SR-BI (the reverse cholesterol transport hypothesis) is protective from CHD in humans. Next, we functionally examined one of the first novel loci from genome-wide association studies (GWAS) for HDL-C, GALNT2. Through discovery of humans with genetic GALNT2 LOF and additional studies in rodents and nonhuman primates, we showed that GALNT2 LOF lowers HDL-C across mammals. We also identify one physiological mechanism linking GALNT2 to HDL-C through its enzymatic function. Thirdly, we studied the mechanism of protection of the APOC3 A43T variant recently reported to lower TGs and CHD risk from exome sequencing. Studies in human carriers and animal models suggest that A43T accelerates renal clearance of circulating ApoC-III, thus hindering its function in delaying TG-rich lipoprotein turnover. These data establish ApoC-III clearance mechanisms as potential therapeutic targets for TG lowering. Finally, we adapted a targeted sequencing approach to increase discovery of causal rare coding and noncoding variants at candidate loci influencing HDL-C and TGs. Collectively, this work provides a sampling of approaches for leveraging the spectrum of genomic methods to identify clinically relevant variants impacting HDL, TG and CHD risk. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Daniel J. Rader
Human versus machine: Analyzing video game user reviews for plot and narrative

Video game users have shown strong interests in having subject metadata to find games. However, creating and maintaining subject metadata is costly and difficult. This study explores the utility of an automated approach for generating subject metadata for video games, focusing on plot and narrative. By comparing two methods to analyze the reviews—qualitative analysis conducted by a human researcher vs. automated text analysis using topic modeling—the researchers investigate if an automated method can generate subject terms that are comparable to the ones generated by qualitative analysis. Findings suggest that even with a smaller set of sample dataset, qualitative analysis could create a better set of terms than automated text analysis. However, terms generated from the automated text analysis indicate that its capability to retrieve themes of the video game may be useful in future libraries.
Dysfunctional Innate Immune Responses and Severe Dengue

Although infection with the dengue virus (DENV) causes severe dengue, it causes a mild self-limiting illness in the majority of individuals. There is emerging evidence that an aberrant immune response in the initial stages of infection lead to severe disease. Many inflammatory cytokines, chemokines, and lipid mediators are significantly higher in patients with severe dengue compared to those who develop mild infection, during febrile phase of illness. Monocytes, mast cells, and many other cells of the immune system, when infected with the DENV, especially in the presence of poorly neutralizing antibodies, leads to production of pro-inflammatory cytokines and inhibition of interferon signaling pathways. In addition, production of immunosuppressive cytokines such as IL-10 further leads to inhibition of cellular antiviral responses. This dysregulated and aberrant immune response leads to reduced clearance of the virus, and severe dengue by inducing a vascular leak and excessive inflammation due to high levels of inflammatory cytokines. Individuals with comorbid illnesses could be prone to more severe dengue due to low grade endotoxemia, gut microbial dysbiosis and an altered phenotype of innate immune cells. The immunosuppressive and inflammatory lipid mediators and altered phenotype of monocytes are likely to further act on T cells and B cells leading to an impaired adaptive immune response to the virus. Therefore, in order to identify therapeutic targets for treatment of dengue, it would be important to further characterize these mechanisms in order for early intervention. In this review, we discuss the differences in the innate immune responses in those who progress to develop severe dengue, compared to those with milder disease in order to understand the mechanisms that lead to severe dengue.
Modifying and Integrating in vitro and ex vivo Respiratory Models for Inhalation Drug Screening

For the past 50 years, the route of inhalation has been utilized to administer therapies to treat a variety of respiratory and pulmonary diseases. When compared with other drug administration routes, inhalation offers a targeted, non-invasive approach to deliver rapid onset of drug action to the lung, minimizing systemic drug exposure and subsequent side effects. However, despite advances in inhaled therapies, there is still a need to improve the preclinical screening and the efficacy of inhaled therapeutics. Innovative in vitro models of respiratory physiology to determine therapeutic efficacy of inhaled compounds have included the use of organoids, micro-engineered lung-on-chip systems and sophisticated bench-top platforms to enable a better understanding of pulmonary mechanisms at the molecular level, rapidly progressing inhaled therapeutic candidates to the clinic. Furthermore, the integration of complementary ex vivo models, such as precision-cut lung slices (PCLS) and isolated perfused lung platforms have further advanced preclinical drug screening approaches by providing in vivo relevance. In this review, we address the challenges and advances of in vitro models and discuss the implementation of ex vivo inhaled drug screening models. Specifically, we address the importance of understanding human in vivo pulmonary mechanisms in assessing strategies of the preclinical screening of drug efficacy, toxicity and delivery of inhaled therapeutics.
Governing for Child-Friendliness? Perspectives on Children as Users Among Swedish and Danish Urban Open Space Managers

Despite the acknowledged importance of outdoor environment quality in supporting children's health and well-being, little is known about how contemporary urban open space management caters for children. In this study, Swedish (n = 54) and Danish (n = 25) local governments were surveyed regarding how they manage urban open space for children, e.g., through a child-centered perspective which might include children's perspectives (participation and governance approaches). The results revealed organizational differences and more active consideration of children as urban open space users in Sweden than in Denmark. A general ambition to increase children's participation was reported, but also associated challenges, including budget limitations and lack of knowledge among managers. More ambitious and child-centered urban open space management units work collaboratively and broadly, through governance processes. This includes going beyond conventional structures and perceptions of what are “places for children” and consider all levels of strategic management (policy, tactical, and operational) in developing child-friendly environments within urban open spaces. The large differences between various management units indicates the importance of individual employees' knowledge and dedication, and the value of exchanging knowledge and experiences.
Long-Term Effects of Maternal Deprivation on the Volume of Dopaminergic Nuclei and Number of Dopaminergic Neurons in Substantia Nigra and Ventral Tegmental Area in Rats

Early life adversities leave long-lasting structural and functional consequences on the brain, which may persist later in life. Dopamine is a neurotransmitter that is extremely important in mood and motor control. The aim of this study was to investigate the effect of maternal deprivation during the ninth postnatal day on the volume of dopaminergic nuclei and the number of dopaminergic neurons in adolescence and adulthood. Maternally deprived and control Wistar rats were sacrificed on postnatal day 35 or 60, and the dopaminergic neurons were stained in coronal histological sections of ventral midbrain with the tyrosine hydroxylase antibody. The volume of dopaminergic nuclei and the number of dopaminergic neurons in the substantia nigra (SN) and ventral tegmental area (VTA) were analyzed in three representative coordinates. Maternal deprivation caused weight loss on postnatal day 21 (weaning) and corticosterone blood level elevation on postnatal days 35 and 60 in stressed compared to control rats. In maternally deprived animals, the volumes of SN and VTA were increased compared to the controls. This increase was accompanied by an elevation in the number of dopaminergic neurons in both nuclei. Altogether, based on somatic and corticosterone level measurements, maternal deprivation represents a substantial adversity, and the phenotype it causes in adulthood includes increased volume of the dopaminergic nuclei and number of dopaminergic neurons.
Impact of Se supplementation on the oxidation stability of eggs

Se supplementation in feed can be used to increase human Se intake, and this has showed significant progress in the area of healthy nutrition in recent years. It has been proven that the antioxidant function of Se is likely to contribute to better shelf life in animal products. Egg freshness can be monitored by assessment of albumen and yolk pH, fatty acid profile, malondialdehyde content, yolk vitelline membrane strength, carbonyl content and yolk pigment stability. It has been proven that Se reduces oxidation processes inside the egg and hence the pH of its contents does not increase too rapidly when stored. Several studies have reported that the rate of fatty acid oxidation and the production of lipid oxidation products (malondialdehyde, MDA) are lower in Se enriched eggs compared to non-enriched eggs. These results have been explained by an increase in gluthation peroxidase (GSH-Px) levels and activity in eggs after supplementation of laying hens with Se, which is an essential component of GSH-Px. Se has a positive effect on the stability of yolk pigments, which is linked to the oxidation stability of yolk lipids. According to several studies, Se decreases the carbonyl, which is a marker of protein oxidation. The yolk vitelline membrane consists of a high amount of protein incorporating Se, which explains the increased vitelline membrane strength after Se supplementation.
Soil and water conservation, and soil fertility management effects on rain water productivity of maize hybrid in Burkina Faso

In the evaluation of Soil and Water Conservation (SWC) techniques, little attention is paid to the rain water productivity of crops. The aim of this research work, is to assess the combined effects of SWC practices and soil fertility management on rain water productivity of maize hybrid. On-farm experiments were carried out in the districts of Hounde and Peni both located in the Hauts-Bassins region in Burkina Faso. The treatments were built as association of two SWC technologies combined with three fertilization options. The SWC combinations were: Stone rows and zai pits (SR+Zai), Grass strips and zai pits (GS+Zai), Earth bunds and contour ploughing (EB+CP). The fertilization options were: 5 t ha-1 organic fertilizer (OM), OM + 100 kg ha-1 urea (46% N), OM + 200 kg ha-1 NPK (14-23-14) + urea. The treatments were laid out in a randomized block design where each farmer constituted a replication. As result, the combination of GS+ Zai+ OM+ NPK+ Urea gave 26% additional maize grain yield and maize rain water productivity of 4.51 kg ha-1 mm-1 in the South-Sudan agro-ecological zone. While the combination of SR+ Zai+ OM+ NPK+ Urea increased maize yield by 106 % and water productivity of maize was 6.61 kg ha-1 mm-1 in the North-Sudan agro-ecological zone. To improve maize yields and water productivity in rainfed agriculture, the use of the combination of soil and water conservation techniques and optimum organic and mineral fertilizer application is recommended. Key words: Crop, water use, nutrients, maize yield, harvest index, Burkina Faso.
Yield response, water productivity, and seasonal water production functions for maize under deficit irrigation water management in southern Taiwan

Abstract As the challenges toward increasing water for irrigation become more prevalent, knowledge of crop yield response to water can facilitate the development of irrigation strategies for improving agricultural productivity. Experiments were conducted to quantify maize yield response to soil moisture deficits, and assess the effects of deficit irrigation (DI) on water productivity (water and irrigation water use efficiency, WUE and IWUE). Five irrigation treatments were investigated: a full irrigation (I1) with a water application of 60 mm and four deficit treatments with application depths of 50 (I2), 40 (I3), 30 (I4), and 20 mm (I5). On average, the highest grain yield observed was 1008.41 g m−2 in I1, and water deficits resulted in significant (p < .05) reduction within range of 6 and 33%. This reduction was significantly correlated with a decline in grain number per ear, 1000-grain weight, ear number per plant, and number of grain per row. The highest correlation was found between grain yield and grain number per ear. The WUE and IWUE were within range of 1.52–2.25 kg m−3 and 1.64–4.53 kg m−3, respectively. High water productivity without significant reduction in yield (<13%) for I2 and I3 compared to the yield in I1 indicates that these water depths are viable practices to promote sustainable water development. Also, for assessing the benefits of irrigation practices in the region crop water production functions were established. Maize yield response to water stress was estimated as . 92, suggesting the environmental conditions are conducive for implementing DI strategies.
Cross‐disciplinary data practices in earth system science: Aligning services with reuse and reproducibility priorities

As a data intensive field that unites researchers from many disciplines, Earth System Science (ESS) is an ideal site for examining evolving cross‐disciplinary data practices. This paper reports on results from a survey examining data sharing, data reuse, and research reproducibility practices of ESS researchers, aimed at informing improvements in data services for interdisciplinary sciences. Data reuse was found to be very high for new and comparative analyses but very limited for reproducing research. Data sharing was also strong, mostly through supplements to published papers, with moderate use of open access repositories. At the same time, there was interesting variability in both data sharing and reuse among ESS disciplines. The most pronounced challenges to reuse and reproducibility stem from limited documentation on how data are collected and managed, practices that are poorly supported by institutions, funders, and publishers. A more refined approach to “reproducibility” is needed that aligns with priorities and practices within the research community. Just as importantly, advances in data service models for ESS and other interdisciplinary fields need to account for the diverse and distributed system of repositories and build a workforce with deeper knowledge of the complex data and methods that drive integrative systems science.
A Study on Fabrication and Structural Characterization of PbS Thin Films

PbS thin films are fabricated from 99.9% PbS powder on glass substrates using the vacuum evaporation method. Some of the samples are then treated in an advanced process called annealing. Samples are annealed in temperatures of 80, 100, 120 and 150°C for two h. Characterization using an X-Ray Diffractometer (XRD) resulted in values of lattice constant of the films ranging from (5.782±0,010) A to (5.919±0,006) A. These values are quite different from the standard, probably because the films are stressed and strained. The grains have sizes ranging from (266.440±0.001) A to (694.059±0.002) A, where the greatest grain size was found as deposited thin film because it was directly condensed from powder vapor during the deposition process and after they are annealed, the grain size becomes smaller. The average internal stress has values ranging from (0.36±0,006) × 109 N/m2 to (3.247±0.010) ×109 N/m2 and microstrain ranging from (2,864±0.006) × 10-3 to (25.94±0,01) ×10-3. It was found that the film which has the greatest stress and microstrain is the film with the annealing temperature of 150°C, showing that the annealing process exerts force on the film following the rising of temperature. Use of a Scanning Electron Microscope (SEM) shows the surface pictures of the deposited thin film and the film annealed at 120°C. Furthermore, the thickness of the samples is obtained by using the cross section of the films and showed that the thickness of the deposited thin film is between 0.63 and 1.30 microns and the thickness of the film annealed at 120°C is between 3.37 and 4.34 microns. The best quality thin film from this research is that annealed at 120°C, because it showed more peaks than the other samples. It can be concluded that the annealing process had effects on the structures, grain size, strain and stress of the crystals.