Miracle-dz/UniFAR-FTUs huggingface dataset:
A flexible and versatile framework for statistical design and analysis of quantitative mass spectrometry-based proteomic experiments

Choi, Meena PhD, Purdue University, May 2016. A Flexible and Versatile Framework For Statistical Design and Analysis of Quantitative Mass Spectrometry-Based Proteomic Experiments. Major Professor: Olga Vitek. Quantitative mass spectrometry (MS)-based proteomics is an indispensable technology for biological and clinical research. As the proteomics field grows, MS-based proteomic workflows are becoming more complex and diverse. The accuracy and the throughput of the MS measurements and of the signal processing tools dramatically increased. However, many existing statistical tools and workflows have not followed the technological development. Therefore, there is a need for flexible statistical tools, which reflect diverse and complex workflows, are computationally efficient for large datasets, and maximize the reproducibility of the results. We propose a family of linear mixed effects models, and a split-plot view of the experimental design, that represent measurements from quantitative mass spectrometrybased proteomics. The whole plot part of the design reflects the structure of the biological variation of the experiment, such as case-control design, paired design, or time-course design. The subplot part of the design reflects the structure of the technological variation, such as fragmentation patterns, labeling strategy, and presence of multiple peptides per protein. We propose an estimation procedure that separately estimates the parameters of the subplot and the whole plot parts of the design, to maximize the flexibility of the model, increase the speed of the analysis, and facilitate the interpretation. The proposed modeling framework was validated using 10 controlled mixtures and 10 experimental datasets from targeted Selected Reaction Monitoring (SRM), DataDependent Acquisition (DDA or shotgun), and Data-Independent Acquisition (DIA
Bladder preservation versus radical cystectomy in transitional cell carcinoma and squamous cell carcinoma muscle invasive bladder cancer

Abstract Background: Randomizing patients to bladder preservation or radical cystectomy (RC) for the treatment of bladder cancer has not been practical, due to patient and physician preferences. Therefore, continually comparing the 2 treatment modalities is needed, in order to make the proper choice for each patient. Patients and methods: The records of T1–4N0M0 bladder cancer patients, who presented to the South Egypt Cancer Institute between 2007 and 2017 and were treated by either bladder preservation or RC were reviewed. Results: Out of the 166 included patients, 81 (48.8%) patients were treated by bladder preservation and 85 (51.2%) patients had RC. For the patients treated by bladder preservation and the patients treated by RC, the 5-year overall survival (OS) was 56% and 60% (p = 0.67), the 5-year local recurrence-free survival was 69% and 73% (p = 0.69), and the 5-year disease-free survival was 45% and 53% (p = 0.16), respectively. After propensity matching analysis, the mean 5-year OS was 58% for the bladder preservation patients and 61% for the RC patients (p = 0.51). It is notable that among the bladder preservation group, 8 patients (10%) had squamous cell carcinoma (SCC) pathology and refused RC. Their OS was 56% compared to 53% for the SCC patients treated by RC (p = 0.6). Conclusion: Bladder preservation is a safe alternative to cystectomy in transitional cell carcinoma stages T1–4aN0M0, and its use in SCC bladder cancer should be further studied, as it could be feasible to spare them from initial cystectomy.
Developing and validating a competence framework for improving the productivity of smallholder farmers: a case study from Ethiopia

ABSTRACT Purpose Enhancing the relevance of rural extension services requires aligning extension education to the roles, tasks, activities and competencies of smallholder farmers. The objective of this study is to follow up on previous competence studies and to construct a validated competence framework. Design/Methodology/Approach Competence frameworks are generally being used to articulate performance requirements for certain jobs or professions. Whereas most competence frameworks display generic competencies and long lists of tasks, this study combines generic competencies, behavioural aspects, and content specifications of the job fields. The competence framework was empirically validated through workshops, focus-group discussions, and surveys involving 76 participants from stakeholder groups. Findings The results reveal nine roles: 1. Learner, 2. Manager, 3. Communicator, 4. Co-operator, 5. Professional, 6. Innovator, 7. Entrepreneur, 8. Planner, and 9. Producer. Furthermore, six job fields are defined, based on the content of the farmers' jobs: 1. Pre-planting, 2. During-planting, 3. After-planting, 4. During-harvesting, 5. Post-harvesting, and 6. Facilitating all farming activities. Combining the roles and the job fields results in the identification of 23 tasks and 25 competencies. Practical implications The competence framework validated in this study can serve as a starting point for extension workers to develop courses, training programs, and interactions with smallholder farmers. Theoretical implications The study demonstrates a research approach involving the contextualization of competencies, rendering them meaningful for improving rural innovation and the productivity of smallholder farming. Originality/Value The integrated approach used to develop the competence framework can be applied in any other context, and result in a comprehensive understanding of the respective job/profession.
Bleeding complications at the access sites during catheter directed thrombolysis for acute limb ischaemia: Mini review

Acute and subacute ischemia of the lower limbs represents a major emergency with a high in-hospital mortality, complication, and leg amputation rates. Treatment options for acute limb ischemia include systemic anticoagulation, followed by various catheter based options including infusion of fibrinolytic agents (pharmacological thrombolysis), pharmacomechanical thrombolysis, catheter-mediated thrombus aspiration, mechanical thrombectomy, and any combination of the above or open surgical intervention (thromboembolectomy or surgical bypass). Minor and major bleeding complication during catheter directed thrombolysis (CDT) especially at access site are frequent. Bleeding complications require often an interruption or termination of CDT affecting clinical outcome of the patients. Recently we examined a new access site bleeding protection device during CDT.
The effect of pulsed electric field on drying kinetics, color, and microstructure of carrot

ABSTRACT The aim of the study was to investigate the impact of pulsed electric field (PEF) treatment on the convective drying kinetics of a carrot and color and microstructure changes of the dried product. Samples were treated by PEF with the specific energy input equal to 5.63, 8 and 80 kJ · kg−1. After PEF treatment, thermal conductivity and electrical conductivity were measured. Drying time of the PEF-treated samples was reduced up to 8.2% (Ws = 8 kJ · kg−1, 5 kV · cm−1; 10 pulses) in comparison to intact tissue. Statistical analysis showed that Midilli et al.’s model was considered to describe the kinetics of the process the most precisely. Pulsed electric field treatment increased the effective water diffusion coefficient up to 16.7%. Moreover, PEF treatment and drying caused the alteration of the sample color. After drying, the lightness and chroma were higher or unchanged in comparison to the intact tissue. The dried PEF-treated samples exhibited significantly higher redness (higher value of a* parameter) in comparison to the untreated dried samples. Moreover, the visual inspection of scanning electron microscope images revealed that PEF pretreatment performed at high electric field intensity (5 kV · cm−1, regardless of pulse number) provoked the material to form greater cavities during drying in comparison to the untreated material.
Tertiary Level Saudi EFL Learners’ Reading Strategies in Relation to Gender and Proficiency

Abstract This research addressed some current issues in L2 reading strategy research (the nature of any gender effect, and the use of multiple data gathering instruments) as well as an important problem at tertiary level in Saudi Arabia (low English reading proficiency). It examined which reading strategies were most widely reported by 120 Saudi EFL intensive English course students in a Saudi state university. Two different methods were used to collect data. First a 5-point Likert-scale questionnaire composed of 30 items, chosen based on a preliminary study, was administered to the students. Think-Aloud Protocols (TAP) were then elicited from 14 of the male students while they performed a reading rask. Reading strategies from both sources were analyzed over three phases – pre-reading, while-reading, and post-reading. The results of the TAP analysis revealed that 19 different strategies were used, mostly by more proficient readers. The students’ questionnaire responses showed that there were many significant differences based on student proficiency level, where more proficient students reported using more strategies than less proficient ones, especially top own ones, but few by gender, where females significantly outdid males in a few instances only. There was some evidence for an unanticipated reading purpose effect associated with the two instruments. The implication for contexts like that in Saudi Arabia is that more student training in carefully selected reading strategies is needed.
Population structure and conservation status of the white gorgonian Eunicella singularis (Esper, 1791) in Tunisian waters (Central Mediterranean)

The white gorgonian, Eunicella singularis, is thriving in Mediterranean hard-bottom communities; however, data regarding its distribution and ecology remain absent and insufficient, particularly in the southern Mediterranean Sea.In this study, the population structure and disturbance levels of the most common gorgonian in Tunisia were assessed for the first time. During two years (2015-2016), a total of 818 colonies of E. singularis was surveyed in five coastal sites, by scuba diving, between 7 to 40 m depth. Collected data included density, colony height, and extent of injury. Mean population density was 11.91 ± 7.42 colonies per m2 (mean ± SD). Mean and maximum colony heights were 16.49 ± 5.59 cm and 51 cm, respectively. Among populations, mean extent of tissue injury differed considerably, ranging from 12.47% to 58.88% and most affected colonies showed old necrosis. These data regarding the demographic structure and level of injuries are needed to provide insights into the conservation status of the Tunisian population of E. singularis. Indeed, data on the amount of necrosis could highlight the strength of the colonies’ exposure to mechanical impacts and are consequently crucial to study changes in their demographic structure over time. In fact, the size, structures, and the high level of tissue necrosis of the colonies suggest a low conservation status of the studied Tunisian populations.
Projection‐based and cross‐validated estimation in high‐dimensional Cox model

We propose a projection‐based cross‐validation method for estimating a low‐dimensional parameter in the presence of a high‐dimensional nuisance parameter in the Cox regression model. We show that the proposed estimator is asymptotically normal, which enables us to conduct hypothesis test for the parameter of interest with high‐dimensional nuisance parameters. Three decision rules are presented to avoid the influence of random splitting of samples. Simulation studies indicate that our method is more powerful than that of Fang et al. (2017, JRSSB) when the coefficients of predictors are high‐dimensional and not very sparse. As an illustrative example, we apply our procedure to a breast cancer study.
X-ray Fluorescence Uptake Measurement of Functionalized Gold Nanoparticles in Tumor Cell Microsamples

Quantitative cellular in vitro nanoparticle uptake measurements are possible with a large number of different techniques, however, all have their respective restrictions. Here, we demonstrate the application of synchrotron-based X-ray fluorescence imaging (XFI) on prostate tumor cells, which have internalized differently functionalized gold nanoparticles. Total nanoparticle uptake on the order of a few hundred picograms could be conveniently observed with microsamples consisting of only a few hundreds of cells. A comparison with mass spectroscopy quantification is provided, experimental results are both supported and sensitivity limits of this XFI approach extrapolated by Monte-Carlo simulations, yielding a minimum detectable nanoparticle mass of just 5 pg. This study demonstrates the high sensitivity level of XFI, allowing non-destructive uptake measurements with very small microsamples within just seconds of irradiation time.
Application of Mathematical and Computational Methods to Identify Women’s Priorities in Transport

It is well established that the transport sector is not an equalitarian sector. To develop a sustainable society, a more equalitarian and safe transport system for both users and transport sector employees is needed. This work prioritizes the needs and barriers previously identified as relevant among transport system users and employees for four different transport scenarios (railways, autonomous vehicles (AVs), bicycle-sharing services (BSSs), and employment). The aim of this paper is to prioritize the factors affecting women in these four transport scenarios with the help of a survey followed by the application of mathematical and computational algorithms based on the analytic hierarchy process (AHP) methodology. The identification of factors with higher influence in the fair participation of women in the transport sector will help transport planners, bike-sharing system owners, decision-makers, transport companies, and regulatory professionals to develop measures that could plausibly increase the proportion of women as users of BSSs, users of rail public transport, and AVs, as well as employees in the transport sector for a sustainable society. The results indicated that safety and security were the most challenging factors for railways. Weather, topography, and family responsibilities were shown to have a high influence on the use of BSSs. In the case of autonomous vehicles, the simultaneity and trust in the technology are the main opportunities to influence the acceptance of such vehicles. Finally, for transport employment, caring and parenting responsibilities were the factors that had the largest effect. Some differences in priorities were found for different profiles of women.
LINKAGES BETWEEN STOCK AND CRYPTOCURRENCY MARKETS DURING THE COVID-19 OUTBREAK: AN INTRADAY ANALYSIS

This study explores the return and volatility spillovers between S and P 500 and cryptocurrencies [Litecoin (LTC), Bitcoin (BTC) and Ethereum (ETH)] during the pre-COVID-19 period and COVID-19 period using the VAR-BEKK-AGARCH model on hourly data Furthermore, this study also quantifies the optimal portfolio weights and hedge ratios during both sample periods The findings of study show that the return and volatility spillovers between the US stock and cryptocurrency markets are not significant during the pre-COVID-19 period However, the study finds unidirectional return transmission from S and P 500 to all the cryptocurrencies during the COVID-19 period During the COVID-19 period, the volatility spillover is unidirectional from S and P 500 to Litecoin, whereas the volatility transmissions are not significant for the pairs of S and P 500-Bitcoin and S and P 500-Ethereum Based on optimal weights, the portfolio managers are recommended to slightly decrease their investments in S and P 500 for the portfolios of S and P 500/BTC, S and P 500/ETH and S and P 500/LTC during the COVID-19 period Finally, during the COVID-19 period, all hedge ratios were found to be higher, implying higher hedging costs during the COVID-19 period compared to the pre-COVID-19 period Our research offers valuable insights to the fund managers, investors and policymakers regarding diversification opportunities, hedging, optimal asset allocation and risk management © 2021 World Scientific Publishing Company
So You Think This Baby Has Appendicitis? The Subtle Clues and Deceptive Signs

Diagnosing appendicitis in infants is challenging due to varied and heterogenous presentations. Whilst the condition is uncommon, the consequences of missing this in a busy Emergency Department (ED) can be catastrophic. We report an 8-month-old infant who presented to ED with a brief history of reduced feeding, lethargy and vomiting with normal observations. Excessive crying was noted when the child was supine, he was consolable when placed prone. Due to these paroxysms of crying which varied with position, investigations were commenced. He had a good clinical outcome. A high degree of suspicion is needed in preverbal children. Clinical examination, observation of the behaviour of the child and parental concern remain key to diagnosis. Through this paper we aim to explore the clinical conundrum of making the diagnosis in this age group and the modalities which help in decision making.
Species abundance fluctuations over 31 years are associated with plant–soil feedback in a species‐rich mountain meadow

Increasing evidence suggest that plant–soil interactions play an essential role in plant community assembly processes. Empirical investigations show that plant species abundance in the field is often related to plant–soil biota interactions; however, the direction of these relations have yielded inconsistent results. We combined unique 31‐year long field data on species abundances from a species‐rich mountain meadow with single time point plant–soil feedback greenhouse experiments of 24 co‐occurring plant species. We tested whether these relations were dynamic in time, whether coupled increases and decreases in abundance between years were related to plant–soil feedback and whether these changes were underlain by years in which manuring was applied. The prevailingly negative relationship between plant–soil feedback and plant relative abundance in the field was significantly time‐dependent, which may reconcile the contrasting results in literature. Furthermore, significantly coupled oscillations appeared between species relative abundance changes and plant–soil feedback, which were likely moderated by years in which manuring was applied. Our results are consistent with the notion that the more abundant species are stabilised by negative plant–soil feedback, and the less abundant species co‐vary with the fluctuations of these more competitive species. Synthesis. Our results project plant–soil feedback as an important regulatory mechanism in plant communities, operating in conjunction with species' competitive ability and soil nutrient availability. We suggest that negative feedback is particularly prominent in more abundant plant species that profit from more readily available soil nutrients than less abundant species with positive feedback. Negative plant–soil feedback may thus prevent more abundant plant species from out‐competing less abundant plant species, facilitating stable species co‐existence.
Role of Ecologic ACE I/D Polymorphism Data Towards Prediction of COVID-19 Epidemiology

COVID-19 displays marked variability in the clinical course as well as regional epidemiology. Abnormalities in RAAS system especially stemming from genetic variability in ACE and ACE2 expression (including ACE I/D polymorphism) have been proposed to explain underlying pathogenesis and variability in SARS-CoV-2 infection. In a meta-regression data set of 30 countries, we found significant associations of ACE I/D ratio and COVID-19 prevalence, deaths and recovery rate but not when adjusted for possible confounders. This ecological study suggests potential of ACE I/D data as predictive biomarker COVID-19 risk and severity in a population specific manner, subject to validation in large genetic epidemiological and functional studies.
Investigation of the Corrosion Behavior of Electroless Ni-P Coating in Flue Gas Condensate

The corrosion behavior of Ni-P coating deposited on 3003 aluminum alloy in flue gas condensate was investigated by electrochemical approaches. The results indicated that nitrite acted as a corrosion inhibitor. The inhibiting effect of nitrite was reduced in solutions containing sulfate or nitrate. Chloride and sulfate accelerated the corrosion of Ni-P coatings greatly. This can provide important information for the researchers to develop special Ni-P coatings with high corrosion resistance in the flue gas condensate.
Tourist Taxonomies of International Tourists Visiting Zimbabwe Using an Extended International Tourist Role Scale

Tourist typologies are generally criticized for having spatial biases because most of them were constructed in the context of the Western world. The study used an Extended International Tourist Role (EITR) scale to determine the typologies of international tourists to Zimbabwe. The augmented scale was subjected to reliability and validity tests, which yielded positive results. A factor–cluster analysis of 569 international tourists, yielded three distinct subgroups though with similar traits in certain dimensions. The clusters were named the independent tourist, the indifferent tourist, and the cautious new tourist. In the context of Zimbabwe, the cautious new tourist taxon is the most viable subgroup because of its size and available destination resources. However, for strategic planning, Zimbabwe should begin to embrace the independent tourist. The cautious new tourist is likely to mature into the independent tourist status, if the contemporary trends are anything to go by.
A new species of Amphisbaena (Squamata: Amphisbaenidae) from the Orinoquian region of Colombia

In northern South America, amphisbaenians are rarely seen among the herpetofauna.Thus, general knowledge about them is very poor. During a herpetological survey in 2012 at Casanare, Colombia, we found two specimens of an unusual Amphisbaena. A third specimen sharing the same morphotype labeled Amphisbaena sp. from Vichada department was found deposided in an Colombian reptile collection. Based on morphological analyses together with phylogenetic analyses of 1029 base pairs of the mitochondrial DNA (mtDNA), we describe a new species of Amphisbaena that inhabits in the Orinoquian region of Colombia. The new species is part of a phylogenetic clade together with A. mertensii and A. cunhai (central-southern Brazil), exhibiting a great genetic distance (26.1–28.9%) between the newly identified lineage versus those taxa, and versus the sympatric taxa A. alba and A. fuliginosa. Morphologically, this new Amphisbaena can be distinguished from their congeners by characters combination of number of preocloacal pores, absence of malar scale, postgenial scales and body and caudal annuli counts. Amphisbaena gracilis is on morphology grounds the most similar species. However, the new species can be distinguished from it by having higher body annuli counts, angulus ories aliegned with the edges of the ocular scales and center of frontal scales, less number of large middorsal segments of the first and second body annulus, and rostral scale visible from above. The description of this new Amphisbaena species points out the urgent need to increase the knowledge of worm lizards in Colombia