Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical Significance of Fusobacterium nucleatum and Microsatellite Instability in Evaluating Colorectal Cancer Prognosis

Objective: Both genetic and microbial factors play important roles in colorectal cancer (CRC) development. The effects of Fusobacterium nucleatum ( F. nucleatum ) and microsatellite instability (MSI) on CRC prognosis require more clinical evidence. We aimed to investigate the role of F. nucleatum and MSI as biomarkers in predicting the prognosis of CRC. Methods: CRC patients in various TNM stages were enrolled. MSI status and F. nucleatum were detected by immunohistochemical staining of formalin-fixed paraffin-embedded (FFPE) specimens. The associations between MSI status and F. nucleatum and clinical parameters were analyzed. Results: MSI tumors were more frequently observed in the colon than in the rectum. Cancerous tissues had higher levels of F. nucleatum than adjacent noncancerous tissues. There were no significant differences in F. nucleatum abundance in different age, sex, tumor stage, location, and tumor marker groups. MSI status was associated with tumor location and stage. Survival analyses revealed that disease-free survival (DFS) was significantly longer in the F. nucleatum -negative, younger age, and TNM stage I–II groups (p< 0.05), and age, advanced TNM stage (III and IV), and F. nucleatum status were independent factors for poor prognosis. Multivariate Cox regression and receiver operating characteristic (ROC) curve analyses showed that conventional tumor biomarkers of CRC had more prognostic value than F. nucleatum and MSI. Conclusion: Age, advanced TNM stage, and F. nucleatum positivity were independent factors of poor prognosis, suggesting that F. nucleatum and MSI may contribute to the identification of new strategies for the prevention and treatment of CRC.
Human-Robot Collaboration Using Commonsense Knowledge in Smart Manufacturing Contexts

Human-robot collaboration (HRC), where humans and robots work together on specific tasks, is a growing part of smart manufacturing that entails artificial intelligence (AI) techniques in manufacturing processes. Robots need to be able to dynamically understand their working environments and human partners both accurately and quickly, as inaccurate or slow predictions can be dangerous to humans and collaborative tasks. To handle challenging environments, robots need to utilize commonsense knowledge (CSK), which is everyday knowledge about fundamental concepts, such as how basic objects interact with each other, what their properties are, and how they are associated. Human beings utilize CSK regularly, and robots can effectively collaborate with humans through it. This thesis outlines the fundamentals of CSK to provide prerequisite information and demonstrates how robots utilize it to collaborate with humans. The thesis also demonstrates the effectiveness of CSK and HRC through simulation studies and real-world human-robot collaboration experiments by deploying commonsense knowledge priorities and mathematical modeling for task optimization in robot action planning. Human-robot collaboration is compared with humans working without aid from robots. This thesis presents the results of this work along with a survey of relevant literature, as well as open issues for further research. To the best of our knowledge, ours is pioneering work on proposing a specific approach based on commonsense knowledge for human-robot collaboration in smart manufacturing.
A Note on Testing the LATE Assumptions

In this paper we show that the testable implications derived in Huber and Mellace (2013) are the best possible to detect invalid instruments, in the presence of heterogeneous treatment effects and endogeneity. We also provide a formal proof of the fact that those testable implications are only necessary but not sufficient conditions for instrument validity.
Role of Nanofluid Minimum Quantity Lubrication (NMQL) in Machining Application

Gaining grounds as a potential heat transfer fluid due to its superior thermal and tribological properties, Nanofluid Minimum Quantity Lubrication (NMQL) has been classified as an environmentally friendly technique and has already been successfully applied in several machining processes. This paper presents a review of the role of NMQL for different machining processes. The mechanisms of the MQL technique are thoroughly explained for achieving optimal performance based on parameters like nozzle feed position, angle of elevation, distance from the nozzle tip to cutting zone, flow rate, and air pressure. NMQL is shown to enhance cooling performance and lubrication, as well as the tribological properties of the fluid and cutting performance. With government legislative and public opinion pushing manufacturing companies towards sustainable production techniques and practices, the implementation of MQL-nanofluid can slowly prevent the adverse effects that conventional cutting fluids contribute.
Global Methylation Analysis Using MSAP Reveals Differences in Chilling-Associated DNA Methylation Changes during Dormancy Release in Contrasting Sweet Cherry Varieties

Dormancy is an adaptive strategy developed by temperate perennial crops to protect overwinter tissues from unfavorable environmental conditions. Sweet cherry (Prunus avium L.), a member of the Rosaceae family, requires chilling to overcome dormancy. The time of harvest is directly correlated with chilling requirements in sweet cherries. Consequently, early and late season varieties have low and high chilling requirements, respectively. There is evidence that the expression of dormancy-related genes is regulated by DNA methylation. In this work, methylation-sensitive amplified polymorphism (MSAP) was applied to study genome-wide DNA methylation changes associated with dormancy in two low-chill varieties, ‘Royal Dawn’ and ‘Glen Red’, and one high-chill variety, ‘Kordia’. Our primary results suggest that the occurrence of progressive DNA demethylation is associated with chilling accumulation during dormancy in the three varieties, independent of their chilling requirements. Genes were identified with different methylation status changes, detected by MSAP, related to cell wall remodeling and energy metabolism. Several MSAP profiles among the varieties were observed, suggesting that fine epigenetic control is required to coordinate hormonal and environmental signals that induce dormancy and its release.
Evaluation of Ranavirus Major Capsid Protein Gene Sequence Mutations in United States East Coast Frog and Tadpole Populations

Infectious disease is a leading cause of death in ectothermic taxa including amphibians, reptiles, and bony fish. Frog Virus 3 (FV3) Ranavirus is a prominent pathogen that infects frog and tadpole populations with lethal consequences, especially for pre-metamorphosed individuals. Wood frogs (Lithobates sylvaticus) are particularly susceptible to FV3 infection and mortality events. Conservation of this animal is a critical effort for the maintenance of these ecologically significant animals. Amphibians contribute to the regulation of insect pest levels, energy transfer between aquatic and terrestrial habitats, algae community productivity and function, and vertebrate biomass. Understanding genetic variations of FV3 is crucial to understanding the evolution of this virus and host susceptibility. Diagnostic testing is key for preventing the spread of the virus and reducing the mass mortality events observed in tadpole populations. Populations studied originate from 5 US states, Delaware, Maryland, New Jersey, Pennsylvania, and Virginia. This study explored the validity of current Real Time-PCR diagnostic testing methods and sought out genetic variations that may account for inconsistent diagnostic results brought forth by previous studies. Despite symptom observations in the field and positive fluorescence during diagnostic testing, 416 individuals have been deemed negative as they did not meet the melting temperature (Tm) criteria currently in place. This study presents findings that support the hypothesis that many, if not all, of these individuals are in fact positive for the virus. Due to the prior conflicting diagnostic results the Tm range currently in place may not account for new mutations within a ~530 base pair targeted region of the viral major capsid protein (MCP) gene sequence. Molecular techniques were used to evaluate the amplified DNA of the targeted region of the MCP gene. Traditional PCR and gel electrophoresis results provided evidence of infection in 41 individuals from nine populations. This was followed by sequence analysis of the PCR EVALUATION OF RANAVIRUS MAJOR CAPSID PROTEIN MUTATIONS 2 product for 22 of those individuals. Sequence results confirmed Ranavirus infections in 15 individuals from seven populations. A single base pair mutation was located in six individuals from a New Jersey population. EVALUATION OF RANAVIRUS MAJOR CAPSID PROTEIN MUTATIONS 3 MONTCLAIR STATE UNIVERSITY Evaluation of Ranavirus Major Capsid Protein Gene Sequence Mutations in United States East Coast Frog and Tadpole Populations by
F, G, K, M SPECTRAL STANDARDS IN THE Y BAND (0.95–1.11 μm)

We take advantage of good atmospheric transparency and the availability of high-quality instrumentation in the 1 μm near-infrared atmospheric window to present a grid of F, G, K, and M spectral standards observed at high spectral resolution (R ≈ 25, 000). In addition to a spectral atlas, we present a catalog of atomic line absorption features in the 0.95–1.11 μm range. The catalog includes a wide range of line excitation potentials, from 0–13 eV, arising from neutral and singly ionized species, most frequently those of Fe i and Ti i at low excitation, Cr i, Fe i, and Si i at moderate excitation, and C i, S i, and Si i having relatively high excitation. The spectra also include several prominent molecular bands from CN and FeH. For the atomic species, we analyze trends in the excitation potential, line depth, and equivalent width across the grid of spectroscopic standards to identify temperature and surface gravity diagnostics near 1 μm. We identify the line ratios that appear especially useful for spectral typing as those involving Ti i and C i or S i, which are temperature sensitive in opposite directions, and Sr ii, which is gravity sensitive at all spectral types. ASCII versions of all spectra are available in the online version of the journal.
Open Research Online Phylogenetic and ecological correlates of pollen morphological diversity in a Neotropical rainforest Journal Item

Morphology varies enormously across clades, and the morphology of a trait may reflect ecological function or the retention of ancestral features. We examine the tension between ecological and phylogenetic correlates of morphological diversity through a case study of pollen grains produced by angiosperms in Barro Colorado Island, Panama (BCI). Using a molecular phylogeny of 730 taxa, we demonstrate a statistically significant association between morphological and genetic distance for these plants. However, the relationship is non-linear, and while close relatives share more morphological features than distant relatives, above a genetic distance of ~ 0.7 increasingly distant relatives are not more divergent in phenotype. The pollen grains of biotically pollinated and abiotically pollinated plants overlap in morphological space, but certain pollen morphotypes and individual morphological traits are unique to these pollination ecologies. Our data show that the pollen grains of biotically pollinated plants are significantly more morphologically diverse than those of abiotically pollinated plants. Abstract in Spanish is available with online material. for in the morphological diversity of each pollination group—abiotic, biotic—using pairwise Wilcoxon rank sum tests, which are non-parametric and computed using wilcox.test(x, y)
Pulse-Field Analysis Diversity of Extended Spectrum Beta Lactamases Producing Gram Negative Bacteria Isolated from Periplaneta americana (Cockroaches)

Extended spectrum beta lactamase (ESBL) producing bacteria are organisms of public health significance that have been implicated in prolonged hospital stay, treatment failures and higher fatalities. These organisms were originally thought to be widely distributed in hospital, but have since grown in terms of their epidemiological coverage. This study was therefore aimed at using pulse-field gel electrophoresis (PFGE) to understand the diversity of ESBL producing organisms originating from cockroaches in Ago-Iwoye, Nigeria. The diversity was determined by using a set of twenty six (26) ESBL producing bacterial strains isolated from cockroaches sampled in Ago-Iwoye community, Ogun State, Nigeria. PFGE analysis revealed three pulsotypes (distinct profile) with no distinct isolates present on a pulsotype. It was however observed that no pulsotype had less than two (2) isolates in any case, while isolates from different communities displayed identical profiles. In conclusion, clonal distributions of ESBL producing organisms on cockroaches are without bias to specimens and/or the community sampled. Keywords: ESBL; Gram negative bacteria; PFGE; Diversity;
Roadkill Encounters and Affective Solidarity: Exploring Multispecies Fellowship through Disgust, Pain, and Mourning

This article examines visual images of roadkill and the bodily affects they invoke. Exploring specifically the affects of grief, disgust, and pain, I suggest they are important modalities in the act of mourning the unmourned, changing the perception of roadkill as merely collateral damage. I explore encounters with roadkill through an analysis of photographs by Steve Baker (2011) which capture animals’ corpses on country lanes in the UK. Drawing on a multidisciplinary apparatus, I utilise various tools from affect theory and photography in social and cultural studies. I demonstrate how affective encounters offer an intervention into the prevalent unconcern and indifference to nonhuman suffering and ecological damage – a dynamic of address and rejection that enables possibilities of solidarity and creaturely fellowship.
Milk-Gelling Properties of Proteases Extracted from the Fruits of Solanum Elaeagnifolium Cavanilles

There is little information on the milk coagulation process by plant proteases combined with chymosins. This work is aimed at studying the capability of protease enclosed in the ripe fruits of Solanum elaeagnifolium (commonly named trompillo) to form milk gels by itself and in combination with chymosin. For this purpose, proteases were partially purified from trompillo fruits. These proteases had a molecular weight of ~60 kDa, and results suggest cucumisin-like serine proteases, though further studies are needed to confirm this observation. Unlike chymosins, trompillo proteases had high proteolytic activity (PA = 50.23 UTyr mg protein−1) and low milk-clotting activity (MCA = 3658.86 SU mL−1). Consequently, the ratio of MCA/PA was lower in trompillo proteases (6.83) than in chymosins (187 to 223). Our result also showed that milk gels formed with trompillo proteases were softer (7.03 mPa s) and had a higher release of whey (31.08%) than the milk gels clotted with chymosin (~10 mPa s and ~4% of syneresis). However, the combination of trompillo proteases with chymosin sped up the gelling process (21 min), improved the firmness of milk gels (12 mPa s), and decreased the whey release from milk curds (3.41%). Therefore, trompillo proteases could be combined with chymosin to improve the cheese yield and change certain cheese features.
Working Memory Capacity, Cognitive Regulation, and Their Relationship to Academic Achievement in University Students

The present study investigates the relationship between working memory capacity, cognitive regulation, and academic achievement for university students. Additionally, it examines whether working memory capacity and/or cognitive regulation can predict academic achievement. For the 139 university students who took part in the study, working memory capacity was measured via a digit span test, cognitive regulation was measured via the MAI (Metacognitive Awareness Inventory), and academic achievement was measured via GPA. The results indicate that there is a significant relationship between working memory capacity and cognitive regulation ability, that cognitive regulation had a marginally stronger correlation with GPA than working memory capacity did, and that the working memory ability and cognitive regulation model was a good predictor of academic achievement for the sample studied.
The more experienced, the better prepared? New evidence on the relation between teachers' experience and their readiness for online teaching and learning

In the present study, we tested the common assumption that teachers with more experience consider themselves better prepared for online teaching and learning (OTL). Utilizing an international data set of 731 teachers in higher education at the beginning of the COVID-19 pandemic, we performed structural equation and network modeling to quantify the experience-readiness relationship. In contrast to the linearity assumption “the more experienced, the better prepared”, we found robust evidence for a curvilinear relationship. Teachers’ readiness for OTL increased first and then decreased with more experience—this applied especially to the self-efficacy dimension of readiness. Further analyses suggested that the experience-readiness relationship does not only exist at the level of aggregated constructs but also at the level of indicators, that is, specific areas of knowledge, teaching, and support. We argue that both novice and experienced teachers in higher education could benefit from experience-appropriate, pedagogical, and content-related support programs for OTL.
Seismic imaging and inversion based on spectral-element and adjoint methods

One of the most important topics in seismology is to construct detailed tomographic images beneath the surface, which can be interpreted geologically and geochemically to understand geodynamic processes happening in the interior of the Earth. Classically, these images are usually produced based upon linearized traveltime anomalies involving several particular seismic phases, whereas nonlinear inversion fitting synthetic seismograms and recorded signals based upon the adjoint method becomes more and more favorable. The adjoint tomography, also referred to as waveform inversion, is advantageous over classical techniques in several aspects, such as better resolution, while it also has several drawbacks, e.g., slow convergence and lack of quantitative resolution analysis. In this dissertation, we focus on solving these remaining issues in adjoint tomography, from a theoretical perspective and based upon synthetic examples. To make the thesis complete by itself and easy to follow, we start from development of the spectral-element method, a wave equation solver that enables access to accurate synthetic seismograms for an arbitrary Earth model, and the adjoint method, which provides Frechet derivatives, also named as sensitivity kernels, of a given misfit function. Then, the sensitivity kernels for waveform misfit functions are illustrated, using examples from exploration seismology, in other words, for migration purposes. Next, we show step by step how these gradient derivatives may be utilized in minimizing the misfit function, which leads to iterative refinements on the Earth model. Strategies needed to speed up the inversion, ensure convergence and improve resolution, e.g., preconditioning, quasi-Newton methods, multi-scale measurements and combination of traveltime and waveform misfit functions, are discussed. Through comparisons between the adjoint tomography and classical tomography, we address the resolution issue by calculating the point-spread function, the action of the Hessian on an arbitrarily-chosen model perturbation, and the resolution function, the action of the resolution matrix on the arbitrarily-chosen model perturbation. Inner products between the two functions and the chosen model perturbation (properly normalized) are two scalars – the point-spread parameter and the resolution parameter. The two functions serve as trade-off maps between the chosen model perturbation and all other model parameters, whereas the two parameters indicate whether the chosen model perturbation is well resolved in the inversion. While the point-spread function and the point-spread parameter work in relative sense, the resolution function and the resolution parameter are absolute quantities, regardless of the misfit function used in the inversion. Besides the optimization point of view, we also treat inverse problems from Tarantola's perspective – the Bayesian inference, where each Earth model is associated with certain probability, preferably obeying multivariate normal distribution by choosing Cartesian model…
Prosocial intentions towards religious ingroup and outgroup members among adolescents from public and religious schools

Prosocial behaviour is a very important component in harmonious social relationships, especially within a diverse community such as Indonesia. Public and religion-based schools provide different opportunities for students in terms of interaction with peers from different religions, and in turn may affect attitudes toward ingroup and outgroup religious members. This study compared prosocial intentions towards religion-based ingroup and outgroup peer members in adolescents from heterogeneous (public) schools and homogenous (Islamic) schools. Participants were 220 Muslim middle school students aged 11-15 years, who attended public schools (N= 130; M=48, F=82) and religious schools (N= 90; M=46, F=44). They were recruited through snowball sampling and convenience sampling. This research is a quasi-experimental study, by using the Scenario-based Prosocial Intention Questionnaire (SBPIQ) to measure prosocial intentions, which was modified to include manipulations on the targets of prosocial intention. Two-way mixed ANOVA results showed that the level of prosocial intention was highest toward the ingroup target (M=3,411; SD=0,392), followed by those toward the outgroup (M=3,357; SD=0,403) and neutral targets (M=3,234; SD=0,411). Furthermore, prosocial intentions towards ingroup, outgroup, and neutral targets were all higher in students from public schools. These results implied that there were biases in students’ prosocial behaviors toward ingroup/outgroup religious members. It is crucial for both public and Islamic schools to facilitate positive interactions with members of other religious group in order to overcome these biases.
Estimation Variance is not Model Structure Independent

This paper establishes that when using a least squares criterion to estimate an output error type model structure, then the measurement noise induced variability of the frequency response estimate depends on the estimated (and hence also on the true) pole positions. This dependence on pole position is perhaps counter to prevailing wisdom that for any ‘shift invariant’ model structure, the variability depends only on model order, data length, and input and noise spectral densities. That is, it is counter to the belief that variance error is model-structure independent.