Miracle-dz/UniFAR-FTUs huggingface dataset:
Metabolic fate of endogenous molecular damage: Urinary glutathione conjugates of DNA-derived base propenals as markers of inflammation

Significance Endogenous DNA damage is mechanistically linked to inflammation and cancer, yet the multitude of DNA damage products have not emerged as significant biomarkers partly due to poor understanding of their metabolic fate following formation in tissues. Using a systematic approach of metabolite profiling, we identified 15 candidate metabolites of a common DNA lesion, thymine propenal (Tp), of which three and seven compounds were found in the urine and bile, respectively, of Tp-treated rats. Only one metabolite, a bis-mercapturate derivative, was observed in urine from untreated rats and increased approximately three- to fourfold upon treatment with toxicants producing oxidative stress and DNA oxidation. This metabolite thus represents a strong biomarker candidate for inflammation and oxidative stress. Although mechanistically linked to disease, cellular molecules damaged by endogenous processes have not emerged as significant biomarkers of inflammation and disease risk, due in part to poor understanding of their pharmacokinetic fate from tissue to excretion. Here, we use systematic metabolite profiling to define the fate of a common DNA oxidation product, base propenals, to discover such a biomarker. Based on known chemical reactivity and metabolism in liver cell extracts, 15 candidate metabolites were identified for liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) quantification in urine and bile of rats treated with thymine propenal (Tp). Analysis of urine revealed three metabolites (6% of Tp dose): thymine propenoate and two mercapturate derivatives of glutathione conjugates. Bile contained an additional four metabolites (22% of Tp dose): cysteinylglycine and cysteine derivatives of glutathione adducts. A bis-mercapturate was observed in urine of untreated rats and increased approximately three- to fourfold following CCl4-induced oxidative stress or treatment with the DNA-cleaving antitumor agent, bleomycin. Systematic metabolite profiling thus provides evidence for a metabolized DNA damage product as a candidate biomarker of inflammation and oxidative stress in humans.
The composition of milk from free‐living common marmosets (Callithrix jacchus) in Brazil

Common marmosets, one of the smallest anthropoid primates, have a relatively high reproductive rate, capable of producing twins or triplets twice per year. Growth and development of infants is relatively rapid, and lactation is relatively short at less than 3 months. Although mean values for the proximate composition (dry matter, protein, fat and sugar) of captive common marmoset milks fall within anthropoid norms, composition is highly variable among individual samples, with concentrations of milk fat ranging from below 1 to over 10%. To examine the extent to which this variation might be a consequence of captive conditions, we collected milk samples from wild common marmosets freely living on a farm in the state of Rio de Janeiro, Brazil. The proximate composition of the milk samples was assayed using identical techniques as used for the captive marmoset milks. The composition of the milk of wild common marmosets was also variable, but tended to be lower in dry matter, fat, protein and gross energy, and higher in sugar than milks from captive animals. Interestingly, the percentage of estimated gross energy from the protein fraction of the milks was relatively constant in both wild and captive marmosets and did not differ between wild and captive animals: 1 kcal of common marmoset milk contains on average (±SEM) 0.035±. 001 g of protein regardless of the gross energy content of the milk or whether the milk was from a wild or captive animal. In contrast, in 1 kcal of low‐energy milks, the amount of sugar was significantly higher and the amount of fat significantly lower than in 1 kcal of high‐energy milks. Thus, common marmoset milk exhibits axes of variability (especially fat concentration) as well as a significant stability in the relative amount of protein. Am. J. Primatol. 70:78–83, 2008. © 2007 Wiley‐Liss, Inc.
New Evidence on Conditional Factor Models

We estimate conditional multifactor models over a large cross section of stock returns matching 25 CAPM anomalies. Using conditioning information associated with different instruments improves the performance of the Hou, Xue, and Zhang (HXZ) (2015) and Fama and French (FF) (2015), (2016) models. The largest increase in performance holds for momentum, investment, and intangibles-based anomalies. Yet, there are significant differences in the performance of scaled models: HXZ clearly dominates FF in explaining momentum and profitability anomalies, while the converse holds for value–growth anomalies. Thus, the asset pricing implications of alternative investment and profitability factors (in a conditional setting) differ in a nontrivial way.
Time-Varying Effective Connectivity during Visual Object Naming as a Function of Semantic Demands

Accumulating evidence suggests that visual object understanding involves a rapid feedforward sweep, after which subsequent recurrent interactions are necessary. The extent to which recurrence plays a critical role in object processing remains to be determined. Recent studies have demonstrated that recurrent processing is modulated by increasing semantic demands. Differentially from previous studies, we used dynamic causal modeling to model neural activity recorded with magnetoencephalography while 14 healthy humans named two sets of visual objects that differed in the degree of semantic accessing demands, operationalized in terms of the values of basic psycholinguistic variables associated with the presented objects (age of acquisition, frequency, and familiarity). This approach allowed us to estimate the directionality of the causal interactions among brain regions and their associated connectivity strengths. Furthermore, to understand the dynamic nature of connectivity (i.e., the chronnectome; Calhoun et al., 2014) we explored the time-dependent changes of effective connectivity during a period (200–400 ms) where adding semantic-feature information improves modeling and classifying visual objects, at 50 ms increments. First, we observed a graded involvement of backward connections, that became active beyond 200 ms. Second, we found that semantic demands caused a suppressive effect in the backward connection from inferior frontal cortex (IFC) to occipitotemporal cortex over time. These results complement those from previous studies underscoring the role of IFC as a common source of top-down modulation, which drives recurrent interactions with more posterior regions during visual object recognition. Crucially, our study revealed the inhibitory modulation of this interaction in situations that place greater demands on the conceptual system.
Transient and Sustained Bacterial Adaptation following Repeated Sublethal Exposure to Microbicides and a Novel Human Antimicrobial Peptide

ABSTRACT Microbicides (biocides) play an important role in the prevention and treatment of infections. While there is currently little evidence for in-use treatment failures attributable to acquired reductions in microbicide susceptibility, the susceptibility of some bacteria can be reduced by sublethal laboratory exposure to certain agents. In this investigation, a range of environmental bacterial isolates (11 genera, 18 species) were repeatedly exposed to four microbicides (cetrimide, chlorhexidine, polyhexamethylene biguanide [PHMB], and triclosan) and a cationic apolipoprotein E-derived antimicrobial peptide (apoEdpL-W) using a previously validated exposure system. Susceptibilities (MICs and minimum bactericidal concentrations [MBCs]) were determined before and after 10 passages (P10) in the presence of an antimicrobial and then after a further 10 passages without an antimicrobial to determine the stability of any adaptations. Bacteria exhibiting >4-fold increases in MBCs were further examined for alterations in biofilm-forming ability. Following microbicide exposure, ≥4-fold decreases in susceptibility (MIC or MBC) occurred for cetrimide (5/18 bacteria), apoEdpL-W (7/18), chlorhexidine (8/18), PHMB (8/18), and triclosan (11/18). Of the 34 ≥4-fold increases in the MICs, 15 were fully reversible, 13 were partially reversible, and 6 were nonreversible. Of the 26 ≥4-fold increases in the MBCs, 7 were fully reversible, 14 were partially reversible, and 5 were nonreversible. Significant decreases in biofilm formation in P10 strains occurred for apoEdpL-W (1/18 bacteria), chlorhexidine (1/18), and triclosan (2/18), while significant increases occurred for apoEdpL-W (1/18), triclosan (1/18), and chlorhexidine (2/18). These data indicate that the stability of induced changes in microbicide susceptibility varies but may be sustained for some combinations of a bacterium and a microbicide.
A radiosensitivity gene signature in predicting glioma prognostic via EMT pathway

A 31-gene signature derived by integrating four different microarray experiments, has been found to have a potential for predicting radiosensitivity of cancer cells, but it was seldom validated in clinical cancer samples. We proposed that the gene signature may serve as a predictive biomarker for estimating the overall survival of radiation-treated patients. The significance of gene signature was tested in two previously published datasets from Gene Expression Omnibus (GEO) and The Cancer Genome Altas (TCGA), respectively. In GEO data set, patients predicted to be radiosensitive(RS) had an improved overall survival when compared with radioresistant(RR) patients in either radiotherapy(RT)-treated or non radiotherapy(RT)-treated subgroups(p<0.0001 in the RT-treated group). Multivariate Cox regression analysis showed that the gene signature is the strongest predictor(p=0.0093) in the RT-treated subgroup of patients. However, it does not remain significant (p=0.7668) in non radiotherapy-treated group when adjusting for age and Karnofsky performance score (KPS) as covariates. Similarly, in the TCGA data set, radiotherapy-treated glioblastoma multiforme(GBM) patients assigned to RS group had an improved overall survival compared with RR group(p<0.0001). Geneset enrichment analysis(GSEA) analysis revealed that enrichment of epithelial mesenchymal transition(EMT) pathway was observed with radioresistant phenotype. These results suggest that the signature is a predictive biomarker for radiation-treated glioma patients' prognostic.
Acceptance of imagined versus experienced Virtual Reality Shopping Environments: Insights from two Experiments

As first Virtual Reality (VR) shopping environments have begun to appear on the market, the question arises whether users will adopt them for doing their shopping. However, the evaluation of systems that have not yet diffused the market is potentially challenging because it requires bringing larger samples of respondents into a VR laboratory. Therefore, by conducting two experimental studies we shed light on the research question of whether evaluating the acceptance requires that respondents experience the immersive and interactive shopping environment. Our results reveal that particularly the hedonic variable perceived enjoyment as well as the VR specific variable perceived telepresence are underestimated when participants only imagine (based on a video) being in a VR shopping environment while there is no difference with respect to the behavioral intention to use the system. In addition, we show that particularly the hedonic variable perceived enjoyment and the utilitarian variable perceived usefulness influence the intention to use the shopping environment in the future. Overall, we conclude that experiencing the VR shopping environment is essential for users to be able to evaluate the respective technology.
A macroscopic model of an aggregation experiment using embodied agents in groups of time-varying sizes

In this paper, we present a mathematical model of an aggregation experiment carried out using multiple embodied agents in teams of time-varying sizes. The aggregation experiment is concerned with the gathering and the clustering of small objects initially scattered in an enclosed arena. The number of active agents engaged in the aggregation task is varying according to a local, distributed stimulus-response law, similar to the behavior observed in ant colonies. We use a set of differential equations to describe the dynamics of the system at the macroscopic level. We validate the predictions of this model by comparing them to experimental data obtained using a sensor-based embodied simulator. Results show that the proposed approach delivers accurate predictions and constitutes a computationally efficient tool for studying aggregation experiments with groups of constant or variable sizes. The simplicity of the model suggests that it is easily applicable to other aggregation or segregation experiments characterized by different agent capabilities and individual control algorithms.
A web-based incident reporting system and multidisciplinary collaborative projects for patient safety in a Japanese hospital

Problem: When patient safety programs were mandated for Japanese health care institutions, a safety culture, a tool for collecting incident reports, an organizational arrangement for multidisciplinary collaboration, and interventional methods for improvement had to be established. Design: Observational study of effects of new patient safety programs. Setting: Osaka University Hospital, a large government-run teaching hospital. Strategy for change: A voluntary and anonymous web-based incident reporting system was introduced. For the new organizational structure a clinical risk management committee, a department of clinical quality management, and area clinical risk managers were established with their respective roles clearly defined to advance the plan-do-study-act cycle and to integrate efforts. For preventive action, alert procedures, staff education, ward rounds by peers, a system oriented approach for reducing errors, and various feedback channels were introduced. Effects of change: Continuous incident reporting by all hospital staff has been observed since the introduction of the new system. Several error inducing situations have been improved: wrong choice of drug in computer prescribing, maladministration of drugs due to a look-alike appearance or confusion about the manipulation of a medical device, and poor after hours service of the blood transfusion unit. Staff participation in educational seminars has been dramatically improved. Ward rounds have detected problematic procedures which needed to be dealt with. Lessons learnt: Patient safety programs based on a web-based incident reporting system, responsible persons, staff education, and a variety of feedback procedures can help promote a safety culture, multidisciplinary collaboration, and strong managerial leadership resulting in system oriented improvement.
CHAPTER 3 On the Law of Primacy

There exists a highly familiar phenomenon in learning and memory: first encounters with new situations, people, events, objects, and facts have greater impact on subsequent thought and behavior than later encounters of similar kinds. These "primacy effects" are well known from everyday life: the first day of school, the first romantic kiss, the graduation day, the first scientific paper accepted for publication , and many other "firsts" of the same kind are remembered vividly, and sometimes for the rest of one's life. Primacy effects have been intensely studied under the controlled conditions in the laboratory where they are ubiquitous. They are found in many kinds of memory tasks and situations as diverse as impression formation
The Power Spectrum of Supersonic Turbulence in Perseus

We test a method of estimating the power spectrum of turbulence in molecular clouds based on the comparison of power spectra of integrated intensity maps and single-velocity-channel maps, suggested by A. Lazarian and D. Pogosyan. We use synthetic 13CO data from non-LTE radiative transfer calculations based on density and velocity fields of a simulation of supersonic hydrodynamic turbulence. We find that the method yields the correct power spectrum with good accuracy. We then apply the method to the Five College Radio Astronomy Observatory 13CO map of the Perseus region, from the COMPLETE Web site. We find a power-law power spectrum with slope β = 1.81 ± 0.10. The values of β as a function of velocity resolution are also confirmed using the lower resolution map of the same region obtained with the AT&T Bell Laboratories antenna. Because of its small uncertainty, this result provides a useful constraint for numerical codes used to simulate molecular cloud turbulence.
Incidence of impacted mandibular and maxillary third molars: a radiographic study in a Southeast Iran population

Objectives: The aim of this study is to evaluate the position of impacted third molars based on the classifications of Pell & Gregory and Winter in a sample of Iranian patients. Study design: In this retrospective study, up to 1020 orthopantomograms (OPG) of the patients who were referred to the radiology clinics from October 2007 to January 2011 were evaluated. Data including the age, gender, the angulation type, width and depth of impaction were evaluated by statistical tests. Results: Among 1020 patients, 380(27.3%) were male and 640(62.7%) were female with the sex ratio was 1:1.7. Of the 1020 OPGs, 585 cases showed at least one impacted third molar, with significant difference between males (205; 35.1%) and females (380; 64.9%) (P = 0.0311). Data analysis showed that impacted third molars were 1.9 times more likely to occur in the mandible than in the maxilla (P =0.000). The most common angulation of impaction in the mandible was mesioangular impaction (48.3%) and the most common angulation of impaction in the maxilla was the vertical (45.3%). Impaction in the level IIA was the most common in both maxilla and mandible. There was no significant diffe-rence between the right and left sides in both the maxilla and the mandible. Conclusion: The pattern of third molar impaction in the southeast region of Iran is characterized by a high prevalence of impaction, especially in the mandible. Female more than male have teeth impaction. The most common angulation was the mesioangular in the mandible, and the vertical angulation in the maxilla. The most common level of impaction was the A and there was no any significant difference between the right and left sides in both jaws. Key words:Third molar, impaction, incidence, Iran.
Volatility Stylized Facts

This paper investigates a variety of features exhibited by the amplitude of stock returns. Some of these "stylized facts" have already attracted a great deal of attention from researchers, while some others have been documented only recently. - Horizontal dependence of volatility: Volatility is not constant, it is mean-reverting and it tends to cluster (meaning that high volatility is likely to be followed by high volatility periods, and vice-versa). Moreover, volatility exhibits a significant autocorrelation even for very long lags; it is therefore said to have long-memory. - Extreme events: The number of large (either positive or negative) returns is far bigger than what is expected on the basis of modern finance theory - stated differently, the returns distribution has fat tails. Moreover, shocks have a strong impact on volatility and generally lead to a number of aftershocks - this is again a feature that most financial models are unable to replicate. - The "leverage effect" (also known as the asymmetric volatility phenomenon): Volatility has a negative correlation with returns. Moreover, this relation is asymmetric: when returns are negative, volatility increases rapidly; but, when returns are positive, volatility decreases to a much lesser extent. - Vertical dependence and asymmetric vertical dependence: Volatility measured at different frequencies (e.g. intraday, daily or monthly) has different information content. Low-frequency volatility has a stronger explanatory power on subsequent high-frequency volatility than the other way around. Furthermore, an increase in volatility at low-frequencies has more impact on volatility at high-frequencies than a decrease. This paper extends the existing literature by studying all these stylized facts for both emerging and mature markets, and for both bull and bear market conditions. We are able to confirm the existence of all those stylized facts and to describe them in a more precise way than in the existing literature.
Histamine, Histamine Receptors, and their Role in Immunomodulation: An Updated Systematic Review

Histamine, a biological amine, is considered as a principle mediator of many pathological processes regulating several essential events in allergies and autoimmune diseases. It stimulates different biological activities through differen- tial expression of four types of histamine receptors (H1R, H2R, H3R and H4R) on secretion by effector cells (mast cells and basophils) through various immunological or non-immunological stimuli. Since H4R has been discovered very re- cently and there is paucity of comprehensive literature covering new histamine receptors, their antagonists/agonists, and role in immune regulation and immunomodulation, we tried to update the current aspects and fill the gap in existing litera- ture. This review will highlight the biological and pharmacological characterization of histamine, histamine receptors, their antagonists/agonists, and implications in immune regulation and immunomodulation.
Language and Identity Development Among Syrian Adult Refugees in Canada: A Bourdieusian Analysis

Framed by Bourdieu’s work, this article focuses on the intersections between language learning experiences, capital, and identities of Syrian refugees now living in Regina, Saskatchewan. In this qualitative study, data were collected during a series of focus groups with Syrian women and men. Based on the study findings, we contend that the participants’ multiple identities as hard-working, employed, independent, Muslim mothers or fathers, and wives or husbands developed in Syria were gradually eroded or altered by the realities they experienced in Canada, yet they had a strong desire to re-establish their identity constructions from back home in the new context. We assert that the loss of their linguistic capital from back home limited their employment prospects, impacted their abilities to form social relationships with native English speakers, and led to a shift in traditional gender roles. It is imperative to adapt language training programs in order to support refugees in re-establishing themselves in their professional fields and daily living activities.