Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic Characteristics and Selection Signatures in Indigenous Chongming White Goat (Capra hircus)

The Chongming white goat (CM) is an indigenous goat breed exhibits unique traits that are adapted to the local environment and artificial selection. By performing whole-genome re-sequencing, we generated 14–20× coverage sequences from 10 domestic goat breeds to explore the genomic characteristics and selection signatures of the CM breed. We identified a total of 23,508,551 single-nucleotide polymorphisms (SNPs) and 2,830,800 insertion–deletion mutations (indels) after read mapping and variant calling. We further specifically identified 1.2% SNPs (271,713) and 0.9% indels (24,843) unique to the CM breed in comparison with the other nine goat breeds. Missense (SIFT < 0.05), frameshift, splice-site, start-loss, stop-loss, and stop-gain variants were identified in 183 protein-coding genes of the CM breed. Of the 183, 36 genes, including AP4E1, FSHR, COL11A2, and DYSF, are involved in phenotype ontology terms related to the nervous system, short stature, and skeletal muscle morphology. Moreover, based on genome-wide FST and pooled heterozygosity (Hp) calculation, we further identified selection signature genes between the CM and the other nine goat breeds. These genes are significantly associated with the nervous system (C2CD3, DNAJB13, UCP2, ZMYND11, CEP126, SCAPER, and TSHR), growth (UCP2, UCP3, TSHR, FGFR1, ERLIN2, and ZNF703), and coat color (KITLG, ASIP, AHCY, RALY, and MC1R). Our results suggest that the CM breed may be differentiated from other goat breeds in terms of nervous system owing to natural or artificial selection. The whole-genome analysis provides an improved understanding of genetic diversity and trait exploration for this indigenous goat breed.
MR-Guided Drug Release From Liposomes Triggered by Thermal and Mechanical Ultrasound-Induced Effects

One of the most challenging tasks of the cancer research is the enhancement of the amount of the chemotherapeutic agent that can reach the target site. To achieve this goal, nanovectors capable of encapsulating the drug and releasing it following a specific stimulus have been developed. In light of this, a key point is the necessity to monitor the effective drug release through a safe and highly performing imaging technology such as Magnetic Resonance Imaging (MRI). Liposomes are highly biocompatible nanovesicles that consist of bilayered phospholipid-based membrane encompassing an aqueous core. Almost 20 drug-loaded liposomes are currently approved for clinical use in USA and EU countries. If a liposomal nanomedicine is loaded with an MRI agent whose contrast is sensitive to the microenvironment and with a release kinetics similar to the co-transported drug, the system can act as an imaging reporter of drug release. This Perspective will offer a critical and brief overview of using MRI not only to verify and monitor the release process but also as a valuable tool to predict the therapeutic outcome. In particular, it will be presented representatives preclinical studies illustrating the in vivo potential of MRI-guided drug release protocols triggered by thermal and mechanical ultrasound-induced effects. Considering the therapeutic advantages of this approach, the possible benefits in reducing the side effects and the good results reported at preclinical level, there is a reasonable hope that the near future could witness the entrance in clinical routine of MRI-guided procedures supporting ultrasound-induced drug release protocols.
Effectiveness and Cost-Effectiveness of Internet-Based Cognitive Behavioral Therapy for Insomnia in Clinical Settings

Background Internet-delivered cognitive-behavior treatment for insomnia (iCBT-I) has the potential to fill the gap created by the discrepancy between insomnia cases and number of trained professionals. Although the effectiveness of this method was proven in multiple studies conducted in research settings, its feasibility in routine care is still unclear. Predictors, mediators, and moderators of treatment effect remain uncertain since previous studies often give contradictory results. The present study aims to investigate clinical effectiveness and cost-effectiveness of an internet-based CBT-I program Sleepsy in comparison with care as usual (CAU) among patients with CI recruited from clinical settings. Baseline data will be further analyzed to find predictors of treatment outcome. Methods/Design The proposed study is a parallel-group randomized controlled trial comparing CAU plus iCBT-I with CAU in a clinical setting. One hundred ten participants will be referred from the medical doctors in Moscow. Both groups will have access to CAU, which corresponds to the treatment prescribed by the referring doctor. Patients of the first group will additionally get access to the iCBT-I program with the opportunity to contact a specialist (guidance on request) in a secured environment. The primary outcome is insomnia severity change from pre- to post-treatment. Secondary outcomes include change of subjective sleep characteristics, life quality, fatigue, daytime sleepiness, comorbid affective disorders, dysfunctional beliefs about sleep, sleep hygiene, healthcare consumption, productivity losses, and longer term outcomes at 3 months follow-up. Predictor analysis will include baseline scores of the aforementioned outcomes along with treatment expectancies and personality traits. Discussion The proposed study is one of the first studies evaluating whether iCBT-I also works in routine care. We expect that recruitment of the participants let us determine the target group more precisely and exclude health problems interfering with treatment. Using CAU as control condition may result in a loss of power to detect a meaningful difference. Nevertheless, this approach is reasonable since it reconstructs the clinical situation faced by practicing doctors.
Urinary Cortisol Increases During a Respiratory Outbreak in Wild Chimpanzees

Abstract: In mammals, the excretion of cortisol can provide energy toward restoring homeostasis and is a major component of the stress response. However, chronically elevated cortisol levels also have suppressive effects on immune function. As mounting an immune response is energetically costly, sick individuals may conserve energy by exhibiting certain sickness behaviors, such as declining activity levels. Due to the complex interplay between immune function and sickness behaviors, endocrinological correlates have received growing attention in the medical community, but so far, this subject was investigated rarely. Furthermore, given the complexities of studying illnesses and immunity in natural settings, correlates of sickness behaviors have yet to be studied in non-human primates in the wild. Methods: We measured urinary cortisol levels using liquid chromatography–mass spectrometry in a group of wild habituated chimpanzees in Taï National Park, Côte d'Ivoire, before, during, and after a respiratory disease outbreak (main causative pathogen: human respiratory syncytial virus A, with coinfections of Streptococcus pneumoniae). Changes in cortisol levels were then related to urinary neopterin levels, a biomarker of immune system activation. Results: Urinary cortisol levels were found to be more than 10-fold higher during the outbreak in comparison with levels before and after the outbreak period. Increasing cortisol levels were also associated with increasing neopterin levels. Interestingly, rather atypical patterns in a diurnal decline of cortisol levels were found during infection periods, such that levels remained raised throughout the day. Conclusion: In conclusion, cortisol increase was related to cellular immune response. Our results suggest that cortisol is a mediator of infectious disease pathogenicity through its impact on the immune system and that wild chimpanzees may be facing energetic stress when sick. By monitoring immune challenges in wild-living animals, our study demonstrates that immune defenses have costs and that these costs are context-specific.
Chloroflexi Dominate the Deep-Sea Golf Ball Sponges Craniella zetlandica and Craniella infrequens Throughout Different Life Stages

Deep-sea sponge grounds are underexplored ecosystems that provide numerous goods and services to the functioning of the deep-sea. This study assessed the prokaryotic diversity in embryos, recruits, and adults of Craniella zetlandica and Craniella infrequens, common and abundant representatives of deep-sea sponge grounds in the North Atlantic. Our results reveal that symbiont transmission in the two Craniella sponge species likely occurs vertically, as highly similar microbial consortia have been identified in adults, embryos, and recruits. Moreover, transmission electron microscopy revealed high abundances of sponge-associated microorganisms, among which Chloroflexi (SAR202) were identified as common representatives by amplicon sequencing and fluorescence in situ hybridization (FISH). Equal diversity metrices, a similar overall prokaryotic community composition and a distinct dominance of the phylum Chloroflexi within all life stages are the key findings of our analyses. Information such as presented here provide understanding on the recruitment of deep-sea sponge holobionts which is needed to develop integrated management tools of such vulnerable marine ecosystems.
Population Structure and Biomass Allocation of the Naturalized Shrub Lonicera maackii (Rupr.) Maxim. in Forest and Open Habitats

Open-grown populations of Lonicera maackii (Rupr.) Maxim. in north- ern Kentucky had significantly (P? 0.05) higher aboveground net primary produc- tion (NPP) per stem and per shrub, and a significantly (P ? 0.05) higher percentage of aboveground biomass in leaves than forest-grown populations. The contribution of current (young-of-the-year) stems to aboveground NPP was significantly (P ? 0.05) higher in forest-grown populations. Stem demography was habitat-specific. Open-grown populations were character- ized by unimodal ageand size-class distributions, low stem recruitment and low stem mortality. Forest-grown populations were characterized by right-skewed, bimo- dal, unimodal and random ageand size-class distributions, high stem recruitment and high mortality of small stems. In open-grown populations, intragenet regulation of basal stem sprouting after 3- 5 years assures that future NPP will be allocated primarily to residual (> 1 year old) stems. In forest-grown populations, continued production of current basal stems means that the subcanopy environment is annually tested for changes in resource availability. The results suggest that future NPP in forest-grown populations will be allocated to a mixture of current and residual basal stems.
DETECTION OF HBLA AND BAL GENES IN BACILLUS CEREUS ISOLATES FROM CHEESE SAMPLES USING THE POLYMERASE CHAIN REACTION

Background: Bacillus cereus is a Gram-positive spore-forming bacterium, which causes food poisoning. Spores enable the persistence of B. cereus in the environment, and B. cereus strains can tolerate adverse environmental conditions, such as temperature and insufficient nutrients. B. cereus causes food poisoning via the production of two enterotoxins. Most isolates produce toxins leading to diarrhea (enterotoxins) and vomiting (emetic forms). Diarrhea is caused by the production of three different heat-labile enterotoxins: HBL, NHE, and cytotoxin K. A heat-stable toxin, cereulide, is responsible for emesis. Objectives: This study aimed to detect enterotoxigenic B. cereus isolates in cheese samples using the polymerase chain reaction (PCR). Materials and Methods: Two-hundred pasteurized (n = 100) and nonpasteurized (n = 100) cheese samples were collected. The initial isolation was performed on PEMBA specific medium. Antibiotic susceptibility testing was performed using several antibiotic disks, according to the guidelines of the Clinical Laboratory and Standards Institute. Specific primers amplifying the hblA enterotoxinencoding gene and bal hemolysin-encoding gene were used for the molecular detection of the toxins. Results: Ten samples were positive for the presence of B. cereus, with both Gram staining and biochemical reactions. All the isolates were resistant to penicillin and ampicillin but susceptible to vancomycin, erythromycin, and ciprofloxacin. Six and three isolates were resistant to tetracycline and trimethoprim-sulfamethoxazole, respectively. The hblA and bal genes were amplified in all the B. cereus isolates. Conclusions: The prevalence of B. cereus among the cheese samples was low. All the isolates were positive for genes encoding the hblA enterotoxin and bal toxin.
Specific protein interactions with the 5’- and 3’-untranslated regions of coxsackievirus B3 RNA

In recent years, studies of the molecular pathogenesis of coxsackievirus B3 (CVB3) have revealed that the viral 5' and 3' untranslated regions (UTRs) contain determinants of viral tissue tropism, translation efficiency, and cardiovirulence. However, the mechanism that links the UTRs to these phenotypic observations remains unknown. Thus, the study of protein-UTR interactions is important to understand the underlying mechanism of functions mediated by the CVB3 UTRs. My dissertation addresses this subject by the identification and characterization of cellular proteins that bind to the CVB3 UTRs. To achieve these goals, I sub-cloned the CVB3 5' and 3'-UTR by a PCR-based strategy. The 5'-UTR sequences of nt 1-209, 210-529 and 530-630 were cloned in consideration of their respective structural and functional significance. At the same time, the 3'-UTR wild type sequence of nt 7299-7399 [+ poly(A) tail] and five mutated 3'UTR clones were generated. Mutations in these 3'-UTR clones were previously reported to cause tertiary (but not secondary) structural changes in the 3'-UTR, leading to specific inhibition of viral replication. By using radiolabeled RNA transcripts of these UTR sequences in gel mobility shift and competitive UV cross-linking assays, fifteen specific CVB3 5'-UTR-binding proteins in the HeLa cell were identified. The molecular weight of six important 5'-UTRbinding proteins resembled those of the eukaryotic translation initiation factors (eIF4A, 4B, 4G), the death associated protein-5, La autoantigen and the polypyrimidine tract binding proteins. Using the same method, protein interactions with the 3'-UTR and its various mutants were also investigated. Two small proteins (22 and 24 kDa) that bound specifically to the mutated 3'UTRs were observed. As these corresponding mutations were previously shown to inhibit viral replication, a functional role of these two protein-3'-UTR interactions was inferred. Also, the poly(A) tail of the 3'-UTR was found to be important in mediating HeLa cell protein
Génétique des populations

La genetique des populations s'enseigne dans de nombreuses formations universitaires, scientifiques et medicales. Ce livre presente les principaux concepts comme l'equilibre de Hardy-Weinberg, la consanguinite, la derive genetique, la selection ou l'effet des mutations. Le principe et la realisation des tests statistiques sont rappeles. L'ensemble est illustre par une trentaine d'exemples et d'exercices corriges.
National park entrance fee increase: a conceptual framework

Abstract With decreasing appropriation from public funding and increasing operational costs, public nature-tourism managers are facing ongoing pressure to increase self-generated revenue, such as entrance fees to sustain current services. However, raising fees often arouses resistance from visitors, and thus managing negative reactions is critical to the success of a new fee initiative. Following a three-step process of rendering conceptual relationships from textual data, this study analyzed a large volume of public comments submitted regarding the National Park Service’s entrance fee increase proposal and developed a conceptual framework to understand support/opposition of fee increases on public lands. The conceptual framework identified five constructs affecting support/opposition of fee increases: right-based opposition to public land fees, distributive justice principles, fee increase magnitude, place attachment, and trust in government. Theoretical and practical implications were also discussed.
Evaluation of the Phosphorus Provided by Animal Proteins in the Diet of Broiler Chickens

Abstract This study attempted to determine the biological availability of phosphorus in a chick feeding trial. Researchers compared the phosphorus in six samples of poultry byproduct meal and eleven samples of meat and bone meal to a feed-grade mono-dicalcium phosphate. The samples were analyzed to determine moisture, crude protein, fat, ash, crude fiber, calcium, phosphorus, and amino acid content; metabolizable energy was calculated from proximate composition. Diets had adequate but not excessive amounts of all essential nutrients. “Summit” diets containing 0.447% nonphytate phosphorus (NPP) used each of the animal protein sources or the mono-dicalcium phosphorus as the sole source of supplemental phosphorus; these were then blended with a low-phosphorus (0.12% NPP) basal to provide a range on NPP levels. These data indicate no significant difference in relative biological availability of phosphorus in any of the animal protein sources vs. the feed grade mono-dicalcium phosphorus.
Testing the Stationarity Assumption in Software Effort Estimation Datasets

Software effort estimation (SEE) models are typically developed based on an underlying assumption that all data points are equally relevant to the prediction of effort for future projects. The dynamic nature of several aspects of the software engineering process could mean that this assumption does not hold in at least some cases. This study employs three kernel estimator functions to test the stationarity assumption in three software engineering datasets that have been used in the construction of software effort estimation models. The kernel estimators are used in the generation of non-uniform weights which are subsequently employed in weighted linear regression modeling. Prediction errors are compared to those obtained from uniform models. Our results indicate that, for datasets that exhibit underlying non-stationary processes, uniform models are more accurate than non-uniform models. In contrast, the accuracy of uniform and non-uniform models for datasets that exhibited stationary processes was essentially equivalent. The results of our study also confirm prior findings that the accuracy of effort estimation models is independent of the type of kernel estimator function used in model development.
Activated carbon from longan seed: its activation model and adsorption of water vapor and benzene

THAI). I ABSTRACT (ENGLISH) . III ACKNOWLEDGEMENTS . V TABLE OF CONTENTS. VII LIST OF TABLES . XV LIST OF FIGURES. XVIII SYMBOLS AND ABBREVIATIONS . XXVI CHAPTER
Racism and media, in a moment of crisis and opportunity

ABSTRACT This article provides the author's reply to the four book responses by Dreher, Georgiou, James and Saha. The discussion focuses on how their analytical engagement with the book's treatment of the ambivalences of digital media culture raise pertinent questions for focusing on anti-racism in media work and practices. It does so while reflecting on the extraordinary conditions of antiracist protest and revolt during which it was written in June 2020.
Volunteer tourism (VT) traveler behavior: merging norm activation model and theory of planned behavior

Abstract While volunteer tourism has been gaining in popularity around the world, few studies have looked into the travelers’ re-participation intention within a pro-social context. This study aimed to develop and test a new conceptual framework that explains the volunteer travelers’ behavioral intention formation in the context of a pro-social activity. It employed three theories, which include the norm activation model, the theory of planned behavior, and the personal values, as a theoretical basis that considers the altruistic and egoistic aspects of the travelers’ psychological response to volunteer tourism. A total of 375 quantitative surveys were obtained from Korean travelers who voluntarily completed a non-profit global volunteer tourism program during the spring in 2019. Using a structural equation modelling analysis, the study’s results verified that the proposed model connecting the personal values, the norm activation model, and the theory of planned behavior was a satisfactory predictive model that explains the travelers’ re-participation intention in volunteer tourism. Additionally, subjective well-being was found to be a significant moderator between the re-participation intention and its predictors. The study sheds light on the role of personal and social factors in volunteer tourism.
Application research development of plastein reaction

The plastein reaction, a reversal of enzymatic proteolysis, was applied to prepare a higher-molecular, protein-like substance in which the amino acids supplemented were held in a state of peptide bonding. Although the reaction was described 100 years ago, the reaction mechanism was still relatively unkown. Its application development prospects were discussed.
Time-Aware Models for Software Effort Estimation

It seems logical to assert that the dynamic nature of software engineering practice would mean that software effort estimation (SEE) modelling should take into account project start and completion dates. That is, we should build models for future projects based only on data from completed projects; and we should prefer data from recent similar projects over data from older similar projects. Research in SEE modelling generally ignores these recommendations. In this study two different model development approaches that take project timing into account are applied to two publicly available datasets and the outcomes are compared to those drawn from three baseline (non-time-aware) models. Our results indicate: that it is feasible to build accurate effort estimation models using project timing information; that the models differ from those built without considering time, in terms of the parameters included and their weightings; and that there is no statistical significance difference as to which of the two model building approaches is superior in terms of accuracy.
Detecting and Modeling Method-level Hotspots in Architecture Design Flaws

—In large-scale software systems, the majority of change-prone ﬁles are usually architecturally connected, and their architectural connections often exhibit design ﬂaws, which propagate change-proneness among ﬁles and increase maintenance costs. Complementary to the identiﬁcation and deﬁnition of the ﬁles involved architecture design ﬂaws, the automatic detection at the method level is important for developers to understand ﬁne-grained contributors to the architecture ﬂaws that have incurred high maintenance costs. In this paper, we propose an approach to identify method-level hotspots. Each hotspot contains a group of evolutionarily connected methods or attributes that participate in architecture design ﬂaws and continuously accumulate maintenance difﬁculties. Our investigations on six large-scale projects show that the attributes or methods captured in method-level hotspots are more change-prone than the others. The results also show that the growth trend of the maintenance effort spent on each method-level hotspot could be modeled and monitored by our approach, which sheds light in the decision of design refactoring.