Miracle-dz/UniFAR-FTUs huggingface dataset:
"Brachyspira hampsonii" associated diarrhea in pigs: virulence assessment and host-pathogen interactions

This thesis aimed to verify the causal association between "B. hampsonii" and the re-emergence of mucohaemorrhagic diarrhea in North American swine farms, to investigate the role of the intestinal microbiome as a predisposing factor for infection, to develop a porcine colon in vitro culture model and to apply this model in investigating early host-pathogen interactions. Two infection trials were conducted to determine the pathogenicity of "B. hampsonii" clade II and clade I. Weanling pigs were divided into control (n=6) and inoculated (n=12) groups. In each trial, pigs were inoculated with "B. hampsonii" clade II (tissue homogenate or pure culture) or clade I (pure culture) or sterile culture media. Animals were monitored for clinical signs of diarrhea and upon observation of bloody diarrhea they were necropsied for characterization of lesions. Fecal shedding of "B. hampsonii" was monitored throughout the trials using culture and quantitative real-time PCR. Pre and post-diarrhea fecal samples from the clade II infection trial were used to study the microbiome response to "B. hampsonii" infection and to determine if pre-inoculation microbiome composition differed between pigs that did or did not develop clinical disease. For in vitro model development, numerous factors associated with explant survivability in culture were investigated to develop a protocol for culture of porcine colon explants. The optimized model was used to study the first 12 hours of "B. hampsonii" clade II interaction with the host using a combination of histopathology and gene expression analysis. Pigs inoculated with "B. hampsonii" clade I (9/11) and clade II (9/12 and 8/12 in the tissue homogenate and pure culture experiments, respectively) developed mucohaemorrhagic diarrhea and colitis within 14 days of inoculation. In all trials, mucohaemorrhagic diarrhea was significantly more common in inoculated pigs than controls. No significant differences in richness, diversity or taxonomic composition distinguished the pre-inoculation microbiomes of affected or unaffected clade II inoculated pigs. After the development of diarrhea, the fecal microbiome of diarrheic pigs was more dense and had a had a lower Bacteroidetes:Firmicutes ratio when compared to inoculated but unaffected or control pigs. Cultured porcine colon explants displayed differentiated epithelium and crypts after 5 days in culture, while expressing GAPDH at a constant rate. For explants to thrive in vitro our results suggested the use of distal spiral colon, processed immediately after euthanasia, and cultured in an oxygen-rich gas mix with air-liquid culture interface in media containing antibiotics and antifungals. Explants exposed to "B. hampsonii" for 12 hours had a greater number of necrotic cells and thicker catarrhal exudate than control explants. Interaction of spirochaetes with the epithelium, necrotic cells and crypts was visible under optical microscopy, and a trend of increased expression of IFN-γ and e-cadherin in inoculated explants relative to control explants was…
Examination of the indirect effect of childhood emotional trauma on internalizing symptoms through distress intolerance

Abstract Objectives Extant studies document a prospective link between early childhood trauma and internalizing symptoms, such as anxiety and depression. Less is known regarding specific cognitive-affective mechanisms. The current study sought to examine distress intolerance (DI) as a mechanism that may explain the relation between early childhood emotional abuse and internalizing symptoms. Participants and methods Participants (N = 230; 54.3% women; mean age = 19.72, SD = 2.28) completed multiple self-report indices of early childhood emotional abuse, DI, and internalizing symptom indices. Using structural equation modeling, a series of mediation models was run to examine the indirect effect of childhood emotional abuse on latent and specific internalizing symptom indices through a latent index of subjective DI. Results Childhood emotional abuse was significantly associated with internalizing symptoms through DI (effect size range = .083–.227, medium to large). Conclusions The results provide preliminary evidence for DI as a mechanism of interest in the relation between early childhood emotional abuse and internalizing symptoms.
RUNX Binding Sites Are Enriched in Herpesvirus Genomes, and RUNX1 Overexpression Leads to Herpes Simplex Virus 1 Suppression

Infecting 90% of the global population, HSV-1 and HSV-2 represent some of the most prevalent viruses in the world. Much of their success can be attributed to their ability to establish lifelong latent infections in the dorsal root ganglia (DRG). It is still largely unknown, however, how host transcription factors are involved in establishing this latency. Here, we report that RUNX1, expressed highly in DRG, binds HSV-1 genome, represses transcription of numerous viral genes, and suppresses productive in vitro infection. Our computational work further suggests this strategy may be used by other herpesviruses to reinforce latency in a cell-specific manner. ABSTRACT Herpes simplex virus 1 (HSV-1) and HSV-2 can efficiently establish lifelong, transcriptionally silent latency states in sensory neurons to escape host detection. While host factors have previously been associated with long-range insulators in the viral genome, it is still unknown whether host transcription factors can repress viral genes more proximately to promote latency in dorsal root ganglion (DRG) neurons. Here, we assessed whether RUNX (runt-related transcription factor) transcription factors, which are critical in the development of sensory neurons, could be binding HSV-1 genome directly to suppress viral gene expression and lytic infection. Using previously published transcriptome sequencing data, we confirmed that mouse DRG neurons highly express Runx1 mRNA. Through computational analysis of HSV-1 and HSV-2 genomes, we observed that putative RUNX consensus binding sites (CBSs) were more enriched and more closely located to viral gene transcription start sites than would be expected by chance. We further found that RUNX CBSs were significantly more enriched among genomes of herpesviruses compared to those of nonherpesviruses. Utilizing an in vitro model of HSV-1 infection, we found that overexpressed RUNX1 could bind putative binding sites in the HSV-1 genome, repress numerous viral genes spanning all three kinetic classes, and suppress productive infection. In contrast, knockdown of RUNX1 in neuroblastoma cells induced viral gene expression and increased HSV-1 infection in vitro. In sum, these data support a novel role for RUNX1 in directly binding herpesvirus genome, silencing the transcription of numerous viral genes, and ultimately limiting overall infection. IMPORTANCE Infecting 90% of the global population, HSV-1 and HSV-2 represent some of the most prevalent viruses in the world. Much of their success can be attributed to their ability to establish lifelong latent infections in the dorsal root ganglia (DRG). It is still largely unknown, however, how host transcription factors are involved in establishing this latency. Here, we report that RUNX1, expressed highly in DRG, binds HSV-1 genome, represses transcription of numerous viral genes, and suppresses productive in vitro infection. Our computational work further suggests this strategy may be used by other herpesviruses to reinforce latency in a cell-specific manner.
Biogeochemical Importance of the Bacterial Community in Uranium Waste Deposited at Key Lake, Northern Saskatchewan

ABSTRACT The long-term stability of immobilized elements of concern in uranium tailings deposited in the Deilmann Tailings Management Facility (DTMF), northern Saskatchewan, is dependent upon maintenance of highly oxic conditions within the tailings mass. The main objective of this study was to investigate the effect of stimulating microbial activity on the redox potential and state of ferrihydrite, which are considered to be the primary controlling condition and mineral phase, respectively, within the tailings. To determine the potential for biologically mediated decreases in redox potential and ferrihydrite reduction, a series of microcosm assays were performed. Non-sterile material from the tailings–water interface of the DTMF site was inoculated with indigenous flora previously isolated from the tailings material and enriched with a carbon source (50 ppm trypticase soy broth) and incubated under continuous-flow or intermittent-flow conditions, and compared with an uninoculated, no-carbon control that received continuous flow. Highly reducing conditions with redox potentials of less than −300 mV were detected after 2 days of incubation within the carbon-enriched tailings of microcosms receiving continuous flow, and less than −280 mV after 11 days of incubation within carbon-enriched tailings in microcosms receiving intermittent flow. The lowest recorded Eh value (−545 mV) was recorded after 14 days in a carbon-enriched microcosm receiving intermittent flow. In contrast, the redox conditions in the control microcosm never dropped below −93 mV; thus, it was clear that microbial activity and available carbon drove the Eh conditions to become highly reducing. The occurrence of low redox conditions was concomitant with the bulk chemical detection of Fe (II) in the effluent of treated microcosms. Sites of microbial ferrihydrite reduction were also detected using scanning transmission X-ray microscopy where Fe (II) species were observed in close proximity with bacterial cells. Analysis of the microbial diversity present within the microcosms confirmed that microbes indigenous to the DTMF system have the potential to generate conditions suitable for the proliferation of sulfate and iron reducing bacteria, such as Desulfosporosinus, which was detected by high-throughput 16S rRNA gene sequencing.
A Tabu Search Method for K-anonymity in database privacy protection

In this paper, we introduce a new Tabu method to get K-anonymity character in database information privacy protection. We use the conception of lattice to form the solution space for K-anonymity Character and sear ch the solution area in this solution space to achieve the best or best approach modification solution for the information in the database. We then compared the Tabu method with other traditional heuristic method and our method show a better solution in most of the cases.
Prehistoric activity and Roman rural settlement at Blacklands, Staverton: excavations in 2007

Excavation revealed a pit containing Beaker pottery and a few other features with Bronze Age and Iron Age pottery. The lack of Late Iron Age material suggests that this low level activity had ceased by the time of the establishment of a small early Roman farmstead which contained at least two roundhouses. By the mid 3rd century these houses had been abandoned and replaced by a new set of enclosures probably associated with the construction of a villa evidenced by architectural fragments in later features. Four inhumation burials were found. Five pottery sherds attest post-Roman, possibly preAnglo-Saxon, activity. Prehistoric activity and Roman rural settlement at Blacklands, Staverton: excavations in 2007 by Alistair Barber, Jörn Schuster and Neil Holbrook with contributions by Sarah Cobain, Peter Davenport, Kevin Hayward, Lorrain Higbee, Harriet Jacklin, E. R. McSloy, Kathryn Price, Fiona Roe and Jane Timby Wiltshire Archaeological & Natural History Magazine, vol. 106 (2013), pp. 16-51
Molecular studies of the structure and function of pseudomonas aeruginosa OprD: an imipenem specific porin

Pseudomonas aeruginosa OprD is a specific porin which facilitates the uptake of basic amino acids and imipenem, a carbapenem antibiotic with high potency against P. aeruginosa. To permit further studies of OprD, the oprD structural gene was cloned and expressed in Escherichia coli on a 2.1-kb BamHIIKpnI fragment. DNA sequencing predicted a 420 amino acid mature OprD protein with a 23 amino acid signal peptide. In addition, a putative oprD regulatory gene opdE was sequenced, which predicted a hydrophobic protein of 402 amino acids. A set ofF. aeruginosa isogenic strains with genetically defined levels of OprD were constructed and utilized to characterize the in vivo function of OprD. The results clearly demonstrated that OprD could be utilized by imipenem and meropenem but, even when substantially overexpressed, could not be signfficantly utilized by other p-lactams, quinolones or aminoglycosides. Regarding its function in uptake of nutrients, OprD selectively facilitated the diffusion of basic amino acids and gluconate under growth-rate limiting conditions. Competition experiments confirmed that imipenem shared common binding sites with basic amino acids in the OprD channel, but not with gluconate or glucose. In vitro functional studies using purified OprD provided direct evidence for the presence of a specific binding site(s) for imipenem in the OprD channel, with an I value of 1.4 . tM. An OprD topology model was proposed based on sequence alignment with E.
Process and Content Model of CSR Decision-making – A Stakeholder Approach

This paper examines the process and factors that determine the decision for taking Corporate Social Responsibility (CSR) initiatives by businesses globally. Specifically, it investigates the stages of decision making and the factors that drive the decision making in each stage. A process and content model of decision making is proposed based on the factors determined from literature. The model consist of four stages in which the first stage is the pre-finalization stage in which the initial reasons for carrying out the CSR initiatives are explored, second stage is the finalization stage where the reasons for carrying out CSR initiatives are finalized, third stage is the context building for acting according to those reasons and subsequently carrying forward the CSR initiatives and the last stage is the implementation and execution of CSR initiatives. The review of previous literature reveals that major studies have focused only on one aspect of CSR namely, the reasons for CSR initiatives. This study opens up the direction for studying these factors deeply, so that it can be of use and importance to the businesses who are involved in the decision making of CSR initiatives. The interdependency of factors, as explained in the study, will aid decision makers at different levels of planning and implementation stages. It provides valuable inputs for those decision makers who are planning for CSR initiatives as well as to those who are seeking solutions for unsatisfactory results of these initiatives in their organizations.
Project description — Multi-objective MAPF

Coordinating the movement of a fleet of agents or robotsis a decades-old family of problems that has been intensively studied by the robotics and artificial intelligence communities. Applications of this family of problems can be found in diverse settings including assembly [7], evacuation [9], formation [8] and search-and-rescue [6]. One specific application of this general problem that gained significant interest in the research community is the warehouse domain. Here, storage locations host inventory pods that hold one or more kinds of goods. A large number (several hundreds and some times even several thousands) of robots operate autonomously in the warehouse picking up, carrying and putting down the inventory pods. The robots move the pods from their storage locations to designated dropoff locations where the needed goods are manually removed from the inventory pods (to be packaged and then shipped to customers). Each pod is then carried back by a robot to a (possibly different) storage location [13]. The successful use of such robots in warehouse applications led to a multi-billion industry led by tech-giants such as Amazon robotics and Alibaba [1]. For a visualization, see Fig. 1.
The Impact of Recovery Practices Adopted by Professional Tennis Players on Fatigue Markers According to Training Type Clusters

Introduction: Modern tennis players face congested schedules that force the adoption of various recovery strategies. Thus, recovery must be fine-tuned with an accurate quantification of its impacts, especially with regards to training-induced fatigue. The present study aimed to examine the training type clusters and recovery practices adopted by elite tennis players under ecological training conditions. The respective impacts of training type clusters and recovery techniques on subjective variables, which reflect the players' recovery perceptions, were subsequently determined. Methods: During 15 consecutive months, a total of 35 elite tennis players filled out questionnaires to report their daily training load, training session content, adopted recovery modalities after training, and perceived recovery. Results: The hierarchical analysis identified three clusters: “combined tennis and S&C training,” “predominant tennis training” and “predominant S&C training. ” Muscle soreness and perceived fatigue were not significantly different among these three clusters (p = 0.07–0.65). Across the 146 recorded training and recovery sessions, players primarily employed a combination of 2 or 3 modalities, with cooling strategies being the most widely used technique (87.6%). Mixed linear models revealed that independent of training clusters, cooling strategies significantly reduced muscle soreness (Δmuscle soreness: β = −1.00, p = 0.02). Among the cooling techniques used, whole-body cryotherapy induced a greater perceived recovery than cold-water immersion (p = 0.02). Conclusion: These results showed that perceived recovery was not sensitive to training clusters or the associated acute training load. However, cooling strategies were relevant for the alleviation of tennis training-induced soreness. This study represents an initial step toward a periodized approach of recovery interventions, based on the interactions between training load, training contents, and perceived recovery.
The Suppression of Taboo Word Spoonerisms Is Associated With Altered Medial Frontal Negativity: An ERP Study

The constant internal monitoring of speech is a crucial feature to ensure the fairly error-free process of speech production. It has been argued that internal speech monitoring takes place through detection of conflict between different response options or “speech plans. ” Speech errors are thought to occur because two (or more) competing speech plans become activated, and the speaker is unable to inhibit the erroneous plan(s) prior to vocalization. A prime example for a speech plan that has to be suppressed is the involuntary utterance of a taboo word. The present study seeks to examine the suppression of involuntary taboo word utterances. We used the “Spoonerisms of Laboratory Induced Predisposition” (SLIP) paradigm to elicit two competing speech plans, one being correct and one embodying either a taboo word or a non-taboo word spoonerism. Behavioral data showed that inadequate speech plans generally were effectively suppressed, although more effectively in the taboo word spoonerism condition. Event-related potential (ERP) analysis revealed a broad medial frontal negativity (MFN) after the target word pair presentation, interpreted as reflecting conflict detection and resolution to suppress the inadequate speech plan. The MFN was found to be more pronounced in the taboo word spoonerism compared to the neutral word spoonerism condition, indicative of a higher level of conflict when subjects suppressed the involuntary utterance of taboo words.
Core Mycobiome and Their Ecological Relevance in the Gut of Five Ips Bark Beetles (Coleoptera: Curculionidae: Scolytinae)

Bark beetles are destructive forest pests considering their remarkable contribution to forest depletion. Their association with fungi is useful against the challenges of survival on the noxious and nutritionally limited substrate, i.e., conifer tissues. Fungal symbionts help the beetles in nutrient acquisition and detoxification of toxic tree secondary metabolites. Although gut is the prime location for food digestion and detoxification, limited information is available on gut-mycobiome of bark beetles. The present study screened the gut-mycobiont from six bark beetles (five Ips and one non-Ips) from Scolytinae subfamily using high-throughput sequencing and explored their putative role in symbiosis with the host insect. Results revealed the predominance of four fungal classes- Sordariomycetes, Saccharomycetes, Eurothiomycetes, and Dothidomycetes in all bark beetles. Apart from these, Agaricomycetes, Leothiomycetes, Incertae sedis Basidiomycota, Tremellomycetes, Lecanoromycetes, and Microbotryomycetes were also documented in different beetles. Five Ips bark beetles share a consortium of core fungal communities in their gut tissues consisting of 47 operational taxonomic units (OTUs) belonging to 19 fungal genera. The majority of these core fungal genera belong to the phylum Ascomycota. LEfSe analysis revealed a set of species-specific fungal biomarkers in bark beetles. The present study identified the gut mycobiont assemblage in bark beetles and their putative ecological relevance. An enriched understanding of bark beetle-fungal symbiosis is not only filling the existing knowledge gap in the field but may also unleash an unforeseen potential for future bark beetle management.
Identifying Early Mild Cognitive Impairment by Multi-Modality MRI-Based Deep Learning

Mild cognitive impairment (MCI) is a clinical state with a high risk of conversion to Alzheimer's Disease (AD). Since there is no effective treatment for AD, it is extremely important to diagnose MCI as early as possible, as this makes it possible to delay its progression toward AD. However, it's challenging to identify early MCI (EMCI) because there are only mild changes in the brain structures of patients compared with a normal control (NC). To extract remarkable features for these mild changes, in this paper, a multi-modality diagnosis approach based on deep learning is presented. Firstly, we propose to use structure MRI and diffusion tensor imaging (DTI) images as the multi-modality data to identify EMCI. Then, a convolutional neural network based on transfer learning technique is developed to extract features of the multi-modality data, where an L1-norm is introduced to reduce the feature dimensionality and retrieve essential features for the identification. At last, the classifier produces 94.2% accuracy for EMCI vs. NC on an ADNI dataset. Experimental results show that multi-modality data can provide more useful information to distinguish EMCI from NC compared with single modality data, and the proposed method can improve classification performance, which is beneficial to early intervention of AD. In addition, it is found that DTI image can act as an important biomarker for EMCI from the point of view of a clinical diagnosis.