Miracle-dz/UniFAR-FTUs huggingface dataset:
A stochastic model for MRSA transmission within a hospital ward incorporating environmental contamination

SUMMARY Methicillin-resistant Staphylococcus aureus (MRSA) transmission in hospital wards is associated with adverse outcomes for patients and increased costs for hospitals. The transmission process is inherently stochastic and the randomness emphasized by the small population sizes involved. As such, a stochastic model was proposed to describe the MRSA transmission process, taking into account the related contribution and modelling of the associated microbiological environmental contamination. The model was used to evaluate the performance of five common interventions and their combinations on six potential outcome measures of interest under two hypothetical disease burden settings. The model showed that the optimal intervention combination varied depending on the outcome measure and burden setting. In particular, it was found that certain outcomes only required a small subset of targeted interventions to control the outcome measure, while other outcomes still reported reduction in the outcome distribution with up to all five interventions included. This study describes a new stochastic model for MRSA transmission within a ward and highlights the use of the generalized Mann–Whitney statistic to compare the distribution of the outcome measures under different intervention combinations to assist in planning future interventions in hospital wards under different potential outcome measures and disease burden.
Prebiotic Potential of Herbal Medicines Used in Digestive Health and Disease

Abstract Introduction: The prebiotic potential of herbal medicines has been scarcely studied. Methods: The authors therefore used anaerobic human fecal cultivation to investigate whether three herbal medicines commonly used in gastrointestinal health and disease in Ayurveda alter the growth and abundance of specific bacterial species. Results: Profiling of cultures supplemented with Glycyrrhiza glabra, Ulmus rubra, or triphala formulation by 16S rDNA sequencing revealed profound changes in diverse taxa in human gut microbiota. Principal coordinate analysis highlights that each herbal medicine drives the formation of unique microbial communities. The relative abundance of approximately one-third of the 299 species profiled was altered by all 3 medicines, whereas additional species displayed herb-specific alterations. Herb supplementation increased the abundance of many bacteria known to promote human health, including Bifidobacterium spp. , Lactobacillus spp. , and Bacteroides spp. Herb supplementation resulted in the reduced relative abundance of many species, including potential pathogens such as Citrobacter freundii and Klebsiella pneumoniae. Herbal medicines induced blooms of butyrate- and propionate-producing species. U. rubra and triphala significantly increased the relative abundance of butyrate-producing bacteria, whereas G. glabra induced the largest increase in propionate-producing species. To achieve greater insight into the mechanisms through which herbal medicines alter microbial communities, the authors assessed the shifts in abundance of glycosyl hydrolase families induced by each herbal medicine. Herb supplementation, particularly G. glabra, significantly increased the representation and potential expression of several glycosyl hydrolase families. Discussion: These studies are novel in highlighting the significant prebiotic potential of medicinal herbs and suggest that the health benefits of these herbs are due, at least in part, to their ability to modulate the gut microbiota in a manner predicted to improve colonic epithelium function, reduce inflammation, and protect from opportunistic infection. Forthcoming studies in human clinical trials will test the concordance of the results generated in vitro and the predictions made by genome analyses.
Early Maternal Withdrawal and Nonverbal Childhood IQ as Precursors for Substance Use Disorder in Young Adulthood: Results of a 20-Year Prospective Study.

The relation between early mother–infant interaction and later socio-emotional development has been well established. The present study addresses the more recent interest in the impact of maternal caregiving on cognitive development and their role in decision-making in young adulthood. Using data from a prospective longitudinal study on attachment, prediction from early mother–infant interactions at age 18 months and from verbal and nonverbal cognitive skill at age 5 were examined as predictors of a substance use disorder (abuse/dependence) in young adulthood (age 20) on the Structured Clinical Interview for DSM-TV (SCID). Results reveal that the mother's withdrawal from interaction with the infant at age 18 months, coded using the AMBIANCE coding system (Atypical Maternal Behavior Instrument for Assessment and Classification), was associated with the child's lower nonverbal cognitive scores but not verbal cognitive scores at age 5. In addition, maternal withdrawal at 18 months predicted a clinical diagno.
Laparoscopic Appendicostomy Low-Profile Balloon Button for Antegrade Enemas in Children.

INTRODUCTION The Malone appendicostomy is a continent channel used for antegrade enemas. It requires daily cannulation and is susceptible to stenosis. We use an indwelling low-profile balloon button tube inserted through the appendix into the cecum for antegrade enemas. We hypothesized that this method is effective at managing constipation or fecal incontinence and is associated with a low rate of stenosis. METHODS Children who underwent laparoscopic appendicostomy balloon button placement at our institution from January 2011 to April 2017 were identified. The primary outcome was success in managing constipation or fecal continence as measured by the Malone continence scale. Postoperative complications were analyzed. RESULTS Thirty-six children underwent the procedure, 35 of which met the inclusion criteria. Thirty-one patients (88.5%) underwent the operation for idiopathic constipation, 3 patients (8.6%) for anorectal malformation, and 1 patient (2.9%) for hypermobility. Rate of open conversion was 3%. A full response was obtained in 24 patients (68.6%), partial response in 9 patients (25.7%), and 2 patients failed (5.7%). One patient developed an internal hernia requiring laparotomy and later developed mucosal prolapse. One patient developed a stricture noted at button change. Seven patients (20%) underwent reversal of their appendicostomy tube: 5 due to return of normal bowel function and 2 due to discomfort with flushes. CONCLUSION A laparoscopic appendicostomy with a balloon button tube is an effective means of addressing chronic constipation or fecal incontinence. The stenosis rate associated with tube appendicostomy may be lower than those reported for Malone antegrade continence enema procedures.
Mosquitoes as Suitable Vectors for Alphaviruses

Alphaviruses are arthropod-borne viruses and are predominantly transmitted via mosquito vectors. This vector preference by alphaviruses raises the important question of the determinants that contribute to vector competence. There are several tissue barriers of the mosquito that the virus must overcome in order to establish a productive infection. Of importance are the midgut, basal lamina and the salivary glands. Infection of the salivary glands is crucial for virus transmission during the mosquito’s subsequent bloodfeed. Other factors that may contribute to vector competence include the microflora and parasites present in the mosquito, environmental conditions, the molecular determinants of the virus to adapt to the vector, as well as the effect of co-infection with other viruses. Though mosquito innate immunity is a contributing factor to vector competence, it will not be discussed in this review. Detailed understanding of these factors will be instrumental in minimising transmission of alphaviral diseases.
Radiation Effects on Thermal Properties of Polymers. II. Polytetrafluoroethylene

The second paper in a set of reviews of radiation effects on thermal properties of polymers is devoted to polytetrafluoroethylene (PTFE). The specificity of the radiation physics and chemistry of this material is relatively well investigated and it is widely used in different applications under radiation impact. Degradation of thermal and structure properties is discussed, and models for the description of these effects are presented. Specific problems such as the action of different kinds of radiation, dose rate effects, especially under vacuum, and deviation of PTFE structure from the two-phase model are also examined.
Bacterial analysis of barbecued meat (Suya) from selected locations within Abuja, Nigeria

Barbecued meat, popularly known as ‘Suya’ in Nigeria, is eaten by most Nigerians. However, the raw meat is sometimes prepared in unhygienic environments. This study examines the possibility of contracting infectious food and water borne diseases as a result of eating microbial contaminated barbecued meat. Meat samples were collected from four locations-Baze University, Kubwa, Lugbe and Maitama within FCT, Abuja, Nigeria. Microbial analysis of the samples showed bacterial contamination of all the barbecued meat sampled from the different locations. These meat samples were contaminated with indicator bacteria such as Escherichia coli, Staphylococcus aureus, Providencia spp, Bacillus spp, and Pseudomonas aeroginosa. Comparative analysis of the total aerobic bacterial count revealed a significantly higher concentration of bacteria in the barbecued meat compared to the raw meat samples. The specific bacteria were on average about 1.5–5.9 times higher in the barbecued meat relative to the raw meat samples. This alarming trend was observed in all selected locations. In addition, the bacterial contamination of the barbecued meat sampled from Baze University was significantly lower (6.0 × 105 CFU/g) in comparison to the barbecued meat from the other locations: Lugbe − 31.2 ×105 CFU/g, Kubwa − 34.0 × 105 CFU/g and Maitama − 42.6 × 105 CFU/g, with the latter being the most contaminated. The implications of this result in relation to human health and hygiene are discussed.
Around and Beyond the Isomorphism Problem for Interval Graphs

The class of problems solvable in logarithmic space has recently replenished with the isomorphism testing for interval graphs. We discuss this result, prospects of its extension to larger classes of graphs, and related issues such as constructing canonical models of intersection graphs and solving the Star System Problem for restricted classes of graphs.
Primary Rectal Cancer: Repeatability of Global and Local-Regional MR Imaging Texture Features

Purpose To assess the day-to-day repeatability of global and local-regional magnetic resonance (MR) imaging texture features derived from primary rectal cancer. Materials and Methods After ethical approval and patient informed consent were obtained, two pretreatment T2-weighted axial MR imaging studies performed prospectively with the same imaging unit on 2 consecutive days in 14 patients with rectal cancer (11 men [mean age, 61.7 years], three women [mean age, 70.0 years]) were analyzed to extract (a) global first-order statistical histogram and model-based fractal features reflecting the whole-tumor voxel intensity histogram distribution and repeating patterns, respectively, without spatial information and (b) local-regional second-order and high-order statistical texture features reflecting the intensity and spatial interrelationships between adjacent in-plane or multiplanar voxels or regions, respectively. Repeatability was assessed for 46 texture features, and mean difference, 95% limits of agreement, within-subject coefficient of variation (wCV), and repeatability coefficient (r) were recorded. Results Repeatability was better for global parameters than for most local-regional parameters. In particular, histogram mean, median, and entropy, fractal dimension mean and standard deviation, and second-order entropy, homogeneity, difference entropy, and inverse difference moment demonstrated good repeatability, with narrow limits of agreement and wCVs of 10% or lower. Repeatability was poorest for the following high-order gray-level run-length (GLRL) gray-level zone size matrix (GLZSM) and neighborhood gray-tone difference matrix (NGTDM) parameters: GLRL intensity variability, GLZSM short-zone emphasis, GLZSM intensity nonuniformity, GLZSM intensity variability, GLZSM size zone variability, and NGTDM complexity, demonstrating wider agreement limits and wCVs of 50% or greater. Conclusion MR imaging repeatability is better for global texture parameters than for local-regional texture parameters, indicating that global texture parameters should be sufficiently robust for clinical practice. Online supplemental material is available for this article.
Metatranscriptomic Profiling Reveals Linkages between the Active Rumen Microbiome and Feed Efficiency in Beef Cattle

ABSTRACT Exploring compositional and functional characteristics of the rumen microbiome can improve the understanding of its role in rumen function and cattle feed efficiency. In this study, we applied metatranscriptomics to characterize the active rumen microbiomes of beef cattle with different feed efficiencies (efficient, n = 10; inefficient, n = 10) using total RNA sequencing. Active bacterial and archaeal compositions were estimated based on 16S rRNAs, and active microbial metabolic functions including carbohydrate-active enzymes (CAZymes) were assessed based on mRNAs from the same metatranscriptomic data sets. In total, six bacterial phyla (Proteobacteria, Firmicutes, Bacteroidetes, Spirochaetes, Cyanobacteria, and Synergistetes), eight bacterial families (Succinivibrionaceae, Prevotellaceae, Ruminococcaceae, Lachnospiraceae, Veillonellaceae, Spirochaetaceae, Dethiosulfovibrionaceae, and Mogibacteriaceae), four archaeal clades (Methanomassiliicoccales, Methanobrevibacter ruminantium, Methanobrevibacter gottschalkii, and Methanosphaera), 112 metabolic pathways, and 126 CAZymes were identified as core components of the active rumen microbiome. As determined by comparative analysis, three bacterial families (Lachnospiraceae, Lactobacillaceae, and Veillonellaceae) tended to be more abundant in low-feed-efficiency (inefficient) animals (P < 0.10), and one archaeal taxon (Methanomassiliicoccales) tended to be more abundant in high-feed-efficiency (efficient) cattle (P < 0.10). Meanwhile, 32 microbial metabolic pathways and 12 CAZymes were differentially abundant (linear discriminant analysis score of >2 with a P value of <0.05) between two groups. Among them, 30 metabolic pathways and 11 CAZymes were more abundant in the rumen of inefficient cattle, while 2 metabolic pathways and 1 CAZyme were more abundant in efficient animals. These findings suggest that the rumen microbiomes of inefficient cattle have more diverse activities than those of efficient cattle, which may be related to the host feed efficiency variation. IMPORTANCE This study applied total RNA-based metatranscriptomics and showed the linkage between the active rumen microbiome and feed efficiency (residual feed intake) in beef cattle. The data generated from the current study provide fundamental information on active rumen microbiome at both compositional and functional levels, which serve as a foundation to study rumen function and its role in cattle feed efficiency. The findings that the active rumen microbiome may contribute to variations in feed efficiency of beef cattle highlight the possibility of enhancing nutrient utilization and improve cattle feed efficiency through modification of rumen microbial functions.
Laparoscopic vs Percutaneous Cryotherapy for Renal Tumors: A Systematic Review and Meta-Analysis.

BACKGROUND Cryoablation has emerged as an alternative to the more invasive partial nephrectomy for small renal masses. The approach can be carried out by two techniques, either laparoscopic cryoablation (LCA) or percutaneous cryoablation, (PCA) with CT guidance. We aimed to compare between the two procedures. MATERIALS AND METHODS A systematic review and meta-analysis was conducted, including studies comparing the two techniques. Outcomes included incomplete ablation, late local recurrence, cancer-specific survival, procedure time, transfusion rates, hospital stay, and complications. RESULTS A total of 1475 patients were included, 788 patients in the laparoscopic group and 687 patients in the percutaneous group. There was statistical difference favoring the laparoscopic group with regard to having less incomplete ablation (p = 0.0008) and higher cancer-specific survival patients (p = 0.04). However, there was longer hospital stays in the LCA group (p < 0.00001) and was found to be more costly than the PCA group. There was significantly more Clavien-I complications in the PCA group (p = 0.001) and more Clavien-III complications in the LCA group (p = 0.001). Otherwise, there were no differences in any other outcome parameter. CONCLUSION LCA was found to have less incomplete tumor ablation rates and higher cancer-specific survival rates, however, higher hospitalization time, more major complications (Clavien III), and was costlier compared with PCA.
Distress tolerance among substance users is associated with functional connectivity between prefrontal regions during a distress tolerance task

Distress tolerance (DT), defined as the ability to persist in goal directed behavior while experiencing affective distress, is implicated in the development and maintenance of substance use disorders. While theory and evidence indicate that cortico‐limbic neural dysfunction may account for deficits in goal directed behavior while experiencing distress, the neurobiological mechanisms of DT have yet to be examined. We modified a computerized DT task for use in functional magnetic resonance imaging (fMRI), the Paced Auditory Serial Addition Task (PASAT‐M), and examined the neural correlates and functional connectivity of DT among a cohort of substance users (n = 21; regular cocaine and nicotine users) and healthy controls (n = 25). In response to distress during the PASAT‐M, we found greater activation in a priori cortico‐limbic network ROIs, namely the right insula, anterior cingulate cortex (ACC), bilateral medial frontal gyrus (MFG), right inferior frontal gyrus (IFG) and right ventromedial prefrontal cortex (vmPFC) significantly predicted higher DT among substance users, but not healthy controls. In addition, greater task‐specific functional connectivity during distress between the right MFG and bilateral vmPFC/sgACC was associated with higher DT among substance users, but not healthy controls. The observed positive relationship between DT and neural activation in cortico‐limbic structures, as well as functional connectivity between the rMFG and vmPFC/sgACC, is in line with theory and research suggesting the importance of these structures for persisting in goal directed behavior while experiencing affective distress.
Surface nanoengineering of titanium alloys for biomedical applications

ii Acknowledgments . iv Declaration . vi List of publications . vii Table of contents . viii List of figures . xiii List of tables . xxii List of abbreviations . xxiv Chapter
Intra-operative femoral head vascularity assessment: An innovative and simple technique

Background: Documentation of femoral head blood flow before, during and after head preserving surgery is important for safeguarding vascularity to the femoral head and for documentation in patients in whom the blood flow is compromised. Laser Doppler flowmetry and microsensor intracranial pressure (ICP) transducers have been used to satisfactorily depict such changes. However, these devices are expensive and not universally available in orthopedic operating rooms. We describe a new technique for the assessment of intra-operative blood flow to the femoral head. This is a technical description of a simple system utilized in eight patients to assess the femoral head vascularity using equipment available with the anesthetist. Materials and Methods: A standard epidural catheter attached to an arterial pressure transducer is introduced into the femoral head from the margin of the articular surface via a small hole drilled with a K wire. The pressure wave within the epiphysis is detected on the anesthesia monitor. Pressure within the femoral head is used as a surrogate for blood flow. The pressure and the wave form are correlated with the electrocardiogram (ECG) wave on the anesthetic machine. The technique was used in eight children with hip pathology requiring hip dislocation for documenting the hip vascularity status. Result: There was good correlation between the pressure wave and the ECG for a patient with presumed normal femoral head vascularity, whereas the pressure measurements were greatly reduced and the wave form was absent in a femoral head wih radiographic or bone scan evidence of avascular necrosis. Conclusion: This new technique is a cheap and readily accessible alternative to Laser Doppler flowmetery and ICPs monitoring probes for the assessment of blood flow to the femoral head.
Event Detection and Key Posts Discovering in Social Media Data Streams

Microblogging, as a popular social media service, has become a new information channel for users to receive and exchange the most up-to-date information on current events. Consequently, it is crucial to detect new emerging events and to discover the key posts which have the potential to actively disseminate the events through microblogging. However, traditional event detection models require human intervention for detecting the number of topics to be explored, which significantly reduces the efficiency and accuracy of event detection. Most of the existing methods focus only on event detection and are unable to discover the key posts related to the events, making it challenging to track momentous events in timely manner. To tackle these problems, a HITS (Hypertext Induced Topic Search) based topic decision method, named TD-HITS is proposed. TD-HITS can automatically detect the number of topics as well as discovering associated key posts from a large number of posts. The experimental results are based on a Twitter dataset to demonstrate the effectiveness of our proposed methods for both detecting events and identifying key posts.
Effect of Compounding and Injection Molding on the Mechanical Properties of Flax Fiber Polypropylene Composites

The present study focuses on short flax fiber, as well as long flax fiber-reinforced polypropylene (flax/PP) composites, manufactured by the injection molding method. Compounding of flax with two different grades of PP (with and without maleic anhydride (MA-PP) grafting) is carried out by four methods: kneading process, Henschel kinetic mixer, extrusion compounding, and production of long fiber thermoplastic (LFT) granules through pultrusion. The effect of the compounding method and injection molding on the fiber length and mechanical properties of the composites is being investigated. Furthermore, the effect of fiber—matrix adhesion on the mechanical response is being discussed. It can be concluded that the reduction in fiber length, associated with injection molding, did not affect the tensile properties significantly for the studied systems due to improvements in fiber orientation along the polymer flow direction and increased fiber efficiency through dimensional changes due to fiber opening. The addition of MA-PP led to improvements in the tensile strength of injection-molded composites. Kneader compounded composites showed maximum tensile strength as well as stiffness when compared with other compounding methods.