Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular identification of Ehrlichia, Anaplasma, Babesia and Theileria in African elephants and their ticks

Although historical records indicate the presence of Ehrlichia and Babesia in African elephants, not much is known about their prevalence and diversity in elephants and their ticks, Amblyomma thollonii and Rhipicephalus humeralis. We amplified and sequenced the hypervariable V4 region of the 18S rRNA gene of Babesia and Theileria and the heat shock protein gene (groEL) of Ehrlichia/Anaplasma in DNA extracted from elephant blood (n = 104) and from elephant ticks (n = 52). Our results showed that the African elephants were infected with a novel Babesia spp. while A. thollonii was infected with Theileria bicornis and Theileria cf. velifera. This is the first record of T. bicornis; a protozoan that is linked to fatal infection in rhinoceros in a tick. Elephants and their ticks were all infected with a species of Ehrlichia like that identified in Japanese deer. The prevalence of Babesia spp. , Theileria spp. and Ehrlichia spp. in ticks was higher than that of their elephant hosts. About 13.5% of elephants were positive for Theileria or Babesia while 51% of A. thollonii ticks and 27% of R. humeralis ticks were positive for Theileria or Babesia. Moreover, 5.8% of elephants were positive for Ehrlichia or Anaplasma compared to 19.5% in A. thollonii and 18% in R. humeralis. There was no association between the positive result in ticks and that of their elephant hosts for either Babesia spp. , Theileria spp. or Ehrlichia spp. Our study reveals that the African elephants are naturally infected with Babesia spp and Ehrlichia spp and opens up an opportunity for further studies to determine the role of elephant as reservoirs of tick-borne pathogens, and to investigate their potential in spreading these pathogens as they range extensively. The presence of T. bicornis in A. thollonii also suggests a need for experiments to confirm its vector competence.
Methylsulfonylmethane increases osteogenesis and regulates the mineralization of the matrix by transglutaminase 2 in SHED cells

Methylsulfonylmethane (MSM) is a naturally occurring, sulfate-containing, organic compound. It has been shown to stimulate the differentiation of mesenchymal stem cells into osteoblast-like cells and bone formation. In this study, we investigated whether MSM influences the differentiation of stem cells from human exfoliated deciduous teeth (SHED) into osteoblast-like cells and their osteogenic potential. Here, we report that MSM induced osteogenic differentiation through the expression of osteogenic markers such as osterix, osteopontin, and RUNX2, at both mRNA and protein levels in SHED cells. An increase in the activity of alkaline phosphatase and mineralization confirmed the osteogenic potential of MSM. These MSM-induced effects were observed in cells grown in basal medium but not osteogenic medium. MSM induced transglutaminase-2 (TG2), which may be responsible for the cross-linking of extracellular matrix proteins (collagen or osteopontin), and the mineralization process. Inhibition of TG2 ensued a significant decrease in the differentiation of SHED cells and cross-linking of matrix proteins. A comparison of mineralization with the use of mineralized and demineralized bone particles in the presence of MSM revealed that mineralization is higher with mineralized bone particles than with demineralized bone particles. In conclusion, these results indicated that MSM could promote differentiation and osteogenic potential of SHED cells. This osteogenic property is more in the presence of mineralized bone particles. TG2 is a likely cue in the regulation of differentiation and mineral deposition of SHED cells in response to MSM.
Segmentation of Brain Tumor from MRI Image Blocks using SVM Classifier

Tumors are one of the most dangerous diseases that are difficult to cure completely when detected after its initial stage. Early detection of this will help to get proper treatment. Tumors cause changes in tissues which can be detected using many imaging techniques like Magnetic Resonance Imaging (MRI). The system is proposed for the autonomous segmentation of tumor tissues from normal tissues in MRI images using Gray Level CoOccurrence Matrix (GLCM) features extraction and Support Vector Machine (SVM) classifier.
Quantitative atomic spectroscopy, a review of progress in the optical-UV region and future opportunities

Abstract The development of tunable dye lasers and a simple atomic and ionic beam source for all elements were critical in establishing a reliable absolute scale for atomic transition probabilities in the optical to near UV regions. The laboratory astrophysics program at the University of Wisconsin - Madison (UW) concentrates on neutral and singly-ionized species transitions that are observable in astronomical spectra of cool stars, emphasizing the rare earth n(eutron)-capture elements and the Fe-group elements that are important inputs to early Galactic nucleosynthesis studies. The UW program is one of several productive efforts on atomic transition probabilities. These programs generally use time-resolved laser-induced-fluorescence (TR-LIF) to accurately measure total decay rates and data from high resolution Fourier transform spectrometers (FTSs) to determine emission branching fractions (BFs). The UW laboratory results almost always are directly linked to astronomical chemical composition efforts. There are good opportunities to extend similar research to other wavelength regions.
DGCR8 microprocessor defect characterizes familial multinodular goiter with schwannomatosis.

BACKGROUND DICER1 is the only miRNA biogenesis component associated with an inherited tumor syndrome, featuring multinodular goiter (MNG) and rare pediatric-onset lesions. Other susceptibility genes for familial forms of MNG likely exist. METHODS Whole exome sequencing of a kindred with early-onset MNG and schwannomatosis was followed by investigation of germline pathogenic variants that fully segregated with the disease. Genome wide analyses were performed on 13 tissue samples from familial and non-familial DGCR8-E518K positive tumors, including MNG, schwannomas, papillary thyroid cancers (PTC) and Wilms Tumors. MiRNA profiles of four tissue types were compared, and sequencing of miRNA, pre-miRNA and mRNA was performed in a subset of 9 schwannomas, four of which harbor DGCR8-E518K. RESULTS We identified c.1552G>A;p.E518K in DGCR8, a microprocessor located in 22q, in the kindred. The variant identified is a somatic hotspot in Wilms Tumors and has been identified in two PTCs. Copy number loss of chromosome 22q, leading to loss of heterozygosity at the DGCR8 locus, was found in all 13 samples harboring c.1552G>A;p.E518K. miRNA profiling of PTC, MNG, schwannomas and Wilms Tumors revealed a common profile among E518K hemizygous tumors. In vitro cleavage demonstrated improper processing of pre-miRNA by DGCR8-E518K. MicroRNA and RNA profiling show that this variant disrupts precursor microRNA production, impacting populations of canonical microRNAs and mirtrons. CONCLUSIONS We identified DGCR8 as the cause of an unreported autosomal dominant mendelian tumor susceptibility syndrome: familial multinodular goiter with schwannomatosis.Funded by CIHR, Compute Canada, Alex's Lemonade Stand Foundation, and the Mia Neri Foundation for Childhood Cancer.
Growth Performance of Broilers as Influenced by Different Levels and Sources of Methionine Plus Cysteine

Simple Summary The current work evaluated the utilization of different sources of methionine either from DL-methionine (DL-Met) or L-methionine (L-Met) using different concentrations of dietary methionine plus cystine (Met + Cyst) in broiler chickens. Results showed that a better edible meat yield could be obtained by supplementing Met + Cyst at the rate of 80% of the digestible lysine. Abstract The objective of this work was to evaluate the utilization of methionine from DL-methionine (DL-Met) and L-methionine (L-Met) with different levels of dietary methionine plus cystine (Met + Cyst) in broilers. The experimental diets were formulated by using three levels of Met + Cyst, i.e., 74%, 77% and 80% of digestible lysine. Met + Cyst was provided either from DL-Met or L-Met. A total of 450 day-old broilers were divided into six groups (five replicates of 15 birds each) in a 3 × 2 factorial arrangement under completely randomized design. Weight gain (WG), feed intake (FI) and feed conversion ratio (FCR) was determined. At the end of the experiment (35 days), two birds from each replicate were slaughtered to determine carcass characteristics and serum homocysteine. Results indicate that the combined effect of L-Met and DL-Met significantly affected (p < 0.05) the WG in the starter period and FI in the finisher period. Neither source nor level of methionine influenced (p > 0.05) the FI, WG and FCR of broilers during the starter, finisher or overall phase of growth. The interaction between sources and levels of methionine did not influence (p > 0.05) the feed intake, weight gain and FCR during the overall phase of growth. Source of methionine had no (p > 0.05) effect on carcass characteristics. Methionine levels had a significant effect (p < 0.05) on carcass weight, chest weight and thigh weight. The interaction between sources and levels of methionine had a significant (p < 0.05) effect on the liver weight. The sources of methionine had significant (p < 0.05) effects on the liver and heart weight, while methionine levels significantly influenced (p < 0.05) the liver and gizzard weight. Finally, it was concluded that if DL-Met and L-Met are included in feed at a standard level, they are equally effective as a source of methionine for broilers.
Expert insights: The potential role of the gut microbiome‐bile acid‐brain axis in the development and progression of Alzheimer's disease and hepatic encephalopathy

Recent epidemiological and molecular studies have linked the disruption of cholesterol homeostasis to increased risk for developing Alzheimer's disease (AD). Emerging evidence also suggests that brain cholesterol accumulation contributes to the progression of hepatic encephalopathy (HE) via bile acid (BA)‐mediated effects on the farnesoid X receptor. In this perspective paper, we reviewed several recently published studies that suggested a role for the gut microbiota transformation of BAs as a factor in AD and HE development/progression. We hypothesize that in addition to cholesterol elimination pathways, alteration of the gut microbiota and subsequent changes in both the serum and brain BA profiles are mechanistically involved in the development of both AD and HE, and thus, are a potential target for the prevention and treatment of the two diseases. Our understanding of the microbiome‐BAs‐brain axis in central nervous system disease is still evolving, and critical questions regarding the emerging links among central, peripheral, and intestinal metabolic failures contributing to brain health and disease during aging have yet to be addressed.
Visual Hallucinations and Impaired Conscious Visual Perception in Parkinson Disease

Visual hallucinations (VHs) are common in patients with Parkinson disease (PD), especially those with dementia, whereas auditory hallucinations are quite rare. Recent studies have revealed the involvement of several regions along the visual information-processing system that contribute to the pathophysiological mechanism of VHs: the eyes and retina, retinofugal projection, lateral geniculate nucleus, striate cortex, ventral pathways in the temporal cortices, and frontal and parietal cortices. In addition, the concurrent involvement of other systems in the brainstem and basal forebrain further modify VHs in PD. In this review, we discuss the pathophysiological association between the regional involvement of these areas and VHs.
Analysis of the Molecular Signaling Signatures of Muscle Protein Wasting Between the Intercostal Muscles and the Gastrocnemius Muscles in db/db Mice

Type 2 diabetes (T2D) patients suffer from dyspnea, which contributes to disease-related morbidity. Although T2D has been reported to induce a catabolic state in skeletal muscle, whether T2D induces muscle wasting in respiratory muscles has not yet been investigated. In this study, we examine the difference in the molecular signaling signature of muscle wasting between the intercostal and gastrocnemius muscles using db/db mice, a well-known diabetic mouse model. Akt phosphorylation was significantly decreased in both the intercostal and gastrocnemius muscles of db/db mice and was accompanied by a decrease in mTORC1 activity. In addition, FoxO phosphorylation was suppressed, and ubiquitin-proteasome degradation, characterized by the level of Atrogin-1 and MuRF1, was subsequently enhanced in both muscle types of db/db mice. An increase in LC3BII levels and a decrease in p62 levels marked the occurrence of substantial autophagy in the gastrocnemius muscle but not in the intercostal muscles of db/db mice. Therefore, we suggest that the signaling events of muscle wasting in the intercostal muscles of db/db mice are different from those in the gastrocnemius muscle of db/db mice.
Sleep Quality and Quality of Life Among Healthy High School Athletes

We examined the association between sleep quality and quality of life (QOL) among uninjured high school athletes. Participants completed the Pittsburgh Sleep Quality Index (PSQI) and the Patient-Reported Outcomes Measurement Information System (PROMIS) Pediatric Profile 25 questionnaire. One hundred ten athletes reported poor sleep quality (mean PSQI: 6.6 ± 2.0; mean age: 15.3 ± 1.1; 62% female); 162 athletes reported good sleep quality (mean PSQI: 2.3 ± 1.3; mean age: 15.1 ± 1.7; 33% female). After adjusting for sex and age, worse sleep quality was associated with higher physical function/mobility (β = 0.034; 95% confidence interval [CI] = 0.007-0.060; P = .01), anxiety (β= 0.391; 95% CI = 0.263-0.520; P < .001), depressive symptom (β = 0.456; 95% CI = 0.346-0.565; P < .001), fatigue (β = 0.537; 95% CI = 0.438-0.636; P < .001), pain interference (β = 0.247; 95% CI = 0.119-0.375; P < .001), and pain intensity (β = 0.103; 95% CI = 0.029-0.177; P = .006) ratings. Poor self-reported sleep quality among adolescent athletes was associated with worse QOL ratings. Clinicians should consider assessing sleep hygiene to provide guidance on issues pertaining to reduced QOL.
Screening colonoscopy and flexible sigmoidoscopy for reduction of colorectal cancer incidence: A case-control study

Background Flexible sigmoidoscopy and colonoscopy are both recommended colorectal cancer screening options, but their relative effectiveness needs clarification. The aim of this study was to compare the effectiveness of colonoscopy and flexible sigmoidoscopy for reduction of colorectal cancer incidence. Methods We conducted a case-control study within the linked Surveillance, Epidemiology, and End Results (SEER)-Medicare database. Cases were subjects age 70–85 years in the SEER-Medicare database diagnosed with CRC during 2004–2013. Up to 3 controls were matched to each case by birth year, sex, race, and SEER region. Receipt of screening colonoscopy or flexible sigmoidoscopy was ascertained from Medicare claims. Conditional logistic regression models were developed to estimate the odds ratios (ORs) and 95% confidence intervals (CI) for a history of screening in cases vs. controls. We conducted secondary analyses by sex, race, endoscopist characteristics, and with varying timing and duration of the look-back period. Results Receipt of screening colonoscopy and sigmoidoscopy was associated with a 59% (OR 0.41, 95%CI 0.39, 0.43) and 22% reduction (OR 0.78, 95%CI 0.67, 0.92) in colorectal cancer incidence, respectively. Colonoscopy was associated with greater reduction in the distal colorectal cancer incidence (OR 0.22, 95%CI 0.20, 0.24) than proximal colorectal cancer incidence (OR 0.62, 95%CI 0.59, 0.66). Sigmoidoscopy was associated with a 52% reduction in distal colorectal cancer incidence (OR 0.48, 95%CI 0.37, 0.63), but with no reduction in proximal colorectal cancer incidence. These associations were stronger in men than in women. No differences by race or endoscopist characteristics were observed. Conclusion Both screening colonoscopy and sigmoidoscopy were associated with reductions in overall colorectal cancer incidence, with a greater magnitude of reduction observed with colonoscopy.
Genetic and morphological divergence in the warm-water planktonic foraminifera genus Globigerinoides

The planktonic foraminifera genus Globigerinoides provides a prime example of a species-rich genus in which genetic and morphological divergence are uncorrelated. To shed light on the evolutionary processes that lead to the present-day diversity of Globigerinoides, we investigated the genetic, ecological and morphological divergence of its constituent species. We assembled a global collection of single-cell barcode sequences and show that the genus consists of eight distinct genetic types organized in five extant morphospecies. Based on morphological evidence, we reassign the species Globoturborotalita tenella to Globigerinoides and amend Globigerinoides ruber by formally proposing two new subspecies, G. ruber albus n.subsp. and G. ruber ruber in order to express their subspecies level distinction and to replace the informal G. ruber “white” and G. ruber “pink”, respectively. The genetic types within G. ruber and Globigerinoides elongatus show a combination of endemism and coexistence, with little evidence for ecological differentiation. CT-scanning and ontogeny analysis reveal that the diagnostic differences in adult morphologies could be explained by alterations of the ontogenetic trajectories towards final (reproductive) size. This indicates that heterochrony may have caused the observed decoupling between genetic and morphological diversification within the genus. We find little evidence for environmental forcing of either the genetic or the morphological diversification, which allude to biotic interactions such as symbiosis, as the driver of speciation in Globigerinoides.
Ionic Liquids under Confinement: From Systematic Variations of the Ion and Pore Sizes toward an Understanding of the Structure and Dynamics in Complex Porous Carbons

We use molecular simulations of an ionic liquid in contact with a range of nanoporous carbons to investigate correlations between the ion size, pore size, pore topology, and properties of the adsorbed ions. We show that diffusion coefficients increase with the anion size and, surprisingly, with the quantity of adsorbed ions. Both findings are interpreted in terms of confinement: when the in-pore population increases, additional ions are located in less-confined sites and diffuse faster. Simulations in which the pores are enlarged while keeping the topology constant support these observations. The interpretation of properties across structures is more challenging. An interesting point is that smaller pores do not necessarily lead to a larger confinement. In this work, the highest degrees of confinement are observed for intermediate pore sizes. We also show a correlation between the quantity of adsorbed ions and the ratio between the maximum pore diameter and the pore limiting diameter.
‘Optimal Virtualized In-Network Processing with Applications to Aggregation and Multicast’

Computer networks become more and more virtualized and software-defined, introducing new opportunities for innetwork (a.k.a. in situ) processing and flexible traffic engineering. In order to make efficient use of in-network node resources (such as computation or storage) and bandwidth resources, the two resource types must be jointly optimized: traffic-steering mechanisms are needed to reroute traffic through the in-network node resources, potentially introducing longer paths. Matthias Rost’s thesis takes a first look at this important tradeoff, which is not only relevant in the context of SDN/NFV, but can also be seen as an interesting generalization of classic multicast and aggregation problems, with applications in optical networks, sensor networks, or even network analytics. The main contribution of the thesis is VirtuCast, an exact single-commodity algorithm which is based on an interesting path decomposition algorithm. The thesis also stands out by its broad treatment of the topic as well as the in-depth analytical study and rigorous evaluation.
Nosocomial infections among patients admitted in general ICU: study from a tertiary-care hospital in South India

Background: Nosocomial infections (NI) are also called hospital-associated infections that comprise almost all clinically apparent infections that are not arising as a result of patients’ original admitting diagnosis. NI defined as localized and systemic conditions that result from adverse reaction owing to the presence of an infectious agents and was not present or incubating at the time of admission to the hospital. The rate of NI varies from 2.85% to 34.6% among the hospitalized patients. Objective: To investigate NIs among the patients admitted in intensive care unit (ICU) and to evaluate the prevalence, risk factors, the causative bacteria, and their resistance pattern to antimicrobial agents. Materials and Methods: The study was carried out over a period of 12 months from July 2014 to June 2015. Patients admitted in the general ICU were monitored for the development of NIs. Samples were collected from suspected patients depending on the type of NI, to detect the causative organisms and their antimicrobial susceptibility. Extended spectrum beta-lactamase (ESBL)-positive isolates were tested by double disc synergy test for ESBL production. Result: The study included 260 patients admitted into general ICU. The prevalence of NI was 19.2%. Female subjects were more affected (60%) than male subjects (40%). Risk factors identified were urinary catheterization, female sex, advanced age, mechanical ventilation, and increased hospitalization. Ventilator-associated pneumonia was the most common NI, constituting 36%, followed by urinary tract infections (26%). Esherichia coli were the predominant organisms among the Gram-negative bacteria. Imipenem was majorly used antibiotic for empirical treatment of ICU infections before getting the antibiotic sensitivity report. Conclusion: Indiscriminate use of antibiotics should be avoided in order to curtail the emergence and the spread of drug resistance among nosocomial pathogens. This study gives insight into the incidence of NIs and in revising antibiotic policy and guiding clinicians in preventing emergence of carbapenem resistance among the patients.
EFFICACY OF A LEBANESE ISOLATE OF BEAUVERIA SP. FOR THE BIOCONTROL OF BEMISIA TABACI

Farah Baroudy, Elvis Gerges, Lucia Hanna, Hana Sobh, Nabil Nemer and Yusuf Abou-Jawdah. 2018. Efficacy of a Lebanese isolate of Beauveria sp. for the biocontrol of Bemisia tabaci. Lebanese Science Journal, 19(1): 74-84. The sweetpotato/cotton whitefly, Bemisia tabaci (Gennadius) is a major pest of several crops worldwide. In addition to the direct damage induced, it has the ability to transmit some of the most dangerous plant viruses rendering it a very critical pest. The development of whitefly resistance to several groups of pesticides forced farmers and researchers to adopt integrated pest management strategies and to look for alternative control measures. Studies using molecular markers showed the coexistence in Lebanon of two species, the “Middle East-Asia Minor 1 species” also known as biotype B and the “Mediterranean species” also known as biotype Q. In greenhouse trials, the Beauveria pseudobassiana isolated in Lebanon was found to be quite efficient for the management of B. tabaci. Sprays containing spore suspensions of 10 spores/mL caused around 75% mortality of the early growth stages: egg, crawler, second and third instar larvae. The addition of a surfactant such as corn oil improved the mortality level that reached 98% in the egg /crawler stage and 84% in the second and third instar larvae at a spore concentration as low as 10 conidia/mL. In view of the promising results, further medium size trials under commercial greenhouse conditions are planned.