Miracle-dz/UniFAR-FTUs huggingface dataset:
Survival of Bifidobacteria and their usefulness in Faecal Source Tracking

Abstract: Bifidobacteria have long since been recommended as indicators of human and animal pollution. Concentration ratio (tracking ratio) of the sorbitol-utilising bifidobacteria (SUB) and the total bifidobacteria (TB) can be used to distinguish between animal and human sources of faecal water contamination. The cut-off value needs to be calibrated in a given geographical area. Seven sites with permanent faecal contamination were selected in South Africa. Concentrations of SUB ranged from 10-50000 cells/100 mL, while TB ranged from 0-8000 cells/100 mL. The tracking ratio ranged from 0.10 to 6.25, but no clear cut-off value could be established. The YN-17 agar was replaced for TB with the modified Beerens medium with pH = 5.70, to suppress the growth of faecal streptococci. Tracking ratios observed are most likely the results of different survival rates of SUB and TB. Bifidobacteria die-off due to nutrients was not found to be significant using design of experiment. Thus a lack of continuous input or oxygen levels in water may be major factors. This would limit the ratios used as a faecal source tracking method.
Prevalence of non-communicable diseases among individuals with HIV infection by antiretroviral therapy status in Dar es Salaam, Tanzania

Background Long-term antiretroviral therapy has modified the clinical course of HIV infection to a chronic condition associated with increased risk of developing non-communicable diseases (NCDs). Information is scant, from sub-Saharan Africa, on the prevalence of NCDs and associated factors among individuals on ART. Methodology We consecutively enrolled individuals with HIV infection who were ART naïve and those on ART for ≥5 years (LTART) attending health facilities in Dar es Salaam. Participant's blood pressure, anthropometric measurements, and fasting blood glucose were recorded. Participants with impaired fasting blood glucose underwent an oral glucose tolerance test. A venous blood sample was sent to the lab for biochemical tests. Chi-square test was used to compare proportions, Poisson regression with robust standard errors was used to determine associations between variables. Results Overall, 612 individuals with HIV infection were enrolled, half of whom were ART naïve. Females comprised 71.9% and 68.0% of participants in the LTART and ART naïve study arms, respectively, p = 0.290. The mean age (±SD) was 44.9 ± 12.7 years and 37.5 ± 11.8 years among LTART and ART naïve participants, respectively, p<0.001. Hypertension was documented in 25.2% in those on LTART compared to 6.9% among ART naïve subjects, p<0.001. Impaired glucose tolerance was found in 22.9% and 4.6% among LTART compared to ART naïve subjects, p<0.001. Diabetes mellitus was detected in 17.0% of those on LTART compared to 3.9% ART naïve participants, p<0.001. Hypercholesterolemia was found in 30.4% of individuals on LTART compared to 16.7% of ART naïve subjects, p<0.001, and hypertriglyceridemia was found in 16.0% of participants on LTART compared to 9.5% of ART naïve, p = 0.015. LTART use, age ≥40 years, history of smoking, and body mass index were independently associated with NCDs. Conclusion Hypertension, impaired glucose tolerance, diabetes mellitus, hypercholesterolemia, and hypertriglyceridemia were associated with long-term use of antiretroviral drugs.
Delineation of the Genera Struvea Bonder and Phyllodictyon J. E. Gray (Cladophorales, Chlorophyta)

Plants of the stalked, net‐forming green alga Struvea plumosa Sender, the type species of the genus Struvea, divide segregatively at every stage of their multicellular differentiation. The segregative process results in virtually simultaneous internal cleavage of the cytoplasts of parent axes or laterals into uniseriate series of nearly identically sized daughter cells m which intercalary cross‐wall formation never takes place. Several branch orders result through a repeated process by which each daughter cell produces a pair of opposite protrusions at its distal end; the protruded arms subsequently undergo segregative divisions themselves after reaching a sufficient length. Struvea elegans Børgesen is seemingly the only other member of the genus in which the thallus divides by this segregative process. The remaining species appear to lack segregative cell division, their septation resulting from non‐synchronous, centripetal wall ingrowths that divide parent cells into more or less equal halves. Intercalary cell divisions are common, this process being easily seen in the most widely distributed member of the genus, Struvea anastomosans (Harv.) Pice, et Grunov ex Pice. Phyllodictyon J. E. Gray, based on Phyllodictyon putcherrimum. is currently considered a synonym of Struvea but should be reinstated to accommodate those former species of Struvea that have Cladophoratype. as opposed to segregative, cell division. Although the two genera thus differ substantially in their modes of cytokinesis and are assumed to represent independent developmental lines, both Struvea and Phyllodictyon are assigned to the Cladophorales on the basis of molecular studies by others showing that recognition of the separate order Siphonocladales renders the Cladophorales paraphyletic.
Computerized Cognitive Rehabilitation Training for Ugandan Seniors Living with HIV: A Validation Study

The feasibility, acceptability and preliminary efficacy of computerized cognitive rehabilitation therapy (CCRT) for mitigating neurocognitive decline was evaluated in African adults ≥50 years old. Eighty-one Ugandans with (n = 40) and without (n = 41) chronic human immunodeficiency viruses (HIV) were allocated CCRT—i.e., 20–45-min cognitive training sessions with culturally adapted video games delivered via Captain’s Log Software, or standard of care (SOC). Pre and post (i.e., 8-weeks later) intervention performance based neurocognitive tests, quality of life (QOL) and frailty related phenotype (FRP) were determined in all respondents. Multivariable linear regression estimated CCRT- vs. SOC-related differences (β) in neurocognitive batteries, QOL and FRP. Effect sizes (ES) for estimated β were calculated. CCRT protocol was completed by 92.8% of persons allocated to it. Regardless of HIV status, CCRT was associated with higher performance in learning tests than SOC—interference list (β = 1.00, 95%CI: (0.02, 1.98); ES = 0.43) and delayed recall (β = 1.04, 95%CI: (0.06, 2.02); ES = 0.47). CCRT effect on verbal fluency was clinically important (ES = 0.38), but statistical significance was not reached (β = 1.25, 95%CI: (−0.09, 2.58)). Among HIV-positive adults, clinically important post-CCRT improvements were noted for immediate recall (ES = 0.69), working memory (ES = 0.51), verbal fluency (ES = 0.51), and timed gait (ES = −0.44) tasks. Among HIV-negative adults, CCRT resulted in moderate post-intervention improvement in learning tests (ES = 0.45) and large decline in FRP (ES = −0.71), without a positive effect on simple attention and visuomotor coordination tasks. CCRT intervention is feasible among older Ugandan adults with potential benefit for learning and verbal fluency tests regardless of HIV status and lowering FRP in HIV-negative older adults.
Establishment of a novel miniature veno-venous extracorporeal membrane oxygenation (V-V ECMO) model in the rat.

Recently, veno-venous extracorporeal membrane oxygenation (V-V ECMO) has been commonly used in the world to support patients with severe respiratory failure. However, V-V ECMO is a new technology compared to veno-arterial extracorporeal membrane oxygenation and cardiopulmonary bypass, and there are few reports of basic research. Although continuing research is desired, clinical research that standardizes conditions such as patients' background characteristics is difficult. The purpose of this study was to establish a simple and stably maintainable miniature V-V ECMO model to study the mechanisms of the biological reactions in circulation during V-V ECMO. The V-V ECMO system consisted of an original miniature membrane oxygenator, polyvinyl chloride tubing line, and roller pump. The priming volume of this system was only 8 mL. Polyethylene tubing was used to cannulate the right femoral vein as the venous return cannula for the V-V ECMO system. A 16-G cannula was passed through the right internal jugular vein and advanced into the right atrium as the conduit for venous uptake. The animals were divided into 2 groups: SHAM group and V-V ECMO group. V-V ECMO was initiated and maintained at 50-60 mL/kg/min, and oxygen was added into the oxygenator during V-V ECMO at a concentration of 100% (pump flow:oxygen = 1:10). Blood pressure was measured continuously, and blood cells were measured by blood collection. During V-V ECMO, the blood pressure and hemodilution rate were maintained around 80 mmHg and 20%, respectively. Hb was kept at >10 g/dL, and V-V ECMO could be maintained without blood transfusion. It was possible to confirm oxygenation of and carbon dioxide removal from the blood. Likewise, the pH was adequately maintained. There were no problems with this miniature V-V ECMO system, and extracorporeal circulation progressed safely. In this study, a novel miniature V-V ECMO model was established in the rat. A miniature V-V ECMO model appears to be very useful for studying the mechanisms of the biological reactions during V-V ECMO and to perform basic studies of circulation assist devices.
Impact of contract-farming in staple food chains: the case of rice in Benin

Research on the impact of smallholder contract-farming largely focuses on exportoriented high-value commodities. Little is known about the possibility of contract-farming for upgrading in staple food chains. While theoretical insights predict contract-farming to be infeasible for lower-value staple food crops, empirical evidence from such sectors is extremely scarce. In this paper, we provide evidence on smallholder contract-farming in the rice sector in Benin. We use cross-sectional household data and propensity score matching methods to analyze the impact of contract-farming on selected farm performance indicators. The findings indicate that contract-farming has a positive impact on rice productivity and income.
Date Seed Extract Diminished Apoptosis Event in Human Colorectal Carcinoma Cell Line

Apoptosis, or programmed cell death, is an essential process to remove the damaged or abnormal cancerous cells. Therefore, the study of apoptosis-inducing agents helps identifying new drugs for cancer therapy. The aim of this study was to evaluate the apoptotic effect of methanolic extract of date seed in human colon cancer cell. HT29 cells were cultured and exposed to different concentrations of date seed extract (100, 200 and 400µg/ml). Neutral comet assay was used and the patterns were classified into four groups based on the tail length and head size. Results showed that the extract has not been able to induce apoptosis in HT29 cells. Amazingly, the rate of apoptosis observed in the HT29 cells exposed to the extract, was lower than the negative control group that received no treatment. While the methanolic extract of date seed did not induce apoptosis in colon tumor cells its supporting effect on HT29 cells survival may fuels more investigation.
Evidence of Host-Associated Populations of Cryptosporidium parvum in Italy

Recent studies have revealed extensive genetic variation among isolates of Cryptosporidium parvum , an Apicomplexan parasite that causes gastroenteritis in both humans and animals worldwide. The parasite’s population structure is inﬂuenced by the intensity of transmission, the host-parasite interaction, and husbandry practices. As a result, C. parvum populations can be panmictic, clonal, or even epidemic on both a local scale and a larger geographical scale. To extend the study of C. parvum populations to an unexplored region, 173 isolates of C. parvum collected in Italy from humans and livestock (calf, sheep, and goat) over a 10-year period were genotyped using a multilocus scheme based on 7 mini- and microsatellite loci. In agreement with other studies, extensive polymorphism was observed, with 102 distinct multilocus genotypes (MLGs) identiﬁed among 173 isolates. The presence of linkage disequilibrium, the conﬁnement of MLGs to individual farms, and the relationship of many MLGs in-ferred using network analysis (eBURST) suggest a predominantly clonal population structure, but there is also evidence that part of the diversity can be explained by genetic exchange. MLGs from goats were found to differ from bovine and sheep MLGs, sup-porting the existence of C. parvum subpopulations. Finally, MLGs from isolates collected
Identification and characterization of adipose surface epitopes

Adipose tissue is a central regulator of metabolism and an important pharmacological target to treat the metabolic consequences of obesity, such as insulin resistance and dyslipidemia. Among the various cellular compartments, the adipocyte cell surface is especially appealing as a drug target as it contains various proteins that when activated or inhibited promote adipocyte health, change its endocrine function and eventually maintain or restore whole-body insulin sensitivity. In addition, cell surface proteins are readily accessible by various drug classes. However, targeting individual cell surface proteins in adipocytes has been difficult due to important functions of these proteins outside adipose tissue, raising various safety concerns. Thus, one of the biggest challenges is the lack of adipose selective surface proteins and/or targeting reagents. Here, we discuss several receptor families with an important function in adipogenesis and mature adipocytes to highlight the complexity at the cell surface and illustrate the problems with identifying adipose selective proteins. We then discuss that, while no unique adipocyte surface protein might exist, how splicing, posttranslational modifications as well as protein/protein interactions can create enormous diversity at the cell surface that vastly expands the space of potentially unique epitopes and how these selective epitopes can be identified and targeted.
Fast Geometric Distortion Correction Using a Deep Neural Network: Implementation for the 1 Tesla MRI-Linac System.

PURPOSE Combining high-resolution magnetic resonance imaging (MRI) with a linear accelerator (Linac) as a single MRI-Linac system provides the capability to monitor intra-fractional motion and anatomical changes during radiotherapy, which facilitates more accurate delivery of radiation dose to the tumour and less exposure to healthy tissue. The gradient non-linearity (GNL) induced distortions in MRI; however, hinder the implementation of MRI-Linac system in image-guided radiotherapy where highly accurate geometry and anatomy of the target tumour is indispensable. METHODS To correct the geometric distortions in MR images, in particular, for the 1 Tesla (T) MRI-Linac system, a deep fully-connected neural network was proposed to automatically learn the intricate relationship between the undistorted (theoretical) and distorted (real) space. A data set, consisting of spatial samples acquired by phantom measurement that covers both inside and outside the working diameter of spherical volume (DSV), was utilised for training the neural network; which offers the ability to describe subtle deviations of the GNL field within the entire region of interest (ROI). RESULTS The performance of the proposed method was evaluated on MR images of a three-dimensional (3D) phantom and the pelvic region of an adult volunteer scanned in the 1T MRI-Linac system. The experimental results showed that the severe geometric distortions within the entire ROI had been successfully corrected with an error less than the pixel size. Also, the presented network is highly efficient, which achieved significant improvement in terms of computational efficiency compared to existing methods. CONCLUSIONS The feasibility of the presented deep neural network for characterising the GNL field deviations in the 1T MRI-Linac system was demonstrated in this study, which shows promise in facilitating the MRI-Linac system to be routinely implemented in real-time MRI-guided radiotherapy.
Adherence of Giardia lamblia Trophozoites to Int-407 Human Intestinal Cells

Attachment of Giardia lamblia trophozoites to enterocytes is essential for colonization of the small intestine and is considered a prerequisite for parasite-induced enterocyte dysfunction and clinical disease. In this work, coincubation of Giardia with Int-407 cells, was used as an in vitro model to study the role of cytoskeleton and surface lectins involved in the attachment of the parasite. This interaction was also studied by scanning and transmission electron microscopy. Adherence was dependent on temperature and was maximal at 37°C. It was reduced by 2.5 mM colchicine (57%), mebendazole (10 m g/ml) (59%), 100 mM glucose (26%), 100 mM mannose (22%), 40 mM mannose-6-phosphate (18%), and concanavalin A (100 m g/ml) (21%). No signiﬁcant modiﬁcation was observed when Giardia was pretreated with cytochalasins B and D and with EDTA. Giardia attachment was also diminished by preincubating Int-407 cells with cytochalasin B and D (5 m g/ml) (16%) and by glutaraldehyde ﬁxation of intestinal cells and of G. lamblia trophozoites (72 and 100%, respectively). Ultrastructural studies showed that Giardia attaches to the Int-407 monolayer predominantly by its ventral surface. Int-407 cells contact trophozoites with elongated microvilli, and both trophozoite imprints and interactions of Giardia ﬂagella with intestinal cells were also observed. Transmission electron microscopy showed that Giardia lateral crest and ventrolateral ﬂange were important structures in the adherence process. Our results suggest a combination of mechanical and hydrodynamic forces in trophozoite attachment; surface lectins also seem to mediate binding and may be involved in speciﬁc recognition of host cells. Controls. For all experiments, the results were compared with an equal num- ber of control attachment assays. These assays were done at the same time as test wells under identical conditions but without the alteration of the coculture parameter on the compound being tested. Further control experiments were done in medium containing DMSO (1%). Statistical analysis. Each determination was carried out in duplicate and in at least three separate experiments. Results were compared with values for controls that had been run concomitantly and are expressed as mean values 6 standard deviations ( n $ 6) unless otherwise noted. Student’s t test was used to assess differences, with a P of , 0.05 being considered signiﬁcant.
An evaluation of alternative procedures using the Bou-Rouch method for sampling hyporheic invertebrates

This study assesses the influence of well design, pumping rate, and sample volume on hyporheic invertebrate density and richness estimates in three streams differing in sediment composition. A comparison of five well designs, i.e., temporary wells with no pores and with 4-, 6-, and 8-mm pores along the lower 15 cm and permanent wells with 6-mm pores, revealed no significant differences in either total invertebrate densities or taxon richness. Pumping rates, i.e., 1.5 versus 4 L·min -1 , significantly affected density estimates at two streams and taxon richness at one of the three streams, shown by higher values at the faster pumping rate. A comparison of five sample volume sizes, i.e., 0.5, 1.0, 1.5, 2.0, and 2.5 L, indicated that smaller sample volumes produced significantly higher estimates of density, while larger sample volumes gave significantly higher estimates of taxon richness. These results underscore the importance of maintaining consistent pumping rates and sample volume sizes throughout the course of a study.
Stress-induced Mouse Model of the Cardiac Manifestations of Friedreich's Ataxia Corrected by AAV-mediated Gene Therapy.

Friedreich's ataxia (FA), an autosomal recessive disorder caused by a deficiency in the expression of frataxin (FXN), is characterized by progressive ataxia and hypertrophic cardiomyopathy. Although cardiac dysfunction is the most common cause of mortality in FA, the cardiac disease remains subclinical for most of the clinical course because the neurologic disease limits muscle oxygen demands. Previous FXN knockout mouse models exhibit fatal cardiomyopathy similar to human FA but in contrast to the human condition, untreated mice become moribund by 2 months of age unlike humans where the cardiac disease often does not manifest until the 3rd decade. The study was designed to create a mouse model for early FA disease relevant to the time for which a gene therapy would likely be most effective. To generate a cardiac-specific mouse model of FA cardiomyopathy similar to the human disease, we used a cardiac promoter (αMyhc) driving Cre-recombinase cardiac-specific excision of FXN exon 4 to generate a mild cardiac-specific FA model that is normal at rest but exhibits the cardiac phenotype with stress. The hearts of αMyhc mice had decreased levels of FXN and activity of mitochondrial complex II/complex IV respiratory chain. At rest, the αMyhc mice exhibited normal cardiac function as assessed by echocardiographic assessment of ejection fraction and fractional shortening, but when the heart was stressed chemically with dobutamine, αMyhc mice compared to littermate control mice had a 62% reduction in stress ejection fraction (p<2×10-4) and 71% reduction in stress-related fractional shortening (p<10-5). When assessing functional cardiac performance using running on an inclined treadmill, αMyhc mice stayed above the midline 3-fold less than littermate controls (p<0.02). A one-time intravenous administration of 1011 genome copies of AAVrh.10hFXN, an adeno-associated virus serotype rh10 gene transfer vector expressing human FXN, corrected the stress-induced ejection fraction and fractional shortening phenotypes. Treated αMyhc mice exhibited exercise performance on a treadmill indistinguishable from littermate controls (p>0.07). These αMyhc mice provide an ideal model to study long-term cardiac complications due to FA and AAV-mediated gene therapy correction of stress-induced cardiac phenotypes typical of human FA.
Methotrexate and rheumatoid arthritis associated interstitial lung disease

Question addressed by the study Methotrexate (MTX) is a key anchor drug for rheumatoid arthritis (RA) management. Fibrotic interstitial lung disease (ILD) is a common complication of RA. Whether MTX exposure increases the risk of ILD in patients with RA is disputed. We aimed to evaluate the association of prior MTX use with development of RA-ILD. Methods Through a case–control study design with discovery and international replication samples, we examined the association of MTX exposure with ILD in 410 patients with chronic fibrotic ILD associated with RA (RA-ILD) and 673 patients with RA without ILD. Estimates were pooled over the different samples using meta-analysis techniques. Results Analysis of the discovery sample revealed an inverse relationship between MTX exposure and RA-ILD (adjusted OR 0.46, 95% CI 0.24–0.90; p=0.022), which was confirmed in the replication samples (pooled adjusted OR 0.39, 95% CI 0.19–0.79; p=0.009). The combined estimate using both the derivation and validation samples revealed an adjusted OR of 0.43 (95% CI 0.26–0.69; p=0.0006). MTX ever-users were less frequent among patients with RA-ILD compared to those without ILD, irrespective of chest high-resolution computed tomography pattern. In patients with RA-ILD, ILD detection was significantly delayed in MTX ever-users compared to never-users (11.4±10.4 years and 4.0±7.4 years, respectively; p<0.001). Answer to the question Our results suggest that MTX use is not associated with an increased risk of RA-ILD in patients with RA, and that ILD was detected later in MTX-treated patients. This multi-ethnic case–control study showed that methotrexate use is not associated with an increased risk of interstitial lung disease in patients with rheumatoid arthritis https://bit.ly/3fC8skd