Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence of gastrointestinal parasitic infections in wild mammals of a safari park and a zoo in Bangladesh

Abstract In safari parks and zoos, wild animals are kept mainly for recreational purposes. Animals in these enclosures are also crucial for the education, research, and conservation aspect. To ensure better management and good health of wild animals in captivity, it is essential to monitor the occurrence of gastrointestinal (GI) parasitic (helminths and protozoa) infections. The current investigation was undertaken to investigate the prevalence of GI parasitic infections in wild mammals at Bangabandhu Sheikh Mujib (BSM) safari park and Chattogram (CTG) zoo of Bangladesh. A total of 72 individual faecal samples were collected from 25 species of wild mammals. Routine qualitative (e.g. direct smear, sedimentation, and flotation) and quantitative (e.g. McMaster technique) tests were performed to identify the eggs or oocysts of helminths and protozoa. Results demonstrated that wild mammals of both BSM safari park and CTG zoo were infected with a total of 17 genera/species of helminths and protozoa. The overall prevalence of GI parasitic infections in wild mammals of both zoological parks was 65.3% (95% confidence interval [CI]: 53.14–76.12), whereas it was 72.4% (95% CI: 52.76–87.27) in the BSM safari park and 60.5% (95% CI: 44.41–75.02) in the CTG zoo. In both zoological parks, infection with nematodes was more frequent compared to other helminth into the wild mammals. The herbivores were more infected with GI parasites than carnivores and omnivores of both BSM safari park and CTG zoo. The mean eggs/oocysts per gram of faeces was the highest in the carnivores compared to herbivores and omnivores of both enclosures. The findings of the current study demonstrated that wild mammals of both BSM safari park and CTG zoo suffered from various GI parasitic infections. Regular monitoring along with proper therapeutic measures may reduce the severe consequences of GI parasitic infections in captive wild animals.
Polygenic Scores Help Reduce Racial Disparities in Predictive Accuracy of Automated Type 1 Diabetes Classification Algorithms.

OBJECTIVE Automated algorithms to identify individuals with type 1 diabetes using electronic health records are increasingly used in biomedical research. It is not known whether the accuracy of these algorithms differs by self-reported race. We investigated whether polygenic scores improve identification of individuals with type 1 diabetes. RESEARCH DESIGN AND METHODS We investigated two large hospital-based biobanks (Mass General Brigham [MGB] and BioMe) and identified individuals with type 1 diabetes using an established automated algorithm. We performed medical record reviews to validate the diagnosis of type 1 diabetes. We implemented two published polygenic scores for type 1 diabetes (developed in individuals of European or African ancestry). We assessed the classification algorithm before and after incorporating polygenic scores. RESULTS The automated algorithm was more likely to incorrectly assign a diagnosis of type 1 diabetes in self-reported non-White individuals than in self-reported White individuals (odds ratio 3.45; 95% CI 1.54-7.69; P = 0.0026). After incorporating polygenic scores into the MGB Biobank, the positive predictive value of the type 1 diabetes algorithm increased from 70 to 97% for self-reported White individuals (meaning that 97% of those predicted to have type 1 diabetes indeed had type 1 diabetes) and from 53 to 100% for self-reported non-White individuals. Similar results were found in BioMe. CONCLUSIONS Automated phenotyping algorithms may exacerbate health disparities because of an increased risk of misclassification of individuals from underrepresented populations. Polygenic scores may be used to improve the performance of phenotyping algorithms and potentially reduce this disparity.
CrAssphage May Be Viable Markers of Contamination in Pristine and Contaminated River Water

Rivers support substantial populations and provide important ecosystem services. Despite the application of fecal coliform tests and other markers, we lack rapid and reproducible approaches for determining fecal contamination in rivers. ABSTRACT Viruses are the most biologically abundant entities and may be ideal indicators of fecal pollutants in water. Anthropogenic activities have triggered drastic ecosystem changes in rivers, leading to substantial shifts in chemical and biological attributes. Here, we evaluate the viability of using the presence of crAssphage as indicators of fecal contamination in South African rivers. Shotgun analysis revealed diverse crAssphage viruses in these rivers, which are impacted by chemical and biological pollution. Overall, the diversity and relative abundances of these viruses was higher in contaminated sites compared to pristine locations. In contrast to fecal coliform counts, crAssphage sequences were detected in pristine rivers, supporting the assertion that the afore mentioned marker may be a more accurate indicator of fecal contamination. Our data demonstrate the presence of diverse putative hosts which includes members of the phyla Bacteroidota, Pseudomonadota, Verrucomicrobiota, and Bacillota. Phylogenetic analysis revealed novel subfamilies, suggesting that rivers potentially harbor distinct and uncharacterized clades of crAssphage. These data provide the first insights regarding the diversity, distribution, and functional roles of crAssphage in rivers. Taken together, the results support the potential application of crAssphage as viable markers for water quality monitoring. IMPORTANCE Rivers support substantial populations and provide important ecosystem services. Despite the application of fecal coliform tests and other markers, we lack rapid and reproducible approaches for determining fecal contamination in rivers. Waterborne viral outbreaks have been reported even after fecal indicator bacteria (FIB) were suggested to be absent or below regulated levels of coliforms. This indicates a need to develop and apply improved indicators of pollutants in aquatic ecosystems. Here, we evaluate the viability of crAssphage as indicators of fecal contamination in two South African rivers. We assess the abundance, distribution, and diversity of these viruses in sites that had been predicted pristine or contaminated by FIB analysis. We show that crAssphage are ideal and sensitive markers for fecal contamination and describe novel clades of crAss-like phages. Known crAss-like subfamilies were unrepresented in our data, suggesting that the diversity of these viruses may reflect geographic locality and dependence.
Cytogenotoxic, insecticidal, and phytotoxic activity from biomass extracts of the freshwater algae Nitella furcata

ABSTRACT Agroecology, the application of ecological concepts to agricultural production, has been developing over the last years with consequent promotion for discovery of bioactive compounds to control pests and abolish crop diseases. In this context, algae from Nitella genus are characterized by high potential for bioeconomic applications due to (1) available biomass for harvesting or cultivation and (2) production of allelochemicals, which present a potential to protect field crops from insect infestation. Therefore, this study aimed to determine primary and secondary metabolites derived from aqueous and hydroethanolic extracts of Nitella furcata and to evaluate phytotoxic, cytogenotoxic, insecticidal, and pro-oxidative activities of these extracts. Determination of metabolites showed the presence predominantly of carbohydrates, proteins, phenols, and flavonoids in hydroethanolic extract. Both extracts of N. furcata interfered in the germination of seeds and development of seedlings of Lactuca sativa, with hydroethanolic extract exhibiting greater inhibition. Both extracts also interfered with meristematic cells of Allium cepa as evidenced by chromosomal alterations and higher pro-oxidative activity. Aqueous extract at 5 and 0 mg/ml produced 100% insect mortality. Further, hydroethanolic extract at 0 mg/ml was lethal immediately upon exposure. Therefore, results demonstrate that N. furcata is potential algae species to be considered for development of environmental and ecotoxicological studies as a source of compounds with potential use in agroecological strategies.
Experimental kS estimation: A comparison of methods for Corynebacterium glutamicum from lab to microfluidic scale

Knowledge about the specific affinity of whole cells toward a substrate, commonly referred to as kS, is a crucial parameter for characterizing growth within bioreactors. State‐of‐the‐art methodologies measure either uptake or consumption rates at different initial substrate concentrations. Alternatively, cell dry weight or respiratory data like online oxygen and carbon dioxide transfer rates can be used to estimate kS. In this work, a recently developed substrate‐limited microfluidic single‐cell cultivation (sl‐MSCC) method is applied for the estimation of kS values under defined environmental conditions. This method is benchmarked with two alternative microtiter plate methods, namely high‐frequency biomass measurement (HFB) and substrate‐limited respiratory activity monitoring (sl‐RA). As a model system, the substrate affinity kS of Corynebacterium glutamicum ATCC 13032 regarding glucose was investigated assuming a Monod‐type growth response. A kS of <70.7 mg/L (with 95% probability) with HFB, 8.55 ± 1.38 mg/L with sl‐RA, and 2.66 ± 0.99 mg/L with sl‐MSCC was obtained. Whereas HFB and sl‐RA are suitable for a fast initial kS estimation, sl‐MSCC allows an affinity estimation by determining tD at concentrations less or equal to the kS value. Thus, sl‐MSCC lays the foundation for strain‐specific kS estimations under defined environmental conditions with additional insights into cell‐to‐cell heterogeneity.
Orphans in Syria and Iraq Juggling Balls: Wars, COVID-19, and the NGO’s financial crisis

ABSTRACT The COVID-19 pandemic’s impact varies between and within nations, causing new forms of inequality. Refugee and orphan children in conflicted areas are more likely to suffer due to poverty, vulnerability, and limited access to essential services including reduction in donor funding. This qualitative study is the first to assess the effects of the COVID-19 pandemic and the financial crisis on Iraqi and Syrian orphaned children and their mothers. The Modified Grounded Theory was used for the preliminary analysis to expand the range of themes. This study has identified five major themes: financial crisis, low educational attainment, child labour, mental health issues, violence, and social problems. The impact of COVID-19 children and adolescents’ mental health is of great concern. These multiple crises may significantly impact orphan children and adolescents’ cognitive, mental health, and physical development. It is critical to address mental health issues during the current crisis and to plan for possible future pandemics and their intersecting outcomes. A Holistic approach requires providers to be aware of their clients’ intersecting circumstances and needs using a range of lenses, including the person in the environment, family dynamics, culture, politics, and structural challenges. Offering food, medical supplies, and housing are considered basic needs.
Molecular characterization of the intact mouse muscle spindle using a multi-omics approach

The proprioceptive system is essential for the control of coordinated movement, posture, and skeletal integrity. The sense of proprioception is produced in the brain using peripheral sensory input from receptors such as the muscle spindle, which detects changes in the length of skeletal muscles. Despite its importance, the molecular composition of the muscle spindle is largely unknown. In this study, we generated comprehensive transcriptomic and proteomic datasets of the entire muscle spindle isolated from the murine deep masseter muscle. We then associated differentially expressed genes with the various tissues composing the spindle using bioinformatic analysis. Immunostaining verified these predictions, thus establishing new markers for the different spindle tissues. Utilizing these markers, we identified the differentiation stages the spindle capsule cells undergo during development. Together, these findings provide comprehensive molecular characterization of the intact spindle as well as new tools to study its development and function in health and disease.
Clinicopathological and prognostic value of chemokine receptor CCR7 expression in head and neck squamous cell carcinoma: a systematic review and meta-analysis

ABSTRACT Objectives This study aimed to identify the clinicopathological characteristics and prognostic value of CC chemokine receptor 7 (CCR7) expression in patients with head and neck squamous cell carcinoma (HNSSC). Methods The Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines were followed in this meta-analysis. Up to the 2nd of July 2022 a search was conducted using five databases: PubMed, Embase, Scopus, ProQuest, and Web of Science. The methodological standards for the epidemiological research scale were used to assess the quality of the included articles, and Stata software was used to synthesize the meta-analysis. Results We considered 13 of the 615 studies which included 1005 HNSCC patients. High expression of CCR7 increased the pooled odds ratio (OR) of advanced stage, tumor size, metastasis and recurrence by 2.82 [95% confidence interval (CI) 1.84 to 4.33], 2.48 (95% CI 1.68, to 3.67), 3.57, 95% CI 2.25 to 5.05) and 3.93 (95% CI 2.03 to 7.64), respectively. High CCR7 reduced overall patient survival [hazard ratio 2.62 (95% CI 1.59 to 4.32)]. Conclusion This study showed that high expression of CCR7 in HNSCC tumors was significantly associated with worse clinicopathological and survival outcomes, suggesting that CCR7 and its pathway could be potential therapeutic strategies for HNSCC.
Segmented filamentous bacteria impede rotavirus infection via retinoic acid receptor-mediated signaling

ABSTRACT Prevention of rotavirus (RV) infection by gut-resident segmented filamentous bacteria (SFB) is an example of the influence of gut microbiota composition on enteric viral infection. Yet, the mechanism by which SFB prevents RV infection is poorly understood. A recent report that SFB colonization of germfree mice generates retinoic acid (RA) thus activating RA receptor (RAR) signaling, which protected against Citrobacter rodentium infection, prompted us to investigate whether this pathway might contribute to SFB’s protection against RV infection. Colonization of conventional mice by SFB indeed increased intestinal RA levels and direct administration of RA partially mimicked the protection against RV infection conferred by SFB. Moreover, blockade of RAR signaling eliminated SFB’s protection against RV infection. Blockade of RAR signaling did not impact RV infection in the absence of SFB, nor did it alter the protection against RV infection conferred by bacterial flagellin, which in contrast to SFB, is dependent upon IL-22 signaling. SFB/RA-mediated prevention of RV infection was associated with an RA-dependent increase in enterocyte migration, consistent with the notion that enhanced anoikis is the ultimate means by which SFB, IL-22, and RA impede RV infection.
Denuded Descemet’s membrane supports human embryonic stem cell-derived retinal pigment epithelial cell culture

Recent clinical studies suggest that retinal pigment epithelial (RPE) cell replacement therapy may preserve vision in retinal degenerative diseases. Scaffold-based methods are being tested in ongoing clinical trials for delivering pluripotent-derived RPE cells to the back of the eye. The aim of this study was to investigate human embryonic stem cell-derived retinal pigment epithelial (hESC-RPE) cells survival and behaviour on a decellularized Descemet’s Membrane (DM), which may be of clinical relevance in retinal transplantation. DMs were isolated from human donor corneas and treated with thermolysin. The DM surface topology and the efficiency of the denudation method were evaluated by atomic force microscope, scanning electron microscopy and histology. hESC-RPE cells were seeded onto the endothelial-side surface of decellularized DM in order to determine the potential of the membrane to support hESC-RPE cell culture, alongside maintaining their viability. Integrity of the hESC-RPE monolayer was assessed by measuring transepithelial resistance. RPE-specific gene expression and growth factors secretion were assessed to confirm maturation and functionality of the cells over the new substrate. Thermolysin treatment did not affect the integrity of the tissue, thus ensuring a reliable method to standardize the preparation of decellularized DM. 24 hours post-seeding, hESC-RPE cell attachment and initial proliferation rate over the denuded DM were higher than hESC-RPE cells cultured on tissue culture inserts. On the new matrix, hESC-RPE cells succeeded in forming an intact monolayer with mature tight junctions. The resulting cell culture showed characteristic RPE cell morphology and proper protein localization. Gene expression analysis and VEGF secretion demonstrate DM provides supportive scaffolding and inductive properties to enhance hESC-RPE cells maturation. Decellularized DM was shown to be capable of sustaining hESC-RPE cells culture, thus confirming to be potentially a suitable candidate for retinal cell therapy.
Note-On the Optimality of Integer Lot Size Ratios in Economic Lot Size Determination in Multi-Stage Assembly Systems

The proof of a well known theorem by Crowston and Wagner in Crowston, Wagner, and Williams Crowston, W. B. , M. H. Wagner, J. F. , Williams. 1973. Economic lot size determination in multi-stage assembly systems. Management Sci.19 5, January 517-527. is shown here to be defective. According to this theorem, an optimal solution to the batch size determination problem for multi-echelon production/inventory assembly structures is characterized by a set of lot sizes, such that the lot size at each stage must be an integer multiple of the lot size at its successor stage. The theorem has been said to apply to uncapacitated assembly systems having constant final product demand over an infinite horizon, with no backlogs or lost sales permitted, where lot sizes must be rational numbers and time invariant. While the theorem supposedly applied to the case of both finite production rates and infinite production rates, the proof dealt only with the case of instantaneous production. Also, the proof implicitly assumed that lots were processed at any given stage only after unchanging spans of time. In this paper we show that with or without this implicit assumption, the theorem does hold true for the special case of instantaneous processing in two-level assembly systems; that is, configurations where there is only one successor stage in the entire system. However, we also show by counterexample that without this implicit assumption, the theorem is invalid for more general assembly structures. Furthermore, in the appendix of this paper we show that the proof is defective at the point where Crowston and Wagner extend their results for two-level systems to more general assembly systems. Thus it is an open question whether or not the theorem is valid for all assembly structures when processing at any given stage must occur only after unchanging spans of time.
The multifaceted virulence of adherent-invasive Escherichia coli

ABSTRACT The surge in inflammatory bowel diseases, like Crohn’s disease (CD), is alarming. While the role of the gut microbiome in CD development is unresolved, the frequent isolation of adherent-invasive Escherichia coli (AIEC) strains from patient biopsies, together with their propensity to trigger gut inflammation, underpin the potential role of these bacteria as disease modifiers. In this review, we explore the spectrum of AIEC pathogenesis, including their metabolic versatility in the gut. We describe how AIEC strains hijack the host defense mechanisms to evade immune attrition and promote inflammation. Furthermore, we highlight the key traits that differentiate AIEC from commensal E. coli. Deciphering the main components of AIEC virulence is cardinal to the discovery of the next generation of antimicrobials that can selectively eradicate CD-associated bacteria.
Assembly‐free quantification of vagrant DNA inserts

Inserts of DNA from extranuclear sources, such as organelles and microbes, are common in eukaryote nuclear genomes. However, sequence similarity between the nuclear and extranuclear DNA, and a history of multiple insertions, make the assembly of these regions challenging. Consequently, the number, sequence and location of these vagrant DNAs cannot be reliably inferred from the genome assemblies of most organisms. We introduce two statistical methods to estimate the abundance of nuclear inserts even in the absence of a nuclear genome assembly. The first (intercept method) only requires low‐coverage (<1×) sequencing data, as commonly generated for population studies of organellar and ribosomal DNAs. The second method additionally requires that a subset of the individuals carry extranuclear DNA with diverged genotypes. We validated our intercept method using simulations and by re‐estimating the frequency of human NUMTs (nuclear mitochondrial inserts). We then applied it to the grasshopper Podisma pedestris, exceptional for both its large genome size and reports of numerous NUMT inserts, estimating that NUMTs make up 0.056% of the nuclear genome, equivalent to >500 times the mitochondrial genome size. We also re‐analysed a museomics data set of the parrot Psephotellus varius, obtaining an estimate of only 0.0043%, in line with reports from other species of bird. Our study demonstrates the utility of low‐coverage high‐throughput sequencing data for the quantification of nuclear vagrant DNAs. Beyond quantifying organellar inserts, these methods could also be used on endosymbiont‐derived sequences. We provide an R implementation of our methods called “vagrantDNA” and code to simulate test data sets.
Safety and effectiveness of self-managed abortion using misoprostol alone acquired from an online telemedicine service in the United States.

OBJECTIVES To evaluate self-reported outcomes and serious adverse events following self-managed medication abortion using misoprostol alone provided from an online service. STUDY DESIGN We conducted a retrospective record review of self-managed abortion outcomes using misoprostol obtained from Aid Access, an online telemedicine organization serving United States (US) residents, between June 1, 2020, and June 30, 2020. The main outcomes were the proportion of people who reported ending their pregnancy without instrumentation intervention and the proportion who received treatment for serious adverse events. RESULTS During the study period, 1016 people received prescriptions for misoprostol. We obtained follow-up information for 610 (60%) of whom 568 confirmed use of the medication and 42 confirmed non-use. When taking the medication, 96% were at or less than 10 weeks' gestation and 4% were more than 10 weeks. Overall, 88% (95% CI: 84.6-90.2) reported successfully ending their pregnancy without instrumentation intervention. Of the 568 who took the misoprostol, 12 (2%) reported experiencing one or more serious adverse events and 20 (4%) reported experiencing a symptom of a potential complication. CONCLUSIONS Self-managed medication abortion using misoprostol provided by an online telemedicine service has a high rate of effectiveness and a low rate of serious adverse events. Outcomes compare favorably to other service delivery models using a similar regimen. As mifepristone continues to be over-regulated and the 2022 US Supreme Court ruling allows states to severely restrict access to in-clinic abortion care, this regimen is a promising option for self-managed abortion in the US.