Miracle-dz/UniFAR-FTUs huggingface dataset:
Applying QuEChERS Method in Screening for Polychlorinated Biphenyls (PCBs) from Raw and Wastewater from Gaborone (Botswana) and Mafikeng (South Africa)

Wastewater contains a variety of chemical substances owing to the different sources that contribute to affluent into sewage treatment plants. Raw and wastewater samples were obtained from the surface of the water bodies at depths of 50 and 100 metres but at different locations in each sampling site. The water samples were subjected to extraction of polychlorinated biphenyls (PCBs) using QuEChERS (Quick, Easy, Cheap, Effective, Rugged and Safe) extraction kit before analysis using the Gas Chromatography Mass Spectrometer (GC-MS). The control samples had turbidity, temperature and pH values within the acceptable levels as per Botswana, South Africa and WHO drinking water standards. Turbidity values were rather higher than the set standards for raw and wastewater, with water samples from Modimola/Setumo dam having recorded the highest range of 25.0 – 200 Nephelometric Turbidity Units (NTU). The same sampling site also had water samples with pH higher at 9.01 to 9.78. Wastewater effluent in Notwane Sewage Treatment Plant, Gaborone Dam (both in Gaborone) and Disaneng Dam (South Africa) have polychlorinated biphenyls (PCBs) below detectable levels by the Agilent Gas Chromatography Mass Spectrometer (GC-MS). Only traces of PCBs were detected from wastewater from Modimola dam in Mafikeng. This may be due to the different industries in Mafikeng producing various chemicals compared to Gaborone. The water in Modimola dam therefore requires thorough treatment before it can be returned for domestic consumption as PCBs are toxic compounds that are found to trigger cancer in humans and also affect the reproduction system resulting in low IQ.
Rapid re‐transplantation safety following early kidney graft loss

Early graft loss is a devastating kidney transplant complication associated with high mortality and an increased risk of sensitization to antigens from the failed graft. Moreover, if rapid re‐transplantation were to occur, given that the human leukocyte antigen antibodies identification may not be reliable until several weeks after transplantation, the recipient's immunological status would be uncertain. Hence, there could be an increased immunological risk. To date, there is no information on whether a rapid re‐transplantation after early graft loss, without a new reliable anti‐HLA determination, is safe.
The synaptic blocker botulinum toxin A decreases the density and complexity of oligodendrocyte precursor cells in the adult mouse hippocampus

Oligodendrocyte progenitor cells (OPCs) are responsible for generating oligodendrocytes, the myelinating cells of the CNS. Life‐long myelination is promoted by neuronal activity and is essential for neural network plasticity and learning. OPCs are known to contact synapses and it is proposed that neuronal synaptic activity in turn regulates their behavior. To examine this in the adult, we performed unilateral injection of the synaptic blocker botulinum neurotoxin A (BoNT/A) into the hippocampus of adult mice. We confirm BoNT/A cleaves SNAP‐25 in the CA1 are of the hippocampus, which has been proven to block neurotransmission. Notably, BoNT/A significantly decreased OPC density and caused their shrinkage, as determined by immunolabeling for the OPC marker NG2. Furthermore, BoNT/A resulted in an overall decrease in the number of OPC processes, as well as a decrease in their lengths and branching frequency. These data indicate that synaptic activity is important for maintaining adult OPC numbers and cellular integrity, which is relevant to pathophysiological scenarios characterized by dysregulation of synaptic activity, such as age‐related cognitive decline, Multiple Sclerosis and Alzheimer's disease.
TRAUMATIC BRAIN INJURY MECHANISMS IN THE GOTTINGEN MINIPIG IN RESPONSE TO TWO UNIQUE INPUT MODES

Traumatic brain injury (TBI) continues to be a widespread problem in the United States with approximately 1.7 million occurrences annually. Current automotive crash test standards use the Head Injury Criterion (HIC) to assess head injury potential, but this metric does not relate an impact to underlying damage. For an injury metric to effectively predict TBI, it is crucial to relate level of impact to resulting injury. The research presented in this dissertation explains the development and repeatability of two novel injury devices, impact response characterization over the course of 24 hours in the Göttingen minipig and the relationships between metabolite changes, underlying disruption, and impact kinematics, and the characterization of impact response over the course of 72 hours. The translation-input and combined translation and rotation-input injury devices were shown to be repeatable, minimizing the number of animals needed for testing. Impact response over the course of 24 hours showed axonal disruption through immunostaining and proton magnetic resonance spectroscopy. The translation-input injury group metabolite analyses revealed the initial stages of glutamate excitotoxicity while the combined-input injury group showed a clear pathway for glutamate excitotoxicity. Numerous correlative relationships and potential underlying disruption predictors were found between metabolites, immunostaining, and kinematics. The most promising predictor combination for the translation-input injury device was N-acetylaspartylglutamate/Scyllo at 24 hours compared to 1 hour and linear speed for predicting underlying light neurofilament disruption. For the combined-input injury device, the strongest predictor combination was Glutamine/N-acetylaspartylglutamate at 24 hours compared to baseline and angular acceleration for predicting underlying light neurofilament disruption. Statistically significant predictors were found between Glutamate+Glutamine/Total Creatine at 24 hours compared to baseline and all kinematics and injury metrics with an angular component for predicting heavy neurofilament disruption. Analyses over the course of 72 hours revealed persistent axonal disruption and metabolite perturbations. Overall, this dissertation and the complementary parts of this project have many societal implications. Due to the high incidence of traumatic brain injury, there is a need for prevention, mitigation, and treatment strategies. Developing a new injury metric will help improve prevention strategies, especially in the automotive, sporting, and military environments.
Microgrid Scheduling for Reliable, Cost-Effective, and Environmentally Friendly Energy Management

There has been a growing interest in microgrids because of various advantages such as environmental benefits through its integration with renewables, possible cost-efficient replacement of the electricity infrastructure in isolated areas, and improvement of reliability and resilience using multiple energy sources. However, the microgrid faces various challenges in operational management because it deals with a multitude of energy sources mainly comprising renewables (municipal solid waste incineration and solar and wind energy), fuels (natural gas, hydrogen, and biofuel), and batteries. In this work, we developed a mixed-integer linear programming model for cost-efficient and environmentally friendly scheduling in the microgrid operation. The model provides optimal schedules with minimal cost or reduced environmental impacts, e.g., global warming potential, while satisfying the balance of electricity supply and demand. Notably, an additional set of diversity constraints is incorporated within the model to.
The Promise of Tubule Biomarkers in Kidney Disease: A Review.

For over 70 years, serum creatinine has remained the primary index for detection and monitoring of kidney disease. Tubulo-interstitial damage and fibrosis are highly prognostic for subsequent kidney failure in biopsy studies, yet this pathology is invisible to the clinician in the absence of a biopsy. Recent discovery of biomarkers that reflect distinct aspects of kidney tubule disease have led to investigations of whether these markers can provide additional information on risk of CKD progression and associated adverse clinical endpoints, above and beyond eGFR and albuminuria. These biomarkers can be loosely grouped into those that mark tubule cell injury (e.g. KIM-1, MCP-1), and those that mark tubule cell dysfunction (e.g. α1M, UMOD). These kidney tubule biomarkers provide new opportunities to monitor response to therapeutics used to treat CKD patients. In this review, we describe results from some unique contributions in this area, and discuss current challenges and requirements in the field to bring these markers to clinical practice. We advocate for a broader assessment of kidney health that moves beyond a focus on the glomerulus, and we highlight how such tools can improve diagnostic accuracy and earlier assessment of therapeutic efficacy or harm in CKD patients.
Exploring surveillance data biases when estimating the reproduction number: with insights into subpopulation transmission of COVID-19 in England

The time-varying reproduction number (Rt: the average number of secondary infections caused by each infected person) may be used to assess changes in transmission potential during an epidemic. While new infections are not usually observed directly, they can be estimated from data. However, data may be delayed and potentially biased. We investigated the sensitivity of Rt estimates to different data sources representing COVID-19 in England, and we explored how this sensitivity could track epidemic dynamics in population sub-groups. We sourced public data on test-positive cases, hospital admissions and deaths with confirmed COVID-19 in seven regions of England over March through August 2020. We estimated Rt using a model that mapped unobserved infections to each data source. We then compared differences in Rt with the demographic and social context of surveillance data over time. Our estimates of transmission potential varied for each data source, with the relative inconsistency of estimates varying across regions and over time. Rt estimates based on hospital admissions and deaths were more spatio-temporally synchronous than when compared to estimates from all test positives. We found these differences may be linked to biased representations of subpopulations in each data source. These included spatially clustered testing, and where outbreaks in hospitals, care homes, and young age groups reflected the link between age and severity of the disease. We highlight that policy makers could better target interventions by considering the source populations of Rt estimates. Further work should clarify the best way to combine and interpret Rt estimates from different data sources based on the desired use. This article is part of the theme issue ‘Modelling that shaped the early COVID-19 pandemic response in the UK’.
Changes in the nutritional content of children's lunches after the Food Dudes healthy eating programme

Abstract Previous research into the effectiveness of healthy eating programmes has shown increases in healthful eating behaviour in primary schools; however, data collection methods have not been sufficiently sensitive to detect micronutrient changes. The present study extends the literature by measuring individual children's intake of macro- and micronutrients at lunchtime, before and after a programme targeting children's consumption of fruit and vegetables, to identify evidence-based health benefits of programme participation. Baseline data were collected over 4 d at lunchtime in two primary schools. The Food Dudes programme was then implemented in the intervention school. Follow-up data were collected over 4 d in each school 2 months after baseline. We employed a validated and sensitive photographic method to estimate individual children's (N 112) consumption of fruit, vegetables, and their intake of calories, macro- and selected micronutrients. Significant changes were observed in the intervention school but not in the control school: Children's consumption of fruit, vegetables, vitamin C and E intake increased, while their total energy consumption, fat, saturated fat, and sodium intake decreased. The present results show that the Food Dudes programme produced a positive nutritional change, with implications for its application as a healthy eating and obesity prevention intervention. These optimistic conclusions should be tested by further research to establish the longevity of the positive effects presented here.
Business and Economics Students’ Self-Reports on Academic Reading in English as L2: A Factor Analysis

Abstract Adequate reading behaviour is vital for text comprehension across fields. In today’s professional environment, a well-developed reading skill is also expected in English as a second language (EL2), which happens already in college, although transition to college-level reading may be difficult even in the first language. It is therefore useful to analyse students’ use of reading strategies to facilitate their academic progress. This study investigates the reading behaviour of junior students of business/economics when reading academic texts in EL2. We conducted an exploratory factor analysis (N=134) of a 45-item questionnaire about students’ awareness of reading strategies and their reading confidence (i.e. self-perceived competence in text retelling). The majority of the items were based on self-reports found in the literature (Kolić-Vehovec, Bajšanski, 2001; Mokhtari, Reichard, 2002; Taraban, Kerr, Rynearson, 2004) and several items were added to the questionnaire (e.g. questions related to note taking). Five factors were interpretable: four factors related to Metacognitive Awareness of Reading Strategies (Repeated Reading, Monitoring/Regulation, Note Taking and Elaboration) and the fifth factor covering self-perceived competence in text retelling (Reading Confidence). Internal consistency of the factors indicated by standardized Cronbach’s alphas were 0.83 (Repeated Reading), 0.80 (Monitoring and Regulation), 0.77 (Note Taking), 0.63 (Elaboration) and 0.75 (Reading Confidence). Three strategies positively correlated with each other (Repeated Reading, Monitoring/Regulation and Elaboration), while negative correlation was found between Note Taking and Reading Confidence. The results provide valuable information on the patterns in student reading as a baseline for further analysis of L2 text comprehension in college.
Sustained Ability of a Natural Microbial Community to Remove Nitrate from Groundwater

Microbial-mediated nitrate removal from groundwater is widely recognized as the predominant mechanism for nitrate attenuation in contaminated aquifers and is largely dependent on the presence of a carbon-bearing electron donor. The repeated exposure of a natural microbial community to an electron donor can result in the sustained ability of the community to remove nitrate; this phenomenon has been clearly demonstrated at the laboratory scale. However, in situ demonstrations of this ability are lacking. For this study, ethanol (electron donor) was repeatedly injected into a groundwater well (treatment) for six consecutive weeks to establish the sustained ability of a microbial community to remove nitrate. A second well (control) located up-gradient was not injected with ethanol during this time. The treatment well demonstrated strong evidence of sustained ability as evident by concomitant ethanol and nitrate removal and subsequent sulfate removal upon consecutive exposures. Both wells were then monitored for six additional weeks under natural (no injection) conditions. During the final week, ethanol was injected into both treatment and control wells. The treatment well demonstrated sustained ability as evident by concomitant ethanol and nitrate removal whereas the control did not. Surprisingly, the treatment well did not indicate a sustained and selective enrichment of a microbial community. These results suggested that the predominant mechanism(s) of sustained ability likely exist at the enzymatic- and/or genetic-levels. The results of this study demonstrated that the in situ ability of a microbial community to remove nitrate can be sustained in the prolonged absence of an electron donor. Moreover, these results implied that the electron-donor exposure history of nitrate-contaminated groundwater can play an important role nitrate attenuation. Article Impact Statement Groundwater microbes sustain ability to remove nitrate in absence of carbon and energy source.
Manganese transport by Streptococcus sanguinis in acidic conditions and its impact on growth in vitro and in vivo

Streptococcus sanguinis is an oral commensal and an etiological agent of infective endocarditis. Previous studies have identified the SsaACB manganese transporter as essential for endocarditis virulence; however, the significance of SsaACB in the oral environment has never been examined. Here we report that a ΔssaACB mutant of strain SK36 exhibits reduced growth and manganese uptake under acidic conditions. Further studies revealed that these deficits resulted from the decreased activity of TmpA, shown in the accompanying paper to function as a ZIP-family manganese transporter. Transcriptomic analysis of fermentor-grown cultures of SK36 WT and ΔssaACB strains identified pH-dependent changes related to carbon catabolite repression in both strains, though their magnitude was generally greater in the mutant. In strain VMC66, which possesses a MntH transporter, loss of SsaACB did not significantly alter growth or cellular manganese levels under the same conditions. Interestingly, there were only modest differences between SK36 and its ΔssaACB mutant in competition with Streptococcus mutans in vitro and in a murine oral colonization model. Our results suggest that the heterogeneity of the oral environment may provide a rationale for the variety of manganese transporters found in S. sanguinis and point to strategies for enhancing the safety of oral probiotics. Graphical Abstract Depiction of methods. Streptococcal strains used are depicted at the top. The four methods illustrated are: 1. S. sanguinis cells were grown in media at pH 7.3 and pH 6.2 and quantified by plating. 2. S. sanguinis cells were grown in a fermentor vessel for RNA-sequencing and metal analysis. 3. S. sanguinis and S. mutans cells were grown in 12-well plates singly or in competition, then plated and the pH of the media measured. 4. S. sanguinis and S. mutans cells were inoculated into the mouths of mice. Oral swabs and dental biofilms from molars were assayed for bacterial composition by qPCR. (Biorender)
Zones of cellular damage around pulsed-laser wounds

After a tissue is wounded, cells surrounding the wound adopt distinct wound-healing behaviors to repair the tissue. Considerable effort has been spent on understanding the signaling pathways that regulate immune and tissue-resident cells as they respond to wounds, but these signals must ultimately originate from the physical damage inflicted by the wound. Tissue wounds comprise several types of cellular damage, and recent work indicates that different types of cellular damage initiate different types of signaling. Hence to understand wound signaling, it is important to identify and localize the types of wound-induced cellular damage. Laser ablation is widely used by researchers to create reproducible, aseptic wounds in a tissue that can be live-imaged. Because laser wounding involves a combination of photochemical, photothermal and photomechanical mechanisms, each with distinct spatial dependencies, cells around a pulsed-laser wound will experience a gradient of damage. Here we exploit this gradient to create a map of wound-induced cellular damage. Using genetically-encoded fluorescent proteins, we monitor damaged cellular and sub-cellular components of epithelial cells in living Drosophila pupae in the seconds to minutes following wounding. We hypothesized that the regions of damage would be predictably arrayed around wounds of varying sizes, and subsequent analysis found that all damage radii are linearly related over a 3-fold range of wound size. Thus, around laser wounds, the distinct regions of damage can be estimated after measuring any one. This report identifies several different types of cellular damage within a wounded epithelial tissue in a living animal. By quantitatively mapping the size and placement of these different types of damage, we set the foundation for tracing wound-induced signaling back to the damage that initiates it.
Integration and comparison of multi-omics profiles of NGLY1 deficiency plasma and cellular models to identify clinically relevant molecular phenotypes

NGLY1 (N-glycanase 1) deficiency is a rare congenital recessive disorder of protein deglycosylation unaddressed by the current standard of care. Using combined metabolomics and proteomics profiling, we show that NGLY1 deficiency activates the immune response and disturbs lipid metabolism, biogenic amine synthesis, and glutathione metabolism. These alterations were also observed in NGLY1 deficient patient-derived induced pluripotent stem cells (iPSCs) and differentiated neural progenitor cells (NPCs), which serve as personalized cellular models of the disease. These findings provide molecular insight into the pathophysiology of NGLY1 deficiency and suggest potential therapeutic strategies.
Short- and long-term effects of amoxicillin/clavulanic acid or doxycycline on the gastrointestinal microbiome of growing cats

Antibiotic treatment in early life influences gastrointestinal (GI) microbial composition and function. In humans, the resultant intestinal dysbiosis is associated with an increased risk for certain diseases later in life. The objective of this study was to determine the temporal effects of antibiotic treatment on the GI microbiome of young cats. Fecal samples were collected from cats randomly allocated to receive either amoxicillin/clavulanic acid (20 mg/kg q12h) for 20 days (AMC group; 15 cats) or doxycycline (10 mg/kg q24h) for 28 days (DOX group;15 cats) as part of the standard treatment of upper respiratory tract infection. In addition, feces were collected from healthy control cats (CON group;15 cats). All cats were approximately two months of age at enrolment. Samples were collected on days 0 (baseline), 20 or 28 (AMC and DOX, respectively; last day of treatment), 60, 120, and 300. DNA was extracted and sequencing of the 16S rRNA gene and qPCR assays were performed. Fecal microbial composition was different on the last day of treatment for AMC cats, and 1 month after the end of antibiotic treatment for DOX cats, compared to CON cats. Species richness was significantly greater in DOX cats compared to CON cats on the last day of treatment. Abundance of Enterobacteriales was increased, and that of Erysipelotrichi was decreased in cats of the AMC group on the last day of treatment compared to CON cats. The abundance of the phylum Proteobacteria was increased in cats of the DOX group on days 60 and 120 compared to cats of the CON group. Only minor differences in abundances between the treatment groups and the control group were present on day 300. Both antibiotics appear to delay the developmental progression of the microbiome, and this effect is more profound during treatment with amoxicillin/clavulanic acid and one month after treatment with doxycycline. Future studies are required to determine if these changes influence microbiome function and whether they have possible effects on disease susceptibility in cats.