Miracle-dz/UniFAR-FTUs huggingface dataset:
Genotypic Characterization of Uropathogenic Escherichia coli from Companion Animals: Predominance of ST372 in Dogs and Human-Related ST73 in Cats

Extraintestinal pathogenic Escherichia coli (ExPEC) account for over 80% and 60% of bacterial urinary tract infections (UTIs) in humans and animals, respectively. As shared uropathogenic E. coli (UPEC) strains have been previously reported among humans and pets, our study aimed to characterize E. coli lineages among UTI isolates from dogs and cats and to assess their overlaps with human UPEC lineages. We analysed 315 non-duplicate E. coli isolates from the UT of dogs (198) and cats (117) collected in central Germany in 2019 and 2020 utilizing whole genome sequencing and in silico methods. Phylogroup B2 (77.8%), dog-associated sequence type (ST) 372 (18.1%), and human-associated ST73 (16.6%), were predominant. Other STs included ST12 (8.6%), ST141 (5.1%), ST127 (4.8%), and ST131 (3.5%). Among these, 58.4% were assigned to the ExPEC group and 51.1% to the UPEC group based on their virulence associated gene (VAG) profile (ExPEC, presence of ≥VAGs: papAH and/or papC, sfa/focG, afaD/draBC, kpsMTII, and iutA; UPEC, additionally cnf1 or hlyD). Extended-spectrum cephalosporin (ESC) resistance mediated by extended-spectrum β-lactamases (ESBL) and AmpC-β-lactamase was identified in 1.9% of the isolates, along with one carbapenemase-producing isolate and one isolate carrying a mcr gene. Low occurrence of ESC-resistant or multidrug-resistant (MDR) isolates (2.9%) in the two most frequently detected STs implies that E. coli isolated from UTIs of companion animals are to a lesser extent associated with resistance, but possess virulence-associated genes enabling efficient UT colonization and carriage. Detection of human-related pandemic lineages suggests interspecies transmission and underscores the importance of monitoring companion animals.
Characteristics and susceptibility pattern of catheter-associated urinary tract infections (CAUTI) bacteria in Indonesia: A study in a national reference hospital of Sumatra region 2020–2021

Catheter-associated urinary tract infection (CAUTI) is defined as a urinary tract infection associated with catheter placement for more than two consecutive days. Hence, antibiotic resistance in the context of CAUTIs represents a substantial challenge. The aim of this study was to present the characteristics of patients with CAUTI and the susceptibility pattern of CAUTI bacteria in the national reference hospital of the Sumatra region of Indonesia. A cross-sectional study was conducted at H. Adam Malik General Hospital, Medan, Indonesia, from 2020 to 2021, using a total sampling. All CAUTI patients included were on catheterization and diagnosed based on the Centers for Disease Control and Prevention (CDC) guidelines. The patient’s urine culture and antibiotic susceptibility test were carried out on the patient’s admitted urine sample for further assessment. Identification of bacteria, antibiotic susceptibility test, and the extended-spectrum beta-lactamase (ESBL) test for Escherichia coli and Klebsiella pneumoniae were conducted using the VITEK-2 Compact. A total of 74 CAUTI patients were included in the study, 59.5% were female, 54.1% were 46–65 years old, and a third had cardiovascular disease comorbidities (33.8%). A total of 83 CAUTI-associated bacteria were isolated. The majority were Gram-negative bacteria (74.7%), and the most bacteria isolated was E. coli (31.3%), followed by K. pneumoniae, Enterococcus faecalis, Acinetobacter baumannii, and Enterococcus faecium. The ESBL test was positive mostly in K. pneumoniae (100%) and E. coli (76.9%). CAUTI-associated E. coli was susceptible to tigecycline, meropenem, ertapenem, nitrofurantoin, and gentamicin. The isolated K. pneumoniae was susceptible to tigecycline, meropenem, ertapenem, and amikacin. While E. faecalis showed susceptibility to tigecycline, nitrofurantoin, vancomycin, imipenem, linezolid, ampicillin, piperacillin/tazobactam, amoxicillin/clavulanic acid, ampicillin/sulbactam, and piperacillin.
Properties and Applications of Essential Oils: A Review

Essential oils are complex mixtures of volatile compounds obtained from plants where they play aromatic, communicative and defensive roles. They have been used for centuries in medicine, agriculture and industry due to their broad spectrum of biological activity. They exhibit antimicrobial, antiviral, anti-inflammatory, antioxidant and smooth muscle relaxant properties. Due to their lipophilicity and small molecular size, essential oil components easily penetrate biological membranes and exert therapeutic effects. Currently, research is underway on the use of essential oils for the treatment of viral infections, cancer prevention and inflammatory diseases. These agents may provide a valuable alternative to conventional therapies due to their natural origin and high tolerability. However, ensuring the appropriate quality and standardization of preparations is crucial to guarantee their efficacy and safe use. This paper provides an overview of the properties of essential oils, the methods used to obtain them, their composition, and their medical and therapeutic applications.
Cerebellar stroke in a young female associated with elevated homocysteine levels and heterozygous MTHFR C677T gene:  A case report.

Homocysteine is an amino acid, which is an intermediate in the metabolism of methionine and cysteine. Elevated homocysteine levels are recognized as a cause for both arterial and venous thrombotic phenomena. Methylenetetrahydrofolatereductase -encoded by MTHFR gene- is the rate-limiting enzyme of the remethylation of homocysteine to methionine. Homozygous MTHFR T677T gene mutation can independently cause raised homocysteine levels and increase the risk of thrombosis whereas heterozygous MTHFR C677T gene mutation usually does with an acquired cause such as folate or vitamin B12 deficiency, and is with lesser risk for thrombosis. We report a case of a previously healthy 23-year-old female, who was excluded from other inherited and acquired thrombophilic conditions, but was found to be having heterozygous MTHFR C677T gene mutation and elevated level of homocysteine presented late with right cerebellar stroke. Therefore, when young patients present with thrombotic phenomena, homocysteine levels should be assessed in the absence of other common thrombophilic conditions.
Cannabinoids and the Endocannabinoid System in Early SARS-CoV-2 Infection and Long COVID-19—A Scoping Review

Coronavirus disease-19 (COVID-19) is a highly contagious illness caused by the SARS-CoV-2 virus. The clinical presentation of COVID-19 is variable, often including symptoms such as fever, cough, headache, fatigue, and an altered sense of smell and taste. Recently, post-acute “long” COVID-19 has emerged as a concern, with symptoms persisting beyond the acute infection. Vaccinations remain one of the most effective preventative methods against severe COVID-19 outcomes and the development of long-term COVID-19. However, individuals with underlying health conditions may not mount an adequate protective response to COVID-19 vaccines, increasing the likelihood of severe symptoms, hospitalization, and the development of long-term COVID-19 in high-risk populations. This review explores the potential therapeutic role of cannabinoids in limiting the susceptibility and severity of infection, both pre- and post-SARS-CoV-19 infection. Early in the SARS-CoV-19 infection, cannabinoids have been shown to prevent viral entry, mitigate oxidative stress, and alleviate the associated cytokine storm. Post-SARS-CoV-2 infection, cannabinoids have shown promise in treating symptoms associated with post-acute long COVID-19, including depression, anxiety, post-traumatic stress injury, insomnia, pain, and decreased appetite. While current research primarily focuses on potential treatments for the acute phase of COVID-19, there is a gap in research addressing therapeutics for the early and post-infectious phases. This review highlights the potential for future research to bridge this gap by investigating cannabinoids and the endocannabinoid system as a potential treatment strategy for both early and post-SARS-CoV-19 infection.
Water quality analysis based on the presence of aquatic macroinvertebrates applied to water springs covered with soil-cement technique

Human activities, such as deforestation and inappropriate waste disposal have had negative impact on watercourses, including water spring areas. The soil-cement technique is a low-cost and easily implementable option to safeguard water springs and to preserve watercourses. The aim of the preset study is to assess water quality in water springs in Prudentópolis City, Brazil by using this technique based on aquatic macroinvertebrate communities and land use in this location. In total, 1,236 macroinvertebrates belonging to 18 taxa were collected from 5 water springs. Species belonging to family Chironomidae prevailed in points A, B, C and E, since they represent approximately 42% of all collected insects. Tree Cover was the primary land use form in the assessed points. According to Canonical Correspondence Analysis (CCA), different taxonomic groups had different responses to the assessed environmental factors. In conclusion, soil preservation, sustainable management and the cement technique, in combination to a set of preventive actions, were effective measures to ensure the conservation of aquatic ecosystems and water quality.
Cause and Significance of the Ultra-low Water Saturation in Gas-enriched Shale Reservoir

During the exploitation of shale gas,it is necessary to conduct reservoir reconstruction for the purpose of economic recovery.Workers in North America and China now adopt the method of combining drilling and completion of horizontal well with massive hydraulic fracturing,which needs enormous amount of water and sand.The interaction of these fluids and reservoir rocks lays the foundation for the success of reservoir reconstruction,whereas the initial water saturation of reservoirs and the understanding of causes of this state are premises of the method.With studies of the marine shale gas reservoirs in southern China, it is found that gas-enriched reservoir often has ultra-low water saturation,which is caused by hydrocarbon generation,consumption and evaporation,etc.Ultra-low water saturation improves adsorption capacity of shale,extends the movable pore throat radius,and increases the gas phase permeability.However,it also accelerates the water-base rates of adsorption and permeation,deteriorates water and hydrocarbon phase trapping problems,and brings more potential damages to aqueous phase trapping of shale gas.Under this circumstance,more attention needs to be paid to the negative effect of ultra-low water saturation and its work damage during the evaluation,reconstruction,and development of shale gas reservoirs.
EEG Network Analysis of Depressive Emotion Interference Spatial Cognition Based on a Simulated Robotic Arm Docking Task

Depressive emotion (DE) refers to clinically relevant depressive symptoms without meeting the diagnostic criteria for depression. Studies have demonstrated that DE can cause spatial cognition impairment. However, the brain network mechanisms underlying DE interference spatial cognition remain unclear. This study aimed to reveal the differences in brain network connections between DE and healthy control (HC) groups during resting state and a spatial cognition task. The longer operation time of the DE group during spatial cognition task indicated DE interference spatial cognition. In the resting state stage, the DE group had weaker network connections in theta and alpha bands than the HC group had. Specifically, the electrodes in parietal regions were hubs of the differential networks, which are related to spatial attention. Moreover, in docking task stages, the left frontoparietal network connections in delta, beta, and gamma bands were stronger in the DE group than those of the HC group. The enhanced left frontoparietal connections in the DE group may be related to brain resource reorganization to compensate for spatial cognition decline and ensure the completion of spatial cognition tasks. Thus, these findings might provide new insights into the neural mechanisms of depressive emotion interference spatial cognition.
Effects of Mining on Benthic Macroinvertebrate Communities and Monitoring Strategy

The benthic macroinvertebrate community of the Animas River watershed study area has been impaired by more than a century of hard-rock mining. Currently, remediation of mine sites is being done to restore ecosystem health in this watershed. Ecological recovery of the community depends on the degree that remediation improves water quality and reduces erosion of mill tailings into the river, resulting in improved habitat quality. Benthic macroinvertebrate data were collected in fall 1996, spring 1997, and fall 1997 to measure existing ecosystem health and to evaluate the response of the benthic community to remediation activities. Macroinvertebrate samples were obtained from 25 impaired and 11 unimpaired sites. Sampling methods were proposed to determine time of year, frequency, and location for collection of pre-remediation data and to qualitatively and statistically compare those data to the post-remediation data. Two methods were proposed: (1) a single site assessment where only one sample site exists downstream from each remediation site, and (2) a multiple site assessment where a minimum three sample sites are used for each remediation site. At least 3 years of pre-remediation data and 3 years of post-remediation data from the same site must be collected to distinguish between the effectiveness of remediation and temporal variation inherent in natural populations. If post-remediation data are not significantly different from pre-remediation data, then subsequent data collection should be delayed until further remediation is completed, the benthos has had more time to recover, or macroinvertebrates have had more time to recolonize the impaired reaches. If a significant difference is evident between pre- and post-remediation data, a minimum of 2 years of additional post-remediation data should be collected.
Bitter Phytochemicals as Novel Candidates for Skin Disease Treatment

Skin diseases represent a global healthcare challenge due to their rising incidence and substantial socio-economic burden. While biological, immunological, and targeted therapies have brought a revolution in improving quality of life and survival rates for certain dermatological conditions, there remains a stringent demand for new remedies. Nature has long served as an inspiration for drug development. Recent studies have identified bitter taste receptors (TAS2Rs) in both skin cell lines and human skin. Additionally, bitter natural compounds have shown promising benefits in addressing skin aging, wound healing, inflammatory skin conditions, and even skin cancer. Thus, TAS2Rs may represent a promising target in all these processes. In this review, we summarize evidence supporting the presence of TAS2Rs in the skin and emphasize their potential as drug targets for addressing skin aging, wound healing, inflammatory skin conditions, and skin carcinogenesis. To our knowledge, this is a pioneering work in connecting information on TAS2Rs expression in skin and skin cells with the impact of bitter phytochemicals on various beneficial effects related to skin disorders.
Integration of Riboflavin-Modified Carbon Fiber Mesh Electrode Systems in a 3D-Printed Catheter Hub

Background: Catheter line infection is a common complication within clinical environments, and there is a pressing need for technological options to aid in reducing the possibility of sepsis. The early identification of contamination could be pivotal in reducing cases and improving outcomes. Method: A sensing rationale based on a riboflavin-modified electrode system integrated within a modified 3D-printed catheter needle-free connector is proposed, which can monitor changes in pH brought about by bacterial contamination. Results: Riboflavin, vitamin B2, is a biocompatible chemical that possesses a redox-active flavin core that is pH dependent. The oxidation peak potential of the adsorbed riboflavin responds linearly to changes in pH with a near-Nernstian behavior of 63 mV/pH unit and is capable of accurately monitoring the pH of an authentic IV infusate. Conclusions: The proof of principle is demonstrated with an electrode-printed hub design offering a valuable foundation from which to explore bacterial interactions within the catheter lumen with the potential of providing an early warning of contamination.
Enhancement of Medicago Sativa Plant Growth and Yield after Treatment with Rhizobium spp.

Rhizobium plays an important role in cultivation of legumes throughout the nitrogen fixation process. In the pres - ent study, the growth of alfalfa ( Medicago sativa ) was studied after treatment with Rhizobium spp. isolated from two different sites in Jordan. The effect of the two isolates (RS1 and RS2) and co-inoculation of the two isolates (RS1+RS2) was tested on alfalfa. Chlorophyll contents, relative water content, leaf area, shoot length, stem diameter and plant biomass (leaf, root and shoot dry weight) were studied under growth chamber conditions (day/night temperatures of 25 ° C; 16:8 h photoperiod) using different inoculum doses (10 ml, 20 ml and 40 ml). The effect of Rhizobium isolates on alfalfa was compared with rhizosphere plant growth-promoting rhizobacteria (PGPR) collected from the same soil samples. The results indicated that RS1 at high dose (40 ml) and RS2 at any dose significantly enhanced alfalfa growth in all measured parameters compared with control plants (without bacterial inoculation). RS2 was better than RS1 in most measured parameters even at low inoculum dose (10 ml), whereas no significant differences between the two strains were found at high inoculum doses. Co-inoculation of the two isolates was less effective than each isolate alone. On the other hand, the PGPR showed a significant enhancement of alfalfa growth as they enhanced significantly all measured parameters compared to the control plants at all doses.
Using Vegetation Indices as Input into Random Forest for Soybean and Weed Classification

Weed management is a major component of a soybean (Glycine max L.) production system; thus, managers need tools to help them distinguish soybean from weeds. Vegetation indices derived from light reflectance properties of plants have shown promise as tools to enhance differences among plants. The objective of this study was to evaluate normalized difference vegetation indices derived from multispectral leaf reflectance data as input into random forest machine learner to differentiate soybean and three broad leaf weeds: Palmer amaranth (Amaranthus palmeri L.), redroot pigweed (A. retroflexus L.), and velvetleaf (Abutilon theophrasti Medik). Leaf reflectance measurements were acquired from plants grown in two separate greenhouse experiments conducted in 2014. Twelve normalized difference vegetation indices were derived from the reflectance measurements, including advanced, green, greenred, green-blue, and normalized difference vegetation indices, shortwave infrared water stress indices, normalized difference pigment and red edge indices, and structure insensitive pigment index. Using the twelve vegetation indices as input variables, the conditional inference version of random forest (cforest) readily distinguished soybean and velvetleaf from the two pigweeds (Palmer amaranth and redroot pigweed) and from each other with classification accuracies ranging from 93.3% to 100%. The greatest errors were observed between the two pigweed classes, with classification accuracies ranging from 70% to 93.3%. Results suggest combining them into one class to increase classification accuracy. Vegetation indices results were equivalent to or slightly better than results obtained with sixteen multispectral bands used as input data into cforest. This research further supports using vegetation indices and machine learning algorithms such as cforest as decision support tools for weed identification.
The DUX4–HIF1α Axis in Murine and Human Muscle Cells: A Link More Complex Than Expected

FacioScapuloHumeral muscular Dystrophy (FSHD) is one of the most prevalent inherited muscle disorders and is linked to the inappropriate expression of the DUX4 transcription factor in skeletal muscles. The deregulated molecular network causing FSHD muscle dysfunction and pathology is not well understood. It has been shown that the hypoxia response factor HIF1α is critically disturbed in FSHD and has a major role in DUX4-induced cell death. In this study, we further explored the relationship between DUX4 and HIF1α. We found that the DUX4 and HIF1α link differed according to the stage of myogenic differentiation and was conserved between human and mouse muscle. Furthermore, we found that HIF1α knockdown in a mouse model of DUX4 local expression exacerbated DUX4-mediated muscle fibrosis. Our data indicate that the suggested role of HIF1α in DUX4 toxicity is complex and that targeting HIF1α might be challenging in the context of FSHD therapeutic approaches.
Vertical Stratification of Peatland Microbial Communities Follows a Gradient of Functional Types across Hummock–Hollow Microtopographies

ABSTRACT Microbes play crucial roles in global carbon cycles, particularly in peatland ecosystems that store vast quantities of carbon. Boreal peatlands are under stress from commercial extraction of peat, drainage for conversion to forestry and agricultural lands, and climate change. In this study, we identify key microbial groups and their ecological functions across peatland depth profiles and provide insight into how environmental changes related to water table may alter microbial communities. We examined the diversity and composition of prokaryotic communities across a microtopographic hummock–hollow gradient using Illumina sequencing. Communities formed a gradient of species and functional groups with depth, with overlap in functional groups at lower layers of hummocks and upper layers of hollows. Yet, overall, we found significantly different prokaryotic communities in hollows than hummocks. Surfaces of hummocks were typified by aerobic chemoorganotrophs, methanotrophs and chemoheterotrophs, mid-depths were typified by aerobic chemoorganotrophs, nitrogen-fixing bacteria and anaerobic nitrate reducers, while lower depths in hollows were typified by anaerobic and facultative anaerobic chemoorganotrophs, nitrate reducers and methanogenic archaea. Microbial composition as a function of hydrology and moisture regimes suggests that environmental changes that alter hydrological regimes (e.g., climate change, peatland draining) may alter carbon and nutrient cycling regimes.