Miracle-dz/UniFAR-FTUs huggingface dataset:
Network pharmacology to investigate the pharmacological mechanisms of muscone in Xingnaojing injections for the treatment of severe traumatic brain injury

Background Xingnaojing injections (XNJI) are widely used in Chinese medicine to mitigate brain injuries. An increasing number of studies have shown that XNJI may improve neurological function. However, XNJI’s active ingredients and molecular mechanisms when treating traumatic brain injury (TBI) are unknown. Methods XNJI’s chemical composition was acquisited from literature and the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. We used the “absorption, distribution, metabolism, and excretion” (ADME) parameter-based virtual algorithm to further identify the bioactive components. We then screened data and obtained target information regarding TBI and treatment compounds from public databases. Using a Venn diagram, we intersected the information to determine the hub targets. Cytoscape was used to construct and visualize the network. In accordance with the hub proteins, we then created a protein–protein interaction (PPI) network using STRING 11.0. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed according to the DAVID bioinformatics resource database (ver. 6.8). We validated the predicted compound’s efficacy using the experimental rat chronic constriction injury (CCI) model. The neuronal apoptosis was located using the TUNEL assay and the related pathways’ hub proteins were determined by PCR, Western blot, and immunohistochemical staining. Results We identified 173 targets and 35 potential compounds belonging to XNJI. STRING analysis was used to illustrate the protein–protein interactions and show that muscone played a fundamental role in XNJI’s efficacy. Enrichment analysis revealed critical signaling pathways in these components’ potential protein targets, including PI3K/AKT1, NF-kB, and p53. Moreover, the hub proteins CASP3, BCL2L1, and CASP8 were also involved in apoptosis and were associated with PI3K/AKT, NF-kB, and p53 signaling pathways. We showed that muscone and XNJI were similarly effective 168 h after CCI, demonstrating that the muscone in XNJI significantly attenuated neuronal apoptosis through the PI3K/Akt1/NF-kB/P53 pathway. Conclusion We verified the neuroprotective mechanism in muscone for the first time in TBI. Network pharmacology offers a new approach for identifying the potential active ingredients in XNJI.
Single origin of three plasmids bearing blaCTX-M-15 from different Klebsiella pneumoniae clones.

OBJECTIVES To determine and compare the complete nucleotide sequences of plasmids carrying blaCTX-M-15 from three different Klebsiella pneumoniae clones. METHODS IncFII-type plasmids pKP02022, pKP09085 and pKP007 were extracted from three K. pneumoniae strains. These strains belong to sequence types (STs) ST15, ST48 and ST23, respectively, and were isolated in Korea. Plasmids were sequenced using the 454 Genome Sequencer FLX system. RESULTS The three plasmids, pKP02022 (203577 bp), pKP09085 (213019 bp) and pKP007 (246 176 bp), all exhibited a very similar structure, with a pKPN3-like backbone and a resistance region including blaOXA-1, aac(6')-Ib-cr and cat genes as well as blaCTX-M-15. They were also very similar to pUUH239.2, previously isolated in Sweden. Iron (III) uptake-related genes were found in pKP007 from the ST23 strain, which has been reported to be associated with liver abscesses. The resistance region contained several insertion sequences, such as IS26, which may play an important role in structural rearrangements of plasmids. CONCLUSIONS The very similar structure of the three plasmids, extracted from different clones, suggests that the spread of CTX-M-producing K. pneumoniae isolates might result from the horizontal transfer of plasmids and subsequent integration and recombination.
causalizeR: a text mining algorithm to identify causal relationships in scientific literature

Complex interactions among multiple abiotic and biotic drivers result in rapid changes in ecosystems worldwide. Predicting how specific interactions can cause ripple effects potentially resulting in abrupt shifts in ecosystems is of high relevance to policymakers, but difficult to quantify using data from singular cases. We present causalizeR (https://github.com/fjmurguzur/causalizeR), a text-processing algorithm that extracts causal relations from literature based on simple grammatical rules that can be used to synthesize evidence in unstructured texts in a structured manner. The algorithm extracts causal links using the relative position of nouns relative to the keyword of choice to extract the cause and effects of interest. The resulting database can be combined with network analysis tools to estimate the direct and indirect effects of multiple drivers at the network level, which is useful for synthesizing available knowledge and for hypothesis creation and testing. We illustrate the use of the algorithm by detecting causal relationships in scientific literature relating to the tundra ecosystem.
A Comprehensive Review of Transaminitis and Irritable Bowel Syndrome

We observed in the literature that irritable bowel syndrome (IBS) may be linked to irregular parameters of the metabolic system (MS) and liver function. For that reason, we conducted this systematic review to comprehensively analyze the association of transaminitis (elevated alanine transaminase (ALT)) with IBS. This review was designed by following methods described in the Cochrane Handbook for Systematic Reviews of Interventions. Published peer-reviewed journal articles were included. Data were extracted based on study design, age, gender, author, date of publication or availability online, publication type, participants, gender (M/F), and types of IBS. Our electronic multiple databases yielded a total of 519 preliminary studies; we then removed duplicate studies and left with 326 studies. After reviewing the full text of these articles, a total of 83 studies were eliminated and lastly, three studies were selected for this systematic review for quantitative and qualitative analysis. All the enrolled subjects in included studies were diagnosed with IBS by the Rome II and III criteria and among these subjects, 50.4% had IBS-D, 13.8% had IBS-C, 30.3% had IBS-M, and 3.5% had IBS-U. The prevalence of elevated ALT with other liver enzymes (γ-GT levels and aspartate aminotransferase (AST)) in patients with irritable bowel syndrome whether their body mass index (BMI) was high or not (16.9% vs. 7.7%; p=0.015) and γ-GT (24.1% vs. 11.5%; p=0.037), Lee et al., 2016. The IBS-D subtype was seen more commonly in patients whose alcohol intake was significantly high however their study data showed no significant change in elevation of ALT. The upper limits normal values for serum liver enzymes were defined as 41 international per liter in males and 31 international units per liter in females for ALT. No significant relationships were observed between IBS status and elevated γ-GT (OR, 1.647; 95% CI, 0.784-3.461). The review study proposes a potential relation between elevated ALT levels, MS, and IBS, and this review might be the first review in IBS patients to observe the association of elevated ALT in the IBS population. Although further additional trials with a large sample size will be required to confirm these results. Furthermore, for assessing the efficacy of the manipulation of gut microbiota randomized controlled trials in a large population of IBS patients are needed to establish a causal-resultant relationship between IBS, MS, and liver damage.
Deciphering Trifolium pratense L. holobiont reveals a microbiome resilient to future climate changes

The plant microbiome supports plant growth, fitness, and resistance against climate change. Trifolium pratense (red clover), an important forage legume crop, positively contributes to ecosystem sustainability. However, T. pratense is known to have limited adaptive ability toward climate change. Here, the T. pratense microbiomes (including both bacteria and fungi) of the rhizosphere and the root, shoot, and flower endospheres were comparatively examined using metabarcoding in a field located in Central Germany that mimics the climate conditions projected for the next 50–70 years in comparison with the current climate conditions. Additionally, the ecological functions and metabolic genes of the microbial communities colonizing each plant compartment were predicted using FUNGuild, FAPROTAX, and Tax4Fun annotation tools. Our results showed that the individual plant compartments were colonized by specific microbes. The bacterial and fungal community compositions of the belowground plant compartments did not vary under future climate conditions. However, future climate conditions slightly altered the relative abundances of specific fungal classes of the aboveground compartments. We predicted several microbial functional genes of the T. pratense microbiome involved in plant growth processes, such as biofertilization (nitrogen fixation, phosphorus solubilization, and siderophore biosynthesis) and biostimulation (phytohormone and auxin production). Our findings indicated that T. pratense microbiomes show a degree of resilience to future climate changes. Additionally, microbes inhabiting T. pratense may not only contribute to plant growth promotion but also to ecosystem sustainability.
Single-cell DNA methylome analysis of circulating tumor cells

Objective Previous investigations of circulating tumor cells (CTCs) have mainly focused on their genomic or transcriptomic features, leaving their epigenetic landscape relatively uncharacterized. Here, we investigated the genome-wide DNA methylome of CTCs with a view to understanding the epigenetic regulatory mechanisms underlying cancer metastasis. Methods We evaluated single-cell DNA methylome and copy number alteration (CNA) in 196 single cells, including 107 CTCs collected from 17 cancer patients covering six different cancer types. Our single-cell bisulfite sequencing (scBS-seq) covered on average 11.78% of all CpG dinucleotides and accurately deduced the CNA patterns at 500 kb resolution. Results We report distinct subclonal structures and different evolutionary histories of CTCs inferred from CNA and DNA methylation profiles. Furthermore, we demonstrate potential tumor origin classification based on the tissue-specific DNA methylation profiles of CTCs. Conclusions Our work provides a comprehensive survey of genome-wide DNA methylome in single CTCs and reveals 5-methylcytosine (5-mC) heterogeneity in CTCs, addressing the potential epigenetic regulatory mechanisms underlying cancer metastasis and facilitating the future clinical application of CTCs.
The Expression of miR-365 in Serum of Hypertension Patients with Left Ventricular Hypertrophy Was Up-Regulated, Which Was Positively Correlated with Left Ventricular Mass Index

Objective The present study aims to investigate micro ribonucleic acid-365 (miR-365) serum expression and its correlation with left ventricular hypertrophy (LVH) in patients with hypertension (HT). Methods Eighty-four patients were selected as study subjects and divided into three groups: the experimental group (n = 28), the observation group (n = 29), and the control group (n = 27). The experimental group included patients with LVH-accompanied HT who were treated in the People’s Hospital of Hebei Province between November 2019 and November 2020, the observation group included patients with HT unaccompanied by LVH, and the control group included healthy age and gender-matched subjects who underwent health examinations in our physical examination center. The cardiac echocardiography, 24-h Holter electrocardiogram, and circulating miR-365 levels in all subjects were measured. The differences in circulating miR-365 expression levels among the three groups were compared, and the correlations between the miR-365 expression levels and the blood pressure parameters (24-h mean systolic blood pressure [SBP] and 24-h mean diastolic blood pressure [DBP]), inter-ventricular septal thickness (IVST), left ventricular posterior wall thickness (LVPWT), left ventricular internal diameter (LVID), left ventricular mass (LVM), LVM index (LVMI), and LVH-related indicators were analyzed. Results The relative miR-365 expressions in the experimental, observation, and control groups were 2.08 (1.60, 2.34), 0.62 (0.44, 0.83), and 0.66 (0.35, 0.86), respectively. Patient miR-365 expression was significantly higher in the experimental group than in the observation group and the control group; the differences were statistically significant (p < 0.000). Furthermore, miR-365 expression was significantly correlated with SBP, DBP, IVST, LVPWT, LVID, LVM, and LVMI; the greatest correlation was with LVMI. Further univariate linear regression analysis revealed that miR-365 expression was linearly and positively correlated with LVMI and that miRNA-365 expression increased with the LVMI value. Conclusion The miR-365 serum expression in patients with LVH-accompanied HT was increased compared with the observation group and the control group and positively correlated with the LVH degree.
Exenatide loaded PLGA microspheres for long-acting antidiabetic therapy: preparation, characterization, pharmacokinetics and pharmacodynamics

Clinical application of exenatide, a peptide drug widely used for the treatment of type 2 diabetes mellitus, is greatly limited due to its short plasma half-life of 2.4 hours. To prolong the half-life of exenatide, a water in oil in oil (W/O/O) method was employed to prepare exenatide-loaded PLGA microspheres with a satisfactory particle size of 75.22 μm and a span value of 1.13. Optimized exenatide-loaded microspheres were endowed with high entrapment efficiency (83.8 ± 1.3%) and low initial burst release (1.31 ± 0.13%). Degradation pattern of the peptide-loaded microspheres was investigated by monitoring the changes in molecular weight, appearance, and release profile. Histological study proved the safety of the microspheres. In the pharmacokinetics and pharmacodynamics study, the long acting formulation had relative bioavailability of 70.31% and it achieved a hypoglycemic activity for up to 3 weeks in diabetic mice. A single subcutaneous injection of exenatide-loaded microspheres exhibited a comparable effect on controlling blood glucose to exenatide solution, which was injected twice per day at the same dose of exenatide. In conclusion, the exenatide-loaded microspheres might be a promising long acting formulation for glycemic control with low initial burst release and reduced risk of gastrointestinal intolerance and hypoglycemia.
Human Polycomb Protein 2 (hPC2) as a Novel Independent Prognostic Marker in Nasopharyngeal Carcinoma

Purpose Human polycomb protein 2(hPC2) is a vital component of polycomb repressive complex 1(PRC1). It plays a critical role in tumorigenesis and progression. However, whether HPC2 expression affects the prognosis of patients with nasopharyngeal carcinoma (NPC) is currently unclear. In the present study, we investigated the expression of hPC2and elucidated its clinical prognostic significance in NPC. Patients and Methods The expression of hPC2 in 180 NPCs samples was examined by immunohistochemistry (IHC) and evaluated by H-score staining intensity. Receiver operator characteristic (ROC) curve analysis was performed to determine cut-off values of hPC2 expression. The chi-square test, Kaplan–Meier (Log rank test), and the Cox proportional hazards model were utilized to analyze the data. Results We found hPC2 is highly expressed in 48.3% of NPC specimens, which significantly correlated with T stage (p=0.032), N stage (p=0.006), and clinical stage (p=0.003). Kaplan–Meier analysis indicated that NPCs with high hPC2 expression tended to have a lower cumulative rates of overall survival (OS, p<0.001), recurrence-free survival (RFS, p=0.001), and distant metastasis-free survival (DMFS, p=0.003). In the NPCs subgroup, T3–T4, N2–N3, and stages III–IV, high hPC2 expression also had a prognostic impact on worse outcome in terms of OS, RFS, and DMFS. More importantly, multivariate analyses demonstrated that hPC2 expression was an independent prognostic factor for OS (hazard ratio [HR], 95% (confidence interval [CI]), p=0.001), RFS (HR, 95% CI, p=0.018), and DMFS (HR, 95% CI, p=0.022). Conclusion We present evidence that high expression of hPC2 correlated with poorer prognosis in NPC. hPC2 could serve as a novel prognostic biomarker and might be a promising therapeutic target for NPC.
The Effects of the COVID-19 Lockdowns on the Composition of the Troposphere as Seen by IAGOS

Abstract. The European Research Infrastructure IAGOS (In-service Aircraft for a Global Observing System) equips commercial aircraft with a system for measuring atmospheric composition. A range of essential climate variables and air quality parameters are measured throughout the flight, from take-off to landing, giving high resolution information in the vertical in the vicinity of international airports, and in the upper-troposphere/lower-stratosphere during the cruise phase of the flight. Six airlines are currently involved in the programme, achieving a quasi-global coverage under normal circumstances. During the COVID-19 crisis, many airlines were forced to ground their fleets due to a fall in passenger numbers and imposed travel restrictions. Deutsche Lufthansa, a partner in IAGOS since 1994 was able to operate a IAGOS-equipped aircraft during the COVID-19 lockdown, providing regular measurements of ozone and carbon monoxide at Frankfurt airport. The data form a snapshot of an unprecedented time in the 27 year time-series. In May 2020, we see a 39 % increase in ozone near the surface with respect to the 26 year climatology, a magnitude similar to that of the 2003 heatwave. The anomaly in May is driven by an increase in ozone at nighttime which might be linked to the reduction of NO during the COVID-19 lockdowns. The anomaly diminishes with altitude becoming a slightly negative anomaly in the free troposphere. The ozone precursor carbon monoxide shows an 11 % reduction in MAM near the surface. There is only a small reduction of CO in the free troposphere due to the impact of long-range transport on the CO from emissions in regions outside Europe. This is confirmed by IASI-SOFRID CO retrievals which display a clear drop of CO at 800 hPa over Europe in March but otherwise show little change to the abundance of CO in the free troposphere.
Curriculum Design for Postgraduate Program of Islamic Study at UIN Raden Fatah Palembang During the Covid-19 Pandemic

During the Covid-19 pandemic, the learning process at the Islamic Studies Study Program, Postgraduate Program, UIN Raden Fatah Palembang was carried out online (long distance), so that lecturers were required to be creative in designing the learning curriculum. The curriculum design is structured as concise and as simple as possible, so that the delivery of course material (lecture method) can be implemented effectively and efficiently. The Semester Learning Plan (RPS) does not have to be changed, but needs to be adjusted to a learning process that is suitable for the conditions during the Covid-19 pandemic, which is the e-learning process. Keywords—the Covid-19 epidemic, learning curriculum design and SI study program
HEAVY METAL CONTENT AND MICROBIOLOGICAL QUALITY OF YAJI (COMPLEX SPICE MIXTURE) SOLD WITHIN KANO

Abdulsalam, L Department Of Microbiology, Bayero University, P.M. B. 3011 Kano, Nigeria. Correspondence Author ABSTRACT In recent years, food biosafety has been a priority, as such a study was carried out on the microbiological and heavy metal contents of yaji; a complex spice mixture sold within Kano metropolis. A total of nine stores within Kano metropolis and compared with 3 The result of the analysis showed that the total aerobic mesophilic count, fungal count and coliform count ranged 9.60×10cfu/g, and 3.6 >1100MPN/g respectively. Staphylococcus aureus, Escherichia coli, Salmonella, Enterobacter Fusarium, Rhizopus and Aspergillus sp The counts obtained were higher than the maximum acceptable levels provided by the ISO and FAO. The ranges of the concentration of heavy metals in dry weight were; lead 0.001 – 0.003, nickel 0.001 0.005, co 0.009 g/Kg. The levels of metals found in the samples were within the standard limits approved by WHO. This study showed that the samples were not contaminated with the studied heavy metals but were foun health hazard to consumers. It is therefore recommended that strict hygienic measures should be taken during yaji preparation since the laboratory prepared yaji were less contaminated. Public enlightenment be provided as continuous/routine consumption may result to the bioaccumulation of harmful metals in the body.
Attitudes and Behaviors Causal Relationships: Uncovering Latent Segments Within A Heterogeneous Population

This project aimed at unraveling the contemporaneous relationship that exists between attitudes and choice behaviors. Attitudes, perceptions, and preferences may shape behaviors; likewise, behavioral choices exercised by individuals may offer experiences that shape attitudes. While it is likely that these relationships play out over time, the question of whether attitudes affect behaviors or behaviors affect attitudes at a specific cross-section in time remains unanswered and a fruitful area of inquiry. Various studies in the literature have explored this question, but have done so without explicitly recognizing the heterogeneity that may exist in the population. In other words, the causal structure at play at any point in time may differ across individuals, thus motivating the development of an approach that can account for the presence of multiple segments in the population, each following a different causal structure. Results suggest that there is considerable heterogeneity in the population with the contemporaneous causal structures in which behaviors shape attitudes more prevalent than those in which attitudes affect choice behaviors. These findings have important implications for transport modeling and policy development.
Saturated Hydraulic Conductivity of Sand-Based Golf Putting Green Root Zones Affected by Sodium

Abstract Sodium hazard recommendations are primarily based on research conducted on fine-textured soils with moderate to high clay contents. However, sand-based golf putting greens typically contain very little clay (<3% by weight), and there is little evidence to suggest that sodium negatively affects saturated hydraulic conductivity (Ksat) of sand-based root zones with a low clay content. This study was designed to evaluate the effects of sodium on sand-based putting green soils. Putting green root zones were constructed with various amendments and saturated in solutions to create a range of base cation saturations. Saturated hydraulic conductivity was measured and compared with exchangeable sodium percentage (ESP) on soil cation exchange sites. In five of six root zone mixes, increasing ESP did not affect Ksat; only an 80:20 mixture by volume of sand/loam containing 4.8% clay had significantly lower Ksat as ESP increased to 25%. These findings suggest that current sodium hazard recommendations should be adjusted to account for soils with a low clay content. However, this research did not evaluate the effect of sodium on unsaturated flow or the effect of localized areas of a high clay content (clay lenses). The clay in this study was uniformly distributed through the profiles, and future work should evaluate clay accumulation at depth in these soils. The concept of soil plasticity is proposed as a quantitative assessment of sodium hazard, where only soils that exhibit plastic properties would be negatively affected by sodium.