Miracle-dz/UniFAR-FTUs huggingface dataset:
Improved normalization of species count data in ecology by scaling with ranked subsampling (SRS): application to microbial communities

Background Analysis of species count data in ecology often requires normalization to an identical sample size. Rarefying (random subsampling without replacement), which is the current standard method for normalization, has been widely criticized for its poor reproducibility and potential distortion of the community structure. In the context of microbiome count data, researchers explicitly advised against the use of rarefying. Here we introduce a normalization method for species count data called scaling with ranked subsampling (SRS) and demonstrate its suitability for the analysis of microbial communities. Methods SRS consists of two steps. In the scaling step, the counts for all species or operational taxonomic units (OTUs) are divided by a scaling factor chosen in such a way that the sum of scaled counts equals the selected total number of counts Cmin. The relative frequencies of all OTUs remain unchanged. In the subsequent ranked subsampling step, non-integer count values are converted into integers by an algorithm that minimizes subsampling error with regard to the population structure (relative frequencies of species or OTUs) while keeping the total number of counts equal Cmin. SRS and rarefying were compared by normalizing a test library representing a soil bacterial community. Common parameters of biodiversity and population structure (Shannon index H’, species richness, species composition, and relative abundances of OTUs) were determined for libraries normalized to different size by rarefying as well as SRS with 10,000 replications each. An implementation of SRS in R is available for download (https://doi.org/10.20387/BONARES-2657-1NP3). Results SRS showed greater reproducibility and preserved OTU frequencies and alpha diversity better than rarefying. The variance in Shannon diversity increased with the reduction of the library size after rarefying but remained zero for SRS. Relative abundances of OTUs strongly varied among libraries generated by rarefying, whereas libraries normalized by SRS showed only negligible variation. Bray–Curtis index of dissimilarity among replicates of the same library normalized by rarefying revealed a large variation in species composition, which reached complete dissimilarity (not a single OTU shared) among some libraries rarefied to a small size. The dissimilarity among replicated libraries normalized by SRS remained negligibly low at each library size. The variance in dissimilarity increased with the decreasing library size after rarefying, whereas it remained either zero or negligibly low after SRS. Conclusions Normalization of OTU or species counts by scaling with ranked subsampling preserves the original community structure by minimizing subsampling errors. We therefore propose SRS for the normalization of biological count data.
Nurses' Knowledge and Attitude towards Postoperative Pain Management in Ghana

Background Pain management is a very important aspect of nursing care among postoperative patients. Deficit in the knowledge and bad attitude towards pain management among nurses remain a problem in Ghana. In order to manage pain better in the surgical wards, nurses should be well equipped with knowledge of pain assessment and management. Purpose The purpose of the study was to determine nurse's knowledge and attitude towards pain management among postoperative patients in surgical units in Ghana. Methodology. This study used the quantitative study approach with a descriptive cross-sectional study design. A sample of 211 nurses was recruited using the convenience sampling method. Data were collected using a questionnaire regarding postoperative pain management. Descriptive statistics, Pearson's correlation coefficient, and the chi-squared test were used to analyze the data using SPSS version 16.0. Results The mean age of the nurses was 29.77, with the youngest nurse being 23 years and oldest being 39 years. Majority (72.5%) of nurses had moderate knowledge, and 89.6% of the nurses had negative attitude towards pain management. There was no significant relationship between nurse's knowledge and years of experience as a nurse (r = −0.03, p=0.64), as well as no significant relationship between knowledge and number of years working in the surgical ward (r = 0.06, p=0.36). Also, there was no significant relationship between nurses' knowledge and nurses' attitude (r = 0.06, p=0.36). Conclusion and recommendation. The level of knowledge and attitude towards postoperative management were generally inadequate among nurses. Therefore, there is the need to implement in-service training on pain management for nurses working in the surgical units frequently.
Gan-Qing-Ning Formula Inhibits the Growth of Hepatocellular Carcinoma by Promoting Apoptosis and Inhibiting Angiogenesis in H22 Tumor-Bearing Mice

Objective Gang-Qing-Ning (GQN) is a traditional Chinese medicine formula that has been used in the treatment of hepatocellular carcinoma (HCC) in the folk population for decades. However, scientific validation is still necessary to lend credibility to the traditional use of GQN against HCC. This study investigates the antitumor effect of GQN on H22 tumor-bearing mice and its possible mechanism. Methods Fifty H22 tumor-bearing mice were randomly assigned to five groups. Three groups were treated with high, medium, and low dosages of GQN (27.68, 13.84, and 6.92 g/kg, respectively); the positive control group was treated with cytoxan (CTX) (20 mg/kg) and the model group was treated with normal saline. After 10 days' treatment, the tumor inhibitory rates were calculated. Pathological changes in tumor tissue were observed, and the key proteins and genes of the mitochondrial apoptosis pathway were measured, as well as the mRNA expression levels of VEGF in tumor tissue. Results The tumor inhibitory rates of high, medium, and low dosages of GQN groups were 47.39%, 38.26%, and 22.17%, respectively. The high dosage of the GQN group significantly increased the protein and mRNA expression levels of Bax, Cyt-C, and cleaved Caspase 3 (or Caspase 3) (P < 0.01) but decreased the expression levels of Bcl-2, VEGF, and microvessel density (MVD) (P < 0.01). Conclusions The high dosage of GQN can significantly inhibit the tumor growth in H22 tumor-bearing mice. It exerts the antitumor effect by enhancing proapoptotic factors and inhibiting the antiapoptotic factor of the mitochondrial apoptosis pathway and inhibiting tumor angiogenesis.
Proteins from Lignosus tigris with selective apoptotic cytotoxicity towards MCF7 cell line and suppresses MCF7-xenograft tumor growth

Background Lignosus tigris, a recently discovered species of the unique Lignosus family, has been traditionally used by the indigenous communities in Peninsular Malaysia to treat various ailments and as an alternative medicine for cancer treatment. The L. tigris cultivar sclerotia (Ligno TG-K) was found to contain numerous bioactive compounds with beneficial biomedicinal properties and the sclerotial extract exhibited potent antioxidant activity. However, the anticancer property of the Ligno TG-K including in vitro and in vivo antitumor effects as well as its anticancer active compounds and the mechanisms has yet to be investigated. Methods The cytotoxicity of the Ligno TG-K against human breast (MCF7), prostate (PC3) and lung (A549) adenocarcinoma cell lines was evaluated using MTT cytotoxicity assay. The cytotoxic mechanisms of the active high molecular weight proteins (HMWp) fraction were investigated through detection of caspases activity and apoptotic-related proteins expression by Western blotting. The in vivo antitumor activity of the isolated HMWp was examined using MCF7 mouse xenograft model. Shotgun LC-MS/MS analysis was performed to identify the proteins in the HMWp. Results and Discussion Cold water extract of the sclerotia inhibited proliferation of MCF7, A549 and PC3 cells with IC50 ranged from 28.9 to 95.0 µg/mL. Bioassay guided fractionation of the extract revealed that HMWp exhibited selective cytotoxicity against MCF7 cells via induction of cellular apoptosis by the activation of extrinsic and intrinsic signaling pathways. HMWp activated expression of caspase-8 and -9 enzymes, and pro-apoptotic Bax protein whilst inhibiting expression of tumor survivor protein, Bcl-2. HMWp induced tumor-cell apoptosis and suppressed growth of tumor in MCF-7 xenograft mice. Lectins, serine proteases, RNase Gf29 and a 230NA deoxyribonuclease are the major cytotoxic proteins that accounted for 55.93% of the HMWp. Conclusion The findings from this study provided scientific evidences to support the traditional use of the L. tigris sclerotia for treatment of breast cancer. Several cytotoxic proteins with high abundance have been identified in the HMWp of the sclerotial extract and these proteins have potential to be developed into new anticancer agents or as adjunct cancer therapy.
Identification and verification of the prognostic value of the glutathione S-transferase Mu genes in gastric cancer

Gastric cancer (GC) is one of the most frequently diagnosed gastrointestinal cancer types in the world. Novel prognostic biomarkers are required to predict the progression of GC. Glutathione S-transferase Mu (GSTM) belongs to a family of phase II enzymes that have been implicated in a number of cancer types. However, the prognostic value of the GSTM genes has not been previously investigated in GC. The Cancer Genome Atlas (TCGA) was used to evaluate mRNA expression levels of GSTMs in GC tissue samples. Overall survival (OS) rates, hazard ratios (HRs) and 95% CIs were calculated using the Cox logistic regression model and Kaplan-Meier (KM) analysis was performed. In addition, the KM plotter online database was used to validate mRNA expression and the prognostic value of GSMT family members in patients with GC. To predict the function of GSTM genes in these patients, several bioinformatics tools, including the Database for Annotation, Visualization and Integrated Discovery, gene multiple association network integration algorithm, Search Tool for the Retrieval of Interacting Genes/Proteins, Gene Set Enrichment Analysis (GSEA), nomogram and genome-wide co-expression analysis were used. In the present study, high expression of GSTM5 was indicated to be strongly associated with lower OS in patients with GC, according to the TCGA and KM plotter online databases (HR=1.47, 95% CI: 1.06-2.04, P=0.021; and HR=1.69, 95% CI: 1.42-2.01, P=1.6×10−9, respectively). The results from the GSEA and genome-wide co-expression analysis indicated that GSTM5 expression associated with several biological process terms, including ‘adhesion’, ‘angiogenesis’, ‘apoptotic process’, ‘cell growth’, ‘proliferation’, ‘migration’, ‘Hedgehog signaling’, ‘MAPK signaling’ and the ‘TGF-β signaling pathway’. In conclusion, the present results indicated that GSTM5 may serve as a biomarker for GC prognosis and may be a potential therapeutic target for GC.
Repeatability of Scotopic Sensitivity and Dark Adaptation Using a Medmont Dark-Adapted Chromatic Perimeter in Age-related Macular Degeneration

Purpose Functional studies of rods in age-related macular degeneration using the Medmont Dark-Adapted Chromatic Perimeter (DACP) have demonstrated impairments in scotopic sensitivities and dark adaptation (DA). We investigated the intersession repeatability of scotopic sensitivity and DA parameters including the rod intercept time recorded from the Medmont DACP. Methods Scotopic thresholds (14 test points) and DA using a 30% photobleach (eight test points) were measured on two separate days from participants 50 years of age or older with a range of age-related macular degeneration severity at loci superior and inferior to the fovea. Repeatability coefficients were calculated for prebleach scotopic sensitivity, and for DA parameters including rod intercept time. Results Twelve participants (mean age, 79.7 ± 8.1 years) repeated Medmont DACP testing within 50 days. Repeatability coefficients for prebleach scotopic sensitivity to long wavelength (red, 625 nm) and short wavelength (cyan, 505 nm) were 5.9 dB and 7.2 dB, respectively. The DA curve-derived repeatability coefficients for cone threshold was 3.9 dB, final threshold 5.3 dB, with an R value of 0.075 decades/min, rod intercept time 7.6 minutes, and RITslope 0.54 min/degree. Conclusions This study establishes repeatability coefficients for scotopic thresholds and multiple DA parameters obtained with the Medmont DACP in patients with age-related macular degeneration. These repeatability coefficients will serve as the basis for determining clinically meaningful change in rod function in future clinical trials. Translational Relevance Measures of repeatability parameters of scotopic thresholds and DA are essential to the accurate interpretation of results in future studies and trials using these measures.
A Hard Case to Swallow: Crucifix Esophageal Foreign Body in a Nonverbal Patient

Delayed presentation of esophageal foreign bodies places patients at high risk for esophageal perforation and infection. In nonverbal patients as well as children and adults with other concomitant illnesses, it is important to consider a broad differential diagnosis for presentations with upper respiratory complaints. The authors present a case of a nonverbal, elderly woman who presented after several days of mild, dry cough and was ultimately found to have a large esophageal foreign body that had been present for an unclear amount of time.
IMPACTO DEL ESTRÉS CALÓRICO SOBRE LA ACTIVIDAD REPRODUCTIVA EN BOVINOS Y CONSIDERACIONES PARA MITIGAR SUS EFECTOS SOBRE LA REPRODUCCIÓN

Mammalian like all living organisms must cover their nutritional requirements in order to achieve both survival and evolution of their species for which reason the conditions that ensure their welfare, depend from the nutrient exploitation. The phases of development involving reproductive processes imply high nutritional requirements and high metabolic activity, which may be affected by severe weather. The heat stress has adverse effects on gametogenesis, hormonal pulses, estrus expression, the oocyte, fertilization, implantation, embryonic development and basal metabolism, even in the response to functional alteration of the neuroendocrine axis. In tropical countries is important to adopt some strategies to reduce the thermal shock in animals, to improve their productive and reproductive performance. The first option is to use animals that have evolved in similar climatic conditions and thus have reached a certain degree of adaptation. Another measure is the use of systems that offer animals less direct exposure to sunlight, either through silvopastoral systems, the use of shading coefficient, the use of direct cooling systems with water sprinklers or fans that have shown to improve conception rates. Currently the implementation of reproductive biotechnology is aiming to supply hormone-like failures with techniques such as FTAI (fixed time artificial insemination). The present review is aimed to study the effects of heat stress over cow reproductive activity in the tropics and to consider implementing some measures intended to mitigate the negative impact of climatic conditions in the tropic.
Pingkui Enema Alleviates TNBS-Induced Ulcerative Colitis by Regulation of Inflammatory Factors, Gut Bifidobacterium, and Intestinal Mucosal Barrier in Rats

Background Ulcerative colitis (UC) is a chronic recurrent inflammation of the colon, and clinical outcome of UC is still unsatisfied. Pingkui enema, a traditional Chinese medicine prescription, has been safely applied for the treatment of diarrhea and dysentery in clinic for many years. However, its mechanism is still elusive. The present study is designed to investigate the effect of Pingkui enema on trinitrobenzene sulfonic acid- (TNBS-) induced ulcerative colitis (UC) and possible mechanism in rats. Methods UC was induced by intracolonic instillation of TNBS in male Sprague-Dawley rats, which were treated with different dosages of Pingkui enema (low, medium, and high) or sulfasalazine for ten days. Survival rate was calculated. A clinical disease activity score was evaluated. Histological colitis severity was analyzed by hematoxylin-eosin (HE) staining. Content of Bifidobacterium in intestinal tissue was analyzed by RT-PCR. Concentration of IL-8, IL-13, TNF-α, D-lactic acid (D-LA), and diamine oxidase (DAO) in serum and contents of adhesin and receptor of Bifidobacterium adhesion in rat intestinal mucus were measured by ELISA. Results The results showed that Pingkui enema treatment with high dosage markedly improved the survival rate compared with untreated and sulfasalazine treated groups. All dosages of Pingkui enema reduced pathological score. High dosage of Pingkui enema and sulfasalazine treatments significantly reduced the serum concentration of IL-8, TNF-α, D-LA, and DAO and markedly increased the serum concentration of IL-13. In addition, high-dose Pingkui enema and sulfasalazine treatments increased gut content of Bifidobacterium, gut mucus expressions of adhesin, and adhesin receptor of Bifidobacterium. Conclusions Pingkui enema has therapeutic effect on TNBS-induced UC, and possible mechanism may be via regulation of gut probiotics (Bifidobacterium) and inflammatory factors and protection of intestinal mucosal barrier.
The Canine Erythrocyte Sedimentation Rate (ESR): Evaluation of a Point-of-Care Testing Device (MINIPET DIESSE)

The erythrocyte sedimentation rate (ESR) in canine medicine has been replaced by the evaluation of a few sensitive markers of the acute-phase proteins. The aim of the study was to evaluate the ESR using a point-of-care (MINIPET, DIESSE Diagnostica Senese S.p.A.) device (ESR-MP) and to compare the results with the gold standard Westergren method (ESR-W) in dogs. One hundred and nineteen K3-EDTA blood samples for complete blood count were randomly selected and assayed for ESR. The reference interval (RI) was established using the percentile method. The coefficient of variation (CV) in intra-assay and interassay precision of ESR-MP was calculated. The analytical sensitivity (Se), specificity (Sp), positive predictive values (PPVs), and negative predictive values (NPVs) were calculated. Agreement between ESR-MP and ESR-W was assessed with Pearson correlation coefficient (r), Cohen concordance test (K), Passing-Bablok regression, and Bland–Altman plots. Ten canine samples (8.4%) were ruled out because of flag-error by the MINIPET instrument (4.2%) or because they showed the diphasic pattern in ESR-W (4.2%). The canine RI of ESR-MP was 0–10 mm/h. Precision was excellent in intra-assay (CV = 0.02) and interassay (CV = 0.32). The analytical characteristics of ESR-MP in nonanemic samples were as follows: Se = 0.82, Sp = 0.95, PPV = 0.82, and NPV = 0.95. The accuracy of ESR-MP was better than ESR-W in nonanemic samples (r = 0.87; K = 0.77) and lower in anemic subjects (Hct <37%) (r = 0.76; K = 0.69). The Passing-Bablok regression showed the presence of systematic error and the absence of proportional error only in nonanemic blood samples. The Bland–Altman plots gave negative average values due to the difference in RIs and an agreement in both ESRs. The ESR-MP results can be obtained with the same K3-EDTA tubes used for the blood count, in shortcut time, and at reduced costs using the MINIPET device. These investigations highlight that ESR-MP could be useful in canine clinical settings.
Midregional Proadrenomedullin (MRproADM) Serum Levels in Critically Ill Patients Are Associated with Short-Term and Overall Mortality during a Two-Year Follow-Up

Adrenomedullin (ADM) is a peptide with pleiotropic effects in systemic inflammation. Its more stable precursor protein midregional proadrenomedullin (MRproADM) can be measured more reliably compared to ADM. Our objective was to investigate the potential role of MRproADM as a diagnostic and prognostic biomarker in critically ill patients at the intensive care unit (ICU). We therefore measured MRproADM in 203 ICU patients and 66 healthy controls. We found that MRproADM levels are significantly increased in critically ill patients as compared to healthy controls. MRproADM levels are significantly increased in patients with sepsis, but its diagnostic value for identifying sepsis is numerically lower than that of established markers (e.g., interleukin-6, C-reactive protein, and procalcitonin). MRproADM levels are closely correlated to endothelial and organ dysfunction, inflammation, and established clinical scores (APACHE II, SOFA, and SAPS2). MRproADM concentrations correlate with vasopressor use but not fluid balance. Increased MRproADM levels (cut − off > 1.4 nmol/L) in critically ill patients are independent predictors of ICU and overall mortality during a follow-up of up to 26 months (OR 3.15 for ICU mortality, 95% CI 1.08-9.20, p = 0.036; OR for overall mortality 2.4, 95% CI 1.12-5.34, p = 0.026). Our study demonstrates the potential of MRproADM serum levels as a prognostic biomarker in critical illness for ICU mortality and long-term survival during follow-up.
Quantitative Proteomic Analyses To Reveal the Key Features of Proteins in New Onset Ankylosing Spondylitis Patients

Ankylosing spondylitis (AS) is a chronic immune-mediated disease. Various immune cells play an essential role in the AS pathogenesis. However, the specific pathogenesis of AS has not been well understood. Proteomic profiles of peripheral blood mononuclear cells (PBMCs) were applied to reveal the specific pathogenesis of AS. Quantitative proteomic analyses were performed using liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based methods to investigate the protein profiling of PBMCs from new-onset AS patients (n = 9) and healthy controls (n = 9). We identified 782 differentially expressed proteins (DEPs) and 527 differentially phosphorylated proteins (DPPs) between AS patients and healthy controls. The subcellular location of DEPs and DPPs showed that most of the DEPs were from the cytoplasm (n = 296, 38%), were extracellular (n = 141, 18%), and from the nucleus (n = 114, 15%); most of the DPPs were from the cytoplasm (n = 37, 34%), nucleus (n = 35, 32%), and plasma membrane (n = 10, 9%). We further identified 89 proteins with both expression and phosphorylation differences. The functional annotation of the 89 differentially expressed and phosphorylated proteins enriched in the antigen processing and presentation pathway. Four DEPs with six phosphorylated positions were found in the antigen processing and presentation pathway. The differentially expressed and phosphorylated proteins may be helpful to uncover the pathogenesis of AS. The six AS-specific proteins may serve as candidate markers for AS diagnosis and new treatment targets.