Miracle-dz/UniFAR-FTUs huggingface dataset:
Characteristics of Soluble and Exchangeable Acidity in an Extremely Acidified Acid Sulfate Soil

An extremely acidified acid sulfate soil (ASS) was investigated to characterize its soluble and exchangeableacidity. The results showed that soluble acidity of a sample determined by titration with a KOH solutionwas much significantly greater than that indicated by pH measured using a PH meter, particularly for theextremely acidic soil samples. This is because the total soluble acidity of the extremely acidic soil sampleswas mainly composed of various soluble Al and Fe species, possibly in forms of Al sulfate complexes (e.g.,AISO4) and ferrous Fe (Fe2+). It is therefore suggested not to use pH alone as an indicator of soluble acidityin ASS, particularly for extremely acidic ASS. It is also likely that AISO4+ actively pericipated in cationexchange reactions. It appears that the possible involvement of this Al sulfate canon in the canon adsorptionhas significant effect on increasing the amount of acidity being adsorbed by the soils.
Time to recovery from COVID-19 and its predictors among patients admitted to treatment center of Wollega University Referral Hospital (WURH), Western Ethiopia: Survival analysis of retrospective cohort study

Introduction Despite its alarming spread throughout the world, no effective drug and vaccine is discovered for COVID-19 so far. According to WHO, the recovery time from COVID-19 was estimated to be 2 weeks for patients with mild infection, and 3 to 6 weeks for those with serious illnesses. A studies regarding the median recovery time and its predictors are limited globally and specifically in Ethiopia. Therefore, the aim of this study was to estimate the median time to recovery from COVID-19 and its predictors among COVID-19 cases admitted to WURH, Western Ethiopian. Methods This was a hospital-based retrospective cohort study conducted among 263 adult patients admitted with COVID-19 in WURH treatment center from March 29, 2020 through September 30, 2020. Epidata version 3.2 was used for data entry, and STATA version 14 for analysis. A Cox proportional hazard regression model was fitted to determine factors associated with recovery time. A variable with P-value ≤ 0.25 at bivariable Cox regression analysis were selected for multivariable Cox proportional model. Multivariable Cox regression model with 95% CI and Adjusted Hazard Ratio (AHR) was used to identify a significant predictor of time to recovery from COVID-19 at P-value < 0.05. Results The mean age of patient was 36.8 (SD± 10.68) years. At the end of follow up, two hundred twenty seven observations were developed an event (recovered) with median time to recovery of 18 days with IQR of 10–27 days. The overall incidence rate of recovery was of 4.38 per 100 (95% CI: 3.84, 4.99) person-days observations. Being older age (AHR = 1.59, 95% CI: 1.02, 2.49), presence of fever on admission (AHR = 1.78, 95% CI: 1.21, 2.62), and comorbidity (AHR = 0.56, 95% CI, 0.34, 0.90) were found to have statistically significant association with recovery time. Conclusion and recommendations In general, the median recovery time of patients with COVID-19 cases was long, and factors such as older age group, presence of fever, and comorbidity was an independent predictors of delayed recovery from COVID-19. Intervention to further reduce recovery time at treatment center has to focus on patients those shows symptoms and with comorbidities.
P2RX7 gene variation mediates the effect of childhood adversity and recent stress on the severity of depressive symptoms

The P2X purinoceptor 7 (P2RX7) mediates inflammatory microglial responses and is implicated in neuroimmune mechanisms of depression and neurodegenerative disorders. A number of studies suggest that psychosocial stress may precipitate depression through immune activation. Genetic association studies of P2RX7 variants with depression have been inconclusive. However, nearly all studies have focused on only one single-nucleotide polymorphism (SNP) and have not considered interaction with psychosocial stress. We investigated the effect of several variations in P2RX7 gene using a clumping method in interaction with early adversities and recent stress on depression severity. 1752 subjects provided information on childhood adversities, recent life events, and current depression severity. Participants were genotyped for 681 SNPs in the P2RX7 gene, 335 of them passed quality control and were entered into linear regression models followed by a clumping procedure for main effect and interactions. No significant main effect was observed. Rs74892325 emerged as a top SNP for interaction with childhood adversities and rs61953400 for interaction with recent life events. Our study is the first to investigate several variants in the P2RX7 gene and in interaction with two types of stress, extending our understanding of neuroinflammation in depression, and supporting that the majority of genes influence depression by enhancing sensitivity to stressors.
Prognostic value of preoperative circulating tumor cells counts in patients with UICC stage I-IV colorectal cancer

Colorectal cancer (CRC) is one of the leading causes of cancer death worldwide. There is an urgent need to identify prognostic markers for patients undergoing curative resection of CRC. The detection of circulating tumor cells in peripheral blood is a promising approach to identify high-risk patients with disseminated disease in colorectal cancer. This study aims to evaluate the prognostic relevance of preoperative CTCs using the Cellsearch® system (CS) in patients, who underwent resection with curative intent of different stages (UICC I-IV) of colorectal cancer. Out of 91 Patients who underwent colorectal resection, 68 patients were included in this study. CTC analysis was performed in patients with CRC UICC stages I-IV immediately before surgery. Data were correlated with clinicopathological parameters and patient outcomes. One or more CTCs/7.5 mL were detected in 45.6% (31/68) of patients. CTCs were detected in all stages of the Union of International Cancer Control (UICC), in stage I (1/4, 25%), in stage II (4/12, 33.3%), in stage III (5/19, 26.3%) and in stage IV (21/33, 63.6%). The detection of ≥ 1 CTCs/ 7.5ml correlated to the presence of distant overt metastases (p = 0.014) as well as with shorter progression-free (p = 0.008) and overall survival (p = 0.008). Multivariate analyses showed that the detection of ≥ 1 CTCs/ 7.5ml is an independent prognostic indicator for overall survival (HR, 3.14; 95% CI, 1.18–8.32; p = 0.021). The detection of CTCs is an independent and strong prognostic factor in CRC, which might improve the identification of high-risk patients in future clinical trials.
Key circular RNAs identified in male osteoporosis patients by whole transcriptome sequencing

Background Osteoporosis (OP) is a systemic disease with bone loss and microstructural deterioration. Numerous noncoding RNAs (ncRNAs) have been proved to participate in various diseases, especially circular RNAs (circRNAs). However, the expression profile and mechanisms underlying circRNAs in male osteoporosis have not yet been explored. Methods The whole transcriptome expression profile and differences in mRNAs, circRNAs, and microRNAs (miRNAs) were investigated in peripheral blood samples of patients with osteoporosis and healthy controls consisting of males ≥ 60-years-old. Results A total of 398 circRNAs, 51 miRNAs, and 642 mRNAs were significantly and differentially expressed in osteoporosis compared to healthy controls. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the host genes of significantly differentially expressed circRNAs were mainly enriched in the regulation of cell cycle process: biological process (BP), organelle part cellular components (CC), protein binding molecular function (MF), Toll-like receptor signaling pathway, tumor necrosis factor (TNF) signaling pathway, and thyroid hormone signaling pathway. circRNA-miRNA-mRNA regulatory network was constructed using the differentially expressed RNAs. Moreover, key circRNAs (hsa_circ_0042409) in osteoporosis were discovered and validated by qPCR. Conclusions The key cicrRNAs plays a major role in the pathogenesis of osteoporosis and could be used as potential biomarkers or targets in the diagnosis and treatment of osteoporosis.
Modified double guiding catheter ‘Ping Pong’ technique to treat large coronary perforation: a case report

Abstract Background Despite improvement in available tools and techniques, procedural complications like coronary perforation can occur during percutaneous coronary intervention (PCI). Severe proximal coronary perforations are usually caused by balloon and vessel size mismatch but can also occur with appropriately sized balloons or stents if the coronary vessel has very eccentric calcification or if there is negative remodelling of the vessel. Case summary A 74-year-old man with a history of type II diabetes mellitus, hypertension, and chronic coronary syndrome (previous PCI 10 years before) presented with unstable angina of 2 weeks of duration. Coronary angiography revealed a patent stent in left anterior descending artery, significant disease in left circumflex artery and diffuse calcified lesion in dominant right coronary artery (RCA). During angioplasty of RCA, the patient developed severe Ellis grade III perforation, which was successfully managed with modified double guiding catheter ‘Ping Pong’ technique. In this technique, the already engaged 7 French (F) Amplatz Left 1 guide catheter was used to deliver the bulky covered stent in highly tortuous and calcified RCA while a second 6F guide catheter (Judkin Right) introduced through contralateral femoral access was used for introducing the balloon, which initially sealed the perforation and subsequently acted as a distal anchor to provide strong support to deliver the covered stent. Conclusion In a case of severe coronary perforation, modified Ping Pong technique using a small-sized second guide catheter complimentary to the first guide catheter, can be used to deploy bulky covered stent.
The complete chloroplast genome sequence of Trapa incisa Sieb. & Zucc. (Lythraceae)

Abstract Trapa L. , an annual floating-leaved herb, is widely distributed in the old world and has important edible and medicinal values. However, the taxonomy and phylogeny of Trapa are unclear. Here, we reported the complete chloroplast genome of a wild species with small nuts, T. incisa. The complete chloroplast genome size of T. incisa was 155, 453 bp, consisting of two inverted repeat (IR) regions (24, 388 bp), one large single copy (LSC) region (88, 398 bp) and one small single copy (SSC) region (18, 279 bp). A total of 129 genes were annotated, including 83 protein-coding genes, 38 tRNA genes and 8 rRNA genes. Among them, 19 genes were duplicated (6 protein-coding genes, 9 tRNA genes and 4 rRNA genes). The phylogenomic analysis suggested a close relationship between T. incisa and T. maximowiczii.
When face masks signal social identity: Explaining the deep face-mask divide during the COVID-19 pandemic

With the COVID-19 pandemic still raging and the vaccination program still rolling out, there continues to be an immediate need for public health officials to better understand the mechanisms behind the deep and perpetual divide over face masks in America. Using a random sample of Americans (N = 615), following a pre-registered experimental design and analysis plan, we first demonstrated that mask wearers were not innately more cooperative as individuals than non-mask wearers in the Prisoners’ Dilemma (PD) game when information about their own and the other person’s mask usage was not salient. However, we found strong evidence of in-group favouritism among both mask and non-mask wearers when information about the other partner’s mask usage was known. Non-mask wearers were 23 percentage points less likely to cooperate than mask wearers when facing a mask-wearing partner, and 26 percentage points more likely to cooperate than mask wearers when facing a non-mask-wearing partner. Our analysis suggests social identity effects as the primary reason behind people’s decision whether to wear face masks during the pandemic.
Combination of (interferon beta-1b, lopinavir/ritonavir and ribavirin) versus favipiravir in hospitalized patients with non-critical COVID-19: A cohort study

Objectives Our study aims at comparing the efficacy and safety of IFN-based therapy (lopinavir/ritonavir, ribavirin, and interferon β-1b) vs. favipiravir (FPV) in a cohort of hospitalized patients with non-critical COVID-19. Methods Single center observational study comparing IFN-based therapy (interferon β-1b, ribavirin, and lopinavir/ritonavir) vs. FPV in non-critical hospitalized COVID-19 patients. Allocation to either treatment group was non-random but based on changes to national treatment protocols rather than physicians’ selection (quasi-experimental). We examined the association between IFN-based therapy and 28-day mortality using Cox regression model with treatment as a time-dependent covariate. Results The study cohort included 222 patients, of whom 68 (28%) received IFN-based therapy. Antiviral therapy was started at a median of 5 days (3–6 days) from symptoms onset in the IFN group vs. 6 days (4–7 days) for the FPV group, P <0.0001. IFN-based therapy was associated with a lower 28-day mortality as compared to FPV (6 (9%) vs. 18 (12%)), adjusted hazard ratio [aHR] (95% Cl) = 0.27 (0.08–0.88)). No difference in hospitalization duration between the 2 groups, 9 (7–14) days vs. 9 (7–13) days, P = 0.732 was found. IFN treated group required less use of systemic corticosteroids (57%) as compared to FPV (77%), P = 0.005 after adjusting for disease severity and other confounders. Patients in the IFN treated group were more likely to have nausea and diarrhea as compared to FPV group (13%) vs. (3%), P = 0.013 and (18%) vs. (3%), P<0.0001, respectively. Conclusion Early IFN-based triple therapy was associated with lower 28-days mortality as compared to FPV.
Efficacy of anti-vascular endothelial growth factor agents for treating neovascular age-related macular degeneration in vitrectomized eyes

Purpose To evaluate the efficacy of intravitreal anti-vascular endothelial growth factor (anti-VEGF) agents for treatment of neovascular age-related macular degeneration (nAMD) in vitrectomized eyes. Methods The medical records were reviewed of nAMD patients treated with anti-VEGF agents who previously underwent pars plana vitrectomy (PPV). PPV was performed with complete posterior vitreous detachment induction. Results A total of 44 eyes from 44 patients were included. The mean central foveal thickness (CFT) was 478.50 ± 156.93 μm at baseline, 414.25 ± 143.55 μm (86.6% of baseline) at 1 month after first injection (P < 0.001), and 386.75 ± 141.45 μm (80.8% of baseline) after monthly multiple injections (2.30 ± 1.07; range, 1–5) (P < 0.001). The mean logarithm of the minimum angle of resolution best-corrected visual acuity visual acuity (BCVA) was 0.85 ± 0.57 at baseline, 0.86 ± 0.63 after the first injection, and 0.84 ± 0.64 after monthly multiple injections. BCVA improved in 39.5% at 1 month after first injection and 45.2% at 1 month after monthly multiple injections. In the subgroup analysis, CFT of eyes with the posterior capsule decreased significantly to 85.8% and 79.8% of baseline values at 1 month after the first injection and after monthly multiple injections, respectively. CFT of eyes without the posterior capsule decreased to 91.6% and 87.4% of baseline values at 1 month after the first injection and after monthly multiple injections, respectively, without statistical significance. Conclusion Monthly injections of Intravitreal anti-VEGF agents induced favorable anatomical improvement and vision maintenance in vitrectomized eyes with nAMD.
Ocrelizumab after natalizumab in JC-virus positive relapsing remitting multiple sclerosis patients

Ocrelizumab is often used as an alternative therapy in natalizumab-treated MS patients at risk for progressive multifocal leukoencephalopathy (PML). Our objective was to assess efficacy and safety of JC-virus positive patients switching (either directly or indirectly) from natalizumab to ocrelizumab. Forty-two patients were included from an observational cohort (median follow-up 21 months). No evidence of disease activity was found in 83% of direct switchers and 50% of indirect switchers. Two direct switchers were diagnosed with carry-over PML. Our data support a direct switch for adequate disease suppression, although carry-over PML illustrates the dilemma when choosing between a direct or indirect switch.
Cell cycle kinetics in hematologic malignancies studied with flow cytometry

Brons PPT, Linssen PCM, Speth PAJ, Wessels JMC & Haanen C: Cellular Pharmacokine­ tic Study of Amsacrine in Human Nucleated Hematopoietic Cells. Proc Fifth NCI/ EORTC Symp New Drugs Cancer Therapy. Amsterdam, The Netherlands, October 22-24, 1986. Brons PPT, Pennings A, Boezeman JBM & Haanen C: Pseudo DNA-aneuploïdie in hematopoietische cellen door verschillen in excitatie spectra. Ned Tijdschr GeneesM 132:984,1988. Brons PPT, Linssen PCM, Speth PAJ, Wessels JMC & Haanen C: Human Cellular and Plasma Pharmacokinetics of Amsacrine Administered as a 3-H Infusion. Proc Sixth NCI/ EORTC Symp New Drugs Cancer Therapy. Amsterdam, The Netherlands, March 21-23, 1989. Minderman H, Brons Ρ, Linssen Ρ, Speth Ρ, Pennings A, Boezeman J, Wessels J & Haanen C: Doxorubicin induces a dose-dependent deceleration in the cell cycle progres­ sion in a human leukemic cell line (MOLT-4). Proc Sixth NCI/EORTC Symp New Drugs Cancer Therapy Amsterdam, The Netherlands, March 21-23,1989. Brons PPT, Pennings A, Haanen C, Wessels JMC & Boezeman JBM: Simultaneous Flow Cytometric Measurement of Cell-Surface Immunofluorescence and DNA content in Normal and Leukemic Human Bone Marrow Using a Novel Single Laser Method. Ami Cellular Pathol 1:328,1989. Brons PPT, Raemaekers JMM, Bogman MJJT, Holdrinet RSG, Pennings AHM & Wessels HMC: Simultaneous Flow Cytometric Measurement of DNA Content and Cell-Surface Immunofluorescence: A New Tool For Studying Proliferation activity in Non-Hodgkin's Lymphoma. Proc Symp Biology of Human Malignant Lymphomas. Bordeaux, France, March 5-6,1990. Brons PPT, Haanen C, Boezeman JBM, Raemaekers JMM, Pennings AHM & Wessels HMC: Cell Kinetics in Non-Hodgkin's Lymphoma Studied With in Vivo Administration of Iododeoxyuridine, Nuclear Ki-67 Staining and Flow Cytometry. Proc Symp Biology of Human Malignant Lymphomas. Bordeaux, France, March 5-6,1990.
Adsorption of phenol from aqueous solution using carbonized maize tassels

The adsorption of phenol which is one of the most important organic pollutant was studied using carbon from maize tassels. The effect of contact time, adsorbent dosage and temperature on the adsorption capacity was investigated. The maximum phenol adsorption was obtained as 54% at a temperature of 75oC and at a pH of 6. Freundlich and Langmuir adsorption models were used for mathematical description of the adsorption equilibrium. The experimental data fitted well into the Langmuir isotherm.
Cytokines: From Clinical Significance to Quantification

Cytokines are critical mediators that oversee and regulate immune and inflammatory responses via complex networks and serve as biomarkers for many diseases. Quantification of cytokines has significant value in both clinical medicine and biology as the levels provide insights into physiological and pathological processes and can be used to aid diagnosis and treatment. Cytokines and their clinical significance are introduced from the perspective of their pro‐ and anti‐inflammatory effects. Factors affecting cytokines quantification in biological fluids, native levels in different body fluids, sample processing and storage conditions, sensitivity to freeze‐thaw, and soluble cytokine receptors are discussed. In addition, recent advances in in vitro and in vivo assays, biosensors based on different signal outputs and intracellular to extracellular protein expression are summarized. Various quantification platforms for high‐sensitivity and reliable measurement of cytokines in different scenarios are discussed, and commercially available cytokine assays are compared. A discussion of challenges in the development and advancement of technologies for cytokine quantification that aim to achieve real‐time multiplex cytokine analysis for point‐of‐care situations applicable for both biomedical research and clinical practice are discussed.
Sequence dynamics of three influenza A virus strains grown in different MDCK cell lines, including those expressing different sialic acid receptors

Viruses are often cultured in cell lines for research and vaccine development, and those often differ from the natural hosts or tissues. Cell lines can also differ in the presence of virus receptors, such as the sialic acid (Sia) receptors used by influenza A viruses (IAV), which can vary in linkage (α2,3‐ or α2,6‐linkage) and form (N‐glycolylneuraminic acid [Neu5Gc] or N‐acetylneuraminic acid [Neu5Ac]). The selective pressures resulting from passaging viruses in cell types with host‐specific variations in viral receptors are still only partially understood. IAV are commonly cultured in MDCK cells which are both derived from canine kidney tubule epithelium and inherently heterogeneous. MDCK cells naturally present Neu5Ac and α2,3‐linked Sia forms. Here, we examine natural MDCK variant lineages, as well as engineered variants that synthesize Neu5Gc and/or α2,6‐linkages. We determined how viral genetic variation occurred within human H3N2, H1N1 pandemic and canine H3N2 IAV populations when serially passaged in MDCK cell lines that vary in cell type (MDCK‐Type I or MDCK‐Type II clones) and in Sia display. Deep sequencing of viral genomes showed small numbers of consensus‐level mutations, mostly within the hemagglutinin (HA) gene. Both human IAV showed variants in the HA stem and the HA receptor‐binding site of populations passaged in cells displaying Neu5Gc. Canine H3N2 showed variants near the receptor‐binding site when passaged in cells displaying Neu5Gc or α2,6‐linkages. Viruses replicated to low titres in MDCK‐Type II cells, suggesting that not all cell types in heterogeneous MDCK cell populations are equally permissive to infection.
Scaling of subcellular actin structures with cell length through decelerated growth

How cells tune the size of their subcellular parts to scale with cell size is a fundamental question in cell biology. Until now, most studies on the size control of organelles and other subcellular structures have focused on scaling relationships with cell volume, which can be explained by limiting pool mechanisms. Here, we uncover a distinct scaling relationship with cell length rather than volume, revealed by mathematical modeling and quantitative imaging of yeast actin cables. The extension rate of cables decelerates as they approach the rear of the cell, until cable length matches cell length. Further, the deceleration rate scales with cell length. These observations are quantitatively explained by a ‘balance-point’ model, which stands in contrast to limiting pool mechanisms, and describes a distinct mode of self-assembly that senses the linear dimensions of the cell.
International survey of strategies to mitigate transfusion‐transmitted Trypanosoma cruzi in non‐endemic countries, 2016–2018

Chagas disease, caused by Trypanosoma cruzi, is endemic to Mexico, Central and South America. While initially limited to the Americas, emigration of infected persons triggered geographically broader blood safety challenges. To mitigate transfusion‐transmitted Chagas (TTC), transfusion services implemented approaches including risk factor questions and serologic testing. We sought to understand and compare strategies in non‐endemic countries.