Miracle-dz/UniFAR-FTUs huggingface dataset:
Composition and distribution of suprabenthic fauna in the southeastern Weddell Sea and off King George Island

: Composition, abundance, and distribution of suprabenthos froma depth between 1 and 1.33 mabove the seafloor were analysed. The samples were taken during ANT XVl3 with RV Polarstern in February and March 1998 by means of the supranet of an epibenthic sledge along two transects in the southern Weddell Sea (Vestkapp and Halley Bay) and one east of King George Island. At each of these three transects, five to six stations were taken in water depth between 200 and 2000 m. In total, 34 057 specimens were sampled at 16 stations, yielding 1 205 050 individuals for all stations standardized to 1000 m3 hauls. Of these, copepods were usually the most abundant group in the supranet (805 822 ind 1000 m-9. The suprabenthic fauna of the south-west of Vestkapp (Weddell Sea) transect was dominated by planktonic taxa in terms of individual numbers especially at the deeper stations (938-1983 m). At Halley Bay the total abundance ofplankton was lower but its relative abundance (> 80%) was also high, whilst off King George Island peracarid crustaceans were an important fraction.
Application of Flow Cytometry to Segregated Kinetic Modeling Based on the Physiological States of Microorganisms (cid:1)

Flow cytometry (FC) has been introduced to characterize and to assess the physiological states of micro- organisms in conjunction with the classical plate-counting method. To show the applicability of the technique, in particular for the development of kinetic models, pure culture fermentation experiments were followed over time, using both prokaryotic ( Lactobacillus hilgardii ) and eukaryotic ( Saccharomyces cerevisiae ) microorganisms growing in standard culture media (MRS and YPD). The differences observed between the active and viable cells determined by FC and CFU, respectively, allowed us to determine that a large number of cells were in a viable but nonculturable (VBNC) state, which resulted in a subpopulation much larger than the damaged-cell (double-stained) subpopulation. Finally, the determination of the evolution of viable, the VBNC, and the dead cells allowed us to develop a segregated kinetic model to describe the yeast and the bacteria population dynamics and glucose consumption in batch cultures. This model, more complete than that which is tradi-tionally used, based only on viable cell measurements, describes better the behavior and the functionality of the cultures, giving a deeper knowledge in real time about the status and the course of the bioprocesses. Accurate measurements of biomass, substrate consumption, and product formation are the most important parameters for bioprocess and evaluation. Measurement of active biomass is essential for determining growth rates and cell yields
The yeast telomerase recruitment module requires a specific RNA architecture.

: Telomerases are ribonucleoprotein (RNP) enzymes that are related to reverse transcriptases. While they maintain genome stability, their composition varies significantly between species. Yeast telomerase RNPs contain an RNA that is comparatively large and its overall folding shows long helical segments with distal functional parts. Here we investigated the essential stem IVc module of the budding yeast telomerase RNA, called Tlc1. The distal part of stem IVc includes a conserved sequence element CS2a and structurally conserved features to which bind the Pop1/Pop6/Pop7 proteins and which together function analogously to the P3 domains of the RNase P/MRP RNPs. A more proximal bulged stem with the CS2 element is thought to associate with Est1. Previous data showed that changes in CS2a cause a loss of all of the proteins, not just the Pop-proteins, from stem IVc. The results here show that the association of Est1 with stem IVc indeed requires both the proximal bulged stem and the presence of the Tlc1 P3 domain with the associated Pop-proteins. Separating the P3-domain from the Est1 binding site by inserting only 2 base pairs into the helical stem between the two sites causes a complete loss of Est1 from the RNP and hence a telomerase-negative phenotype in vivo. Still, the distal P3 domain with the associated Pop-proteins remains intact . Moreover, the P3 domain also ensures Est2 stability on the RNP independently of the Est1 association. Therefore, the recruitment module of the Tlc1 RNA requires a very tight architectural organization for telomerase function in vivo .
Irreducible many-body correlations in topologically ordered systems

Topologically ordered systems exhibit large-scale correlation in their ground states, which may be characterized by quantities such as topological entanglement entropy. We propose that the concept of irreducible many-body correlation (IMC), the correlation that cannot be implied by all local correlations, may also be used as a signature of topological order. In a topologically ordered system, we demonstrate that for a part of the system with holes, the reduced density matrix exhibits IMCs which become reducible when the holes are removed. The appearance of these IMCs then represents a key feature of topological phase. We analyze the many-body correlation structures in the ground state of the toric code model in external magnetic fields, and show that the topological phase transition is signaled by the IMCs.
Tracheostomy in children promotes persistent neutrophilic airway inflammation

Background: Tracheostomies in children are associated with significant morbidity, poor quality of life, excess healthcare costs, and excess mortality. The underlying mechanisms facilitating adverse respiratory outcomes in tracheostomised children are poorly understood. We aimed to characterise airway host defence in tracheostomised children using serial molecular analyses. Methods: Tracheal aspirates, tracheal cytology brushings, nasal swabs and stool samples were prospectively collected from children with a tracheostomy and controls. Transcriptomic, proteomic, and metabolomic methods were applied to characterise the impact of tracheostomy on host immune response and the airway microbiome. Results: Children followed up serially from the time of tracheostomy up to three months post-procedure (n=9) were studied. A validation cohort of children with a long-term tracheostomy was also enrolled (n=24). Controls (n=13) comprised children without a tracheostomy undergoing bronchoscopy. Tracheostomy was associated with new, rapidly emergent and sustained airway neutrophilic inflammation, superoxide production and evidence of proteolysis when compared with controls. In contrast, reduced airway microbial diversity was established pre-tracheostomy and sustained thereafter. Conclusions: Childhood tracheostomy is associated with rapidly emergent and persistent airway neutrophil recruitment and activation, with sustained proteolysis and superoxide generation. These findings suggest neutrophil recruitment and activation as potential exploratory targets in seeking to prevent recurrent airway complications in this vulnerable group of patients.
Correlation of patient serum IgG, IgA and IgM antigen binding with COVID-19 disease severity using multiplexed SARS-CoV-2 antigen microarray and maintained relative IgA and IgM antigen binding over time

Zoonotic spillover of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to humans in December 2019 caused the coronavirus disease 2019 (COVID-19) pandemic. Serological monitoring is critical for detailed understanding of individual immune responses to infection and protection to guide clinical therapeutic and vaccine strategies. We developed a high throughput multiplexed SARS-CoV-2 antigen microarray incorporating spike (S) and nucleocapsid protein (NP) and fragments expressed in various hosts which allowed simultaneous assessment of serum IgG, IgA, and IgM responses. Antigen glycosylation influenced antibody binding, with S glycosylation generally increasing and NP glycosylation decreasing binding. Purified antibody isotypes demonstrated a binding pattern and intensity that differed from the same isotype in the presence of other isotypes in whole serum, probably due to competition. Using purified antibody isotypes from naive Irish COVID-19 patients, we correlated antibody isotype binding to different panels of antigens with disease severity, with significance for binding to the S region S1 expressed in insect cells (S1 Sf21) for all three antibody isotypes. Assessing longitudinal response for constant concentrations of antibody isotypes for a subset of patients demonstrated that while the relative proportion of antigen-specific IgGs decreased over time for severe disease, the relative proportion of antigen-specific IgA binding remained at the same magnitude at 5 and 9 months post-first symptom onset. Further, the relative proportion of IgM binding decreased for S antigens but remained the same for NP antigens. This may support antigen specific serum IgA and IgM playing a role in maintaining longer-term protection, of importance for developing and assessing vaccine strategies. Overall, these data demonstrate the multiplexed platform as a sensitive and useful platform for expanded humoral immunity studies, allowing detailed elucidation of antibody isotypes response against multiple antigens. This approach will be useful for monoclonal antibody therapeutic studies and screening of donor polyclonal antibodies for patient infusions.
ETDRS letter scoring method improves the accuracy of 1.25% low-contrast visual acuity measurement in optic neuritis eyes in MS

Objectives: To examine whether the accuracy of 1.25% low-contrast visual acuity (LCVA) measurement in MS patients with optic neuritis (ON) can be improved by using the Early Treatment Diabetic Retinopathy Study (ETDRS) letter scoring method. Methods: 51 relapsing-remitting MS patients with a history of unilateral ON were enrolled. LCVA was tested using 2.5% and 1.25% low contrast ETDRS-style 4m Sloan letter charts. When [≥]20 letters were read correctly, the letter score was equal to letter count plus 30. If <20 letters were read correctly, the letter score was equal to letter count at 4m plus the total number of letters read correctly at 1m. Results: 60.8% ON eyes had a 1.25% LCVA letter count worse than 1 line (5 letters). In ON eyes with <20 letter count, ETDRS letter score showed a significantly improved correlation with macular GCIPL thickness (r=0.71, p<0.0001; vs r=0.31, p=0.08 for letter count) and VEP latency (r=-0.47, p=0.003; vs r=-0.15, p=0.4 for letter count). Discussion: Given ON with VEP monitoring has been frequently used as a model in MS remyelination trials, this ETDRS-style letter scoring method may be considered to enhance the functional outcome measure, which is necessary for regulatory approval.
IMPROVING EFFECT OF FISH OIL, OLIVE OIL AND MELATONIN ON INDUCED HYPERCHOLESTEROLEMIA IN ADULT MALE RATS.

This study aims to evaluate the possible improving effects of fish oil, olive oil and melatonin on the induced hypercholesterolemia in adult male rats. 50 rats were used in this study and were divided into 5 groups 10 rats each. Rats of group 1 were fed on a standard diet and those of group 2 were fed on a standard diet enriched with 1% cholesterol (cholesterol fed group) for 10 weaks. Groups 3-5 were fed as in group 2 then the diet was replaced by standard diet and fish oil in group 3 (fish oil group), standard diet and olive oil in group 4 (olive oil group) and standard diet and melatonin in group 5 (melatonin group) for 2 weeks . Then, blood samples were taken from all animals and the aorta of each animal was obtained after slaughtering and examined histologically to assess the presence of atherosclerosis. Parameters of the lipogram [total plasma cholesterol (TPC), high density lipoprotein (HDL), low density lipoprotein (LDL) and triglycerides (TG)], superoxide dismutase (SOD), total thiol, nitric oxide (NO) and lipid peroxide (LP) were measured. fibrous plaques nearly to the same extent in all groups but absence of well developed fibrous cap which was found in the cholesterol fed group denoting slight improvement. It was concluded that diet additives as fish oil, olive oil or melatonin injection have modulating effect on the parameters of the lipogram, oxidative stress markers and histological features of atherosclerotic lesion and that the improvement of the aortic wall was slight due to the short period of treatment (2 weeks only) to produce marked change in the aortic wall.
Modern Contraceptive Utilization and Associated Factors Among Married Women in Liberia: Evidence from the 2019 Liberia Demographic and Health Survey

Background: Contraceptive methods help individuals control the number, interval, and timing of pregnancies and prevent unwanted pregnancies. Objective: This study aimed to assess the prevalence of modern contraceptive utilization and associated factors among married reproductive-age women in Liberia. Methods: This study was based on a large community-based cross-sectional survey, conducted from October 16, 2019, to February 12, 2020, in Liberia. The survey employed a multistage cluster sampling technique to recruit study participants. Binary logistic regression was used to identify associated factors of contraceptive utilization. A p-value of <0.05 and a 95% confidence interval were used to declare statistical significance. Results: The overall modern contraceptive utilization among reproductive-age women in Liberia was 23.87% (95% CI: 27.3, 29.9). Women with the age group of 20 and 24 years [AOR = 2.08 (95% CI:1.37, 3.14)], 25–29 years [AOR = 1.73 (95% CI: 1.13, 2.65)], 45–49 years [AOR = 0.46, 95% CI: 0.27, 0.76], being Muslim [AOR = 0.52, 95% CI: 0.399, 0.67], residing in South Eastern Regions (B) [AOR = 1.40, 95% CI: 1.11, 1.79], south central [AOR=0.48 95% CI:0.37, 0.61] and North Central region [AOR = 0.48, 95% CI: 0.37, 0.61], being employed [AOR = 1.26, 95% CI:1.06, 1.51], having 1–2 child/children [AOR = 2.81, 95% CI:1.80, 4.39] 3–4 children [AOR = 3.87, 95% CI:3.87, 6.24] and 5 and above [AOR = 7.06, 95% CI: 4.27, 11.69], completed primary [AOR = 1.52, 95% CI: 1.22, 1.88] and higher education [AOR = 1.72, 95% CI: 1.01, 2.94], having educated husband [AOR = 1.35, 95% CI: 1.12, 1.63], being from richer households [AOR = 1.41, 95% CI:1.09, 1.82], and had declared infecund [AOR = 0.13, 95% CI: 0.046, 0.36] were independently associated with modern contraceptive utilization among married women in Liberia. Conclusion: The prevalence of modern contraceptive utilization among reproductive-age women in Liberia was low. Contraceptive utilization was affected by partners’ education and participants’ socio-demographic and obstetric attributes. Thus, public health interventions are urgently required to enhance use of contraceptives among this group of population.
Nominal Debt and the Heterogeneous Effects of Forward Guidance ∗

We develop an incomplete-markets heterogeneous agent New-Keynesian (HANK) model in which households are allowed to borrow using nominal debt. We show that, in this framework, forward guidance, that is the promise by the central bank to lower future interest rates, can be a powerful policy tool, especially when the economy is in a liquidity trap. In our model, expected lower rates imply a future transfer of wealth from savers to borrowers, reducing precautionary motives and stimulating current demand and inﬂation. In addition, at the time of the policy announcement, debt deﬂation generates also a wealth transfer towards constrained agents, who have high marginal propensity to consume, further increasing aggregate consumption and inﬂation, and igniting a positive feedback loop. These results contrast with previous research on HANK models, which focused on frameworks where agents were not allowed to borrow, and which found negligible effects of forward guidance.
Dose, Duration and Strain of Bacillus Calmette-Guerin in the Treatment of Non-Muscle Invasive Bladder Cancer: Systematic Review and Meta-Analysis of Randomized Clinical Trials

i Abstract instillation is widely used as an adjuvant therapy after transurethral resection of bladder tumor (TURBT) in patients with intermediate-and high-risk non-muscle invasive bladder cancer (NMIBC). However, the effective dose, duration and strain of BCG have not yet been clearly determined. We aimed to elucidate the relationship between dose, duration, and strain of BCG and clinical outcomes in NMIBC patients treated with TURBT. Methods: We conducted a literature search in Embase, Scopus, and PubMed databases for all relevant articles published up to October 2016 in accordance with the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) guidelines. The relative risks of clinical outcomes, including recurrence, progression, cancer-specific mortality, and all-cause mortality according to dose (standard versus low), duration (induction versus maintenance), and strain of BCG were presented as the pooled risk ratio (RR) and 95% confidence interval (CI). Results: Nineteen studies meeting the inclusion criteria were finally selected in this meta-analysis. The risk of recurrence was significantly highly observed in case of low dose BCG (RR, 1.17; 95% CI 1.06-1.30) and induction BCG (RR, 1.33; 95% CI 1.17-1.50) only group. While there were no significant differences between dose or duration and other clinical outcomes. Chi-square-based Q statistic and Higgins I-squared statistic test revealed that there was no significant inter-study heterogeneity in all analyses. On direct comparison in each study comparing BCG strains, the Tice strain showed a relatively high probability of recurrence compared with the Connaught (RR, 1.29; 95% CI 1.01-1.64) and RIVM (RR, 2.04, 95% CI 1.28-3.25) strains. Funnel plot testing revealed no significant publication bias. Conclusions: The use of standard dose and maintenance BCG instillation may be effective to reduce recurrence rate after TURBT for NMIBC. Further large scale, well-designed and prospective studies, with stratification of the patients into risk group at randomization, will be required to determine the optimal guideline of BCG use to improve clinical outcomes in NMIBC.
The Mortality Rate of Two Different Breeds of Broilers after Brooding Stage to Maturity

: This study critically examined whether there is any different in the mortality rate of two different breeds of broilers after the brooding stage to maturity. The experiment was performed in the Departmental Poultry farm of Tai Solarin University of Education, Ijebu-Ode, Ogun State under the same environment and Managemental condition. The birds were four weeks old at the commencement of the study and they were reared for seven weeks. The birds were divided into two groups based on their breeds. In-group A we have the Arbour Acres and in group B, Anak 2000. The research started with 55 birds in-group A and ended with 48 birds and in-group B, there were 59 birds at the beginning of the research and ended with 55 birds. The results were analyzed using the percentage and Chi-square methods. The analysis revealed that there is very high significant different (p<0.001) in the mortality rate of the two breeds. It was also revealed that group A has higher mortality (12.73%) compare to group B with lower mortality (6.78%). Based on this, it can be concluded that the Anak 2000 is better than the Arbour Acres in terms of mortality rate pattern.
The DNA methylation landscape of advanced prostate cancer.

The androgen receptor (AR) antagonist enzalutamide is one of the principal treatments for men with castration-resistant prostate cancer (CRPC). However, not all patients respond, and resistance mechanisms are largely unknown. We hypothesized that genomic and transcriptional features from metastatic CRPC biopsies prior to treatment would be predictive of de novo treatment resistance. To this end, we conducted a phase II trial of enzalutamide treatment (160 mg/d) in 36 men with metastatic CRPC. Thirty-four patients were evaluable for the primary end point of a prostate-specific antigen (PSA)50 response (PSA decline ≥ 50% at 12 wk vs. base-line). Nine patients were classified as nonresponders (PSA decline < 50%), and 25 patients were classified as responders (PSA decline ≥ 50%). Failure to achieve a PSA50 was associated with shorter progression-free survival, time on treatment, and overall survival, demonstrating PSA50 ’ s utility. Targeted DNA-sequencing was performed on 26 of 36 biopsies, and RNA- sequencing was performed on 25 of 36 biopsies that contained sufficient material. Using computational methods, we measured AR transcriptional function and performed gene set enrichment analysis (GSEA) to identify pathways whose activity state corre- lated with
E ﬀ ect of Clay Colloid Particles on Formaldehyde Transport in Unsaturated Porous Media

: This study examines the e ﬀ ects of two representative colloid-sized clay particles (kaolinite, KGa-1b and montmorillonite, ST x -1b) on the transport of formaldehyde (FA) in unsaturated porous media. The transport of FA was examined with and without the presence of clay particles under various ﬂow rates and various levels of saturation in columns packed with quartz sand, under unsaturated conditions. The experimental results clearly suggested that the presence of clay particles retarded by up to ~23% the transport of FA in unsaturated packed columns. Derjaguin–Landau–Verwey–Overbeek (DLVO) interaction energy calculations demonstrated that permanent retention of clay colloids at air-water interfaces (AWI) and solid-water interfaces (SWI) was negligible, except for the pair (ST x -1b)–SWI. The experimental results of this study showed that signiﬁcant clay colloid retention occurred in the unsaturated column, especially at low ﬂow rates. This deviation from DLVO predictions may be explained by the existence of additional non-DLVO forces (hydrophobic and capillary forces) that could be much stronger than van der Waals and double layer forces. The present study shows the important role of colloids, which may act as carriers of contaminants.
Differential Regulation of Cathepsin S and Cathepsin L in Interferon (cid:2) –treated Macrophages

Cathepsin S (catS) and cathepsin L (catL) mediate late stages of invariant chain (Ii) degradation in discrete antigen-presenting cell types. Macrophages (M (cid:3) s) are unique in that they express both proteases and here we sought to determine the relative contribution of each enzyme. We observe that catL plays no significant role in Ii cleavage in interferon (IFN)- (cid:2) –stimulated M (cid:3) s. In addition, our studies show that the level of catL activity is significantly decreased in M (cid:3) s cultured in the presence of IFN- (cid:2) whereas catS activity increases. The decrease in catL activity upon cytokine treatment occurs despite the persistence of high levels of mature catL protein, suggesting that a specific inhibitor of the enzyme is up-regulated in IFN- (cid:2) –stimulated peritoneal M (cid:3) s. Similar inhibition of activity is observed in dendritic cells engineered to overexpress catL. Such enzymatic inhibition in M (cid:3) s exhibits only partial dependence upon Ii and therefore, other mechanisms of catL inhibition are regulated by IFN- (cid:2) . Thus, during a T helper cell type 1 immune response catL inhibition in M (cid:3) s results in preferential usage of catS, such that major histocompatibility complex class II presentation by all bone marrow–derived antigen-presenting cell is regulated by catS.