Miracle-dz/UniFAR-FTUs huggingface dataset:
Improvement of Xylanase Production by Bacillus subtilis in Submerged Fermentation after UV and Chemicals Mutagenesis

Aims: Bacillus subtilis is one of the most utilized industrial microorganisms for its high capability of producing large amount of extracellular enzymes including xylanase. This extracellular enzyme has been used extensively for many years in food and detergents industry. In recent years, many attempts have been made for the improvement of microbial xylanase production by inducing mutagenesis. Thus, the objectives of this study are to produce mutants of B. subtilis using UV and chemicals mutagenesis, subsequently to elucidate the xylanase activity and finally to identify the most effective mutagenic agent for overproduction of this enzyme. Methodology: In this study, ultraviolet (UV) irradiation and chemical mutagens of ethyl methanesulfonate (EMS) and acridine orange (AO) have been selected because of their simplicity of handling and cost-effectiveness as compared to recombinant DNA technology. The efficiency of these mutagenesis was further assessed in submerged fermentation in shake flask culture compared with the non-treated wild type control strain. Results: Based on our results, B. subtilis that had been induced with 50 μg/mL of AO for 30 min exhibited the overproduction of xylanase with 1.580±0.027 U/mL in submerged fermentation. Indeed, the highest xylanase overproduction reached the maximum peak of 1.638±0.027 U/mL after Original Research Article Ho and Chor; JABB, 3(2): 42-57, 2015; Article no.JABB. 2015.031 43 30 min of induction using 100 ug/mL of EMS. Apparently, when compared to the non-treated control, xylanase activity experienced the highest percentage of overproduction as much as 15.68% from EMS mutagenesis induced for 30 min in contrast to only 11.58% from B. subtilis that had been induced with 50 μg/mL of AO for 30 min. Conclusion: In a nutshell, based on our results, EMS evidenced among the most promising mutagenic agent of inducing B. subtilis that capable of overproduction of xylanase to the greater extend as compared to UV irradiation and mutagenic agent of AO.
Emerging Role of Extracellular Vesicles in Prostate Cancer

Abstract Prostate cancer (PCa) is the second most common cancer among men in the United States. While the use of prostate-specific antigen has improved the ability to screen and ultimately diagnose PCa, there still remain false positives due to noncancerous conditions in the prostate gland itself and other prognostic biomarkers for PCa are needed. Contents within extracellular vesicles (EVs) have emerged as promising biomarkers that can give valuable information about disease state, and have the additional benefit of being acquired through noninvasive liquid biopsies. Meaningful communication between cancer cells and the microenvironment are carried by EVs, which impact important cellular processes in prostate cancer such as metastasis, immune regulation, and drug resistance.
Lichen fungi do not depend on the alga for ATP production

Lichen fungi live in a symbiotic association with unicellular phototrophs and have no known aposymbiotic stage. A recent study postulated that some of them have lost mitochondrial oxidative phosphorylation and rely on their algal partners for ATP. This claim originated from an apparent lack of ATP9, a gene encoding one subunit of ATP synthase, from a few mitochondrial genomes. Here we show that while these fungi indeed have lost the mitochondrial ATP9, each retain a nuclear copy of this gene. Our analysis reaffirms that lichen fungi produce their own ATP.
Intensive Care Unit Volume of Sepsis Patients Does Not Affect Mortality: Results of a Nationwide Retrospective Analysis

Background: There is little research evaluating outcomes from sepsis in intensive care units (ICUs) with lower sepsis patient volumes as compared to ICUs with higher sepsis patient volumes. Our objective was to compare the outcomes of septic patients admitted to ICUs with different sepsis patient volumes. Materials and Methods: We included all patients from the eICU-CRD database admitted for the management of sepsis with blood lactate ≥ 2mmol/L within 24 hours of admission. Our primary outcome was ICU mortality. Secondary outcomes included hospital mortality, 30-day ventilator free days, and initiation of renal replacement therapy (RRT). ICUs were grouped in quartiles based on the number of septic patients treated at each unit. Results: 10,716 patients were included in our analysis; 272 (2.5%) in low sepsis volume ICUs, 1,078 (10.1%) in medium-low sepsis volume ICUs, 2,608 (24.3%) in medium-high sepsis volume ICUs, and 6,758 (63.1%) in high sepsis volume ICUs. On multivariable analyses, no significant differences were documented regarding ICU and hospital mortality, and ventilator days in patients treated in lower versus higher sepsis volume ICUs. Patients treated at lower sepsis volume ICUs had lower rates of RRT initiation as compared to high volume units (medium-high vs. high: OR = 0.78, 95%CI = 0.66-0.91, P-value = 0.002 and medium-low vs. high: OR = 0.57, 95%CI = 0.44-0.73, P-value < 0.001). Conclusion: The previously described volume-outcome association in septic patients was not identified in an intensive care setting.
Lifting and Toning of Arms and Calves Using High-Intensity Focused Electromagnetic Field (HIFEM) Procedure Documented by Ultrasound Assessment.

OBJECTIVE The HIFEM procedure demonstrates positive outcomes on abdomen and buttock. This multi-center study aims to investigate its effect on adipose tissue and muscle mass located in upper arms and calves. MATERIALS AND METHODS Twenty subjects (45.10±15.19 years, 24.44±3.22 kg/m2) who underwent a HIFEM procedure (4 sessions; 20 minutes per muscle group) on arms and calves were evaluated. Overall, 7 patients were treated over biceps and triceps, 4 patients over calves, and 9 patients underwent treatment of both upper arms and calves. The changes in adipose and muscle tissue of musculus biceps brachii, triceps brachii, and gastrocnemius were evaluated by using ultrasound. The results from a 1-month, 3-month, and 6-month follow-up were compared to the baseline. Digital photographs, weight measurements, satisfaction, and comfort questionnaires were assessed at baseline and follow-ups. RESULTS Ultrasound images revealed a significant (P<0.05) increase in the muscle mass of all studied muscles, with the most noticeable improvement in biceps brachii (+16.13% at 3 months). The fat deposits over arms and calves showed significant improvement (P<0.05), reaching -15.12% at 3 months. The results peaked at 3 months and were sustained up to 6 months with a slight but insignificant decline. Aesthetic enhancement of treated areas was documented while patients were highly satisfied. CONCLUSIONS The achieved outcomes showed that the HIFEM procedure is effective for muscle toning and fat reduction in arms and calves. The results suggest that the use of the HIFEM procedure is not limited only to abdominal and buttock shaping but is also effective for toning of arms and calves. J Drugs Dermatol. 2021;20(7):755-759. doi:10.36849/JDD.5878.
Engineering large-scale chromosomal deletions by CRISPR-Cas9

Abstract Large-scale chromosomal deletions are a prevalent and defining feature of cancer. A high degree of tumor-type and subtype specific recurrencies suggest a selective oncogenic advantage. However, due to their large size it has been difficult to pinpoint the oncogenic drivers that confer this advantage. Suitable functional genomics approaches to study the oncogenic driving capacity of large-scale deletions are limited. Here, we present an effective technique to engineer large-scale deletions by CRISPR-Cas9 and create isogenic cell line models. We simultaneously induce double-strand breaks (DSBs) at two ends of a chromosomal arm and select the cells that have lost the intermittent region. Using this technique, we induced large-scale deletions on chromosome 11q (65 Mb) and chromosome 6q (53 Mb) in neuroblastoma cell lines. A high frequency of successful deletions (up to 30% of selected clones) and increased colony forming capacity in the 11q deleted lines suggest an oncogenic advantage of these deletions. Such isogenic models enable further research on the role of large-scale deletions in tumor development and growth, and their possible therapeutic potential.
Characterization of G4 DNA formation in mitochondrial DNA and their potential role in mitochondrial genome instability

Mitochondria possess their own genome which can be replicated independently of nuclear DNA. Mitochondria being the powerhouse of the cell produce reactive oxygen species, due to which the mitochondrial genome is frequently exposed to oxidative damage. Previous studies have demonstrated an association of mitochondrial deletions to aging and human disorders. Many of these deletions were present adjacent to non‐B DNA structures. Thus, we investigate noncanonical structures associated with instability in mitochondrial genome. In silico studies revealed the presence of > 100 G‐quadruplex motifs (of which 5 have the potential to form 3‐plate G4 DNA), 23 inverted repeats, and 3 mirror repeats in the mitochondrial DNA (mtDNA). Further analysis revealed that among the deletion breakpoints from patients with mitochondrial disorders, majority are located at G4 DNA motifs. Interestingly, ~ 50% of the deletions were at base‐pair positions 8271–8281, ~ 35% were due to deletion at 12362–12384, and ~ 12% due to deletion at 15516–15545. Formation of 3‐plate G‐quadruplex DNA structures at mitochondrial fragile regions was characterized using electromobility shift assay, circular dichroism (CD), and Taq polymerase stop assay. All 5 regions could fold into both intramolecular and intermolecular G‐quadruplex structures in a KCl‐dependent manner. G4 DNA formation was in parallel orientation, which was abolished in the presence of LiCl. The formation of G4 DNA affected both replication and transcription. Finally, immunolocalization of BG4 with MitoTracker confirmed the formation of G‐quadruplex in mitochondrial genome. Thus, we characterize the formation of 5 different G‐quadruplex structures in human mitochondrial region, which may contribute toward formation of mitochondrial deletions.
Determination of monosaccaride and disaccaride in condensed Siwu Decoction by HPLC-ELSD

Object To establish a method by high performance liquid chromatography/evaporative light scattering detector (HPLC-ELSD) for the determination of contents of D-fructose, D-glucose, and sucrose in Siwu Decoction (SWD). Methods Condensed SWD was analyzed by HPLC-ELSD after dilution, precipitation by ethanol. Results Condensed SWD, 1 mL, contained (33.4±1.5) mg of D-fructose, (24.2±0.9) mg of D-glucose and (112.7±6.1) mg of sucrose. The standard curves were linear within the range of 0.15—3.75 mg/mL for D-fructose and 0.15—5 mg/mL for D-glucose and sucrose. The recovery rates were 128.5% for D-fructose, 114.7% for D-glucose, and 124.7% for sucrose. The relative standard deviations (RSD) within-days were 3.0% for D-fructose, 3.2% for D-glucose, and 4.4% for sucrose. Conclusion SWD contains abundant monosaccharide and disaccharide. HPLC-ELSD can be used to analyse the monosaccharide and disaccharide in SWD.
Some approximations in applications of X. cap alpha. theory

An approximate X.cap alpha. functional is proposed from which the charge density fitting equations follow variationally. LCAO X.cap alpha. calculations on atomic nickel and diatomic hydrogen show the method independent of the fitting (auxiliary) bases to within 0.02 eV. Variational properties associated with both orbital and auxiliary basis set incompleteness are used to approach within 0.2 eV the X.cap alpha. total energy limit for the nitrogen molecule.
Changes in pectinesterase, polygalacturonase and cellulase activity during mango fruit ripening

Changes in the activities of the cell wall degrading enzymes pectinesterase (PE), polygalacturonase (PG) and cellulase were studied during the ripening of fruit from ‘Kitch- ner’, ‘Dr Knight’ and ‘Abu-Samaka’ mango cultivars. PE activity decreased continuously during ripening of ‘Kitchner’ and ‘Dr Knight’, while that of ‘Abu-Samaka’ increased up to firmness 88 N, and subsequently decreased. Activities of PG and cellulase increased progressively during the ripening of fruit of the three cultivars with a high correlation between the increase in the activity of the two enzymes and the loss of fruit firmness. A key role of PE in controlling fruit softening rate in mango was identified.
Pan-caspase inhibition as a potential host-directed immunotherapy against MRSA and other bacterial skin infections

A pan-caspase inhibitor, Q-VD-OPH, has therapeutic efficacy against preclinical methicillin-resistant Staphylococcus aureus skin infection. Anti-infection immunotherapy Antibiotic-resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA) are increasingly prevalent and difficult to treat. Alphonse et al. show that a pan-caspase inhibitor called Q-VD-OPH functioned as an effective immunotherapy in mouse models of community-acquired MRSA, Streptococcus pyogenes, and Pseudomonas aeruginosa skin infections. Q-VD-OPH reduced apoptosis in neutrophils and monocytes and increased necroptosis in macrophages, thereby increasing TNF production and infection clearance in mice. This work suggests a potential strategy to target bacterial infections without requiring the use of antibiotics. Staphylococcus aureus causes most skin infections in humans, and the emergence of methicillin-resistant S. aureus (MRSA) strains is a serious public health threat. There is an urgent clinical need for nonantibiotic immunotherapies to treat MRSA infections and prevent the spread of antibiotic resistance. Here, we investigated the pan-caspase inhibitor quinoline–valine–aspartic acid–difluorophenoxymethyl ketone (Q-VD-OPH) for efficacy against MRSA skin infection in mice. A single systemic dose of Q-VD-OPH decreased skin lesion sizes and reduced bacterial burden compared with vehicle-treated or untreated mice. Although Q-VD-OPH inhibited inflammasome-dependent apoptosis-associated speck-like protein containing caspase activation and recruitment domain (ASC) speck formation and caspase-1–mediated interleukin-1β (IL-1β) production, Q-VD-OPH maintained efficacy in mice deficient in IL-1β, ASC, caspase-1, caspase-11, or gasdermin D. Thus, Q-VD-OPH efficacy was independent of inflammasome-mediated pyroptosis. Rather, Q-VD-OPH reduced apoptosis of monocytes and neutrophils. Moreover, Q-VD-OPH enhanced necroptosis of macrophages with concomitant increases in serum TNF and TNF-producing neutrophils, monocytes/macrophages, and neutrophils in the infected skin. Consistent with this, Q-VD-OPH lacked efficacy in mice deficient in TNF (with associated reduced neutrophil influx and necroptosis), in mice deficient in TNF/IL-1R and anti-TNF antibody-treated WT mice. In vitro studies revealed that combined caspase-3, caspase-8, and caspase-9 inhibition reduced apoptosis, and combined caspase-1, caspase-8, and caspase-11 inhibition increased TNF, suggesting a mechanism for Q-VD-OPH efficacy in vivo. Last, Q-VD-OPH also had a therapeutic effect against Streptococcus pyogenes and Pseudomonas aeruginosa skin infections in mice. Collectively, pan-caspase inhibition represents a potential host-directed immunotherapy against MRSA and other bacterial skin infections.
Combination of targeted monitoring and Breeding Bird Survey data improves population trend estimation and species distribution modeling for the Common Nighthawk

ABSTRACT Standardized monitoring is critical for conservation because reliable survey data are used to inform the necessity, type, and effectiveness of conservation actions. Many of the avian monitoring data used for conservation are collected by “comprehensive” programs that survey for all species observed; however, there are some species that have low availability for detection during comprehensive surveys and are instead monitored with targeted programs. Unfortunately, those targeted programs are rarely evaluated relative to existing programs and management objectives to inform allocation of effort. We assessed the statistical performance of the comprehensive North American Breeding Bird Survey (BBS), the targeted Canadian Nightjar Survey (CNS), and the two programs combined for the Common Nighthawk (Chordeiles minor). First, we used parameters from the existing datasets to simulate population declines and determined the probability of detecting those declines. Analyses that combined both datasets resulted in higher probability of detecting a 30% population decline (BBS: 38%, CNS: 64%, combined: 69%). Next, we built probability of occurrence models and assessed the predictive performance of those models. Combined analyses had similar predictive performance to the CNS and moderated poor performance of the BBS in the north (mean Cohen's kappa; BBS: 0.40, CNS: 0.46, combined: 0.50). Our results suggest that data from targeted monitoring is important for evaluation of Common Nighthawk population trend and habitat relationships but is best combined with BBS data. Comprehensive and targeted monitoring programs may be better when considered together, and exploration of data combination should become the rule, not the exception. We suggest that the framework we present can be used as a starting point for evaluating targeted monitoring programs relative to defined objectives and existing programs, with the potential to explore hypothetical management scenarios. LAY SUMMARY Not all species are well detected during “comprehensive” bird surveys like the Breeding Bird Survey. Targeted monitoring at particular times of day or in specific locations can help detect those species and help wildlife managers conserve them. The Common Nighthawk is a crepuscular bird that is poorly detected during comprehensive dawn surveys. We showed that the targeted Canadian Nightjar Survey improves the precision of Common Nighthawk population trends and accuracy of habitat predictions. Combining information from the Breeding Bird Survey and the Canadian Nightjar Survey can further improve population trend estimates and habitat predictions. Our study suggests that targeted monitoring can be important for some species and that combining it with comprehensive monitoring is important for evaluating existing and proposed conservation programs.
Measuring Legacies of Collective Racial Violence

The “legacy effect” of lynchings and other forms of racialized violence has shaped patterns of inequality in America. While past studies have been relatively similar in their design—relating basic counts of lynchings to various contemporary outcomes—I argue for and demonstrate a more nuanced approach. I show that if we think of racialized violence as more than just the act of lynching, and consider both the temporal and spatial proximity between historic events of racial violence and contemporary inequality, we can establish this relationship in a more fulsome way. In the case of this study, the relationship is drawn to housing segregation. I argue that expanding the conceptualization of racial violence is critical for both empirical inquiry and shaping community efforts around redress.
Functional Effectiveness of Commodity Futures Market: A Comparative Assessment of Agricultural and Metal Commodities

The study focuses on examining the price discovery process, short run disturbances and hedging mechanism of agricultural and metal commodities futures market for the period January 2010 to December 2018. Contango and normal backwardation have also been taken into deliberation for select commodities which are traded in MCX and NCDEX, India which is a valuable addition to the existing body of literature in derivatives market. Johansen’s co-integration, VECM, Granger causality test and OLS are employed for understanding the price discovery and constant hedging for select commodities. Further, existence contango and normal backwardation have been observed by comparing the spot and futures prices. It has been found that spot market is acting as a leader in the longer period and laggard in short run investors can be benefitted to take short run or long run investment decision.
Numerical prediction of heat transfer in supersonic inlets

The prediction of the performances of supersonic inlets heavily depends on the ability to model Shock-Wave/Turbulent-Boundary-Layer Interactions (SWBLI). A joint experimental and computational study is carried out to identify the dierent flow regimes occuring in supersonic conditions (Mach 4) between two sharp ns mounted on a flat plate. The three examined congurations (77 ,7 11 ,1 515) cover a representative range of interaction strengths. The distributions of pressure and Stanton number are related to the identied flow regimes. Experiments and computations agree on the primary features of the flow, but they diverge on the secondary features and the level of the heat transfer in these regions, where it may be over-predicted by a factor of 2 2:5. The SWBLI heat transfer issue might be due to unsteadiness problems and turbulence modeling deciencies.
Primary instability of a visco-plastic film down an inclined plane: experimental study

Abstract We study experimentally the primary instability of a visco-plastic film flow down an inclined plane. The experimental set-up is a channel with a varying slope angle, in which a permanent flow of a Herschel–Bulkley fluid (carbopol or kaolin) is established. Controlled perturbations are imposed at the entrance of the channel to generate surface waves, and their downstream evolution is observed with a laser sensor system measuring the local fluid thickness. Growth rates and cutoff frequencies are obtained after processing the thickness signal, and experimental critical Reynolds and Bingham numbers are deduced. We find that the experimental stability map obtained is well described by the pseudo-plug model of Balmforth & Liu (J. Fluid Mech., vol, 519, 2004, pp. 33–54), a model obtained after neglecting the film thickness compared with its length. This is not the case for dispersion effects (growth rates, cutoff frequencies, phase speeds), for which a more accurate model is needed.
Statics and dynamics of a viscous ligament drawn out of a pure-liquid bath

Abstract In this paper we investigate the statics and the dynamics of large-viscosity ligaments attached to a rod and drawn out of a pure-liquid bath. Following the similar work of films pulling out of a bath (Champougny et al., J. Fluid Mech., vol. 811, 2017, pp. 499–524), a one-dimensional model is applied to describe the ligaments drawn at constant velocities. We focus on the whole drawing dynamics of the ligament up to breakup, for which the breakup height is determined. The breakup height coincides with the maximum static meniscus height for very slow drawing, whose process can be described by quasi-static solutions. We present the numerical results of the static menisci and analytically unravel the mechanism in the low gravity case. Starting from a stable static meniscus, the breakup height of faster drawing depends separately on the rod radius and the drawing velocity, the latter dependency being fully determined by considering the agravic limit. Next, it is shown that the entire lifetime of the ligament drawing can be sequenced into a ductility stage, a capillarity stage and a pinch-off stage, the latter being shown to be almost instantaneous. The ductility and capillarity stages are decorrelated with the help of an approximate solution of the ductility stage, and the transition between the two stages corresponds to the time at which the capillarity-induced contraction velocity exceeds the ductility-induced one. The one-dimensional predictions of the breakup height and the entrained liquid volume attached to the rod quantitatively agree with experimental results of silicone oil ligaments, and the deviations are rationalized in comparison with a two-dimensional model.