Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA‐stable isotope probing (DNA‐SIP) identifies marine sponge‐associated bacteria actively utilizing dissolved organic matter (DOM)

Summary Sponges possess exceptionally diverse associated microbial communities and play a major role in (re)cycling of dissolved organic matter (DOM) in marine ecosystems. Linking sponge‐associated community structure with DOM utilization is essential to understand host–microbe interactions in the uptake, processing, and exchange of resources. We coupled, for the first time, DNA‐stable isotope probing (DNA‐SIP) with 16S rRNA amplicon sequencing in a sponge holobiont to identify which symbiotic bacterial taxa are metabolically active in DOM uptake. Parallel incubation experiments with the sponge Plakortis angulospiculatus were amended with equimolar quantities of unlabelled (12C) and labelled (13C) DOM. Seven bacterial amplicon sequence variants (ASVs), belonging to the phyla PAUC34f, Proteobacteria, Poribacteria, Nitrospirae, and Chloroflexi, were identified as the first active consumers of DOM. Our results support the predictions that PAUC34f, Poribacteria, and Chloroflexi are capable of organic matter degradation through heterotrophic carbon metabolism, while Nitrospirae may have a potential mixotrophic metabolism. We present a new analytical application of DNA‐SIP to detect substrate incorporation into a marine holobiont with a complex associated bacterial community and provide new experimental evidence that links the identity of diverse sponge‐associated bacteria to the consumption of DOM.
Nanoparticles in nanomedicine: a comprehensive updated review on current status, challenges and emerging opportunities

Abstract The fast progress in nanomedicine and nanoparticles (NP) materials presents unconventional solutions which are expected to revolutionise health care with great potentials including, enhanced efficacy, bioavailability, drug targeting, and safety. This review provides a comprehensive update on widely used organic and inorganic NP with emphasis on the recent development, challenges and future prospective for bio applications where, further investigations into innovative synthesis methodologies, properties and applications of NP would possibly reveal new improved biomedical relevance. NP exhibits exceptional physical and chemical properties due to their high surface area to volume ratio and nanoscale size, which led to breakthroughs in therapeutic, diagnostic and screening techniques repeated line. Finally, an update of FDA-approved NP is explored where innovative design engineering allowed a paradigmatic shift in their market share. This review would serve as a discerning comprehensive source of information for learners who are seeking a cutting-edge review but have been astounded by the size of publications.
Nanostructured Thermoplastic Vulcanizates by Selectively Cross-Linking a Thermoplastic Blend with Similar Chemical Structures

Ethylene vinyl acetate rubber (vinyl acetate (VA) content = 50 wt %) (EVM) and ethylene vinyl acetate copolymer (VA content 900% elongation at break), nice elasticity (only about 19% remnant strain at 100% stretching), and good flexibility but also superior oil resistance.
The measurement of ocular axial length in normal human eyes based on an improved Twyman‐Green interferometer

In order to meet the demands of myopia prevention, as well as the increasing needs of measurement for refractive and cataract operations in China, a new axial length (AL) measurement system combining an improved Twyman‐Green interferometer with digital signal processing has been established. The ALs of 33 eyes of different optical refractive subjects (−8.50 ~ 0.50 D) were measured with the New AL and intraocular lens (IOL) master. The repeatability of measurements with the New AL was assessed using coefficient of variation (CoV) and intra‐group correlation coefficient (ICC). Comparison, correlation, linear regression and agreement of AL between devices were analyzed. There was good repeatability (CoV = 0.0617%, ICC = 0.9999) with the New AL and great agreement has been obtained with both devices. These show that the New AL is capable of providing precise AL values over the normal AL range compared to the IOL master, and indicate that the New AL developed can be used for routine clinical AL measurements.
Isoniazid Population Pharmacokinetics and Dose Recommendation for Korean Patients With Tuberculosis Based on Target Attainment Analysis

The wide variability of isoniazid (INH) pharmacokinetics is mainly attributed to the trimodal N‐acetyltransferase 2 (NAT2) acetylator phenotype, that is, rapid, intermediate, and slow. Consequently, a uniform INH dose in current clinical practice may lead to treatment failure and emergence of drug resistance. There is a lack of studies on specific doses of INH for different NAT2 acetylator phenotypes among tuberculosis (TB) patients. Therefore, we aimed to provide insight into the optimal dosing of INH for each NAT2 acetylator phenotype with respect to the probability of achieving a pharmacokinetic (PK)/pharmacodynamic target. PK, the NAT2 genotype, and clinical data were collected in a multicenter prospective cohort study conducted at 13 clinical centers in Korea. Population PK modeling and simulation were carried out. Data from 454 TB patients were divided into a training data set and a test data set at a ratio of 4 to 1. The PK of the training data were best described by a 2‐compartment model with allometric scaling for body size effect. Importantly, NAT2 acetylator phenotypes significantly affected the apparent clearance. Our model, which provided better predictive performance compared with previously published models, was evaluated by external validation using the test set. The simulation for assessing target efficacy and toxicity indicated that the best INH dosing regimens for Korean tuberculosis patients were once‐daily doses of 400, 300, and 200 mg for rapid, intermediate, and slow acetylators, respectively. In conclusion, our study provides a step forward in precision dosing for antituberculosis management.
Efficiency-fairness trade-offs in evacuation management of urban floods: The effects of the shelter capacity and zone prioritization

With increasing flood risk, evacuation has become an important research topic in urban flood management. Urban flood evacuation is a complex problem due to i) the complex interactions among several components within a city and ii) the need to consider multiple, often competing, dimensions/objectives in evacuation analysis. In this study, we focused on the interplay between two such objectives: efficiency and fairness. We captured the evacuation process in a conceptual agent-based model (ABM), which was analyzed under different hard infrastructure and institutional arrangement conditions, namely, various shelter capacity distributions as a hard infrastructure property and simultaneous/staged evacuation as an institutional arrangement. Efficiency was measured as the time it takes for a person to evacuate to safety. Fairness was defined by how equally residents suffered from floods, and the level of suffering depended on the perceived risk and evacuation time. Our findings suggested that efficiency is more sensitive to the shelter capacity distribution, while fairness changes more notably according to the evacuation priority assigned to the divided zones in staged evacuation. Simultaneous evacuation generally tended to be more efficient but unfairer than staged evacuation. The efficiency-fairness trade-off was captured by Pareto-optimal strategies, among which uniform capacity cases led to a higher efficiency while prioritizing high-risk residents increases fairness. Strategies balancing efficiency and fairness featured a uniform capacity and prioritized high-risk residents at an intermediate time delay. These findings more clearly exposed the interactions between different factors and could be adopted as benchmarks to inform more complicated evacuation ABMs.
Obeticholic Acid and Fibrates in Primary Biliary Cholangitis: Comparative Effects in a Multicentric Observational Study

INTRODUCTION: Obeticholic acid (OCA) and fibrates therapy results in biochemical improvement in placebo-controlled trials in patients with primary biliary cholangitis and insufficient response to ursodeoxycholic acid. There is scarce information outside of clinical trials. Therefore, we have assessed the effectiveness and adverse events of these treatments. METHODS: Data from patients included in the ColHai registry treated with OCA, fibrates, or both were recorded during a year, as well as adverse events and treatment discontinuation. RESULTS: Eighty-six patients were treated with OCA, 250 with fibrates (81% bezafibrate; 19% fenofibrate), and 15 with OCA plus fibrates. OCA group had baseline significantly higher alkaline phosphatase (ALP) (P = 0.01) and lower platelets (P = 0.03) than fibrates. Both treatments significantly decreased ALP, gamma-glutamyl transferase (GGT), and transaminases and improved Globe score. Albumin and immunoglobulin type M improved in the fibrates group. ALP decrease was higher under fibrates, whereas alanine aminotransferase decline was higher under OCA. Although baseline transaminases and GGT were higher in patients with OCA plus fibrates, significant ALP, GGT, alanine aminotransferase, and Globe score improvement were observed during triple therapy. Adverse events were reported in 14.7% of patients (21.3% OCA; 17.6% fenofibrate; 10.7% bezafibrate), mainly pruritus (10.1% with OCA). Discontinuation was more frequent in fenofibrate treatment mainly because of intolerance or adverse events. DISCUSSION: Second-line therapy with OCA or fibrates improves hepatic biochemistry and the GLOBE score in primary biliary cholangitis patients with suboptimal response to ursodeoxycholic acid. Simultaneous treatment with OCA and fibrates improved ALP as well.
Validation of BRCA testing on cytologic samples of high‐grade serous carcinoma

Testing for BRCA1/2 gene alterations in patients with high‐grade serous carcinoma (HGSC) is a critical determinant of treatment eligibility for poly(adenosine diphosphate‐ribose) polymerase inhibitors in addition to providing vital information for genetic counselling. Many patients present with effusions necessitating therapeutic drainage, and this makes cytologic specimens (CySs) the initial diagnostic material for HGSC, often before histologic sampling. Initiating somatic BRCA testing on a CyS allows the BRCA status to be determined sooner, and this affects clinical management.
Evaluation of a Low-Cost Virtual Reality Surround-Screen Projection System

Two of the most popular mediums for virtual reality are head-mounted displays and surround-screen projection systems, such as CAVE Automatic Virtual Environments. In recent years, HMDs suffered a significant reduction in cost and have become widespread consumer products. In contrast, CAVEs are still expensive and remain accessible to a limited number of researchers. This study aims to evaluate both objective and subjective characteristics of a CAVE-like monoscopic low-cost virtual reality surround-screen projection system compared to advanced setups and HMDs. For objective results, we measured the head position estimation accuracy and precision of a low-cost active infrared (IR) based tracking system, used in the proposed low-cost CAVE, relatively to an infrared marker-based tracking system, used in a laboratory-grade CAVE system. For subjective characteristics, we investigated the sense of presence and cybersickness elicited in users during a visual search task outside personal space, beyond arms reach, where the importance of stereo vision is diminished. Thirty participants rated their sense of presence and cybersickness after performing the VR search task with our CAVE-like system and a modern HMD. The tracking showed an accuracy error of 1.66 cm and . 4 mm of precision jitter. The system was reported to elicit presence but at a lower level than the HMD, while causing significant lower cybersickness. Our results were compared to a previous study performed with a laboratory-grade CAVE and support that a VR system implemented with low-cost devices could be a viable alternative to laboratory-grade CAVEs for visual search tasks outside the user's personal space.
Correlation of minimum inhibitory concentrations between human and animal antimicrobials against Escherichia coli isolated from livestock

We analyzed the correlation between minimum inhibitory concentrations (MICs) of antimicrobials used in humans and those used in animals to enable comparison of antimicrobial susceptibility between Escherichia coli isolated from humans and those from animals. We compared the following pairs of MIC data: piperacillin (PIPC) to ampicillin (ABPC), amikacin (AMK) to kanamycin (KM), minocycline (MINO) to oxytetracycline (OTC), and levofloxacin (LVFX) to enrofloxacin (ERFX) using 103 isolates of E. coli from healthy livestock (cattle, pigs, broiler chickens, and layer chickens). Kappa analysis of the agreement for resistance and susceptibility between PIPC and ABPC, AMK and KM, MINO and OTC, and LVFX and ERFX showed almost perfect (κ = 0.81), slight (κ = 0.12), fair (κ = 0.37), and moderate (κ = 0.46) agreement, respectively. Within the antimicrobial pairs, all isolates resistant to the human antimicrobial were also resistant to the veterinary antimicrobial. However, there was less agreement within the pairs for those isolates that were sensitive to the human antimicrobial. The percentage agreement for susceptibility, defined as the percentage of isolates sensitive to both antimicrobials compared with isolates sensitive to both antimicrobials, as well as those sensitive only to the human antimicrobial, was 89.9%, 87.3%, 64.0%, and 89.9% for PIPC and ABPC, AMK and KM, MINO and OTC, and LVFX and ERFX, respectively. Our results suggest that the possibility of missing the resistance for antimicrobials used in human medicine by examining MICs for the equivalent antimicrobials used in veterinary medicine is low.
Weight Loss by Low-Calorie Diet Versus Gastric Bypass Surgery in People With Diabetes Results in Divergent Brain Activation Patterns: A Functional MRI Study

OBJECTIVE Weight loss achieved with very-low-calorie diets (VLCDs) can produce remission of type 2 diabetes (T2D), but weight regain very often occurs with reintroduction of higher calorie intakes. In contrast, bariatric surgery produces clinically significant and durable weight loss, with diabetes remission that translates into reductions in mortality. We hypothesized that in patients living with obesity and prediabetes/T2D, longitudinal changes in brain activity in response to food cues as measured using functional MRI would explain this difference. RESEARCH DESIGN AND METHODS Sixteen participants underwent gastric bypass surgery, and 19 matched participants undertook a VLCD (meal replacement) for 4 weeks. Brain responses to food cues and resting-state functional connectivity were assessed with functional MRI pre- and postintervention and compared across groups. RESULTS We show that Roux-en-Y gastric bypass surgery (RYGB) results in three divergent brain responses compared with VLCD-induced weight loss: 1) VLCD resulted in increased brain reward center food cue responsiveness, whereas in RYGB, this was reduced; 2) VLCD resulted in higher neural activation of cognitive control regions in response to food cues associated with exercising increased cognitive restraint over eating, whereas RYGB did not; and 3) a homeostatic appetitive system (centered on the hypothalamus) is better engaged following RYGB-induced weight loss than VLCD. CONCLUSIONS Taken together, these findings point to divergent brain responses to different methods of weight loss in patients with diabetes, which may explain weight regain after a short-term VLCD in contrast to enduring weight loss after RYGB.
C/EBPβ/AEP Signaling Regulates the Oxidative Stress in Malignant Cancers, Stimulating the Metastasis

Solid tumors start as a local disease, but some are capable of metastasizing to the lymph nodes and distant organs. The hypoxic microenvironment, which is critical during cancer development, plays a key role in regulating cancer progression and metastasis. However, the molecular mechanisms mediating the disseminated cancer cell metastasis remain incompletely understood. Here, we show that C/EBPβ/AEP signaling that is upregulated in breast cancers mediates oxidative stress and lung metastasis, and inactivation of asparagine endopeptidase (AEP, also known as legumain) robustly regulates breast cancer reactive oxygen species (ROS) and metastasis. AEP, a protease activated in acidic conditions, is overexpressed in numerous types of cancer and promotes metastasis. Employing a breast cancer cell line MDA-MD-231, we show that C/EBPβ, an oxidative stress or inflammation-activated transcription factor, and its downstream target AEP mediate ROS production as well as migration and invasion in cancer cells. Deficiency of AEP in the MMTV-PyMT transgenic breast cancer mouse model significantly regulates oxidative stress and suppresses lung metastasis. Administration of an innovative AEP inhibitor substantially mitigates ROS production and cancer metastasis. Hence, our study demonstrates that pharmacologic inhibition of AEP activity might provide a disease-modifying strategy to suppress cancer metastasis.
PHOSPHATE FRACTIONS AND AVAILABILITY IN VERTISOLS OF SOUTH-WESTERN SPAIN

Phosphorus (P) is the most limiting element in the Vertisols of southwestern Spain. There are few studies about P status, and crop responses to recommended P-fertilizer applications are erratic in these soils. The objectives of this work were (i) to investigate the P status and inorganic P fractions in these soils and (ii) to evaluate the relationships between soil inorganic P fractions, available P indices, and P uptake by plants. Total P, organic P, available P indices, and soil inorganic P fractions were studied in surface samples of 19 Vertisols of southwestern Spain. Total P uptake by Agrostis tennuis was determined after 11 weeks of plant growth in a greenhouse, and was used to measure plant available soil P. Total P ranged from 168 to 482 mg P kg−1; soil organic P ranged from 42 to 125 mg P kg−1 and averaged 28% of the total P. Soil inorganic P fractions were determined by a sequential-fractionation procedure (NH4Cl-P, NH4F-P, 0.1 M NaOH, CDB-P, 1 M NaOH-P, and H2SO4-P). Comparative rankings of the various inorganic P fraction quantities were H2SO4-P > NH4F-P > 0.1 M NaOH = 1 M NaOH-P > CDB-P > NH4Cl-P. Most of the inorganic P occurs in the least available form as Ca-P. The following soil test P extracted increasingly higher average amounts of P: Saunder (11.4 mg P kg−1), Truog (14.7 mg P kg−1), Olsen (17.8 mg P kg−1), Jackson (38.4 mg P kg−1) and Bray 2 (119.4 mg P kg−1). Jackson-P showed higher correlation with P uptake by the crop (r = 0.87) than did Olsen-P and Bray-P (r = 0.61 and 0.37, respectively), which are used to evaluate available P in the soils of the region studied. The results suggest that Jackson extractants removed easily soluble P as well as P from Fe and Al oxides. Moreover, organic P was an important fraction in supplying available P. A multiple regression model with Jackson-P, organic carbon, and cation-exchange capacity as independent variables explained 91% of the total variation in total plant P uptake. This implies that P availability and dynamics in these soils are influenced strongly by organic compounds and clay minerals.
Nitrate removal from aqueous solution using carbon nanotubes magnetized by nano zero-valent iron

Background and purpose:�Nitrate is one of the most common chemical pollutants in groundwater in the world. Adsorption has been considered as an effective and efficient method of removing pollutants, particularly nitrate from aqueous solutions and so the aim of this study was to magnetization of the carbon nanotubes with zero- valent iron and using it as an adsorbent for the removal of nitrate from aquatic environments. Materials and methods:�In this study, reduction method for converting divalent iron into zero-valent iron and co-precipitation method for iron particles deposition on carbon nanotubes was used. Characteristics of absorbent were analyzed by SEM (Scanning electron microscopy), XRD (X-ray powder diffraction), and VSM (Vibrating Sample Magnetometer) techniques. In this study, the effect of the pH, contact time, mixer speed, temperature, adsorbent dosage and the concentration of nitrate was investigated by one factor at the time method and then was optimized. Results: The pH equal to 3, 60 min contact time, 200 rpm stirring speed and 1 g/l absorbent was obtained as the optimum conditions in the adsorption of nitrate. Investigating the isotherm and kinetic models showed that the experimental data correlate to the Langmuir adsorption isotherm model (R 2 > 0.997) and pseudo-second order kinetic (R 2 > 0.993). The reaction thermodynamic study also expressed endothermic and spontaneous reaction. Conclusion: In optimal conditions, carbon nanotubes modified by zero-valent iron has well potential to quickly and effectively remove nitrate and simply be separated from the solution by the magnet due to its magnetic property.
New Implementation of Semi-classical Dynamic Simulation on the Photoisomerization of cis- and trans-Isomers of Free Stilbene

New implementation of semi-classical trajectory surface hopping dynamic simulation has been developed and applied to the photoisomerization of cis- and trans- isomers on the gas phase. This method not only uses the exponential model to the modification of the originally analytical non-adiabatic transition probability formula, but also involves the con- strained Hamiltonian system into the constrained molecular dynamic simulation. Two-dimensional potential energy surfaces of ground S0 and excited S1 states are constructed analytically fitting to ab initio calculations in terms of torsion angle and one dihedral angle around the central ethylenic C=C bond as variables, and the other internal coordinates are all fixed at configuration of one-bond flip conical intersection. The analytical PESs are quite accurate and the mean absolute error is less than 2.4 kcalmol -1 , and much less than 1.0 kcalmol -1 around conical intersection region. A straight seam line is found on potential energy surfaces that simply separates the cis-area with the trans-area. The constrained Hamiltonian system is em- ployed to run trajectories in the Cartesian coordinate system and surface hopping in terms of the two internal dihedral angles. Typical trajectories are found in which the torsion angle changes monotonically for both cis- to trans- and trans- to cis- isomerizations. This is an exact picture of one-bond flip mechanism of photoisomerization around the conical intersection. Quantum yield for trans- to cis- isomerization is simulated as 60.45% in very good agreement with experimental value 55.0%, while quantum yield for cis- to trans- isomerization is simulated as 42.3% in comparison with experimental value 35.0%. As the S1 energy in local minimum of cis-area is higher than that in trans-area, and thus cis- to trans- isomerization is quite possible to access to another Hula-Twist conical intersection. These simulation results demonstrate that the computed cumulative quantum yield and reaction mechanism are consistent with the previously experimental and theoretical results. This means that the present trajectory surface hopping method would be good at the dynamic simulation on the large system with or without constraint Hamiltonian in comparison with the quantum molecular dynamics. Keywords new implementation of semi-classical dynamic simulation; constrained Hamiltonian system; Zhu-Nakamura theory; isomerization of cis- and trans-stilbene; two dimensional analytical potential energy surfaces