Miracle-dz/UniFAR-FTUs huggingface dataset:
On the Catalytic Activity of the Engineered Coiled-Coil Heptamer Mimicking the Hydrolase Enzymes: Insights from a Computational Study

Recently major advances were gained on the designed proteins aimed to generate biomolecular mimics of proteases. Although such enzyme-like catalysts must still suffer refinements for improving the catalytic activity, at the moment, they represent a good example of artificial enzymes to be tested in different fields. Herein, a de novo designed homo-heptameric peptide assembly (CC-Hept) where the esterase activity towards p-nitro-phenylacetate was obtained for introduction of the catalytic triad (Cys-His-Glu) into the hydrophobic matrix, is the object of the present combined molecular dynamics and quantum mechanics/molecular mechanics investigation. Constant pH Molecular Dynamics simulations on the apoform of CC-Hept suggested that the Cys residues are present in the protonated form. Molecular dynamics (MD) simulations of the enzyme–substrate complex evidenced the attitude of the enzyme-like system to retain water molecules, necessary in the hydrolytic reaction, in correspondence of the active site, represented by the Cys-His-Glu triad on each of the seven chains, without significant structural perturbations. A detailed reaction mechanism of esterase activity of CC-Hept-Cys-His-Glu was investigated on the basis of the quantum mechanics/molecular mechanics calculations employing a large quantum mechanical (QM) region of the active site. The proposed mechanism is consistent with available esterases kinetics and structural data. The roles of the active site residues were also evaluated. The deacylation phase emerged as the rate-determining step, in agreement with esterase activity of other natural proteases.
DEFOLIATION AND GROWTH IN AN UNDERSTORY PALM: QUANTIFYING THE CONTRIBUTIONS OF COMPENSATORY RESPONSES

We analyzed to what extent and by what mechanisms plants of the tropical understory palm Chamaedorea elegans are able to mitigate the negative effects of defoliation on performance (i.e., plant size, total growth, leaf lamina growth, and reproduction) and how this is related to light availability. For this purpose we developed a new approach that allowed us to quantify the performance of defoliated plants relative not only to the performance of undamaged plants, but also relative to the estimated performance of hypothetical defoliated plants that do not exhibit any mechanisms of compensatory growth. The latter provides a way to quantify the adaptive value of compensation with reference to a hypothetical noncompensating alternative state. C. elegans plants were grown in a greenhouse at two light levels (5% and 16% of natural daylight) and subjected to five defoliation treatments (a control and four levels of defoliation). Defoliation was repeated every three months. Growth analysis revealed that defoliated.
Effective Object Localization in Images by Calculating Ratio and Distance Between Pixels

In this paper, two novel similarity functions which consider the spatial and brightness relations between pixels for object localization in images are presented. We explore different advantages of our functions and compare them to others that use only spatial connection between pixels. It is shown, that one of them is robust to linear change in pixel brightness levels of the compared images. Comparison of computational cost and localization accuracy of shifted object for our similarity functions with others is given in the paper. The presented experimental results confirm the effectiveness of the proposed approach for object localization.
Improving cardiology fellow education of right heart catheterization using a simulation based curriculum

Medical procedures are traditionally taught informally at patients' bedside through observation and practice using the adage “see one, do one, teach one. ” This lack of formalized training can cause trainees to be unprepared to perform procedures independently. Simulation based education (SBE) increases competence, reduces complications, and decreases costs. We developed, implemented, and evaluated the efficacy of a right heart catheterization (RHC) SBE curriculum.
A Digital Clinical Guideline Based on HL7 Arden Syntax for the Treatment of Children with Traumatic Brain Injury.

BACKGROUND Intracranial hypertension is a serious complication accompanying the intensive care of children with traumatic brain injury. Intensive care of these patients is based on internationally accepted guidelines and their local editions. OBJECTIVE The goal was to develop a software system for digital implementation of the clinical protocol for the treatment of intracranial hypertension in children, based on HL7 Arden Syntax clinical decision support. METHODS Arden Syntax, an HL7 medical knowledge representation and processing standard, was used to develop a digital version of the local guideline. RESULTS Comparison of 37 patients given conventional treatment with a second group of 84 patients treated with the digital clinical guideline yielded statistically significant differences. CONCLUSION The digital clinical guideline system undoubtedly improves the doctor's awareness of the patient's existing condition and potential complications of intracranial hypertension.
Machine Learning Modeling of Wine Sensory Profiles and Color of Vertical Vintages of Pinot Noir Based on Chemical Fingerprinting, Weather and Management Data

Important wine quality traits such as sensory profile and color are the product of complex interactions between the soil, grapevine, the environment, management, and winemaking practices. Artificial intelligence (AI) and specifically machine learning (ML) could offer powerful tools to assess these complex interactions and their patterns through seasons to predict quality traits to winegrowers close to harvest and before winemaking. This study considered nine vintages (2008–2016) using near-infrared spectroscopy (NIR) of wines and corresponding weather and management information as inputs for artificial neural network (ANN) modeling of sensory profiles (Models 1 and 2 respectively). Furthermore, weather and management data were used as inputs to predict the color of wines (Model 3). Results showed high accuracy in the prediction of sensory profiles of vertical wine vintages using NIR (Model 1; R = 0.92; slope = 0.85), while better models were obtained using weather/management data for the prediction of sensory profiles (Model 2; R = 0.98; slope = 0.93) and wine color (Model 3; R = 0.99; slope = 0.98). For all models, there was no indication of overfitting as per ANN specific tests. These models may be used as powerful tools to winegrowers and winemakers close to harvest and before the winemaking process to maintain a determined wine style with high quality and acceptability by consumers.
Advantages of Highly Spherical Gold Nanoparticles as Labels for Lateral Flow Immunoassay

The use of lateral flow immunoassays (LFIAs) for rapid on-site testing is restricted by their relatively high limit of detection (LoD). One possible way to decrease the LoD is to optimize nanoparticle properties that are used as labels. We compare two types of Au nanoparticles: usual quasispherical gold nanoparticles (C-GNPs), obtained by the Turkevich–Frens method, and superspherical gold nanoparticles (S-GNPs), obtained by a progressive overgrowth technique. Average diameters were 18.6–47.5 nm for C-GNPs and 20.2–90.4 nm for S-GNPs. Cardiomarker troponin I was considered as the target analyte. Adsorption and covalent conjugation with antibodies were tested for both GNP types. For C-GNPs, the minimal LoD was obtained with 33.7 nm nanoparticles, reaching 12.7 ng/mL for covalent immobilization and 9.9 ng/mL for adsorption. The average diameter of S-GNPs varied from 20.2 to 64.5 nm, which resulted in a decrease in LoD for an LFIA of troponin I from 3.4 to 1.2 ng/mL for covalent immobilization and from 2.9 to 2.0 ng/mL for adsorption. Thus, we obtained an 8-fold decrease in LoD (9.9 to 1.2 ng/mL) by using S-GNPs. This effect can be related to more effective antibody immobilization and improved S-GNP optical properties. The obtained results can improve LFIAs for various practically significant analytes.
Quantifying trait selection driving community assembly: a test in herbaceous plant communities under contrasted land use regimes

Plant traits are particularly important in determining plant community structure. However, how can one identify which traits are the most important in driving community assembly? Here we propose a method 1) to quantify the direction and strength of trait selection during community assembly and 2) to obtain parsimonious lists of traits that can predict species relative abundances in plant communities. We tested our method using floristic data from 32 plots experiencing different treatments (fertilisation and grazing) in southern France. Twelve functional traits were measured on 68 species. We determined the direction and strength of selection on these 12 traits using a metric derived from a maximum entropy model (i.e. lambda). We then determined our parsimonious list of traits using a backward selection of traits based on these lambda values (for all treatments and in each treatment separately). We finally compared our method to two other methods: one based on iterative RLQ and the other based on an entropy-based forward selection of traits. We found major differences in the direction and strength of selection across the 12 traits and treatments. From the 12 traits, plant vegetative and reproductive heights, leaf dry matter content leaf nitrogen content, specific leaf area, and leaf phosphorus content were particularly important for predicting species relative abundances when considering all treatments together. Our method yielded results similar to those produced by the entropy-based approach but differed from those produced by the iterative RLQ, whose selected traits could not significantly predict species relative abundances. Together these results suggest that the assembly of these communities is primarily driven by a small number of key functional traits. We argue that our method provides an objective way of determining a parsimonious list of traits that together accurately predict community structure and which, despite its complementarities with entropy-based method, offers significant advantages.
Biosensors for D-Amino Acids: Detection Methods and Applications

D-enantiomers of amino acids (D-AAs) are only present in low amounts in nature, frequently at trace levels, and for this reason, their biological function was undervalued for a long time. In the past 25 years, the improvements in analytical methods, such as gas chromatography, HPLC, and capillary electrophoresis, allowed to detect D-AAs in foodstuffs and biological samples and to attribute them specific biological functions in mammals. These methods are time-consuming, expensive, and not suitable for online application; however, life science investigations and industrial applications require rapid and selective determination of D-AAs, as only biosensors can offer. In the present review, we provide a status update concerning biosensors for detecting and quantifying D-AAs and their applications for safety and quality of foods, human health, and neurological research. The review reports the main challenges in the field, such as selectivity, in order to distinguish the different D-AAs present in a solution, the simultaneous assay of both L- and D-AAs, the production of implantable devices, and surface-scanning biosensors. These innovative tools will push future research aimed at investigating the neurological role of D-AAs, a vibrant field that is growing at an accelerating pace.
Tescalcin is an unfavorable prognosis factor that regulats cell proliferation and survival in hepatocellular carcinoma patients

Abstract Background Hepatocellular carcinoma (HCC) is a major health problem and a primary cause of cancer‐related death worldwide. Although great advances have achieved recently by large‐scale high‐throughput analysis, the precise molecular mechanism underlying HCC progression remains to be clearly elucidated. We investigated the relationship between Tescalcin (TESC), a candidate oncogene, and clinicopathological features of HCC patients and explored the role of TECS in HCC development. Methods To identify new genes involved in HCC development, we analyzed The Cancer Genome Atlas liver cancer database, and TESC was selected for further investigation. HCC tissue microarray analysis for TESC and its association with clinicopathological features were performed to investigate its clinical significance. TESC was knocked down by using short‐hairpin RNAs. Cell proliferation was analyzed by WST‐1 assay and cell counting. Cell apoptosis was tested by fluorescence‐activated cell sorting. A subcutaneous xenograft tumor model in nude mice was established to determine the in vivo function of TESC. Affymetrix microarray was used to identify its molecular mechanism. Results TESC was significantly increased in HCC tissues compared with the adjacent normal liver tissues. High expression of TESC was detected in 61 of 172 HCC patients by tissue microarray. Large tumor (> 5 cm) and elevated total bilirubin were associated with high TESC expression (both P < 0.050). In multivariate analysis, TESC was identified as an independent prognostic factor for short overall survival of HCC patients. TESC knockdown impaired HCC cell growth in vitro and in vivo. TESC knockdown significantly increased cell apoptosis in HCC cell lines. Furthermore, Affymetrix microarray analysis revealed that TESC knockdown inhibited tumor proliferation‐related pathways while activated cell death‐related pathways. Conclusion TESC was identified as an independent prognostic factor for short overall survival of HCC patients, and was critical for HCC cell proliferation and survival.
Population genetic structure of the Gulf of St. Lawrence aster, Symphyotrichum laurentianum (Asteraceae), a threatened coastal endemic.

The Gulf of St. Lawrence aster (Symphyotrichum laurentianum (Fernald) G.L. Nesom) is an endemic annual of saline habitats in the southern Gulf of St. Lawrence. It is listed as a threatened species, and has recently experienced popu- lation declines in much of its range. We used 11 allozyme markers to assay population genetic variation in six wild popu- lations of S. laurentianum from the Magdalen Islands, Quebec (QC), the only remaining wild population from Prince Edward Island National Park (PEI), and a greenhouse population founded in 1999 with seed collected from PEI. Symphyo- trichum laurentianum harbours moderate genetic diversity (Ps = 0.36, As = 1.54), with only modest spatial genetic structure (pairwise FST < 0.15) and no significant isolation by distance. The PEI population had greatly reduced allelic diversity compared with the populations from the Magdalen Islands, which likely act as a reservoir of genetic variation in S. laurentianum. Recent loss of alleles during population decline in PEI is suggested by the retention of greater allelic di- versity in the greenhouse population. Estimates of breeding structure suggest small but nonzero rates of outcross pollina- tion (FIS = 0.73, 95% CI = 0.48-0.97; outcrossing rate *16%). Population genetic structure in S. laurentianum can inform those forming and carrying out conservation and recovery plans for this threatened species.
Exploring the acceptability of HIV partner notification in prisons: Findings from a survey of incarcerated people living with HIV in Indonesia

Assisted HIV partner notification services provide a safe and effective way for people living with HIV (PLHIV) to inform their partners about the possibility of exposure and to offer them testing, treatment, and support. This study examined whether or not PLHIV in prison might be willing to participate in assisted HIV partner notification services and their reasons for and against disclosing their HIV-positive status to their partners. PLHIV (n = 150) recruited from Jakarta’s two largest all-male prisons completed an interviewer-administered questionnaire collecting demographic and risk behavior data, and attitudes toward HIV disclosure and partner services. Among those who were sexually active and/or injecting drugs before incarceration, two-thirds (66.4%, 91/137) endorsed provider referral as an acceptable way to notify their sex partners, and nearly three quarters (72.4%, 89/123) endorsed provider referral to notify their drug-injecting partners. Only a quarter (25.1%) of participants reported that their main sex partner had ever received an HIV test. Participants with anticipated stigma were less likely to endorse provider referral for sex partners (adjusted odds ratio [aOR] = 0.58, 95% CI: 0.35, 0.96) and drug-injecting partners (aOR = 0.54, 95% CI: 0.29, 1.00). Relationship closeness was associated with higher odds of endorsing provider referral for drug-injecting partners (aOR = 2.08, 95% CI: 1.25, 3.45). Protecting partners from infection and a moral duty to inform were main reasons to disclose, while stigma and privacy concerns were main reasons not to disclose. Most incarcerated PLHIV have at-risk partners in the community who they would be willing to notify if provided with assistance. Assisted partner notification for prison populations offers a promising public health approach to accelerate diagnosis, treatment, and prevention of HIV infection in the community, particularly among women.
A Method of Developing a Checkable Self-Recovery Floating-Point Pipeline System

The objective nature observed in the development of the computer world makes it possible to predict requests for the development of promising computer systems. The parallelism and fuzziness of the natural world encourages the development of pipeline systems for the processing of approximate data. The progressive development of high-risk objects increases the requirements for safety-related systems in improving the checkable and fault-tolerant solutions used in them. A method for developing a checkable fault-tolerant floating-point pipeline system is proposed. Matrix circuits of pipeline sections are unified in the form of lines of identical elements. The operands and floating-point results obtain an additional bit excluded from the calculations. Its movement creates many versions of calculation execution, ensuring the checkability of circuits and their fault tolerance in the form of self-recovery when selecting a version that excludes a faulty element. The method uses the synergy of different types of performed functions to simplify the system and to counter faults.
Concentrations of abscisic acid and other solutes in xylem sap from root systems of tomato and castor-oil plants are distorted by wounding and variable sap flow rates

We investigated if concentrations of abscisic acid (ABA) and other solutes measured in the first few droplets of xylem sap from detopped root systems, are good estimates of those in the transpiration stream as it enters the shoot-base of whole plants. Xylem sap from root systems of pot-grown tomato plants (Lycopersicon esculentum Mill., cv. Ailsa Craig), at the seven-leaf stage, was obtained by placing root systems in chambers pressurized to 0.3 MPa with air. The first sample was taken from the cut-surface of the hypo-cotyl stump within 30 s of removing the shoot. ABA, sucrose and other osmolytes were more concentrated in the initial 100–200 mm3 of xylem sap than in subsequent samples. This suggested the sap was contaminated and not unchanged transpiration fluid. The effect was reproduced on the same plant, several times, by recutting the hypocotyl prior to reassembling the sap collecting set-up and repressurizing. Similar results were found with castor-oil plants (Ricinus communis L., cv. Gibsonii). However, neither release of ABA from the cut surface of the hypocotyl stump, nor the effects of pressure to the roots caused the contamination. Instead, small radial pressures exerted by a rubber sleeve attached to the hypocotyl stump, for collecting the sap, were responsible. The effect was reproduced by lightly squeezing the hypocotyl by hand. The possibility was examined that reliable estimates of ABA concentrations in transpiration stream fluid may be obtained from sap samples taken immediately after rejecting the initial, contaminated 200 mm3. However, ABA concentrations in these later samples were also unsatisfactory since they changed with rate of sap flow. The problem may be overcome by analysing sap induced to flow through detached root systems at rates close to those of whole-plant transpiration.
The use of safe wallows to improve water quality in deer farmed catchments

Abstract The pastoral grazing of farmed red deer (Cervus elaphus) is common in New Zealand. However, red deer have a natural instinct to seek out water and wallow in it. In headwater catchments, red deer frequently create a wallow in a wet area connected to a waterway causing substantial contamination via excretal returns and erosion. It is not sufficient to fence off wallows as deer will make new ones nearby. Hence, this study aimed to determine whether the fencing‐off of the old wallow and the creation of a “safe” wallow unconnected to a stream would mitigate contaminant loss. The study used paired catchments with the calibration year establishing the relationship between the catchments for fortnightly base flow samples and storm flow samples taken at the same time in each catchment. After a year, the treatment (safe wallow and fencing‐off) was imposed and a new relationship established. During the calibration year, median concentrations in stream flow of nitrogen (N) and phosphorus (P) species, suspended sediment (SS), and the faecal indicator bacteria, E. coli were generally in excess of recommended guidelines for lowland water quality and contact recreation in New Zealand (guidelines = 9 μg dissolved reactive P litre‐1, 30 μg total P litre‐1, 444 μg nitrate‐ and nitrite‐N litre‐1, 0.9 mg NH4 +‐N litre‐1 at pH 7, 4 mg SS litre‐1, and 260 MPN 100 ml‐1). Loads of P(up to c. 3 kg Pha‐1) and SS (up to 4 Mg ha‐1) were among the highest measured for pastoral catchments in New Zealand. However, after the treatment was imposed, loads decreased by up to 90%. Analysis indicated that the decreases were significant for P species, SS, and E. coli, while the decrease in NH4 +‐N was not significant (P = 0.053). The use of safe wallows in conjunction with fencing off and planting the old wallow is recommended as a method for mitigating water quality problems associated with deer wallows.