Miracle-dz/UniFAR-FTUs huggingface dataset:
Reduced Graphene Oxide and Polyaniline Nanofibers Nanocomposite for the Development of an Amperometric Glucose Biosensor

The control of glucose concentration is a crucial factor in clinical diagnosis and the food industry. Electrochemical biosensors based on reduced graphene oxide (rGO) and conducting polymers have a high potential for practical application. A novel thermal reduction protocol of graphene oxide (GO) in the presence of malonic acid was applied for the synthesis of rGO. The rGO was characterized by scanning electron microscopy, X-ray diffraction analysis, Fourier-transform infrared spectroscopy, and Raman spectroscopy. rGO in combination with polyaniline (PANI), Nafion, and glucose oxidase (GOx) was used to develop an amperometric glucose biosensor. A graphite rod (GR) electrode premodified with a dispersion of PANI nanostructures and rGO, Nafion, and GOx was proposed as the working electrode of the biosensor. The optimal ratio of PANI and rGO in the dispersion used as a matrix for GOx immobilization was equal to 1:10. The developed glucose biosensor was characterized by a wide linear range (from 0.5 to 50 mM), low limit of detection (0.089 mM), good selectivity, reproducibility, and stability. Therefore, the developed biosensor is suitable for glucose determination in human serum. The PANI nanostructure and rGO dispersion is a promising material for the construction of electrochemical glucose biosensors.
The Lanostane Triterpenoids in Poria cocos Play Beneficial Roles in Immunoregulatory Activity

Poria cocos (Schwein) F.A. Wolf (syn. Wolfiporia cocos) dried sclerotium, called fuling, is an edible, saprophytic fungus commonly used as a tonic and anti-aging traditional Chinese medicine. It is traditionally used in combination with other traditional Chinese medicines to enhance immunity. This study showed that P. cocos extract (Lipucan®) containing lanostane triterpenoids has no immunotoxicity and enhances non-specific (innate) immunity though activating natural killer cells and promotes interferon γ (IFN-γ) secretion by Type 1 T-helper (Th1) cells immune response. In addition, P. cocos extract significantly decreased interleukin (IL-4 and IL-5) secretion by Type 2 T-helper (Th2) cells immune response, which are related to the allergy response. The purified lanostane triterpenoids were first identified as active ingredients of P. cocos with enhanced non-specific immunity by promoting interferon γ (IFN-γ) secretion in a preliminary study. Our findings support that the P. cocos extract plays beneficial roles in immunoregulatory activity.
Learnable Weighting of Intra-Attribute Distances for Categorical Data Clustering with Nominal and Ordinal Attributes

The success of categorical data clustering generally much relies on the distance metric that measures the dissimilarity degree between two objects. However, most of the existing clustering methods treat the two categorical subtypes, i.e., nominal and ordinal attributes, in the same way when calculating the dissimilarity without considering the relative order information of the ordinal values. Moreover, there would exist interdependence among the nominal and ordinal attributes, which is worth exploring for indicating the dissimilarity. This paper will therefore study the intrinsic difference and connection of nominal and ordinal attribute values from a perspective akin to the graph. Accordingly, we propose a novel distance metric to measure the intra-attribute distances of nominal and ordinal attributes in a unified way, meanwhile preserving the order relationship among ordinal values. Subsequently, we propose a new clustering algorithm to make the learning of intra-attribute distance weights and partitions of data objects into a single learning paradigm rather than two separate steps, whereby circumventing a suboptimal solution. Experiments show the efficacy of the proposed algorithm in comparison with the existing counterparts.
Loop-Mediated Isothermal Amplification in Schistosomiasis

Human schistosomiasis is one of the most important parasitic diseases, causing around 250 million cases (mostly in Africa) and 280,000–500,000 deaths every year. Due to the limited resources and the far-removed nature of many endemic areas, the implementation of new, sensitive and specific diagnostic tools has had little success. This is particularly true for PCR-based molecular methods that require expensive equipment and trained personnel to be executed. Loop-mediated isothermal amplification (LAMP) along with other isothermal techniques appeared in the early 21st century as an alternative to those methods, overcoming some of the aforementioned limitations and achieving a more inexpensive diagnostic. However, to this date, neither LAMP nor any other isothermal technique have signified a meaningful change in the way schistosomiasis diagnosis is routinely performed. Here, we present the recent developments in LAMP-based schistosomiasis diagnosis. We expose the main advantages and disadvantages of LAMP technology over PCR and other classical diagnostic methods focusing in various research approaches on intermediate hosts, animal models and patients. We also examine its potential clinical application in post-therapy monitoring, as well as its usefulness as a point-of-care test.
Application of Proper Orthogonal Decomposition to Study Coherent Flow Structures in a Saccular Aneurysm.

Aneurysms are localized expansions of weakened blood vessels that can be debilitating or fatal upon rupture. Previous studies have shown that flow in an aneurysm exhibits complex flow structures that are correlated with its inflow conditions. Therefore, the objective of this study was to demonstrate the application of Proper Orthogonal Decomposition (POD) to study the impact of different inflow conditions on energetic flow structures and their temporal behavior in an aneurysm. To achieve this objective, experiments were performed on an idealized rigid sidewall aneurysm model. A piston pump system was used for precise inflow control, i.e., peak Reynolds number ($Re_p$) and Womersley number ($\alpha$) were varied from 50-270 and 2-5, respectively. The velocity flow field measurements at the mid-plane location of the idealized aneurysm model were performed using Particle Image Velocimetry (PIV). The results demonstrate the efficacy of POD in decomposing complex data, and POD was able to capture the energetic flow structures unique to each studied inflow condition. Furthermore, the time-varying coefficient results highlighted the interplay between the coefficients and their corresponding POD modes, which in turn helped explain how POD modes impact certain flow features. The low-order reconstruction results were able to capture the flow evolution and provide information on complex flow in an aneurysm. The POD and low-order reconstruction results also indicated that vortex formation, evolution, and convection varied with an increase in $\alpha$, while vortex strength and formation of secondary structures were correlated with an increase in $Re_p$.
Completion of neuronal remodeling prompts myelination along developing motor axon branches

Postnatal motor neurons undergo extensive competitive remodeling and synchronously myelinate. Wang et al. now reveal that axon remodeling and myelination intersect. While myelination does not predetermine competition outcome, completing remodeling allows myelination to accelerate. This involves cytoskeletal maturation, which enables increased delivery of promyelinating signals.
The transcription factor Ndt80 is a repressor of Candida parapsilosis virulence attributes

ABSTRACT Candida parapsilosis is an emergent opportunistic yeast among hospital settings that affects mainly neonates and immunocompromised patients. Its most remarkable virulence traits are the ability to adhere to prosthetic materials, as well as the formation of biofilm on abiotic surfaces. The Ndt80 transcription factor was identified as one of the regulators of biofilm formation by C. parapsilosis; however, its function in this process was not yet clarified. By knocking out NDT80 (CPAR2-213640) gene, or even just one single copy of the gene, we observed substantial alterations of virulence attributes, including morphogenetic changes, adhesion and biofilm growth profiles. Both ndt80Δ and ndt80ΔΔ mutants changed colony and cell morphologies from smooth, yeast-shaped to crepe and pseudohyphal elongated forms, exhibiting promoted adherence to polystyrene microspheres and notably, forming a higher amount of biofilm compared to wild-type strain. Interestingly, we identified transcription factors Ume6, Cph2, Cwh41, Ace2, Bcr1, protein kinase Mkc1 and adhesin Als7 to be under Ndt80 negative regulation, partially explaining the phenotypes displayed by the ndt80ΔΔ mutant. Furthermore, ndt80ΔΔ pseudohyphae adhered more rapidly and were more resistant to murine macrophage attack, becoming deleterious to such cells after phagocytosis. Unexpectedly, our findings provide the first evidence for a direct role of Ndt80 as a repressor of C. parapsilosis virulence attributes. This finding shows that C. parapsilosis Ndt80 functionally diverges from its homolog in the close related fungal pathogen C. albicans.
Learning to Approximate Density Functionals.

ConspectusDensity functional theory (DFT) calculations are used in over 40,000 scientific papers each year, in chemistry, materials science, and far beyond. DFT is extremely useful because it is computationally much less expensive than ab initio electronic structure methods and allows systems of considerably larger size to be treated. However, the accuracy of any Kohn-Sham DFT calculation is limited by the approximation chosen for the exchange-correlation (XC) energy. For more than half a century, humans have developed the art of such approximations, using general principles, empirical data, or a combination of both, typically yielding useful results, but with errors well above the chemical accuracy limit (1 kcal/mol). Over the last 15 years, machine learning (ML) has made major breakthroughs in many applications and is now being applied to electronic structure calculations. This recent rise of ML begs the question: Can ML propose or improve density functional approximations? Success could greatly enhance the accuracy and usefulness of DFT calculations without increasing the cost.In this work, we detail efforts in this direction, beginning with an elementary proof of principle from 2012, namely, finding the kinetic energy of several Fermions in a box using kernel ridge regression. This is an example of orbital-free DFT, for which a successful general-purpose scheme could make even DFT calculations run much faster. We trace the development of that work to state-of-the-art molecular dynamics simulations of resorcinol with chemical accuracy. By training on ab initio examples, one bypasses the need to find the XC functional explicitly. We also discuss how the exchange-correlation energy itself can be modeled with such methods, especially for strongly correlated materials. Finally, we show how deep neural networks with differentiable programming can be used to construct accurate density functionals from very few data points by using the Kohn-Sham equations themselves as a regularizer. All these cases show that ML can create approximations of greater accuracy than humans, and is capable of finding approximations that can deal with difficult cases such as strong correlation. However, such ML-designed functionals have not been implemented in standard codes because of one last great challenge: generalization. We discuss how effortlessly human-designed functionals can be applied to a wide range of situations, and how difficult that is for ML.
Hormone-sensitive lipase couples intergenerational sterol metabolism to reproductive success

Triacylglycerol (TG) and steryl ester (SE) lipid storage is a universal strategy to maintain organismal energy and membrane homeostasis. Cycles of building and mobilizing storage fat are fundamental in (re)distributing lipid substrates between tissues or to progress ontogenetic transitions. In this study, we show that Hormone-sensitive lipase (Hsl) specifically controls SE mobilization to initiate intergenerational sterol transfer in Drosophila melanogaster. Tissue-autonomous Hsl functions in the maternal fat body and germline coordinately prevent adult SE overstorage and maximize sterol allocation to embryos. While Hsl-deficiency is largely dispensable for normal development on sterol-rich diets, animals depend on adipocyte Hsl for optimal fecundity when dietary sterol becomes limiting. Notably, accumulation of SE but not of TG is a characteristic of Hsl-deficient cells across phyla including murine white adipocytes. In summary, we identified Hsl as an ancestral regulator of SE degradation, which improves intergenerational sterol transfer and reproductive success in flies.
Accurate haplotype-resolved assembly reveals the origin of structural variants for human trios

Abstract Motivation Achieving a near complete understanding of how the genome of an individual affects the phenotypes of that individual requires deciphering the order of variations along homologous chromosomes in species with diploid genomes. However, true diploid assembly of long-range haplotypes remains challenging. Results To address this, we have developed Haplotype-resolved Assembly for Synthetic long reads using a Trio-binning strategy, or HAST, which uses parental information to classify reads into maternal or paternal. Once sorted, these reads are used to independently de novo assemble the parent-specific haplotypes. We applied HAST to cobarcoded second-generation sequencing data from an Asian individual, resulting in a haplotype assembly covering 94.7% of the reference genome with a scaffold N50 longer than 11 Mb. The high haplotyping precision (∼99.7%) and recall (∼95.9%) represents a substantial improvement over the commonly used tool for assembling cobarcoded reads (Supernova), and is comparable to a trio-binning-based third generation long-read-based assembly method (TrioCanu) but with a significantly higher single-base accuracy [up to 99.99997% (Q65)]. This makes HAST a superior tool for accurate haplotyping and future haplotype-based studies. Availability and implementation The code of the analysis is available at https://github.com/BGI-Qingdao/HAST Supplementary information Supplementary data are available at Bioinformatics online.
Deciphering bacterial mechanisms of root colonization

Summary Bacterial colonization of the rhizosphere is critical for the establishment of plant–bacteria interactions that represent a key determinant of plant health and productivity. Plants influence bacterial colonization primarily through modulating the composition of their root exudates and mounting an innate immune response. The outcome is a horizontal filtering of bacteria from the surrounding soil, resulting in a gradient of reduced bacterial diversity coupled with a higher degree of bacterial specialization towards the root. Bacteria–bacteria interactions (BBIs) are also prevalent in the rhizosphere, influencing bacterial persistence and root colonization through metabolic exchanges, secretion of antimicrobial compounds and other processes. Traditionally, bacterial colonization has been examined under sterile laboratory conditions that mitigate the influence of BBIs. Using simplified synthetic bacterial communities combined with microfluidic imaging platforms and transposon mutagenesis screening approaches, we are now able to begin unravelling the molecular mechanisms at play during the early stages of root colonization. This review explores the current state of knowledge regarding bacterial root colonization and identifies key tools for future exploration.
Cardio-ankle vascular index represents the best surrogate for 10-year ASCVD risk estimation in patients with primary hypertension

ABSTRACT Background: Identification of target organ damage and/or risk-enhancing factors help treatment decisions in hypertensive and hyperlipidaemic patients who reside in borderline to an intermediate risk category based on 10-year atherosclerotic cardiovascular disease (ASCVD) risk estimates. Aim: In the present study, we aimed to investigate the comparative efficacy of certain hypertension-mediated organ damage markers (HMOD) for the prediction of 10-year ASCVD risk ≥10%, in patients with primary hypertension without established CVD. Methods: One-hundred thirty-seven asymptomatic hypertensive patients ≥40 years of age were enrolled in the present study. Ten-year ASCVD risks were estimated by Pooled Cohort Equations. The following HMOD markers; pulse pressure (PP), left ventricular mass index (LVMI), carotid intima-media thickness (CIMT), ankle-brachial index (ABI), cardio-ankle vascular index (CAVI) and estimated glomerular filtration rate (eGFR) were evaluated with respect to efficacy for predicting ≥10% ASCVD risk with ROC analysis. Results: CAVI gave the greatest Area Under Curve (AUC = 0.736, p < .000), and followed by CIMT (AUC = 0.727, p < .000), LVMI (AUC = O.630, p = .01), and PP (AUC = 0.623, p = .02). ABI and eGFR were not found to be predictive. CAVI correlated best with estimated 10-year ASCVD risk (r = 0.460, p < .000). A CAVI value ≥8 was found 71% sensitive and 72% specific for predicting ≥10% risk in 10-year ASCVD risk scale. CAVI gave the best graded response to increments in 10-year ASCVD risk categories. Conclusion: We suggest that CAVI is the best surrogate for 10-year ASCVD risk, among several HMOD markers.
Preservation of the Implant in Nipple-Sparing Mastectomies: A Retrospective Cohort Study

Background Mastectomies are an integral part of breast cancer treatment for many patients.1 Of those patients, a significant number have previously undergone breast augmentation before being diagnosed with breast cancer. Therefore, we developed the novel technique of performing nipple- and implant-sparing mastectomies (NISMs) for women with prior breast augmentations. This study will assess the plausibility of using NISMs versus nipple-sparing mastectomies (NSMs) in this subgroup of patients by comparing the complication rates. Methods Data were collected on age, tumor size, tumor grade, receptors, and the interval between mastectomy and implant exchange for both groups. Descriptive statistics were used to summarize patient characteristics. Independent samples t tests, χ2 tests, and Fisher exact tests were used to compare the NISM and NSM cohorts. Logistic regression was used to assess the association between complications and mastectomy type and was summarized as an odds ratio with a 95% confidence interval. Results Fifteen patients underwent an NISM and 35 patients underwent an NSM. The overall rate of complications was less in NISM cases than in NSM cases (20% vs 27%). However, this difference was not statistically significant (odds ratio, 0.54; 95% confidence interval, 0.18–1.64; P = 0.278). Conclusions The overall complication rate was lower with NISMs compared with NSMs. Nipple- and implant-sparing mastectomy is a novel, viable, and safe option for patients with breast cancer and a history of submuscular breast augmentation.
General considerations for sample size estimation in animal study

The aim of this paper is to introduce basic concepts and methods for calculating sample size in animal studies. At the planning stage of clinical studies, the determination of the sample size is a very important process to show the validity, accuracy, and reliability of the study. However, not all studies require a sample size to be calculated. Before conducting the study, it is essential to determine whether the study objectives suggest a pilot and exploratory study, as well as the purpose of testing the hypothesis of interest. Since most animal experiments are pilot and exploratory studies, it would be more appropriate to review other considerations for conducting an experiment while maintaining scientific and qualitative levels rather than sample size estimation. Sample size is calculated in various situations in animal studies. Therefore, it can be estimated according to the situations and objectives through the methods of precision analysis, power analysis, and so on. In some cases, nonparametric methods can be employed if the assumptions of normality is not met or a small sample is available for the study.
A model experiment for de-astringency of persimmon fruit with high carbon dioxide treatment: In vitro gelation of kaki-tannin by reacting with acetaldehyde

In order to explain the mechanism for removing the astringency from persimmon fruit by high carbon dioxide treatment, we studied in vitro whether purified kaki-tannin, a kind of polymeric proanthocyanidin, reacts with acetaldehyde to become a gel under mild conditions or not.Kaki-tannin reacted with acetaldehyde in a relatively short time to become a gel in phosphate buffer at pH 6 to 8. Phosphate, malate and citrate accelerated the gel formation, whereas ethanol, ascorbate and Tricine buffer prevented it. Formaldehyde was more effective, and propylaldehyde was less effective than acetaldehyde in causing gelation.We suggest that the de-astringency is due to the insolubilization of kaki-tannin, which occurs by means of reacting with acetaldehyde produced in the fruit during high carbon dioxide treatment.
Über die Beziehungen zwischen Phosphathaushalt und Photosynthese I

1. Chlorella pyrenoidosa wurde in phosphatfreiem Medium suspendiert und nach entsprechender Vorbehandlung in 6-proz. Trichloressigsäure (TES) abgetötet und extrahiert. Das im TES-Auszug bestimmbare anorganische Phosphat wies in den ersten 30 Sek. nach Beginn der Belichtung eine Verminderung um 20%, in den ersten 90 Sek. nach der Verdunklung eine Vermehrung um 30% auf, während die stationären Licht- und Dunkelzustände keine wesentlichen Verschiebungen hervorriefen. 2. Eine kurzdauernde Atmungssteigerung im Anschluß an eine Belichtungsperiode konnte beobachtet und mit den Phosphatspiegelschwankungen in Zusammenhang gebracht werden. 3. In diesen Beobachtungen wird der Beweis für die seit einiger Zeit diskutierte Ansicht, daß ein Teil der Lichtenergie auf dem Wege über das energiereiche Phosphat in „chemische Energie“ umgewandelt wird, gesehen. 4. Die Möglichkeiten der Phosphatbindung im Rahmen der photochemischen Reaktionskette werden besprochen und in entsprechende Schemata eingebaut. 5. Als primäre Produkte der Photoreaktion werden ein an einen H-Acceptor mittleren Potentials gebundener Wasserstoff und energiereiche Phosphate angesehen. Mit deren Hilfe könnte nicht nur die CO2-Assimilation, sondern auch die Reduktion und der Einbau von Nitrat und Sulfat und der Umbau von Kohlenhydraten und anderer sauerstoffreicher Verbindungen zu sekundären Pflanzenstoffen und Wuchsstoffen durchgeführt werden. Ein entsprechendes Schema der Photosynthese wird entworfen.
Analytical modeling of silicon etch process in high density plasma

Plasma etching of silicon is one of the important etching processes used in modern integrated circuit manufacturing and micro-electro-mechanical systems fabrication. A good understanding of this process leads to better models which are the key to easier and less costly plasma etching process design. The main focus of this paper is on the simulation of the ion reflection from feature sidewalls and the resulting microtrenches. Pure Cl2 plasma was used for experiments because of the simple chemistry. SPEEDIE (Stanford etching and deposition profile simulator) was used in this work. Langmuir adsorption model was used for etching kinetics. Self-consistent calculations were done for fluxes using surface coverage dependent sticking probabilities. For ion reflection, it was assumed that the reflected ions come off with a distribution about the specular reflection angle. This distribution is modeled as cosnθ (θ is the deviation from the specular angle) and is important in getting the correct shape for microtrenche.