bluuebunny/crossref_metadata_2025 huggingface dataset:
EasyAmber: A comprehensive toolbox to automate the molecular dynamics simulation of proteins
Authors: Suplatov Dmitry , Sharapova Yana , Švedas Vytas
Published: June 2020

Conformational plasticity of the functionally important regions and binding sites in protein/enzyme structures is one of the key factors affecting their function and interaction with substrates/ligands. Molecular dynamics (MD) can address the challenge of accounting for protein flexibility by predicting the time-dependent behavior of a molecular system. It has a potential of becoming a particularly important tool in protein engineering and drug discovery, but requires specialized training and skills, what impedes practical use by many investigators. We have developed the easyAmber — a comprehensive set of programs to automate the molecular dynamics routines implemented in the Amber package. The toolbox can address a wide set of tasks in computational biology struggling to account for protein flexibility. The automated workflow includes a complete set of steps from the initial “static” molecular model to the MD “production run”: the full-atom model building, optimization/equilibration of the molecular system, classical/conventional and accelerated molecular dynamics simulations. The easyAmber implements advanced MD protocols, but is highly automated and easy-to-operate to attract a broad audience. The toolbox can be used on a personal desktop station equipped with a compatible gaming GPU-accelerator, as well as help to manage huge workloads on a powerful supercomputer. The software provides an opportunity to operate multiple simulations of different proteins at the same time, thus significantly increasing work efficiency. The easyAmber takes the molecular dynamics to the next level in terms of usability for complex processing of large volumes of data, thus supporting the recent trend away from inefficient “static” approaches in biology toward a deeper understanding of the dynamics in protein structures. The software is freely available for download at https://biokinet.belozersky.msu.ru/easyAmber, no login required.
Scalable classification of organisms into a taxonomy using hierarchical supervised learners
Authors: Sohsah Gihad N. , Ibrahimzada Ali Reza , Ayaz Huzeyfe , Cakmak Ali
Published: June 2020

Accurately identifying organisms based on their partially available genetic material is an important task to explore the phylogenetic diversity in an environment. Specific fragments in the DNA sequence of a living organism have been defined as DNA barcodes and can be used as markers to identify species efficiently and effectively. The existing DNA barcode-based classification approaches suffer from three major issues: (i) most of them assume that the classification is done within a given taxonomic class and/or input sequences are pre-aligned, (ii) highly performing classifiers, such as SVM, cannot scale to large taxonomies due to high memory requirements, (iii) mutations and noise in input DNA sequences greatly reduce the taxonomic classification score. In order to address these issues, we propose a multi-level hierarchical classifier framework to automatically assign taxonomy labels to DNA sequences. We utilize an alignment-free approach called spectrum kernel method for feature extraction. We build a proof-of-concept hierarchical classifier with two levels, and evaluated it on real DNA sequence data from barcode of life data systems. We demonstrate that the proposed framework provides higher f1-score than regular classifiers. Besides, hierarchical framework scales better to large datasets enabling researchers to employ classifiers with high classification performance and high memory requirement on large datasets. Furthermore, we show that the proposed framework is more robust to mutations and noise in sequence data than the non-hierarchical classifiers.
Asymptotic expansions, partial theta functions, and radial limit differences of mock modular and modular forms
Authors: Folsom Amanda
Published: June 2020

In 1920, Ramanujan studied the asymptotic differences between his mock theta functions and modular theta functions, as [Formula: see text] tends towards roots of unity singularities radially from within the unit disk. In 2013, the bounded asymptotic differences predicted by Ramanujan with respect to his mock theta function [Formula: see text] were established by Ono, Rhoades, and the author, as a special case of a more general result, in which they were realized as special values of a quantum modular form. Our results here are threefold: we realize these radial limit differences as special values of a partial theta function, provide full asymptotic expansions for the partial theta function as [Formula: see text] tends towards roots of unity radially, and explicitly evaluate the partial theta function at roots of unity as simple finite sums of roots of unity.
Dedekind sums arising from newform Eisenstein series
Authors: Stucker T. , Vennos A. , Young M. P.
Published: June 2020

For primitive nontrivial Dirichlet characters [Formula: see text] and [Formula: see text], we study the weight zero newform Eisenstein series [Formula: see text] at [Formula: see text]. The holomorphic part of this function has a transformation rule that we express in finite terms as a generalized Dedekind sum. This gives rise to the explicit construction (in finite terms) of elements of [Formula: see text]. We also give a short proof of the reciprocity formula for this Dedekind sum.
Iterated integrals on products of one variable multiple polylogarithms
Authors: Li Jiangtao
Published: June 2020

In this paper, we show that the iterated integrals on products of one variable multiple polylogarithms from [Formula: see text] to [Formula: see text] are actually in the algebra of multiple zeta values if they are convergent. In the divergent case, we define the regularized iterated integrals from [Formula: see text] to [Formula: see text]. By the same method, we show that the regularized iterated integrals are also in the algebra of multiple zeta values. As an application, we give new series representations for multiple zeta values and calculate some interesting examples of iterated integrals.
Real-Time Principal Component Analysis
Authors: Chowdhury Ranak Roy , Adnan Muhammad Abdullah , Gupta Rajesh K.
Published: June 2020

We propose a variant of Principal Component Analysis (PCA) that is suited for real-time applications. In the real-time version of the PCA problem, we maintain a window over the most recent data and project every incoming row of data into a lower-dimensional subspace, which we generate as the output of the model. The goal is to reduce the reconstruction error of the output from the input and to retain major components pertaining to previous distributions of the data. We use the reconstruction error as the termination criteria to update the eigenspace as new data arrives. We then propose two variants of this algorithm that are progressively more time efficient. To verify whether our proposed model can capture the essence of the changing distribution of large datasets in real time, we have implemented the algorithms and compared performance against carefully designed simulations that change distributions of data sources over time in a controllable manner. Furthermore, we have demonstrated that proposed algorithms can capture the changing distributions of real-life datasets by running simulations on datasets from a variety of real-time applications, e.g., localization, activity recognition, customer expenditure, and so forth. Results show that straightforward modifications to convert PCA to use a sliding window of datasets do not work because of the difficulties associated with determination of optimal window size. Instead, we propose algorithmic enhancements that rely on spectral analysis to improve dimensionality reduction. Results show that our methods can successfully capture the changing distribution of data in a real-time scenario, thus enabling real-time PCA.
Thriving in a crowded and changing world: C++ 2006–2020
Authors: Stroustrup Bjarne
Published: June 2020

By 2006, C++ had been in widespread industrial use for 20 years. It contained parts that had survived unchanged since introduced into C in the early 1970s as well as features that were novel in the early 2000s. From 2006 to 2020, the C++ developer community grew from about 3 million to about 4.5 million. It was a period where new programming models emerged, hardware architectures evolved, new application domains gained massive importance, and quite a few well-financed and professionally marketed languages fought for dominance. How did C++ -- an older language without serious commercial backing -- manage to thrive in the face of all that?

This paper focuses on the major changes to the ISO C++ standard for the 2011, 2014, 2017, and 2020 revisions. The standard library is about 3/4 of the C++20 standard, but this paper's primary focus is on language features and the programming techniques they support.

The paper contains long lists of features documenting the growth of C++. Significant technical points are discussed and illustrated with short code fragments. In addition, it presents some failed proposals and the discussions that led to their failure. It offers a perspective on the bewildering flow of facts and features across the years. The emphasis is on the ideas, people, and processes that shaped the language.

Themes include efforts to preserve the essence of C++ through evolutionary changes, to simplify its use, to improve support for generic programming, to better support compile-time programming, to extend support for concurrency and parallel programming, and to maintain stable support for decades' old code.

The ISO C++ standard evolves through a consensus process. Inevitably, there is competition among proposals and clashes (usually polite ones) over direction, design philosophies, and principles. The committee is now larger and more active than ever, with as many as 250 people turning up to week-long meetings three times a year and many more taking part electronically. We try (not always successfully) to mitigate the effects of design by committee, bureaucratic paralysis, and excessive enthusiasm for a variety of language fashions.

Specific language-technical topics include the memory model, concurrency and parallelism, compile-time computation, move-semantics, exceptions, lambda expressions, and modules. Designing a mechanism for specifying a template's requirements on its arguments that is sufficiently flexible and precise yet doesn't impose run-time costs turned out to be hard. The repeated attempts to design ``concepts'' to do that have their roots back in the 1980s and touch upon many key design issues for C++ and for generic programming.

The description is based on personal participation in the key events and design decisions, backed by the thousands of papers and hundreds of meeting minutes in the ISO C++ standards committee's archives.
History of coarrays and SPMD parallelism in Fortran
Authors: Reid John , Long Bill , Steidel Jon
Published: June 2020

The coarray programming model is an expression of the Single-Program-Multiple-Data (SPMD) programming model through the simple device of adding a codimension to the Fortran language. A data object declared with a codimension is a coarray object. Codimensions express the idea that some objects are located in local memory while others are located in remote memory. Coarray syntax obeys most of the same rules for normal array syntax. It is familiar to the Fortran programmer so the use of coarray syntax is natural and intuitive. Although the basic idea is quite simple, inserting it into the language definition turned out to be difficult.

In addition, the process was complicated by rapidly changing hardware and heated arguments over whether parallelism should be supported best as an interface to language-independent libraries, as a set of directives superimposed on languages, or as a set of specific extensions to existing languages.

In this paper, we review both the early history of coarrays and also their development into a part of Fortran 2008 and eventually into a larger part of Fortran 2018. Coarrays have been used, for example, in weather forecasting and in neural networks and deep learning.
A history of the Groovy programming language
Authors: King Paul
Published: June 2020

This paper describes the history of the Groovy programming language. At the time of Groovy’s inception, Java was a dominant programming language with a wealth of useful libraries. Despite this, it was perceived by some to be evolving slowing and to have shortcomings for scripting, rapid prototyping and when trying to write minimalistic code. Other languages seemed to be innovating faster than Java and, while overcoming some of Java’s shortcomings, used syntax that was less familiar to Java developers. Integration with Java libraries was also non-optimal.

Groovy was created as a complementary language to Java—its dynamic counterpart. It would look and feel like Java but focus on extensibility and rapid innovation. Groovy would borrow ideas from dynamic languages like Ruby, Python and Smalltalk where needed to provide compelling JVM solutions for some of Java’s shortcomings.

Groovy supported innovation through its runtime and compile-time metaprogramming capabilities. It supported simple operator overloading, had a flexible grammar and was extensible. These characteristics made it suitable for growing the language to have new commands (verbs) and properties (nouns) specific to a particular domain, a so called Domain Specific Language (DSL). While still intrinsically linked with Java, over time Groovy has evolved from a niche dynamic scripting language into a compelling mainstream language.

After many years as a principally dynamically-typed language, a static nature was added to Groovy. Code could be statically type checked or when dynamic features weren’t needed, they could be turned off entirely for Java-like performance. A number of nuances to the static nature came about to support the style of coding used by Groovy developers.

Many choices made by Groovy in its design, later appeared in other languages (Swift, C#, Kotlin, Ceylon, PHP, Ruby, Coffeescript, Scala, Frege, TypeScript and Java itself). This includes Groovy’s dangling closure, Groovy builders, null-safe navigation, the Elvis operator, ranges, the spaceship operator, and flow typing. For most languages, we don’t know to what extent Groovy played a part in their choices. We do know that Kotlin took inspiration from Groovy’s dangling closures, builder concept, default
it
parameter for closures, templates and interpolated strings, null-safe navigation and the Elvis operator.

The leadership, governance and sponsorship arrangements of Groovy have evolved over time, but Groovy has always been a successful highly collaborative open source project driven more by the needs of the community than by a vision of a particular company or person.
A history of MATLAB
Authors: Moler Cleve , Little Jack
Published: June 2020

The first MATLAB (the name is short for “Matrix Laboratory”) was not a programming language. Written in Fortran in the late 1970s, it was a simple interactive matrix calculator built on top of about a dozen subroutines from the LINPACK and EISPACK matrix software libraries. There were only 71 reserved words and built-in functions. It could be extended only by modifying the Fortran source code and recompiling it.

The programming language appeared in 1984 when MATLAB became a commercial product. The calculator was reimplemented in C and significantly enhanced with the addition of user functions, toolboxes, and graphics. It was available initially on the IBM PC and clones; versions for Unix workstations and the Apple Macintosh soon followed.

In addition to the matrix functions from the calculator, the 1984 MATLAB included fast Fourier transforms (FFT). The Control System Toolbox appeared in 1985 and the Signal Processing Toolbox in 1987. Built-in support for the numerical solution of ordinary differential equations also appeared in 1987.

The first significant new data structure, the sparse matrix, was introduced in 1992. The Image Processing Toolbox and the Symbolic Math Toolbox were both introduced in 1993.

Several new data types and data structures, including single precision floating point, various integer and logical types, cell arrays, structures, and objects were introduced in the late 1990s.

Enhancements to the MATLAB computing environment have dominated development in recent years. Included are extensions to the desktop, major enhancements to the object and graphics systems, support for parallel computing and GPUs, and the “Live Editor”, which combines programs, descriptive text, output and graphics into a single interactive, formatted document.

Today there are over 60 Toolboxes, many programmed in the MATLAB language, providing extended capabilities in specialized technical fields.
Sequential Electrochemical Flow Cell for Complex Multicomponent Electrocatalysis
Authors: Pounds T. , Benn E. E. , Carter A. , Erlebacher J.
Published: June 2020

A highly efficient flow cell for sequential electrolysis containing two complete electrochemical cells, capable of generating reactive species at the upstream working electrode and transporting them to the downstream working electrode, is demonstrated. Deconvolution of the intermixed electrode circuits is accomplished through analysis of the inherent resistance of the electrolyte, which allows for precise and independent control of the electrochemical potential at each electrode without altering concentrations of supporting or background electrolyte species. Sequential electrolysis involving oxidation of hydrogen and reduction of the generated protons downstream is demonstrated at nearly 100% efficiency on Pt-decorated dealloyed porous Nb catalysts. The conversion efficiency of the catalysts is discussed in terms of their geometries and active surface composition, elucidating strategies for use of sequential electrolysis cells for fundamental and applied studies.
Aluminum Deposition and Dissolution in [EMIm]Cl-Based Ionic Liquids–Kinetics of Charge–Transfer and the Rate–Determining Step
Authors: Böttcher Rene , Mai Sebastian , Ispas Adriana , Bund Andreas
Published: June 2020

The kinetics of the dissolution and deposition of aluminum from a first generation ionic liquid consisting of AlCl3/1-ethyl-3-methylimidazolium chloride (molar ratio 2:1) was studied. Electrochemical impedance spectroscopy shows that the double layer capacitance and the charge–transfer resistance depend on the state of the electrode surface. The impedance spectra are strongly influenced by mass transport. The rate–determining step of the aluminum deposition, as determined from the cathodic Tafel slope evaluated from current step experiments, was found to be either a chemical step, releasing the complexing agent chloride, while aluminum is in the divalent oxidation state (AlCl3
− → AlCl2 + Cl−) or an electron transfer from the divalent to the monovalent aluminum occurring twice for the overall reaction to occur once (Al2+ + e− → Al+). The rate–determining step for aluminum dissolution was found to be the transfer of an electron from elemental aluminum to the monovalent oxidation state (Al0 → Al+ + e−). A linear slope in the low cathodic overpotential region of the Tafel plot suggests a change in the cathodic rate–determining step. The Tafel slope indicates a chemical step, releasing the complexing agent chloride, after the last electron transfer (AlCl− → Al0 + Cl−) to be the rate–determining step for overpotentials below 50 mV. Density functional theory calculations support the proposed reduction and oxidation mechanisms.
Ion Transport Mechanisms in the Oxide Film Formed on 316L Stainless Steel Surfaces Studied by ToF-SIMS with 18O2 Isotopic Tracer
Authors: Wang Luntao , Seyeux Antoine , Marcus Philippe
Published: June 2020

The composition and structure of the native and passive oxide films formed on 316 L stainless steel have been studied in situ by ToF-SIMS. High temperature re-oxidation experiments in isotopic 18O2 gas have also been done to assess the ion transport mechanisms in the native and passive oxide films. Duplex oxides with an inner Cr rich layer and an outer layer rich in Fe and Mo oxide have been observed on native and passive oxide films. Exposure of the oxide films to isotopic 18O2 tracer at 300 °C reveals that the outward cationic diffusion governs the inner oxide growth. The outer Mo-rich layer prevents the continued transport of Cr to the outermost surface. The passive film, due to its composition and structure, exhibits a markedly lower oxidation rate compared to native oxide films.
Fabrication of Tetra-Substituted Copper(II) Phthalocyanine-Graphene Modified Pencil Graphite Electrode for Amperometric Detection of Hydrogen Peroxide
Authors: Gorduk Ozge , Gorduk Semih , Sahin Yucel
Published: June 2020

In this study, tetra-substituted copper(II) phthalocyanine-graphene modified pencil graphite electrode (CuPc-Gr/PGE) was developed for the amperometric determination of hydrogen peroxide (H2O2) for the first time in the literature. The developed non-enzymatic electrode platform was electrochemically characterized by cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) methods. Scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS) methods were also used for surface characterization of the modified electrode. The response to H2O2 at the working potential of −0.4 V is linear in the 0.1 μM to 100 μM concentration range in PBS pH 7.0. The limit of detection (LOD) and limit of quantitation (LOQ) are 0.045 and 0.15 μM, respectively. Good selectivity was observed within physiological interference species such as ascorbic acid, dopamine, uric acid, and glucose. Additionally, amount of H2O2 was determined using the novel produced non-enzymatic sensor with satisfactory results in beverage samples. These consequences imply that the CuPc-Gr/PGE displays effective electrocatalytic activity for the reduction of H2O2, indicating it has capability use for the detection of H2O2.
Impacts of Climatic Change on Reference Crop Evapotranspiration across Different Climatic Zones of Ningxia at Multi-Time Scales from 1957 to 2018
Authors: Zhao Ziyang , Wang Hongrui , Wang Cheng , Li Wangcheng , Chen Hao , Gong Shuxin
Published: June 2020

The impact of global climate change on agroecosystems is growing, affecting reference crop evapotranspiration (ET0) and subsequent agricultural water management. In this study, the climate factors temporal trends, the spatiotemporal variation, and the climate driving factors of ET0 at different time scales were evaluated across the Northern Yellow River Irrigation Area (NYR), Central Arid Zone (CAZ), and Southern Mountain Area (SMA) of Ningxia based on 20 climatic stations’ daily data from 1957 to 2018. The results showed that the Tmean (daily mean air temperature), Tmax (daily maximum air temperature), and Tmin (daily minimum air temperature) all had increased significantly over the past 62 years, whilst RH (relative humidity), U2 (wind speed at 2 m height), and SD (sunshine duration) had significantly decreasing trends across all climatic zones. At monthly scale, the ET0 was mainly concentrated from April to September. And at annual and seasonal scales, the overall increasing trends were more pronounced in NX, NYR, and SMA, while CAZ was the opposite. For the spatial distribution, ET0 presented a trend of rising first and then falling at all time scales. The abrupt change point for climatic factors and ET0 series was obtained at approximately 1990 across all climatic zones, and the ET0 had a long period of 25a and a short period of 10a at annual scale, while it was 15a and 5a at seasonal scale. RH and Tmax were the most sensitive climatic factors at the annual and seasonal scales, while the largest contribution rates were Tmax and SD. This study not only is important for the understanding of ET0 changes but also provides the preliminary and elementary reference for agriculture water management in Ningxia.
Comparison of Machine Learning Methods and Conventional Logistic Regressions for Predicting Gestational Diabetes Using Routine Clinical Data: A Retrospective Cohort Study
Authors: Ye Yunzhen , Xiong Yu , Zhou Qiongjie , Wu Jiangnan , Li Xiaotian , Xiao Xirong
Published: June 2020

Background. Gestational diabetes mellitus (GDM) contributes to adverse pregnancy and birth outcomes. In recent decades, extensive research has been devoted to the early prediction of GDM by various methods. Machine learning methods are flexible prediction algorithms with potential advantages over conventional regression. Objective. The purpose of this study was to use machine learning methods to predict GDM and compare their performance with that of logistic regressions. Methods. We performed a retrospective, observational study including women who attended their routine first hospital visits during early pregnancy and had Down’s syndrome screening at 16-20 gestational weeks in a tertiary maternity hospital in China from 2013.1.1 to 2017.12.31. A total of 22,242 singleton pregnancies were included, and 3182 (14.31%) women developed GDM. Candidate predictors included maternal demographic characteristics and medical history (maternal factors) and laboratory values at early pregnancy. The models were derived from the first 70% of the data and then validated with the next 30%. Variables were trained in different machine learning models and traditional logistic regression models. Eight common machine learning methods (GDBT, AdaBoost, LGB, Logistic, Vote, XGB, Decision Tree, and Random Forest) and two common regressions (stepwise logistic regression and logistic regression with RCS) were implemented to predict the occurrence of GDM. Models were compared on discrimination and calibration metrics. Results. In the validation dataset, the machine learning and logistic regression models performed moderately (AUC 0.59-0.74). Overall, the GBDT model performed best (AUC 0.74, 95% CI 0.71-0.76) among the machine learning methods, with negligible differences between them. Fasting blood glucose, HbA1c, triglycerides, and BMI strongly contributed to GDM. A cutoff point for the predictive value at 0.3 in the GBDT model had a negative predictive value of 74.1% (95% CI 69.5%-78.2%) and a sensitivity of 90% (95% CI 88.0%-91.7%), and the cutoff point at 0.7 had a positive predictive value of 93.2% (95% CI 88.2%-96.1%) and a specificity of 99% (95% CI 98.2%-99.4%). Conclusion. In this study, we found that several machine learning methods did not outperform logistic regression in predicting GDM. We developed a model with cutoff points for risk stratification of GDM.
Antimalarial Plants Used across Kenyan Communities
Authors: Omara Timothy
Published: June 2020

Malaria is one of the serious health problems in Africa, Asia, and Latin America. Its treatment has been met with chronic failure due to pathogenic resistance to the currently available drugs. This review attempts to compile phytotherapeutical information on antimalarial plants in Kenya based on electronic data. A comprehensive web search was conducted in multidisciplinary databases, and a total of 286 plant species from 75 families, distributed among 192 genera, were retrieved. Globally, about 139 (48.6%) of the species have been investigated for antiplasmodial (18%) or antimalarial activities (97.1%) with promising results. However, there is no record on the antimalarial activity of about 51.4% of the species used although they could be potential sources of antimalarial remedies. Analysis of ethnomedicinal recipes indicated that mainly leaves (27.7%) and roots (19.4%) of shrubs (33.2%), trees (30.1%), and herbs (29.7%) are used for preparation of antimalarial decoctions (70.5%) and infusions (5.4%) in Kenya. The study highlighted a rich diversity of indigenous antimalarial plants with equally divergent herbal remedy preparation and use pattern. Further research is required to validate the therapeutic potential of antimalarial compounds from the unstudied claimed species. Although some species were investigated for their antimalarial efficacies, their toxicity and safety aspects need to be further investigated.
Changes in Vitamin E and β-Carotene Contents in Various Edible Cassava Leaves (Manihot esculenta Crantz) of Different Ages across Multiple Seasons
Authors: Laya Alphonse , Koubala Benoît B.
Published: June 2020

Vitamin E and carotenoids belong to a group of bioactive compounds that have an important effect on human health. The present study aims to investigate for the first time the concentration of vitamin E, α-, γ-, and δ-tocopherol, and β-carotene in edible cassava leaves during different ages. The analysis was performed using colorimetry and high-performance liquid chromatograph (HPLC) methods. A significant difference was found among α-, γ-, and δ-tocopherol concentrations in leaves; γ- and α-tocopherol isomer contents were the predominant in amount, respectively. Among the leaves, AD variety harvested at 6 months after planting (MAP) was the highest in total vitamin E (222 μgα-TE/g). However, the highest γ-tocopherol content (2782 μg/100g) and the content of biologically active vitamin E (1244 μg/100g) were found in EN variety at 6MAP, whereas the highest value (42 μg/g) of β-carotene was found in AD variety at 12MAP. Total vitamin E and tocopherol isomers composition varied among varieties and seasons as did β-carotene. The effects of varieties and harvest ages on the biosynthesis regulation of these compounds were confirmed by principal component analysis (F1x F2: 74.34%). Edible cassava leaves can be considered as sources of vitamin E for natural dietary antioxidant during different ages, and the best time to harvest EN and AD varieties is at 6MAP on the basis of α-tocopherol equivalent or content of biologically active vitamin E content, and EN and AD varieties performed the overall best. Thus, the edible cassava leaves are among the leafy vegetables that could be helpful to suggest as a part of daily meal for health benefits and pharmaceutical purposes.
SecureBP from Homomorphic Encryption
Authors: Liu Qinju , Lu Xianhui , Luo Fucai , Zhou Shuai , He Jingnan , Wang Kunpeng
Published: June 2020

We present a secure backpropagation neural network training model (SecureBP), which allows a neural network to be trained while retaining the confidentiality of the training data, based on the homomorphic encryption scheme. We make two contributions. The first one is to introduce a method to find a more accurate and numerically stable polynomial approximation of functions in a certain interval. The second one is to find a strategy of refreshing ciphertext during training, which keeps the order of magnitude of noise at O˜e33.
Role of Long Noncoding RNAs in Parkinson’s Disease: Putative Biomarkers and Therapeutic Targets
Authors: Lv Qiankun , Wang Ziyu , Zhong Zhen , Huang Wei
Published: June 2020

Parkinson’s disease (PD) is a neurodegenerative disease characterized by bradykinesia, rigidity, and tremor. Age is the main risk factor. Long noncoding RNAs (lncRNAs) are novel RNA molecules of more than 200 nucleotides in length. They may be involved in the regulation of many pathological processes of PD. PD has a variety of pathophysiological mechanisms, including alpha-synuclein aggregate, mitochondrial dysfunction, oxidative stress, calcium homeostasis, axonal transport, and neuroinflammation. Among these, the impacts of lncRNAs on the pathogenesis and progression of PD need to be highlighted. lncRNAs may serve as putative biomarkers and therapeutic targets for the early diagnosis of PD. This study aimed to investigate the role of lncRNAs in various pathological processes of PD and the specific lncRNAs that might be used as putative diagnostic biomarkers and therapeutic targets of PD.
Verification and Defined Dosage of Sodium Pentobarbital for a Urodynamic Study in the Possibility of Survival Experiments in Female Rat
Authors: Xu Sheng-Fei , Du Guang-Hui , Abulikim Kuerbanjiang , Cao Peng , Tan Hui-bing
Published: June 2020

Objectives. To evaluate the effects of pentobarbital dosages on lower urinary tract function and to define an appropriate dosage of sodium pentobarbital that would be suitable for urodynamic studies in which recovery from anesthesia and long term survive were needed for subsequent experiment. Methods. Twenty‐four 8‐week‐old, female, virgin, Sprague‐Dawley rats (200‐250 g) were used in this study. Rats in study groups received gradient doses of pentobarbital intraperitoneally, and those in the control group received urethane intraperitoneally. External urethral sphincter electromyography (EUS‐EMG) was recorded simultaneously during cystometry and leak point pressure tests. The toe‐pinch reflex was used to determine the level of anesthesia. Results. Micturition was normally induced in both the urethane group and 32 mg/kg pentobarbital group. However, in groups of 40 mg/kg or 36 mg/kg pentobarbital, micturition failed to be induced; instead, nonvoiding contractions accompanied by EUS‐EMG tonic activity were observed. There were no significant differences in leak point pressure or EUS‐EMG amplitude or frequency between the urethane and 32 mg/kg pentobarbital groups. Conclusions. This study confirmed significant dose‐dependent effects of pentobarbital on lower urinary tract function and 32 mg/kg pentobarbital as an appropriate dosage for recovery urodynamic testing, which enable the achievement of expected essential micturition under satisfactory anesthesia in female rats.
A Combination Therapy of pHRE-Egr1-HSV-TK/Anti-CD133McAb-131I/MFH Mediated by FePt Nanoparticles for Liver Cancer Stem Cells
Authors: Lin Mei , Xiao Yanhong , Jiang Xingmao , Zhang Jun , Guo Ting , Shi Yujuan
Published: June 2020

It has been evidenced that liver cancer stem cells (LCSCs) are to blame hepatocellular carcinoma (HCC) occurrence, development, metastasis, and recurrence. Using iron-platinum nanoparticles (FePt-NPs) as a carrier and CD133 antigen as a target, a new strategy to targetly kill LCSCs by integrating HSV-TK suicide gene, 131I nuclide irradiation, and magnetic fluid hyperthermia (MFH) together was designed and investigated in the present study. The results showed that FePt-NPs modified with PEI (PEI-FePt-NPs) could bind with DNA, and the best binding ratio was 1 : 40 (mass ratio). Moreover, DNA binding to PEI-FePt-NPs could refrain from Dnase1 enzyme digestion and could release under certain conditions. LCSCs (CD133+ Huh-7 cells) were transfected with pHRE-Egr1-HSV-TK by PEI-FePt-NPs, and the transfection efficiency was 53.65±3.40%. These data showed a good potential of PEI-FePt-NPs as a gene transfer carrier.131I was labeled with anti-CD133McAb in order to facilitate therapy targeting. The combined intervention of pHRE-Egr1-HSV-TK/anti-CD133McAb-131I/MFH mediated by PEI-FePt-NPs could greatly inhibit LCSCs’ growth and induce cell apoptosis in vitro, significantly higher than any of the individual interventions (p<0.05). This study offers a practicable idea for LCSC treatment, and PEI-FePt-NPs may act as novel nonviral gene vectors and a magnetic induction medium.
Adaptation Evolution and Phylogenetic Analyses of Species in Chinese Allium Section Pallasia and Related Species Based on Complete Chloroplast Genome Sequences
Authors: Xie Fu-Min , Xie Deng-Feng , Xie Chuan , Yu Yan , Zhou Song-Dong , He Xing-Jin
Published: June 2020

The section Pallasia is one of the components of the genus Allium subgenus Allium (Amaryllidaceae), and species relationship in this section is still not resolved very well, which hinders further evolutionary and adaptive studies. Here, the complete chloroplast genomes of five sect. Pallasia species were reported, and a comparative analysis was performed with other three related Allium species. The genome size of the eight species ranged from 151,672 bp to 153,339 bp in length, GC content changed from 36.7% to 36.8%, and 130 genes (except Allium pallasii), 37 tRNA, and 8 rRNA were identified in each genome. By analyzing the IR/LSC and IR/SSC boundary, A. pallasii exhibited differences compared with other seven species. Phylogenetic analysis achieved high supports in each branch, seven of the eight Allium species cluster into a group, and A. pallasii exhibit a close relationship with A. obliquum. Higher pairwise Ka/Ks ratios were found in A. schoenoprasoides compared to A. caeruleum and A. macrostemon while a lower value of Ka/Ks ratios was detected between A. caeruleum and A. macrostemon. This study will be a great contribution to the future phylogenetic and adaptive research in Allium.
The Role of circRNA‐SETD2/miR‐519a/PTEN Axis in Fetal Birth Weight through Regulating Trophoblast Proliferation
Authors: Wang Dan , Na Quan , Song Guiyu , Wang Ying , Wang Yang
Published: June 2020

Abnormal birth weight is the one of the major causes of adulthood diseases such as obesity, metabolic syndrome, cardiovascular disease, type 2 diabetes, and hypertension. Accumulating evidence has suggested that the placental trophoblast is one of the most important reasons that influence birth weight. Our previous study showed that miR‐519a are correlated with low fetal birth weight through regulating trophoblast proliferation. To further clarify the detailed mechanisms on how it is regulated, we screened the placental‐specific circular RNAs (circRNAs) via microarray assay. The result identified that circ‐SETD2 was highly expressed in the placenta of the patients with fetal macrosomia compared with healthy donors. Furthermore, bioinformatic analyses and the luciferase reporter assay revealed that miR‐519a possessing the binding sites for both circ‐SETD2 and phosphate and tensin homolog was deleted on chromosome 10 (PTEN). Interestingly, upregulation of circ‐SETD2 enhanced the proliferation and invasion of the human trophoblast‐like cell line HTR8/SVneo cell. A parallel study performed by Western blotting showed that overexpression of circ‐SETD2 reduced miR‐519a levels and increased PTEN levels in HTR8/SVneo cells. Importantly, the enhancement of HTR8/SVneo cell activity by circ‐SETD2 overexpression was nullified when the cells were cotransfected by circ‐SETD2 and miR‐519a, suggesting the involvement of the circ‐SETD2/miR‐519a/PTEN axis in trophoblast activity. Taken together, we illustrate the role of circ‐SETD2, as an upstream signaling of miR‐519a/PTEN, in placenta development via regulating trophoblast proliferation and invasion. These findings improve our understanding of the mechanisms of progression of fetal macrosomia and will guide future development of therapeutic strategies against the disease by targeting the circ‐SETD2/miR‐519a/PTEN axis.
Sleep-Disordered Breathing in Children with Prader-Willi Syndrome in Relation to Growth Hormone Therapy Onset
Authors: Zimmermann Maja , Laemmer Constanze , Woelfle Joachim , Fimmers Rolf , Gohlke Bettina
Published: June 2020

Objective: The aim of this study was to consider sleep apnea in Prader-Willi syndrome (PWS) children depending on age at growth hormone (GH) therapy onset. Study Design: We analyzed longitudinally cardiorespiratory polygraphy of 62 PWS children (aged 0–2.5 years at baseline). Twenty-one children (Group A) started GH-therapy during and 41 children (Group B) after their first year of life. Data were acquired before, at 3 and 6 months, then 1.2, 2.2, and 3.2 years after GH onset. Outcomes were determined with the obstructive apnea hypopnea index (OAHI), central apnea index (CAI), oxygen desaturation index (ODI), and by measuring obstructive sleep apnea (OSA) and peripheral blood oxygen saturation (SpO2). Results: We observed no significant differences in OAHI, CAI, ODI, and SpO2 depending on treatment onset. At baseline, 5/21 patients (23.8%) in Group A versus 15/41 patients (36.6%) in Group B showed pathological sleep apnea (OAHI ≥1.5). Pathological OSA increased significantly in Group A during the first 3 months of therapy but dropped below baseline after 1 year in both groups. ODI changed during GH therapy in both groups (from 4.0 to 2.6 in Group A, and 3.6 to 1.6 in Group B; baseline to 3.2 years; p < 0.05). Conclusions: OSA in PWS children appears to develop independently of treatment onset. Treatment may therefore safely be initiated early but should be accompanied by regular sleep analysis.
Effects of Erythropoietin-Stimulating Agents on Blood Pressure in Patients with Non-Dialysis CKD and Renal Anemia
Authors: Ohki Kohji , Wakui Hiromichi , Uneda Kazushi , Azushima Kengo , Haruhara Kotaro , Kinguchi Sho , Urate Shingo , Yamada Takayuki , Yamaji Takahiro , Kobayashi Ryu , Kanaoka Tomohiko , Minegishi Shintaro , Ishigami Tomoaki , Fujikawa Tetsuya , Toya Yoshiyuki , Tamura Kouichi
Published: June 2020

Introduction: Erythropoietin-stimulating agents (ESAs) are used to treat renal anemia in patients with non-dialysis CKD, but this can lead to increases in blood pressure (BP). Objective: We investigated the effects of continuous erythropoietin receptor activator (CERA) and darbepoetin alfa (DA) on office/ambulatory BP in 36 patients with non-dialysis CKD and renal anemia who did not receive ESA treatment. Methods: Participants were randomly assigned to CERA or DA, and received ESA treatment for 24 weeks. ESA doses were adjusted to maintain hemoglobin (Hb) at 10–12 g/dL. Primary outcomes were office/ambulatory BP after 24 weeks of ESA treatment. Hb levels were within the target range at 24 weeks. Results: Office/ambulatory BP, renal function, and other parameters were not significantly different between groups. However, we could not exclude the possibility that differences may exist because our sample size was small. Therefore, we also performed analysis of all of the data that were compiled from the groups of per-protocol population. Although office/ambulatory BP profiles had not worsened after 24 weeks of ESA treatment, more than half of the patients required an increase in the antihypertensive agent dose. Conclusions: CERA and DA may have similar effects on BP profiles in patients with non-dialysis CKD and renal anemia. ESA treatment often requires increases in the doses of antihypertensive agents.
Activation, Deficiency, and Reduced IFN-γ Production of Mucosal-Associated Invariant T Cells in Patients with Inflammatory Bowel Disease
Authors: Ju Jae Kyun , Cho Young-Nan , Park Ki-Jeong , Kwak Han Deok , Jin Hye-Mi , Park Seon-Young , Kim Hyun Soo , Kee Seung-Jung , Park Yong-Wook
Published: June 2020

Mucosal-associated invariant T (MAIT) cells are innate-like T cells that can activate either in response to T-cell receptor (TCR) engagement or through activating cytokines and play an important role in autoimmune disorders. The study examined the level and function of MAIT cells in patients with inflammatory bowel disease (IBD). Circulating MAIT cell levels were significantly reduced in IBD patients. This MAIT cell deficiency was correlated with IBD disease activity grades, hemoglobin, and CRP. IFN-γ production of circulating MAIT cells in response to both MHC class 1b-like related protein (MR1)-dependent and -independent stimulations was decreased in IBD patients, which was partially associated with reduced activation of nuclear factor of activated T cells 1 (NFAT1) transcription factor, a main regulator of IFN-γ production. Expression levels of CD69, programmed death-1 (PD-1), and annexin V in MAIT cells were elevated in IBD patients. CCL20, CXCL10, CXCL16, and CCL25 were expressed higher in inflamed intestinal tissues than in noninflamed tissues. This study demonstrates that circulating MAIT cells are activated and numerically and functionally deficient in IBD patients. Furthermore, activated MAIT cells have the potential to migrate to inflamed tissues. These findings suggest an important role of MAIT cells in mucosal immunity in IBD.
Peritoneal Dialysis Zoonotic Bacterial Peritonitis with Staphylococcus pseudintermedius
Authors: Dahbour Layth , Gibbs Jeffrey , Coletta Christian , Hummell Jeannine , Al-Sarie Mohammad , Kahlon Navkirat Pannu , Akpunonu Basil
Published: June 2020

We present the first reported case of peritoneal dialysis-associated peritonitis caused by Staphylococcus pseudintermedius, an organism that had been misclassified as S. aureus in the past. S. pseudintermedius is well recognized in the veterinary literature and noted as flora in the mouth, nares, and anus of domesticated animals. It has been associated with soft tissue infections in pets and is now being reported in increased frequency as the causative agent in various human infections. It also has a different antibiotic sensitivity profile. The patient had close contact with her pet dog and was successfully treated with intravenous antibiotics in the hospital followed by oral doxycycline for 10 days after discharge. The patient has not had any recurrent infection after obtaining and applying appropriate hygienic education and precautions.
A Novel Atypical Presentation of Frontal Fibrosing Alopecia Involving the Frontoparietal Scalp
Authors: Goldman Chloe , Diaz Aisleen , Miteva Mariya
Published: June 2020

Frontal fibrosing alopecia (FFA) is a progressive scarring alopecia of unknown etiology that classically presents with a band of hair loss along the frontotemporal scalp. We report a case of FFA involving a band of alopecia along the frontotemporal scalp extending into 2 symmetrical triangles along the parietal scalp reminiscent of the Greek letter upsilon (υ). Trichoscopy demonstrated loss of follicular ostia and peripilar casts. Histology demonstrated altered follicular architecture with decreased follicular density and focal perifollicular fibrosis with a lichenoid infiltrate. Both the trichoscopy and histology support a diagnosis of FFA.
A new Drusinae species from the western Alps with comments on the subfamily and an updated key to filtering carnivore larvae of Drusinae species (Insecta: Trichoptera: Limnephilidae)
Authors: VITECEK SIMON , GRAF WOLFRAM , MARTINI JAN , ZITTRA CARINA , HANDSCHUH STEPHAN , KUHLMANN HENDRIK C. , VIEIRA ARIANE , HESS MONIKA , HECKES ULLRICH , ERZINGER FELICITAS , PAULS STEFFEN U. , WARINGER JOHANN
Published: June 2020

A new Drusinae species, Drusus katagelastos sp. nov., of the Drusus chapmani Species Complex, is described based on a male and associated larvae. Adult-larval association was achieved through DNA barcoding. The male of the new species differs from that of its congeners in the formation of the intermediate appendages and parameres. Information on the morphology of the larva is given, and important diagnostic features are discussed. In the context of filtering carnivore Drusinae, the larva of the new species can be separated from other filtering carnivore species by the dense cover of long translucent bristles within the frontal cavity surrounded by a circular corona of long bristles. Drusus katagelastos sp. nov. is known from only northwestern Italy (Piemonte).
A new species of Characidium (Characiformes: Crenuchidae) from the upper rio São Francisco basin, Minas Gerais, Brazil
Authors: ZANATA ANGELA M. , RIBEIRO THIAGO C. , ARAÚJO-PORTO FELIPE A. , PESSALI TIAGO C. , OLIVEIRA-SILVA LEONARDO
Published: June 2020

Characidium cacah, new species, apparently endemic to the rio das Velhas sub-basin, upper rio São Francisco basin, Brazil, is described. The new species is easily distinguished from congeners, except C. chicoi, C. helmeri, C. mirim, C. nana, C. nupelia, C. stigmosum and C. xavante, by having an incomplete lateral line and for lacking an adipose fin. The new species can be diagnosed from the aforementioned species by a series of characters, including the presence of 12 circumpeduncular scales, the isthmus completely scaled, a thin inconspicuous or dashed midlateral dark stripe, the absence of a conspicuous peduncular blotch, and humeral blotch and basicaudal spot variably marked.