bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNSS2: Improved ab initio protein secondary structure prediction using advanced deep learning architectures
Authors: Guo Zhiye , Hou Jie , Cheng Jianlin 
Published: September 2020

AbstractAccurate prediction of protein secondary structure (alpha‐helix, beta‐strand and coil) is a crucial step for protein inter‐residue contact prediction and ab initio tertiary structure prediction. In a previous study, we developed a deep belief network‐based protein secondary structure method (DNSS1) and successfully advanced the prediction accuracy beyond 80%. In this work, we developed multiple advanced deep learning architectures (DNSS2) to further improve secondary structure prediction. The major improvements over the DNSS1 method include (a) designing and integrating six advanced one‐dimensional deep convolutional/recurrent/residual/memory/fractal/inception networks to predict 3‐state and 8‐state secondary structure, and (b) using more sensitive profile features inferred from Hidden Markov model (HMM) and multiple sequence alignment (MSA). Most of the deep learning architectures are novel for protein secondary structure prediction. DNSS2 was systematically benchmarked on independent test data sets with eight state‐of‐art tools and consistently ranked as one of the best methods. Particularly, DNSS2 was tested on the protein targets of 2018 CASP13 experiment and achieved the Q3 score of 81.62%, SOV score of 72.19%, and Q8 score of 73.28%. DNSS2 is freely available at: https://github.com/multicom-toolbox/DNSS2.
Open Chemistry, JupyterLab, REST, and quantum chemistry
Authors: Hanwell Marcus D. , Harris Chris , Genova Alessandro , Haghighatlari Mojtaba , El Khatib Muammar , Avery Patrick , Hachmann Johannes , de Jong Wibe Albert 
Published: September 2020

AbstractQuantum chemistry must evolve if it wants to fully leverage the benefits of the internet age, where the worldwide web offers a vast tapestry of tools that enable users to communicate and interact with complex data at the speed and convenience of a button press. The Open Chemistry project has developed an open‐source framework that offers an end‐to‐end solution for producing, sharing, and visualizing quantum chemical data interactively on the web using an array of modern tools and approaches. These tools build on some of the best open‐source community projects such as Jupyter for interactive online notebooks, coupled with 3D accelerated visualization, state‐of‐the‐art computational chemistry codes including NWChem and Psi4, and emerging machine learning and data mining tools such as ChemML and ANI. They offer flexible formats to import and export data, along with approaches to compare computational and experimental data.
The impact of endometrial injury on reproductive outcomes: results of an updated meta‐analysis
Authors: Nahshon Chen , Sagi‐Dain Lena , Dirnfeld Martha 
Published: September 2020

AbstractBackgroundIt is still unclear whether endometrial injury (EI) has a beneficial effect on reproductive outcomes, and if so, the optimal procedure characteristics are not clear. All previous papers concluded that more research is needed, and as additional studies were recently published, the insights on EI have changed significantly.MethodsSearches were conducted in MEDLINE, Embase, Web of Science, and Cochrane Library, to identify randomized controlled trials examining the EI effect on IVF outcomes in women at least one previous failed cycle.Results2015 references were identified through database searching. Ultimately, 17 studies were included, involving 3016 patients. Clinical pregnancy rate (CPR) (RR = 1.19, [95% CI 1.06–1.32],P= .003) and live birth rate (LBR) (RR = 1.18, [95%CI 1.04–1.34],P= .009) were significantly improved after EI. Number of previous failed cycles, maternal age, and hysteroscopy were found to be relevant confounders. Higher CPR and LBR were found when EI was performed twice, while performing EI once did not significantly improve reproductive rates.ConclusionAccording to the present meta‐analysis, EI may be offered to younger patients with few previous failed cycles and should be additionally studied in an RCT comparing different timing and more than one EI before treatment.
Potential of mesenchymal stem cells as topical immunomodulatory cell therapies for ocular surface inflammatory disorders
Authors: Beeken Lydia J. , Ting Darren S.J. , Sidney Laura E. 
Published: September 2020

Abstract
Ocular surface inflammatory disorders (OSIDs) are a group of highly prevalent, heterogeneous diseases that display a variety of aetiologies and symptoms and are risk factors for serious complications, including ocular and cornea impairment. Corneal inflammation is a common factor of all OSIDs, regardless of their cause or symptoms. Current medications include over-the-counter lubricating eye drops, corticosteroids, and ciclosporin, which either do not treat the corneal inflammation or have been associated with multiple side effects leading to alternative treatments being sought. Regenerative medicine cell therapies, particularly mesenchymal stem cells (MSCs), have shown great promise for immunosuppression and disease amelioration across multiple tissues, including the cornea. However, for successful development and clinical translation of MSC therapy for OSIDs, significant problems must be addressed. This review aims to highlight considerations, including whether the source of MSC isolation impacts the efficacy and safety of the therapy, in addition to assessing the feasibility of MSC topical application to the cornea and ocular surface through analysis of potential scaffolds and cell carriers for application to the eye. The literature contains limited data assessing MSCs incorporated into scaffolds for corneal administration, thus here we highlight the necessity of further investigations to truly exploit the potential of an MSC-based cell therapy for the treatment of OSIDs.
Synthesis, Characterization, and Anticancer Studies of Some Pyrazole‐Based Hybrid Heteroatomics
Authors: Kuthyala Sharanya , Sheikh Sareen , Prabhu Ashwini , Rekha P. D. , Karikannar Nagaraja G. , Shankar Madan K. 
Published: September 2020

AbstractDefined with a dual‐mode of action, the hybrid molecule synthesis is an attractive strategy to endure the scientific challenges in drug discovery. Besides worthy development in cancer therapy, it is still a leading cause of death across the globe. Failure in terms of efficacy, selectivity and toxicity, the statistics of a potential drug to concrete the cancer is rather in bleak. In the present study, synthesized hybrid molecules were well characterized by spectroscopy techniques. The single‐crystal X‐ray crystallography study revealed the monoclinic crystal system of Dimethyl 1,4‐dihydro‐2,6‐dimethyl‐4‐(3‐(5‐methyl‐1‐phenyl‐1H‐pyrazol‐4‐yl)‐1H‐pyrazol‐4‐yl)pyridine‐3,5‐dicarboxylate (5 b) with spacegroup C2/c. MTT assay provided the anticancer property of the compounds Diethyl1,4‐dihydro‐3,5‐dimethyl‐4‐(3‐(5‐methyl‐1‐phenyl‐1H‐pyrazol‐4‐yl)‐1H‐pyrazol‐4‐yl)pyridine‐2,6‐dicarboxylate (5 a) and 5‐methyl‐1‐phenyl‐4‐(4‐(4,5‐diphenyl‐1H‐imidazol‐2‐yl)‐1H‐pyrazol‐3‐yl)‐1H‐pyrazole (6 a) against A549 cell lines with the IC50 values of 42.79 μM and 55.13 μM respectively. The AO‐EB staining assay for cell death analysis confirmed the selective action of both 5 a and 6 a. Further, molecular docking confirmed the effective binding with cyclin‐dependent kinase (CDK2) protein, suggesting that the target compounds are remarkable inhibitors in dysregulating the CDK2 protein in cancer cells.
Engineering Inorganic Nanoflares with Elaborate Enzymatic Specificity and Efficiency for Versatile Biofilm Eradication
Authors: Liang Meijuan , Wang Yanbing , Ma Kang , Yu Shanshan , Chen Yingying , Deng Zhao , Liu Yi , Wang Fuan 
Published: September 2020

AbstractNanozyme has emerged as a versatile nanocatalyst yet is constrained with limited catalytic efficiency and specificity for various biomedical applications. Herein, by elaborately integrating the recognition/transduction carbon dots (CDs) with platinum nanoparticles (PtNPs), an exquisite CDs@PtNPs (CPP) nanoflare is engineered as an efficient and substrate‐specific peroxidase‐mimicking nanozyme for high‐performance biosensing and antibacterial applications. The intelligent CPP‐catalyzed hydrogen peroxide (H2O2)‐generated reactive oxygen species realize the sensitive diagnosis‐guided enhanced disinfection of pathogens. Significantly, the CPP nanozyme shows the prominent biofilm eradication and wound healing in vivo by virtue of endogenous H2O2 in acidic infection tissues, which can substantially preclude the annoying antibiotics resistance. A fundamental understanding on the present CPP nanoflare would not only facilitate the advancement of various prospective biocatalysts, but also establish a multifunctional means for versatile biosensing and smart diagnostic applications.
Toward Controlling Filament Size and Location for Resistive Switches via Nanoparticle Exsolution at Oxide Interfaces
Authors: Spring Jonathan , Sediva Eva , Hood Zachary D. , Gonzalez‐Rosillo Juan Carlos , O'Leary Willis , Kim Kun Joong , Carrillo Alfonso J. , Rupp Jennifer L. M. 
Published: September 2020

AbstractMemristive devices are among the most prominent candidates for future computer memory storage and neuromorphic computing. Though promising, the major hurdle for their industrial fabrication is their device‐to‐device and cycle‐to‐cycle variability. These occur due to the random nature of nanoionic conductive filaments, whose rupture and formation govern device operation. Changes in filament location, shape, and chemical composition cause cycle‐to‐cycle variability. This challenge is tackled by spatially confining conductive filaments with Ni nanoparticles. Ni nanoparticles are integrated on the bottom La0.2Sr0.7Ti0.9Ni0.1O3−δ electrode by an exsolution method, in which, at high temperatures under reducing conditions, Ni cations migrate to the perovskite surface, generating metallic nanoparticles. This fabrication method offers fine control over particle size and density and ensures strong particle anchorage in the bottom electrode, preventing movement and agglomeration. In devices based on amorphous SrTiO3, it is demonstrated that as the exsolved Ni nanoparticle diameter increases up to ≈50 nm, the ratio between the ON and OFF resistance states increases from single units to 180 and the variability of the low resistance state reaches values below 5%. Exsolution is applied for the first time to engineer solid–solid interfaces extending its realm of application to electronic devices.
Characterization of potential superspreader farms for bovine tuberculosis: A review
Authors: Fielding Helen R. , McKinley Trevelyan J. , Delahay Richard J. , Silk Matthew J. , McDonald Robbie A. 
Published: September 2020

AbstractBackgroundVariation in host attributes that influence their contact rates and infectiousness can lead some individuals to make disproportionate contributions to the spread of infections. Understanding the roles of such ‘superspreaders’ can be crucial in deciding where to direct disease surveillance and controls to greatest effect. In the epidemiology of bovine tuberculosis (bTB) in Great Britain, it has been suggested that a minority of cattle farms or herds might make disproportionate contributions to the spread of Mycobacterium bovis, and hence might be considered ‘superspreader farms’.Objectives and MethodsWe review the literature to identify the characteristics of farms that have the potential to contribute to exceptional values in the three main components of the farm reproductive number ‐ Rf: contact rate, infectiousness and duration of infectiousness, and therefore might characterize potential superspreader farms for bovine tuberculosis in Great Britain.ResultsFarms exhibit marked heterogeneity in contact rates arising from between‐farm trading of cattle. A minority of farms act as trading hubs that greatly augment connections within cattle trading networks. Herd infectiousness might be increased by high within‐herd transmission or the presence of supershedding individuals, or infectiousness might be prolonged due to undetected infections or by repeated local transmission, via wildlife or fomites.ConclusionsTargeting control methods on putative superspreader farms might yield disproportionate benefits in controlling endemic bovine tuberculosis in Great Britain. However, real‐time identification of any such farms, and integration of controls with industry practices, present analytical, operational and policy challenges.
Yang-Baxter deformations of the AdS5×S5 supercoset sigma model from 4D Chern-Simons theory
Authors: Fukushima Osamu , Sakamoto Jun-ichi , Yoshida Kentaroh 
Published: September 2020

Abstract
We present homogeneous Yang-Baxter deformations of the AdS5×S5 supercoset sigma model as boundary conditions of a 4D Chern-Simons theory. We first generalize the procedure for the 2D principal chiral model developed by Delduc et al. [5] so as to reproduce the 2D symmetric coset sigma model, and specify boundary conditions governing homogeneous Yang-Baxter deformations. Then the conditions are applicable for the AdS5×S5 supercoset sigma model case as well. In addition, homogeneous bi-Yang-Baxter deformation is also discussed.
Pattern Recognition Receptors: Significance of Expression in the Liver
Authors: Żeromski Jan , Kierepa Agata , Brzezicha Bartosz , Kowala-Piaskowska Arleta , Mozer-Lisewska Iwona 
Published: September 2020

AbstractPattern recognition receptors (PRRs) are a pivotal part of the immune system. They are distributed in almost every site of higher organisms, able to recognize foreign pathogens or unwanted remnants of metabolism and mount innate immune response. Moreover, PRRs create bridging signaling to initiate adaptive immunity. The liver being the largest organ of the body, exposed to myriads of foreign substances often being immunogenic, is well equipped with PRRs. They act as sentinels of the organ, both in health and disease. In viral hepatitis C at least two of them, RIG-1 and TLR3 sense HCV, induce protective interferon production and create proinflammatory status. The hepatitis B virus is apparently invisible to PRRs, which has recently been denied. Besides, they are active in the course of infection. In liver injury and hepatic fibrogenesis Toll-like receptors (TLRs), predominantly TLR4, TLR3 and TLR9 are associated with gut microflora-related products and DNA from dying hepatocytes, lead to the activation of hepatic stellate cells. The latter initiate production of fibrillar collagens, the main agents forming hepatic fibrosis. Tumor cells of primary liver cancer also express PRRs, mainly TLRs. In concert with non-resolving liver inflammation, they are considered pivotal factors leading to carcinogenesis.
Development of a fast liquid chromatography-tandem mass spectrometry method for simultaneous quantification of neurotransmitters in murine microdialysate
Authors: Helmschrodt Christin , Becker Susen , Perl Stefanie , Schulz Anja , Richter Angelika 
Published: September 2020

AbstractThe continuous measurement of multiple neurotransmitters in microdialysate of freely moving mice to study neurochemical changes in specific brain regions requires a rapid and very sensitive quantitative analytical method. The quantitative analysis of 11 neurotransmitters and metabolites, including serotonin (5-HT), 5-hydroxyindoleacetic acid (5-HIAA), melatonin (ME), dopamine (DA), levodopa (l-DOPA), 3-methoxytyramine (3-MT), norepinephrine (NE), epinephrine (EP), acetylcholine (ACh), choline (Ch), and γ-aminobutyric acid (GABA), was performed using a biphenyl column coupled to an API-QTrap 3200 (AB SCIEX) mass spectrometer in positive electrospray ionization mode. To the microdialysate samples, 0.5 ng of isotopically labeled standard was added for analyte quantification. A rapid liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed and validated for the simultaneous analysis of monoamines, their precursor, and metabolites, as well as ACh, Ch, and GABA in murine microdialysate within 7.0 min. The limit of detection in artificial CSF ranged from 0.005 ng/mL (ME) to 0.75 ng/mL (NE and GABA). A comprehensive pre-analytical protocol was validated. Recovery was between 87 and 117% for neurotransmitter concentrations from 0.6 to 45 ng/mL with an inter-day accuracy of below 20%. Basal neurotransmitter values were determined in the striatum of mice over a time period of 3 h. This LC-MS/MS method, including a short and gentle sample preparation, is suitable for simultaneous measurements of neurotransmitters in murine cerebral microdialysate and enables the determination of basal neurotransmitter levels in specific brain regions to detect disease-related and drug-induced neurochemical changes.Graphical abstract
Standing waves of the quintic NLS equation on the tadpole graph
Authors: Noja Diego , Pelinovsky Dmitry E. 
Published: September 2020

AbstractThe tadpole graph consists of a circle and a half-line attached at a vertex. We analyze standing waves of the nonlinear Schrödinger equation with quintic power nonlinearity equipped with the Neumann–Kirchhoff boundary conditions at the vertex. The profile of the standing wave with the frequency $$\omega \in (-\infty ,0)$$

ω
∈
(
-
∞
,
0
)

is characterized as a global minimizer of the quadratic part of energy constrained to the unit sphere in $$L^6$$

L
6

. The set of standing waves includes the set of ground states, which are the global minimizers of the energy at constant mass ($$L^2$$

L
2

-norm), but it is actually wider. While ground states exist only for a certain interval of masses, the standing waves exist for every $$\omega \in (-\infty ,0)$$

ω
∈
(
-
∞
,
0
)

and correspond to a bigger interval of masses. It is proven that there exist critical frequencies $$\omega _1$$

ω
1

and $$\omega _0$$

ω
0

with $$-\infty< \omega _1< \omega _0 < 0$$

-
∞
<

ω
1

<

ω
0

<
0

such that the standing waves are the ground state for $$\omega \in [\omega _0,0)$$

ω
∈
[

ω
0

,
0
)

, local constrained minima of the energy for $$\omega \in (\omega _1,\omega _0)$$

ω
∈
(

ω
1

,

ω
0

)

and saddle points of the energy at constant mass for $$\omega \in (-\infty ,\omega _1)$$

ω
∈
(
-
∞
,

ω
1

)

. Proofs make use of the variational methods and the analytical theory for differential equations.
Sensitivity of nasopharyngeal, oropharyngeal, and nasal wash specimens for SARS-CoV-2 detection in the setting of sampling device shortage
Authors: Calame Adrien , Mazza Léna , Renzoni Adriana , Kaiser Laurent , Schibler Manuel 
Published: September 2020

AbstractIn the context of an unprecedented shortage of nasopharyngeal swabs (NPS) or sample transport media during the coronavirus disease 2019 (COVID-19) crisis, alternative methods for sample collection are needed. To address this need, we validated a cell culture medium as a viral transport medium, and compared the analytical sensitivity of SARS-CoV-2 RT-PCR in nasal wash (NW), oropharyngeal swab (OPS), and NPS specimens. Both the clinical and analytical sensitivity were comparable in these three sample types. OPS and NW specimens may therefore represent suitable alternatives to NPS for SARS-CoV-2 detection.
Muscle-driven and torque-driven centrodes during modeled flexion of individual lumbar spines are disparate
Authors: Rockenfeller Robert , Müller Andreas , Damm Nicolas , Kosterhon Michael , Kantelhardt Sven R. , Frank Rolfdieter , Gruber Karin 
Published: September 2020

AbstractLumbar spine biomechanics during the forward-bending of the upper body (flexion) are well investigated by both in vivo and in vitro experiments. In both cases, the experimentally observed relative motion of vertebral bodies can be used to calculate the instantaneous center of rotation (ICR). The timely evolution of the ICR, the centrode, is widely utilized for validating computer models and is thought to serve as a criterion for distinguishing healthy and degenerative motion patterns. While in vivo motion can be induced by physiological active structures (muscles), in vitro spinal segments have to be driven by external torque-applying equipment such as spine testers. It is implicitly assumed that muscle-driven and torque-driven centrodes are similar. Here, however, we show that centrodes qualitatively depend on the impetus. Distinction is achieved by introducing confidence regions (ellipses) that comprise centrodes of seven individual multi-body simulation models, performing flexion with and without preload. Muscle-driven centrodes were generally directed superior–anterior and tail-shaped, while torque-driven centrodes were located in a comparably narrow region close to the center of mass of the caudal vertebrae. We thus argue that centrodes resulting from different experimental conditions ought to be compared with caution. Finally, the applicability of our method regarding the analysis of clinical syndromes and the assessment of surgical methods is discussed.
Functionalization of polymers and nanomaterials for water treatment, food packaging, textile and biomedical applications: a review
Authors: Makvandi Pooyan , Iftekhar Sidra , Pizzetti Fabio , Zarepour Atefeh , Zare Ehsan Nazarzadeh , Ashrafizadeh Milad , Agarwal Tarun , Padil Vinod V. T. , Mohammadinejad Reza , Sillanpaa Mika , Maiti Tapas Kumar , Perale Giuseppe , Zarrabi Ali , Rossi Filippo 
Published: September 2020

AbstractThe inert nature of most commercial polymers and nanomaterials results in limitations of applications in various industrial fields. This can be solved by surface modifications to improve physicochemical and biological properties, such as adhesion, printability, wetting and biocompatibility. Polymer functionalization allows to graft specific moieties and conjugate molecules that improve material performances. In the last decades, several approaches have been designed in the industry and academia to graft functional groups on surfaces. Here, we review surface decoration of polymers and nanomaterials, with focus on major industrial applications in the medical field, textile industry, water treatment and food packaging. We discuss the advantages and challenges of polymer functionalization. More knowledge is needed on the biology behind cell–polymer interactions, nanosafety and manufacturing at the industrial scale.
Bounded Responsibility and Bounded Ethics of Science and Technology
Authors: Abel Günter 
Published: September 2020

AbstractThe leading question of this paper is: Where does the normativity of the ethics of science and technology come from? This is a challenging question given that the traditional reservoirs of convenience (like metaphysical universalism) are no longer at our disposal the way they used to be. The paper is divided into eight sections: (1) It is specified what challenges a non-foundationalist justification and normativity has to meet. (2) A three-dimensional conception of responsibility is developed based on the human triangular I–We–World relations. (3) The concepts of bounded responsibility and bounded ethics of science and technology are formulated. (4) The principle of reflective equilibrium is introduced as a principle of rationality, and it is shown how this principle generates rational and reasonable justifications in the ethics of science and technology. (5) Against this background, a reconception of internal and external responsibilities of science is given. (6) The type of responsibility demanded is exemplified by today’s climate research. (7) The paper argues for a hand-in-hand model of uncertainties in the sciences and for ethical obligations to preserve the conditions of human life on earth. The ethical argument is spelled out in terms of ethical care, preservation, and precaution. (8) Additionally, some arguments are developed to answer the question of why it is reasonable at all to preserve human life on earth.