bluuebunny/crossref_metadata_2025_split huggingface dataset:
DRoP: Automated detection of conserved solvent‐binding sites on proteins
Authors: Kearney Bradley M. , Schwabe Michael , Marcus Kendra C. , Roberts Daniel M. , Dechene Michelle , Swartz Paul , Mattos Carla 
Published: July 2019

AbstractWater and ligand binding play critical roles in the structure and function of proteins, yet their binding sites and significance are difficult to predict a priori. Multiple solvent crystal structures (MSCS) is a method where several X‐ray crystal structures are solved, each in a unique solvent environment, with organic molecules that serve as probes of the protein surface for sites evolved to bind ligands, while the first hydration shell is essentially maintained. When superimposed, these structures contain a vast amount of information regarding hot spots of protein‐protein or protein‐ligand interactions, as well as conserved water‐binding sites retained with the change in solvent properties. Optimized mining of this information requires reliable structural data and a consistent, objective analysis tool. Detection of related solvent positions (DRoP) was developed to automatically organize and rank the water or small organic molecule binding sites within a given set of structures. It is a flexible tool that can also be used in conserved water analysis given multiple structures of any protein independent of the MSCS method. The DRoP output is an HTML format list of the solvent sites ordered by conservation rank in its population within the set of structures, along with renumbered and recolored PDB files for visualization and facile analysis. Here, we present a previously unpublished set of MSCS structures of bovine pancreatic ribonuclease A (RNase A) and use it together with published structures to illustrate the capabilities of DRoP.
Nuclear magnetic resonance solution structure of Pisum sativum defensin 2 provides evidence for the presence of hydrophobic surface‐clusters
Authors: Pinheiro‐Aguiar Ramon , do Amaral Virginia S. G. , Pereira Iuri B. , Kurtenbach Eleonora , Almeida Fabio C. L. 
Published: July 2019

Abstract
Pisum sativum defensin 2 (Psd2) is a small (4.7 kDa) antifungal peptide whose structure is held together by four conserved disulfide bridges. Psd2 shares the cysteine‐stabilized alpha‐beta (CSαβ) fold, which lacks a regular hydrophobic core. All hydrophobic residues are exposed to the surface, except for leucine 6. They are clustered in the surface formed by two loops, between β1 and α‐helix and β2 and β3 sheets. The observation of surface hydrophobic clusters reveals a remarkable evolution of the CSαβ fold to expose and reorganize hydrophobic residues, which facilitates creating versatile binding sites.
Quantum Spin Hall Materials
Authors: Cao Chuanwu , Chen Jian‐Hao 
Published: July 2019

AbstractThe quantum spin Hall (QSH) effect describes the state of matter in certain 2D electron systems, in which an insulating bulk state arises together with helical states at the edge of the sample. In stark contrast to its closest kin, the integer quantum Hall state, the QSH state exists only in time‐reversal symmetric system (e.g., in non‐magnetic materials and without the application of external magnetic field). This article reviews the development of the understanding and construction of the QSH states after their first theoretical proposal, with an emphasis on the materials perspective. Certain semiconductor quantum wells and 2D materials with strong spin–orbit coupling have been found to support QSH states.
Data‐based optimal Denial‐of‐Service attack scheduling against robust control based on Q‐learning
Authors: An Liwei , Yang Guang‐Hong 
Published: July 2019

SummaryAttack optimization is an important issue in securing cyber‐physical systems. This paper investigates how an attacker should schedule its denial‐of‐service attacks to degrade the robust performance of a closed‐loop system. The measurements of system states are transmitted to a remote controller over a multichannel network. With limited resources, the attacker only has the capacity to jam sparse channels and to decide which channels should be attacked. Under an
framework, a data‐based optimal attack strategy that uses Q‐learning is proposed to maximize the effect on the closed‐loop system. The Q‐learning algorithm can adaptively learn the optimal attack using data sniffed over the wireless network without requiring a priori knowledge of system parameters. Simulation results sustain the performance of the proposed attack scenario.
Synthesis and Catalytic Application of Poly(2‐acrylamido‐2‐methyl‐1‐propanesulfonic acid‐co‐acrylamide) Grafted on Graphene Oxide
Authors: Boroujeni Kaveh Parvanak , Tohidiyan Zeinab , Fadavi Abdulhamid , Eskandari Mohammad Mehdi , Shahsanaei Hekmat Allah 
Published: July 2019

AbstractGraphene oxide was grafted with poly(2‐acrylamido‐2‐methyl‐1‐propanesulfonic acid‐co‐acrylamide) (GO–poly(AMPS–co–AM)) by free radical copolymerization of the corresponding monomers namely acrylamide (AM) and 2‐acrylamido‐2‐methyl‐1‐propanesulfonic acid (AMPS). The benzoyl peroxide (BPO) was used as initiator. The GO–poly(AMPS–co–AM) was characterized by Fourier transform infrared spectroscopy (FT–IR), Raman spectroscopy, X–ray diffraction (XRD), thermal gravimetric analysis (TGA), differential thermal analysis (DTA), scanning electron microscopy (SEM), energy‐dispersive X–ray spectroscopy (EDX), UV–Vis and fluorescence spectroscopy, and elemental analysis. The GO–poly(AMPS–co–AM) exhibited the acidic site loading of 0.85 mmol g−1, the maximum degradation temperatures (Tmax) of 212, 292, and 406 °C, the char yield of 30% at 800 °C, the limiting oxygen index (LOI) of 29.5, an estimated band gap of 4.7 eV, and the fluorescence emission bands of 722, 800, and 880 nm at the excitation wavelengths (λmax) of 360, 400, and 440 nm, respectively. The GO–poly(AMPS–co–AM) was used as a reusable catalyst for the preparation of 1,8‐dioxo‐octahydroxanthenes through the condensation of an aldehyde with 5,5‐dimethyl‐1,3‐cyclohexanedione (dimedone) in H2O/EtOH (1:1) as green solvents at room temperature.
SiCx/TiCx Nanostructured Material from Ti3SiC2 for High Rate Performance of Lithium Storage
Authors: Li Chenyang , Xue Zhe , Qin Jiaqian , Sawangphruk Montree , Rajendran Saravanan , Zhang Xinyu , Liu Riping 
Published: July 2019

AbstractA new SiCx/TiCx electrode material has been synthesized by ball‐milling of Ti3SiC2 MAX phase. To demonstrate the possible applications for lithium‐ion batteries, the electrochemical properties of the SiCx/TiCx nanocomposite was studied. The results indicate that this new material has a higher specific capacity (170 mAh/g) than those of pure SiC (93 mAh/g), TiC (75 mAh/g), and the mixture of SiC‐TiC (122 mAh/g) at current density of 100 mA/g for 300 cycles. Furthermore, the SiCx/TiCx nanocomposite has a specific capacity of 110 mAh/g, better than those of artificial graphite (labeled: SAG−R, 26 mAh/g) and mesocarbon microbeads (labeled: MCMB, 21 mAh/g), at current density of 1 A/g for 1000 cycles. The enhancement mechanism of the SiCx/TiCx nanostructure has been discussed by the DFT calculation. Further development of this anode material may enable practical applications for long cycling and fast charge‐discharge anode in rechargeable batteries.
Super‐Elastic Magnetic Structural Color Hydrogels
Authors: Zhang Yalan , Wang Yu , Wang Huan , Yu Ying , Zhong Qifeng , Zhao Yuanjin 
Published: July 2019

AbstractStructural color hydrogels are promising candidates as scaffold materials for tissue engineering and for matrix cell culture and manipulation, while their super‐elastic features are still lacking due to the irreconcilable interfere of the precursor and the self‐assembly unit. This hinders many of their practical biomedical applications where elasticity is required. Herein, hydrophilic and size‐controllable Fe3O4@poly(4‐styrenesulfonic acid‐co‐maleic acid) (PSSMA)@SiO2 magnetic response photonic crystals are fabricated as the assembly units of the structural color hydrogels by orderly packing of core–shell colloidal nanocrystal clusters via a two‐step facile synthesis approach. These units are capable of responding instantaneously to an external magnetic field with resistance to interference of ions, thus, by integrating super‐elastic hydrogels, super‐elastic magnetic structural color hydrogels can be achieved. The structural color arises from the dynamic ordering of the magnetic nanoparticles through the contactless control of external magnetic field, allowing regional polymerization of hydrogels via changing orientation and strength of external magnetic field. These regionally polymerized super‐elastic magnetic structural color hydrogels can work as anti‐counterfeiting labels with super‐elastic identification, which may be widely used in the future.
Screening a genomic library for genes involved in propionate tolerance in Yarrowia lipolytica
Authors: Park Young‐Kyoung , Nicaud Jean‐Marc 
Published: July 2019

AbstractMicrobial oils are regarded as promising alternatives to fossil fuels. For bio‐oil production to be sustainable over the long term, utilizing low‐cost substrates like volatile fatty acids (VFAs) is crucial. Increasing attention is being paid to one of the most common VFAs: propionate, a substrate that could be used to produce the odd‐chain FAs of industrial interest. However, little is known about microbial responses to propionate‐induced stress and the genes involved. Using genomic library screening, we identified two genes involved in propionate tolerance in Yarrowia lipolytica—MFS1 and RTS1. Strains containing each of the genes displayed enhanced tolerance to propionate even when the genes were expressed in truncated form via a replicative plasmid. Compared with the control strain, the strain overexpressing MFS1 under a constitutive promoter displayed greater tolerance to propionate: It had a shorter lag phase and higher growth rate in propionate medium (0.047 hr−1 versus 0.030 hr−1 for the control in 40 g/L propionate); it also accumulated more total lipids and more odd‐chain lipids (10% and 3.3%, respectively) than the control. The strain overexpressing RTS1 showed less tolerance for propionate than the strains harboring the truncated form (0.057 hr−1 versus 0.065 hr−1 in 40 g/L propionate medium) but still had higher tolerance than the control strain. Furthermore, the overexpression of RTS1 seemed to confer tolerance to other weak acids such as lactate, formic acid, malic acid, and succinic acid. This work provides a basis for better understanding the response to propionate‐induced stress in Y. lipolytica.
Schauder Estimates for a Class of Potential Mean Field Games of Controls
Authors: Bonnans J. Frédéric , Hadikhanloo Saeed , Pfeiffer Laurent 
Published: July 2019

AbstractAn existence result for a class of mean field games of controls is provided. In the considered model, the cost functional to be minimized by each agent involves a price depending at a given time on the controls of all agents and a congestion term. The existence of a classical solution is demonstrated with the Leray–Schauder theorem; the proof relies in particular on a priori bounds for the solution, which are obtained with the help of a potential formulation of the problem.
Quality Improvement of Damage Control Laparotomy: Impact of the Establishment of a Single Korean Regional Trauma Center
Authors: Kang Wu Seong , Jo Young Goun , Park Yun Chul 
Published: July 2019

AbstractBackgroundDamage control laparotomy (DCL) is a lifesaving technique to minimize the lethal triad of coagulopathy, hypothermia, and acidosis. The government has nominated and supported our center as one of the regional trauma centers of South Korea since 2014. This study aimed to investigate the improving outcomes of patients undergoing DCL before and after the establishment of the trauma center.MethodThe period from January 2011 to December 2017 was divided into pre‐trauma center (pre‐TC) (2011–2013) and trauma center (TC) (2014–2017) periods. Multivariable logistic regression was performed to identify the risk factors and risk‐adjusted cumulative sum (RA‐CUSUM), and graphs were used to monitor the change in mortality.ResultOf the 485 patients who underwent trauma laparotomy, DCL was performed for 119 patients (24.5%). The operation time (99 vs. 80 min, p = 0.022), time from admission to operation (125 vs. 112 min, p = 0.010), time from admission to first treatment (119 vs. 99 min, p = 0.004), and time from admission to first transfusion (70 vs. 52 min, p = 0.009) were significantly shortened in the TC period. The ratio of plasma to packed red blood cells in massive transfusions (≥PRBCs 10 units within the first 24 h) was significantly increased in the TC period (0.56 vs. 0.72, p = 0.004). RA‐CUSUM curves revealed that the risk‐adjusted 30‐day mortality improved and then plateaued in the TC period.ConclusionAfter the implementation of a trauma center, more prompt intervention and damage control resuscitation could be achieved. Moreover, risk‐adjusted mortality of DCL was improved.
Comparison of Topical, Systemic, and Combined Therapy with Steroids on Idiopathic Granulomatous Mastitis: A Prospective Randomized Study
Authors: Çetin Kenan , Sıkar Hasan E. , Göret Nuri E. , Rona Günay , Barışık Nagehan Ö. , Küçük Hasan F. , Gulluoglu Bahadır M. 
Published: July 2019

AbstractBackgroundIdiopathic granulomatous mastitis (IGM) is a benign disorder of the breast, for which the optimal treatment modality remains missing.MethodsA total of 124 patients with a histopathologically proven diagnosis of IGM were enrolled in a prospective, randomized parallel arm study. Patients were treated with topical steroids in Group T (n: 42), systemic steroids (0.8 mg/kg/day peroral) in Group S (n: 42), and combined steroids (0.4 mg/kg/day peroral + topical) in Group C (n: 40). Compliance with the therapy, response to the therapy, the duration of therapy, side effects and the recurrence rates were compared.ResultsSixteen patients did not comply with the treatment, and the highest ratio of compliance with therapy was seen in Group T (p < 0.05). Complete clinical regression (CCR) was observed in 90 (83.3%) patients. Response to the treatment (RT) was evaluated radiologically and observed in 89.8% of the patients. There was no statistically significant difference between groups regarding CCR, RT and the recurrence rate. The longest duration of therapy was observed in Group T (22 ± 9.1‐week), whereas the shortest was observed in Group S (11.7 ± 5.5‐week) (p < 0.001). The systemic side effects were significantly lower in Group T in comparison with Groups S and C (2.4% vs. 38.2% and 30.3%, respectively) (p < 0.001).ConclusionsThe efficiency of the treatment was similar for all groups, both clinically and radiologically. Although the duration of therapy was longer in Group T, the lack of systemic side effects increased the compliance of the patients with the therapy. Therefore, topical steroids would be among first‐line treatment options of IGM.
Combinatorial expression of different β-carotene hydroxylases and ketolases in Escherichia coli for increased astaxanthin production
Authors: Wu Yuanqing , Yan Panpan , Liu Xuewei , Wang Zhiwen , Tang Ya-Jie , Chen Tao , Zhao Xueming 
Published: July 2019

Abstract
In natural produced bacteria, β-carotene hydroxylase (CrtZ) and β-carotene ketolase (CrtW) convert β-carotene into astaxanthin. To increase astaxanthin production in heterologous strain, simple and effective strategies based on the co-expression of CrtZ and CrtW were applied in E. coli. First, nine artificial operons containing crtZ and crtW genes from different sources were constructed and, respectively, introduced into E. coli ZF237T, a β-carotene producing host. Among the nine resulting strains, five accumulated detectable amounts of astaxanthin ranging from 0.49 to 8.07 mg/L. Subsequently, the protein fusion CrtZ to CrtW using optimized peptide linkers further increased the astaxanthin production. Strains expressing fusion proteins with CrtZ rather than CrtW attached to the N-terminus accumulated much more astaxanthin. The astaxanthin production of the best strain ZF237T/CrtZAs-(GS)1-WBs was 127.6% and 40.2% higher than that of strains ZF237T/crtZ As W Bs and ZF237T/crtZ Bs W Ps, respectively. The strategies depicted here also will be useful for the heterologous production of other natural products.
Soy Isoflavone Improved Female Sexual Dysfunction of Mice Via Endothelial Nitric Oxide Synthase Pathway
Authors: Zhang Jing , Zhu Yuan , Pan Lianjun , Xia Haiping , Ma Jiehua , Zhang Aixia 
Published: July 2019

Abstract

Introduction
Female sexual dysfunction (FSD) is a common endocrine disease that impairs the quality of life for many women. The existing therapy strategies still have many disadvantages. It is necessary to explore new pharmacologic treatments that are effective and safe.

Aim
The aim of this study was to explore the effects of soy isoflavone (SI) on FSD in mice and the underlying mechanisms.

Methods and Main Outcome Measures
Laser Doppler flowmetry was used to determine vaginal blood flow. Serum hormone levels and histologic changes of the vagina were analyzed by enzyme-linked immunosorbent assay (ELISA) and by hematoxylin and eosin (H&E) and Masson’s trichome staining. The mRNA and protein expression of endothelial nitric oxide synthase (eNOS) was then evaluated by quantitative real-time polymerase chain reaction and western blot assays.

Results
Vaginal blood flow was found to be remarkably lower in adult mice, and SI was shown to increase vaginal blood flow in a dose-dependent manner (P &lt; .05). The results of ELISA and H&E and Masson’s trichome staining suggest that SI had a positive effect on FSD, as evidenced by the levels of hormones in serum and histologic changes of the vagina, which changed consistently. In addition, the level of eNOS was positively correlated with the concentration of SI, and eNOS inhibitor was able to reverse the improvement in sexual function induced by SI.

Conclusion
Our study demonstrated that SI could improve sexual function by upregulating the eNOS pathway. Therefore, SI might serve as a promising candidate for the treatment of sexual dysfunction.
Shear stress-driven flow: the state space of near-wall turbulence as
Authors: Doohan Patrick , Willis Ashley P. , Hwang Yongyun 
Published: July 2019

An inner-scaled, shear stress-driven flow is considered as a model of independent near-wall turbulence as the friction Reynolds number $Re_{\unicode[STIX]{x1D70F}}\rightarrow \infty$. In this limit, the model is applicable to the near-wall region and the lower part of the logarithmic layer of various parallel shear flows, including turbulent Couette flow, Poiseuille flow and Hagen–Poiseuille flow. The model is validated against damped Couette flow and there is excellent agreement between the velocity statistics and spectra for the wall-normal height $y^{+}<40$. A near-wall flow domain of similar size to the minimal unit is analysed from a dynamical systems perspective. The edge and fifteen invariant solutions are computed, the first discovered for this flow configuration. Through continuation in the spanwise width $L_{z}^{+}$, the bifurcation behaviour of the solutions over the domain size is investigated. The physical properties of the solutions are explored through phase portraits, including the energy input and dissipation plane, and streak, roll and wave energy space. Finally, a Reynolds number is defined in outer units and the high-$Re$ asymptotic behaviour of the equilibria is studied. Three lower branch solutions are found to scale consistently with vortex–wave interaction (VWI) theory, with wave forcing localising around the critical layer.
Deformation partitioning in mountain belts: insights from analogue modelling experiments and the Taiwan collisional orogen
Authors: Malavieille Jacques , Dominguez Stephane , Lu Chia-Yu , Chen Chih-Tung , Konstantinovskaya Elena 
Published: July 2019

AbstractMany orogens on the planet result from plate convergence involving subduction of a continental margin. The lithosphere is strongly deformed during mountain building involving subduction of a plate composed generally of accreted continental margin units and some fragments of downgoing oceanic crust and mantle. A complex deformation involving strong partitioning of deformation modes and kinematics produces crustal shortening, accompanied by crustal thickening. Partitioning depends on three main factors: (1) rheologic layering of the lithosphere; (2) interaction between tectonics and surface processes; (3) subduction kinematics and 3D geometry of continental margins (oblique convergence, shape of indenters). Here we present an original view and discussion on the impact of deformation partitioning on the structure and evolution of orogens by examining the Taiwan mountain belt as a case study. Major unsolved questions are addressed through geological observations from the Taiwan orogen and insights from analogue models integrating surface processes. Some of these questions include: What is the role played by décollements or weak zones in crustal deformation and what is the impact of structural heterogeneities inherited from the early extensional history of a rifted passive continental margin? What is the relationship between deep underplating, induced uplift and flow of crustal material during erosion (finite strain evolution during wedge growth)? Are syn-convergent normal faults an effect of deformation partitioning and erosion? What is the role of strain partitioning on the location of major seismogenic faults in active mountain belts? What can be learned about the long-term and the present-day evolution of Taiwan?
The effect of child death on birth spacing in Nigeria
Authors: Ewemade Jude , Akinyemi Joshua , DeWet Nicole 
Published: July 2019

AbstractStudies have focused on the effect of short birth spacing on childhood mortality, yet very little attention has been paid to the possibility of an inverse relationship such that child mortality might also positively or negatively affect birth spacing. In Nigeria, where both fertility and child mortality are high, this inverse relationship is a possible reason for the country’s high fertility. The objective of this study was to examine the effect of child death on time to birth of the next child. Data were drawn from the 2013 Nigerian Demographic Health Survey. The study sample comprised 188,986 live births born to women aged 15–49 years within the five years preceding the survey. A multivariate Cox proportional hazard regression model was fitted to the data, and hazard ratios with 95% confidence intervals calculated. More than half of the mothers (68%) already had a next birth by 36 months after the death of the index child. Controlling for other covariates, the Cox regression model showed that the likelihood of next birth was higher when the index child had died compared with when the index child survived (HR: 2.21; CI: 2.03–2.41). Sub-group analysis by geo-political regions in Nigeria showed that in all regions there was a higher likelihood of having a next birth following the death of a preceding child. Death of the index child was found to be a major factor that shortens the length of birth intervals in Nigeria. It is therefore important that the Government of Nigeria intensifies efforts aimed at reducing infant mortality and encouraging adequate birth spacing.