bluuebunny/crossref_metadata_2025_split huggingface dataset:
An ontology-driven, case-based clinical decision support model for removable partial denture design
Authors: Chen Qingxiao , Wu Ji , Li Shusen , Lyu Peijun , Wang Yong , Li Miao 
Published: June 2016

AbstractWe present the initial work toward developing a clinical decision support model for specific design of removable partial dentures (RPDs) in dentistry. We developed an ontological paradigm to represent knowledge of a patient’s oral conditions and denture component parts. During the case-based reasoning process, a cosine similarity algorithm was applied to calculate similarity values between input patients and standard ontology cases. A group of designs from the most similar cases were output as the final results. To evaluate this model, the output designs of RPDs for 104 randomly selected patients were compared with those selected by professionals. An area under the curve of the receiver operating characteristic (AUC-ROC) was created by plotting true-positive rates against the false-positive rate at various threshold settings. The precision at position 5 of the retrieved cases was 0.67 and at the top of the curve it was 0.96, both of which are very high. The mean average of precision (MAP) was 0.61 and the normalized discounted cumulative gain (NDCG) was 0.74 both of which confirmed the efficient performance of our model. All the metrics demonstrated the efficiency of our model. This methodology merits further research development to match clinical applications for designing RPDs. This paper is organized as follows. After the introduction and description of the basis for the paper, the evaluation and results are presented in Section 2. Section 3 provides a discussion of the methodology and results. Section 4 describes the details of the ontology, similarity algorithm, and application.
Intracellular ROS mediates gas plasma-facilitated cellular transfection in 2D and 3D cultures
Authors: Xu Dehui , Wang Biqing , Xu Yujing , Chen Zeyu , Cui Qinjie , Yang Yanjie , Chen Hailan , Kong Michael G. 
Published: June 2016

AbstractThis study reports the potential of cold atmospheric plasma (CAP) as a versatile tool for delivering oligonucleotides into mammalian cells. Compared to lipofection and electroporation methods, plasma transfection showed a better uptake efficiency and less cell death in the transfection of oligonucleotides. We demonstrated that the level of extracellular aqueous reactive oxygen species (ROS) produced by gas plasma is correlated with the uptake efficiency and that this is achieved through an increase of intracellular ROS levels and the resulting increase in cell membrane permeability. This finding was supported by the use of ROS scavengers, which reduced CAP-based uptake efficiency. In addition, we found that cold atmospheric plasma could transfer oligonucleotides such as siRNA and miRNA into cells even in 3D cultures, thus suggesting the potential for unique applications of CAP beyond those provided by standard transfection techniques. Together, our results suggest that cold plasma might provide an efficient technique for the delivery of siRNA and miRNA in 2D and 3D culture models.
A comparative genomic analysis of targets of Hox protein Ultrabithorax amongst distant insect species
Authors: Prasad Naveen , Tarikere Shreeharsha , Khanale Dhanashree , Habib Farhat , Shashidhara L. S. 
Published: June 2016

AbstractIn the fruitfly Drosophila melanogaster, the differential development of wing and haltere is dependent on the function of the Hox protein Ultrabithorax (Ubx). Here we compare Ubx-mediated regulation of wing patterning genes between the honeybee, Apis mellifera, the silkmoth, Bombyx mori and Drosophila. Orthologues of Ubx are expressed in the third thoracic segment of Apis and Bombyx, although they make functional hindwings. When over-expressed in transgenic Drosophila, Ubx derived from Apis or Bombyx could suppress wing development, suggesting evolutionary changes at the level of co-factors and/or targets of Ubx. To gain further insights into such events, we identified direct targets of Ubx from Apis and Bombyx by ChIP-seq and compared them with those of Drosophila. While majority of the putative targets of Ubx are species-specific, a considerable number of wing-patterning genes are retained, over the past 300 millions years, as targets in all the three species. Interestingly, many of these are differentially expressed only between wing and haltere in Drosophila but not between forewing and hindwing in Apis or Bombyx. Detailed bioinformatics and experimental validation of enhancer sequences suggest that, perhaps along with other factors, changes in the cis-regulatory sequences of earlier targets contribute to diversity in Ubx function.
Virulence determinants associated with the Asian community-associated methicillin-resistant Staphylococcus aureus lineage ST59
Authors: Li Min , Dai Yingxin , Zhu Yuanjun , Fu Chih-Lung , Tan Vee Y. , Wang Yanan , Wang Xing , Hong Xufen , Liu Qian , Li Tianming , Qin Juanxiu , Ma Xiaowei , Fang Jingyuan , Otto Michael 
Published: June 2016

AbstractUnderstanding virulence is vital for the development of novel therapeutics to target infections with community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA), which cause an ongoing epidemic in the United States and are on a global rise. However, what defines virulence particularly of global CA-MRSA lineages is poorly understood. Threatening a vast population, the predominant Asian CA-MRSA lineage ST59 is of major epidemiological importance. However, there have been no molecular analyses using defined virulence gene deletion mutants in that lineage as of yet. Here, we compared virulence in skin, lung and blood infection models of ST59 CA-MRSA isolates with geographically matched hospital-associated MRSA isolates. We selected a representative ST59 CA-MRSA isolate based on toxin expression and virulence characteristics and produced isogenic gene deletion mutants of important CA-MRSA virulence determinants (α-toxin, PSM α, Agr) in that isolate for in-vitro and in-vivo analyses. Our results demonstrate strongly enhanced virulence of ST59 CA-MRSA over hospital-associated lineages, supporting the notion that enhanced virulence is characteristic for CA-MRSA. Furthermore, they show strong and significant contribution of Agr, α-toxin and PSMα to pathogenesis of ST59 CA-MRSA skin, lung and blood infection, emphasizing the value of drug development efforts targeted toward those virulence determinants.
60-GHz Millimeter-wave Over Fiber with Directly Modulated Dual-mode Laser Diode
Authors: Tsai Cheng-Ting , Lin Chi-Hsiang , Lin Chun-Ting , Chi Yu-Chieh , Lin Gong-Ru 
Published: June 2016

AbstractA directly modulated dual-mode laser diode (DMLD) with third-order intermodulation distortion (IMD3) suppression is proposed for a 60-GHz millimeter-wave over fiber (MMWoF) architecture, enabling new fiber-wireless communication access to cover 4-km single-mode-fiber (SMF) and 3-m wireless 16-QAM OFDM transmissions. By dual-mode injection-locking, the throughput degradation of the DMLD is mitigated with saturation effect to reduce its threshold, IMD3 power and relative intensity noise to 7.7 mA, −85 dBm and −110.4 dBc/Hz, respectively, providing huge spurious-free dynamic range of 85.8 dB/Hz2/3. This operation suppresses the noise floor of the DMLD carried QPSK-OFDM spectrum by 5 dB. The optical receiving power is optimized to restrict the power fading effect for improving the bit error rate to 1.9 × 10−3and the receiving power penalty to 1.1 dB. Such DMLD based hybrid architecture for 60-GHz MMW fiber-wireless access can directly cover the current optical and wireless networks for next-generation indoor and short-reach mobile communications.
Improved catalytic efficiency, thermophilicity, anti-salt and detergent tolerance of keratinase KerSMD by partially truncation of PPC domain
Authors: Fang Zhen , Zhang Juan , Du Guocheng , Chen Jian 
Published: June 2016

AbstractThe keratinase from Stenotrophomonas maltophilia (KerSMD) is known for its high activity and pH stability in keratin degradation. However, catalytic efficiency and detergent tolerability need to be improved in order to be used for industrial application. In this work, we obtained several keratinase variants with enhanced catalytic efficiency, thermophilicity and anti-salt and detergent tolerability by partially truncating the PPC domain of KerSMD. The variants all showed improved catalytic efficiency to synthetic substrate AAPF, with the V355 variant having the highest kcat /Km value of 143.6 s−1 mM−1. The truncation of keratinase had little effect on alkaline stability but obviously decreased collagenase activity, developing its potential application in leather treatment. The variants V380, V370 and V355 were thermophilic, with a 1.7-fold enhancement of keratinlytic activity at 60 °C when compared to the wild type. The entire truncation of PPC domain obtained the variant V355 with improved tolerance to alkalinity, salt, chaotropic agents and detergents. The V355 variant showed more than a 40% improvement in activity under 15% (w/v) NaCl or 4% (w/v) SDS solution, showing excellent stability under harsh washing and unhairing conditions. Our work investigated how protein engineering affects the function of PPC domain of KerSMD.
Volumetric (3D) bladder dose parameters are more reproducible than point (2D) dose parameters in vaginal vault high-dose-rate brachytherapy
Authors: Sapienza Lucas Gomes , Flosi Adriana , Aiza Antonio , de Assis Pellizzon Antonio Cassio , Chojniak Rubens , Baiocchi Glauco 
Published: June 2016

AbstractThere is no consensus on the use of computed tomography in vaginal cuff brachytherapy (VCB) planning. The purpose of this study was to prospectively determine the reproducibility of point bladder dose parameters (DICRU and maximum dose), compared with volumetric-based parameters. Twenty-two patients who were treated with high-dose-rate (HDR) VCB underwent simulation by computed tomography (CT-scan) with a Foley catheter at standard tension (position A) and extra tension (position B). CT-scan determined the bladder ICRU dose point in both positions and compared the displacement and recorded dose. Volumetric parameters (D0.1cc, D1.0cc, D2.0cc, D4.0cc and D50%) and point dose parameters were compared. The average spatial shift in ICRU dose point in the vertical, longitudinal and lateral directions was 2.91 mm (range: 0.10–9.00), 12.04 mm (range: 4.50–24.50) and 2.65 mm (range: 0.60–8.80), respectively. The DICRU ratio for positions A and B was 1.64 (p < 0.001). Moreover, a decrease in Dmax was observed (p = 0.016). Tension level of the urinary catheter did not affect the volumetric parameters. Our data suggest that point parameters (DICRU and Dmax) are not reproducible and are not the ideal choice for dose reporting.
Reactivation of Tert in the medial prefrontal cortex and hippocampus rescues aggression and depression of Tert−/− mice
Authors: Zhou Q-G , Wu H-Y , Zhou H , Liu M-Y , Lee H-W , Liu X , Devkota S , Ro E J , Zhu D-Y , Suh H 
Published: June 2016

AbstractThe role of telomerase reverse transcriptase (TERT) has been extensively investigated in the contexts of aging and cancer. Interestingly, Tert−/− mice exhibit additional but unexpected aggressive and depressive behaviors, implying the potential involvement of TERT function in mood control. Our conditional rescue experiments revealed that the depressive and aggressive behaviors of Tert−/− mice originate from Tert deficiency in two distinct brain structures. Reactivation of Tert in the hippocampus was sufficient to normalize the depressive but not the aggressive behaviors of Tert−/− mice. Conversely, re-expression of Tert in the medial prefrontal cortex (mPFC) reversed the aggressive but not the depressive behavior of Tert−/− mice. Mechanistically, decreased serotonergic signaling and increased nitric oxide (NO) transmission in the hippocampus transduced Tert deficiency into depression as evidenced by our observation that the infusion of a pharmacological agonist for serotonin receptor 1a (5-HTR1A) and a selective antagonist for neuronal NO synthase into the hippocampus successfully normalized the depressive behavior of Tert−/− mice. In addition, increased serotonergic transmission by the 5-HTR1A agonist in the mPFC was sufficient to rescue the aggressive behavior of Tert−/− mice. Thus, our studies revealed a novel function of TERT in the pathology of depression and aggression in a brain structure-specific manner, providing direct evidence for the contribution of TERT to emotional control.
Obesity and age-related alterations in the gene expression of zinc-transporter proteins in the human brain
Authors: Olesen R H , Hyde T M , Kleinman J E , Smidt K , Rungby J , Larsen A 
Published: June 2016

AbstractThe incidence of Alzheimer's disease (AD) is increasing. Major risk factors for AD are advancing age and diabetes. Lately, obesity has been associated with an increased risk of dementia. Obese and diabetic individuals are prone to decreased circulating levels of zinc, reducing the amount of zinc available for crucial intracellular processes. In the brain, zinc co-localizes with glutamate in synaptic vesicles, and modulates NMDA receptor activity. Intracellular zinc is involved in apoptosis and fluctuations in cytoplasmic Zn2+ affect modulation of intracellular signaling. The ZNT and ZIP proteins participate in intracellular zinc homeostasis. Altered expression of zinc-regulatory proteins has been described in AD patients. Using microarray data from human frontal cortex (BrainCloud), this study investigates expression of the SCLA30A (ZNT) and SCLA39A (ZIP) families of genes in a Caucasian and African-American sample of 145 neurologically and psychiatrically normal individuals. Expression of ZNT3 and ZNT4 were significantly reduced with increasing age, whereas expression of ZIP1, ZIP9 and ZIP13 were significantly increased. Increasing body mass index (BMI) correlated with a significant reduction in ZNT1 expression similar to what is seen in the early stages of AD. Increasing BMI also correlated with reduced expression of ZNT6. In conclusion, we found that the expression of genes that regulate intracellular zinc homeostasis in the human frontal cortex is altered with increasing age and affected by increasing BMI. With the increasing rates of obesity throughout the world, these findings warrant continuous scrutiny of the long-term consequences of obesity on brain function and the development of neurodegenerative diseases.
Carryover effects drive competitive dominance in spatially structured environments
Authors: Van Allen Benjamin G. , Rudolf Volker H. W. 
Published: June 2016

Significance
Communities do not exist in a vacuum; instead, they are connected to each other through dispersal of interacting species. As a result, understanding how changes to the quality of habitat patches affect communities across the whole landscape is critical in our human-dominated world and changing climate. When individuals disperse, they “carry” traits shaped by their natal environment to their destinations. Using replicated laboratory landscapes with two competing species, we show that these historic effects of natal habitats have dramatic influences on community structure at all spatial scales and multiple dispersal rates. Such historic effects are ubiquitous in nature, suggesting that changes to local habitat quality can have important effects on regional community structure.
Hierarchical structures of amorphous solids characterized by persistent homology
Authors: Hiraoka Yasuaki , Nakamura Takenobu , Hirata Akihiko , Escolar Emerson G. , Matsue Kaname , Nishiura Yasumasa 
Published: June 2016

Significance
Persistent homology is an emerging mathematical concept for characterizing shapes of data. In particular, it provides a tool called the persistence diagram that extracts multiscale topological features such as rings and cavities embedded in atomic configurations. This article presents a unified method using persistence diagrams for studying the geometry of atomic configurations in amorphous solids. The method highlights hierarchical structures that conventional techniques could not have treated appropriately.
OX40L blockade protects against inflammation-driven fibrosis
Authors: Elhai Muriel , Avouac Jérôme , Hoffmann-Vold Anna Maria , Ruzehaji Nadira , Amiar Olivia , Ruiz Barbara , Brahiti Hassina , Ponsoye Matthieu , Fréchet Maxime , Burgevin Anne , Pezet Sonia , Sadoine Jérémy , Guilbert Thomas , Nicco Carole , Akiba Hisaya , Heissmeyer Vigo , Subramaniam Arun , Resnick Robert , Molberg Øyvind , Kahan André , Chiocchia Gilles , Allanore Yannick 
Published: June 2016

SignificanceFibrosis is a leading cause of death in industrialized countries. Until now, there has been no effective therapy to prevent or counteract the fibrotic process. This article describes the effect of the blockade of a late costimulatory molecule to prevent inflammation-driven skin, lung, and vessel fibrosis and to induce regression of established dermal fibrosis in vivo in complementary murine models of systemic sclerosis, a prototypic autoimmune fibrotic disease. This article also reveals an unexpected role of this protein as a biomarker of worsening fibrosis that might help delineate the prognosis of patients in clinical practice more accurately.
Disentangling mechanisms involved in collagen pyridinoline cross-linking: The immunophilin FKBP65 is critical for dimerization of lysyl hydroxylase 2
Authors: Gjaltema Rutger A. F. , van der Stoel Miesje M. , Boersema Miriam , Bank Ruud A. 
Published: June 2016

SignificanceCollagens are structural extracellular matrix proteins that provide mechanical support to tissues. To gain stability, collagens can form pyridinoline cross-links via enzymatically formed intermediates initiated by lysyl hydroxylase (LH) 2. Individuals with mutations in the gene encoding LH2 share highly overlapping traits with individuals with mutations in the gene encoding the immunophilin FKBP65 that shows no LH activity. We found that FKBP65 is necessary for the dimerization of LH2, which is required for activity of LH2. Collagen cross-linking plays important roles in bone diseases as well as in such pathologies as cancer and fibrosis. Our study has elucidated a mechanism of how to interfere in a specific type of collagen cross-linking and can help advance the design of new treatments toward these pathologies.
Shock synthesis of quasicrystals with implications for their origin in asteroid collisions
Authors: Asimow Paul D. , Lin Chaney , Bindi Luca , Ma Chi , Tschauner Oliver , Hollister Lincoln S. , Steinhardt Paul J. 
Published: June 2016

SignificanceThe singular occurrence, to date, of natural quasicrystals requires an explanation both of the possibility and of the rarity of their formation outside of the laboratory. Successful synthesis by an experimental shock, with starting materials similar to the exotic intermetallic alloys in the Khatyrka meteorite, demonstrates a mechanism that is feasible in space but not in any natural setting on Earth. The previously unrecognized composition of the synthesized quasicrystal, the first, to our knowledge, to be created by shocking discrete bulk starting materials, demonstrates a method for discovery of previously unknown quasicrystal compositions.
Liquid drops attract or repel by the inverted Cheerios effect
Authors: Karpitschka Stefan , Pandey Anupam , Lubbers Luuk A. , Weijs Joost H. , Botto Lorenzo , Das Siddhartha , Andreotti Bruno , Snoeijer Jacco H. 
Published: June 2016

Significance
The Cheerios effect is the attraction of solid particles floating on liquids, mediated by surface tension forces. We demonstrate experimentally that a similar interaction can also occur for the inverse case, liquid particles on the surface of solids, provided that the solid is sufficiently soft. Remarkably, depending on the thickness of the solid layer, the interaction can be either purely attractive or become repulsive. A theoretical model, in excellent agreement with the experimental data, shows that the interaction requires both elasticity and capillarity. Interactions between objects on soft substrates could play an important role in phenomena of cell–cell interaction and cell adhesion to biological tissues, and be exploited to engineer soft smart surfaces for controlled drop coalescence and colloidal assembly.
Real-time transposable element activity in individual live cells
Authors: Kim Neil H. , Lee Gloria , Sherer Nicholas A. , Martini K. Michael , Goldenfeld Nigel , Kuhlman Thomas E. 
Published: June 2016

Significance
We have followed in real time how transposable elements, or “jumping genes,” move around in the genome of a living organism. Using a simple plasmid-borne transposable element, we have measured directly and precisely how frequently cells are affected by transposable elements and what factors contribute to their activity. We find the activity of this simple transposable element to be surprisingly rich, depending upon the host cell’s growth and environmental factors. Application of this system to more complex natural transposable elements will enable a quantitative understanding of these fundamental dynamical elements of all genomes, informing our understanding of genome plasticity and the mutations that can give rise to disease and drive evolution.
Chemical properties of lipids strongly affect the kinetics of the membrane-induced aggregation of α-synuclein
Authors: Galvagnion Céline , Brown James W. P. , Ouberai Myriam M. , Flagmeier Patrick , Vendruscolo Michele , Buell Alexander K. , Sparr Emma , Dobson Christopher M. 
Published: June 2016

Significance
Parkinson’s disease is the second most prevalent neurodegenerative disorder and is characterized by the presence in the brains of patients of proteinaceous deposits whose main component is α-synuclein. This protein interacts with membranes as part of its biological function, but this interaction also modulates its kinetics of aggregation. Here, we show that, despite the fact that α-synuclein binds to different types of membranes, it only forms amyloid fibrils in the presence of the most soluble lipids investigated here. This finding is of particular significance because it shows that modifications of the chemical properties of lipids, such as those associated with oxidation and ageing, could be a key determinant of the switch between functional and deleterious interactions between α-synuclein and membranes.
Achieving climate connectivity in a fragmented landscape
Authors: McGuire Jenny L. , Lawler Joshua J. , McRae Brad H. , Nuñez Tristan A. , Theobald David M. 
Published: June 2016

Significance
Many plants and animals will need to move large distances to track preferred climates, but fragmentation and barriers limit their movements. We asked to what degree and where species will be able to track suitable climates. We demonstrate that only 41% of US natural land area is currently connected enough to allow species to track preferred temperatures as the planet warms over the next 100 years. If corridors allowed movement between all natural areas, species living in 65% of natural area could track their current climates, allowing them to adjust to 2.7 °C more temperature change. The greatest benefits result from connecting low-lying natural areas, especially in the southeastern United States. Facilitating movement will be crucial for preventing biodiversity losses.