bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maximal violation of Bell inequalities under local filtering
Authors: Li Ming , Qin Huihui , Wang Jing , Fei Shao-Ming , Sun Chang-Pu 
Published: April 2017

AbstractWe investigate the behavior of the maximal violations of the CHSH inequality and Vèrtesi’s inequality under the local filtering operations. An analytical method has been presented for general two-qubit systems to compute the maximal violation of the CHSH inequality and the lower bound of the maximal violation of Vértesi’s inequality over the local filtering operations. We show by examples that there exist quantum states whose non-locality can be revealed after local filtering operation by the Vértesi’s inequality instead of the CHSH inequality.
Multiple p-n junction subwavelength gratings for transmission-mode electro-optic modulators
Authors: Lee Ki Young , Yoon Jae Woong , Song Seok Ho , Magnusson Robert 
Published: April 2017

AbstractWe propose a free-space electro-optic transmission modulator based on multiple p-n-junction semiconductor subwavelength gratings. The proposed device operates with a high-Q guided-mode resonance undergoing electro-optic resonance shift due to direct electrical control. Using rigorous electrical and optical modeling methods, we theoretically demonstrate a modulation depth of 84%, on-state efficiency 85%, and on-off extinction ratio of 19 dB at 1,550 nm wavelength under electrical control signals within a favorably low bias voltage range from −4 V to +1 V. This functionality operates in the transmission mode and sustainable in the high-speed operation regime up to a 10-GHz-scale modulation bandwidth in principle. The theoretical performance prediction is remarkably advantageous over plasmonic tunable metasurfaces in the power-efficiency and absolute modulation-depth aspects. Therefore, further experimental study is of great interest for creating practical-level metasurface components in various application areas.
A New Approach to Evaluating Aberrant DNA Methylation Profiles in Hepatocellular Carcinoma as Potential Biomarkers
Authors: Yang Yuan , Zhao Linghao , Huang Bo , Hou Guojun , Zhou Beibei , Qian Jin , Yuan Shengxian , Xiao Huasheng , Li Minghui , Zhou Weiping 
Published: April 2017

AbstractHypermethylation of CpG islands in the promoter region of tumor suppressor genes (TSGs) and their subsequent silencing is thought to be one of the main mechanisms of carcinogenesis. MBD2b enrichment coupled with a NimbleGen array was applied to examine the genome-wide CpG island methylation profile of hepatocellular carcinoma (HCC). Hypermethylated DNA of 58 pairs of HCC and adjacent tissue samples was enriched and hybridized in the same array. Aberrant hypermethylated peaks of HCC and adjacent tissues were screened and annotated after data processing using NimbleScan2.5 and our newly developed Weighting and Scoring (WAS) method, respectively. Validation using bisulfite sequencing of randomly selected ANKRD45, APC, CDX1, HOXD3, PTGER and TUBB6 genes demonstrated significant hypermethylation modification in HCC samples, consistent with the array data.
Chronic social defeat reduces myelination in the mouse medial prefrontal cortex
Authors: Lehmann Michael L. , Weigel Thaddeus K. , Elkahloun Abdel G. , Herkenham Miles 
Published: April 2017

AbstractThe medial prefrontal cortex (mPFC) plays a key role in top-down control of the brain’s stress axis, and its structure and function are particularly vulnerable to stress effects, which can lead to depression in humans and depressive-like states in animals. We tested whether chronic social defeat produces structural alterations in the mPFC in mice. We first performed a microarray analysis of mPFC gene expression changes induced by defeat, and biological pathway analysis revealed a dominant pattern of down-regulation of myelin-associated genes. Indeed, 69% of the most significantly down-regulated genes were myelin-related. The down regulation was confirmed by in situ hybridization histochemistry for two strongly down-regulated genes, myelin oligodendrocyte glycoprotein (Mog) and ermin (Ermn), and by immunohistochemistry for myelin basic protein. To test for stress-induced changes in myelin integrity, aurophosphate (Black Gold) myelin staining was performed on mPFC sections. Quantitative stereologic analysis showed reduced myelinated fiber length and density. Behavioral analysis confirmed that the 14-day social defeat sessions resulted in induction of depressive-like states measured in social interaction and light/dark tests. The combined data suggest that chronic social defeat induces molecular changes that reduce myelination of the prefrontal cortex, which may be an underlying basis for stress-induced depressive states.
Excitability in the p53 network mediates robust signaling with tunable activation thresholds in single cells
Authors: Mönke Gregor , Cristiano Elena , Finzel Ana , Friedrich Dhana , Herzel Hanspeter , Falcke Martin , Loewer Alexander 
Published: April 2017

AbstractCellular signaling systems precisely transmit information in the presence of molecular noise while retaining flexibility to accommodate the needs of individual cells. To understand design principles underlying such versatile signaling, we analyzed the response of the tumor suppressor p53 to varying levels of DNA damage in hundreds of individual cells and observed a switch between distinct signaling modes characterized by isolated pulses and sustained oscillations of p53 accumulation. Guided by dynamic systems theory we show that this requires an excitable network structure comprising positive feedback and provide experimental evidence for its molecular identity. The resulting data-driven model reproduced all features of measured signaling responses and is sufficient to explain their heterogeneity in individual cells. We present evidence that heterogeneity in the levels of the feedback regulator Wip1 sets cell-specific thresholds for p53 activation, providing means to modulate its response through interacting signaling pathways. Our results demonstrate how excitable signaling networks can provide high specificity, sensitivity and robustness while retaining unique possibilities to adjust their function to the physiology of individual cells.
Accessing Forbidden Glass Regimes through High-Pressure Sub-Tg Annealing
Authors: Svenson Mouritz N. , Mauro John C. , Rzoska Sylwester J. , Bockowski Michal , Smedskjaer Morten M. 
Published: April 2017

AbstractDensity and hardness of glasses are known to increase upon both compression at the glass transition temperature (Tg) and ambient pressure sub-Tg annealing. However, a serial combination of the two methods does not result in higher density and hardness, since the effect of compression is countered by subsequent annealing and vice versa. In this study, we circumvent this by introducing a novel treatment protocol that enables the preparation of high-density, high-hardness bulk aluminosilicate glasses. This is done by first compressing a sodium-magnesium aluminosilicate glass at 1 GPa at Tg, followed by sub-Tg annealing in-situ at 1 GPa. Through density, hardness, and heat capacity measurements, we demonstrate that the effects of hot compression and sub-Tg annealing can be combined to access a “forbidden glass” regime that is inaccessible through thermal history or pressure history variation alone. We also study the relaxation behavior of the densified samples during subsequent ambient pressure sub-Tg annealing. Density and hardness are found to relax and approach their ambient condition values upon annealing, but the difference in relaxation time of density and hardness, which is usually observed for hot compressed glasses, vanishes for samples previously subjected to high-pressure sub-Tg annealing. This confirms the unique configurational state of these glasses.
Interactive Book Reading to Accelerate Word Learning by Kindergarten Children With Specific Language Impairment: Identifying Adequate Progress and Successful Learning Patterns
Authors: Storkel Holly L. , Komesidou Rouzana , Fleming Kandace K. , Romine Rebecca Swinburne 
Published: April 2017

Purpose
The goal of this study was to provide guidance to clinicians on early benchmarks of successful word learning in an interactive book reading treatment and to examine how encoding and memory evolution during treatment contribute to word learning outcomes by kindergarten children with specific language impairment (SLI).

Method
Twenty-seven kindergarten children with SLI participated in a preliminary clinical trial using interactive book reading to teach 30 new words. Word learning was assessed at 4 points during treatment through a picture naming test.

Results
The results indicate that the following performance during treatment was cause for concern, indicating a need to modify the treatment: naming 0–1 treated words correctly at Naming Test 1; naming 0–2 treated words correctly at Naming Test 2; naming 0–3 treated words correctly at Naming Test 3. In addition, the results showed that encoding was the primary limiting factor in word learning, but memory evolution also contributed (albeit to a lesser degree) to word learning success.

Conclusion
Case illustrations demonstrate how a clinician's understanding of a child's word learning strengths and weaknesses develop over the course of treatment, substantiating the importance of regular data collection and clinical decision-making to ensure the best possible outcomes for each individual child.
Step-by-Step Multifunctionalization of Isoxazoles Based On SEAr Reactions and C–H Direct Arylations
Authors: Fuse Shinichiro , Morita Taiki , Nakamura Hiroyuki 
Published: April 2017

Functionalized isoxazoles are important as pharmaceuticals and agrochemicals. Generally, electrophilic aromatic substitution or generation of carbanions/electrophilic trapping approach is used to introduce functional groups into unsubstituted heteroaromatics. However, these approaches have not been simple to apply to unsubstituted isoxazoles due to their poor nucleophilicity and instability under basic conditions. Recently several approaches have been reported to overcome these problems. This review summarizes the functionalization of isoxazoles, including SEAr reactions and C–H direct arylations, towards the step-by-step multifunctionalization of isoxazoles.1	Introduction2	SEAr Reaction of Isoxazoles3	Preparation of Isoxazolyl Anions and Their Use for the Synthesis of Functionalized Isoxazoles4	Other C–C and C–N Bond Formations of Isoxazoles5	Transition-Metal-Catalyzed C–H Direct Functionalization of Isoxazoles6	Step-by-Step Multifunctionalization of Isoxazoles7	Summary and Outlook
Beyond Hammer: the first run market and the prestige horror film in the early 1960s
Authors: Jancovich Mark 
Published: April 2017

AbstractAlthough 1960s horror was supposedly dominated by Hammer, Heffernan has pointed out that Hammer (and AIP) were both trying hard to break out of the low bracket market and into the middle bracket. This article focuses on the prestige horror films of the early 1960s, and not only looks at them as a coherent production trend (rather than as a series of individual or anomalous films) but in the process, offers a new context for an understanding of 1960s horror; that is, it demonstrates that the 1960s horror film was not simply low budget cinema but that it operated in almost all the key American film markets—the first run cinema, the low budget and the art cinema. Consequently, we cannot only see that Hammer and AIP, rather than simply the dominant form, were actually defined by their attempt to steer a course between different sectors of the market (they were from the low budget end but trying to move into the first run market, whilst also drawing on some of the distinction associated with the art cinema); but also that the prestige horror films had their own very specific problems to negotiate. These negotiations would also lay the foundations for the industry-wide transformations of the late 1960s. This article is published as part of a collection on gothic and horror.
Structural and functional innovations in the real-time evolution of new (βα)
8
barrel enzymes
Authors: Newton Matilda S. , Guo Xiaohu , Söderholm Annika , Näsvall Joakim , Lundström Patrik , Andersson Dan I. , Selmer Maria , Patrick Wayne M. 
Published: April 2017

Significance
New proteins can evolve by duplication of the genes that encode them, followed by specialization of the different copies. However, how the growth rate of an organism is coupled to the changes in a protein’s structure and function occurring during this process is not known. Here we show at atomic resolution how selection for the growth of a bacterium led to the evolution of HisA proteins with either a new function or two functions (old and new). We found that a distinct protein conformation is responsible for each function, and that a better enzyme leads to faster growth only up to a certain threshold. This study provides insight into how evolution works, from atomic to whole-organism levels.
Relocation and Recolonization of Coho Salmon in Two Tributaries to the Elwha River: Implications for Management and Monitoring
Authors: Liermann Martin , Pess George , McHenry Mike , McMillan John , Elofson Mel , Bennett Todd , Moses Raymond 
Published: April 2017

AbstractIn 2012 the lower of two Elwha River dams was breached, restoring access of anadromous salmonids to the middle Elwha River (between the two dams), including two distinct tributaries, Indian Creek and Little River. While comparable in size, Indian Creek is considerably less steep than Little River (mean slope of 1.0% versus 3.5%, respectively) and has a warmer stream temperature regime due to its source, Lake Sutherland. During and after breaching, Coho Salmon Oncorhynchus kisutch were relocated to these tributaries from lower Elwha River hatcheries (below the dams) to determine if individuals from a hatchery‐dominated population would successfully spawn and seed the systems with juveniles and to assess differences in recolonization between the streams. Transplantation led to immediate spawning, which resulted in levels of smolt out‐migrants per stream kilometer comparable with other established Coho Salmon populations in the Pacific Northwest. During the first 2 years of the relocation, redd densities in the two systems were similar but Indian Creek produced four to five times as many smolts per kilometer as Little River. In addition, fry out‐migration occurred 2 to 4 weeks earlier in Indian Creek, as predicted by the warmer incubation temperatures. In the first years of the study, there was little evidence of natural colonization of the two tributaries by adults. However, in 2016 over half of the observed adults returning to the two tributaries were not transplanted, suggesting that the progeny from the transplanted fish were returning to their natal waters. This work demonstrates that transplanting hatchery‐dominated Coho Salmon adults into newly available habitat can result in immediate freshwater production that is comparable to other systems and that density and timing of juvenile out‐migrants can differ dramatically based on the seeded habitat.Received December 9, 2016; accepted March 30, 2017 Published online July 28, 2017
Incorporating interaction networks into the determination of functionally related hit genes in genomic experiments with Markov random fields
Authors: Robinson Sean , Nevalainen Jaakko , Pinna Guillaume , Campalans Anna , Radicella J Pablo , Guyon Laurent 
Published: April 2017

Abstract

Motivation
Incorporating gene interaction data into the identification of ‘hit’ genes in genomic experiments is a well-established approach leveraging the ‘guilt by association’ assumption to obtain a network based hit list of functionally related genes. We aim to develop a method to allow for multivariate gene scores and multiple hit labels in order to extend the analysis of genomic screening data within such an approach.

Results
We propose a Markov random field-based method to achieve our aim and show that the particular advantages of our method compared with those currently used lead to new insights in previously analysed data as well as for our own motivating data. Our method additionally achieves the best performance in an independent simulation experiment. The real data applications we consider comprise of a survival analysis and differential expression experiment and a cell-based RNA interference functional screen.

Availability and implementation
We provide all of the data and code related to the results in the paper.

Supplementary information
Supplementary data are available at Bioinformatics online.
Age of Migration Differentials in Life Expectancy With Cognitive Impairment: 20-Year Findings From the Hispanic-EPESE
Authors: Garcia Marc A , Saenz Joseph L , Downer Brian , Chiu Chi-Tsun , Rote Sunshine , Wong Rebeca 
Published: April 2017

Abstract

Background and Objectives
To examine differences in life expectancy with cognitive impairment among older Mexican adults according to nativity (U.S.-born/foreign-born) and among immigrants, age of migration to the United States.

Research Design and Methods
This study employs 20 years of data from the Hispanic Established Populations for the Epidemiologic Study of the Elderly to estimate the proportion of life spent cognitively healthy and cognitively impaired prior to death among older Mexican adults residing in the southwestern United States. We combine age-specific mortality rates with age-specific prevalence of cognitive impairment, defined as a Mini-Mental Status Exam score of less than 21 points to calculate Sullivan-based life table models with and without cognitive impairment in later life.

Results
Foreign-born Mexican immigrants have longer total life expectancy and comparable cognitive healthy life expectancy regardless of gender compared to U.S.-born Mexican-Americans. However, the foreign-born spend a greater number of years after age 65 with cognitive impairment relative to their U.S.-born counterparts. Furthermore, we document an advantage in life expectancy with cognitive impairment and proportion of years after age 65 cognitively healthy among mid-life immigrant men and women relative to early- and late-life migrants.

Discussion and Implications
The relationship between nativity, age of migration, and life expectancy with cognitive impairment means that the foreign-born are in more need of support and time-intensive care in late life. This issue merits special attention to develop appropriate and targeted screening efforts that reduce cognitive decline for diverse subgroups of older Mexican-origin adults as they age.
Hybrid de novo genome assembly of the Chinese herbal fleabane Erigeron breviscapus
Authors: Yang Jing , Zhang Guanghui , Zhang Jing , Liu Hui , Chen Wei , Wang Xiao , Li Yahe , Dong Yang , Yang Shengchao 
Published: April 2017

Abstract
Background: The plants in the Erigeron genus of the Compositae (Asteraceae) family are commonly called fleabanes, possibly due to the belief that certain chemicals in these plants repel fleas. In the traditional Chinese medicine, Erigeron breviscapus, which is native to China, was widely used in the treatment of cerebrovascular disease. A handful of bioactive compounds, including scutellarin, 3,5-dicaffeoylquinic acid, and 3,4-dicaffeoylquinic acid, have been isolated from the plant. With the purpose of finding novel medicinal compounds and understanding their biosynthetic pathways, we propose to sequence the genome of E. breviscapus. Findings: We assembled the highly heterozygous E. breviscapus genome using a combination of PacBio single-molecular real-time sequencing and next-generation sequencing methods on the Illumina HiSeq platform. The final draft genome is approximately 1.2 Gb, with contig and scaffold N50 sizes of 18.8 kb and 31.5 kb, respectively. Further analyses predicted 37 504 protein-coding genes in the E. breviscapus genome and 8172 shared gene families among Compositae species. Conclusions: The E. breviscapus genome provides a valuable resource for the investigation of novel bioactive compounds in this Chinese herb.
An Unanticipated Complication of Atopic Dermatitis
Authors: MacGillivray Megan E. , Fiorillo Loretta 
Published: April 2017

Abstract
An infant with a history of atopic dermatitis presented to the emergency department on 5 occasions with flulike symptoms. Eventually, this child presented with signs of infection and increased intracranial pressure: fever, bulging anterior fontanel, and leukocytosis. A computed tomography scan identified a large frontal lobe brain abscess. The abscess was surgically drained; culture was positive for Staphylococcus aureus. The initial source of the infected brain abscess was explored. Ultimately, it was thought to be secondary to impetiginized atopic dermatitis, an unusual but serious consequence of a common skin condition.
The Evaluation of Trauma Care
Authors: Bal Alkan , Cooper Michael , Lee Amanda , Anil Murat , Hennes Halim 
Published: April 2017

Objective
The purpose of the study is to compare the outcomes of pediatric trauma patients with motor vehicle crashes (MVCs) and motor vehicle versus pedestrian crashes (MPCs) at a level 1 pediatric trauma center in the United States and a pediatric trauma center in Turkey.

Methods
The medical records of all pediatric MVC and MPC subjects presenting to the emergency departments (EDs) of a level 3 hospital in Turkey (Izmir Tepecik Training and Research Hospital [ITTRH]) and a level 1 pediatric trauma center in the United States (Children's Medical Center Dallas [CMCD]) over a 1-year period were reviewed. Data that were collected include patient demographics, prehospital report (mechanism of injury, mode of transportation), injury severity score (ISS), abbreviated injury scale score, Glasgow Coma Scale score, ED length of stay, ED interventions, ED and hospital disposition, and mortality. Patients with moderate (ISS, 5–15) and severe (ISS, >15) trauma scores were included in the study.

Results
One hundred six patient charts from the ITTRH and 125 patient charts from the CMCD with moderate and severe ISS due to MVCs and MPCs were reviewed. Most of the patients were pedestrians (86%) in the ITTRH group and passengers (60%) in the CMCD group. The percentage of patients transferred by ambulance (ground or air) to the CMCD and the ITTRH was 97.9% and 85%, respectively. Fifteen percent of ITTRH patients and 2.1% of CMCD patients arrived by private vehicle. Emergency department arrival ISS and Glasgow Coma Scale were similar between the 2 hospitals (P > 0.05). The overall mortality rate in the study population was 8.8% (11/125) at the CMCD and 4.7% (5/106) at the ITTRH. (P = 0.223). Blood product utilization was significantly higher in the CMCD group compared with the ITTRH group (P = 0.005). The use of hypertonic saline/mannitol/hyperventilation in patients with significant head trauma and increased intracranial pressure was higher in the ITTRH group (P = 0.000).

Conclusions
This is the first study that compared pediatric trauma care and outcome at a level 1 pediatric trauma center in the United States and a pediatric hospital in Turkey. Our findings highlight the opportunities to improve pediatric trauma care in Turkey. Specifically, there is a need for national trauma registries, enhanced trauma education, and standardized trauma patient care protocols. In addition, efforts should be directed toward improving prehospital care through better integration within the health care system and physician participation in educating prehospital providers. Data and organized trauma care will be instrumental in system-wide improvement and developing appropriate injury-prevention strategies.