bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Comprehensive Analysis of Metabolomics and Transcriptomics in Cervical Cancer
Authors: Yang Kai , Xia Bairong , Wang Wenjie , Cheng Jinlong , Yin Mingzhu , Xie Hongyu , Li Junnan , Ma Libing , Yang Chunyan , Li Ang , Fan Xin , Dhillon Harman S. , Hou Yan , Lou Ge , Li Kang 
Published: February 2017

AbstractCervical cancer (CC) still remains a common and deadly malignancy among females in developing countries. More accurate and reliable diagnostic methods/biomarkers should be discovered. In this study, we performed a comprehensive analysis of metabolomics (285 samples) and transcriptomics (52 samples) on the potential diagnostic implication and metabolic characteristic description in cervical cancer. Sixty-two metabolites were different between CC and normal controls (NOR), in which 5 metabolites (bilirubin, LysoPC(17:0), n-oleoyl threonine, 12-hydroxydodecanoic acid and tetracosahexaenoic acid) were selected as candidate biomarkers for CC. The AUC value, sensitivity (SE), and specificity (SP) of these 5 biomarkers were 0.99, 0.98 and 0.99, respectively. We further analysed the genes in 7 significantly enriched pathways, of which 117 genes, that were expressed differentially, were mainly involved in catalytic activity. Finally, a fully connected network of metabolites and genes in these pathways was built, which can increase the credibility of our selected metabolites. In conclusion, our biomarkers from metabolomics could set a path for CC diagnosis and screening. Our results also showed that variables of both transcriptomics and metabolomics were associated with CC.
The promotion of cooperation by the poor in dynamic chicken games
Authors: Ito Hiromu , Katsumata Yuki , Hasegawa Eisuke , Yoshimura Jin 
Published: February 2017

AbstractThe evolution of cooperative behavior is one of the most important issues in game theory. Previous studies have shown that cooperation can evolve only under highly limited conditions, and various modifications have been introduced to games to explain the evolution of cooperation. Recently, a utility function basic to game theory was shown to be dependent on current wealth as a conditional (state) variable in a dynamic version of utility theory. Here, we introduce this dynamic utility function to several games. Under certain conditions, poor players exhibit cooperative behavior in two types of chicken games (the hawk-dove game and the snowdrift game) but not in the prisoner’s dilemma game and the stag hunt game. This result indicates that cooperation can be exhibited by the poor in some chicken games. Thus, the evolution of cooperation may not be as limited as has been suggested in previous studies.
Catch and Release: rare cell analysis from a functionalised medical wire
Authors: Chen Shukun , El-Heliebi Amin , Tauber Gerlinde , Langsenlehner Tanja , Pötscher Michaela , Kashofer Karl , Czyż Zbigniew T. , Polzer Bernhard , Riethdorf Sabine , Kuske Andra , Leitinger Gerd , Pantel Klaus , Kroneis Thomas , Sedlmayr Peter 
Published: February 2017

AbstractEnumeration and especially molecular characterization of circulating tumour cells (CTCs) holds great promise for cancer management. We tested a modified type of an in vivo enrichment device (Catch&Release) for its ability to bind and detach cancer cells for the purpose of single-cell molecular downstream analysis in vitro. The evaluation showed that single–cell analysis using array comparative genome hybridization (array-CGH) and next generation sequencing (NGS) is feasible. We found array-CGH to be less noisy when whole genome amplification (WGA) was performed with Ampli1 as compared to GenomePlex (DLRS values 0.65 vs. 1.39). Moreover, Ampli1-processed cells allowed detection of smaller aberrations (median 14.0 vs. 49.9 Mb). Single-cell NGS data obtained from Ampli1-processed samples showed the expected non-synonymous mutations (deletion/SNP) according to bulk DNA. We conclude that clinical application of this refined in vivo enrichment device allows CTC enumeration and characterization, thus, representing a promising tool for personalized medicine.
Highly accurate and power‐efficient battery charger with charging current compensator for wearable devices
Authors: Jung Y.‐H. , Hong S.‐K. , Kwon O.‐K. 
Published: February 2017

Highly accurate and power‐efficient hybrid battery charger is proposed which includes the switching and linear chargers as well as a charging current compensator. The proposed current compensator operates the switching charger in the constant current (CC) mode to achieve high power efficiency and to improve the charging current accuracy with a small‐sized inductor. It also operates the linear charger to minimise the charging current variation in the trickle current (TC) mode and to reduce the battery charging voltage error in the constant voltage (CV) mode. The proposed battery charger was fabricated using a 0.18 μm CMOS process and occupies a chip area of 1.63 mm2. The measurement results show that the proposed battery charger achieves a charging current accuracy of 96.2% in the CC mode, which is improved by 15.8% at a target current of 500 mA, as well as a power dissipation of 0.26 W. In addition, the charging current variation and charging voltage error are measured to be <2 mAP−P in the TC mode and 0.48% in the CV mode.
Titanium Mesh Nasal Repair without Nasal Lining
Authors: Kao Katherine , Chen Collin , Gross Jennifer , Hahn Samuel , Chi John , Branham Gregory , Zenga Joseph 
Published: February 2017

AbstractThe objective of this study was to describe outcomes for patients who underwent titanium mesh reconstruction of full-thickness nasal defects without internal lining repair. This is a retrospective cohort study. Patients with through-and-through nasal defects were identified at a single academic institution between 2008 and 2016. Nasal reconstruction was performed with either titanium mesh and external skin reconstruction without repair of the intranasal lining or traditional three-layer closure. Five patients underwent titanium mesh reconstruction and 11 underwent traditional three-layer repair. Median follow-up was 11 months (range, 2–66 months). The only significant difference between groups was older age in patients undergoing titanium reconstruction (mean, 81 vs. 63 years; difference of 18; 95% confidence interval [CI], 4–32 years). Defect extent including overall size and structures removed was similar between groups (p > 0.05). Paramedian forehead flap was the most common external reconstruction in both groups (100% for titanium mesh and 73% for three-layer closure). Time under anesthesia was significantly shorter for titanium mesh reconstruction (median, 119 vs. 314 minutes; difference of 195; 95% CI, 45–237). Estimated blood loss and length of hospital stay were similar between groups (p > 0.05). Complication rates were substantial although not significantly different, 40 and 36% in titanium and three-layer reconstruction, respectively (p > 0.05). All patients with complications after titanium reconstruction had prior or postoperative radiotherapy. Titanium mesh reconstruction of through-and-through nasal defects can successfully be performed without reconstruction of the intranasal lining, significantly decreasing operative times. This reconstructive technique may not be suitable for patients who undergo radiotherapy.
Principles of Nasal Reconstruction
Authors: Branham Gregory , Spataro Emily 
Published: February 2017

AbstractThe rise in cutaneous malignancies over the past 20 years has led to significant advances in reconstructing the nose from an aesthetic and functional standpoint. The principles of nasal reconstruction center on application of the nasal subunit principle, three-layered reconstruction, nasal skin characteristics, and patient factors. Reconstructive planning starts with proper defect analysis, followed by application of the reconstructive ladder for soft-tissue repair, adequate structural support, and repair of nasal lining deficits. Optimal reconstructive methods depend on the location and size of the defect. Finally, refinement of the reconstruction is achieved through dermabrasion, scar revision, and flap thinning techniques.
Phenotypic and genetic evidence for a unifactorial structure of spatial abilities
Authors: Rimfeld Kaili , Shakeshaft Nicholas G. , Malanchini Margherita , Rodic Maja , Selzam Saskia , Schofield Kerry , Dale Philip S. , Kovas Yulia , Plomin Robert 
Published: February 2017

SignificanceSpatial ability is a strong predictor of several important outcomes, including success in science, technology, engineering, and mathematics (STEM) subjects and careers. This ability is widely believed to be multifactorial, with numerous components and subdomains, such as “mental rotation,” “scanning,” and “mechanical reasoning.” This large twin study allows the genetic and environmental etiology of diverse putative spatial abilities to be explored. The results indicate that this domain is in fact unifactorial, albeit dissociable from general intelligence, suggesting that its structure is much simpler than the sprawling literature suggests. This will aid gene-hunting efforts and allow this ability and its consequences to be examined with greater precision.
C-terminal phosphorylation regulates the kinetics of a subset of melanopsin-mediated behaviors in mice
Authors: Somasundaram Preethi , Wyrick Glenn R. , Fernandez Diego Carlos , Ghahari Alireza , Pinhal Cindy M. , Simmonds Richardson Melissa , Rupp Alan C. , Cui Lihong , Wu Zhijian , Brown R. Lane , Badea Tudor Constantin , Hattar Samer , Robinson Phyllis R. 
Published: February 2017

Significance
Intrinsically photosensitive retinal ganglion cells (ipRGCs) respond to light via both rod/cone-driven synaptic input and intrinsic melanopsin-based phototransduction; however, these two pathways are not functionally redundant. Melanopsin-based phototransduction in ipRGCs is critical for the regulation of the pupillary light reflex (PLR), circadian light responses, masking, and sleep. Therefore, understanding the kinetics and shutoff mechanisms for the melanopsin-based photoresponse will reveal how it contributes to a myriad of behaviors that are controlled by ipRGCs. Here, we show that the melanopsin photoresponse shutoff due to C-terminal phosphorylation determines the kinetics of the intrinsic light response in ipRGCs, the PLR, and reentrainment, but not masking and phase angle of entrainment. These results highlight the elaborate control of how the melanopsin photoresponse regulates vastly different light-mediated behaviors.
Robust sampling of decision information during perceptual choice
Authors: Vandormael Hildward , Herce Castañón Santiago , Balaguer Jan , Li Vickie , Summerfield Christopher 
Published: February 2017

Significance
When making decisions, humans and other primates move their eyes freely to gather information about their environment. A large literature has explored the factors that determine where the eyes fall during natural scene perception and visual search, concluding that deviant or surprising perceptual information attracts attention and gaze. Here, we describe a sampling policy that paradoxically shows that in a decision-making task, the eyes are attracted to expected rather than unexpected information: When classifying the average of an array of numbers, human observers looked by preference at the numbers that were closest to the mean. This policy drove a behavioral tendency to discount the influence of outliers when making choices, leading to “robust” choices about the stimulus array.
A signal sequence suppressor mutant that stabilizes an assembled state of the twin arginine translocase
Authors: Huang Qi , Alcock Felicity , Kneuper Holger , Deme Justin C. , Rollauer Sarah E. , Lea Susan M. , Berks Ben C. , Palmer Tracy 
Published: February 2017

Significance
The twin-arginine translocation (Tat) system transports folded proteins across the prokaryotic inner membrane and the thylakoid membrane of plant chloroplasts. Proteins are targeted to the Tat system by signal peptides containing a highly conserved twin arginine motif. We isolated suppressors in the TatB component that allowed a Tat substrate with a defective twin arginine motif to be transported. The strongest of these suppressors, TatB F13Y, resulted in the constitutive assembly of the Tat translocase in the absence of signal peptide binding. These results show that Tat signal peptides have two separable roles: they target their passenger proteins to the Tat machinery but they also trigger the assembly of the active Tat transporter.
Nondestructive nanostraw intracellular sampling for longitudinal cell monitoring
Authors: Cao Yuhong , Hjort Martin , Chen Haodong , Birey Fikri , Leal-Ortiz Sergio A. , Han Crystal M. , Santiago Juan G. , Paşca Sergiu P. , Wu Joseph C. , Melosh Nicholas A. 
Published: February 2017

Significance
Cell content analysis has rapidly become one of the most important new tools for measuring cell phenotype and behavior. However, the central limitation of current sampling technologies is they are destructive and must lyse the cells to measure the contents. This destruction prevents knowledge of prior or future states of the cell, which is particularly important for dynamic cell processes, such as development and differentiation. Here, we show a nondestructive longitudinal sampling and analysis platform that can sample repeatedly and accurately from the same single cell or group of cells over a long time period. We demonstrate sampling of both proteins and mRNA for cell lines as well as human-derived cardiomyocytes and astrocytes.
Architecture and coevolution of allosteric materials
Authors: Yan Le , Ravasio Riccardo , Brito Carolina , Wyart Matthieu 
Published: February 2017

Significance
In allosteric proteins, binding a ligand affects activity at a distant site. The physical principles allowing for such an action at a distance are not well understood. Here we introduce a numerical scheme to evolve allosteric materials in which the number of solutions, their spatial architectures, and the correlations among them can be computed. We show that allostery in these materials uses recently discovered elastic edge modes near the active site to transmit information, and that correlations generated during evolution alone can reveal key aspects of this architecture.
Serum-borne bioactivity caused by pulmonary multiwalled carbon nanotubes induces neuroinflammation via blood–brain barrier impairment
Authors: Aragon Mario J. , Topper Lauren , Tyler Christina R. , Sanchez Bethany , Zychowski Katherine , Young Tamara , Herbert Guy , Hall Pamela , Erdely Aaron , Eye Tracy , Bishop Lindsey , Saunders Samantha A. , Muldoon Pretal P. , Ottens Andrew K. , Campen Matthew J. 
Published: February 2017

Significance
Inhaled particulates, such as multiwalled carbon nanotubes, can induce neuroinflammatory outcomes. The present study shows that acute neuroinflammation is dependent on the impairment of blood-brain barrier function. Pharmacologic restoration of blood-brain barrier integrity prevented the neuroinflammatory responses to pulmonary multiwalled carbon nanotube exposure. Circulating factors, including possibly thrombospondin-1, recapitulate inflammatory responses in cultured cerebrovascular endothelial cells, suggesting a mechanism for indirect systemic effects of inhaled nanoparticles.
Membrane integration of an essential β-barrel protein prerequires burial of an extracellular loop
Authors: Wzorek Joseph S. , Lee James , Tomasek David , Hagan Christine L. , Kahne Daniel E. 
Published: February 2017

Significance
Membrane proteins must be assembled to adopt a mature functional form. Integral membrane proteins with β-barrel structure are found in the outer membranes of Gram-negative bacteria, mitochondria, and chloroplasts. To understand the mechanism by which these proteins are assembled, intermediate states in the process must be accumulated and characterized. Here, we study assembly-defective mutants of the β-barrel protein BamA. Our findings reveal that a highly conserved, hydrophilic loop is buried within the β-barrel of BamA before membrane integration, suggesting that one barrier to assembly is the translocation of hydrophilic sequences across the membrane. The specific interactions we identify in this early assembly step could potentially be used for design of mechanism-based inhibitors with antibiotic activity.
Integrated view of internal friction in unfolded proteins from single-molecule FRET, contact quenching, theory, and simulations
Authors: Soranno Andrea , Holla Andrea , Dingfelder Fabian , Nettels Daniel , Makarov Dmitrii E. , Schuler Benjamin 
Published: February 2017

Significance
The dynamics of proteins, which are essential for both folding and function, are known to be strongly dependent on solvent viscosity and friction. However, an increasing number of experiments have demonstrated the importance of a contribution to protein dynamics independent of solvent friction. Such “internal friction” has recently been detected even in unfolded proteins, although they are more expanded and solvent-accessible than folded proteins. Based on two complementary experimental methods, simulations, and theory, our results provide a coherent view of internal friction in unfolded proteins and constitute an important basis for understanding the molecular origin of this phenomenon and its role for the folding of proteins and for the functional dynamics of intrinsically disordered proteins.
Identification of productive and futile encounters in an electron transfer protein complex
Authors: Andrałojć Witold , Hiruma Yoshitaka , Liu Wei-Min , Ravera Enrico , Nojiri Masaki , Parigi Giacomo , Luchinat Claudio , Ubbink Marcellus 
Published: February 2017

Significance
Paramagnetic NMR spectroscopy is exquisitely sensitive for sparsely populated states in protein–protein interactions, and thus, it can provide important information on how protein–protein complexes form and evolve toward their productive state. However, the description of ensembles of protein–protein orientations is nontrivial, and great care must be taken when deriving biologically relevant results. We have applied an algorithm that restricts the conformational space sampled by the two partners to the maximum allowed for by the data. These ensembles can then be reduced assuming the principle of scarcity. We found that some states are linked to the main state through electrostatic pathways. Such paths help to identify those minor states that are able to evolve into the productive complex.
PEMapper and PECaller provide a simplified approach to whole-genome sequencing
Authors: Johnston H. Richard , Chopra Pankaj , Wingo Thomas S. , Patel Viren ,   International Consortium on Brain and Behavior in 22q11.2 Deletion Syndrome, Epstein Michael P. , Mulle Jennifer G. , Warren Stephen T. , Zwick Michael E. , Cutler David J. , Morrow Bernice , Emanuel Beverly , McDonald-McGinn Donna M. , Scherer Steve , Bassett Anne , Chow Eva , Vermeesch Joris , Swillen Ann , Gur Raquel , Bearden Carrie , Kates Wendy , Shashi Vandana , Simon Tony , Chopra Pankj , Cubells Joseph , Cutler David J. , Epstein Michael P. , Johnston H. Richard , Mulle Jennifer , Patel Viren , Warren Stephen T. , Wingo Thomas S. , Zwick Michael E. , Campbell Linda , Repetto Gabriela , Vorstman Jacob , Van Amelsvoort Therese , Eliez Stephen , Philip Nicole , Gothelf Doron , Van Den Bree Marianne , Owen Michael , Murphy Clodagh , Murphy Declan , Garcia-Minaur Sixto , Neine-Suner Damian , Murphy Kieran , Armando Marco , Vicari Stefano 
Published: February 2017

Significance
PEMapper and PECaller are paired software programs that simplify mapping and variant calling for whole-genome datasets. Whole-genome sequencing data are fast becoming the most natural dataset for all genetic studies. Analysis tools for data at this scale are essential. This manuscript describes tools, which solve the challenges of data analysis at whole-genome scale, using an approach involving 16-mer mapping and SNP calling based on a Pólya–Eggenberger distribution for SNP genotypes. We show that our software package is faster (cheaper to run), uses much less disk space (cheaper to store results), requires no previous knowledge of existing genetic variation (easier to deploy to nonhuman species), and achieves calling results that are as good as Genome Analysis Toolkit best practices.
Oogenesis and reproductive investment of Atlantic herring are functions of not only present but long-ago environmental influences as well
Authors: dos Santos Schmidt Thassya C. , Slotte Aril , Kennedy James , Sundby Svein , Johannessen Arne , Óskarsson Gudmundur J. , Kurita Yutaka , Stenseth Nils C. , Kjesbu Olav Sigurd 
Published: February 2017

Significance
Fish stock advice and management have a focus on protecting the reproductive capacity of a stock. Central to the associated research undertaken is whether spawning stock biomass is a proxy for total egg production. Here we demonstrate for the planktivorous Atlantic herring that the standard use of season-independent potential fecundity formulas may cause flaws in these interpretations. In particular, this would happen when the adults have experienced poor feeding conditions that negatively affect the reservoir of primary oocytes and thereby the future fecundity. Hence, females in excellent condition may show significantly lower-than-expected fecundity that could lead to errors in the judgment of reproductive capacity, especially under “red flag” situations.
Rootworm management: status of GM traits, insecticides and potential new tools.
Authors: Ludwick D. C. , Hibbard B. E. 
Published: February 2017

Abstract

Western corn rootworm (
Diabrotica virgifera virgifera
LeConte) and northern corn rootworm (
Diabrotica barberi
(Smith and Lawrence)) are major pests of maize in the USA. These pests have been managed with a variety of tactics over the last century. Both
Diabrotica
spp. have adapted to crop rotation in different ways in certain regions of the USA as well as to some of the insecticides targeted at them.
D. v. virgifera
has adapted to more of the chemical control measures and transgenic control methods. Discussed in this review are the challenges associated with managing both species, and how current management strategies might be combined and implemented to help manage damage from these species. Also, we discuss the potential for new technologies, such as RNA interference, to be used in the future.
Secondary school leader perceptions about the inclusion of queer materials in the school course curricula
Authors: Steck Andy , Perry David 
Published: February 2017

AbstractThe US school system is dominated by heteronormativity in the formal curriculum that gives preference to binary conceptions of sexuality. School leaders play a role in supporting or disrupting school policies facilitating or inhibiting curricular inclusion of queer content in course materials and an instructional pedagogy that promotes an equitable and inclusive educational process. Using a qualitative design and phenomenographic data analysis method, the purpose of the study was to use a queer/curriculum theory lens to explore secondary level school leaders’ perceptions about their experiences with the inclusion of queer related content in the course curricula in their schools. The sample included seven secondary level educational leaders from schools in a northeastern state in the USA. Using a qualitative design and phenomenographic data analysis methods of in‐depth interviews, five categories of description of leader perceptions were identified: (1) lack of inclusion of queer content in formal state curricula, (2) recognized need for inclusion of queer content in the formal curricula, (3) informal inclusion of queer content in the course curriculum, (4) teacher reluctance to include queer content in the curriculum, and (5) providing teachers with resources and professional development opportunities related to integrating queer content into their course curriculum.