bluuebunny/crossref_metadata_2025_split huggingface dataset:
Platelet mechanosensing of substrate stiffness during clot formation mediates adhesion, spreading, and activation
Authors: Qiu Yongzhi , Brown Ashley C. , Myers David R. , Sakurai Yumiko , Mannino Robert G. , Tran Reginald , Ahn Byungwook , Hardy Elaissa T. , Kee Matthew F. , Kumar Sanjay , Bao Gang , Barker Thomas H. , Lam Wilbur A. 
Published: September 2014

Significance
Platelets are cell fragments in the blood that initiate clot formation at the site of bleeding. Although the biological aspects of this process have been well characterized, whether platelets can detect and physiologically respond to the mechanical aspects of its local environment is unclear. Here, we show that platelets sense the stiffness of the underlying clot substrate, and increasing substrate stiffness increases platelet adhesion and spreading. Importantly, adhesion on stiffer substrates leads to higher levels of platelet activation. Mechanistically, we determined that Rac1, actin, and myosin activity mediate this process. This newfound capability of how platelets adjust their degree of activation based on the mechanical properties of their environment provides new insight into how clots are formed.
Unique semantic space in the brain of each beholder predicts perceived similarity
Authors: Charest Ian , Kievit Rogier A. , Schmitz Taylor W. , Deca Diana , Kriegeskorte Nikolaus 
Published: September 2014

Significance
Everyone is different. Understanding the unique way an individual perceives the world is a fundamental goal of psychology and brain science. Using novel methods for analyzing functional MRI (fMRI) data, we show that each person viewing a set of objects represents the objects uniquely in his or her brain. Moreover, given an individual’s measured brain-activity patterns, idiosyncrasies in his or her perception of the similarities among the objects can be predicted. Prediction accuracy is modest using current technology. However, our results demonstrate that fMRI has the power to reveal individually unique representations of particular objects in the human brain. The novel method might help us understand the biological substrate of individual experience in mental health and disease.
Left–right dissociation of hippocampal memory processes in mice
Authors: Shipton Olivia A. , El-Gaby Mohamady , Apergis-Schoute John , Deisseroth Karl , Bannerman David M. , Paulsen Ole , Kohl Michael M. 
Published: September 2014

Significance
The hippocampus is implicated in memory and spatial navigation. In rodents, in which this bilateral brain structure has been studied extensively, the left and right hippocampi have generally been considered functionally equivalent. However, recent work has revealed unexpected asymmetries in the molecular and morphological characteristics of neuronal connections according to brain hemisphere. To investigate whether this left–right difference has implications for hippocampal function, we acutely inhibited activity in an area-specific and genetically-defined population of hippocampal neurons during various behavioral tasks. We found that silencing the CA3 area of the left hippocampus impaired associative spatial long-term memory, whereas the equivalent manipulation in the right hippocampus did not. Thus, our data show that hippocampal long-term memory processing is lateralized in mice.
Precisely modulated pathogenicity island interference with late phage gene transcription
Authors: Ram Geeta , Chen John , Ross Hope F. , Novick Richard P. 
Published: September 2014

Significance
Highly mobile staphylococcal pathogenicity islands (SaPIs) are the only source of toxic shock toxin and certain other superantigens, especially enterotoxin B. To promote their survival and spread, the SaPIs parasitize and interfere with certain bacteriophages. Unlike the interference of the clustered regularly interspaced short palindromic repeats (CRISPRs), the interference of SaPIs is never complete, allowing horizontal gene transfer and adaptation. We report a novel SaPI-determined interference mechanism that targets a phage gene essential for both phage and SaPI. Because SaPI is not self-destructive, it must modulate this inhibition to ensure production of its own infectious particles, as well as those of the phage, and it does so by means of a novel SaPI protein that binds to the inhibitor.
Epigenetic dysregulation by nickel through repressive chromatin domain disruption
Authors: Jose Cynthia C. , Xu Beisi , Jagannathan Lakshmanan , Trac Candi , Mallela Ramya K. , Hattori Takamitsu , Lai Darson , Koide Shohei , Schones Dustin E. , Cuddapah Suresh 
Published: September 2014

Significance
Histone modifications associated with gene silencing typically mark large contiguous regions of the genome forming repressive chromatin domain structures. Since the repressive domains exist in close proximity to active regions, maintenance of domain structure is critically important. This study shows that nickel, a nonmutagenic carcinogen, can disrupt histone H3 lysine 9 dimethylation (H3K9me2) domain structures genome-wide, resulting in spreading of H3K9me2 marks into the active regions, which is associated with gene silencing. Our results suggest inhibition of DNA binding of the insulator protein CCCTC-binding factor (CTCF) at the H3K9me2 domain boundaries as a potential reason for H3K9me2 domain disruption. These findings have major implications in understanding chromatin dynamics and the consequences of chromatin domain disruption during pathogenesis.
Application of desorption electrospray ionization mass spectrometry imaging in breast cancer margin analysis
Authors: Calligaris David , Caragacianu Diana , Liu Xiaohui , Norton Isaiah , Thompson Christopher J. , Richardson Andrea L. , Golshan Mehra , Easterling Michael L. , Santagata Sandro , Dillon Deborah A. , Jolesz Ferenc A. , Agar Nathalie Y. R. 
Published: September 2014

Significance
This study is the first demonstration, to our knowledge, of the application of desorption electrospray ionization mass spectrometry imaging (DESI-MSI) for discrimination of breast cancer and delineation of tumor margins. Using DESI-MSI, it is possible to discriminate between cancerous and adjacent normal tissue on the basis of the detection and specific spatial distributions of different lipid species. This study proves the feasibility of classifying cancerous and normal breast tissues using ambient ionization MSI. It will allow the surgeon to access to this information in real time so as to make accurate intraoperative decisions quickly. It will result in improved cosmesis and decrease the need for multiple operations for margin reexcision.
Epitaxial growth of large-gap quantum spin Hall insulator on semiconductor surface
Authors: Zhou Miao , Ming Wenmei , Liu Zheng , Wang Zhengfei , Li Ping , Liu Feng 
Published: September 2014

Significance
Quantum phase of matter is of great scientific and technological interest. The quantum spin Hall (QSH) insulator is a newly discovered two-dimensional material that exhibits topological edge state residing inside bulk energy gap, so that its edge is metallic with quantized conductance and its bulk is insulating. For its potential applications in spintronics and quantum computing, a large energy gap is desirable, e.g., for room-temperature application. So far, large-gap QSH insulators have been predicted only in freestanding films. Here we demonstrate the formation of a large-gap QSH state on a semiconductor substrate through epitaxial growth of heavy metal atoms on halogenated Si surface. Our findings not only reveal a new formation mechanism of large-gap QSH insulator, but may also pave the way for its experimental realization.
The cardiac-specific N-terminal region of troponin I positions the regulatory domain of troponin C
Authors: Hwang Peter M. , Cai Fangze , Pineda-Sanabria Sandra E. , Corson David C. , Sykes Brian D. 
Published: September 2014

Significance
Protein–protein interactions typically involve some degree of induced fit, producing complementary surfaces that account for high affinity and specificity. However, there are increasingly more examples of intrinsically disordered regions (IDRs) that exert important biologic effects despite never attaining a rigid structure. Here we show how a particularly disordered region of cardiac troponin I impacts the overall global conformation and function of its binding partner, cardiac troponin C. This newly described role for an IDR is accomplished through electrostatic interactions, which are particularly suited to IDRs. The regulation of electrostatic interactions in IDRs through phosphorylation is an emerging concept in cellular signaling, and troponin I is now another important example, one known by cardiac physiologists for 40 y.
Object and spatial mnemonic interference differentially engage lateral and medial entorhinal cortex in humans
Authors: Reagh Zachariah M. , Yassa Michael A. 
Published: September 2014

SignificanceEpisodic memories are complex records of experience, consisting of “what” happened as well as “where” and “when” it happened. Animal studies have demonstrated distinct brain networks supporting memory for information about what experience occurred and information about where the experience occurred. However, such dissociations have been elusive in humans. Using a memory interference task that pits object (i.e., what) vs. spatial (i.e., where) memories against each other and high-resolution fMRI, we report evidence for two parallel but interacting networks in the human hippocampus and its input regions, supporting prior work in animals. We propose a conceptual model of how object and spatial interference are reduced in the regions providing input to the hippocampus, allowing rich, distinct memories to be built.
Statistical learning of recurring sound patterns encodes auditory objects in songbird forebrain
Authors: Lu Kai , Vicario David S. 
Published: September 2014

Significance
Human infants and adults can extract statistical regularities from a continuous sound stream even when passively exposed. This type of unreinforced learning is important for language acquisition and auditory perception. We exposed songbirds, a well-developed model for studying perception and production of learned vocal signals, to sound streams and then recorded neural activity from the auditory forebrain. Responses demonstrated neuronal recognition of complex recurring patterns present in the stream, even for patterns made of nonadjacent sounds. These results show that passive exposure can create and differentiate representations of recently heard sounds in the neuronal population. Because auditory information about the world is received serially over time, recognition of complex auditory objects may depend on this type of ongoing memory process.
Neuronal mechanism for acute mechanosensitivity in tactile-foraging waterfowl
Authors: Schneider Eve R. , Mastrotto Marco , Laursen Willem J. , Schulz Vincent P. , Goodman Jena B. , Funk Owen H. , Gallagher Patrick G. , Gracheva Elena O. , Bagriantsev Sviatoslav N. 
Published: September 2014

Significance
Like vision, audition, and olfaction, mechanosensation is a fundamental way in which animals interact with the environment, but it remains the least well understood at the cellular and molecular levels. Here, we explored evolutionary changes that contribute to the enhancement of mechanosensitivity in tactile-foraging ducks. We found that the somatosensory neurons that innervate the duck bill can detect physical force much more efficiently than analogous cells in other species, such as mice. Furthermore, ducks exhibit an increase in the number of neurons dedicated to this task in their sensory ganglia and a decrease in the number of neurons that detect temperature. Our findings provide an explanation for the acute mechanosensitivity of the duck bill at the level of somatosensory neurons.
Discontinuity in the responses of ecosystem processes and multifunctionality to altered soil community composition
Authors: Bradford Mark A. , Wood Stephen A. , Bardgett Richard D. , Black Helaina I. J. , Bonkowski Michael , Eggers Till , Grayston Susan J. , Kandeler Ellen , Manning Peter , Setälä Heikki , Jones T. Hefin 
Published: September 2014

Significance
Ecosystem functioning is more strongly affected by biodiversity loss when multiple functions are considered because different species affect different functions. To quantify these biodiversity-functioning relationships, the emerging multifunctionality framework advocates calculation of indices that aggregate responses of individual functions. Data aggregation, however, is notorious for providing misleading information by obscuring true relationships between explanatory and response variables. We test the ability of common multifunctionality indices to reveal effects on key ecosystem functions of changes in soil communities. The multifunctionality indices all decrease with soil animal loss, but the responses of individual functions diverge markedly from these aggregated metrics. Application of the multifunctionality framework for landscape provision of multiple ecosystem services should therefore emphasize understanding relationships between communities and individual functions.
Range of cell-wall alterations enhance saccharification in
Brachypodium distachyon
mutants
Authors: Marriott Poppy E. , Sibout Richard , Lapierre Catherine , Fangel Jonatan U. , Willats William G. T. , Hofte Herman , Gómez Leonardo D. , McQueen-Mason Simon J. 
Published: September 2014

Significance
Bioethanol produced from waste biomass from crops has the potential to provide a sustainable alternative to petroleum-based transportation fuel that does not compete with human food supply. The main obstacle to this approach is the resistance of this biomass to digestion. Thus, expensive energetic pretreatment and high enzyme inputs are needed to increase digestion. In this study, we screened a population of randomly mutated plants for digestibility with the aim of identifying novel factors that impact on this trait. We found a number of mutants with high digestibility and no impairments in growth or fitness. These mutants show a range of alterations in cell-wall composition, and we have mapped and characterized the mutant with the highest increase in digestibility.
Discrete elements for 3D microfluidics
Authors: Bhargava Krisna C. , Thompson Bryant , Malmstadt Noah 
Published: September 2014

Significance
Microfluidic systems promise to improve the analysis and synthesis of materials, biological or otherwise, by lowering the required volume of fluid samples, offering a tightly controlled fluid-handling environment, and simultaneously integrating various chemical processes. To build these systems, designers depend on microfabrication techniques that restrict them to arranging their designs in two dimensions and completely fabricating their design in a single step. This study introduces modular, reconfigurable components containing fluidic and sensor elements adaptable to many different microfluidic circuits. These elements can be assembled to allow for 3D routing of channels. This assembly approach allows for the application of network analysis techniques like those used in classical electronic circuit design, facilitating the straightforward design of predictable flow systems.
Insulin and insulin-like growth factor 1 receptors are required for normal expression of imprinted genes
Authors: Boucher Jeremie , Charalambous Marika , Zarse Kim , Mori Marcelo A. , Kleinridders Andre , Ristow Michael , Ferguson-Smith Anne C. , Kahn C. Ronald 
Published: September 2014

Significance
Imprinted genes are normally selectively expressed, depending on the parent from whom the gene is inherited. These genes play important roles in control of growth and metabolism. We find that the loss of insulin and insulin-like growth factor 1 (IGF1) receptors in cells induces a major decrease in expression of multiple imprinted genes, regardless of whether they would be maternally or paternally expressed. This deregulation is associated with changes in methylation of DNA, but is not due to classical imprinting control. Our results demonstrate a previously unrecognized function of insulin and IGF1 receptors independent of these hormones and provide a new pathway by which insulin and IGF1 receptors may regulate growth and metabolism during early development and thereafter.
Learning bundles of stimuli renders stimulus order as a cue, not a confound
Authors: Qian Ting , Aslin Richard N. 
Published: September 2014

Significance
The effects of stimulus order on human cognition have been previously reported in various cognitive tasks, and the prevalent explanations have been that sensitivity to stimulus order is due to either constraints on cognitive resources (e.g., working memory) or misconceptions about probability axioms. Our work suggests a fundamentally different interpretation: Humans are sensitive to order because it serves as an important cue. This interpretation is philosophically consistent with the burgeoning literature on rational cognition, where human behavior has been shown to (at least approximately) match the statistically optimal solution of a task. We propose that redefining the role of stimulus order as a cue may provide a more general perspective for understanding human cognition.
Dominance of misfolded intermediates in the dynamics of α-helix folding
Authors: Lin Milo M. , Shorokhov Dmitry , Zewail Ahmed H. 
Published: September 2014

Significance
Proteins fill the vast majority of infrastructural and functional roles at the biological nanoscale. Despite their structural variability, most proteins contain α-helix motifs. Aptly described as molecular zippers, α-helices form by first aligning numerous degrees of freedom to stabilize a helical nucleus, after which the helix can presumably rapidly grow. Here, we show that helix zipping in polyalanine can get “caught” by nonhelical contacts that block growth, and that these misfolded intermediates can dominate the folding process, leading to zipping times that are an order of magnitude longer than expected based on unimpeded growth. The dominance of intermediate misfolded structures and their influence on folding dynamics have implications for protein aggregation, which is of significance in diseases such as Alzheimer’s.
Comprehensive large-scale assessment of intrinsic protein disorder
Authors: Walsh Ian , Giollo Manuel , Di Domenico Tomás , Ferrari Carlo , Zimmermann Olav , Tosatto Silvio C. E. 
Published: September 2014

Abstract
Motivation: Intrinsically disordered regions are key for the function of numerous proteins. Due to the difficulties in experimental disorder characterization, many computational predictors have been developed with various disorder flavors. Their performance is generally measured on small sets mainly from experimentally solved structures, e.g. Protein Data Bank (PDB) chains. MobiDB has only recently started to collect disorder annotations from multiple experimental structures.
Results: MobiDB annotates disorder for UniProt sequences, allowing us to conduct the first large-scale assessment of fast disorder predictors on 25 833 different sequences with X-ray crystallographic structures. In addition to a comprehensive ranking of predictors, this analysis produced the following interesting observations. (i) The predictors cluster according to their disorder definition, with a consensus giving more confidence. (ii) Previous assessments appear over-reliant on data annotated at the PDB chain level and performance is lower on entire UniProt sequences. (iii) Long disordered regions are harder to predict. (iv) Depending on the structural and functional types of the proteins, differences in prediction performance of up to 10% are observed.
Availability: The datasets are available from Web site at URL: http://mobidb.bio.unipd.it/lsd .
Contact: silvio.tosatto@unipd.it
Supplementary information: Supplementary data are available at Bioinformatics online.
Stars as resonant absorbers of gravitational waves
Authors: McKernan B. , Ford K. E. S. , Kocsis B. , Haiman Z. 
Published: September 2014

Abstract
Quadrupole oscillation modes in stars can resonate with incident gravitational waves (GWs), and grow non-linear at the expense of GW energy. Stars near massive black hole binaries (MBHBs) can act as GW-charged batteries, discharging radiatively. Mass-loss from these stars can prompt MBHB accretion at near-Eddington rates. GW opacity is independent of amplitude, so distant resonating stars can eclipse GW sources. Absorption by the Sun of GWs from Galactic white dwarf binaries may be detectable with second-generation space-based GW detectors as a shadow within a complex diffraction pattern.
Neuropsychological Functioning and Health‐Related Quality of Life
Authors: Sorensen Lisa G. , Neighbors Katie , Zhang Song , Limbers Christine A. , Varni James W. , Ng Vicky L. , Squires Robert H. , Alonso Estella M. ,   Pediatric Acute Liver Failure Study Group
Published: September 2014

ABSTRACTObjectives:Pediatric acute liver failure (PALF) is a rare but serious event, with poorly understood functional outcomes. The goal was to determine the prevalence of reduced neuropsychological functioning and health‐related quality of life (HRQOL) following PALF.Methods:This multicenter study examined neuropsychological functioning and HRQOL 1 to 6 (median 3.8) years after PALF. Participants ages 6 to 16 (median 9.9) years were recruited from the PALF registry and administered measures of intelligence, visual spatial/visual motor coordination, attention, executive function, depression, and adaptive skills. HRQOL and fatigue were assessed using the Pediatric Quality of Life Inventory 4.0 Generic Core Scales (PedsQL 4.0) and PedsQL Multidimensional Fatigue Scale.Results:A total of 36 patients participated; 50% were boys and 67% were white. Median age at PALF was 5.6 years. A history of grade 3 or 4 hepatic encephalopathy was reported in 5/36 (14%) participants and 23/36 (64%) received a liver transplant. Visual spatial ability was significantly better than norms (P = 0.009), but motor coordination was worse (P = 0.04). Teachers (P = 0.04 to P < 0.0001) and parents (P = 0.005) reported more executive deficits versus norms, and participants had worse attention (P = 0.02). Participants did not differ significantly from norms on IQ, depression, or adaptive functioning. All of the child self‐report PedsQL Generic Core and fatigue scales were significantly lower than a matched healthy sample (P = 0.001 to P < 0.0001) and parent proxy report was lower on the fatigue scales (P = 0.001 to P < 0.0001).Conclusions:Long‐term PALF survivors demonstrate average IQ and visual spatial ability, but greater than expected impairments in motor skills, attention, executive function, HRQOL, and fatigue.