bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting Speech Intelligibility With a Multiple Speech Subsystems Approach in Children With Cerebral Palsy
Authors: Lee Jimin , Hustad Katherine C. , Weismer Gary 
Published: May 2014

Purpose
Speech acoustic characteristics of children with cerebral palsy (CP) were examined with a multiple speech subsystems approach; speech intelligibility was evaluated using a prediction model in which acoustic measures were selected to represent three speech subsystems.

Method
Nine acoustic variables reflecting different subsystems, and speech intelligibility, were measured in 22 children with CP. These children included 13 with a clinical diagnosis of dysarthria (speech motor impairment [SMI] group) and 9 judged to be free of dysarthria (no SMI [NSMI] group). Data from children with CP were compared to data from age-matched typically developing children.

Results

Multiple acoustic variables reflecting the articulatory subsystem were different in the SMI group, compared to the NSMI and typically developing groups. A significant speech intelligibility prediction model was obtained with all variables entered into the model (adjusted
R
2
= .801). The articulatory subsystem showed the most substantial independent contribution (58%) to speech intelligibility. Incremental
R
2
analyses revealed that any single variable explained less than 9% of speech intelligibility variability.

Conclusions
Children in the SMI group had articulatory subsystem problems as indexed by acoustic measures. As in the adult literature, the articulatory subsystem makes the primary contribution to speech intelligibility variance in dysarthria, with minimal or no contribution from other systems.
A seismologically consistent compositional model of Earth’s core
Authors: Badro James , Côté Alexander S. , Brodholt John P. 
Published: May 2014

Significance
It is well known that Earth’s core is made primarily of iron, alloyed with ∼5% nickel and some lighter elements, such as carbon, oxygen, silicon, or sulfur. The amount as well as the chemistry of the light elements is poorly known and still a matter of considerable debate. In this paper we calculate the seismic signature of iron-rich light-element alloys and compare them to the seismic properties of Earth’s core. We find that oxygen is required as a major light element in the core, whereas silicon, sulfur, and carbon are not required. We also find that silicon concentration in the core cannot be higher than 4.5%, and sulfur concentration cannot be higher than 2.4%.
Active learning increases student performance in science, engineering, and mathematics
Authors: Freeman Scott , Eddy Sarah L. , McDonough Miles , Smith Michelle K. , Okoroafor Nnadozie , Jordt Hannah , Wenderoth Mary Pat 
Published: May 2014

Significance
The President’s Council of Advisors on Science and Technology has called for a 33% increase in the number of science, technology, engineering, and mathematics (STEM) bachelor’s degrees completed per year and recommended adoption of empirically validated teaching practices as critical to achieving that goal. The studies analyzed here document that active learning leads to increases in examination performance that would raise average grades by a half a letter, and that failure rates under traditional lecturing increase by 55% over the rates observed under active learning. The analysis supports theory claiming that calls to increase the number of students receiving STEM degrees could be answered, at least in part, by abandoning traditional lecturing in favor of active learning.
Global view of enhancer–promoter interactome in human cells
Authors: He Bing , Chen Changya , Teng Li , Tan Kai 
Published: May 2014

Significance
In eukaryotes, gene expression is controlled by short regulatory DNA sequences called enhancers. Understanding how an enhancer selects its target promoter(s) is a major challenge in the field of gene regulation. Advances in genomic technologies have enabled rapid and comprehensive identification of active promoters and enhancers for many cell types. However, there is a lack of methods to link bona fide enhancers and their target promoters. Here, we develop and integrate multiple genomic features into a statistical predictor for enhancer–promoter interactions. Systematic analyses of the predicted interactions across 12 cell types reveals several global features of enhancer–promoter communication. Our approach presents a systematic and effective strategy to decipher the mechanisms underlying enhancer and promoter communication.
Selection and constraint underlie irreversibility of tooth loss in cypriniform fishes
Authors: Aigler Sharon R. , Jandzik David , Hatta Kohei , Uesugi Kentaro , Stock David W. 
Published: May 2014

Significance
The mechanisms underlying Dollo’s Law, the assertion that the evolutionary loss of complex structures is irreversible, remain poorly characterized. In principle, such mechanisms could involve the improbability either of generating the mutations required for trait reappearance or of selecting for their fixation. Whereas most attention has focused on the former mechanism, we used experimental reversal of dentition reduction in cypriniform fishes to provide evidence for the operation of both within a single system.
DELLA protein functions as a transcriptional activator through the DNA binding of the INDETERMINATE DOMAIN family proteins
Authors: Yoshida Hideki , Hirano Ko , Sato Tomomi , Mitsuda Nobutaka , Nomoto Mika , Maeo Kenichiro , Koketsu Eriko , Mitani Rie , Kawamura Mayuko , Ishiguro Sumie , Tada Yasuomi , Ohme-Takagi Masaru , Matsuoka Makoto , Ueguchi-Tanaka Miyako 
Published: May 2014

SignificanceGibberellin (GA)-dependent degradation of DELLA protein, a key negative regulator, is essential for GA action. However, it is unclear how DELLA regulates downstream gene expression. Although possessing strong transactivation activity, DELLA lacks a DNA-binding domain. Therefore, a model has been proposed in which DELLA acts as a transcriptional coactivator with another transcription factor or factors containing a DNA-binding domain. Here, we show that some members of the INDETERMINATE DOMAIN (IDD) protein family are such intermediate proteins. The DELLA/IDD complex up-regulates the expression of the GA-positive regulatorSCARECROW-LIKE 3(SCL3). Meanwhile, SCL3 protein also interacts with IDD proteins to suppress its own expression. We propose that a coregulator exchange system between DELLA (as coactivator) and SCL3 (as corepressor) regulates the expression ofSCL3.
Repair of DNA double-strand breaks by templated nucleotide sequence insertions derived from distant regions of the genome
Authors: Onozawa Masahiro , Zhang Zhenhua , Kim Yoo Jung , Goldberg Liat , Varga Tamas , Bergsagel P. Leif , Kuehl W. Michael , Aplan Peter D. 
Published: May 2014

Significance
We show that DNA double-strand breaks (DSBs) can be repaired by insertion of 50- to 1,000-bp sequences termed “templated-sequence insertions” (TSIs) derived from distant regions of the genome. Additional experiments indicate that the source of template for repair was primarily nuclear RNA. This mode of DNA-DSB repair by insertion is not restricted to experimentally produced breaks but also occurs at the site of spontaneous DNA DSBs in human cells. These TSIs are polymorphic in the human genome, suggesting that some TSIs occur in germ cells or embryos. Recognition of these TSIs is important in interpreting structural variations in short-read sequencing studies and provides additional polymorphic markers for population and evolution studies. This error-prone form of DNA repair may play a role in genetic diseases.
Integrating phase and composition of secondary organic aerosol from the ozonolysis of α-pinene
Authors: Kidd Carla , Perraud Véronique , Wingen Lisa M. , Finlayson-Pitts Barbara J. 
Published: May 2014

Significance
The phase of atmospheric aerosol particles can have dramatic effects on reactivity, growth, oxidation, and water uptake. As such, it plays a critical role in every aspect of particle evolution. Despite this, our knowledge of the phase of secondary organic aerosol (SOA) and how it changes in relation to conditions during SOA formation, particle history, composition, relative humidity, and temperature remains poor. Recent laboratory experiments suggest that SOA, under certain circumstances, is best described as a semisolid or viscous tar. This work shows how phase/viscosity, water availability during SOA formation, and composition are interrelated and offers mechanistic insights into these relationships.
Childhood bullying involvement predicts low-grade systemic inflammation into adulthood
Authors: Copeland William E. , Wolke Dieter , Lereya Suzet Tanya , Shanahan Lilly , Worthman Carol , Costello E. Jane 
Published: May 2014

Significance
Bullying is a common childhood experience that affects children at all income levels and racial/ethnic groups. Being a bully victim has long-term adverse consequences on physical and mental health and financial functioning, but bullies themselves display few ill effects. Here, we show that victims suffer from greater increases in low-grade systemic inflammation from childhood to young adulthood than are seen in others. In contrast, bullies showed lower increases in inflammation into adulthood compared with those uninvolved in bullying. Elevated systemic low-grade inflammation is a mechanism by which this common childhood social adversity may get under the skin to affect adult health functioning, even many years later.
In vitro assay using engineered yeast vacuoles for neuronal SNARE-mediated membrane fusion
Authors: Ko Young-Joon , Lee Miriam , Kang KyeongJin , Song Woo Keun , Jun Youngsoo 
Published: May 2014

Significance
Although synaptic vesicle fusion plays a crucial role in neurotransmission, studies of its molecular mechanisms have relied heavily on the use of artificial liposomes reconstituted with recombinantly expressed proteins. In this study, we establish an in vitro assay using engineered yeast vacuoles bearing neuronal SNAREs for measuring neuronal SNARE-mediated membrane fusion and show that this assay provides a simple and independent means of investigating synaptic vesicle fusion mechanisms.
Helicase proteins DHX29 and RIG-I cosense cytosolic nucleic acids in the human airway system
Authors: Sugimoto Naoshi , Mitoma Hiroki , Kim Taeil , Hanabuchi Shino , Liu Yong-Jun 
Published: May 2014

Significance
Different molecules act in sensing cytosolic nucleic acids derived from viruses, depending on the cell type and the virus. Epithelial cells and fibroblasts recognize viral invasion through cytosolic nucleic acid sensors and initiate antiviral immune responses by secreting cytokines. Retinoic acid-inducible gene 1 (RIG-I), a member of the DNA/RNA helicase family, plays a significant role as such a sensor. We identified DEAH (Asp-Glu-Ala-His) box polypeptide 29 (DHX29), another member of the family, as a unique cytosolic nucleic acid cosensor in human airway epithelial cells and fibroblasts. DHX29 directly bound nucleic acids, interacted with RIG-I, and triggered downstream signaling. DHX29 may be the optimal target for drug and vaccine design to control viral infections and viral-induced pathology in the airway.
Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes
Authors: Zeng Yonghui , Feng Fuying , Medová Hana , Dean Jason , Koblížek Michal 
Published: May 2014

Significance
Photosynthesis is one of the most fundamental biological processes on Earth. To date, species capable of performing (bacterio)chlorophyll-based phototrophy have been reported in six bacterial phyla. Here we report a phototrophic bacterium belonging to the rare and understudied phylum Gemmatimonadetes. This strain, isolated from a freshwater lake in the Gobi Desert, contains fully functional photosynthetic reaction centers. Its photosynthesis genes appear to originate from an ancient horizontal gene transfer from a purple phototrophic bacterium. Our findings not only demonstrate that Gemmatimonadetes represents a new phototrophic bacterial phylum, but also present, to our knowledge, the first evidence that genes for (bacterio)chlorophyll-based phototrophy can be transferred between distant bacterial phyla.
Air-stable droplet interface bilayers on oil-infused surfaces
Authors: Boreyko Jonathan B. , Polizos Georgios , Datskos Panos G. , Sarles Stephen A. , Collier C. Patrick 
Published: May 2014

Significance
By suspending a lipid bilayer in an aperture or between water droplets, single-molecule transport through membrane channels can be electrically detected. To date, all suspended bilayers have been confined to fluid reservoirs. This study demonstrates that droplet interface bilayers can be created in an ambient environment using noncoalescing water droplets on an oil-infused surface. Air-stable droplet interface bilayers are easy to manipulate and electrically characterize, and could potentially allow for the biosensing of airborne molecules.
Neurons in cortical area MST remap the memory trace of visual motion across saccadic eye movements
Authors: Inaba Naoko , Kawano Kenji 
Published: May 2014

Significance
We found that most medial superior temporal (MST) neurons, but no middle temporal neurons, increased their firing rates when a saccade brought the location of the visual stimulus, which had been visible only before the saccade, into their receptive fields (RFs): so-called “memory remapping.” The distinctive feature of the MST neurons is that they did not respond to stimuli in their future RFs before the saccade, a response known as “predictive remapping.” In other areas (e.g., lateral intraparietal cortex, frontal eye field), neurons showing memory remapping had been recorded together with neurons showing predictive remapping, consistent with their role in guiding goal-directed motor actions such as saccades. Our finding is understandable in the view that MST has a different role, which is to perceive the visual world.
In vivo modulation of hypoxia-inducible signaling by topographical helix mimetics
Authors: Lao Brooke Bullock , Grishagin Ivan , Mesallati Hanah , Brewer Thomas F. , Olenyuk Bogdan Z. , Arora Paramjit S. 
Published: May 2014

Significance
Protein–protein interactions are attractive targets for drug design due to their fundamental role in biological function. However, small molecules that selectively target the intended interactions have been difficult to access using traditional drug discovery approaches. We show that compounds that reproduce key functionality at the interface between transcription factor hypoxia-inducible factor 1α (HIF1α) and coactivator p300 (or CREB binding protein, CBP) can inhibit expression of a multitude of genes under hypoxic environments. The designed inhibitors target the chosen protein–protein interaction in a predictable manner and reduce tumor growth in mouse xenograft models.
Specificity of
O
-glycosylation in enhancing the stability and cellulose binding affinity of Family 1 carbohydrate-binding modules
Authors: Chen Liqun , Drake Matthew R. , Resch Michael G. , Greene Eric R. , Himmel Michael E. , Chaffey Patrick K. , Beckham Gregg T. , Tan Zhongping 
Published: May 2014

Significance
Plant biomass decomposition has broad implications for the global carbon cycle, agriculture, and ecology, and it is primarily accomplished by fungi. Recently, research into fungal biomass degradation mechanisms has been driven by the growing biofuels industry, because enzymes from fungi are among the primary catalysts being investigated for industrial processes to convert polysaccharides into upgradeable sugars. Understanding the mechanisms used by polysaccharide-degrading enzymes and identifying means to improve their performance is of paramount importance because of the scale of enzyme production for biofuels processes. Here, we use glycoprotein synthesis and biophysical measurements to characterize the specific effects of glycosylation on ubiquitous fungal carbohydrate-binding modules for biomass degradation, which reveal key features of the importance of posttranslational modifications on enzyme function.
Compressive mapping of number to space reflects dynamic encoding mechanisms, not static logarithmic transform
Authors: Cicchini Guido Marco , Anobile Giovanni , Burr David C. 
Published: May 2014

Significance
The ability to map numbers onto space is fundamental to measurement and mathematics. The mental “numberline” is an important predictor of math ability, thought to reflect an internal, native logarithmic representation of number, later becoming linearized by education. Here we demonstrate that the nonlinearity results not from a static logarithmic transformation but from dynamic processes that incorporate past history into numerosity judgments. We show strong and significant correlations between the response to the current trial and the magnitude of the previous stimuli and that subjects respond with a weighted average of current and recent stimuli, explaining completely the logarithmic-like nonlinearity. We suggest that this behavior reflects a general strategy akin to predictive coding to cope adaptively with environmental statistics.
Split-gene system for hybrid wheat seed production
Authors: Kempe Katja , Rubtsova Myroslava , Gils Mario 
Published: May 2014

Significance
Global food security demands the development of new technologies to increase and secure cereal production on finite arable land without increasing water and fertilizer use. Although the use of heterosis through hybrid breeding has produced tremendous economic benefits in worldwide crop production, less than 1% of the global wheat area is planted with hybrids. One of the greatest bottlenecks in breeding hybrid wheat is the lack of an efficient sterility system to block self-pollination. This report describes a recessive system for pollination control in wheat. We demonstrate the implementation and feasibility of the system for generation and maintenance of the male-sterile parent, hybrid seed production and full restoration of fertility in the hybrid wheat seed.
Immunoglobulin somatic hypermutation by APOBEC3/Rfv3 during retroviral infection
Authors: Halemano Kalani , Guo Kejun , Heilman Karl J. , Barrett Bradley S. , Smith Diana S. , Hasenkrug Kim J. , Santiago Mario L. 
Published: May 2014

SignificanceAntibodies are important for recovery from viral infections and vaccine efficacy. To improve the ability of antibodies to bind and neutralize viral pathogens, antibody DNA sequences undergo a mutational process driven by the enzyme activation-induced deaminase (AID). However, high levels of antibody mutations are required to potently inhibit global strains of the retrovirus HIV-1. We provide evidence that a related enzyme, apolipoprotein B mRNA-editing enzyme catalytic polypeptide 3 (APOBEC3), can also mutate antibodies during retrovirus infection, but in a different DNA sequence context compared to AID. The findings demonstrate that APOBEC3 acts as a key player in generating virus-specific neutralizing antibodies and highlight a previously unidentified mechanism for antibody diversification that could be harnessed for vaccine development.
Circulating proteolytic signatures of chemotherapy-induced cell death in humans discovered by N-terminal labeling
Authors: Wiita Arun P. , Hsu Gerald W. , Lu Chuanyi M. , Esensten Jonathan H. , Wells James A. 
Published: May 2014

Significance
Many chemotherapeutics function by inducing cellular apoptosis, or programmed cell death, in tumor cells. Here, using a unique enzymatically driven technology, we find that numerous protein fragments are released into the bloodstream from apoptotic cells within hours after chemotherapy. These circulating signatures of cell death, if confidently assigned to tumor cells, may form the foundation for entirely novel, rapid, and inexpensive biomarkers of chemotherapeutic efficacy. Diagnostic tests to rapidly assess cell death after treatment could serve an important role in management for many cancers.
Tolerance induction in memory CD4 T cells requires two rounds of antigen-specific activation
Authors: David Alexandria , Crawford Frances , Garside Paul , Kappler John W. , Marrack Philippa , MacLeod Megan 
Published: May 2014

SignificanceAutoimmune diseases are driven by immune cells that recognize self-tissues. A major goal for treatment strategies for autoimmune diseases is to turn off or tolerize self-reactive immune cells such as CD4 T cells that coordinate tissue damage in many autoimmune diseases. Autoimmune diseases are often diagnosed many years following their onset. The self-reactive CD4 T cells that must be tolerized, therefore, are previously activated or memory CD4 T cells. Little is known about whether tolerance can be induced in memory CD4 T cells. This paper demonstrates that memory CD4 T cells survive initial exposure to tolerance-inducing signals but that a second activation signal leads to cell death. This study has important implications for immunotherapeutic strategies for autoimmune diseases.
Behçet disease-associated MHC class I residues implicate antigen binding and regulation of cell-mediated cytotoxicity
Authors: Ombrello Michael J. , Kirino Yohei , de Bakker Paul I. W. , Gül Ahmet , Kastner Daniel L. , Remmers Elaine F. 
Published: May 2014

SignificanceTo elucidate their role in Behçet disease (BD), we used imputation to analyze MHC class I (MHC-I) alleles and amino acids in a large case-control collection. Several MHC-I alleles influenced BD susceptibility, some conferring risk and others affording protection. The association of MHC-I with BD was mapped to six positions around the peptide-binding groove and to one position in the signal peptide. These residues are critical in defining the peptide-binding specificity of MHC-I molecules, and they also affect the engagement of MHC-I molecules by killer immunoglobulin-like receptors on natural killer and T cells. These data implicate peptide binding by MHC-I in BD pathogenesis and suggest that altered regulation of cytotoxic cells by MHC-I may be pathogenic in BD.
The Role of the Champlain Canal and Erie Canal as Putative Corridors for Colonization of Lake Champlain and Lake Ontario by Sea Lampreys
Authors: Eshenroder Randy L. 
Published: May 2014

AbstractThe origin of populations of the landlocked Sea LampreyPetromyzon marinusin Lakes Champlain and Ontario, whether by artificial canals or by natural colonization following the last ice age, is controversial, in part because the related history and ecology had been poorly documented. This situation favored a native classification for the populations in both lakes based mainly on genetics. A native classification for the Lake Champlain population was predicated on either of two erroneous dates of first record, 1841 and 1894, whereas the correct date, 1929, was much more recent and strongly supports a nonnative classification. The detection of the Sea Lamprey in Lake Champlain occurred shortly after the opening in 1916 of the Champlain Barge Canal, which opened the upper Hudson River to fish passage. The case for a native Lake Ontario population did not account for a watershed breach in 1863 between the Susquehanna River, where the Sea Lamprey had been common, and the Lake Ontario drainage. Shortly after this canal‐related connection was made, Sea Lamprey populations became abundant, nearly simultaneously, in four locations in the Lake Ontario drainage, suggesting this breach was the entry point for the founding population. The genetic distances between the landlocked populations and the Atlantic Ocean population appear to have been caused by recent bottlenecks rather than long‐term residence; a recent genetic bottleneck was detected in the Lake Ontario population. Native classifications rested, in part, on extraordinary ecological scenarios, whereas nonnative classifications are consistent with experience in the upper Great Lakes and with well‐known vectors of range expansion (canals, dam openings, watershed breaches). These findings in aggregate favor a nonnative classification of the Sea Lamprey in both lakes.