bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular investigation of coexistent chronic myeloid leukaemia and peripheral T-cell lymphoma – a case report
Authors: Gruszka Alicja M. , Rabascio Cristina , Cannella Laura , Sammassimo Simona , Andreola Giovanna , Gregato Giuliana , Faretta Mario , Calleri Angelica , De Molfetta Rita , Pruneri Giancarlo , Bertolini Francesco , Alcalay Myriam 
Published: October 2015

AbstractChronic myeloid leukemia (CML) is a myeloproliferative neoplasm underlain by the formation of BCR-ABL1 – an aberrant tyrosine kinase – in the leukaemic blasts. Long-term survival rates in CML prior to the advent of tyrosine kinase inhibitors (TKIs) were dismal, albeit the incidence of secondary malignancies was higher than that of age-matched population. Current figures confirm the safety of TKIs with conflicting data concerning the increased risk of secondary tumours. We postulate that care has to be taken when distinguishing between coexisting, secondary-to-treatment and second in sequence, but independent tumourigenic events, in order to achieve an unbiased picture of the adverse effects of novel treatments. To illustrate this point, we present a case of a patient in which CML and peripheral T-cell lymphoma (PTCL) coexisted, although the clinical presentation of the latter followed the achievement of major molecular response of CML to TKIs.
High resolution structure of an M23 peptidase with a substrate analogue
Authors: Grabowska Maja , Jagielska Elzbieta , Czapinska Honorata , Bochtler Matthias , Sabala Izabela 
Published: October 2015

AbstractLytM is a Staphylococcus aureus autolysin and a homologue of the S. simulans lysostaphin. Both enzymes are members of M23 metallopeptidase family (MEROPS) comprising primarily bacterial peptidoglycan hydrolases. LytM occurs naturally in a latent form, but can be activated by cleavage of an inhibitory N-terminal proregion. Here, we present a 1.45 Å crystal structure of LytM catalytic domain with a transition state analogue, tetraglycine phosphinate, bound in the active site. In the electron density, the active site of the peptidase, the phosphinate and the “diglycine” fragment on the P1′ side of the transition state analogue are very well defined. The density is much poorer or even absent for the P1 side of the ligand. The structure is consistent with the involvement of His260 and/or His291 in the activation of the water nucleophile and suggests a possible catalytic role for Tyr204, which we confirmed by mutagenesis. Possible mechanisms of catalysis and the structural basis of substrate specificity are discussed based on the structure analysis.
Phylum-wide analysis of genes/proteins related to the last steps of assembly and export of extracellular polymeric substances (EPS) in cyanobacteria
Authors: Pereira Sara B. , Mota Rita , Vieira Cristina P. , Vieira Jorge , Tamagnini Paula 
Published: October 2015

AbstractMany cyanobacteria produce extracellular polymeric substances (EPS) with particular characteristics (e.g. anionic nature and presence of sulfate) that make them suitable for industrial processes such as bioremediation of heavy metals or thickening, suspending or emulsifying agents. Nevertheless, their biosynthetic pathway(s) are still largely unknown, limiting their utilization. In this work, a phylum-wide analysis of genes/proteins putatively involved in the assembly and export of EPS in cyanobacteria was performed. Our results demonstrated that most strains harbor genes encoding proteins related to the three main pathways: Wzy-, ABC transporter- and Synthase-dependent, but often not the complete set defining one pathway. Multiple gene copies are mainly correlated to larger genomes and the strains with reduced genomes (e.g. the clade of marine unicellular Synechococcus and Prochlorococcus), seem to have lost most of the EPS-related genes. Overall, the distribution of the different genes/proteins within the cyanobacteria phylum raises the hypothesis that cyanobacterial EPS production may not strictly follow one of the pathways previously characterized. Moreover, for the proteins involved in EPS polymerization, amino acid patterns were defined and validated constituting a novel and robust tool to identify proteins with similar functions and giving a first insight to which polymer biosynthesis they are related to.
Unusual spin dynamics in topological insulators
Authors: Dóra Balázs , Simon Ferenc 
Published: October 2015

AbstractThe dynamic spin susceptibility (DSS) has a ubiquitous Lorentzian form around the Zeeman energy in conventional materials with weak spin orbit coupling, whose spectral width characterizes the spin relaxation rate. We show that DSS has an unusual non-Lorentzian form in topological insulators, which are characterized by strong SOC and the anisotropy of the DSS reveals the orientation of the underlying spin texture of topological states. At zero temperature, the high frequency part of DSS is universal and increases in certain directions as ωd−1 with d = 2 and 3 for surface states and Weyl semimetals, respectively, while for helical edge states, the interactions renormalize the exponent as d = 2K − 1 with K the Luttinger-liquid parameter. As a result, spin relaxation rate cannot be deduced from the DSS in contrast to the case of usual metals, which follows from the strongly entangled spin and charge degrees of freedom in these systems.
Construction of a High-Density Genetic Map and Quantitative Trait Locus Mapping in the Sea Cucumber Apostichopus japonicus
Authors: Tian Meilin , Li Yangping , Jing Jing , Mu Chuang , Du Huixia , Dou Jinzhuang , Mao Junxia , Li Xue , Jiao Wenqian , Wang Yangfan , Hu Xiaoli , Wang Shi , Wang Ruijia , Bao Zhenmin 
Published: October 2015

AbstractGenetic linkage maps are critical and indispensable tools in a wide range of genetic and genomic research. With the advancement of genotyping-by-sequencing (GBS) methods, the construction of a high-density and high-resolution linkage maps has become achievable in marine organisms lacking sufficient genomic resources, such as echinoderms. In this study, high-density, high-resolution genetic map was constructed for a sea cucumber species, Apostichopus japonicus, utilizing the 2b-restriction site-associated DNA (2b-RAD) method. A total of 7839 markers were anchored to the linkage map with the map coverage of 99.57%, to our knowledge, this is the highest marker density among echinoderm species. QTL mapping and association analysis consistently captured one growth-related QTL located in a 5 cM region of linkage group (LG) 5. An annotated candidate gene, retinoblastoma-binding protein 5 (RbBP5), which has been reported to be an important regulator of cell proliferation, was recognized in the QTL region. This linkage map represents a powerful tool for research involving both fine-scale QTL mapping and marker assisted selection (MAS) and will facilitate chromosome assignment and improve the whole-genome assembly of sea cucumber in the future.
Soft-tissue and dermal arrangement in the wing of an Early Cretaceous bird: Implications for the evolution of avian flight
Authors: Navalón Guillermo , Marugán-Lobón Jesús , Chiappe Luis M. , Luis Sanz José , Buscalioni Ángela D. 
Published: October 2015

AbstractDespite a wealth of fossils of Mesozoic birds revealing evidence of plumage and other soft-tissue structures, the epidermal and dermal anatomy of their wing’s patagia remain largely unknown. We describe a distal forelimb of an enantiornithine bird from the Lower Cretaceous limestones of Las Hoyas, Spain, which reveals the overall morphology of the integument of the wing and other connective structures associated with the insertion of flight feathers. The integumentary anatomy and myological and arthrological organization of the new fossil is remarkably similar to that of modern birds, in which a system of small muscles, tendons and ligaments attaches to the follicles of the remigial feathers and maintains the functional integrity of the wing during flight. The new fossil documents the oldest known occurrence of connective tissues in association with the flight feathers of birds. Furthermore, the presence of an essentially modern connective arrangement in the wing of enantiornithines supports the interpretation of these primitive birds as competent fliers.
Chemical recognition of fruit ripeness in spider monkeys (Ateles geoffroyi)
Authors: Nevo Omer , Orts Garri Rosa , Hernandez Salazar Laura Teresa , Schulz Stefan , Heymann Eckhard W. , Ayasse Manfred , Laska Matthias 
Published: October 2015

AbstractPrimates are now known to possess well-developed olfactory sensitivity and discrimination capacities that can play a substantial role in many aspects of their interaction with conspecifics and the environment. Several studies have demonstrated that olfactory cues may be useful in fruit selection. Here, using a conditioning paradigm, we show that captive spider monkeys (Ateles geoffroyi) display high olfactory discrimination performance between synthetic odor mixtures mimicking ripe and unripe fruits of two wild, primate-consumed, Neotropical plant species. Further, we show that spider monkeys are able to discriminate the odor of ripe fruits from odors that simulate unripe fruits that become increasingly similar to that of ripe ones. These results suggest that the ability of spider monkeys to identify ripe fruits may not depend on the presence of any individual compound that mark fruit ripeness. Further, the results demonstrate that spider monkeys are able to identify ripe fruits even when the odor signal is accompanied by a substantial degree of noise.
Use of the second-generation antipsychotic, risperidone, and secondary weight gain are associated with an altered gut microbiota in children
Authors: Bahr S M , Tyler B C , Wooldridge N , Butcher B D , Burns T L , Teesch L M , Oltman C L , Azcarate-Peril M A , Kirby J R , Calarge C A 
Published: October 2015

AbstractThe atypical antipsychotic risperidone (RSP) is often associated with weight gain and cardiometabolic side effects. The mechanisms for these adverse events are poorly understood and, undoubtedly, multifactorial in etiology. In light of growing evidence implicating the gut microbiome in the host’s energy regulation and in xenobiotic metabolism, we hypothesized that RSP treatment would be associated with changes in the gut microbiome in children and adolescents. Thus, the impact of chronic (>12 months) and short-term use of RSP on the gut microbiome of pediatric psychiatrically ill male participants was examined in a cross-sectional and prospective (up to 10 months) design, respectively. Chronic treatment with RSP was associated with an increase in body mass index (BMI) and a significantly lower ratio of Bacteroidetes:Firmicutes as compared with antipsychotic-naïve psychiatric controls (ratio=0.15 vs 1.24, respectively; P<0.05). Furthermore, a longitudinal observation, beginning shortly after onset of RSP treatment, revealed a gradual decrease in the Bacteroidetes:Firmicutes ratio over the ensuing months of treatment, in association with BMI gain. Lastly, metagenomic analyses were performed based on extrapolation from 16S ribosomal RNA data using the software package, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Those data indicate that gut microbiota dominating the RSP-treated participants are enriched for pathways that have been implicated in weight gain, such as short-chain fatty acid production.
Factors Affecting Early Services for Children Who Are Hard of Hearing
Authors: Harrison Melody , Page Thomas A. , Oleson Jacob , Spratford Meredith , Unflat Berry Lauren , Peterson Barbara , Welhaven Anne , Arenas Richard M. , Moeller Mary Pat 
Published: October 2015

Purpose
To describe factors affecting early intervention (EI) for children who are hard of hearing, we analyzed (a) service setting(s) and the relationship of setting to families' frequency of participation, and (b) provider preparation, caseload composition, and experience in relation to comfort with skills that support spoken language for children who are deaf and hard of hearing (CDHH).

Method
Participants included 122 EI professionals who completed an online questionnaire annually and 131 parents who participated in annual telephone interviews.

Results
Most families received EI in the home. Family participation in this setting was significantly higher than in services provided elsewhere. EI professionals were primarily teachers of CDHH or speech-language pathologists. Caseload composition was correlated moderately to strongly with most provider comfort levels. Level of preparation to support spoken language weakly to moderately correlated with provider comfort with 18 specific skills.

Conclusions
Results suggest family involvement is highest when EI is home-based, which supports the need for EI in the home whenever possible. Access to hands-on experience with this population, reflected in a high percentage of CDHH on providers' current caseloads, contributed to professional comfort. Specialized preparation made a modest contribution to comfort level.
Constrained inference of protein interaction networks for invadopodium formation in cancer
Authors: Wang Haizhou , Leung Ming , Wandinger‐Ness Angela , Hudson Laurie G. , Song Mingzhou 
Published: October 2015

Integrating prior molecular network knowledge into interpretation of new experimental data is routine practice in biology research. However, a dilemma for deciphering interactome using Bayes’ rule is the demotion of novel interactions with low prior probabilities. Here the authors present constrained generalised logical network (CGLN) inference to predict novel interactions in dynamic networks, respecting previously known interactions and observed temporal coherence. It encodes prior interactions as probabilistic logic rules called local constraints, and forms global constraints using observed dynamic patterns. CGLN finds constraint‐satisfying trajectories by solving a k ‐stops problem in the state space of dynamic networks and then reconstructs candidate networks. They benchmarked CGLN on randomly generated networks, and CGLN outperformed its alternatives when 50% or more interactions in a network are given as local constraints. CGLN is then applied to infer dynamic protein interaction networks regulating invadopodium formation in motile cancer cells. CGLN predicted 134 novel protein interactions for their involvement in invadopodium formation. The most frequently predicted interactions centre around focal adhesion kinase and tyrosine kinase substrate TKS4, and 14 interactions are supported by the literature in molecular contexts related to invadopodium formation. As an alternative to the Bayesian paradigm, the CGLN method offers constrained network inference without requiring prior probabilities and thus can promote novel interactions, consistent with the discovery process of scientific facts that are not yet in common beliefs.
Effects of lymphocyte profile on development of EBV-induced lymphoma subtypes in humanized mice
Authors: Lee Eun Kyung , Joo Eun Hye , Song Kyung-A , Choi Bongkum , Kim Miyoung , Kim Seok-Hyung , Kim Sung Joo , Kang Myung-Soo 
Published: October 2015

Significance
The mechanism of how Epstein-Barr virus (EBV) contributes to the development of two distinct lymphomas remains unknown. Intriguingly, EBV-associated Hodgkin’s lymphoma was seen exclusively in mice with activated T-cell conditions, whereas EBV-associated non-Hodgkin’s lymphoma was developed in mice with suppressed T-cell conditions, in which immature B cells were predominant at the time of EBV infection. This distinct association provides new insight into the pathogenesis of specific types of EBV-induced lymphomas.
Consequences of zygote injection and germline transfer of mutant human mitochondrial DNA in mice
Authors: Yu Hong , Koilkonda Rajeshwari D. , Chou Tsung-Han , Porciatti Vittorio , Mehta Arpit , Hentall Ian D. , Chiodo Vince A. , Boye Sanford L. , Hauswirth William W. , Lewin Alfred S. , Guy John 
Published: October 2015

Significance
Therapies for Leber hereditary optic neuropathy (LHON), in common with all disorders caused by mutated mtDNA, are inadequate, in part because of the absence of suitable animal models. To test a potential therapy, we introduced mutant human NADH ubiquinone oxidoreductase subunit 4 DNA directly into mitochondria of mouse zygotes to generate transgenic LHON mice. This mutation in mice caused the hallmark visual loss and optic neuropathy seen in LHON patients. We reversed the blindness by gene therapy with the wild-type allele. To our knowledge, this is the first description of a mouse model with the same genotype and phenotype as the human counterpart disorder. This innovative technology has implications not only for creating mouse models of mutant mtDNA but also for treating the mitochondrial dysfunction with gene therapy.
Resource colimitation governs plant community responses to altered precipitation
Authors: Eskelinen Anu , Harrison Susan P. 
Published: October 2015

Significance
Understanding how and why communities vary in their responses to climatic change is critical for global biodiversity conservation. In a 5-y experimental study of a heterogeneous grassland system, we found that the most nutrient-limited communities were relatively insensitive to alterations in rainfall, but that this insensitivity could be reversed by nutrient addition, leading to greatly enhanced productivity, near-complete species turnover, and accelerated diversity loss. Species with slow-growing, resource-conserving traits were especially vulnerable to decline. These results highlight that the ecological principle of colimitation by water and nutrients can lead to powerful predictions about climate change impacts on natural communities.
Bubble nucleation and migration in a lead–iron hydr(oxide) core–shell nanoparticle
Authors: Niu Kaiyang , Frolov Timofey , Xin Huolin L. , Wang Junling , Asta Mark , Zheng Haimei 
Published: October 2015

Significance
An understanding of gas bubble formation in a solid and the materials’ responses at the nanoscale is of technological importance. Tracking nanobubble evolution in a solid during chemical reactions involving a solid, a gas, and a liquid is rarely achieved. Here, we show a breakthrough in materials characterization by monitoring gas bubble nucleation and migration and the associated strain evolution in a lead–iron hydroxide core–shell nanoparticle during dehydration reaction using liquid cell transmission electron microscopy. We found strain coupling can be used to remove gas bubbles from nanostructures, which sheds light on strategies for nanomaterials engineering and novel materials synthetic routes.
Direct link between metabolic regulation and the heat-shock response through the transcriptional regulator PGC-1α
Authors: Minsky Neri , Roeder Robert G. 
Published: October 2015

Significance
In recent years an extensive effort has been made to elucidate the molecular pathways involved in metabolic signaling. Our study shows, surprisingly, a direct link between metabolic regulation and the heat-shock response, a highly conserved transcriptional program that is activated in the presence of various environmental stresses. Specifically, we demonstrate that peroxisome proliferator-activated receptor γ coactivator 1α, a critical and well-established inducible transcriptional coactivator of metabolic genes, acts as a direct transcriptional repressor of heat-shock factor 1, a key regulator of the heat-shock/stress response and a factor more recently demonstrated to be necessary for cancer initiation and survival. Thus, our findings have possible implications both for our understanding of the full scope of metabolically regulated target genes in vivo and, conceivably, for therapeutics.
A respiratory chain controlled signal transduction cascade in the mitochondrial intermembrane space mediates hydrogen peroxide signaling
Authors: Patterson Heide Christine , Gerbeth Carolin , Thiru Prathapan , Vögtle Nora F. , Knoll Marko , Shahsafaei Aliakbar , Samocha Kaitlin E. , Huang Cher X. , Harden Mark Michael , Song Rui , Chen Cynthia , Kao Jennifer , Shi Jiahai , Salmon Wendy , Shaul Yoav D. , Stokes Matthew P. , Silva Jeffrey C. , Bell George W. , MacArthur Daniel G. , Ruland Jürgen , Meisinger Chris , Lodish Harvey F. 
Published: October 2015

SignificanceBoth the mitochondrial respiratory chain and reactive oxygen species (ROS) control numerous physiological and pathological cellular responses. ROS such as hydrogen peroxide (H2O2) are thought to initiate signaling by broadly and nonspecifically redox-modifying signaling molecules, suggesting that H2O2signaling may be distinct from other signal transduction pathways. Here, we provide evidence suggesting that H2O2signaling is under control of what appears to be a typical signal transduction cascade that connects the respiratory chain to the mitochondrial intermembrane space-localized conserved Syk pathway and results in a focused signaling response in diverse cell types. The results thus reveal a mechanism that allows the respiratory chain to communicate with the remainder of the cell in response to ROS.
First Record of Pughead Deformity in Blue Catfish
Authors: Schmitt Joseph D. , Orth Donald J. 
Published: October 2015

AbstractPugheaded fish exhibit anomalous bone structure, often characterized by a steep, bulging forehead and incomplete closure of the mouth. While the pughead deformity has been observed in many species of fish, thescientific literature contains no documented instances of pugheadedness in Blue Catfish Ictalurus furcatus. Pugheadedness is rare, particularly in tidal systems, and most recorded instances have been based on single specimens. We captured several pugheaded Blue Catfish (N = 18) in the tidal Rappahannock River in eastern Virginia, a tributary of the Chesapeake Bay. While Blue Catfish sampling was extensive in the James, Pamunkey, and Mattaponi rivers (N = 4,357 fish at 163 sites), pugheaded specimens were encountered at only six sampling sites within the upper tidal zone of the Rappahannock River, an area known to be susceptible to summertime hypoxia. We encountered pugheaded individuals at a higher rate than reported in most published studies, ranging between 1.89% and 3.68%, much higher than rates detected in other tidal systems. Pugheaded specimens had significantly lower relative weights than nonpugheaded specimens, indicating that this deformity may affect their ability to forage. Hypoxia, pollutants, and genetic anomalies are all explored as potential drivers of high deformity rates within the Rappahannock River.