bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular diagnosis of pediatric patients with citrin deficiency in China: SLC25A13 mutation spectrum and the geographic distribution
Authors: Lin Wei-Xia , Zeng Han-Shi , Zhang Zhan-Hui , Mao Man , Zheng Qi-Qi , Zhao Shu-Tao , Cheng Ying , Chen Feng-Ping , Wen Wang-Rong , Song Yuan-Zong 
Published: July 2016

AbstractCitrin deficiency (CD) is a Mendelian disease due to biallelic mutations of SLC25A13 gene. Neonatal intrahepatic cholestasis caused by citrin deficiency (NICCD) is the major pediatric CD phenotype, and its definite diagnosis relies on SLC25A13 genetic analysis. China is a vast country with a huge population, but the SLC25A13 genotypic features of CD patients in our country remains far from being well clarified. Via sophisticated molecular analysis, this study diagnosed 154 new CD patients in mainland China and identified 9 novel deleterious SLC25A13 mutations, i.e. c.103A > G, [c.329 − 154_c.468 + 2352del2646; c.468 + 2392_c.468 + 2393ins23], c.493C > T, c.755 − 1G > C, c.845_c.848 + 1delG, c.933_c.933 + 1insGCAG, c.1381G > T, c.1452 + 1G > A and c.1706_1707delTA. Among the 274 CD patients diagnosed by our group thus far, 41 SLC25A13 mutations/variations were detected. The 7 mutations c.775C > T, c.851_854del4, c.1078C > T, IVS11 + 1G > A, c.1364G > T, c.1399C > T and IVS16ins3kb demonstrated significantly different geographic distribution. Among the total 53 identified genotypes, only c.851_854del4/c.851_854del4 and c.851_854del4/c.1399C > T presented different geographic distribution. The northern population had a higher level of SLC25A13 allelic heterogeneity than those in the south. These findings enriched the SLC25A13 mutation spectrum and brought new insights into the geographic distribution of the variations and genotypes, providing reliable evidences for NICCD definite diagnosis and for the determination of relevant molecular targets in different Chinese areas.
Polymeric nanocapsules with up-converting nanocrystals cargo make ideal fluorescent bioprobes
Authors: Bazylińska U. , Wawrzyńczyk D. , Kulbacka J. , Frąckowiak R. , Cichy B. , Bednarkiewicz A. , Samoć M. , Wilk K. A. 
Published: July 2016

AbstractAn innovative approach for up-converting nanoparticles adaptation for bio-related and theranostic applications is presented. We have successfully encapsulated multiple, ~8 nm in size NaYF4 nanoparticles inside the polymeric nanocarriers with average size of ~150 nm. The initial coating of nanoparticles surfaces was preserved due to the hydrophobic environment inside the nanocapsules, and thus no single nanoparticle surface functionalization was necessary. The selection of biodegradable and sugar-based polyelectrolyte shells ensured biocompatibility of the nanostructures, while the choice of Tm3+ and Yb3+ NaYF4 nanoparticles co-doping allowed for near-infrared to near-infrared bioimaging of healthy and cancerous cell lines. The protective role of organic shell resulted in not only preserved high up-converted emission intensity and long luminescence lifetimes, without quenching from water environment, but also ensured low cytotoxicity and high cellular uptake of the engineered nanocapsules. The multifunctionality of the proposed nanocarriers is a consequence of both the organic exterior part that is accessible for conjugation with biologically important molecules, and the hydrophobic interior, which in future application may be used as a container for co-encapsulation of inorganic nanoparticles and anticancer drug cargo.
The RNA-binding protein repertoire of Arabidopsis thaliana
Authors: Marondedze Claudius , Thomas Ludivine , Serrano Natalia L. , Lilley Kathryn S. , Gehring Chris 
Published: July 2016

AbstractRNA-binding proteins (RBPs) have essential roles in determining the fate of RNA from synthesis to decay and have been studied on a protein-by-protein basis, or computationally based on a number of well-characterised RNA-binding domains. Recently, high-throughput methods enabled the capture of mammalian RNA-binding proteomes. To gain insight into the role of Arabidopsis thaliana RBPs at the systems level, we have employed interactome capture techniques using cells from different ecotypes grown in cultures and leaves. In vivo UV-crosslinking of RNA to RBPs, oligo(dT) capture and mass spectrometry yielded 1,145 different proteins including 550 RBPs that either belong to the functional category ‘RNA-binding’, have known RNA-binding domains or have orthologs identified in mammals, C. elegans, or S. cerevisiae in addition to 595 novel candidate RBPs. We noted specific subsets of RBPs in cultured cells and leaves and a comparison of Arabidopsis, mammalian, C. elegans, and S. cerevisiae RBPs reveals a common set of proteins with a role in intermediate metabolism, as well as distinct differences suggesting that RBPs are also species and tissue specific. This study provides a foundation for studies that will advance our understanding of the biological significance of RBPs in plant developmental and stimulus specific responses.
Inactivation of Fam20B in Joint Cartilage Leads to Chondrosarcoma and Postnatal Ossification Defects
Authors: Ma Pan , Yan Wenjuan , Tian Ye , Wang Jingya , Feng Jian Q. , Qin Chunlin , Cheng Yi-Shing Lisa , Wang Xiaofang 
Published: July 2016

AbstractDuring endochondral ossification, chondrocytes embed themselves in a proteoglycan-rich matrix during the proliferation-maturation transition. Accumulating evidence shows that proteoglycans are essential components for chondrocyte proliferation and differentiation. When we conditionally inactivated FAM20B (Family with sequence similarity 20 member-B), which is a newly identified xylose kinase essential for glycosaminoglycan (GAG) formation on the protein core of proteoglycans, from the dental mesenchyme using Osr2-Cre, which is also strongly expressed in joint cartilage, we found chondrosarcoma in the knee joint and remarkable defects of postnatal ossification in the long bones. Mechanistic analysis revealed that the defects were associated with gain of function in multiple signaling pathways in the epiphyseal chondrocytes, such as those derived by WNT, BMP, and PTHrP/IHH molecules, suggesting that the FAM20B-catalyzed proteoglycans are critical mediators for a signaling balance in the regulatory network controlling chondrocyte differentiation and proliferation. In particular, we demonstrated that the WNT inhibitor was able to rescue part of the bone defects in Osr2-Cre;Fam20Bfl/fl mice, indicating that FAM20B-catalyzed proteoglycans regulate postnatal endochondral ossification partially through the mediation of WNT signaling.
Identification of an NDM-5-producing Escherichia coli Sequence Type 167 in a Neonatal Patient in China
Authors: Zhu Yuan-qi , Zhao Jing-yi , Xu Cha , Zhao Hui , Jia Nan , Li Yan-nian 
Published: July 2016

AbstractEmergence of New Delhi metallo-β-lactamase-producing Enterobacteriaceae has become a challenging threat to public health. Two carbapenem-resistant Escherichia coli, strain QD28 and QD29, were recovered from the aspirating sputum of a neonate and the urine of an adult in a Chinese hospital in 2013. Molecular typing revealed that both isolates belonged to the sequence type 167, but they were clonally diverse. Both isolates exhibited resistance to carbapenems, cephalosporins, ciprofloxacin, gentamicin, piperacillin-tazobactam and trimethoprim-sulfamethoxazole. In addition, strain QD28 was also resistant to aztreonam and strain QD29 was resistant to amikacin, fosfomycin and minocycline. Antimicrobial resistance gene screening revealed that strain QD28 harbored aac(6′)-Ib, blaCTX-M-14, blaNDM-5, blaTEM-1 and sul1 genes and strain QD29 harbored aac(6′)-Ib, blaCTX-M-3, blaNDM-5, blaTEM-1, rmtB, sul1 and sul2 genes. The blaNDM-5 gene was found to be located on a 46-kb plasmid in two isolates and further sequence analysis showed that this plasmid was highly similar to the previously reported IncX3 plasmid pNDM-MGR194 in India. This is the first identification of blaNDM-5-carrying E. coli in the neonatal infection.
E‐plane metallic RWG‐to‐SIW transition for large‐scale MM‐wave phased array antenna applications
Authors: Abdel‐Wahab W.M. , Ehsandar A. , Al‐Saedi H. , Safavi‐Naeini S. 
Published: July 2016

A novel air‐filled E‐plane rectangular waveguide (RWG) to substrate integrated waveguide (SIW) transition, which is suitable for Ka‐band large‐scale antenna arrays, is presented. The power is coupled between the RWG and SIW through two slots: one etched on the SIW ground plane and the other cut through metallic RWG narrow side wall (E‐plane). A back‐to‐back transition is designed, fabricated, assembled, and tested. Measured results show a good agreement with the simulated ones. An SIW attenuation loss ≤0.33 dB/1 cm and a transition return loss better than 10 dB have been experimentally obtained over the band 28.30–30.8 GHz.
Compact QB‐BPF based on single PMR
Authors: Zhu Chuanming , Xu Jin , Kang Wei , Wu Wen 
Published: July 2016

Compact quint‐band bandpass filter (QB‐BPF) based on a novel penta‐mode resonator (PMR) is presented. The first five resonant modes of the proposed PMR can be independently controlled by shorted high‐impedance section of quarter‐wave stepped impedance resonators, and four loaded open stubs resulting in the independency of centre frequencies and quality factors of five passbands. Meanwhile, due to the multipath propagation induced from cross‐coupling, 11 transmission zeros are realised around five passbands, resulting in high passband selectivity. As an example, a QB‐BPF operating at 0.63/1.2/1.8/2.45/3.5 GHz is designed and fabricated. The fabricated QB‐BPF also has a compact size of 0.18λg × 0.12λg.
Design of a high‐speed electrothermal linear micromotor for microelectromechanical systems safety‐and‐arming devices
Authors: Li Xiuyuan , Zhao Yulong , Hu Tengjiang , Bai Yingwei 
Published: July 2016

The design, fabrication and characterisation of a high‐speed electrothermal linear micromotor for microelectromechanical systems safety‐and‐arming devices are presented. The micromotor consists of a microspring, a barrier plate and four V‐shaped electrothermal actuators with microlever amplifications. The whole device is fabricated on a silicon‐on‐insulator wafer with a 50 µm device layer and the fabrication process is introduced. The micromotor has been successfully operated at a speed of 35.66 mm/s over a range of 500 µm with an output force of 5.27 mN under the applied voltage of 23 V. The chip area of the fabricated micromotor is about 19.20 mm2, which means the micromotor can be easily integrated with other microdevices. The linear micromotor performs well in driving force, mechanical strength and working speed, which signifies the proposed device is suitable for safety‐and‐arming devices.
Single-molecule imaging reveals a common mechanism shared by G-quadruplex–resolving helicases
Authors: Tippana Ramreddy , Hwang Helen , Opresko Patricia L. , Bohr Vilhelm A. , Myong Sua 
Published: July 2016

Significance
G-quadruplex (GQ) is a four-stranded DNA structure that forms in the human genome and influences gene expression and DNA replication. Stably formed GQ structures can act as a physical blockade to disrupt genomic processes. To counteract such an effect, cells possess special helicases dedicated to unfolding GQ structures. In our study, we examined three such GQ-resolving helicases, using single-molecule imaging, that show distinct binding preference to different conformations (folding directions) of GQ DNA. Nevertheless, all three GQ resolvases use the same mechanism, which involves repetitive cycles of GQ unfolding in successive runs. Such activity leads to efficient GQ hybridization with a complementary DNA and dislodging chemical GQ ligand. Our findings have implications for designing new GQ ligands for therapeutic purposes.
DNA damage tolerance pathway involving DNA polymerase ι and the tumor suppressor p53 regulates DNA replication fork progression
Authors: Hampp Stephanie , Kiessling Tina , Buechle Kerstin , Mansilla Sabrina F. , Thomale Jürgen , Rall Melanie , Ahn Jinwoo , Pospiech Helmut , Gottifredi Vanesa , Wiesmüller Lisa 
Published: July 2016

SignificanceDNA damage tolerance pathways like translesion synthesis and recombination facilitate the bypass of replication-blocking lesions. Such events are crucial for the survival of rapidly proliferating cells, including cancer and stem cells undergoing active duplication during tissue renewal. Herein, we characterize an unprecedented damage tolerance pathway that requires the combined function of a highly enigmatic translesion DNA polymerase ι (POLι) and the so-called guardian-of-the-genome, p53. We provide evidence demonstrating that p53 complexed with POLι triggers idling events that decelerate nascent DNA elongation at replication barriers, facilitating the resolution of stalled forks by specialized structure-specific enzymes. Our findings implicate p53 in the protection of quickly growing cancer and stem cells from endogenous and exogenous sources of replication stress.
Minimal basilar membrane motion in low-frequency hearing
Authors: Warren Rebecca L. , Ramamoorthy Sripriya , Ciganović Nikola , Zhang Yuan , Wilson Teresa M. , Petrie Tracy , Wang Ruikang K. , Jacques Steven L. , Reichenbach Tobias , Nuttall Alfred L. , Fridberger Anders 
Published: July 2016

Significance
To perceive speech, the brain relies on inputs from sensory cells located near the top of the spiral-shaped cochlea. This low-frequency region of the inner ear is anatomically difficult to access, and it has not previously been possible to study its mechanical response to sound in intact preparations. Here, we used optical coherence tomography to image sound-evoked vibration inside the intact cochlea. We show that low-frequency sound moves a small portion of the basilar membrane, and that the motion declines in an exponential manner across the basilar membrane. Hence, the response of the hearing organ to speech-frequency sounds is different from the one evident in high-frequency cochlear regions.
Referring expressions and executive functions in bilingualism
Authors: Sorace Antonella 
Published: July 2016

Abstract
Recent research has shown that the bilingual experience has positive effects on non-linguistic cognition (Bialystok 2009; Costa and Sebastian-Gallés 2014) but also negative effects on language, for example on vocabulary size and lexical fluency (Pearson et al. 1993). While most of the linguistic ‘disadvantages’ of bilingualism have been discussed in the lexical domain, this question is scaled up here to the sentence level and a novel theoretical framework is proposed which explicitly connects psychological and linguistic research. It is suggested that the bilingual experience may (a) affect the reciprocal interactions between language and general cognition, and (b) modulate the relation between components of executive functions. These effects may in turn influence the processing of particular linguistic structures, such as anaphoric expressions, and lead to bilingual-monolingual differences that could be regarded as ‘disadvantages’ but are in fact the result of normal adaptive changes due to the bilingual experience. Future experimental research validating this proposal may benefit both linguistic models of anaphora resolution and psychological models of cognitive control in monolinguals and bilinguals.
Optimal welding parameters for small-scale resistance spot welding with response surface methodology
Authors: Yue X. K. , Tong G. Q. , Chen F. , Ma X. L. , Gao X. P. 
Published: July 2016

In this study, Ti–1Al–1Mn thin foils with thickness of 0.05 mm were welded by small-scale resistance spot welding. Welding current, electrode force and welding time have been changed while other welding parameters remained constant. The welded joints were subjected to tensile shear tests for determining the values of shear force and absorption energy. A quadratic model of response surface methodology based on Box–Behnken design was employed in establishing regression equations between input variables (current, electrode force and time) and output variables (shear force, absorption energy, variance of shear force and variance of absorption energy). The models were satisfied in optimising the welding parameters. Besides, the microstructure analysis on the typical spot welds was also conducted. GRAPHICAL ABSTRACT
Combined effects of crystallography, heat treatment and surface polishing on blistering in tungsten exposed to high-flux deuterium plasma
Authors: Zayachuk Y. , Tanyeli I. , Van Boxel S. , Bystrov K. , Morgan T.W. , Roberts S.G. 
Published: July 2016

Abstract
For tungsten exposed to low-energy hydrogen-plasmas, it has been thought that grains with

〈

1

1

1

〉

surface normal are most susceptible to blistering while those with

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0

0

1

〉

surface normal are virtually impervious to it. Here, we report results showing that non-uniformity of blister distribution depends on the state of the surface due to polishing. In electrochemically polished material blisters appear on the grains with all orientations, while in mechanically polished material blister-free areas associated with particular orientations emerge. On the other hand, blistering is shown to have a strong dependence on the level of deformation within particular grains in partially recrystallized material.
Differential paralog divergence modulates evolutionary outcomes in yeast
Authors: Sanchez Monica R. , Miller Aaron W. , Liachko Ivan , Sunshine Anna B. , Lynch Bryony , Huang Mei , DeSevo Christopher G. , Pai Dave A. , Tucker Cheryl M. , Hoang Margaret L. , Dunham Maitreya J. 
Published: July 2016

AbstractEvolutionary outcomes depend not only on the selective forces acting upon a species, but also on the genetic background. However, large timescales and uncertain historical selection pressures can make it difficult to discern such important background differences between species. Experimental evolution is one tool to compare evolutionary potential of known genotypes in a controlled environment. Here we utilized a highly reproducible evolutionary adaptation inSaccharomyces cerevisiaeto investigate whether other yeast species would adopt similar evolutionary trajectories. We evolved populations ofS. cerevisiae, S. paradoxus, S. mikatae, S. uvarum, and interspecific hybrids betweenS. uvarumandS. cerevisiaefor ~200-500 generations in sulfate-limited continuous culture. Wild-typeS. cerevisiaecultures invariably amplify the high affinity sulfate transporter gene,SUL1. However, while amplification of theSUL1locus was detected inS. paradoxusandS. mikataepopulations,S. uvarumcultures instead selected for amplification of the paralog,SUL2. We measured the relative fitness of strains bearing deletions and amplifications of bothSULgenes from different species, confirming that, converse toS. cerevisiae, S. uvarum SUL2contributes more to fitness in sulfate limitation thanS. uvarum SUL1. By measuring the fitness and gene expression of chimeric promoter-ORF constructs, we were able to delineate the cause of this differential fitness effect primarily to the promoter ofS. uvarum SUL1. Our data show evidence of differential sub-functionalization among the sulfur transporters across Saccharomyces species through recent changes in noncoding sequence. Furthermore, these results show a clear example of how such background differences due to paralog divergence can drive significant changes in evolutionary trajectories of eukaryotes.
Antiparallel protocadherin homodimers use distinct affinity- and specificity-mediating regions in cadherin repeats 1-4
Authors: Nicoludis John M. , Vogt Bennett E. , Green Anna G. , Schärfe Charlotta P. I. , Marks Debora S. , Gaudet Rachelle 
Published: July 2016

ABSTRACTProtocadherins (Pcdhs) are cell adhesion and signaling proteins used by neurons to develop and maintain neuronal networks, relying ontranshomophilic interactions between their extracellular cadherin (EC) repeat domains. We present the structure of the antiparallel EC1-4 homodimer of human PcdhYB3, a member of the γ subfamily of clustered Pcdhs. Structure and sequence comparisons of α, β, and γ clustered Pcdh isoforms illustrate that subfamilies encode specificity in distinct ways through diversification of loop region structure and composition in EC2 and EC3, which contains isoform-specific conservation of primarily polar residues. In contrast, the EC1/EC4 interface comprises hydrophobic interactions that provide non-selective dimerization affinity. Using sequence coevolution analysis, we found evidence for a similar antiparallel EC1-4 interaction in non-clustered Pcdh families. We thus deduce that the EC1-4 antiparallel homodimer is a general interaction strategy that evolved before the divergence of these distinct protocadherin families.
Anti-proliferative therapy for HIV cure: a compound interest approach
Authors: Reeves Daniel B. , Duke Elizabeth R. , Hughes Sean M. , Prlic Martin , Hladik Florian , Schiffer Joshua T. 
Published: July 2016

AbstractIn the era of antiretroviral therapy (ART), HIV-1 infection is no longer tantamount to early death. Yet the benefits of treatment are available only to those who can access, afford, and tolerate taking daily pills. True cure is challenged by HIV latency, the ability of chromosomally integrated virus to persist within memory CD4+T cells in a non-replicative state and activate when ART is discontinued. Using a mathematical model of HIV dynamics, we demonstrate that treatment strategies offering modest but continual enhancement of reservoir clearance rates result in faster cure than abrupt, one-time reductions in reservoir size. We frame this concept in terms of compounding interest: small changes in interest rate drastically improve returns over time. On ART, latent cell proliferation rates are orders of magnitude larger than activation and new infection rates. Contingent on subtypes of cells that may make up the reservoir and their respective proliferation rates, our model predicts that coupling clinically available, anti-proliferative therapies with ART could result in functional cure within 2-10 years rather than several decades on ART alone.
Metabolomic-based biomarker discovery for non-invasive lung cancer screening: A case study
Authors: O’Shea Keiron , Cameron Simon J.S. , Lewis Keir E , Lu Chuan , Mur Luis AJ 
Published: July 2016

AbstractBackgroundLung cancer (LC) is one of the leading lethal cancers worldwide, with an estimated 18.4% of all cancer deaths being attributed to the disease. Despite developments in cancer diagnosis and treatment over the previous thirty years, LC has seen little to no improvement in the overall five year survival rate after initial diagnosis.MethodsIn this paper, we extended a recent study which profiled the metabolites in sputum from patients with lung cancer and age-matched volunteers smoking controls using flow infusion electrospray ion mass spectrometry. We selected key metabolites for distinguishing between different classes of lung cancer, and employed artificial neural networks and leave-one-out cross-validation to evaluate the predictive power of the identified biomarkers.ResultsThe neural network model showed excellent performance in clas sification between lung cancer and control groups with the area under the receiver operating characteristic curve of 0.99. The sensitivity and specificity of for detecting cancer from controls were 96% and 94% respectively. Furthermore, we have identified six putative metabolites that were able todiscriminate between sputum samples derived from patients suffering small cell lung cancer (SCLC) and non-small cell lung cancer. These metabolites achieved excellent cross validation performance with a sensitivity of 80% and specificity of 100% for predicting SCLC.ConclusionsThese results indicate that sputum metabolic profiling may have potential for screening of lung cancer and lung cancer recurrence, and may greatly improve effectiveness of clinical intervention.