bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel Locus for Paroxysmal Kinesigenic Dyskinesia Mapped to Chromosome 3q28-29
Authors: Liu Ding , Zhang Yumiao , Wang Yu , Chen Chanjuan , Li Xin , Zhou Jinxia , Song Zhi , Xiao Bo , Rasco Kevin , Zhang Feng , Wen Shu , Li Guoliang 
Published: May 2016

AbstractParoxysmal kinesigenic dyskinesia (PKD) is characterized by recurrent and brief attacks of dystonia or chorea precipitated by sudden movements. It can be sporadic or familial. Proline-Rich Transmembrane Protein 2 (PRRT2) has been shown to be a common causative gene of PKD. However, less than 50% of patients with primary PKD harbor mutations in PRRT2. The aim of this study is to use eight families with PKD to identify the pathogenic PRRT2 mutations, or possible novel genetic cause of PKD phenotypes. After extensive clinical investigation, direct sequencing and mutation analysis of PRRT2 were performed on patients from eight PKD families. A genome-wide STR and SNP based linkage analysis was performed in one large family that is negative for pathogenic PRRT2 mutations. Using additional polymorphic markers, we identified a novel gene locus on chromosome 3q in this PRRT2-mutation-negative PKD family. The LOD score for the region between markers D3S1314 and D3S1256 is 3.02 and we proposed to designate this locus as Episodic Kinesigenic Dyskinesia (EKD3). Further studies are needed to identify the causative gene within this locus.
A persistent northern boundary of Indian Summer Monsoon precipitation over Central Asia during the Holocene
Authors: Ramisch Arne , Lockot Gregori , Haberzettl Torsten , Hartmann Kai , Kuhn Gerhard , Lehmkuhl Frank , Schimpf Stefan , Schulte Philipp , Stauch Georg , Wang Rong , Wünnemann Bernd , Yan Dada , Zhang Yongzhan , Diekmann Bernhard 
Published: May 2016

AbstractExtra-tropical circulation systems impede poleward moisture advection by the Indian Summer Monsoon. In this context, the Himalayan range is believed to insulate the south Asian circulation from extra-tropical influences and to delineate the northern extent of the Indian Summer Monsoon in central Asia. Paleoclimatic evidence, however, suggests increased moisture availability in the Early Holocene north of the Himalayan range which is attributed to an intensification of the Indian Summer Monsoon. Nevertheless, mechanisms leading to a surpassing of the Himalayan range and the northern maximum extent of summer monsoonal influence remain unknown. Here we show that the Kunlun barrier on the northern Tibetan Plateau [~36°N] delimits Indian Summer Monsoon precipitation during the Holocene. The presence of the barrier relocates the insulation effect 1,000 km further north, allowing a continental low intensity branch of the Indian Summer Monsoon which is persistent throughout the Holocene. Precipitation intensities at its northern extent seem to be driven by differentiated solar heating of the Northern Hemisphere indicating dependency on energy-gradients rather than absolute radiation intensities. The identified spatial constraints of monsoonal precipitation will facilitate the prediction of future monsoonal precipitation patterns in Central Asia under varying climatic conditions.
A homology-based pipeline for global prediction of post-translational modification sites
Authors: Chen Xiang , Shi Shao-Ping , Xu Hao-Dong , Suo Sheng-Bao , Qiu Jian-Ding 
Published: May 2016

AbstractThe pathways of protein post-translational modifications (PTMs) have been shown to play particularly important roles for almost any biological process. Identification of PTM substrates along with information on the exact sites is fundamental for fully understanding or controlling biological processes. Alternative computational strategies would help to annotate PTMs in a high-throughput manner. Traditional algorithms are suited for identifying the common organisms and tissues that have a complete PTM atlas or extensive experimental data. While annotation of rare PTMs in most organisms is a clear challenge. In this work, to this end we have developed a novel homology-based pipeline named PTMProber that allows identification of potential modification sites for most of the proteomes lacking PTMs data. Cross-promotion E-value (CPE) as stringent benchmark has been used in our pipeline to evaluate homology to known modification sites. Independent-validation tests show that PTMProber achieves over 58.8% recall with high precision by CPE benchmark. Comparisons with other machine-learning tools show that PTMProber pipeline performs better on general predictions. In addition, we developed a web-based tool to integrate this pipeline at http://bioinfo.ncu.edu.cn/PTMProber/index.aspx. In addition to pre-constructed prediction models of PTM, the website provides an extensional functionality to allow users to customize models.
Alterations in gray matter volume due to unilateral hearing loss
Authors: Wang Xingchao , Xu Pengfei , Li Peng , Wang Zhenmin , Zhao Fu , Gao Zhixian , Xu Lei , Luo Yue-jia , Fan Jin , Liu Pinan 
Published: May 2016

AbstractAlthough extensive research on neural plasticity resulting from hearing deprivation has been conducted, the direct influence of compromised audition on the auditory cortex and the potential impact of long durations of incomplete sensory stimulation on the adult cortex are still not fully understood. In this study, using voxel-based morphometry, we evaluated gray matter (GM) volume changes that may be associated with reduced hearing ability and the duration of hearing impairment in 42 unilateral hearing loss (UHL) patients with acoustic neuromas compared to 24 normal controls. We found significant GM volume increases in the somatosensory and motor systems and GM volume decreases in the auditory (i.e., Heschl’s gyrus) and visual systems (i.e., the calcarine cortex) in UHL patients. The GM volume decreases in the primary auditory cortex (i.e., superior temporal gyrus and Heschl’s gyrus) correlated with reduced hearing ability. Meanwhile, the GM volume decreases in structures involving high-level cognitive control functions (i.e., dorsolateral prefrontal cortex and anterior cingulate cortex) correlated positively with hearing loss duration. Our findings demonstrated that the severity and duration of UHL may contribute to the dissociated morphology of auditory and high-level neural structures, providing insight into the brain’s plasticity related to chronic, persistent partial sensory loss.
Abrupt sand-dune accumulation at the northeastern margin of the Tibetan Plateau challenges the wet MIS3a inferred from numerous lake-highstands
Authors: Long Hao , Fuchs Markus , Yang Linhai , Cheng Hongyi 
Published: May 2016

AbstractOver the Tibetan Plateau and adjacent regions, numerous 14C-based lake records revealed a ubiquitous wet climatic period during 40–25 ka (late MIS 3), which is in contradiction with the global pattern of generally cold and dry climates. This paper focuses on OSL dating results of a large set of sand dunes and alluvial sediments (50 OSL ages) from the Qinwangchuan (QWC) Basin at the northeast edge of the Tibetan Plateau, with the aim to test the validity of the anomalous wet condition for the late MIS 3 interval, evidenced by numerous lake highstands. The abrupt sand dune accumulation as indication of increased aridity in the study area was OSL dated to ~40–13 ka. This dry climatic inference of the sand dune system from QWC apparently shows no wet MIS 3a event. Thus, the anomalous wet conditions revealed by high lake levels for the late MIS 3 phase may not be a universal phenomena across entire western China.
Boosting BCG-primed responses with a subunit Apa vaccine during the waning phase improves immunity and imparts protection against Mycobacterium tuberculosis
Authors: Nandakumar Subhadra , Kannanganat Sunil , Dobos Karen M. , Lucas Megan , Spencer John S. , Amara Rama Rao , Plikaytis Bonnie B. , Posey James E. , Sable Suraj B. 
Published: May 2016

AbstractHeterologous prime–boosting has emerged as a powerful vaccination approach against tuberculosis. However, optimal timing to boost BCG-immunity using subunit vaccines remains unclear in clinical trials. Here, we followed the adhesin Apa-specific T-cell responses in BCG-primed mice and investigated its BCG-booster potential. The Apa-specific T-cell response peaked 32–52 weeks after parenteral or mucosal BCG-priming but waned significantly by 78 weeks. A subunit-Apa-boost during the contraction-phase of BCG-response had a greater effect on the magnitude and functional quality of specific cellular and humoral responses compared to a boost at the peak of BCG-response. The cellular response increased following mucosal BCG-prime–Apa-subunit-boost strategy compared to Apa-subunit-prime–BCG-boost approach. However, parenteral BCG-prime–Apa-subunit-boost by a homologous route was the most effective strategy in-terms of enhancing specific T-cell responses during waning in the lung and spleen. Two Apa-boosters markedly improved waning BCG-immunity and significantly reduced Mycobacterium tuberculosis burdens post-challenge. Our results highlight the challenges of optimization of prime–boost regimens in mice where BCG drives persistent immune-activation and suggest that boosting with a heterologous vaccine may be ideal once the specific persisting effector responses are contracted. Our results have important implications for design of prime–boost regimens against tuberculosis in humans.
Effects of polarization mode dispersion on polarization-entangled photons generated via broadband pumped spontaneous parametric down-conversion
Authors: Lim Hyang-Tag , Hong Kang-Hee , Kim Yoon-Ho 
Published: May 2016

AbstractAn inexpensive and compact frequency multi-mode diode laser enables a compact two-photon polarization entanglement source via the continuous wave broadband pumped spontaneous parametric down-conversion (SPDC) process. Entanglement degradation caused by polarization mode dispersion (PMD) is one of the critical issues in optical fiber-based polarization entanglement distribution. We theoretically and experimentally investigate how the initial entanglement is degraded when the two-photon polarization entangled state undergoes PMD. We report an effect of PMD unique to broadband pumped SPDC, equally applicable to pulsed pumping as well as cw broadband pumping, which is that the amount of the entanglement degradation is asymmetrical to the PMD introduced to each quantum channel. We believe that our results have important applications in long-distance distribution of polarization entanglement via optical fiber channels.
External Volume Expansion Modulates Vascular Growth and Functional Maturation in a Swine Model
Authors: Kao Huang-Kai , Hsu Hsiang-Hao , Chuang Wen-Yu , Chen Sheng-Chih , Chen Bin , Wu Shinn-Chih , Guo Lifei 
Published: May 2016

AbstractDespite increasing application of the pre-grafting expansion during autologous fat transplantation in breast reconstruction, little is known about its mechanism of action. To address that, ventral skins of miniature pigs were treated over a 10-day or 21-day period, with continuous suction at −50 mm Hg via a 7-cm diameter rubber-lined suction-cup device. Soft tissue thickness increased immediately after this external volume expansion (EVE) treatment, such increase completely disappeared by the next day. In the dermis and subcutaneous fat, the EVE treated groups showed significant increases in blood vessel density evident by CD31 staining as well as in vascular networks layered with smooth muscle cells when compared with the control group. This finding was corroborated by the increased percentage of endothelial cells present in the treatment groups. There was no significant difference in the percentages of proliferating basal keratinocytes or adipocytes, nor in epidermal thickness. Moreover, the EVE had no effect on proliferation or differentiation potential of adipose stem cells. Taken together, the major effects of EVE appeared to be vascular remodeling and maturation of functional blood vessels. This understanding may help clinicians optimize the vascularity of the recipient bed to further improve fat graft survival.
An RNA-dependent RNA polymerase gene in bat genomes derived from an ancient negative-strand RNA virus
Authors: Horie Masayuki , Kobayashi Yuki , Honda Tomoyuki , Fujino Kan , Akasaka Takumi , Kohl Claudia , Wibbelt Gudrun , Mühldorfer Kristin , Kurth Andreas , Müller Marcel A. , Corman Victor M. , Gillich Nadine , Suzuki Yoshiyuki , Schwemmle Martin , Tomonaga Keizo 
Published: May 2016

AbstractEndogenous bornavirus-like L (EBLL) elements are inheritable sequences derived from ancient bornavirus L genes that encode a viral RNA-dependent RNA polymerase (RdRp) in many eukaryotic genomes. Here, we demonstrate that bats of the genus Eptesicus have preserved for more than 11.8 million years an EBLL element named eEBLL-1, which has an intact open reading frame of 1,718 codons. The eEBLL-1 coding sequence revealed that functional motifs essential for mononegaviral RdRp activity are well conserved in the EBLL-1 genes. Genetic analyses showed that natural selection operated on eEBLL-1 during the evolution of Eptesicus. Notably, we detected efficient transcription of eEBLL-1 in tissues from Eptesicus bats. To the best of our knowledge, this study is the first report showing that the eukaryotic genome has gained a riboviral polymerase gene from an ancient virus that has the potential to encode a functional RdRp.
The role and indications of aggressive locoregional therapy in metastatic inflammatory breast cancer
Authors: Yan Yi , Tang Lili , Tong Wei , Zhou Jingyu 
Published: May 2016

AbstractWe seek to confirm the effect and explore the indications of aggressive locoregional management in patients with metastatic inflammatory breast cancer (IBC). Between 2003 and 2014, we reviewed the records of 156 patients with metastatic IBC from five large centers of Breast Surgery in the region of central south of China. Clinicopathologic data were collected to access overall survival (OS), prognostic factors and the indications for locoregional treatment. 75 (48%) patients underwent aggressive locoregional therapy. Patients in locoregional therapy group had a median OS of 24 months compared with 17 months of those in no locoregional therapy group. 2-year OS rate of these two groups was 52% and 32%, separately. Locoregional therapy (HR = 0.556; 95% CI 0.385–0.803; p = 0.002) was confirmed to be an independent prognostic factor, which could significantly improve OS of patients with metastatic IBC. For locoregional therapy group, statistical differences were observed in all subgroups stratified by the factors that were significant in univariate analysis except in the subgroups of stable disease, Charlson comorbidity index ≥3 and cerebral metastasis. Therefore, systemic therapy efficacy, Charlson comorbidity index and cerebral metastasis status appeared to be important indexes for choice of locoregional therapy in different individuals.
An investigation into blood microbiota and its potential association with Bacterial Chondronecrosis with Osteomyelitis (BCO) in Broilers
Authors: Mandal Rabindra K. , Jiang Tieshan , Al-Rubaye Adnan A. , Rhoads Douglas D. , Wideman Robert F. , Zhao Jiangchao , Pevzner Igal , Kwon Young Min 
Published: May 2016

AbstractBacterial chondronecrosis with osteomyelitis (BCO) is a common cause of lameness in commercial broiler chickens worldwide. BCO represents substantial production loss and welfare issues of chickens. The bacterial species or communities underlying BCO pathogenesis still remain to be fully characterized. To gain insights on blood microbiota in broilers and its potential association with BCO, blood samples collected from healthy (n = 240) and lame (n = 12) chickens were analyzed by deep sequencing of 16S RNA genes. The chicken blood microbiota were dominated by Proteobacteria (60.58% ± 0.65) followed by Bactroidetes (13.99% ± 0.29), Firmicutes (11.45% ± 0.51), Actinobacteria (10.21% ± 0.37) and Cyanobacteria (1.96% ± 0.21) that constituted 98.18% (± 0.22) of the whole phyla. The bacterial communities consist of 30–40 OTUs in the blood of broiler chickens, regardless of ages and other environmental or host conditions and the blood microbiomes of BCO chickens were largely distinct from those of healthy chickens. In addition, Linear discriminant analysis (LDA) effect size (LEfSe) method revealed that Staphylococcus, Granulicatella and Microbacterium were significantly enriched in BCO chickens as compared to healthy chickens. The results from this study have significant implications in understanding blood microbiota present in broiler chickens and its potential role in BCO pathogenesis.
Changes in inflammatory cytokine networks in myasthenia gravis
Authors: Uzawa Akiyuki , Kanai Tetsuya , Kawaguchi Naoki , Oda Fumiko , Himuro Keiichi , Kuwabara Satoshi 
Published: May 2016

AbstractMyasthenia gravis (MG) is an autoimmunological inflammatory disorder of the neuromuscular junction. Inflammation could be a key player for understanding the pathogenesis of MG. We measured the serum levels of 24 inflammatory cytokines in 43 patients with anti-acetylcholine receptor antibody-positive MG and 25 healthy controls. In patients with MG, serum levels of a proliferation-inducing ligand (APRIL), IL-19, IL-20, IL-28A and IL-35 were significantly increased as compared with controls (p < 0.05). Among them, IL-20, IL-28A and IL-35 were significantly decreased after treatment (p < 0.05). In clinical subtype analyses, APRIL and IL-20 were increased in patients with late-onset MG and IL-28A levels were increased in patients with thymoma-associated MG compared with healthy controls (p < 0.01). The results of the present study demonstrate both anti-inflammatory and inflammatory cytokines are upregulated in MG, reflecting the importance of cytokine-mediated inflammation and its regulation in MG pathophysiology.
Crumpling Damaged Graphene
Authors: Giordanelli I. , Mendoza M. , Andrade J. S. , Gomes M. A. F. , Herrmann H. J. 
Published: May 2016

AbstractThrough molecular mechanics we find that non-covalent interactions modify the fractality of crumpled damaged graphene. Pristine graphene membranes are damaged by adding random vacancies and carbon-hydrogen bonds. Crumpled membranes exhibit a fractal dimension of 2.71 ± 0.02 when all interactions between carbon atoms are considered and 2.30 ± 0.05 when non-covalent interactions are suppressed. The transition between these two values, obtained by switching on/off the non-covalent interactions of equilibrium configurations, is shown to be reversible and independent on thermalisation. In order to explain this transition, we propose a theoretical model that is compatible with our numerical findings. Finally, we also compare damaged graphene membranes with other crumpled structures, as for instance polymerised membranes and paper sheets, that share similar scaling properties.
Targeted next-generation sequencing for the detection of ciprofloxacin resistance markers using molecular inversion probes
Authors: Stefan Christopher P. , Koehler Jeffrey W. , Minogue Timothy D. 
Published: May 2016

AbstractAntibiotic resistance (AR) is an epidemic of increasing magnitude requiring rapid identification and profiling for appropriate and timely therapeutic measures and containment strategies. In this context, ciprofloxacin is part of the first-line of countermeasures against numerous high consequence bacteria. Significant resistance can occur via single nucleotide polymorphisms (SNP) and deletions within ciprofloxacin targeted genes. Ideally, use of ciprofloxacin would be prefaced with AR determination to avoid overuse or misuse of the antibiotic. Here, we describe the development and evaluation of a panel of 44 single-stranded molecular inversion probes (MIPs) coupled to next-generation sequencing (NGS) for the detection of genetic variants known to confer ciprofloxacin resistance in Bacillus anthracis, Yersinia pestis, and Francisella tularensis. Sequencing results demonstrate MIPs capture and amplify targeted regions of interest at significant levels of coverage. Depending on the genetic variant, limits of detection (LOD) for high-throughput pooled sequencing ranged from approximately 300–1800 input genome copies. LODs increased 10-fold in the presence of contaminating human genome DNA. In addition, we show that MIPs can be used as an enrichment step with high resolution melt (HRM) real-time PCR which is a sensitive assay with a rapid time-to-answer. Overall, this technology is a multiplexable upfront enrichment applicable with multiple downstream molecular assays for the detection of targeted genetic regions.
Embryonic and postnatal telomere length decrease with ovulation order within clutches
Authors: Noguera José C. , Metcalfe Neil B. , Reichert Sophie , Monaghan Pat 
Published: May 2016

AbstractTelomere length (TL) in early life has been found to be predictive of subsequent lifespan. Factors such as parental TL, parental age and environmental conditions during development have been shown to contribute to the observed variation in TL among individuals. One factor that has not hitherto been considered is ovulation order, although it is well established that the last hatched/born offspring in a brood or litter often show relatively poor subsequent performance. We examined the within- and across-clutch effect of ovulation order on TL in embryos of zebra finches experiencing the same controlled incubation conditions (N = 151), and tested whether any such ovulation order effects remained detectable in adults (N = 122). Irrespective of clutch and egg size, TL in early-stage embryos (72 h incubation) markedly decreased with within-clutch ovulation order; the difference in TL of first and last-laid embryos was equivalent to the average within-individual telomere loss over the entire period of nestling and juvenile life. This ovulation-order effect occurred only within but not across clutches, and was still evident in adults. Given that TL in early life predicts lifespan, our results suggest that parental effects on telomere length could contribute to the known poor performance of later-ovulated family members.
Increased neuronal death and disturbed axonal growth in the Polμ-deficient mouse embryonic retina
Authors: Baleriola Jimena , Álvarez-Lindo Noemí , de la Villa Pedro , Bernad Antonio , Blanco Luis , Suárez Teresa , de la Rosa Enrique J. 
Published: May 2016

AbstractProgrammed cell death occurs naturally at different stages of neural development, including neurogenesis. The functional role of this early phase of neural cell death, which affects recently differentiated neurons among other cell types, remains undefined. Some mouse models defective in DNA double-strand break (DSB) repair present massive cell death during neural development, occasionally provoking embryonic lethality, while other organs and tissues remain unaffected. This suggests that DSBs occur frequently and selectively in the developing nervous system. We analyzed the embryonic retina of a mouse model deficient in the error-prone DNA polymerase μ (Polμ), a key component of the non-homologous end-joining (NHEJ) repair system. DNA DSBs were increased in the mutant mouse at embryonic day 13.5 (E13.5), as well as the incidence of cell death that affected young neurons, including retinal ganglion cells (RGCs). Polμ−/− mice also showed disturbed RGC axonal growth and navigation, and altered distribution of the axonal guidance molecules L1-CAM and Bravo (also known as Nr-CAM). These findings demonstrate that Polμ is necessary for proper retinal development, and support that the generation of DSBs and their repair via the NHEJ pathway are genuine processes involved in neural development.