bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance comparison of four commercial human whole-exome capture platforms
Authors: Shigemizu Daichi , Momozawa Yukihide , Abe Testuo , Morizono Takashi , Boroevich Keith A. , Takata Sadaaki , Ashikawa Kyota , Kubo Michiaki , Tsunoda Tatsuhiko 
Published: August 2015

AbstractWhole exome sequencing (WXS) is widely used to identify causative genetic mutations of diseases. However, not only have several commercial human exome capture platforms been developed, but substantial updates have been released in the past few years. We report a performance comparison for the latest release of four commercial platforms, Roche/NimbleGen’s SeqCap EZ Human Exome Library v3.0, Illumina’s Nextera Rapid Capture Exome (v1.2), Agilent’s SureSelect XT Human All Exon v5 and Agilent’s SureSelect QXT, using the same DNA samples. Agilent XT showed the highest target enrichment efficiency and the best SNV and short indel detection sensitivity in coding regions with the least amount of sequencing. Agilent QXT had slightly inferior target enrichment than Agilent XT. Illumina, with additional sequencing, detected SNVs and short indels at the same quality as Agilent XT and showed the best performance in coverage of medically interesting mutations. NimbleGen detected more SNVs and indels in untranslated regions than the others. We also found that the platforms, which enzymatically fragment the genomic DNA (gDNA), detected more homozygous SNVs than those using sonicated gDNA. We believe that our analysis will help investigators when selecting a suitable exome capture platform for their particular research.
Label-free single-cell protein quantification using a drop-based mix-and-read system
Authors: Abbaspourrad Alireza , Zhang Huidan , Tao Ye , Cui Naiwen , Asahara Haruichi , Zhou Ying , Yue Dongxian , Koehler Stephan A. , Ung Lloyd W. , Heyman John , Ren Yukun , Ziblat Roy , Chong Shaorong , Weitz David A. 
Published: August 2015

AbstractQuantitative protein analysis of single cells is rarely achieved due to technical difficulties of detecting minute amounts of proteins present in one cell. We develop a mix-and-read assay for drop-based label-free protein analysis of single cells. This high-throughput method quantifies absolute, rather than relative, amounts of proteins and does not involve antibody labeling or mass spectrometry.
Akt2 knock-down reveals its contribution to human lung cancer cell proliferation, growth, motility, invasion and endothelial cell tube formation
Authors: Attoub Samir , Arafat Kholoud , Kamel Hammadi Nasseredine , Mester Jan , Gaben Anne-Marie 
Published: August 2015

AbstractThe Akt/PKB serine/threonine protein kinase consists of three isoforms: Akt-1, −2 and −3. Their overexpression has been detected in human cancers, but their roles in cancer progression are unclear. We investigated the impact of specific silencing of Akt1 and Akt2 on human lung cancer cell proliferation, colony growth, motility and invasion in vitro as well as tumor growth in vivo using human Non-Small Cell Lung Cancer cells LNM35 and on the vascular tube formation using HUVEC cells. Although silencing of Akt1 decreased cellular invasion at least in part via COX-2 inhibition, it had almost no effect on cell motility, proliferation, colony formation and angiogenesis. Transient as well as stable silencing of Akt2 resulted in a strong inhibition of Rb phosphorylation associated with a decrease in cellular proliferation and colony formation, leading to the inhibition of tumor growth in the xenograft model. Silencing of Akt2 also reduced cellular motility and invasion in vitro, presumably via COX-2 inhibition. Moreover, silencing of Akt2 in the HUVEC cells resulted in the inhibition of their spontaneous angiogenic phenotype. Altogether, these results indicate that Akt2 plays an important role in lung cancer progression and can be a promising target for lung cancer therapy.
Advances in nowcasting influenza-like illness rates using search query logs
Authors: Lampos Vasileios , Miller Andrew C. , Crossan Steve , Stefansen Christian 
Published: August 2015

AbstractUser-generated content can assist epidemiological surveillance in the early detection and prevalence estimation of infectious diseases, such as influenza. Google Flu Trends embodies the first public platform for transforming search queries to indications about the current state of flu in various places all over the world. However, the original model significantly mispredicted influenza-like illness rates in the US during the 2012–13 flu season. In this work, we build on the previous modeling attempt, proposing substantial improvements. Firstly, we investigate the performance of a widely used linear regularized regression solver, known as the Elastic Net. Then, we expand on this model by incorporating the queries selected by the Elastic Net into a nonlinear regression framework, based on a composite Gaussian Process. Finally, we augment the query-only predictions with an autoregressive model, injecting prior knowledge about the disease. We assess predictive performance using five consecutive flu seasons spanning from 2008 to 2013 and qualitatively explain certain shortcomings of the previous approach. Our results indicate that a nonlinear query modeling approach delivers the lowest cumulative nowcasting error and also suggest that query information significantly improves autoregressive inferences, obtaining state-of-the-art performance.
Quasi-Static Magnetic Field Shielding Using Longitudinal Mu-Near-Zero Metamaterials
Authors: Lipworth Guy , Ensworth Joshua , Seetharam Kushal , Lee Jae Seung , Schmalenberg Paul , Nomura Tsuyoshi , Reynolds Matthew S. , Smith David R. , Urzhumov Yaroslav 
Published: August 2015

AbstractThe control of quasi-static magnetic fields is of considerable interest in applications including the reduction of electromagnetic interference (EMI), wireless power transfer (WPT) and magnetic resonance imaging (MRI). The shielding of static or quasi-static magnetic fields is typically accomplished through the use of inherently magnetic materials with large magnetic permeability, such as ferrites, used sometimes in combination with metallic sheets and/or active field cancellation. Ferrite materials, however, can be expensive, heavy and brittle. Inspired by recent demonstrations of epsilon-, mu- and index-near-zero metamaterials, here we show how a longitudinal mu-near-zero (LMNZ) layer can serve as a strong frequency-selective reflector of magnetic fields when operating in the near-field region of dipole-like sources. Experimental measurements with a fabricated LMNZ sheet constructed from an artificial magnetic conductor – formed from non-magnetic, conducting, metamaterial elements – confirm that the artificial structure provides significantly improved shielding as compared with a commercially available ferrite of the same size. Furthermore, we design a structure to shield simultaneously at the fundamental and first harmonic frequencies. Such frequency-selective behavior can be potentially useful for shielding electromagnetic sources that may also generate higher order harmonics, while leaving the transmission of other frequencies unaffected.
MiR-210 inhibits NF-κB signaling pathway by targeting DR6 in osteoarthritis
Authors: Zhang Dawei , Cao Xiaorui , Li Jun , Zhao Guangyue 
Published: August 2015

AbstractOsteoarthritis (OA) is characterized by degradation of articular cartilage and joint inflammation. MicroRNAs have been proved to play an important role in the regulation of chondrogenesis. Previous study showed that microRNA-210 (miR-210) was probably associated with osteoarthritis, while the function of miR-210 in osteoarthritis still remains unknown. The aim of the present study was to investigate the protective effect of miR-210 on osteoarthritis. In the in vitro study, miR-210 level in chondrocytes was decreased after treatment with lipopolysaccharide (LPS). Transfection with miR-210 mimic inhibited LPS-induced pro-inflammatory cytokines production, cell viability reduction and cell apoptosis. Results of luciferase activity assay showed that miR-210 targeted 3′-UTR of death receptor 6 (DR6) to inhibit its expression. MiR-210 mimic and DR6 siRNA transfection inhibited the activation of NF-κB pathway and cell apoptosis of chondrocytes. For the in vivo study, OA model was established on rats by anterior cruciate ligament transection (ACLT). MiR-210 expression is reduced in OA rats. MiR-210 over-expressing lentivirus was injected into the OA rats. Cytokines production and NF-κB and DR6 expression in OA rats was inhibited by miR-210 overexpression. The results demonstrated that miR-210 decreased inflammation in articular cavity in OA rats by targeting DR6 and inhibiting NF-κB signaling pathway.
A Novel Role of Numb as A Regulator of Pro-inflammatory Cytokine Production in Macrophages in Response to Toll-like Receptor 4
Authors: Kueanjinda Patipark , Roytrakul Sittiruk , Palaga Tanapat 
Published: August 2015

AbstractActivation of macrophages triggers the release of pro-inflammatory cytokines leading to inflammation. Numb is a negative regulator of Notch signaling, but the role of Numb in macrophages is not fully understood. In this study, the role of Numb as a regulator of inflammatory responses in macrophages was investigated. Murine bone marrow-derived macrophages, in which expression of Numb was silenced, secreted significantly less TNFα, IL-6 and IL-12 and more IL-10 upon activation by lipopolysaccharide (LPS), a ligand for Toll-like receptor 4 (TLR4), despite increased Notch signaling. The Tnfα mRNA levels both in Numb-deficient and wild-type macrophages were not significantly different, unlike those of Il6 and Il12-p40. In Numb-deficient macrophages, the Tnfα mRNAs were degraded at faster rate, compared to those in control macrophages. Activation of p38 MAPK and NF-κΒ p65 were compromised in activated Numb deficient macrophages. Numb was found to interact with the E3 ubiquitin ligase, Itch, which reportedly regulates p38 MAPK. In addition, blocking the Notch signaling pathway in activated, Numb-deficient macrophages did not further reduce TNFα levels, suggesting a Notch-independent role for Numb. A proteomics approach revealed a novel funciton for Numb in regulating complex signaling cascades downstream of TLRs, partially involving Akt/NF-κB p65/p38 MAPK in macrophages.
ADAM12 and ADAM17 are essential molecules for hypoxia-induced impairment of neural vascular barrier function
Authors: Cui Dan , Arima Mitsuru , Takubo Keiyo , Kimura Tokuhiro , Horiuchi Keisuke , Minagawa Takuya , Matsuda Satoshi , Ikeda Eiji 
Published: August 2015

AbstractNeural vascular barrier is essential for the life of multicellular organisms and its impairment by tissue hypoxia is known to be a central of pathophysiology accelerating the progression of various intractable neural diseases. Therefore, the molecules involved in hypoxia-induced impairment of vascular barrier can be the targets to establish new therapies for intractable diseases. Here, we demonstrate that a disintegrin and metalloproteinases (ADAMs) 12 and 17 expressed in endothelial cells are the molecules responsible for the impairment of neural vascular barrier by hypoxia. Brain microvascular endothelial cells in vitro lost their barrier properties immediately after hypoxic stimulation through diminished localization of claudin-5, a tight junction molecule, on cell membranes. Hypoxic disappearance of claudin-5 from cell membranes and the consequent loss of barrier properties were completely suppressed by inhibition of the metalloproteinase activity which was found to be attributed to ADAM12 and ADAM17. Inhibition of either ADAM12 or ADAM17 was sufficient to rescue the in vivo neural vasculature under hypoxia from the loss of barrier function. This is the first report to specify the molecules which are responsible for hypoxia-induced impairment of neural vascular barrier and furthermore can be the targets of new therapeutic strategies for intractable neural diseases.
The de novo synthesis of ubiquitin: identification of deubiquitinases acting on ubiquitin precursors
Authors: Grou Cláudia P. , Pinto Manuel P. , Mendes Andreia V. , Domingues Pedro , Azevedo Jorge E. 
Published: August 2015

AbstractProtein ubiquitination, a major post-translational modification in eukaryotes, requires an adequate pool of free ubiquitin. Cells maintain this pool by two pathways, both involving deubiquitinases (DUBs): recycling of ubiquitin from ubiquitin conjugates and processing of ubiquitin precursors synthesized de novo. Although many advances have been made in recent years regarding ubiquitin recycling, our knowledge on ubiquitin precursor processing is still limited and questions such as when are these precursors processed and which DUBs are involved remain largely unanswered. Here we provide data suggesting that two of the four mammalian ubiquitin precursors, UBA52 and UBA80, are processed mostly post-translationally whereas the other two, UBB and UBC, probably undergo a combination of co- and post-translational processing. Using an unbiased biochemical approach we found that UCHL3, USP9X, USP7, USP5 and Otulin/Gumby/FAM105b are by far the most active DUBs acting on these precursors. The identification of these DUBs together with their properties suggests that each ubiquitin precursor can be processed in at least two different manners, explaining the robustness of the ubiquitin de novo synthesis pathway.
Atlantic hurricane activity during the last millennium
Authors: Burn Michael J. , Palmer Suzanne E. 
Published: August 2015

AbstractHurricanes are a persistent socio-economic hazard for countries situated in and around the Main Development Region (MDR) of Atlantic tropical cyclones. Climate-model simulations have attributed their interdecadal variability to changes in solar and volcanic activity, Saharan dust flux, anthropogenic greenhouse gas and aerosol emissions and heat transport within the global ocean conveyor belt. However, the attribution of hurricane activity to specific forcing factors is hampered by the short observational record of Atlantic storms. Here, we present the Extended Hurricane Activity (EHA) index, the first empirical reconstruction of Atlantic tropical cyclone activity for the last millennium, derived from a high-resolution lake sediment geochemical record from Jamaica. The EHA correlates significantly with decadal changes in tropical Atlantic sea surface temperatures (SSTs; r = 0.68; 1854–2008), the Accumulated Cyclone Energy index (ACE; r = 0.90; 1851–2010) and two annually-resolved coral-based SST reconstructions (1773–2008) from within the MDR. Our results corroborate evidence for the increasing trend of hurricane activity during the Industrial Era; however, we show that contemporary activity has not exceeded the range of natural climate variability exhibited during the last millennium.
Associations of prepregnancy body mass index and gestational weight gain with pregnancy outcomes in nulliparous women delivering single live babies
Authors: Liu Lu , Hong Zhongxin , Zhang Lihong 
Published: August 2015

AbstractThe study was to assess the associations of prepregnancy body mass index (BMI) and gestational weight gain (GWG) with pregnancy outcomes. This was a retrospective analysis of 2973 nulliparous women who delivered single live babies. Prepregnancy BMI was categorized as underweight (<18.5 kg/m2), normal weight (18.5–24.9 kg/m2) or overweight/obese (≥25.0 kg/m2). GWG was categorized as inadequate, adequate or excessive. 567 (19.1%) women were overweight/obese and 1600 (53.8%) exhibited excessive GWG. Compared with women of normal weight, overweight/obese women had a higher incidence of cesarean section (odds ratio, 95% confidence interval: 2.02, 1.59–2.56), postpartum hemorrhage (1.50, 1.05–2.14), preterm delivery (2.51, 1.83–3.45), preterm premature rupture of membranes (2.11, 1.32–3.38), gestational diabetes mellitus (2.04, 1.65–2.53), gestational hypertension (7.68, 4.21–14.00), preeclampsia (1.98, 1.18–3.33) and small for gestational age (2.81, 1.21–6.54). Compared with adequate GWG, excessive GWG increased the incidence of cesarean section (2.02, 1.59–2.56), preterm delivery (1.48, 1.05–2.71), preeclampsia (1.78, 1.34–4.27) and macrosomia (2.61, 1.61–4.25) and reduced the incidence of gestational diabetes mellitus (0.75, 0.62–0.92). High prepregnancy BMI and excessive GWG in nulliparous Chinese women are associated with adverse pregnancy outcomes. Weight control before and during pregnancy could reduce the complications of pregnancy.
Experimental demonstration for high speed integrated visible light communication and multimode fiber communication system
Authors: Huang Xingxing , Wang Yiguang , Wang Yuanquan , Yang Chao , Li Jiehui , Chi Nan 
Published: August 2015

The authors propose and experimentally demonstrate an integrated visible light communication (VLC) and multimode fibre communication (MFC) system. The bit error rate results are under the 7% pre‐forward‐error‐correction limit of 3.8 × 10−3 through 100‐m multimode fibre and 60‐cm free‐space transmission with 600 Mbit/s by 64 quadrature amplitude modulation and orthogonal frequency division multiplexing. The experimental results show that VLC system can serve as an excellent choice for the optical interconnect system, such as MFC system. As far as the authors’ knowledge, this is the first time that MFC has been introduced to VLC system.
Lightning transient characteristics of cable power collection system in wind power plants
Authors: Li Xianqiang , Wang Jianguo , Wang Yu , Fan Yadong , Zhang Baoquan , Wang Shunchao , Zhou Mi , Cai Li 
Published: August 2015

In recent years, frequent accidents due to lightning have occurred in wind power plants, resulting in damages to electrical equipments in the power collection system, especially in the cable power collection system (CPCS) and the nacelle step‐up transformer. In this study, electromagnetic transient simulation of lightning overvoltage in a 35 kV CPCS with the nacelle step‐up transformer was carried out. Influencing factors including the location of the step‐up transformer, the lightning current, the grounding resistance of wind turbine generator (WTG) and distance between WTGs are taken into consideration. The simulation results show that, in the case of 30 Ω grounding resistance for the WTG, the current flowing through the arrester installed at the high voltage winding side of the step‐up transformer will reach up to 27.1 kA when subjected to a 200 kA lightning current, which reveals the damage mechanism of arrester blasting. Based on the calculation results, recommended nominal discharge current value for the arrester as well as the optimal lightning overvoltage protection method are proposed here.
Expressing our internal states and understanding those of others
Authors: Di Cesare Giuseppe , Di Dio Cinzia , Marchi Massimo , Rizzolatti Giacomo 
Published: August 2015

Significance
Vitality form is a term that describes the manner with which actions are performed. Despite their crucial importance in interpersonal communication, vitality forms have been almost completely neglected in neuroscience. Here, using a functional MRI technique, we investigated the neural correlates of vitality forms in three tasks: action observation, imagination, and execution. We found that, in all three tasks, there is a common specific activation of the dorsocentral sector of the insula in addition to the parietofrontal network that is typically active during arm movements production and observation. Thus, the dorsocentral part of the insula seems to represent a fundamental and previously unsuspected node that modulates the cortical motor circuits, allowing individuals to express their vitality forms and understand those of others.
Long‐Term Therapy with Oral Treprostinil in Pulmonary Arterial Hypertension Failed to Lead to Improvement in Important Physiologic Measures: Results from a Single Center
Authors: Chin Kelly Marie , Ruggiero Rosechelle , Bartolome Sonja , Velez‐Martinez Mariella , Darsaklis Konstantina , Kingman Martha , Harden Scarlet , Torres Fernando 
Published: August 2015

Sustained‐release oral treprostinil, an oral prostacyclin, led to significant improvement in 6‐minute walk distance (6MWD) versus placebo in treatment‐naive patients with pulmonary arterial hypertension (PAH) but failed to lead to significant improvement in two 16‐week trials in patients receiving background PAH therapies (FREEDOM studies). Long‐term studies are lacking. Our objective was to evaluate 6MWD, functional class, hemodynamics, and other long‐term outcomes during oral treprostinil administration in PAH. Patients receiving oral treprostinil through the FREEDOM studies at our institution were included and were followed for up to 7 years. The primary end point was change in pulmonary vascular resistance (PVR) at first follow‐up catheterization. Other end points included 6MWD, functional class, and other hemodynamic results. Thirty‐seven patients received oral treprostinil for a median of 948 days, with 81%, 61%, and 47% continuing therapy at 1, 2, and 3 years, respectively. Mean treprostinil dose at 3, 12, and 24 months was 4.3 ± 2.3, 8.6 ± 3.2, and 11.7 ± 5.8 mg/24 h, respectively. Compared with pretreatment values, there was no significant change in 6MWD at 3 or 12 months, no improvement in functional class at 12 months, and no significant change in hemodynamics at the first follow‐up catheterization (N = 34). Oral treprostinil dose was inversely associated with change in PVR (r = −0.42, P < 0.05), and change in PVR was numerically better among patients in the highest dosing quartile. No significant improvement in 6MWD, functional class, or hemodynamics versus pretreatment values was seen with long‐term oral treprostinil therapy, potentially because of inability to achieve a clinically effective dose.
ERC analysis: web-based inference of gene function via evolutionary rate covariation
Authors: Wolfe Nicholas W. , Clark Nathan L. 
Published: August 2015

Abstract
Summary: The recent explosion of comparative genomics data presents an unprecedented opportunity to construct gene networks via the evolutionary rate covariation (ERC) signature. ERC is used to identify genes that experienced similar evolutionary histories, and thereby draws functional associations between them. The ERC Analysis website allows researchers to exploit genome-wide datasets to infer novel genes in any biological function and to explore deep evolutionary connections between distinct pathways and complexes. The website provides five analytical methods, graphical output, statistical support and access to an increasing number of taxonomic groups.
Availability and implementation: Analyses and data at http://csb.pitt.edu/erc_analysis/
Contact: nclark@pitt.edu