bluuebunny/crossref_metadata_2025_split huggingface dataset:
Southern Ocean Biogeochemical Float Deployment Strategy, With Example From the Greenwich Meridian Line (GO‐SHIP A12)
Authors: Talley L. D. , Rosso I. , Kamenkovich I. , Mazloff M. R. , Wang J. , Boss E. , Gray A. R. , Johnson K. S. , Key R. M. , Riser S. C. , Williams N. L. , Sarmiento J. L. 
Published: September 2018

AbstractBiogeochemical Argo floats, profiling to 2,000‐m depth, are being deployed throughout the Southern Ocean by the Southern Ocean Carbon and Climate Observations and Modeling program (SOCCOM). The goal is 200 floats by 2020, to provide the first full set of annual cycles of carbon, oxygen, nitrate, and optical properties across multiple oceanographic regimes. Building from no prior coverage to a sparse array, deployments are based on prior knowledge of water mass properties, mean frontal locations, mean circulation and eddy variability, winds, air‐sea heat/freshwater/carbon exchange, prior Argo trajectories, and float simulations in the Southern Ocean State Estimate and Hybrid Coordinate Ocean Model (HYCOM). Twelve floats deployed from the 2014–2015 Polarstern cruise from South Africa to Antarctica are used as a test case to evaluate the deployment strategy adopted for SOCCOM's 20 deployment cruises and 126 floats to date. After several years, these floats continue to represent the deployment zones targeted in advance: (1) Weddell Gyre sea ice zone, observing the Antarctic Slope Front, and a decadally‐rare polynya over Maud Rise; (2) Antarctic Circumpolar Current (ACC) including the topographically steered Southern Zone chimney where upwelling carbon/nutrient‐rich deep waters produce surprisingly large carbon dioxide outgassing; (3) Subantarctic and Subtropical zones between the ACC and Africa; and (4) Cape Basin. Argo floats and eddy‐resolving HYCOM simulations were the best predictors of individual SOCCOM float pathways, with uncertainty after 2 years of order 1,000 km in the sea ice zone and more than double that in and north of the ACC.
A mitochondrial proteome profile indicative of type 2 diabetes mellitus in skeletal muscles
Authors: Chae Sehyun , Kim Su-Jin , Do Koo Young , Lee Jung Hwa , Kim Hokeun , Ahn Byung Yong , Ha Yong-Chan , Kim Yong-Hak , Jang Mi Gyeong , Koo Kyung-Hoi , Choi Sung Hee , Lim Soo , Park Young Joo , Jang Hak Chul , Hwang Daehee , Lee Sang-Won , Park Kyong Soo 
Published: September 2018

AbstractThe pathogenesis of type 2 diabetes mellitus (T2DM) is closely associated with mitochondrial functions in insulin-responsive tissues. The mitochondrial proteome, compared with the mitochondrial genome, which only contains 37 genes in humans, can provide more comprehensive information for thousands of mitochondrial proteins regarding T2DM-associated mitochondrial functions. However, T2DM-associated protein signatures in insulin-responsive tissues are still unclear. Here, we performed extensive proteome profiling of mitochondria from skeletal muscles in nine T2DM patients and nine nondiabetic controls. A comparison of the mitochondrial proteomes identified 335 differentially expressed proteins (DEPs) between T2DM and nondiabetic samples. Functional and network analyses of the DEPs showed that mitochondrial metabolic processes were downregulated and mitochondria-associated ER membrane (MAM) processes were upregulated. Of the DEPs, we selected two (NDUFS3 and COX2) for downregulated oxidative phosphorylation and three (CALR, SORT, and RAB1A) for upregulated calcium and protein transport as representative mitochondrial and MAM processes, respectively, and then confirmed their differential expression in independent mouse and human samples. Therefore, we propose that these five proteins be used as a potential protein profile that is indicative of the dysregulation of mitochondrial functions in T2DM, representing downregulated oxidative phosphorylation and upregulated MAM functions.
Raman spectroscopy-based identification of toxoid vaccine products
Authors: Silge Anja , Bocklitz Thomas , Becker Bjoern , Matheis Walter , Popp Juergen , Bekeredjian-Ding Isabelle 
Published: September 2018

AbstractVaccines are complex biomedicines. Manufacturing is time consuming and requires a high level of quality control (QC) to guarantee consistent safety and potency. An increasing global demand has led to the need to reduce time and cost of manufacturing. The evolving concepts for QC and the upcoming threat of falsification of biomedicines define a new need for methods that allow the fast and reliable identification of vaccines. Raman spectroscopy is a non-destructive technology already established in QC of classical medicines. We hypothesized that Raman spectroscopy could be used for identification and differentiation of vaccine products. Raman maps obtained from air-dried samples of combination vaccines containing antigens from tetanus, diphtheria and pertussis (DTaP vaccines) were summarized to compile product-specific Raman signatures. Sources of technical variance were emphasized to evaluate the robustness and sensitivity in downstream data analysis. The data management approach corrects for spatial inhomogeneities in the dried sample while offering a proper representation of the original samples inherent chemical signature. Reproducibility of the identification was validated by a leave-one-replicate-out cross-validation. The results highlighted the high specificity and sensitivity of Raman measurements in identifying DTaP vaccine products. The results pave the way for further exploitation of the Raman technology for identification of vaccines in batch release and cases of suspected falsification.
Pattern to Knowledge: Deep Knowledge-Directed Machine Learning for Residue-Residue Interaction Prediction
Authors: Wong Andrew K. C. , Sze-To Ho Yin , Johanning Gary L. 
Published: September 2018

AbstractResidue-residue close contact (R2R-C) data procured from three-dimensional protein-protein interaction (PPI) experiments is currently used for predicting residue-residue interaction (R2R-I) in PPI. However, due to complex physiochemical environments, R2R-I incidences, facilitated by multiple factors, are usually entangled in the source environment and masked in the acquired data. Here we present a novel method, P2K (Pattern to Knowledge), to disentangle R2R-I patterns and render much succinct discriminative information expressed in different specific R2R-I statistical/functional spaces. Since such knowledge is not visible in the data acquired, we refer to it as deep knowledge. Leveraging the deep knowledge discovered to construct machine learning models for sequence-based R2R-I prediction, without trial-and-error combination of the features over external knowledge of sequences, our R2R-I predictor was validated for its effectiveness under stringent leave-one-complex-out-alone cross-validation in a benchmark dataset, and was surprisingly demonstrated to perform better than an existing sequence-based R2R-I predictor by 28% (p: 1.9E-08). P2K is accessible via our web server on https://p2k.uwaterloo.ca.
A multisubstrate reductase from Plantago major: structure-function in the short chain reductase superfamily
Authors: Fellows Rachel , Russo Christopher M. , Silva Catarina S. , Lee Soon Goo , Jez Joseph M. , Chisholm John D. , Zubieta Chloe , Nanao Max H. 
Published: September 2018

AbstractThe short chain dehydrogenase/reductase superfamily (SDR) is a large family of NAD(P)H-dependent enzymes found in all kingdoms of life. SDRs are particularly well-represented in plants, playing diverse roles in both primary and secondary metabolism. In addition, some plant SDRs are also able to catalyse a reductive cyclisation reaction critical for the biosynthesis of the iridoid backbone that contains a fused 5 and 6-membered ring scaffold. Mining the EST database of Plantago major, a medicinal plant that makes iridoids, we identified a putative 5β-progesterone reductase gene, PmMOR (P. major multisubstrate oxido-reductase), that is 60% identical to the iridoid synthase gene from Catharanthus roseus. The PmMOR protein was recombinantly expressed and its enzymatic activity assayed against three putative substrates, 8-oxogeranial, citral and progesterone. The enzyme demonstrated promiscuous enzymatic activity and was able to not only reduce progesterone and citral, but also to catalyse the reductive cyclisation of 8-oxogeranial. The crystal structures of PmMOR wild type and PmMOR mutants in complex with NADP+ or NAD+ and either 8-oxogeranial, citral or progesterone help to reveal the substrate specificity determinants and catalytic machinery of the protein. Site-directed mutagenesis studies were performed and provide a foundation for understanding the promiscuous activity of the enzyme.
The endless visuomotor calibration of reach-to-grasp actions
Authors: Volcic Robert , Domini Fulvio 
Published: September 2018

AbstractIt is reasonable to assume that when we grasp an object we carry out the movement based only on the currently available sensory information. Unfortunately, our senses are often prone to err. Here, we show that the visuomotor system exploits the mismatch between the predicted and sensory outcomes of the immediately preceding action (sensory prediction error) to attain a degree of robustness against the fallibility of our perceptual processes. Participants performed reach-to-grasp movements toward objects presented at eye level at various distances. Grip aperture was affected by the object distance, even though both visual feedback of the hand and haptic feedback were provided. Crucially, grip aperture as well as the trajectory of the hand were systematically influenced also by the immediately preceding action. These results are well predicted by a model that modifies an internal state of the visuomotor system by adjusting the visuomotor mapping based on the sensory prediction errors. In sum, the visuomotor system appears to be in a constant fine-tuning process which makes the generation and control of grasping movements more resistant to interferences caused by our perceptual errors.
A Next-Generation Sequencing-Based Platform for Quantitative Detection of Hepatitis B Virus Pre-S Mutants in Plasma of Hepatocellular Carcinoma Patients
Authors: Teng Chiao-Fang , Huang Hsi-Yuan , Li Tsai-Chung , Shyu Woei-Cherng , Wu Han-Chieh , Lin Chien-Yu , Su Ih-Jen , Jeng Long-Bin 
Published: September 2018

AbstractHepatocellular carcinoma (HCC) is a leading cause of cancer-related death worldwide. Early diagnosis and treatment of HCC remain a key goal for improving patient survival. Chronic hepatitis B virus (HBV) infection is a major risk factor for HCC development. Pre-S mutants harboring deletions in HBV large surface antigen have been well demonstrated as HBV oncoproteins that dysregulate multiple signaling pathways in hepatocytes, leading to HCC formation. The presence of pre-S mutants in plasma represents important predictive and prognostic markers for HCC in patients with chronic HBV infection. However, the method to detect pre-S mutants remains to be optimized. In this study, we developed a platform, based on the next-generation sequencing (NGS) technology, for detection of pre-S mutants in plasma of HBV-related HCC patients. Compared to the current TA cloning-based analysis, the NGS-based analysis could detect pre-S deletion quantitatively, and the detection rate was significantly more sensitive in 49 plasma analyzed (McNemar’s paired proportion test, P value < 0.0001; simple kappa coefficient, κ = 0.29 (95% CI, 0.12 to 0.46)). Our data suggest that the NGS-based platform may hold a promise for improving the clinical application of pre-S mutants in serving as predictive and prognostic markers for HBV-related HCC.
Calcineurin B homologous protein 3 binds with high affinity to the CHP binding domain of the human sodium/proton exchanger NHE1
Authors: Fuchs Simon , Hansen Sierra C. , Markones Marie , Mymrikov Evgeny V. , Heerklotz Heiko , Hunte Carola 
Published: September 2018

AbstractThe Na+/H+ exchanger NHE1 is critical for cell vitality as it controls intracellular pH and cell volume. Its functionality is influenced by calcineurin B homologous proteins (CHPs). The human isoform CHP3 is important for transport of NHE1 to the plasma membrane and for its activity. Here, we characterized the binding interaction of human CHP3 with the regulatory domain of NHE1. The exact binding site of CHP3 was previously debated. CHP3 as well as both regions of NHE1 in question were produced and purified. CHP3 specifically formed stable complexes with the CHP-binding region (CBD) of NHE1 (residues 503–545) in size-exclusion chromatography (SEC), but not with the C-terminal region (CTD, residues 633–815). CTD was functional as shown by Ca2+-dependent binding of calmodulin in SEC analysis. CHP3 bound with high affinity to CBD with an equilibrium dissociation constant (KD) of 56 nM determined by microscale thermophoresis. The high affinity was substantiated by isothermal calorimetry analysis (KD = 3 nM), which also revealed that the interaction with CBD is strongly exothermic (ΔG° = −48.6 kJ/mol, ΔH = −75.3 kJ/mol, −TΔS° = 26.7 kJ/mol). The data provide insights in the molecular mechanisms that underlie the regulatory interaction of CHP3 and NHE1 and more general of calcineurin homologous proteins with their target proteins.
A Clinical Risk Prediction Tool for Peritonitis-Associated Treatment Failure in Peritoneal Dialysis Patients
Authors: Nochaiwong Surapon , Ruengorn Chidchanok , Koyratkoson Kiatkriangkrai , Thavorn Kednapa , Awiphan Ratanaporn , Chaisai Chayutthaphong , Phatthanasobhon Sirayut , Noppakun Kajohnsak , Suteeka Yuttitham , Panyathong Setthapon , Dandecha Phongsak , Chongruksut Wilaiwan , Nanta Sirisak ,   For the Thai Renal Outcomes Research (THOR) Investigators, Ruanta Yongyuth , Tantraworasin Apichart , Wongsawat Uraiwan , Praseartkul Boontita , Sattaya Kittiya , Busapavanich Suporn 
Published: September 2018

AbstractA tool to predict peritonitis-associated treatment failure among peritoneal dialysis (PD) patients has not yet been established. We conducted a multicentre, retrospective cohort study among 1,025 PD patients between 2006 and 2016 in Thailand to develop and internally validate such a tool. Treatment failure was defined as either a requirement for catheter removal, a switch to haemodialysis, or peritonitis-associated mortality. Prediction model performances were analysed using discrimination (C-statistics) and calibration (Hosmer-Lemeshow test) tests. Predictors were weighted to calculate a risk score. In total, 435 patients with 855 episodes of peritonitis were identified; 215 (25.2%) episodes resulted in treatment failure. A total risk score of 11.5 was developed including, diabetes, systolic blood pressure <90 mmHg, and dialysate leukocyte count >1,000/mm3 and >100/mm3 on days 3–4 and day 5, respectively. The discrimination (C-statistic = 0.92; 95%CI, 0.89–0.94) and calibration (P > 0.05) indicated an excellent performance. No significant difference was observed in the internal validation cohort. The rate of treatment failure in the different groups was 3.0% (low-risk, <1.5 points), 54.4% (moderate-risk, 1.5–9 points), and 89.5% (high-risk, >9 points). A simplified risk-scoring scheme to predict treatment failure may be useful for clinical decision making regarding PD patients with peritonitis. External validation studies are needed.
Conscious processing of auditory regularities induces a pupil dilation
Authors: Quirins Marion , Marois Clémence , Valente Mélanie , Seassau Magali , Weiss Nicolas , El Karoui Imen , Hochmann Jean-Rémy , Naccache Lionel 
Published: September 2018

AbstractPupil dilation has been reliably identified as a physiological marker of consciously reportable mental effort. This classical finding raises the question of whether or not pupil dilation could be a specific somatic signature of conscious processing. In order to explore this possibility, we engaged healthy volunteers in the ‘local global’ auditory paradigm we previously designed to disentangle conscious from non-conscious processing of novelty. We discovered that consciously reported violations of global (inter-trials) regularity were associated with a pupil dilation effect both in an active counting task and in a passive attentive task. This pupil dilation effect was detectable both at the group-level and at the individual level. In contrast, unreported violations of this global regularity, as well as unreported violations of local (intra-trial) regularity that do not require conscious access, were not associated with a pupil dilation effect. We replicated these findings in a phonemic version of the ‘local global’. Taken together these results strongly suggest that pupil dilation is a somatic marker of conscious access in the auditory modality, and that it could therefore be used to easily probe conscious processing at the individual level without interfering with participant’s stream of consciousness by questioning him/her.
Design, Construction and Validation of an Electrical Impedance Probe with Contact Force and Temperature Sensors Suitable for in-vivo Measurements
Authors: Ruiz-Vargas Albert , Ivorra Antoni , Arkwright John William 
Published: September 2018

AbstractBioimpedance spectroscopy measurements can be used for tissue characterization. These measurements can be performed in soft tissues by direct contact of a non-invasive probe consisting of two or four electrodes. The amount of force applied by users can be quite different, and the measurements can vary as a result. To compensate for this, we have built an electrical impedance probe (diameter 3.2 mm) with fibre optic contact-force and temperature sensors built in it. The different sensors of the probe were tested individually. The errors in magnitude and phase angle of the probe are <0.9% and <4°, respectively, for a 0.9% NaCl solution. The linear dynamic range of the force sensor was from 0 to 100 grams. An ex-vivo experiment on a section of proximal colon from a guinea-pig was performed. Twenty bioimpedance measurements were taken in a frequency range of 5 kHz to 1 MHz, while simultaneously recording the force applied. For an increase in contact pressure applied to tissue from 0 to 15.4 kPa, the maximum change in resistivity was 33% at 5 kHz and the minimum was 6.6% at 142 kHz. The probe is small enough to be introduced via the instrument port of an endoscope.
The Long-term Outcome After Resection of Upper Cervical Spinal Cord Tumors: Report of 51 Consecutive Cases
Authors: Wang Xin , Gao Jun , Wang Tianyu , Li Zhimin , Li Yongning 
Published: September 2018

AbstractThe literature discussing the long-term outcome after resection of upper cervical spinal cord tumors is limited. The purpose of this study was to review the progression-free survival (PFS), overall survival (OS), and long-term outcomes in a consecutive series of 51 patients with upper cervical spinal cord tumors who underwent surgery at our institution between 2005 and 2010. Patient outcome were evaluated using the Japanese Orthopaedic Association score (JOA) and the McCormick functional schema. Follow-up data was collected completely and the median follow-up time was 6.1 years. Gross total resection (GTR) was performed in 27 patients (52.94%) and subtotal resection (STR) in 24 patients (47.06%). Progression-free survival and overall survival at 5 years was 88.23% and 92.16%, respectively. Good prognosis was defined as 74.51% based on JOA scoring. The univariate analysis showed that patients over 60y, tumors located higher than C2, tumor size greater than 4 cm as well as malignant tumors and subtotal resection were factors indicating a poor prognosis. However, the multivariate regression analyses showed only the level of tumor and tumor size were independent risk factors for a poor prognosis. The gold standard treatment for intraspinal tumors is gross total resection and follow-up should be focused on patients with a high risk of poor prognosis.
Chemical analysis of NGC 6528: one of the most metal-rich bulge globular clusters
Authors: Muñoz C. , Geisler D. , Villanova S. , Saviane I. , Cortés C. C. , Dias B. , Cohen R. E. , Mauro F. , Moni Bidin C. 
Published: September 2018

Context. The bulge globular clusters (GCs) are key tracers of the bulge, a central and ancient component of our Galaxy. It is essential to understand their formation and evolution to study that of the bulge, as well as their relationship with the other Galactic GC systems (halo and disk GCs). High-resolution spectroscopy is a powerful tool for such studies, allowing us to obtain a detailed chemical characterization and kinematics of the clusters and to compare their chemical patterns with those of their halo and disk counterparts.
Aims. Our main goals are to obtain detailed abundances for a sample of seven red giant members of NGC 6528 in order to characterize their chemical composition and study the relationship of this GC with the bulge, and with other bulge, halo, and disk GCs. Moreover, we analyze this cluster’s behavior associated with the multiple-populations phenomenon.
Methods. We obtained the stellar parameters and chemical abundances of light elements (Na, Al), iron-peak elements (V, Cr, Mn, Fe, Co, Ni, Cu), α-elements (O, Mg, Si, Ca, Ti) and heavy elements (Zr, Ba, Eu) in seven red giant members of NGC 6528 using high-resolution spectroscopy from FLAMES-UVES.
Results. In six stars of our sample we obtained a mean iron content of [Fe/H] = − 0.14 ± 0.03 dex, in good agreement with other studies. We found no significant internal iron spread. We detected one candidate variable star, which was excluded from the mean in iron content, and derived a metallicity in this star of [Fe/H] = − 0.55 ± 0.04 dex. Moreover, we found no extended O-Na anticorrelation but instead only an intrinsic Na spread. In addition, NGC 6528 does not exhibit a Mg-Al anticorrelation, and no significant spread in either Mg or Al. The α and iron-peak elements show good agreement with the bulge field star trend. The heavy elements are slightly dominated by the r-process. The chemical analysis suggests an origin and evolution similar to that of typical old Galactic bulge field stars. Finally, we find remarkable agreement in the chemical patterns of NGC 6528 and another bulge GC, NGC 6553, suggesting a similar origin and evolution.
Does Voiding Cystourethrogram Exclude Posterior Urethral Valves in Late Presenting Cases?
Authors: Özen Mehmet , Taşdemir Mehmet , Gündoğdu Gökhan , Bilge Ilmay , Büyükünal Cenk , Eroğlu Egemen 
Published: September 2018

Introduction Delayed presentation of posterior urethral valves (PUVs) is a rare condition. Presentation and diagnosis of the patients with late PUVs are challenging. Voiding cystourethrogram (VCUG) is mainly practiced. In this study, we aimed to evaluate the children with late-presented PUVs, and the reliability of VCUG in this group.
Materials and Methods Between January 2003 and December 2017 records of patients who were diagnosed with late-presented PUVs were analyzed. Delayed presentation of PUV was defined as patients who were diagnosed and treated after infancy. Cases were examined in terms of age at diagnosis, presenting symptoms, urinalysis, urinary ultrasound, urodynamic studies, VCUG, and dimercaptosuccinic acid scintigraphy findings. Postoperative follow-up conditions were also assessed.
Results Seventeen boys were diagnosed with late-presented PUVs (mean age was 7.35 years). The most common symptoms at presentation were frequency (58.8%), day and nighttime incontinence (47%), and febrile urinary infection (41%). PUV was noted by VCUG in 10 patients alone. The classical sign of dilated posterior urethra was detected in 9 patients. The 10th patient had posterior urethral irregularity. Urethra could not be evaluated due to unsuccessful voiding in one patient. Six patients had normally appearing urethra on VCUG. Reflux was detected in nine (52.9%) patients.
Conclusion Late-presented PUVs may be missed on VCUG. Whether a PUV might be present is crucial in boys with a history of recurrent urinary infection, persistent reflux, and repetitive daytime incontinence. Based on our results, we conclude that cystoscopic examination should be preferred for those cases to diagnose PUVs regardless of VCUG results.