bluuebunny/crossref_metadata_2025_split huggingface dataset:
Primary producers or consumers? Increasing phytoplankton bacterivory along a gradient of lake warming and browning
Authors: Wilken Susanne , Soares Margarida , Urrutia‐Cordero Pablo , Ratcovich Jens , Ekvall Mattias K. , Van Donk Ellen , Hansson Lars‐Anders 
Published: November 2017

AbstractEukaryotic phytoplankton form the basis of aquatic food webs and play a key role in the global carbon cycle. Many of these evolutionarily diverse microalgae are also capable of feeding on other microbes, and hence simultaneously act both as primary producers and consumers. The net ecosystem impact of such mixotrophs depends on their nutritional strategy which is likely to alter with environmental change. Many temperate lakes are currently warming at unprecedented rates and are simultaneously increasing in water color (browning) due to increased run‐off of humic substances. We hypothesized that the resulting reduction in light intensity and increased bacterial abundances would favor mixotrophic phytoplankton over obligate autotrophs, while higher temperatures might boost their rates of bacterivory. We tested these hypotheses in a mesocosm experiment simulating a gradient of increasing temperature and water color in temperate shallow lakes as expected to occur over the coming century. Mixotrophs showed a faster increase in abundance under the climate change scenario during spring, when they dominated the phytoplankton community. Furthermore, both bacterial abundances and rates of phytoplankton bacterivory increased under future climate conditions. Bacterivory contributed significantly to phytoplankton resource acquisition under future climate conditions, while remaining negligible throughout most of the season in treatments resembling today's conditions. Hence, to our knowledge, we here provide the first evidence for an increasing importance of bacterivory by phytoplankton in future temperate shallow lakes. Such a change in phytoplankton nutritional strategies will likely impact biogeochemical cycles and highlights the need to conceptually integrate mixotrophy into current ecosystem models.
Influence of parameter accuracy on pharmacokinetic analysis of hyperpolarized pyruvate
Authors: Sun Chang‐yu , Walker Christopher M. , Michel Keith A. , Venkatesan Aradhana M. , Lai Stephen Y. , Bankson James A. 
Published: November 2017

PurposeTo explore the effects of noise and error on kinetic analyses of tumor metabolism using hyperpolarized [1‐13C] pyruvate.MethodsNumerical simulations were performed to systematically investigate the effects of noise, the number of unknowns, and error in kinetic parameter estimates on kinetic analysis of the apparent rate of chemical conversion from hyperpolarized pyruvate to lactate (kPL). A pharmacokinetic model with two physical and two chemical pools of hyperpolarized spins was used to generate and analyze the synthetic data.ResultsThe reproducibility of kPL estimates worsened quickly when peak signal‐to‐noise ratio for hyperpolarized pyruvate was below approximately 20. The accuracy of kPL estimates was most sensitive to errors in high excitation angles, the vascular blood volume fraction (vb), and the rate of pyruvate extravasation (kve), and was least sensitive to errors in the T1 of pyruvate. When vb and/or kve were fit as additional unknowns, the accuracy of kPL estimates suffered, and when the vascular input function of pyruvate was also fit, the reproducibility of kPL estimates worsened.ConclusionsThe accuracy and precision of kPL estimates improve substantially for peak signal‐to‐noise ratio above approximately 20. Accurate estimates of perfusion parameters (combinations of vb, kve, and the pyruvate vascular input function) and transmit calibration at high excitation angles have the greatest effect on the accuracy of kinetic analyses. Magn Reson Med 79:3239–3248, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
Relationships between tissue microstructure and the diffusion tensor in simulated skeletal muscle
Authors: Berry David B. , Regner Benjamin , Galinsky Vitaly , Ward Samuel R. , Frank Lawrence R. 
Published: November 2017

PurposeTo establish a series of relationships defining how muscle microstructure and diffusion tensor imaging (DTI) are related.MethodsThe relationship among key microstructural features of skeletal muscle (fiber size, fibrosis, edema, and permeability) and the diffusion tensor were systematically simulated over physiologically relevant dimensions individually, and in combination, using a numerical simulation application. Stepwise multiple regression was used to identify which microstructural features of muscle significantly predict the diffusion tensor using single‐echo and multi‐echo DTI pulse sequences. Simulations were also performed in models with histology‐informed geometry to investigate the relationship between fiber size and the diffusion tensor in models with real muscle geometry.ResultsFiber size is the strongest predictor of λ2, λ3, mean diffusivity, and fractional anisotropy in skeletal muscle, accounting for approximately 40% of the variance in the diffusion model when calculated with single‐echo DTI. This increased to approximately 70% when diffusion measures were calculated from the short T2 component of the multi‐echo DTI sequence. This nonlinear relationship begins to plateau in fibers with greater than 60‐μm diameter.ConclusionsAs the normal fiber size of a human muscle fiber is 40 to 60 μm, this suggests that DTI is a sensitive tool to monitor muscle atrophy, but may be limited in measurements of muscle with larger fibers. Magn Reson Med 80:317–329, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
Chemische Energiekonversion: aus Wasser und Wind
Authors: Boeltken Tim , Selinsek Manuel , Pfeifer Peter 
Published: November 2017

AbstractWind‐ und Sonnenenergie fallen zeitlich fluktuierend an, werden aber gerade dann oft nicht benötigt. Umgewandelt in synthetische und schadstoffarm verbrennende Kraftstoffe, lassen sich große Mengen solcher Energieformen speichern. Ein Karlsruher Unternehmen zeigt, wie es geht.
Wiederverwertung: alte Reifen fein mahlen
Authors: Kroll Lothar , Hoyer Stefan 
Published: November 2017

AbstractFahrzeugreifen sind hohen Kräften und einer intensiven Verschleißbeanspruchung ausgesetzt, weshalb sie besonders widerstandsfähige Werkstoffe enthalten. Die chemische Zusammensetzung etwa der Verstärkungsfüllstoffe wird am Ende der Nutzungsdauer allerdings zum Problem für das Recycling.
Objectively Measured Physical Activity and Sedentary Behavior in Successful Weight Loss Maintainers
Authors: Ostendorf Danielle M. , Lyden Kate , Pan Zhaoxing , Wyatt Holly R. , Hill James O. , Melanson Edward L. , Catenacci Victoria A. 
Published: November 2017

ObjectiveThe objective of this study was to compare patterns of objectively measured moderate‐to‐vigorous physical activity (MVPA, ≥ 3.00 metabolic equivalents [METs]), light‐intensity physical activity (LPA, 1.50‐2.99 METs), and sedentary behavior (SB, < 1.50 METs) in successful weight loss maintainers (WLMs), normal weight controls (NC), and controls with overweight/obesity (OC).MethodsParticipants (18‐65 y) were recruited in three groups: WLM (maintaining ≥ 13.6‐kg weight loss for ≥ 1 year, n = 30), NC (BMI matched to current BMI of WLM, n = 33), and OC (BMI matched to pre–weight loss BMI of WLM, n = 27). All participants wore the activPAL for 1 week.ResultsCompared with OC and NC, WLM spent more awake time in total MVPA (WLM: 9.6 ± 3.9%, NC: 7.1 ± 2.1%, OC: 5.9 ± 2.0%; P < 0.01) and more time in sustained (≥ 10 min) bouts of MVPA (WLM: 39 ± 33, NC: 17 ± 14, OC: 9 ± 11 min/d; P < 0.01). Compared with OC, WLM and NC spent more awake time in LPA (WLM: 29.6 ± 7.9%, NC: 29.1 ± 8.3%, OC: 24.8 ± 6.7%; P = 0.04) and less awake time sedentary (WLM: 60.8 ± 9.3%, NC: 63.8 ± 9.5%, OC: 69.3 ± 7.5%; P < 0.01).ConclusionsResults provide additional data supporting the important role of MVPA in weight loss maintenance and suggest notable differences in LPA and SB between normal weight individuals and those with overweight/obesity. Increasing LPA and/or decreasing SB may be additional potential targets for weight management interventions.
Hematopoietic stem cell transplantation in Niemann–Pick disease type B monitored by chitotriosidase activity
Authors: Quarello Paola , Spada Marco , Porta Francesco , Vassallo Elena , Timeus Fabio , Fagioli Franca 
Published: November 2017

AbstractHere, we report a patient with Niemann–Pick disease type B, with early severe onset of disease and pulmonary involvement, treated with hematopoietic stem cell transplant (HSCT) from a bone marrow matched unrelated donor. We confirm that HSCT is feasible and potentially beneficial for patients with severe phenotype. Noteworthy, we discussed the potential usefulness of the activity of peripheral chitotriosidase for the longitudinal evaluation of HSCT success and effectiveness.
Single‐cell whole exome and targeted sequencing in NPM1/FLT3 positive pediatric acute myeloid leukemia
Authors: Walter Christiane , Pozzorini Christian , Reinhardt Katarina , Geffers Robert , Xu Zhenyu , Reinhardt Dirk , von Neuhoff Nils , Hanenberg Helmut 
Published: November 2017

AbstractBackgroundThe small portion of leukemic stem cells (LSCs) in acute myeloid leukemia (AML) present in children and adolescents is often masked by the high background of AML blasts and normal hematopoietic cells. The aim of the current study was to establish a simple workflow for reliable genetic analysis of single LSC‐enriched blasts from pediatric patients.ProcedureFor three AMLs with mutations in nucleophosmin 1 and/or fms‐like tyrosine kinase 3, we performed whole genome amplification on sorted single‐cell DNA followed by whole exome sequencing (WES). The corresponding bulk bone marrow DNAs were also analyzed by WES and by targeted sequencing (TS) that included 54 genes associated with myeloid malignancies.ResultsAnalysis revealed that read coverage statistics were comparable between single‐cell and bulk WES data, indicating high‐quality whole genome amplification. From 102 single‐cell variants, 72 single nucleotide variants and insertions or deletions (70%) were consistently found in the two bulk DNA analyses. Variants reliably detected in single cells were also present in TS. However, initial screening by WES with read counts between 50–72× failed to detect rare AML subclones in the bulk DNAs.ConclusionsIn summary, our study demonstrated that single‐cell WES combined with bulk DNA TS is a promising tool set for detecting AML subclones and possibly LSCs.
An investigation of toxicities and survival in Hispanic children and adolescents with ALL: Results from the Dana‐Farber Cancer Institute ALL Consortium protocol 05‐001
Authors: Kahn Justine M. , Cole Peter D. , Blonquist Traci M. , Stevenson Kristen , Jin Zhezhen , Barrera Sergio , Davila Randy , Roberts Emily , Neuberg Donna S. , Athale Uma H. , Clavell Luis A. , Laverdiere Caroline , Leclerc Jean‐Marie , Michon Bruno , Schorin Marshall A. , Welch Jennifer J.G. , Sallan Stephen E. , Silverman Lewis B. , Kelly Kara M. 
Published: November 2017

AbstractPurposeThis study compared the relative incidence of treatment‐related toxicities and the event‐free and overall survival between Hispanic and non‐Hispanic children undergoing therapy for acute lymphoblastic leukemia (ALL) on Dana‐Farber Cancer Institute ALL Consortium protocol 05‐001.Patients and methodsSecondary analysis of prospectively collected data from a phase III multicenter study in children and adolescents of 1–18 years with previously untreated ALL.ResultsBetween 2005 and 2011, 794 eligible patients enrolled on DFCI 05‐001, 730 of whom were included in this analysis (19% [N = 150] Hispanic, 73% [N = 580] non‐Hispanic). Hispanic patients were more likely to be ≥10 years of age (32% vs. 24%, P = 0.045) at diagnosis. Toxicity analyses revealed that Hispanic patients had significantly lower cumulative incidence of bone fracture (P < 0.001) and osteonecrosis (ON; P = 0.047). In multivariable risk regression, the risk of ON was significantly lower in Hispanic patients ≥10 years (HR 0.23; P = 0.006). Hispanic patients had significantly lower 5‐year event‐free survival (EFS) (79.4%; 95% CI: 71.6–85.2) and overall survival (OS) (89.2%; 95% CI: 82.7–93.4) than non‐Hispanic patients (EFS: 87.5%; 95% CI: 84.5–90.0, P = 0.004; OS: 92.7%; 95% CI: 90.2–94.6, P = 0.006). Exploratory analyses revealed differences between Hispanic and non‐Hispanic patients in the frequency of common variants in genes related to toxicity or ALL outcome.ConclusionHispanic children treated for ALL on DFCI 05‐001 had fewer bone‐related toxicities and inferior survival than non‐Hispanic patients. While disease biology is one explanatory variable for outcome disparities, these findings suggest that biologic and non‐biologic mechanisms affecting drug delivery and exposure in this population may be important contributing factors as well.
Proteomic Analysis of IPEC‐J2 Cells in Response to Coinfection by Porcine Transmissible Gastroenteritis Virus and Enterotoxigenic Escherichia coli K88
Authors: Xia Lu , Dai Lei , Zhu Liqi , Hu Weiwei , Yang Qian 
Published: November 2017

ScopePiglet diarrhea causes large economic losses to the swine industry. Epidemiological investigations show that piglet diarrhea is often caused by mixed infections, but the mechanisms by which multiple microorganisms cause disease are unclear.
Experimental designBecause transmissible gastroenteritis virus (TGEV) and enterotoxigenic Escherichia coli K88 (ETEC K88) are important contributors to piglet diarrhea, coinfection experiments are conducted using porcine intestinal columnar epithelial cells (IPEC‐J2) as a model system. In order to evaluate piglet diarrhea caused TGEV and ETEC K88, the authors examin the effects of coinfection in IPEC‐J2 cells. In TGEV pre‐infected IPEC‐J2 cells, ETEC K88 adhesion is enhanced over uninfected cells. ETEC K88 is also found to inhibit the proliferation of TGEV. Additionally, cytokine levels (IL‐1β, IL‐6, IL‐8, and TNF‐α) in coinfected cells are lower than cells infected by TGEV alone, and higher than cells infected by ETEC K88 alone. LCMS/MS coupled to isobaric tags for relative and absolute quantification (iTRAQ) is used to profile expressed proteins in IPEC‐J2 cells infected by TGEV alone, ETEC K88 alone, and by both agents together.Results77, 89, and 136 differentially expressed proteins are identified in TGEV infected, ETEC K88 infected, and coinfected cells, respectively.Conclusion and clinical relevanceBased on these data, the authors suspect that integrin α5 might enable TGEV to promote ETEC K88 adhesion. This study is the first to analyze piglet diarrhea caused by TGEV‐ETEC K88 coinfection using high‐throughput quantitative proteomics. The results advance the understanding of coinfection and its role in causing piglet diarrhea.
Computational design of membrane proteins using RosettaMembrane
Authors: Duran Amanda M. , Meiler Jens 
Published: November 2017

AbstractComputational membrane protein design is challenging due to the small number of high‐resolution structures available to elucidate the physical basis of membrane protein structure, multiple functionally important conformational states, and a limited number of high‐throughput biophysical assays to monitor function. However, structural determination of membrane proteins has made tremendous progress in the past years. Concurrently the field of soluble computational design has made impressive inroads. These developments allow us to tackle the formidable challenge of designing functional membrane proteins. Herein, Rosetta is benchmarked for membrane protein design. We evaluate strategies to cope with the often reduced quality of experimental membrane protein structures. Further, we test the usage of symmetry in design protocols, which is particularly important as many membrane proteins exist as homo‐oligomers. We compare a soluble scoring function with a scoring function optimized for membrane proteins, RosettaMembrane. Both scoring functions recovered around half of the native sequence when completely redesigning membrane proteins. However, RosettaMembrane recovered the most native‐like amino acid property composition. While leucine was overrepresented in the inner and outer‐hydrophobic regions of RosettaMembrane designs, it resulted in a native‐like surface hydrophobicity indicating that it is currently the best option for designing membrane proteins with Rosetta.
%MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on protein folding
Authors: Rodriguez Anabel , Wright Gabriel , Emrich Scott , Clark Patricia L. 
Published: November 2017

AbstractMost amino acids can be encoded by more than one synonymous codon, but these are rarely used with equal frequency. In many coding sequences the usage patterns of rare versus common synonymous codons is nonrandom and under selection. Moreover, synonymous substitutions that alter these patterns can have a substantial impact on the folding efficiency of the encoded protein. This has ignited broad interest in exploring synonymous codon usage patterns. For many protein chemists, biophysicists and structural biologists, the primary motivation for codon analysis is identifying and preserving usage patterns most likely to impact high‐yield production of functional proteins. Here we describe the core functions and new features of %MinMax, a codon usage calculator freely available as a web‐based portal and downloadable script (http://www.codons.org). %MinMax evaluates the relative usage frequencies of the synonymous codons used to encode a protein sequence of interest and compares these results to a rigorous null model. Crucially, for analyzing codon usage in common host organisms %MinMax requires only the coding sequence as input; with a user‐input codon frequency table, %MinMax can be used to evaluate synonymous codon usage patterns for any coding sequence from any fully sequenced genome. %MinMax makes no assumptions regarding the impact of transfer ribonucleic acid concentrations or other molecular‐level interactions on translation rates, yet its output is sufficient to predict the effects of synonymous codon substitutions on cotranslational folding mechanisms. A simple calculation included within %MinMax can be used to harmonize codon usage frequencies for heterologous gene expression.
Coupling of surface air and sea surface temperatures in the CERA‐20C reanalysis
Authors: Feng Xiangbo , Haines Keith , de Boisséson Eric 
Published: November 2017

ECMWF has recently produced its first ocean‐atmosphere coupled twentieth century reanalysis CERA‐20C, with ten ensemble members. CERA‐20C is based on a coupled climate model with data assimilation implemented individually for the atmosphere and ocean components. This article focuses on the relationships between 2 m air temperature (T2m) and sea surface temperature (SST) in this new coupled climate reanalysis from the perspective of ensemble statistics. The results show where the atmosphere or the ocean are driving the ensemble variability of temperature at the air–sea interface on varying time‐scales.In CERA‐20C, the T2m–SST ensemble relationships are changing on diurnal, seasonal and longer time‐scales and also within regions. The T2m ensemble spread is much larger than the SST ensemble spread at high frequencies (3 h), normally with low correlations due to different time‐scales of oceanic and atmospheric dynamics, showing the atmospherically driven variability of T2m. On monthly time‐scales, the T2m spread is mostly slightly lower than the SST spread, with high correlations and strong coupling, reflecting the SST‐forced variability. T2m–SST coupling is strongest where atmospheric and oceanic boundary layers are shallow, e.g. in the summer hemisphere, and weakest where the atmospheric boundary layer becomes deep, e.g. in the ITCZ region. As the twentieth century progresses, ensemble spreads decline, while T2m–SST coupling becomes stronger as both atmosphere and oceans are better constrained to observations. In the Tropics, strong ENSO‐related variability is found in T2m–SST coupling as atmospheric convection centres move interannually to break the SST‐dominated relationships.
Tissue Uptake Mechanisms Involved in the Clearance of Non‐Protein Nanoparticles that Mimic LDL Composition: A Study with Knockout and Transgenic Mice
Authors: Daminelli Elaine N. , Fotakis Panagiotis , Mesquita Carlos H. , Maranhão Raul C. , Zannis Vassilis I. 
Published: November 2017

AbstractLipid core nanoparticles (LDE) resembling LDL behave similarly to native LDL when injected in animals or subjects. In contact with plasma, LDE acquires apolipoproteins (apo) E, A‐I and C and bind to LDL receptors. LDE can be used to explore LDL metabolism or as a vehicle of drugs directed against tumoral or atherosclerotic sites. The aim was to investigate in knockout (KO) and transgenic mice the plasma clearance and tissue uptake of LDE labeled with 3H‐cholesteryl ether. LDE clearance was lower in LDLR KO and apoE KO mice than in wild type (WT) mice (p < 0.05). However, infusion of human apoE3 into the apoE KO mice increased LDE clearance. LDE clearance was higher in apoA‐I KO than in WT. In apoA‐I transgenic mice, LDE clearance was lower than in apoA‐I KO and than in apoA‐I KO infusion with human HDL. Infusion of human HDL into the apoA‐I KO mice resulted in higher LDE clearance than in the apoA‐I transgenic mice (p < 0.05). In apoA‐I KO and apoA‐I KO infused human HDL, the liver uptake was greater than in WT animals and apoA‐I transgenic animals (p < 0.05). LDE clearance was lower in apoE/A‐I KO than in WT. Infusion of human HDL increased LDE clearance in those double KO mice. No difference among the groups in LDE uptake by the tissues occurred. In conclusion, results support LDLR and apoE as the key players for LDE clearance, apoA‐I also influences those processes.
EDUCATING THE NATION: IV. SUBJECT CHOICE
Authors: Mandler Peter 
Published: November 2017

ABSTRACTThis address tracks the choices made by students at English schools (O-Level, GCSE and A-Level) and at British universities (undergraduate degree) of what subjects to study over the whole of the period since the Second World War. There are marked long-term trends towards a greater diversity in subjects studied, especially at A-Level and degree level, and this tended to reduce over time the dominance of science, to the advantage of a range of subjects including social studies, traditional humanities and latterly creative arts. These trends reflect (most of all) the growing size and diversity of the student body staying on to further study, but also the broadening of the labour market which this more diverse body of students is entering, and social and cultural changes favouring creativity and self-expression in education. The address closes with a reflection on the possible significance of a very recent halting and even a reversal of these trends in subject choice, to the apparent benefit of the sciences.