bluuebunny/crossref_metadata_2025_split huggingface dataset:
How similar is the stellar structure of low-mass late-type galaxies to that of early-type dwarfs?
Authors: Janz J. , Laurikainen E. , Laine J. , Salo H. , Lisker T. 
Published: May 2016

Abstract
We analyse structural decompositions of 500 late-type galaxies (Hubble T-type ≥6) from the Spitzer Survey of Stellar Structure in Galaxies (S4G; Salo et al.), spanning stellar mass range of about 107 to a few times 1010 M⊙. Their decomposition parameters are compared with those of the early-type dwarfs in the Virgo cluster from Janz et al. They have morphological similarities, including the fact that the fraction of simple one-component galaxies in both samples increases towards lower galaxy masses. We find that in the late-type two-component galaxies both the inner and outer structures are by a factor of 2 larger than in the early-type dwarfs, for the same stellar mass of the component. While dividing the late-type galaxies to low- and high-density environmental bins, it is noticeable that both the inner and outer components of late types in the high local density galaxies are smaller, and lie closer in size to those of the early-type dwarfs. This suggests that, although structural differences between the late- and early-type dwarfs are observed, environmental processes can plausibly transform their sizes sufficiently, thus linking them evolutionarily.
Extended V-Y Advancement Flap Reconstruction of a Large Posterior Upper Midline Trunk Defect
Authors: Fukudome Eugene Y. , Bharadia Deepak R. , Helm Douglas L. , Sinha Indranil 
Published: May 2016

Summary:
Large posterior upper trunk defects can be challenging to reconstruct. Trapezius or latissimus dorsi myocutaneous flaps are principally utilized for reconstruction; however, some defects may not be amenable to this standard approach. Here, we describe a patient with a full-thickness skin and subcutaneous tissue loss of the upper back and inferior cervical region after dermatofibrosarcoma protuberans resection. A large, extended V-Y flap was used for closure of this wound secondary to its location, size, and orientation. This approach preserves shoulder function, allows for readvancement of the flap as needed, and is a reconstructive option for patients with large upper back defects.
Parenteral or enteral nutrition: do you have the choice?
Authors: Oshima Taku , Singer Pierre , Pichard Claude 
Published: May 2016

Purpose of review
The review focuses on the use of parenteral nutrition and enteral nutrition in critically ill patients to optimize the nutrition care throughout the ICU stay. The key message is: you have the choice!

Recent findings
Enteral nutrition has been recommended for critically ill patients, whereas parenteral nutrition has been considered harmful and to be avoided. However, recent studies have challenged this theory. They demonstrated that enteral nutrition is frequently associated with energy and protein undernutrition, whereas parenteral nutrition becomes deleterious only if overfeeding is induced. Measuring energy expenditure by indirect calorimetry, in most cases, enables accurate determination of the energy needs to optimize the prescription of nutrition. Protein targets should also be considered for adequate feeding. Parenteral nutrition can be used as a supplement or as an alternative to enteral nutrition in case of gastrointestinal intolerance, to enable adequate energy, and protein provision.

Summary
Parenteral nutrition is a powerful tool to optimize nutrition care of critically ill patients to improve clinical outcome, if prescribed according to the individual needs of the patients. After 3–4 days of attempt to feed enterally, enteral nutrition or parenteral nutrition can be used alternatively or combined, as long as the target is reached with special attention to avoid hypercaloric feeding.
Unperturbed vs. post-transplantation hematopoiesis: both in vivo but different
Authors: Busch Katrin , Rodewald Hans-Reimer 
Published: May 2016

Purpose of review
Hematopoietic stem cell (HSC) transplantation has yielded tremendous information on experimental properties of HSCs. Yet, it remains unclear whether transplantation reflects the physiology of hematopoiesis. A limitation is the difficulty in accessing HSC functions without isolation, in-vitro manipulation and readout for potential. New genetic fate mapping and clonal marking techniques now shed light on hematopoiesis under physiological conditions.

Recent findings
Transposon-based genetic marks were introduced across the entire hematopoietic system to follow the clonal dynamics of these tags over time. A polyclonal source downstream from stem cells was found responsible for the production of at least granulocytes. In independent experiments, HSCs were genetically marked in adult mice, and the kinetics of label emergence throughout the system was followed over time. These experiments uncovered that during physiological steady-state hematopoiesis large numbers of HSCs yield differentiated progeny. Individual HSCs were active only rarely, indicating their very slow periodicity of differentiation rather than quiescence.

Summary
Noninvasive genetic experiments in mice have identified a major role of stem and progenitor cells downstream from HSCs as drivers of adult hematopoiesis, and revealed that post-transplantation hematopoiesis differs quantitatively from normal steady-state hematopoiesis.
Lipoprotein(a) apheresis
Authors: Pokrovsky Sergei N. , Afanasieva Olga I. , Ezhov Marat V. 
Published: May 2016

Purpose of review
Currently, different methods for extracorporeal elimination of atherogenic apolipoprotein B100 containing lipoprotein particles are used in clinical practice. Most of them effectively remove both lipoprotein(a) [Lp(a)] and LDL. The aim of this review is to highlight research describing the clinical advantages of specific Lp(a) immunosorption compared with other lipoprotein apheresis systems.

Recent findings
Data on the utility of lipoprotein apheresis in patients with elevated Lp(a) level are limited. However, several longitudinal studies demonstrated improvement in cardiovascular outcomes when both Lp(a) and LDL cholesterol levels were decreased with different apheresis systems. The main limitation of these trials is the absence of a control group. First developed in 1991, studies on apheresis with a specific immunosorbent to Lp(a) were small and noncontrolled before 2000s. The only prospective controlled clinical trial utilising Lp(a) apheresis (Clinicaltrials.gov NCT02133807), demonstrated regression of coronary and carotid atherosclerosis when Lp(a) was removed weekly for 18 months.

Summary
Lipoprotein apheresis usually affects multiple lipoproteins, and there are minimal data regarding the effect of specific removal of Lp(a) alone. There is a need for randomized controlled trial with specific Lp(a) apheresis to investigate its effect on cardiovascular outcomes.
Comparison of Endoscopic Mucosal Resection With Circumferential Incision and Endoscopic Submucosal Dissection for Rectal Carcinoid Tumor
Authors: Chen Ru , Liu Xiang , Sun Siyu , Wang Sheng , Ge Nan , Wang Guoxin , Guo Jintao 
Published: May 2016

Background and Aims:
Endoscopic submucosal dissection (ESD) has been a valuable treatment of choice for rectal carcinoid tumors that are endoscopically treatable because of its satisfactory resection rate and low recurrence rate. For treatment of small rectal carcinoids, endoscopic mucosal resection (EMR) is more often chosen by endoscopists because of its safety and time efficiency. We applied circumferential incision and endoscopic mucosal resection (CI-EMR), which is a modification of EMR, to treat rectal carcinoid tumors and compared their efficacy and safety.

Methods:
Between January 2008 and December 2013, we enrolled 66 patients (30 in the ESD group and 36 in the CI-EMR group) at Shengjing Hospital who were pathologically diagnosed with rectal carcinoid tumors <15 mm in diameter. We retrospectively analyzed en bloc resection rates, pathologic complete resection rates, incidences of complications, follow-up outcomes, and procedure times.

Results:
The en bloc resection rate and the histologic complete resection rate were similar, but the procedure time was longer in the ESD group than in the CI-EMR group. In cases that were incompletely resected, neither local recurrence nor distant metastasis was detected during follow-up. Similarly minor bleeding occurred in both groups, and no perforation occurred after either procedure.

Conclusions:
CI-EMR showed comparable en bloc resection and histologically complete resection rates and is technically simpler and minimally invasive compared with ESD. Because of its easier performance and shorter procedure time, CI-EMR may be preferable to ESD for resection of rectal carcinoid tumors <15 mm in diameter without invasion or distant metastases.
The Effect of Mycophenolate Mofetil on Early Wound Healing in a Rodent Model
Authors: Willems Martine CM , Hendriks Thijs , Lomme Roger MLM , de Man Ben M , van der Vliet J Adam 
Published: May 2016

Background
Immunosuppressant agents are inevitable for solid organ recipients, but may have a negative effect on wound healing that is difficult to measure because of clinical use of a polydrug regime. The evidence on mycophenolate mofetil (MMF) is scarce and contradictory. This study aims to investigate the effect of MMF administration on wound healing.

Methods
Ninety-six male Wistar rats divided into 4 groups underwent anastomotic construction in ileum and colon at day 0. Three groups received daily oral doses of 20 or 40 mg/kg MMF or saline (control group) from day 0 until the end of the experiment. Half of each group was analyzed after 3 days and half after 7 days. Another group started the medication 3 days after the laparotomy and was analyzed after 7 days, half of this group received 20 mg/kg and half 40 mg/kg MMF. Wound strength in anastomoses and in the abdominal wall was measured using bursting pressure, breaking strength, and histology. Trough levels were measured.

Results
Significant differences in wound strength were seen in ileum tissue after 3 days, which surprisingly showed a stronger anastomosis in the experimental groups. Bursting pressure as well as breaking strength was higher in the low-dose and high-dose MMF group compared with the control group. A negative effect was measured in abdominal wall tissue for the highest-dose group, which disappeared when the medication was delayed for 3 days. Histology showed poorer bridging of the submucosal layer and more polymorphonuclear cell infiltration in the ileum specimens of the control group compared with the treatment groups.

Conclusions
As a single agent in a preclinical wound healing model in the rat, MMF has no negative effect on healing of bowel anastomoses but might have a negative effect on the healing of abdominal wall.
Diagnostic assessments of student thinking about stochastic processes
Authors: Klymkowsky Michael W. , Koehler Katja , Cooper Melanie M. 
Published: May 2016

AbstractA number of research studies indicate that students often have difficulties in understanding the presence and/or the implications of stochastic processes within biological systems. While critical to a wide range of phenomena, the presence and implications of stochastic processes are rarely explicitly considered in the course of formal instruction. To help instructors identify gaps in student understanding, we have designed and tested six open source activities covering a range of scenarios, from death rates to noise in gene expression, that can be employed, alone or in combination, as diagnostics to reveal student thinking as a prelude to the presentation of stochastic processes within a course or a curriculum.
Combining complex networks and data mining: why and how
Authors: Zanin M. , Papo D. , Sousa P. A. , Menasalvas E. , Nicchi A. , Kubik E. , Boccaletti S. 
Published: May 2016

AbstractThe increasing power of computer technology does not dispense with the need to extract meaningful in-formation out of data sets of ever growing size, and indeed typically exacerbates the complexity of this task. To tackle this general problem, two methods have emerged, at chronologically different times, that are now commonly used in the scientific community: data mining and complex network theory. Not only do complex network analysis and data mining share the same general goal, that of extracting information from complex systems to ultimately create a new compact quantifiable representation, but they also often address similar problems too. In the face of that, a surprisingly low number of researchers turn out to resort to both methodologies. One may then be tempted to conclude that these two fields are either largely redundant or totally antithetic. The starting point of this review is that this state of affairs should be put down to contingent rather than conceptual differences, and that these two fields can in fact advantageously be used in a synergistic manner. An overview of both fields is first provided, some fundamental concepts of which are illustrated. A variety of contexts in which complex network theory and data mining have been used in a synergistic manner are then presented. Contexts in which the appropriate integration of complex network metrics can lead to improved classification rates with respect to classical data mining algorithms and, conversely, contexts in which data mining can be used to tackle important issues in complex network theory applications are illustrated. Finally, ways to achieve a tighter integration between complex networks and data mining, and open lines of research are discussed.
Millions of Boreal Shield Lakes can be used to Probe Archaean Ocean Biogeochemistry
Authors: Schiff S. L. , Tsuji J. M. , Wu L. , Venkiteswaran J. J. , Molot L. A. , Elgood R. J. , Paterson M. J. , Neufeld J. D. 
Published: May 2016

AbstractLife originated in Archaean oceans, almost 4 billion years ago, in the absence of oxygen and the presence of high dissolved iron concentrations. Early Earth oxidation is marked globally by extensive banded iron formations but the contributing processes and timing remain controversial. Very few aquatic habitats have been discovered that match key physico-chemical parameters of the early Archaean Ocean. All previous whole ecosystem Archaean analogue studies have been confined to rare, low sulfur, and permanently stratified lakes. Here we provide first evidence that millions of Boreal Shield lakes with natural anoxia offer the opportunity to constrain biogeochemical and microbiological aspects of early Archaean life. Specifically, we combined novel isotopic signatures and nucleic acid sequence data to examine processes in the anoxic zone of stratified boreal lakes that are naturally low in sulfur and rich in ferrous iron, hallmark characteristics predicted for the Archaean Ocean. Anoxygenic photosynthesis was prominent in total water column biogeochemistry, marked by distinctive patterns in natural abundance isotopes of carbon, nitrogen, and iron. These processes are robust, returning reproducibly after water column re-oxygenation following lake turnover. Evidence of coupled iron oxidation, iron reduction, and methane oxidation affect current paradigms of both early Earth and modern aquatic ecosystems.
Disruption of Humanastn2Function by ZIKVns4bGene as a Molecular Basis for Zika Viral Microcephaly
Authors: Ganguly Bhaskar , Ganguly Enakshi 
Published: May 2016

ABSTRACTThe present Zika virus (ZIKV) pandemic is being associated with increased incidence of microcephaly in newborns. However, a molecular basis for such pathogenesis is distinctly lacking. Comparative nucleic acid sequence analysis showed similarity between regions of non-structural protein 4B (ns4b) gene of ZIKV and human astrotactin2 (astn2) gene. Based on these findings, a molecular target of Zika viral microcephaly is being proposed.
Coalescent inferences in conservation genetics: should the exception become the rule?
Authors: Montano Valeria 
Published: May 2016

AbstractGenetic estimates of effective population size (Ne) are an established means to develop informed conservation policies. Another key goal to pursue the conservation of endangered species is keeping the connectivity across fragmented environments, to which genetic inferences of gene flow and dispersal greatly contribute. Most current statistical tools for estimating such population demographic parameters are based on Kingman's coalescent (KC). However, KC is inappropriate for taxa displaying skewed reproductive variance, a property widely observed in natural species. Coalescent models that consider skewed reproductive success-called multiple merger coalescent (MMCs)-have been shown to substantially improve estimates of Ne when the distribution of offspring per capita is highly skewed. MMCs predictions of standard population genetic parameters, including the rate of loss of genetic variation and the fixation probability of strongly selected alleles, substantially depart from KC predictions. These extended models also allow studying gene genealogies in a spatial continuum, providing a novel theoretical framework to investigate spatial connectivity. Therefore, development of statistical tools based on MMC's should substantially improve estimates of population demographic parameters with major conservation implications.
Cryptic diversity and population structure at small scales: The freshwater snailAncylus(Planorbidae, Pulmonata) in the Montseny mountain range
Authors: Macher Jan N. , Weiss Martina , Beermann Arne J. , Leese Florian 
Published: May 2016

AbstractAnthropogenic impacts like intensified land use and climate change are severe threats to freshwater biodiversity and effective biodiversity monitoring is therefore one of the most urgent tasks. This is however often hampered by the lack of knowledge regarding the number and ecology of species. Molecular tools have shown many freshwater taxa to comprise morphologically cryptic species, which often occur in sympatry on a small geographic scale. Here, we studied the freshwater snailAncylus fluviatilis(MUELLER, 1774) species complex in the Iberian Montseny Mountains. We hypothesised 1) that several species ofA. fluviatilissensu lato occur in the Montseny, 2) that differentAncylusspecies seldom co-occur in syntopy due to different ecological demands or interspecific competition, and 3) that species show a pattern of strong population structure within streams or catchments due to ecological preferences or local adaptation. We barcoded 180 specimens from 36 sites in the Montseny for the cytochrome c oxidase subunit I (COI) barcoding gene and molecularly identified twoAncylusspecies. These species seldom occurred in syntopy and a species distribution modelling approach showed differing bioclimatic preferences of the species. One species mainly occurs in cooler, higher altitude streams while the second species occurs in lower-altitude areas with higher temperatures. Tests of population structure showed that both species possibly do not disperse well in the study area and that populations within species are likely adapted to certain bioclimatic conditions in different regions of the Montseny. Our results highlight the need to incorporate molecular techniques into routine monitoring programmes.
Circadian rhythms have significant effects on leaf-to-canopy gas exchange under field conditions
Authors: Resco de Dios Víctor , Gessler Arthur , Ferrio Juan Pedro , Alday Josu G , Bahn Michael , del Castillo Jorge , Devidal Sébastien , García-Muñoz Sonia , Kayler Zachary , Landais Damien , Martín Paula , Milcu Alexandru , Piel Clément , Pirhofer-Walzl Karin , Ravel Olivier , Salekin Serajis , Tissue David T , Tjoelker Mark G , Voltas Jordi , Roy Jacques 
Published: May 2016

AbstractMolecular clocks drive oscillations in leaf photosynthesis, stomatal conductance and other cell and leaf level processes over ~24 h under controlled laboratory conditions. The influence of such circadian regulation over whole canopy fluxes remains uncertain and diurnal CO2and H2O vapor flux dynamics in the field are currently interpreted as resulting almost exclusively from direct physiological responses to variations in light, temperature and other environmental factors. We tested whether circadian regulation would affect plant and canopy gas exchange at the CNRS Ecotron. Canopy and leaf level fluxes were constantly monitored under field-like environmental conditions, and also under constant environmental conditions (no variation in temperature, radiation or other environmental cues). Here we show first direct experimental evidence at canopy scales of circadian gas exchange regulation: 20-79% of the daily variation range in CO2and H2O fluxes occurred under circadian entrainment in canopies of an annual herb (bean) and of a perennial shrub (cotton). We also observed that considering circadian regulation improved performance in commonly used stomatal conductance models. Overall, our results show that overlooked circadian controls affect diurnal patterns of CO2and H2O fluxes in entire canopies and in field-like conditions, although this process is currently unaccounted for in models.
C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector
Authors: Abudayyeh Omar O. , Gootenberg Jonathan S. , Konermann Silvana , Joung Julia , Slaymaker Ian M. , Cox David B.T. , Shmakov Sergey , Makarova Kira S. , Semenova Ekaterina , Minakhin Leonid , Severinov Konstantin , Regev Aviv , Lander Eric S. , Koonin Eugene V. , Zhang Feng 
Published: May 2016

AbstractThe CRISPR-Cas adaptive immune system defends microbes against foreign genetic elements via DNA or RNA-DNA interference. We characterize the Class 2 type VI-A CRISPR-Caseffector C2c2 and demonstrate its RNA-guided RNase function. C2c2 from the bacteriumLeptotrichia shahiiprovides interference against RNA phage.In vitrobiochemical analysis show that C2c2 is guided by a single crRNA and can be programmed to cleave ssRNA targets carrying complementary protospacers. In bacteria, C2c2 can be programmed to knock down specific mRNAs. Cleavage is mediated by catalytic residues in the two conserved HEPN domains, mutations in which generate catalytically inactive RNA-binding proteins. These results broaden our understanding of CRISPR-Cas systems and suggest that C2c2 can be used to develop new RNA-targeting tools.
Predicting Peptide-MHC Binding Affinities with Imputed Training Data
Authors: Rubinsteyn Alex , O'Donnell Timothy , Damaraju Nandita , Hammerbacher Jeff 
Published: May 2016

AbstractPredicting the binding affinity between MHC proteins and their peptide ligands is a key problem in computational immunology. State of the art performance is currently achieved by the allele-specific predictor NetMHC and the pan-allele predictor NetMHCpan, both of which are ensembles of shallow neural networks. We explore an intermediate between allele-specific and pan-allele prediction: training allele-specific predictors with synthetic samples generated by imputation of the peptide-MHC affinity matrix. We find that the imputation strategy is useful on alleles with very little training data. We have implemented our predictor as an open-source software package called MHCflurry and show that MHCflurry achieves competitive performance to NetMHC and NetMHCpan.