bluuebunny/crossref_metadata_2025_split huggingface dataset:
The cellular response towards lanthanum is substrate specific and reveals a novel route for glycerol metabolism inPseudomonas putidaKT2440
Authors: Wehrmann Matthias , Toussaint Maxime , Pfannstiel Jens , Billard Patrick , Klebensberger Janosch 
Published: March 2019

AbstractEver since the discovery of the first rare earth element (REE)-dependent enzyme, the physiological role of lanthanides has become an emerging field of research due to the potential environmental implications and biotechnological opportunities. InPseudomonas putidaKT2440, the two pyrroloquinoline quinone-dependent alcohol dehydrogenases (PQQ-ADHs) PedE and PedH are inversely produced in response to La3+-availability. This REE-switch is orchestrated by a complex regulatory network including the PedR2/PedS2 two-component system and is important for efficient growth on several alcoholic volatiles. AsP. putidais exposed to a broad variety of organic compounds in its natural soil habitat, the cellular responses towards La3+during growth on various carbon and energy sources were investigated with a differential proteomic approach. Apart from the Ca2+-dependent enzyme PedE, the differential abundance of most other identified proteins was conditional and revealed a substrate specificity. Concomitant with the proteomic changes, La3+had a beneficial effect on lag-phases while causing reduced growth rates and lower optical densities in stationary phase during growth on glycerol. When these growth phenotypes were evaluated with mutant strains, a novel metabolic route for glycerol utilization was identified that seems to be functional in parallel with the main degradation pathway encoded by theglpFKRDoperon. The newly discovered route is initiated by PedE and/or PedH, which most likely convert glycerol to glyceraldehyde. In the presence of lanthanum, glyceraldehyde seems to be further oxidized to glycerate, which, upon phosphorylation to glycerate-2-phosphate by the glycerate kinase GarK, is finally channelled into the central metabolism.ImportanceThe biological role of rare earth elements has long been underestimated and research has mainly focused on methanotrophic bacteria. We have recently demonstrated thatP. putida,a plant growth promoting bacterium that thrives in the rhizosphere of various feed crops, possesses a REE-dependent alcohol dehydrogenase (PedH), but knowledge about lanthanide-dependent effects on physiological traits in non-methylotrophic bacteria is still scarce. This study demonstrates that the cellular response ofP. putidaKT2440 towards La3+is mostly substrate specific and that during growth on glycerol, La3+has a severe effect on several growth parameters. We provide compelling evidence that the observed physiological changes are linked to the catalytic activity of PedH and thereby identify a novel route for glycerol metabolism in this biotechnological relevant organism. Overall, these findings demonstrate that lanthanides can alter important physiological traits of non-methylotrophic bacteria, which might consequently influence their competitiveness during colonization of various environmental niches.
Characterizing the epigenetic landscape of cellular populations from bulk and single-cell ATAC-seq information
Authors: Gabitto Mariano I. , Rasmussen Anders , Wapinski Orly , Allaway Kathryn , Carriero Nicholas , Fishell Gordon J. , Bonneau Richard 
Published: March 2019

AbstractGiven its ability to map chromatin accessibility with single base pair resolution, ATAC-seq has become a leading technology to probe the epigenomic landscape of single and aggregated cells. Understanding ATAC-seq data presents distinct analysis challenges, compared to RNA-seq technologies, because of the relative sparseness of the data produced and the interaction of complex noise with multiple chromatin structure scales. Methods commonly used to analyze chromatin accessibility datasets are adapted from algorithms designed to process different experimental technologies, disregarding the statistical and biological differences intrinsic to the ATAC-seq technology. Here, we present a Bayesian statistical approach, termed ChromA, to analyze ATAC-seq data. ChromA annotates the cellular epigenetic landscape by integrating information from replicates, producing a consensus de-noised annotation of chromatin accessibility. Our method can analyze single cell ATAC-seq data, improving cell type identification and correcting many of the biases generated by the sparse sampling inherent in single cell technologies. We validate ChromA on several biological systems, including mouse and human immune cells and find it effective at recovering accessible chromatin, establishing ChromA as a top preforming general platform for mapping the chromatin landscape in different cellular populations from diverse experimental designs.
Loss of tau and Fyn reduces compensatory effects of MAP2 for tau and reveals a Fyn-independent effect of tau on glutamate-induced Ca2+response
Authors: Liu Guanghao , Thangavel Ramasamy , Rysted Jacob , Kim Yohan , Francis Meghan B , Adams Eric , Lin Zhihong , Taugher Rebecca J , Wemmie John A , Usachev Yuriy M , Lee Gloria 
Published: March 2019

AbstractMicrotubule-associated protein tau associates with Src family tyrosine kinase Fyn. A tau-Fyn double knockout (DKO) mouse was generated to investigate the role of the complex. DKO mice resembled Fyn KO in cognitive tasks and resembled tau KO mice in motor tasks and protection from pentylenetetrazole-induced seizures. In Ca2+response, Fyn KO was decreased relative to WT and DKO had a greater reduction relative to Fyn KO, suggesting that tau may have a Fyn-independent role. Since tau KO resembled WT in its Ca2+response, we investigated whether MAP2 served to compensate for tau, since its level was increased in tau KO but decreased in DKO mice. We found that like tau, MAP2 increased Fyn activity. Moreover, tau KO neurons had increased density of dendritic MAP2-Fyn complexes relative to WT neurons. Therefore, we hypothesize that in the tau KO, the absence of tau would be compensated by MAP2, especially in the dendrites, where tau-Fyn complexes are of critical importance. In the DKO, decreased levels of MAP2 made compensation more difficult, thus revealing the effect of tau in the Ca2+response.Summary StatementThe downstream effect of the interaction between microtubule-associated protein tau and Src family non-receptor tyrosine kinase Fyn was investigated with a tau/Fyn double KO mouse. We demonstrate that tau has a Fyn-independent role in glutamate-induced calcium response and that MAP2 can compensate for tau in interacting with Fyn in dendrites.
Unexpected higher resilience to distraction during visual working memory in schizophrenia
Authors: Zhao Yijie , Ran Xuemei , Zhang Li , Zhang Ruyuan , Ku Yixuan 
Published: March 2019

ABSTRACTVisual working memory (VWM) and distractibility are two core executive functions in human cognition. It has been suggested that schizophrenia (SZ) patients exhibit worse VWM performance and lower resilience to distraction compared with healthy control (HC) subjects. Previous studies, however, have largely investigated these two functions separately. It still remains unclear what are the mechanisms of the deficits, especially the interactions between the two cognitive domains. Here we modify the standard delay-estimation task in VWM and explicitly add distractors in the task so as to examine the two domains simultaneously. We find that SZ indeed exhibit worse performance compared with HC in almost all VWM load and distraction levels, a result consistent with most prior experimental findings. But adding distractors does not selectively impose larger impacts on SZ performance. Furthermore, unlike most previous studies that only focused on behavioral performance, we use the variable precision model to disentangle the distraction effect on different computational components of VWM (resources and resources allocation variability etc.). Surprisingly, adding distractors significantly elevates resources allocation variability—a parameter describing the heterogeneity of resource allocation across different targets—in HC but not in SZ. This counterintuitive result suggests that the internal VWM process in SZ is less interfered by the distractors. However, this unexpected higher resilience to distraction might be associated with less flexible cognitive control mechanisms. In sum, our work demonstrates that multiple cognitive functions might jointly contribute to dysfunctions in SZ and their interactions might manifest differently from merely summing their independent effects.
ARBoR: An Identity and Security Solution for Clinical Reporting
Authors: Venner Eric , Murugan Mullai , Hale Walker , Jones Jordan , Lu Shan , Yi Victoria , Gibbs Richard A. 
Published: March 2019

ABSTRACTMotivationClinical genome sequencing laboratories return reports containing clinical testing results, signed by an Board Certified clinical geneticist, to the ordering physician. This report is often a pdf, but can also be a physical paper copy or a structured data file. The reports are frequently modified and re-issued, due to changes in variant interpretation or clinical attributes. To precisely track report authenticity we developed ARBoR, an application for tracking the lineage of versioned clinical reports even when they are distributed as pdf or paper copies. ARBoR employs a modified blockchain approach and instead of relying on a computationally intensive consensus mechanism for determining authenticity, we allow supervised and digitally signed writes to an encrypted ledger, which is then exactly replicated to many clients.ResultsARBoR was implemented for clinical reporting in the HGSC-CL Clinical Laboratory, initially as part of the NIH’s Electronic Medical Record and Genomics (eMERGE) project. To date we have issued 15,205 versioned clinical reports tracked by ARBoR. This system has provided us with a simple and tamper-proof mechanism for tracking clinical reports with a complicated update history.
Arabidopsis phytochelatin synthase 1, but not phytochelatin synthesis, functions in extracellular defense against multiple fungal pathogens
Authors: Hematy Kian , Lim Melisa , Cherk Candice , Bednarek Paweł , Piślewska-Bednarek Mariola , Sanchez-Rodriguez Clara , Stein Monica , Fuchs Rene , Klapprodt Christine , Lipka Volker , Molina Antonio , Grill Erwin , Schulze-Lefert Paul , Somerville Shauna 
Published: March 2019

ABSTRACTPhytochelatin synthase (PCS) is a key component of heavy metal detoxification in plants. PCS catalyzes both the synthesis of the peptide phytochelatin from glutathione as well as the degradation of glutathione conjugates via peptidase activity. Here, we describe a hitherto uncharacterized role for PCS in disease resistance against plant pathogenic fungi. The pen4 mutant, which is allelic to cadmium insensitive 1 (cad1/pcs1) mutants, was recovered from a screen for Arabidopsis mutants with reduced resistance to the non-adapted barley fungal pathogen, Blumeria graminis f. sp. hordei. PCS1, which is found in the cytoplasm of cells of healthy plants, translocates upon pathogen attack and colocalizes with the PEN2 myrosinase on the surface of immobilized mitochondria. pcs1 and pen2 mutant plants exhibit a similar metabolic defect in the accumulation of pathogen-inducible indole glucosinolate-derived compounds, suggesting that PEN2 and PCS1 act in the same metabolic pathway. The function of PCS1 in this pathway is independent of phytochelatin synthesis and deglycination of glutathione conjugates, as catalytic-site mutants of PCS1 are still functional in indole glucosinolate metabolism. In uncovering a previously unknown function for PCS1, we reveal this enzyme to be a moonlighting protein important for plant responses to both biotic and abiotic stresses.
Kinematics associated with treadmill walking in Rett Syndrome
Authors: Layne Charles S. , Young David R. , Lee Beom-Chan , Glaze Daniel G. , Schwabe Aloysia , Suter Bernhard 
Published: March 2019

AbstractIndividuals with Rett syndrome suffer from severely impaired cognitive and motor performance. Current movement-related therapeutic programs often include traditional physical therapy activities and assisted treadmill walking routines for those patients who are ambulatory. However, there are no quantitative reports of kinematic gait parameters obtained during treadmill walking. Here we report the results of an investigation of 17 females diagnosed with typical Rett who walked on a treadmill as speed gradually increased. The objective included characterizing lower limb kinematics, including knee and hip joint range of motions, velocities, limb asymmetries, and the variance associated with these measures. Joint kinematics were obtained using a 12 camera motion capture system and associated processing and analysis software. Stride times progressively decreased as treadmill speeds increased although the range of speeds our participant could walk was quite slow: range 0.2 m/s – 0.5 m/s. There were significant main effects of speed on sagittal knee and hip range of motions and hip velocity. There were large joint asymmetries and variance values relative to both healthy walkers and others patient populations although variance values decreased as walking speed increased. There were significant correlations between joint range of motions and stride times and joint velocities and stride times. The results indicate that Rett patients can adapt their kinematic gait patterns in response to increasing treadmill speed but their ability to do so lies within a narrow range of speeds. We suggest that treadmill training for ambulatory individuals with Rett may further promote improved walking kinematics as well as overall health benefits.
Impact of an intra-abdominal cooling device during open kidney transplantation in pigs
Authors: Longchamp Alban , Meier Raphael P. H. , Colucci Nicola , Balaphas Alexandre , Orci Lorenzo , Nastasi Antonio , Longchamp Grégoire , Moll Solange , Klauser Antoine , Pascual Manuel , Lazeyras François , Corpataux Jean-Marc , Bühler Leo 
Published: March 2019

AbstractBackgroundKidney transplantation using deceased donors still suffers from high post-operative dysfunction rate. During implantation into the recipient, the kidney rewarms. This second warm ischemia time, which is not monitored, is harmful especially if prolonged. We recently developed an intra-abdominal cooling device that efficiently prevents kidney rewarming during robotic transplantation, and prevent ischemia-reperfusion injuries. Here, we tested the benefits of this cooling device during open kidney transplantation in pigs.MaterialsKidneys were procured from large pigs by open bilateral nephrectomy. Following procurement, kidneys were flushed with 4°C Institut Georges Lopez-1 preservation solution, and placed on ice for 128.5 ± 23.2 min. The cooling device was used to continuously cool down the kidney during the vascular anastomosis time.MethodsAnimals underwent double sequential autologous open renal transplantation with (n = 7) and without (n = 6) intra-abdominal cooling. Renal cortex temperature and urine output were monitored. The severity of the ischemia reperfusion lesions was analyzed by histology (modified Goujon score).ResultsMean anastomosis time was similar between groups (43.9 ± 13 min). At reperfusion, the renal cortex temperature was lower in the group with cooling (4.3 ± 1.1°C vs 26.5 ± 5.5°C p <0.001). The cooled kidneys tended to be protected from injury, including some histopathological ischemia–reperfusion lesions. With the device, kidneys had a better immediate post-operative urine output (p=0.05).ConclusionsOur results indicate that the intra-abdominal cooling device significantly reduces second warm ischemic time during transplantation, is technically safe, and does not prolong anastomotic time.
Personal bankruptcy prediction using decision tree model
Authors: Syed Nor Sharifah Heryati , Ismail Shafinar , Yap Bee Wah 
Published: March 2019

Purpose
Personal bankruptcy is on the rise in Malaysia. The Insolvency Department of Malaysia reported that personal bankruptcy has increased since 2007, and the total accumulated personal bankruptcy cases stood at 131,282 in 2014. This is indeed an alarming issue because the increasing number of personal bankruptcy cases will have a negative impact on the Malaysian economy, as well as on the society. From the aspect of individual’s personal economy, bankruptcy minimizes their chances of securing a job. Apart from that, their account will be frozen, lost control on their assets and properties and not allowed to start any business nor be a part of any company’s management. Bankrupts also will be denied from any loan application, restricted from travelling overseas and cannot act as a guarantor. This paper aims to investigate this problem by developing the personal bankruptcy prediction model using the decision tree technique.

Design/methodology/approach
In this paper, bankrupt is defined as terminated members who failed to settle their loans. The sample comprised of 24,546 cases with 17 per cent settled cases and 83 per cent terminated cases. The data included a dependent variable, i.e. bankruptcy status (Y = 1(bankrupt), Y = 0 (non-bankrupt)) and 12 predictors. SAS Enterprise Miner 14.1 software was used to develop the decision tree model.

Findings
Upon completion, this study succeeds to come out with the profiles of bankrupts, reliable personal bankruptcy scoring model and significant variables of personal bankruptcy.

Practical implications
This decision tree model is possible for patent and income generation. Financial institutions are able to use this model for potential borrowers to predict their tendency toward personal bankruptcy.

Social implications
Create awareness to society on significant variables of personal bankruptcy so that they can avoid being a bankrupt.

Originality/value
This decision tree model is able to facilitate and assist financial institutions in evaluating and assessing their potential borrower. It helps to identify potential defaulting borrowers. It also can assist financial institutions in implementing the right strategies to avoid defaulting borrowers.
Perfect partial reconstructions for multiple simultaneous sources
Authors: Wittsten Jens , Andersson Fredrik , Robertsson Johan , Amundsen Lasse 
Published: March 2019

ABSTRACTA major focus of research in the seismic industry of the past two decades has been the acquisition and subsequent separation of seismic data using multiple sources fired simultaneously. The recently introduced method of signal apparition provides a new take on the problem by replacing the random time‐shifts usually employed to encode the different sources by fully deterministic periodic time‐shifts. In this paper, we give a mathematical proof showing that the signal apparition method results in optimally large regions in the frequency–wavenumber space where exact separation of sources is achieved. These regions are diamond shaped and we prove that using any other method of source encoding results in strictly smaller regions of exact separation. The results are valid for arbitrary number of sources. Numerical examples for different number of sources (three, respectively, four sources) demonstrate the exact recovery of these diamond‐shaped regions. The implementation of the theoretical proofs in the field is illustrated by the results of a conducted field test.
Estimating the intensity of use by interacting predators and prey using camera traps
Authors: Keim Jonah L. , Lele Subhash R. , DeWitt Philip D. , Fitzpatrick J. Jeremy , Jenni Noemie S. 
Published: March 2019

Abstract

Understanding how organisms distribute themselves in response to interacting species, ecosystems, climate, human development and time is fundamental to ecological study and practice. A measure to quantify the relationship among organisms and their environments is intensity of use: the rate of use of a specific resource in a defined unit of time. Estimating the intensity of use differs from estimating probabilities of occupancy or selection, which can remain constant even when the intensity of use varies. We describe a method to evaluate the intensity of use across conditions that vary in both space and time. We demonstrate its application on a large mammal community where linear developments and human activity are conjectured to influence the interactions between white‐tailed deer (Odocoileus virginianus) and wolves (Canis lupus) with possible consequences on threatened woodland caribou (Rangifer tarandus caribou).

We collect and quantify intensity of use data for multiple, interacting species with the goal of assessing management efficacy, including a habitat restoration strategy for linear developments. We test whether blocking linear developments by spreading logs across a 200‐m interval can be applied as an immediate mitigation to reduce the intensities of use by humans, predator and prey species in a boreal caribou range.

We deployed camera traps on linear developments with and without restoration treatments in a landscape exposed to both timber and oil development. We collected a three‐year dataset and employed spatial recurrent event models to analyse intensity of use by an interacting human and large mammal community across a range of environmental and climatic conditions.

Spatial recurrent event models revealed that intensity of use by humans influenced the intensity of use by all five large mammal species evaluated, and the intensities of use by wolves and deer were inextricably linked in space and time. Conditions that resist travel on linear developments had a strong negative effect on the intensity of human and large mammal use.

Mitigation strategies that resist, or redirect, animal travel on linear developments can reduce the effects of resource development on interacting human and predator–prey interactions. Our approach is easily applied to other continuous time point‐based survey methodologies and shows that measuring the intensity of use within animal communities can help scientists monitor, mitigate and understand ecological states and processes.
P2X7 receptor in cardiovascular disease: The heart side
Authors: Guerra Martinez Camila 
Published: March 2019

SummaryThe P2X7 receptor is a ligand‐gated purinergic receptor activated by extracellular ATP. The receptor is highly expressed in immune cells and in the brain, and, upon activation, the P2X7 receptor allows a cation flux, leading to the distinct activation of intracellular signalling pathways as the secretion of pro‐inflammatory cytokines, and modulation of cell survival. Through these molecular mechanisms, P2X7 is known to play important roles in physiology and pathophysiology of a wide spectrum of diseases, including cancer, inflammatory diseases, neurological, respiratory and more recently cardiovascular diseases. Recent studies demonstrated that the P2X7 could modulate the assembly of the NLRP3 inflammasome, leading to the secretion of pro‐inflammatory factors and worsen the cardiac disease phenotypes. This review discusses the critical molecular function of P2X7 in the modulation of the onset, progression and resolution of cardiovascular diseases and analyses the putative future use of P2X7‐based therapies that modulate the IL‐1β secretion arm and direct P2X7 antagonists.
Statistical Evidence, Assertions and Responsibility
Authors: Levanon Liat 
Published: March 2019

AbstractThe legal system has been ambivalent about naked statistical evidence. Addressing this ambivalence, the article explores the epistemological status of naked statistical evidence and its normative and practical implications. It is suggested that since naked statistical evidence cannot generate knowledge, it cannot be the basis for assertions of facts; and assertions of facts are practically and legally important: they are essential in order to establish the court's responsibility for its decisions and its errors. Such responsibility is needed in order to maintain the legitimacy of the legal system; to avoid unfairness to defendants; and to ensure that legal decision‐makers have no valid claims against the decision‐making arrangement. As a result, the legal system is inclined to avoid statistical evidence altogether.