bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving Nelumbo nucifera genome assemblies using high‐resolution genetic maps and BioNano genome mapping reveals ancient chromosome rearrangements
Authors: Gui Songtao , Peng Jing , Wang Xiaolei , Wu Zhihua , Cao Rui , Salse Jérôme , Zhang Hongyuan , Zhu Zhixuan , Xia Qiuju , Quan Zhiwu , Shu Liping , Ke Wedong , Ding Yi 
Published: March 2018

SummaryGenetic and physical maps are powerful tools to anchor fragmented draft genome assemblies generated from next‐generation sequencing. Currently, two draft assemblies of Nelumbo nucifera, the genomes of ‘China Antique’ and ‘Chinese Tai‐zi’, have been released. However, there is presently no information on how the sequences are assembled into chromosomes in N. nucifera. The lack of physical maps and inadequate resolution of available genetic maps hindered the assembly of N. nucifera chromosomes. Here, a linkage map of N. nucifera containing 2371 bin markers [217 577 single nucleotide polymorphisms (SNPs)] was constructed using restriction‐site associated DNA sequencing data of 181 F2 individuals and validated by adding 197 simple sequence repeat (SSR) markers. Additionally, a BioNano optical map covering 86.20% of the ‘Chinese Tai‐zi’ genome was constructed. The draft assembly of ‘Chinese Tai‐zi’ was improved based on the BioNano optical map, showing an increase of the scaffold N50 from 0.989 to 1.48 Mb. Using a combination of multiple maps, 97.9% of the scaffolds in the ‘Chinese Tai‐zi’ draft assembly and 97.6% of the scaffolds in the ‘China Antique’ draft assembly were anchored into pseudo‐chromosomes, and the centromere regions along the pseudo‐chromosomes were identified. An evolutionary scenario was proposed to reach the modern N. nucifera karyotype from the seven ancestral eudicot chromosomes. The present study provides the highest‐resolution linkage map, the optical map and chromosome level genome assemblies for N. nucifera, which are valuable for the breeding and cultivation of N. nucifera and future studies of comparative and evolutionary genomics in angiosperms.
Diurnal periodicity of assimilate transport shapes resource allocation and whole‐plant carbon balance
Authors: Brauner Katrin , Birami Benjamin , Brauner Horst A. , Heyer Arnd G. 
Published: March 2018

SummaryWhole‐plant carbon balance comprises diurnal fluctuations of photosynthetic carbon gain and respiratory losses, as well as partitioning of assimilates between phototrophic and heterotrophic organs. Because it is difficult to access, the root system is frequently neglected in growth models, or its metabolism is rated based on generalizations from other organs. Here, whole‐plant cuvettes were used for investigating total‐plant carbon exchange with the environment over full diurnal cycles. Dynamics of primary metabolism and diurnally resolved phloem exudation profiles, as proxy of assimilate transport, were combined to obtain a full picture of resource allocation. This uncovered a strong impact of periodicity of inter‐organ transport on the efficiency of carbon gain. While a sinusoidal fluctuation of the transport rate, with minor diel deflections, minimized respiratory losses in Arabidopsis wild‐type plants, triangular or rectangular patterns of transport, found in mutants defective in either starch or sucrose metabolism, increased root respiration at the end or beginning of the day, respectively. Power spectral density and cross‐correlation analysis revealed that only the rate of starch synthesis was strictly correlated to the rate of net photosynthesis in wild‐type, while in a sucrose‐phosphate synthase mutant (spsa1), this applied also to carboxylate synthesis, serving as an alternative carbon pool. In the starchless mutant of plastidial phospho‐gluco mutase (pgm), none of these rates, but concentrations of sucrose and glucose in the root, followed the pattern of photosynthesis, indicating direct transduction of shoot sugar levels to the root. The results demonstrate that starch metabolism alone is insufficient to buffer diurnal fluctuations of carbon exchange.
The CRISPR/Cas revolution reaches the RNA world: Cas13, a new Swiss Army knife for plant biologists
Authors: Wolter Felix , Puchta Holger 
Published: March 2018

SummaryApplication of the bacterial CRISPR/Cas systems to eukaryotes is revolutionizing biology. Cas9 and Cas12 (previously called Cpf1) are widely used as DNA nucleases for inducing site‐specific DNA breaks for different kinds of genome engineering applications, and in their mutated forms as DNA‐binding proteins to modify gene expression. Moreover, histone modifications, as well as cytosine methylation or base editing, were achieved with these systems in plants. Recently, with the discovery of the nuclease Cas13a (previously called C2c2), molecular biologists have obtained a system that enables sequence‐specific cleavage of single‐stranded RNA molecules. The latest experiments with this and also the alternative Cas13b system demonstrate that these proteins can be used in a similar manner in eukaryotes for RNA manipulation as Cas9 and Cas12 for DNA manipulations. The first application of Cas13a for post‐transcriptional regulation of gene expression in plants has been reported. Recent results show that the system is also applicable for combating viral infection in plants. As single‐stranded RNA viruses are by far the most abundant class of viruses in plants, the application of this system is of special promise for crops. More interesting applications are imminent for plant biologists, with nuclease dead versions of Cas13 enabling the ability to visualize RNA molecules in vivo, as well as to edit different kinds of RNA molecules at specific bases by deamination or to modify them by conjugation. Moreover, by combining DNA‐ and RNA‐directed systems, the most complex of changes in plant metabolism might be achievable.
Impact of delayed umbilical cord clamping on public cord blood donations: can we help future patients and benefit infant donors?
Authors: Ciubotariu Rodica , Scaradavou Andromachi , Ciubotariu Ilinca , Tarnawski Michal , Lloyd Sara , Albano Maria , Dobrila Ludy , Rubinstein Pablo , Grunebaum Amos 
Published: March 2018

BACKGROUNDCord blood (CB) is a widely accepted stem cell source and its clinical utilization depends, to a great extent, on its cell content. Birth‐to‐clamping (BTC) time of umbilical cord determines placental transfusion to the newborn, and the remaining blood that can be collected and banked. The 2017 Committee Opinion of the American College of Obstetrics and Gynecologists (ACOG) recommends a delay of “at least 30‐60 seconds” before clamping the cord for all newborns to ensure adequate iron stores. The impact of delayed cord clamping (DCC) on public CB banking can be substantial.STUDY DESIGN AND METHODSCord blood units (CBUs) collected from 1210 mothers at one hospital were evaluated for total nucleated cells (TNCs) and weight/volume based on time to clamping. Bank staff recorded BTC time in seconds as reported by obstetricians; collections were performed ex utero. Immediate clamping was defined as BTC of less than 30 seconds, whereas DCC was defined as BTC of 30 seconds or more.RESULTSCord clamping was immediate in 903 (75%) and delayed in 307 (25%) deliveries. Successful recovery (% clinical CBUs) decreased 10‐fold with DCC of more than 60 seconds (22% vs. 2.4%, p < 0.001). CBUs collected after DCC of more than 60 seconds had significantly lower TNC counts than those after DCC of less than 60 seconds (p < 0.0001). Furthermore, 38% to 46% of CBUs after DCC of more than 60 seconds had volume of less than 40 mL.CONCLUSIONOur study indicates that DCC of 30 to 60 seconds has a small negative impact on collection of high‐TNC‐count CBUs. However, increasing BTC to more than 60 seconds decreases significantly both TNC content and volume, reducing drastically the chances of obtaining clinically useful CBUs.
AutomatedRBCexchange compared to manual exchange transfusion for children with sickle cell disease is cost‐effective and reduces iron overload
Authors: Dedeken Laurence , Lê Phu Quoc , Rozen Laurence , El Kenz Hanane , Huybrechts Sophie , Devalck Christine , Diallo Safiatou , Heijmans Catherine , Ferster Alina 
Published: March 2018

BACKGROUNDChronic transfusion in sickle cell disease (SCD) remains the gold standard therapy for stroke prevention and for patients with severe disease despite adequate hydroxyurea treatment. The aim of our study was to assess the safety and efficacy of automated red blood cell exchange (aRBX) in patients with SCD previously treated with manual exchange transfusion (MET). Costs related to transfusion and chelation overtime were evaluated.STUDY DESIGN AND METHODSBeginning in January 2012, children with SCD who weighed 30 kg or more on MET could switch to aRBX. Clinical, biological, and procedures' data, including costs, were recorded for the last 6 months on MET and compared to those after the first and the second year on aRBX.RESULTSTen patients switched from MET to aRBX at a median age of 11.8 years. After the switch, median hemoglobin S (HbS) increased significantly (33.5% on MET compared to 45% on aRBX; p < 0.001) but remained in the target values for all patients. Median ferritin decreased significantly (663.3 µg/L on MET compared to 126.8 µg/L on aRBX; p < 0.001) and intervals between procedures were significantly longer. The requirements of red blood cells (RBCs)/kg/year were not different on MET (0.88 unit/kg/year) than during the second year on aRBX (1.07 unit/kg/year; p = NS). MET costs were similar compared to aRBX since chelation was stopped in previously treated patients.CONCLUSIONErythrocytapheresis reduces iron overload and allows a longer interval between procedures without a higher RBC requirement from the second year on aRBX. The cost did not increase as estimated in our Belgian Health Care System.
Restored response to ADP downstream of purinergic P2Y12 receptor in apheresis platelets after pathogen‐reducing xenon flash treatment
Authors: Abe Hideki , Abe Takaaki , Shiba Masayuki , Satake Masahiro 
Published: March 2018

BACKGROUNDOur previous study revealed that pathogen‐reducing filtered xenon flash‐treated platelets (fXe‐PLTs) showed sustained aggregation in response to adenosine diphosphate (ADP), but apheresis‐collected PLTs (Aph‐PLTs) showed reversible aggregation.STUDY DESIGN AND METHODSAph‐PLTs, fXe‐PLTs, and freshly prepared PLTs (PRP‐PLTs) from whole blood were used to investigate the following responses to ADP: concentration response and effects of ADP receptor antagonists on aggregation, the cytosolic calcium (Ca2+) flux downstream of P2Y1 receptor signaling, and phosphorylation of vasodilator‐stimulated phosphoprotein (VASP) and signaling intermediate protein Akt downstream of the P2Y12 receptor.RESULTSThe aggregation of Aph‐PLTs by ADP (10 µM) changed from reversible to sustained in an fXe flash dose‐dependent manner. The concentration‐response curve of Aph‐PLTs showed a fivefold higher 50% effective concentration compared with PRP‐PLTs, and fXe treatment decreased it to threefold. While the basal Ca2+ level was higher both in Aph‐ and fXe‐PLTs than in PRP‐PLTs, the increase of cytosolic Ca2+ by ADP remained unchanged in Aph‐ and PRP‐PLTs, but was slightly reduced in fXe‐PLTs. Although the forskolin‐induced VASP phosphorylation was significantly reduced in Aph‐PLTs, and partially restored by the fXe treatment, ADP stimulation attenuated this phosphorylation to an equivalent extent among the three PLT types. The ADP‐stimulated time‐dependent Akt phosphorylation was weak in Aph‐PLTs, whereas fXe‐PLTs and PRP‐PLTs showed a marked increase.CONCLUSIONThese results indicate that the reversible aggregation of Aph‐PLTs is the consequence of insufficient Akt phosphorylation. The fXe treatment restores the increase of phosphorylated Akt, resulting in the sustained aggregation of fXe‐PLTs similar to those of PRP‐PLTs.
In vitro evaluation of di(2‐ethylhexyl)terephthalate–plasticized polyvinyl chloride blood bags for red blood cell storage in AS‐1 and PAGGSM additive solutions
Authors: Graminske Sharon , Puca Kathleen , Schmidt Anna , Brooks Scott , Boerner Amanda , Heldke Sybil , de Arruda Indig Monika , Brucks Mark , Kossor David 
Published: March 2018

BACKGROUNDDi(2‐ethylhexyl)phthalate (DEHP) makes polyvinyl chloride flexible for use in blood bags and stabilizes the red blood cell (RBC) membrane preventing excessive hemolysis. DEHP migrates into the blood product and rodent studies have suggested that DEHP exposure may be associated with adverse health effects albeit at high dosages. Although structurally and functionally similar to DEHP, di(2‐ethylhexyl)terephthalate (DEHT; or Eastman 168 SG [Eastman Chemical Company]) is metabolically distinct with a comprehensive and benign toxicology profile. This study evaluated RBC stability in DEHT‐plasticized bags with AS‐1 and PAGGSM compared to conventional DEHP‐plasticized bags with AS‐1.STUDY DESIGN AND METHODSThirty‐six whole blood units were collected into CPD solution, leukoreduced, centrifuged, and divided into RBCs and plasma. To limit donor‐related variability, three ABO‐identical RBCs were mixed together and then divided equally and stored among the three different plasticizer and additive solution combinations. RBCs from 12 trios were analyzed for a standard panel of in vitro variables on Day 0 and after storage.RESULTSNo individual bag on Day 42 exceeded the US 1.0% hemolysis criteria. While hemolysis during storage was higher in the DEHT bags, the PAGGSM RBCs were close to the control RBCs (0.38% vs. 0.32%, respectively). ATP retention was higher than 70% and potassium levels were similar regardless of plasticizer. Additional RBC variables exhibited some significant differences but were not viewed as clinically important.CONCLUSIONDEHT/PAGGSM provides similar hemolysis protection to that of DEHP/AS‐1. Although hemolysis values with DEHT and AS‐1 are higher than that of DEHP, DEHT is a potential DEHP alternative.
Identification of VIM‐2 metallo‐β‐lactamase‐producing Pseudomonas aeruginosa isolated from dogs with pyoderma and otitis in Korea
Authors: Hyun Jae‐Eun , Chung Tae‐Ho , Hwang Cheol‐Yong 
Published: March 2018

BackgroundPseudomonas aeruginosa is a challenging pathogen cultured from cases of acute and chronic canine otitis and sometimes in cases of deep pyoderma. The spread of antimicrobial resistance, especially carbapenem resistance, is a serious therapeutic challenge worldwide.Hypothesis/ObjectivesTo investigate the identification and characterization of resistant P. aeruginosa clinical canine isolates.MaterialsClinical isolates (n = 80) were collected from dogs with pyoderma (n = 18) and otitis (n = 62) in Korea.MethodsAntimicrobial susceptibility was determined using agar dilution and using Clinical and Laboratory Standards Institute guidelines for recording susceptibility for human Pseudomonas isolates; genetic relatedness of isolates was investigated by multilocus sequence typing (MLST) and SpeI macrorestriction analysis. The class 1 integrons were amplified and sequenced using primer walking.ResultsMost isolates were susceptible to colistin (97.5%), polymyxin B (96.3%), ciprofloxacin (81.3%) and meropenem (80.0%); whereas resistance to aztreonam (80%), piperacillin (52.5%), piperacillin/tazobactam (41.3%) and cefepime (37.5%) was high; 12 carbapenem‐nonsusceptible isolates (15%) were detected. MLST revealed 45 different sequence types (STs) and macrorestriction analysis detected 55 distinct pulsotypes (PTs), which were divided into 25 clonal groups. Among carbapenem‐nonsusceptible isolates, 10 (83.3%) were VIM‐2‐producing strains. Nine VIM‐2‐producing isolates were identified as ST1047 and harboured the same 2.8 kb class 1 integron. One remaining isolate was ST1203 with 2.1 kb class 1 integron.Conclusions and clinical importanceThis study demonstrated the diversity of the phenotype and genotype of clinical P. aeruginosa isolates from dogs with pyoderma and otitis. The identification of VIM‐2‐producing P. aeruginosa in dogs is alarming and warrants further surveillance.
Physiological stress response patterns during a blood donation
Authors: Hoogerwerf M. D. , Veldhuizen I. J. T. , Tarvainen M. P. , Merz E.‐M. , Huis in ‘t Veld E. M. J. , de Kort W. L. A. M. , Sluiter J. K. , Frings‐Dresen M. H. W. 
Published: March 2018

BackgroundDonating blood is associated with increased psychological stress. This study investigates whether a blood donation induces physiological stress and if response patterns differ by gender, donation experience and non‐acute stress.Study design and methodsIn 372 donors, physiological stress [blood pressure, pulse rate, pulse rate variability (PRV)] was measured at seven moments during routine donation. PRV was assessed using time domain [root mean square of successive differences (RMSSD)] and frequency domain [high frequency (HF) and low frequency (LF) power] parameters. Non‐acute stress was assessed by questionnaire. Shape and significance of time course patterns were assessed by fitting multilevel models for each stress measure and comparing men and women, first‐time and experienced donors, and donors with high and low levels of non‐acute stress.ResultsSignificant response patterns were found for all stress measures, where levels of systolic blood pressure (F(1,1315) = 24·2, P < 0·001), RMSSD (F(1,1315) = 24·2, P < 0·001), LF (F(1,1627) = 14·1, P < 0·001) and HF (F(1,1624) = 34·0, P < 0·001) increased towards needle insertion and then decreased to values lower than when arriving at the donation centre. Diastolic blood pressure (F(1,1326) = 50·9, P < 0·001) increased and pulse rate (F(1,1393) = 507·4, P < 0·001) showed a U‐shaped curve. Significant group effects were found, that is, higher systolic blood pressure/pulse rate in women; higher pulse rate in first‐time donors; higher RMSSD at arrival and from screening until leaving in first‐time donors; and higher LF and HF in first‐time donors.ConclusionThis study shows an increase in physiological stress related to needle insertion, followed by a decrease when leaving the donation centre. Some group effects were also found.
Antimicrobial‐resistantEnterobacteriaceaerecovered from companion animal and livestock environments
Authors: Adams R. J. , Kim S. S. , Mollenkopf D. F. , Mathys D. A. , Schuenemann G. M. , Daniels J. B. , Wittum T. E. 
Published: March 2018

SummaryAntimicrobial‐resistant bacteria represent an important concern impacting both veterinary medicine and public health. The rising prevalence of extended‐spectrum beta‐lactamase (ESBL), AmpC beta‐lactamase, carbapenemase (CRE) and fluoroquinolone‐resistantEnterobacteriaceaecontinually decreases the efficiency of clinically important antibiotics. Moreover, the potential for zoonotic transmission of antibiotic‐resistant enteric bacteria increases the risk to public health. Our objective was to estimate the prevalence of specific antibiotic‐resistant bacteria on human contact surfaces in various animal environments. Environmental surface samples were collected from companion animal shelters, private equine facilities, dairy farms, livestock auction markets and livestock areas of county fairs using electrostatic cloths. Samples were screened forEnterobacteriaceaeexpressing AmpC, ESBL, CRE or fluoroquinolone resistance using selective media. Livestock auction markets and county fairs had higher levels of bacteria expressing both cephalosporin and fluoroquinolone resistance than did equine, dairy, and companion animal environments. Equine facilities harboured more bacteria expressing cephalosporin resistance than companion animal shelters, but less fluoroquinolone resistance. The regular use of extended‐spectrum cephalosporins in livestock populations could account for the increased levels of cephalosporin resistance in livestock environments compared to companion animal and equine facilities. Human surfaces, as well as shared human and animal surfaces, were contaminated with resistant bacteria regardless of species environment. Detecting these bacteria on common human contact surfaces suggests that the environment can serve as a reservoir for the zoonotic transmission of antibiotic‐resistant bacteria and resistance genes. Identifying interventions to lower the prevalence of antibiotic‐resistant bacteria in animal environments will protect both animal and public health.
Humanizing the mouse immune system to study splanchnic organ inflammation
Authors: McDaniel Mims Brianyell , Grisham Matthew B. 
Published: March 2018

AbstractIt is well known that alterations in splanchnic organ perfusion and/or immune regulation may produce inflammatory tissue injury similar to that observed in several human disorders such as ischaemia and reperfusion injury, food allergies, diabetes, inflammatory bowel disease and graft‐versus‐host disease. Mouse models have been tremendously important in defining the roles of the circulation, leukocyte trafficking, inflammatory mediator generation, immune regulation and the intestinal microbiota in the pathogenesis of acute and chronic inflammation. However, few of the promising interventions or therapeutics reported in mouse models of inflammatory diseases have been translated to clinically effective treatments in patients. There is growing concern that because of the significant differences that exist between the murine and human immune systems, mouse models may not adequately recapitulate the immuno‐pathogenesis of inflammatory diseases. This inconvenient reality has prompted a number of investigators to undertake a series of studies to humanize the murine immune system via adoptive transfer of human lymphoid or progenitor cells into a new generation of immuno‐deficient recipients. In this review, we summarize the recent advances that have been made in the development of humanized mice and describe how these mouse models are being used to study the pathophysiology of splanchnic organ inflammation. In addition, we discuss the limitations of the different approaches and present potential solutions for the continued improvement of these important animal models.
image
Dorsal and ventral horn atrophy is associated with clinical outcome after spinal cord injury
Authors: Huber Eveline , David Gergely , Thompson Alan J. , Weiskopf Nikolaus , Mohammadi Siawoosh , Freund Patrick 
Published: March 2018

ObjectiveTo investigate whether gray matter pathology above the level of injury, alongside white matter changes, also contributes to sensorimotor impairments after spinal cord injury.MethodsA 3T MRI protocol was acquired in 17 tetraplegic patients and 21 controls. A sagittal T2-weighted sequence was used to characterize lesion severity. At the C2-3 level, a high-resolution T2*-weighted sequence was used to assess cross-sectional areas of gray and white matter, including their subcompartments; a diffusion-weighted sequence was used to compute voxel-based diffusion indices. Regression models determined associations between lesion severity and tissue-specific neurodegeneration and associations between the latter with neurophysiologic and clinical outcome.ResultsNeurodegeneration was evident within the dorsal and ventral horns and white matter above the level of injury. Tract-specific neurodegeneration was associated with prolonged conduction of appropriate electrophysiologic recordings. Dorsal horn atrophy was associated with sensory outcome, while ventral horn atrophy was associated with motor outcome. White matter integrity of dorsal columns and corticospinal tracts was associated with daily-life independence.ConclusionOur results suggest that, next to anterograde and retrograde degeneration of white matter tracts, neuronal circuits within the spinal cord far above the level of injury undergo transsynaptic neurodegeneration, resulting in specific gray matter changes. Such improved understanding of tissue-specific cord pathology offers potential biomarkers with more efficient targeting and monitoring of neuroregenerative (i.e., white matter) and neuroprotective (i.e., gray matter) agents.