bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cytosolic glyceraldehyde‐3‐phosphate dehydrogenases play crucial roles in controlling cold‐induced sweetening and apical dominance of potato (Solanum tuberosum L.) tubers
Authors: Liu Tengfei , Fang Hui , Liu Jun , Reid Stephen , Hou Juan , Zhou Tingting , Tian Zhendong , Song Botao , Xie Conghua 
Published: September 2017

AbstractGlyceraldehyde‐3‐phosphate dehydrogenase (GAPDH) is an important enzyme that functions in producing energy and supplying intermediates for cellular metabolism. Recent researches indicate that GAPDHs have multiple functions beside glycolysis. However, little information is available for functions of GAPDHs in potato. Here, we identified 4 putative cytosolic GAPDH genes in potato genome and demonstrated that the StGAPC1, StGAPC2, and StGAPC3, which are constitutively expressed in potato tissues and cold inducible in tubers, encode active cytosolic GAPDHs. Cosuppression of these 3 GAPC genes resulted in low tuber GAPDH activity, consequently the accumulation of reducing sugars in cold stored tubers by altering the tuber metabolite pool sizes favoring the sucrose pathway. Furthermore, GAPCs‐silenced tubers exhibited a loss of apical dominance dependent on cell death of tuber apical bud meristem (TAB‐meristem). It was also confirmed that StGAPC1, StGAPC2, and StGAPC3 interacted with the autophagy‐related protein 3 (ATG3), implying that the occurrence of cell death in TAB‐meristem could be induced by ATG3 associated events. Collectively, the present research evidences first that the GAPC genes play crucial roles in diverse physiological and developmental processes in potato tubers.
Combined transcriptomic and proteomic analysis constructs a new model for light‐induced anthocyanin biosynthesis in eggplant (Solanum melongena L.)
Authors: Li Jing , Ren Li , Gao Zhen , Jiang Mingmin , Liu Yang , Zhou Lu , He Yongjun , Chen Huoying 
Published: September 2017

AbstractLight is a key environmental factor affecting anthocyanin biosynthesis. Our previous study demonstrated that “Lanshan Hexian” is a light‐sensitive eggplant cultivar, but its regulatory mechanism is unknown. Here, delphinidin‐3‐[4‐(cis‐p‐coumaroyl)‐rhamnosyl‐glucopyranoside]‐5‐glucopyranoside and delphinidin‐3‐[4‐(trans‐p‐coumaroyl)‐rhamnosyl‐glucopyranoside]‐5‐glucopyranoside were identified as the main anthocyanin components in Lanshan Hexian by ultra‐performance liquid chromatography‐tandem mass spectrometry. Three time points of anthocyanin accumulation, including the start point (0 day), fastest point (5 days), and highest point (12 day), were investigated by using ribonucleic acid sequencing and iTRAQ technology. The corresponding correlation coefficients of differentially expressed genes, and differentially expressed proteins were 0.6936, 0.2332, and 0.6672. Anthocyanin biosynthesis was a significantly enriched pathway, and CHI, F3H, 3GT, 5GT, and HY5 were regulated at both transcriptional and translational levels. Moreover, some transcription factors and photoreceptors may participate in light‐induced anthocyanin biosynthesis like the known transcription factors MYB113 and TT8. The transient expression assay indicated that SmMYB35, SmMYB44, and a SmMYB86 isoform might involve in the light‐induced anthocyanin biosynthesis pathway. Finally, a regulatory model for light‐induced anthocyanin biosynthesis in eggplant was constructed. Our work provides a new direction for the study of the molecular mechanisms of light‐induced anthocyanin biosynthesis in eggplant.
Dog skin parasite load, TLR‐2, IL‐10 and TNF‐α expression and infectiousness
Authors: Pereira‐Fonseca D. C. M. , Oliveira‐Rovai F. M. , Rodas L. A. C. , Beloti C. A. C. , Torrecilha R. B. P. , Ito P. K. R. K. , Avanço S. V. , Cipriano R. S. , Utsunomiya Y. T. , Hiramoto R. M. , Calvo‐Bado L. , Courtenay O. , Machado G. F. , Lima V. M. F. , Nunes C. M. 
Published: September 2017

SummaryVisceral leishmaniosis is a zoonotic disease that is transmitted by Lutzomyia longipalpis sandflies. Dogs are the main peri‐urban reservoir of the disease, and progression of canine leishmaniosis is dependent on the type of immune response elaborated against the parasite. Type 1 immunity is characterized by effective cellular response, with production of pro‐inflammatory cytokines such as tumour necrosis factor alpha (TNF‐α). In contrast, Type 2 immunity is predominantly humoral, associated with progression of the disease and mediated by anti‐inflammatory cytokines such as interleukin 10 (IL‐10). Although seemly important in the dynamics of leishmaniosis, other gene products such as toll‐like receptor 2 (TRL‐2) and inducible nitric oxide synthase (iNOS) exert unclear roles in the determination of the type of immune response. Given that the dog skin serves as a micro‐environment for the multiplication of Leishmania spp., we investigated the parasite load and the expression of TLR‐2, iNOS, IL‐10 and TNF‐α in the skin of 29 infected and 8 control dogs. We found that increased parasite load leads to upregulation of TLR‐2, IL‐10 and TNF‐α, indicating that abundance of these transcripts is associated with infection. We also performed a xenodiagnosis to demonstrate that increased parasitism is a risk factor for infectiousness to sandflies.
Sparse Approximations of Fractional Matérn Fields
Authors: Roininen Lassi , Lasanen Sari , Orispää Mikko , Särkkä Simo 
Published: September 2017

AbstractWe consider fast lattice approximation methods for a solution of a certain stochastic non‐local pseudodifferential operator equation. This equation defines a Matérn class random field. We approximate the pseudodifferential operator with truncated Taylor expansion, spectral domain error functional minimization and rounding approximations. This allows us to construct Gaussian Markov random field approximations. We construct lattice approximations with finite‐difference methods. We show that the solutions can be constructed with overdetermined systems of stochastic matrix equations with sparse matrices, and we solve the system of equations with a sparse Cholesky decomposition. We consider convergence of the truncated Taylor approximation by studying band‐limited Matérn fields. We consider the convergence of the discrete approximations to the continuous limits. Finally, we study numerically the accuracy of different approximation methods with an interpolation problem.
Serum IL‐15 and IL‐15Rα levels are decreased in lean and obese physically active humans
Authors: Pérez‐López A. , Valadés D. , Vázquez Martínez C. , de Cos Blanco A. I. , Bujan J. , García‐Honduvilla N. 
Published: September 2017

Circulating IL‐15 presence is required to stimulate anti‐adipogenic effects of the IL‐15/IL‐15Rα axis in adipose tissue. Although exercise increases blood IL‐15 expression post‐exercise, it remains inconclusive whether physical activity can alter the baseline concentrations of this cytokine. The aim of this study was to determine whether physical activity regulates circulating IL‐15 and IL‐15Rα in lean and obese individuals. Two hundred and seventy‐six participants were divided into five groups according to physical activity (PA), body mass and type 2 diabetes mellitus (T2DM) diagnosis: (a) lean PA (N = 25); (b) lean non‐PA (N = 28); (c) obese PA (N = 64); (d) obese non‐PA (N = 79); and (e) obese non‐PA with T2DM (N = 80). Serum IL‐15 and IL‐15Rα, blood glucose/lipid profile and body composition were measured. Serum IL‐15 and IL‐15Rα decreased in PA participants compared to non‐PA (P < .05), while IL‐15 and IL‐15Rα increased in obese with T2DM compared to obese without T2DM (P < .05). No differences were observed between lean non‐PA and obese PA. Serum IL‐15Rα was associated with fasting glucose (R2 = .063), insulin (R2 = .082), HbA1c (R2 = .108), and HOMA (R2 = .057) in obese participants. Circulating IL‐15 and IL‐15Rα are reduced in lean and obese participants who perform physical activity regularly (≥180 min/week), suggesting a regulative role of physical activity on the circulating concentrations of IL‐15 and IL‐15Rα at baseline. Moreover, the relationship observed between IL‐15Rα and glucose profile may indicate a role of the alpha receptor in glucose metabolism.
Can alternating temperatures be used to estimate base temperature for seed germination?
Authors: Masin R , Onofri A , Gasparini V , Zanin G 
Published: September 2017

SummaryModelling weed seedling emergence pattern appears to be a promising approach in the development of effective weed management programmes based on the selection of optimal timing of control operations. Thermal and hydrothermal time models propose that seed germination rates are proportional to the amount by which temperature and water potential exceed threshold values for these environmental factors. Hence, base temperature for seed germination is a fundamental biological parameter for the prediction of weed emergence. A series of laboratory experiments were conducted to estimate base temperature in three weed species belonging to the Asteraceae family, predominant in conservation tillage fields in north‐eastern Italy. The traditional method based on germination assays at constant temperatures was compared with a method based on assays at alternating temperatures. The latter might represent an alternative to the former for those species which do not germinate or only poorly under constant temperatures. Base temperature was estimated by regressing the reciprocal of the median germination time on temperature comparing two functions, a broken‐stick and an exponential‐type model. Both models showed good fit to all data in the whole temperature range and in almost all cases provided similar estimates of base temperature. The main result is that, for the weed species examined in this study, the use of alternating temperatures for base temperature estimation appears to be possible. However, further research is required to test if the use of germination assays performed at alternating temperatures can be a suitable method to estimate base temperature of species that have too low germination at constant temperatures.
Laminar‐specific encoding of texture elements in rat barrel cortex
Authors: Allitt Benjamin J. , Alwis Dasuni S. , Rajan Ramesh 
Published: September 2017

Key points
For rats texture discrimination is signalled by the large face whiskers by stick‐slip events.
Neural encoding of repetitive stick‐slip events will be influenced by intrinsic properties of adaptation.
We show that texture coding in the barrel cortex is laminar specific and follows a power function.
Our results also show layer 2 codes for novel feature elements via robust firing rates and temporal fidelity.
We conclude that texture coding relies on a subtle neural ensemble to provide important object information.
AbstractTexture discrimination by rats is exquisitely guided by fine‐grain mechanical stick‐slip motions of the face whiskers as they encounter, stick to and slip past successive texture‐defining surface features such as bumps and grooves. Neural encoding of successive stick‐slip texture events will be shaped by adaptation, common to all sensory systems, whereby receptor and neural responses to a stimulus are affected by responses to preceding stimuli, allowing resetting to signal novel information. Additionally, when a whisker is actively moved to contact and brush over surfaces, that motion itself generates neural responses that could cause adaptation of responses to subsequent stick‐slip events. Nothing is known about encoding in the rat whisker system of stick‐slip events defining textures of different grain or the influence of adaptation from whisker protraction or successive texture‐defining stick‐slip events. Here we recorded responses from halothane‐anaesthetized rats in response to texture‐defining stimuli applied to passive whiskers. We demonstrate that: across the columnar network of the whisker‐recipient barrel cortex, adaptation in response to repetitive stick‐slip events is strongest in uppermost layers and equally lower thereafter; neither whisker protraction speed nor stick‐slip frequency impede encoding of stick‐slip events at rates up to 34.08 Hz; and layer 2 normalizes responses to whisker protraction to resist effects on texture signalling. Thus, within laminar‐specific response patterns, barrel cortex reliably encodes texture‐defining elements even to high frequencies.
The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes
Authors: Shmakov Sergey A. , Sitnik Vassilii , Makarova Kira S. , Wolf Yuri I. , Severinov Konstantin V. , Koonin Eugene V. 
Published: September 2017

ABSTRACT

Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR-Cas) systems store the memory of past encounters with foreign DNA in unique spacers that are inserted between direct repeats in CRISPR arrays. For only a small fraction of the spacers, homologous sequences, called protospacers, are detectable in viral, plasmid, and microbial genomes. The rest of the spacers remain the CRISPR “dark matter.” We performed a comprehensive analysis of the spacers from all CRISPR-
cas
loci identified in bacterial and archaeal genomes, and we found that, depending on the CRISPR-Cas subtype and the prokaryotic phylum, protospacers were detectable for 1% to about 19% of the spacers (~7% global average). Among the detected protospacers, the majority, typically 80 to 90%, originated from viral genomes, including proviruses, and among the rest, the most common source was genes that are integrated into microbial chromosomes but are involved in plasmid conjugation or replication. Thus, almost all spacers with identifiable protospacers target mobile genetic elements (MGE). The GC content, as well as dinucleotide and tetranucleotide compositions, of microbial genomes, their spacer complements, and the cognate viral genomes showed a nearly perfect correlation and were almost identical. Given the near absence of self-targeting spacers, these findings are most compatible with the possibility that the spacers, including the dark matter, are derived almost completely from the species-specific microbial mobilomes.

IMPORTANCE
The principal function of CRISPR-Cas systems is thought to be protection of bacteria and archaea against viruses and other parasitic genetic elements. The CRISPR defense function is mediated by sequences from parasitic elements, known as spacers, that are inserted into CRISPR arrays and then transcribed and employed as guides to identify and inactivate the cognate parasitic genomes. However, only a small fraction of the CRISPR spacers match any sequences in the current databases, and of these, only a minority correspond to known parasitic elements. We show that nearly all spacers with matches originate from viral or plasmid genomes that are either free or have been integrated into the host genome. We further demonstrate that spacers with no matches have the same properties as those of identifiable origins, strongly suggesting that all spacers originate from mobile elements.
Cell Cycle Inhibition To Treat Sleeping Sickness
Authors: Epting Conrad L. , Emmer Brian T. , Du Nga Y. , Taylor Joann M. , Makanji Ming Y. , Olson Cheryl L. , Engman David M. 
Published: September 2017

ABSTRACTAfrican trypanosomiasis is caused by infection with the protozoan parasiteTrypanosoma brucei. During infection, this pathogen divides rapidly to high density in the bloodstream of its mammalian host in a manner similar to that of leukemia. Like all eukaryotes,T. bruceihas a cell cycle involving thede novosynthesis of DNA regulated by ribonucleotide reductase (RNR), which catalyzes the conversion of ribonucleotides into their deoxy form. As an essential enzyme for the cell cycle, RNR is a common target for cancer chemotherapy. We hypothesized that inhibition of RNR by genetic or pharmacological means would impair parasite growthin vitroand prolong the survival of infected animals. Our results demonstrate that RNR inhibition is highly effective in suppressing parasite growth bothin vitroandin vivo. These results support drug discovery efforts targeting the cell cycle, not only for African trypanosomiasis but possibly also for other infections by eukaryotic pathogens.IMPORTANCEThe development of drugs to treat infections with eukaryotic pathogens is challenging because many key virulence factors have closely related homologues in humans. Drug toxicity greatly limits these development efforts. For pathogens that replicate at a high rate, especially in the blood, an alternative approach is to target the cell cycle directly, much as is done to treat some hematologic malignancies. The results presented here indicate that targeting the cell cycle via inhibition of ribonucleotide reductase is effective at killing trypanosomes and prolonging the survival of infected animals.
Role of ultrasound biomicroscopy in diagnosis of ocular toxocariasis
Authors: Chen Qian , Gu Junxiang , Jiang Rui , Zhou Min , Chang Qing 
Published: September 2017

PurposeTo investigate ultrasound biomicroscopy (UBM) characteristics of patients with ocular toxocariasis (OT) and to explore the role of UBM in the diagnosis and differential diagnosis of OT.DesignCross-sectional study.Methods78 eyes of 77 patients clinically consistent with OT and confirmed by serum and/or intraocular antibodies in a single tertiary centre (Fudan University Eye and ENT Hospital, Shanghai) between July 2009 and July 2016 were included in the study. UBM was performed, and the outcomes were analysed.ResultsMean age of the patients included was 12.8±10.3 years. Positive UBM findings were observed in 72 of 78 eyes (92.3%). The primary imaging feature was peripheral granulomas (66 eyes; 84.6%), of which 78.5% were adjacent to the nasal or temporal side of horizontal meridian and 79.7% located on the surface of the ciliary body, presenting as olivary foci on radical section and botuliform foci on coronal section. Moreover, 12 of the peripherally involved eyes were accompanied with posterior pole granulomas, which could be termed ‘combined type’. Other UBM findings included vitreous strands (53 eyes; 67.9%), peripheral tractional retinal detachment (41 eyes; 52.6%) and tractional cyclodialysis (32 eyes; 41.0%).ConclusionsThe utilisation of UBM verifies the existence of the combined subtype (with both peripheral and posterior pole granulomas) and improves the detection rate of peripheral granulomas, which is of great importance to the diagnosis and differential diagnosis of OT.
Exercise for patients with major depression: a systematic review with meta-analysis and trial sequential analysis
Authors: Krogh Jesper , Hjorthøj Carsten , Speyer Helene , Gluud Christian , Nordentoft Merete 
Published: September 2017

ObjectivesTo assess the benefits and harms of exercise in patients with depression.DesignSystematic reviewData sourcesBibliographical databases were searched until 20 June 2017.Eligibility criteria and outcomesEligible trials were randomised clinical trials assessing the effect of exercise in participants diagnosed with depression. Primary outcomes were depression severity, lack of remission and serious adverse events (eg, suicide) assessed at the end of the intervention. Secondary outcomes were quality of life and adverse events such as injuries, as well as assessment of depression severity and lack of remission during follow-up after the intervention.ResultsThirty-five trials enrolling 2498 participants were included. The effect of exercise versus control on depression severity was −0.66 standardised mean difference (SMD) (95% CI −0.86 to −0.46; p<0.001; grading of recommendations assessment, development and evaluation (GRADE): very low quality). Restricting this analysis to the four trials that seemed less affected of bias, the effect vanished into −0.11 SMD (−0.41 to 0.18; p=0.45; GRADE: low quality). Exercise decreased the relative risk of no remission to 0.78 (0.68 to 0.90; p<0.001; GRADE: very low quality). Restricting this analysis to the two trials that seemed less affected of bias, the effect vanished into 0.95 (0.74 to 1.23; p=0.78). Trial sequential analysis excluded random error when all trials were analysed, but not if focusing on trials less affected of bias. Subgroup analyses found that trial size and intervention duration were inversely associated with effect size for both depression severity and lack of remission. There was no significant effect of exercise on secondary outcomes.ConclusionsTrials with less risk of bias suggested no antidepressant effects of exercise and there were no significant effects of exercise on quality of life, depression severity or lack of remission during follow-up. Data for serious adverse events and adverse events were scarce not allowing conclusions for these outcomes.Systematic review registrationThe protocol was published in the journalSystematic Reviews: 2015; 4:40.
Integrated management of atrial fibrillation including tailoring of anticoagulation in primary care: study design of the ALL-IN cluster randomised trial
Authors: van den Dries Carline J , Oudega Ruud , Elvan Arif , Rutten Frans H , van de Leur Sjef J C M , Bilo Henk J G , Hoes Arno W , Moons Karel G M , Geersing Geert-Jan 
Published: September 2017

IntroductionIn our ageing society, we are at the merge of an expected epidemic of atrial fibrillation (AF). AF management requires an integrated approach, including rate or rhythm control, stroke prevention with anticoagulation and treatment of comorbidities such as heart failure or type 2 diabetes. As such, primary care seems to be the logical healthcare setting for the chronic management of patients with AF. However, primary care has not yet played a dominant role in AF management, which has been in fact more fragmented between different healthcare providers. This fragmentation might have contributed to high healthcare costs. To demonstrate the feasibility of managing AF in primary care, studies are needed that evaluate the safety and (cost-)effectiveness of integrated AF management in primary care.Methods and analysisThe ALL-IN trial is a multicentre, pragmatic, cluster randomised, non-inferiority trial performed in primary care practices in a suburban region in the Netherlands. We aim to include a minimum of 1000 patients with AF aged 65 years or more from around 18 to 30 practices. Duration of the study is 2 years. Practices will be randomised to either the intervention arm (providing integrated AF management, involving a trained practice nurse and collaboration with secondary care) or the control arm (care as usual). The primary endpoint is all-cause mortality. Secondary endpoints are cardiovascular mortality, (non)-cardiovascular hospitalisation, major adverse cardiac events, stroke, major bleeding, clinically relevant non-major bleeding, quality of life and cost-effectiveness.Ethics and disseminationThe protocol was approved by the Medical Ethical Committee of the Isala Hospital Zwolle, the Netherlands. Patients in the intervention arm will be asked informed consent for participating in the intervention. Results are expected in 2019 and will be disseminated through both national and international journals and conferences.Trial registration numberThis trial is registered at the Netherlands Trial Register (NTR5532).