bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preliminary breakdown of intracloud lightning: Initiation altitude, propagation speed, pulse train characteristics, and step length estimation
Authors: Wu Ting , Yoshida Satoru , Akiyama Yasuhiro , Stock Michael , Ushio Tomoo , Kawasaki Zen 
Published: August 2015

AbstractUsing a low‐frequency lightning location system comprising 11 sites, we located preliminary breakdown (PB) processes in 662 intracloud (IC) lightning flashes during the summer of 2013 in Osaka area of Japan. On the basis of three‐dimensional location results, we studied initiation altitude and upward propagation speed of PB processes. PB in most IC flashes has an initiation altitude that ranges from 5 to 10 km with an average of 7.8 km. Vertical speed ranges from 0.5 to 17.8 × 105 m/s with an average of 4.0 × 105 m/s. Vertical speed is closely related with initiation altitude, with IC flashes initiated at higher altitude having lower vertical speed during PB stage. Characteristics of PB pulse trains including pulse rate, pulse amplitude, and pulse width are also analyzed. The relationship between pulse rate and vertical speed has the strongest correlation, suggesting that each PB pulse corresponds to one step of the initial leader during the PB stage. Pulse rate, pulse amplitude, and pulse width all show decreasing trends with increasing initiation altitude and increasing trends with increasing vertical speed. Using a simple model, the step length of the initial leader during the PB stage is estimated. Most of initial leaders have step lengths that range from 40 to 140 m with an average of 113 m. Estimated step length has a strong correlation with initiation altitude, indicating that leaders initiated at higher altitude have longer steps. Based on the results of this study, we speculate that above certain altitude (~12 km), initial leaders in PB stages of IC flashes may only have horizontal propagations. PB processes at very high altitude may also have very weak radiation, so detecting and locating them would be relatively difficult.
On the use of programmable hardware and reduced numerical precision in earth‐system modeling
Authors: Düben Peter D. , Russell Francis P. , Niu Xinyu , Luk Wayne , Palmer T. N. 
Published: August 2015

AbstractProgrammable hardware, in particular Field Programmable Gate Arrays (FPGAs), promises a significant increase in computational performance for simulations in geophysical fluid dynamics compared with CPUs of similar power consumption. FPGAs allow adjusting the representation of floating‐point numbers to specific application needs. We analyze the performance‐precision trade‐off on FPGA hardware for the two‐scale Lorenz '95 model. We scale the size of this toy model to that of a high‐performance computing application in order to make meaningful performance tests. We identify the minimal level of precision at which changes in model results are not significant compared with a maximal precision version of the model and find that this level is very similar for cases where the model is integrated for very short or long intervals. It is therefore a useful approach to investigate model errors due to rounding errors for very short simulations (e.g., 50 time steps) to obtain a range for the level of precision that can be used in expensive long‐term simulations. We also show that an approach to reduce precision with increasing forecast time, when model errors are already accumulated, is very promising. We show that a speed‐up of 1.9 times is possible in comparison to FPGA simulations in single precision if precision is reduced with no strong change in model error. The single‐precision FPGA setup shows a speed‐up of 2.8 times in comparison to our model implementation on two 6‐core CPUs for large model setups.
Chondromyces
Authors: Reichenbach Hans 
Published: August 2015

Chon.dro.my' ces. Gr. masc. n.chondroscartilage; Gr. masc. n.mykesfungus; M.L. masc. n.Chondromycescartilaginous fungus.Proteobacteria / Deltaproteobacteria / Myxococcales / Myxococcaceae / ChondromycesVegetative cells are cylindrical rods with rounded ends.Swarm colonies produce wide, shallow depressions in the agar surface, often with an orange band of cells at the edge, agar sometimes slightly etched. Swarms often penetrate the agar deeply.Clusters of sporangioles borne on long, branched or unbranched white slime stalks. Myxospores resemble vegetative cells in shape but are optically refractile.The mol%G+C of the DNA is: 69–70.Type species:Chondromyces crocatusBerkeley and CurtisinBerkeley 1874, 64.
Thiovulum
Authors: Robertson Lesley A. , Gijs Kuenen J. , Paster Bruce J. , Dewhirst Floyd E. , Vandamme Peter 
Published: August 2015

Thi.o' vu.lum. Gr. n.thiossulfur; L. n.ovumegg; M.L. neut. dim. n.Thiovulumsmall sulfur egg.Proteobacteria / Epsilonproteobacteria / Campylobacterales / Helicobacteraceae / ThiovulumCells are round to ovoid,5–25 μm in diameter. Cytoplasm is often concentrated at one end of the cell, with the remaining space being occupied by a large vacuole. Cytoplasm normally containsorthorhombic sulfur inclusions, which are generally concentrated at one end and often almost filling cells completely (Figure 1). The amount of sulfur present in the cells varies with the H2S supply, and cells may be temporarily fully devoid of sulfur inclusions. The number ofgreenish bodies(up to 5 μm in diameter), thought to bestorage material, increases with decreasing numbers of sulfur globules (Hinze, 1913).Cells are rapidly motileby peritrichous flagella (Figure 2; de Boer et al., 1961). Swimmingvelocity of over 600 μm s‐1, some of the highest recorded in the bacterial world (Garcia‐Pichel, 1989). Forward movement is accompanied by rotation around the long axis. Unlike most motile bacteria,Thiovulumcells do swim backwards or tumble. Cells possess afibrillar, or antapical organelleat the posterior end of the cell. Its function is to secrete aslime stalkor thread (Figure 2) which is used by cells to attach to solid surfaces. No resting stages are known.Type species:Thiovulum majusHinze 1913, 195.
Thiococcus
Authors: Imhoff Johannes F. 
Published: August 2015

Thi.o.coc' cus. Gr. n.thiossulfur; L. masc. n.coccussphere; M.L. masc. n.Thiococcussphere with sulfur.Proteobacteria / Gammaproteobacteria / Chromatiales / Chromatiaceae / ThiococcusCells spherical, with diplococcus‐shaped division stages,non‐motile, multiply by binary fission. Gram negative, belong to theGammaproteobacteria, and contain internalphotosynthetic membranes consisting of bundles of ribbon‐like branched tubescontinuous with the cytoplasmic membrane. Individual cells colorless, color of cell suspensions is yellowish to orange‐brown. Photosynthetic pigments are bacteriochlorophyllband carotenoids.The mol%G+C of the DNA is: 69.4–69.9.Type species:Thiococcus pfennigii(Eimhjellen 1970) Imhoff, Süling and Petri 1998b, 1139 (Thiocapsa pfennigiiEimhjellen 1970, 193.)
Thiospirillum
Authors: Imhoff Johannes F. 
Published: August 2015

Thi' o.spi.ril' lum. Gr. n.thiossulfur; M.L. dim. neut. n.Spirilluma bacterial genus; M.L. neut. n.ThiospirillumsulfurSpirillum.Proteobacteria / Gammaproteobacteria / Chromatiales / Chromatiaceae / ThiospirillumCellscurved rods or spirals(sigmoid), dividing by binary fission,motile by(multitrichous)polar flagella. Cells may be immobile and grow in irregular aggregates surrounded by slime. Gram negative, belong to theGammaproteobacteria, and containinternal photosynthetic membranes of vesicular typein which the photosynthetic pigments bacteriochlorophyllaand carotenoids are located.The mol%G+C of the DNA is: 45.5.Type species:Thiospirillum jenense(Ehrenberg 1838) Migula 1900, 1050 (Ophidomonas jenensisEhrenberg 1838, 44.)
Ectothiorhodospira
Authors: Imhoff Johannes F. 
Published: August 2015

Ec' to.thi' o.rho' do.spi' ra. Gr. prep.ectosoutside; Gr. n.thiossulfur; Gr. n.rhodonthe rose; Gr. n.spirathe spiral; M.L. fem. n.Ectothiorhodospiraspiral rose with sulfur outside.Proteobacteria / Gammaproteobacteria / Chromatiales / Ectothiorhodospiraceae / EctothiorhodospiraCells rod‐shaped or vibrioid, also appearing as true spirals, 0.7–1.5 µm in diameter,motile by a polar tuft of flagella, multiply by binary fission, and may contain gas vesicles.Gram‐negative and belong to theGammaproteobacteria.Internal photosynthetic membranes are lamellar stacksthat are continuous with the cytoplasmic membrane. Photosynthetic pigments are bacteriochlorophyllaand carotenoids.The mol%G+C of the DNA is: 61.4–68.4.Type species:Ectothiorhodospira mobilisPelsh 1936, 120.
Citrobacter
Authors: Frederiksen Wilhelm 
Published: August 2015

Cit.ro.bac' ter. L. n.citruslemon; M.L. n.bactera small rod; M.L. masc. n.Citrobactera citrate‐utilizing rod.Proteobacteria / Gammaproteobacteria / Enterobacteriales / Enterobacteriaceae / CitrobacterStraight rods, ~1.0 µm × 2.0–6.0 µm. Occur singly and in pairs. Conform to the general definition of the familyEnterobacteriaceae. Usually not encapsulated. Gram negative. Usuallymotile by peritrichous flagella. Facultatively anaerobic, having both a respiratory and a fermentative type of metabolism. Grow readily on ordinary media. Colonies on nutrient agar are generally 2–4 mm in diameter, smooth, low convex, moist, translucent or opaque, and gray with a shiny surface and entire edge. Mucoid or rough forms may occur occasionally. Oxidase negative. Catalase positive. Chemoorganotrophic.Citrate can be utilized as a sole carbon source by most strains. Lysine is not decarboxylated. Alginate and pectate are not decomposed.D‐glucose is fermented with the production of acid and gas. The methyl red test is positive; the Voges–Proskauer test is negative. Occur in the feces of humans and some animals; probably normal intestinal inhabitants. Sometimes pathogenic and often isolated from clinical specimens as opportunistic pathogens. Can also be found in soil, water, sewage, and food.The mol%G+C of the DNA is: 50–52 (Tm).Type species:Citrobacter freundii(Braak 1928) Werkman and Gillen 1932, 173 (Bacterium freundiiBraak 1928, 140.)
Yersinia
Authors: Bottone Edward J. , Bercovier Herve , Mollaret Henri H. 
Published: August 2015

Yer.si' ni.a. M.L. fem. n.Yersinianamed for the French bacteriologist A.J.E. Yersin, who first isolated the causal organism of plague in 1894.Proteobacteria / Gammaproteobacteria / Enterobacteriales / Enterobacteriaceae / YersiniaStraight rods to coccobacilli, 0.5–0.8 × 1–3 µm. Endospores are not formed. Capsules are not present, but an envelope occurs inY. pestisstrains grown at 37°C and in cells from clinical sources. Gram negative,nonmotile at 37°C, but motile with peritrichous flagella when grown below 30°C, except forY. pestis, which is always nonmotile. Growth occurs on ordinary bacteriological media. Colonies of yersiniae are translucent to opaque, 0.1–1.0 mm in diameter after 24 h. Optimum growth temperature, 28–29°C. Facultatively anaerobic, having both a respiratory and a fermentative type of metabolism. Oxidase negative. Catalase positive. Nitrate is reduced to nitrite with a few exceptions in specific biovars.D‐glucose and other carbohydrates are fermented withacid production but little or no gas. Phenotypic characteristics are often temperature dependent, and usually more characteristics are expressed by cultures incubated at 25–29°C than at 35–37°C. The enterobacterial common antigen is present in all species investigated. Widely distributed in nature with some species adapted to specific animal hosts and humans. Several species are pathogenic for humans and animals includingY. pestis, the causative agent of plague. A significant cause of food‐borne and waterborne disease. Belongs to theGammaproteobacteria.The mol%G+C of the DNA is: 46–50.Type species:Yersinia pestis(Lehmann and Neumann 1896) Van Loghem 1944, 15 (Bacterium pestisLehmann and Neumann 1896, 194;Yersinia pseudotuberculosissubsp.pestisBercovier, Mollaret, Alonso, Brault, Fanning, Steigerwalt and Brenner 1981a, 383.)
How are different neural networks related to consciousness?
Authors: Qin Pengmin , Wu Xuehai , Huang Zirui , Duncan Niall W. , Tang Weijun , Wolff Annemarie , Hu Jin , Gao Liang , Jin Yi , Wu Xing , Zhang Jianfeng , Lu Lu , Wu Chunping , Qu Xiaoying , Mao Ying , Weng Xuchu , Zhang Jun , Northoff Georg 
Published: August 2015

ObjectiveWe aimed to investigate the roles of different resting‐state networks in predicting both the actual level of consciousness and its recovery in brain injury patients.MethodsWe investigated resting‐state functional connectivity within different networks in patients with varying levels of consciousness: unresponsive wakefulness syndrome (UWS; n = 56), minimally conscious state (MCS; n = 29), and patients with brain lesions but full consciousness (BL; n = 48). Considering the actual level of consciousness, we compared the strength of network connectivity among the patient groups. We then checked the presence of connections between specific regions in individual patients and calculated the frequency of this in the different patient groups. Considering the recovery of consciousness, we split the UWS group into 2 subgroups according to recovery: those who emerged from UWS (UWS‐E) and those who remained in UWS (UWS‐R). The above analyses were repeated on these 2 subgroups.ResultsFunctional connectivity strength in salience network (SN), especially connectivity between the supragenual anterior cingulate cortex (SACC) and left anterior insula (LAI), was reduced in the unconscious state (UWS) compared to the conscious state (MCS and BL). Moreover, at the individual level, SACC‐LAI connectivity was more present in MCS than in UWS. Default‐mode network (DMN) connectivity strength, especially between the posterior cingulate cortex (PCC) and left lateral parietal cortex (LLPC), was reduced in UWS‐R compared with UWS‐E. Furthermore, PCC‐LLPC connectivity was more present in UWS‐E than in UWS‐R.InterpretationOur findings show that SN (SACC‐LAI) connectivity correlates with behavioral signs of consciousness, whereas DMN (PCC‐LLPC) connectivity instead predicts recovery of consciousness. Ann Neurol 2015;78:594–605
Elevated synchrony in Parkinson disease detected with electroencephalography
Authors: Swann Nicole C. , de Hemptinne Coralie , Aron Adam R. , Ostrem Jill L. , Knight Robert T. , Starr Philip A. 
Published: August 2015

ObjectiveParkinson disease (PD) can be difficult to diagnose and treat. Development of a biomarker for PD would reduce these challenges by providing an objective measure of disease. Emerging theories suggest PD is characterized by excessive synchronization in the beta frequency band (∼20Hz) throughout basal ganglia–thalamocortical loops. Recently we showed with invasive electrocorticography that one robust measure of this synchronization is the coupling of beta phase to broadband gamma amplitude (ie, phase–amplitude coupling [PAC]). Other recent work suggests that high‐frequency activity is detectable at the scalp using electroencephalography (EEG). Motivated by these findings, we tested whether beta‐gamma PAC over sensorimotor cortex, recorded noninvasively with EEG, differs between PD patients off and on medications, and healthy control subjects.MethodsResting EEG was compared from 15 PD patients and 16 healthy control subjects. PD patients were tested on and off medications on different days, in a counterbalanced order. For each data set we calculated PAC and compared results across groups.ResultsPAC was elevated in the patients off medications compared to on medications (p = 0.008) and for patients off medications compared to controls (p = 0.009).InterpretationElevated PAC is detectable using scalp EEG in PD patients off medications compared to on medications, and compared to healthy controls. This suggests that EEG PAC may provide a noninvasive biomarker of the parkinsonian state. This biomarker could be used as a control signal for closed‐loop control of deep brain stimulation devices, for adjustment of dopaminergic treatment, and also has the potential to aid in diagnosis. Ann Neurol 2015;78:Ann Neurol 2015;78:679–696
Tracking sensory system atrophy and outcome prediction in spinal cord injury
Authors: Grabher Patrick , Callaghan Martina F. , Ashburner John , Weiskopf Nikolaus , Thompson Alan J. , Curt Armin , Freund Patrick 
Published: August 2015

ObjectiveIn patients with subacute spinal cord injury (SCI), the motor system undergoes progressive structural changes rostral to the lesion, which are associated with motor outcome. The extent to which the sensory system is affected and how this relates to sensory outcome are uncertain.MethodsChanges in the sensory system were prospectively followed by applying a comprehensive magnetic resonance imaging (MRI) protocol to 14 patients with subacute traumatic SCI at baseline, 2 months, 6 months, and 12 months after injury, combined with a full neurological examination and comprehensive pain assessment. Eighteen controls underwent the same MRI protocol. T1‐weighted volumes, myelin‐sensitive magnetization transfer saturation (MT), and longitudinal relaxation rate (R1) mapping provided data on spinal cord and brain morphometry and microstructure. Regression analysis assessed the relationship between MRI readouts and sensory outcomes.ResultsAt 12 months from baseline, sensory scores were unchanged and below‐level neuropathic pain became prominent. Compared with controls, patients showed progressive degenerative changes in cervical cord and brain morphometry across the sensory system. At 12 months, MT and R1 were reduced in areas of structural decline. Sensory scores at 12 months correlated with rate of change in cord area and brain volume and decreased MT in the spinal cord at 12 months.InterpretationThis study has demonstrated progressive atrophic and microstructural changes across the sensory system with a close relation to sensory outcome. Structural MRI protocols remote from the site of lesion provide new insights into neuronal degeneration underpinning sensory disturbance and have potential as responsive biomarkers of rehabilitation and treatment interventions. Ann Neurol 2015;78:Ann Neurol 2015;78:679–696
New practical definitions for the diagnosis of autosomal recessive spastic ataxia of Charlevoix–Saguenay
Authors: Pilliod Julie , Moutton Sébastien , Lavie Julie , Maurat Elise , Hubert Christophe , Bellance Nadège , Anheim Mathieu , Forlani Sylvie , Mochel Fanny , N'Guyen Karine , Thauvin‐Robinet Christel , Verny Christophe , Milea Dan , Lesca Gaëtan , Koenig Michel , Rodriguez Diana , Houcinat Nada , Van‐Gils Julien , Durand Christelle M. , Guichet Agnès , Barth Magalie , Bonneau Dominique , Convers Philippe , Maillart Elisabeth , Guyant‐Marechal Lucie , Hannequin Didier , Fromager Guillaume , Afenjar Alexandra , Chantot‐Bastaraud Sandra , Valence Stéphanie , Charles Perrine , Berquin Patrick , Rooryck Caroline , Bouron Julie , Brice Alexis , Lacombe Didier , Rossignol Rodrigue , Stevanin Giovanni , Benard Giovanni , Burglen Lydie , Durr Alexandra , Goizet Cyril , Coupry Isabelle 
Published: August 2015

ObjectiveAutosomal recessive spastic ataxia of Charlevoix–Saguenay (ARSACS) is caused by mutations in the SACS gene. SACS encodes sacsin, a protein whose function remains unknown, despite the description of numerous protein domains and the recent focus on its potential role in the regulation of mitochondrial physiology. This study aimed to identify new mutations in a large population of ataxic patients and to functionally analyze their cellular effects in the mitochondrial compartment.MethodsA total of 321 index patients with spastic ataxia selected from the SPATAX network were analyzed by direct sequencing of the SACS gene, and 156 patients from the ATAXIC project presenting with congenital ataxia were investigated either by targeted or whole exome sequencing. For functional analyses, primary cultures of fibroblasts were obtained from 11 patients carrying either mono‐ or biallelic variants, including 1 case harboring a large deletion encompassing the entire SACS gene.ResultsWe identified biallelic SACS variants in 33 patients from SPATAX, and in 5 nonprogressive ataxia patients from ATAXIC. Moreover, a drastic and recurrent alteration of the mitochondrial network was observed in 10 of the 11 patients tested.InterpretationOur results permit extension of the clinical and mutational spectrum of ARSACS patients. Moreover, we suggest that the observed mitochondrial network anomalies could be used as a trait biomarker for the diagnosis of ARSACS when SACS molecular results are difficult to interpret (ie, missense variants and heterozygous truncating variant). Based on our findings, we propose new diagnostic definitions for ARSACS using clinical, genetic, and cellular criteria. Ann Neurol 2015;78:871–886
Corticospinal tract lesion load: An imaging biomarker for stroke motor outcomes
Authors: Feng Wuwei , Wang Jasmine , Chhatbar Pratik Y. , Doughty Christopher , Landsittel Douglas , Lioutas Vasileios‐Arsenios , Kautz Steven A. , Schlaug Gottfried 
Published: August 2015

ObjectiveThe aim of this work was to investigate whether an imaging measure of corticospinal tract (CST) injury in the acute phase can predict motor outcome at 3 months in comparison to clinical assessment of initial motor impairment.MethodsA two‐site prospective cohort study followed up a group of first‐ever ischemic stroke patients using the Upper‐Extremity Fugl‐Meyer (UE‐FM) Scale to measure motor impairment in the acute phase and at 3 months. A weighted CST lesion load (wCST‐LL) was calculated by overlaying the patient's lesion map on magnetic resonance imaging with a probabilistic CST constructed from healthy control subjects. Regression models were fit to assess the predictive value of wCST‐LL and compared with initial motor impairment.ResultsSeventy‐six patients (37 from cohort 1 and 39 from cohort 2) completed the study. wCST‐LL as well as assessment of motor impairment (UE‐FM) in the acute phase correlated with motor impairment (UE‐FM) at 3 months in both cohort 1 (R2 = 0.69 vs. R2 = 0.67; p = 0.43) and cohort 2 (R2 = 0.69 vs. R2 = 0.62; p = 0.25). In the severely impaired subgroup (defined as UE‐FM ≤ 10 at baseline), wCST‐LL correlated with outcomes significantly better than clinical assessment (R2 = 0.47 vs. R2 = 0.11; p = 0.03). In the nonseverely impaired subgroup, stroke patients recovered approximately 70% of their maximal recovery potential. All stroke patients in both cohorts had poor motor outcomes at 3 months (defined as UE‐FM ≤ 25) when wCST‐LL was ≥ 7.0 cc (positive predictive value was 100%).InterpretationwCST‐LL, an imaging biomarker determined in the acute phase, can predict poststroke motor outcomes at 3 months, especially in patients with severe impairment at baseline. Ann Neurol 2015;78:860–870
Participation of Alkoxy Groups in Reactions of Acetals: Violation of the Reactivity/Selectivity Principle in a Curtin–Hammett Kinetic Scenario
Authors: Garcia Angie , Sanzone Jillian R. , Woerpel K. A. 
Published: August 2015

AbstractNucleophilic substitution reactions of acetals having benzyloxy groups four carbon atoms away can be highly diastereoselective. The selectivity in several cases increased as the reactivity of the nucleophile increased, in violation of the reactivity/selectivity principle. The increase in selectivity with reactivity suggests that multiple conformational isomers of reactive intermediates can give rise to the products.