bluuebunny/crossref_metadata_2025 huggingface dataset:
Synchrotrons round the bend to make cheaper, better x rays
Authors: Feder Toni
Published: May 2015

After a slow start, a technique that promises deep sample penetration and improved spatial resolution is catching on fast.
A disarmament agenda
Authors: Feder Toni
Published: May 2015

Three members of an independent multinational body that analyzes issues related to nuclear disarmament, arms control, and nonproliferation share their views.
Biomimetics: Lessons on optics from nature’s school
Authors: McPhedran Ross C. , Parker Andrew R.
Published: May 2015

The spectacular colors of living creatures are often produced by intricate arrays of photonic elements, including some that researchers wouldn’t otherwise have thought of.
On the belated discovery of fission
Authors: Pearson J. Michael
Published: May 2015

A remarkable sequence of missteps, misfortune, and oversights delayed the discovery of nuclear fission until the eve of World War II—and likely altered history’s course.
Iron-based superconductors, seven years later
Authors: Chubukov Andrey , Hirschfeld Peter J.
Published: May 2015

Discovery of the new materials raised researchers’ hopes of solving the riddle of high-temperature superconductivity. But the unexpectedly diverse systems turned out to possess their own treasure trove of unusual physics that continues to challenge condensed-matter theorists.
Salty solutions
Authors: Thiel Gregory P.
Published: May 2015

As Earth’s population grows and fresh water becomes an ever more precious resource, scientists and engineers are working to increase the efficiency and decrease the cost of desalination.
Identifying localized changes in large systems: Change-point detection for biomolecular simulations
Authors: Fan Zhou , Dror Ron O. , Mildorf Thomas J. , Piana Stefano , Shaw David E.
Published: May 2015

Significance

With data proliferating across many disciplines, data analysts often wish to identify abrupt changes in complex systems with many measured quantities—a problem complicated by the fact that a given change might affect only a few of these quantities. We developed a method that accurately identifies changes in such systems by searching concurrently for change times and the subset of measured quantities that change at each of these times. This work was motivated by the challenge of detecting biologically interesting structural changes in proteins, but our method may prove useful in diverse application domains.
Differential protein expression and peak selection in mass spectrometry data by binary discriminant analysis
Authors: Gibb Sebastian , Strimmer Korbinian
Published: May 2015

Motivation: Proteomic mass spectrometry analysis is becoming routine in clinical diagnostics, for example to monitor cancer biomarkers using blood samples. However, differential proteomics and identification of peaks relevant for class separation remains challenging.

Results: Here, we introduce a simple yet effective approach for identifying differentially expressed proteins using binary discriminant analysis. This approach works by data-adaptive thresholding of protein expression values and subsequent ranking of the dichotomized features using a relative entropy measure. Our framework may be viewed as a generalization of the ‘peak probability contrast’ approach of Tibshirani et al. (2004) and can be applied both in the two-group and the multi-group setting. Our approach is computationally inexpensive and shows in the analysis of a large-scale drug discovery test dataset equivalent prediction accuracy as a random forest. Furthermore, we were able to identify in the analysis of mass spectrometry data from a pancreas cancer study biological relevant and statistically predictive marker peaks unrecognized in the original study.

Availability and implementation: The methodology for binary discriminant analysis is implemented in the R package binda, which is freely available under the GNU General Public License (version 3 or later) from CRAN at URL http://cran.r-project.org/web/packages/binda/. R scripts reproducing all described analyzes are available from the web page http://strimmerlab.org/software/binda/.

Contact:  k.strimmer@imperial.ac.uk
Geodetic secular velocity errors due to interannual surface loading deformation
Authors: Santamaría-Gómez Alvaro , Mémin Anthony
Published: May 2015

Geodetic vertical velocities derived from data as short as 3 yr are often assumed to be representative of linear deformation over past decades to millennia. We use two decades of surface loading deformation predictions due to variations of atmospheric, oceanic and continental water mass to assess the effect on secular velocities estimated from short time-series. The interannual deformation is time-correlated at most locations over the globe, with the level of correlation depending mostly on the chosen continental water model. Using the most conservative loading model and 5-yr-long time-series, we found median vertical velocity errors of 0.5 mm yr−1 over the continents (0.3 mm yr−1 globally), exceeding 1 mm yr−1 in regions around the southern Tropic. Horizontal velocity errors were seven times smaller. Unless an accurate loading model is available, a decade of continuous data is required in these regions to mitigate the impact of the interannual loading deformation on secular velocities.
γ-ray emission states in the redback millisecond pulsar binary system PSR J1227−4853
Authors: Bednarek W.
Published: May 2015

Long expected transition states between the rotation powered and accretion powered non-thermal emission in the millisecond pulsar binary systems have been recently observed in the case of three objects PSR J1023+0038, PSR J1824−2452, and PSR J1227−4859. Surprisingly, the transition is related to the significant change in the γ-ray flux being a factor of a few higher with the presence of an accretion disc. The origin of this enhanced emission seems to be related to the penetration of the inner pulsar magnetosphere by the accretion disc. We propose that the radiation processes, characteristic for the rotation powered pulsar, can co-exist with the presence of an accretion disc in the inner pulsar magnetosphere. In our scenario additional γ-ray emission is produced by secondary leptons, originated close to the acceleration gap, which Compton up-scatter thermal radiation from the accretion disc to GeV energies. The accretion disc penetrates deep into the pulsar magnetosphere allowing the matter to fall on to the neutron star surface producing pulsed X-ray emission. We show that the sum of the rotation powered pulsar γ-ray emission, produced by the primary electrons in the curvature process, and the γ-ray emission, produced by secondary leptons, can explain the observed high-energy radiation from the redback binary pulsar PSR J1227−4853 in the state with evidences of the accretion disc.
Pulse Photoplethysmographic Analysis Estimates the Sympathetic Activity Directed to Heart and Vessels
Authors: Colombo Riccardo , Marchi Andrea , Borghi Beatrice , Fossali Tommaso , Rech Roberto , Castelli Antonio , Corona Alberto , Guzzetti Stefano , Raimondi Ferdinando
Published: May 2015

AbstractAbstract

In controlled experimental conditions, novel pulse plethysmograhic indices estimated changes of the sympathetic outflow directed to vessels and the sympathovagal balance modulating heart rate.

Background:

Novel pulse photoplethysmographic–derived indices have been proposed as tools to measure autonomic nervous system (ANS) modulation in anesthetized and awake patients, but nowadays their experimental validation is lacking. The authors aimed to investigate the ability of pulse photoplethysmographic amplitude (PPGA), ANS state (ANSS), and ANSS index (ANSSi) to measure changes of ANS modulation in response to sympathetic stimulation.

Methods:

Ten awake healthy volunteers underwent two passive head-up tilts at 45° and 90°. The heart rate variability (HRV) and systolic arterial pressure variability were analyzed in the frequency domain as a measure of ANS modulation directed to the heart and the vessels. HRV, baroreflex sensitivity, and pulse photoplethysmographic indices were measured at baseline and after tilt maneuvers. The agreement between HRV-derived indices and pulse photoplethysmographic indices was assessed using Bland–Altman plots.

Results:

PPGA, ANSS, and ANSSi changed significantly during the study protocol. Head-up tilt decreased PPGA and ANSS and increased ANNSi. There was a good agreement between ANSSi and baroreflex sensitivity explored in the high-frequency band (bias, 0.23; 95% CI, −22.7 to 23.2 normalized units) and between ANSSi and the sympathovagal modulation directed to the heart (bias, 0.96; 95% CI, −8.7 to 10.8 normalized units).

Conclusions:

In controlled experimental conditions, novel pulse plethysmographic indices seem to estimate the changes of the sympathetic outflow directed to the vessels and the sympathovagal balance modulating heart rate. These indices might be useful in the future to monitor the fluctuation of sympathetic activity in anesthetized patients.
Assessment of Cerebral Autoregulation Patterns with Near-infrared Spectroscopy during Pharmacological-induced Pressure Changes
Authors: Moerman Annelies T. , Vanbiervliet Valerie M. , Van Wesemael Astrid , Bouchez Stefaan M. , Wouters Patrick F. , De Hert Stefan G.
Published: May 2015

AbstractAbstract

Paradoxical reactions might be part of a normal physiological autoregulatory response, thereby challenging the conventional paradigm. Intact cerebral autoregulation comprises additional patterns of normal cerebrovascular responses that might be obscured if the existence of different mechanisms is ignored, and analysis is based on the mean response of a group.

Background:

Previous work has demonstrated paradoxical increases in cerebral oxygen saturation (ScO2) as blood pressure decreases and paradoxical decreases in ScO2 as blood pressure increases. It has been suggested that these paradoxical responses indicate a functional cerebral autoregulation mechanism. Accordingly, the authors hypothesized that if this suggestion is correct, paradoxical responses will occur exclusively in patients with intact cerebral autoregulation.

Methods:

Thirty-four patients undergoing elective cardiac surgery were included. Cerebral autoregulation was assessed with the near-infrared spectroscopy–derived cerebral oximetry index (COx), computed by calculating the Spearman correlation coefficient between mean arterial pressure and ScO2. COx less than 0.30 was previously defined as functional autoregulation. During cardiopulmonary bypass, 20% change in blood pressure was accomplished with the use of nitroprusside for decreasing pressure and phenylephrine for increasing pressure. Effects on COx were assessed. Data were analyzed using two-way ANOVA, Kruskal–Wallis test, and Wilcoxon and Mann–Whitney U test.

Results:

Sixty-five percent of patients had a baseline COx less than 0.30, indicating functional baseline autoregulation. In 50% of these patients (n = 10), COx became highly negative after vasoactive drug administration (from −0.04 [−0.25 to 0.16] to −0.63 [−0.83 to −0.26] after administration of phenylephrine, and from −0.05 [−0.19 to 0.17] to −0.55 [−0.94 to −0.35] after administration of nitroprusside). A negative COx implies a decrease in ScO2 with increase in pressure and, conversely, an increase in ScO2 with decrease in pressure.

Conclusions:

In this study, paradoxical changes in ScO2 after pharmacological-induced pressure changes occurred exclusively in patients with intact cerebral autoregulation, corroborating the hypothesis that these paradoxical responses might be attributable to a functional cerebral autoregulation.
Pediatric Tibial Osteomyelitis
Authors: Stone Brad , Street Matthew , Leigh Warren , Crawford Haemish
Published: May 2015

Background:

Osteomyelitis shows a strong predilection for the tibia in the pediatric population and is a significant source of complications. The purpose of this article is to retrospectively review a large series of pediatric patients with tibial osteomyelitis. We compare our experience with that in the literature to determine any factors that may aid diagnosis and/or improve treatment outcomes.

Methods:

A 10-year retrospective review was performed of clinical records of all cases of pediatric tibial osteomyelitis managed at the 2 children’s orthopaedic departments in the Auckland region. The Osteomyelitis Database was used to identify all cases between 1997 and 2007, at Starship Children’s Hospital, and 1998 and 2008 at Middlemore’s Kids First Hospital.

Results:

One hundred ninety-one patients fulfilled the inclusion criteria, and had a review of clinical notes and relevant investigations. The average duration of symptoms before presentation to hospital was 5.7 days. Less than 40% of patients had a recent episode of trauma. Almost 60% of patients could not bear weight on admission. Over 40% of patients had a temperature above 38°C. Erythrocyte sedimentation rate was elevated in 78% and the C-reactive protein was elevated in 90% of patients. In total, 42% of blood cultures and almost 75% of tissue cultures were positive, with Staphylococcus aureus being the most commonly cultured organism. X-rays, bone scans, and magnetic resonance imaging were all used to aid the diagnosis. About 43% of patients had surgery. Treatment length was an average of 2 weeks 6 days of intravenous antibiotics followed by 3 weeks 2 days of oral treatment. Six postsurgical complications and 46 readmissions were noted: 25 for relapse, with the remainder due to social and antibiotic-associated complications.

Conclusions:

Although generally diagnosed on presentation, pediatric tibial osteomyelitis can require more sophisticated investigations and prolonged management. Treatment with intravenous and oral antibiotics and surgical debridement where indicated can lead to a good clinical outcome, although complications are often noted.

Level of Evidence:

Level IV—Prognostic study.
Temporary Percutaneous Pedicle Screw Stabilization Without Fusion of Adolescent Thoracolumbar Spine Fractures
Authors: Cui Shari , Busel Gennadiy A. , Puryear Aki S.
Published: May 2015

Background:

Pediatric spine trauma often results from high-energy mechanisms. Despite differences in healing potential, comorbidities, and length of remaining life, treatment is frequently based on adult criteria; ligamentous injuries are fused and bony injuries are treated accordingly. In this study, we present short-term results of a select group of adolescent patients treated using percutaneous pedicle screw instrumentation without fusion.

Methods:

An IRB-approved retrospective review was performed at a level 1 pediatric trauma center for thoracolumbar spine fractures treated by percutaneous pedicle screw instrumentation. Patients were excluded if arthrodesis was performed or if instrumentation was not removed. Demographics, injury mechanism, associated injuries, fracture classification, surgical data, radiographic measures, and complications were collected. Radiographs were analyzed for sagittal and coronal wedge angles and vertebral body height ratio and statistical comparisons performed on preoperative and postoperative values.

Results:

Between 2005 and 2013, 46 patients were treated surgically. Fourteen patients (5 male, 9 female) met inclusion criteria. Injury mechanisms included 8 motor vehicle collisions, 4 falls, and 2 all-terrain vehicle/motorcycle collisions. There were 8 Magerl type A injuries, 4 type B injuries, and 2 type C injuries. There was 1 incomplete spinal cord injury. Implants were removed between 5 and 12 months in 12 patients and after 12 months in 2 patients. Statistical analysis revealed significant postoperative improvement in all radiographic measures (P<0.05). There were no neurological complications, 1 superficial wound dehiscence, and 2 instrumentation failures (treated with standard removal). At last follow-up, 11 patients returned to unrestricted activities including sports. Average follow-up was 9 months after implant removal and 19.3 months after index procedure.

Conclusions:

Adolescent thoracolumbar fractures present unique challenges and treatment opportunities different from the adult patient. We present a nonconsecutive series of 14 patients temporarily stabilized with percutaneous pedicle screw fixation for injuries including 3-column fracture dislocations and purely ligamentous injuries. Temporary fusionless instrumentation can provide successful management of select thoracolumbar spine injuries in pediatric trauma patients.

Level of Evidence:

Level IV—Retrospective case series.
Correction of Tibial Torsion in Children With Cerebral Palsy by Isolated Distal Tibia Rotation Osteotomy: A Short-term, In Vivo Anatomic Study
Authors: Andrisevic Emily , Westberry David E. , Pugh Linda I. , Bagley Anita M. , Tanner Stephanie , Davids Jon R.
Published: May 2015

Background:

Excessive internal or external tibial torsion is frequently present in children with cerebral palsy. Several surgical techniques have been described to correct excessive tibial torsion, including isolated distal tibial rotation osteotomy (TRO). The anatomic changes surrounding this technique are poorly understood. The goal of the study was to examine the anatomic relationship between the tibia and fibula following isolated distal TRO in children with cerebral palsy.

Methods:

Twenty patients with 29 limbs were prospectively entered for study. CT scans of the proximal and distal tibiofibular (TF) articulations were obtained preoperatively, at 6 weeks, and 1 year postoperatively. Measurements of tibia and fibula torsion were performed at each interval. Qualitative assessments of proximal and distal TF joint congruency were also performed.

Results:

The subjects with internal tibia torsion (ITT, 19 limbs) showed significant torsional changes for the tibia between preoperative, postoperative, and 1 year time points (mean torsion 13.21, 31.05, 34.84 degrees, respectively). Measurement of fibular torsion in the ITT treatment group also showed significant differences between time points (mean −36.77, −26.77, −18.54 degrees, respectively). Proximal and distal TF joints remained congruent at all time points in the study.

Subjects with external tibia torsion (ETT, 10 limbs) showed significant differences between preoperative and postoperative tibial torsion, but not between postoperative and 1 year (mean torsion 54, 19.3, 23.3 degrees, respectively). Measurement of fibular torsion in the ETT treatment group did not change significantly between preoperative and postoperative, but did change significantly between postoperative and 1 year (mean torsion −9.8,−16.9, −30.7 degrees, respectively). Nine of 10 proximal TF joints were found to be subluxated at 6 weeks postoperatively. At 1 year, all 9 of these joints had reduced.

Conclusions:

Correction of ITT by isolated distal tibial external rotation osteotomy resulted in acute external fibular torsion. The fibular torsion alignment remodeled over time to accommodate the corrected tibial torsional alignment and reduce the strain associated with the plastic deformity of the fibula. Correction of ETT by isolated distal internal TRO resulted in acute subluxation of the proximal TF articulation in almost all cases. Subsequent torsional remodeling of the fibula resulted in correction of the TF subluxation in all cases. Acute correction of TT by isolated distal TRO occurs by distinct mechanisms, based upon the direction of rotational correction.

Level of Evidence:

Level II—Diagnostic.
Displaced Tibial Shaft Fractures With Intact Fibula in Children: Nonoperative Management Versus Operative Treatment With Elastic Stable Intramedullary Nailing
Authors: Canavese Federico , Botnari Alexei , Andreacchio Antonio , Marengo Lorenza , Samba Antoine , Dimeglio Alain , Pereira Bruno , Mansour Mounira , Rousset Marie
Published: May 2015

Background:

The main objective of this study was to retrospectively evaluate the clinical and radiographic outcomes of displaced tibial shaft fractures with intact fibula in children after nonoperative management and operative treatment by elastic stable intramedullary nailing.

Methods:

A study was performed on 80 consecutive children, 56 males, 24 females from 2 Institutions, with displaced and closed tibial shaft fracture with intact fibula. All patients underwent regular clinical and radiographic follow-up visits for at least 2 years after injury.

Results:

In total, 26 patients (group A-Institution I) were treated surgically by elastic stable intramedullary nailing and 54 patients (18 patients from group B-Institution I and 36 patients from group C-Institution II) were treated nonoperatively with closed reduction and casting. groups A, B, and C did not significantly differ on sex (P=0.37), side (P=0.54), and fracture site (P=0.14).

Valgus deformity was significantly controlled in group A patients only (P=0.001); during follow-up in group B patients (P=0.017), and showed no significant change between pretreatment images and last follow-up in group C patients (P=0.71). Procurvatum deformity was significantly controlled in group A patients only (P=0.001); it showed no significant improvement after conservative treatment in group B (P=0.73) and C patients (P=0.8). Recurvatum was significantly improved in group A (P<0.001) and C patients (P<0.001) but remained unchanged in group B patients (P=0.15). Varus deformity improved significantly in all patient groups.

Immobilization time was significantly shorter in group A compared with group B and C patients (P<0.001).

However, numerical differences, although statistically significant, were not clinically relevant for all variables but immobilization time.

Conclusions:

This study showed good functional and radiologic outcomes in the pediatric population who had sustained closed, traumatic, displaced fracture of tibial diaphysis without associated fibula fracture.

On the basis of the findings reported here, it is not contraindicated to operate skeletally immature patients with displaced fracture of tibial diaphysis without associated fibula fracture. However, results were essentially the same and either method is a satisfactory choice for pediatric tibia shaft fractures with an intact fibula. In particular, we found that conservative treatment was as efficacious as surgical treatment apart from the length of time for immobilization.

Level of Evidence:

Level III.
Operative Versus Conservative Management of Displaced Tibial Shaft Fracture in Adolescents
Authors: Kinney Matthew C. , Nagle David , Bastrom Tracey , Linn Michael S. , Schwartz Alexandra K. , Pennock Andrew T.
Published: May 2015

Background:

Displaced tibial shaft fractures are common in adolescent patients, yet there is no standardized management strategy. We compared surgical fixation and closed reduction and casting (CRC) of these fractures to assess treatment outcomes and determine predictors of failure.

Methods:

We retrospectively reviewed all patients aged 12 to 18 who presented with a displaced tibial shaft fracture that required reduction over an 8-year period. Exclusion criteria included open fractures and lack of follow-up to radiographic union or to 6 months from the index procedure. Fractures were initially treated based on surgeon preference either with CRC or with immediate intramedullary nailing. Seventy-four patients met inclusion criteria: 57 were initially managed with CRC and 17 with operative fixation. Radiographic healing was defined as bridging of 3 cortices and adequacy of final alignment was defined as <5 degrees of angular deformity in both planes and <1.0 cm of shortening. Outcomes were analyzed both on intent-to-treat principles and by definitive treatment method.

Results:

Although all fractures in both groups achieved bony healing, 23 of the 57 patients who underwent CRC failed closed treatment and ultimately required surgery (40.3%). Multivariate analysis of patient and fracture characteristics revealed fracture displacement of >20% (odds ratio=7.8, P<0.05) and the presence of a fibula fracture (odds ratio=5.06, P=0.05) as predictors of closed treatment failure. Patients ultimately managed with intramedullary nailing trended toward increased adequacy of final alignment (92.5% vs. 72.4%, P=0.10) but required longer hospitalization (5.4 vs. 1.9 d, P<0.001) and had a higher incidence of anterior knee pain (20% vs. 0%, P<0.01). There was no significant difference between groups with respect to time to healing.

Conclusions:

Treatment outcomes between initial operative fixation and closed reduction of displaced tibia fractures in adolescents are similar, but patients must be counseled about the high failure rates with CRC. Predictors of CRC failure include initial fracture displacement and the presence of a fibula fracture—these variables should be considered when selecting a treatment method.

Level of Evidence:

Level III—Therapeutic study.
Halovulum dunhuangense gen. nov., sp. nov., isolated from a saline terrestrial spring
Authors: Sun Fengqin , Du Yaping , Liu Xiupian , Lai Qiliang , Shao Zongze
Published: May 2015

A bacterial strain, YYQ-30T, isolated from a mixed water–sand–sediment sample collected from a terrestrial spring located in Dunhuang, China, was characterized with respect to its morphology, physiology and taxonomy. Cells of the strain were Gram-stain-negative, aerobic, oxidase- and catalase-positive, non-flagellated, oval to rod-shaped (0.5–1.0 μm wide and 1.1–6.6 μm long) and divided by binary fission. Growth was observed in the presence of 0–10.0 % (w/v) NaCl with optimal growth at 0–3.0 %, at pH 6.0–9.0 (optimum pH 7.0–8.5) and at 10–45 °C (optimum 30–37 °C). The isolate could reduce nitrate to nitrite and hydrolyse aesculin and gelatin (weakly), but was unable to degrade Tween 80 or starch. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YYQ-30T belongs to the family Rhodobacteraceae and forms a distinct lineage with the type strain of Albimonas donghaensis and forms a branch within a cluster constituted by the type strains of species of the genera Albimonas, Rhodovulum, Albidovulum, Haematobacter and Tropicimonas; levels of 16S rRNA gene sequence similarity between strain YYQ-30T and members of related genera ranged from 94.1 to 89.7  %. Strain YYQ-30T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 70.0  %), C18 : 0 (9.5  %), summed feature 2 (one or more of C14  :  0 3-OH, iso-C16  :  1 I and C12  :  0 aldehyde; 6.9  %) and 11-methyl C18  :  1ω7c (6.0  %) as the principal fatty acids. The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified phospholipids, two unidentified aminolipids and five unknown lipids. The pufLM gene was detected. The G+C content of the genomic DNA was 71.7 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data obtained in this study, strain YYQ-30T is considered to represent a novel species in a new genus within the family Rhodobacteraceae, for which the name Halovulum dunhuangense gen. nov., sp. nov. is proposed. The type strain of Halovulum dunhuangense is YYQ-30T ( = LMG 27418T = MCCC 1A06483T).
Sphingomonas psychrolutea sp. nov., a psychrotolerant bacterium isolated from glacier ice
Authors: Liu Qing , Liu Hong-Can , Zhang Jian-Li , Zhou Yu-Guang , Xin Yu-Hua
Published: May 2015

A Gram-stain-negative, rod-shaped, orange bacterium (strain MDB1-AT) was isolated from ice samples collected from Midui glacier in Tibet, south-west China. Cells were aerobic and psychrotolerant (growth occurred at 0–25 °C). Phylogenetic analysis based on 16S rRNA gene sequences showed that it was a member of the genus Sphingomonas, with its closest relative being Sphingomonas glacialis C16yT (98.9 % similarity). Q-10 was the predominant ubiquinone. C17 : 1ω6c and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) were the major cellular fatty acids. The predominant polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and sphingoglycolipid. The polyamines detected were sym-homospermidine, spermidine and spermine. The G+C content of the genomic DNA was 63.6 %. Based on data from this polyphasic analysis, strain MDB1-AT represents a novel species of the genus Sphingomonas, for which the name Sphingomonas psychrolutea sp. nov. is proposed. The type strain is MDB1-AT ( = CGMCC 1.10106T = NBRC 109639T).
Cyberlindnera xylosilytica sp. nov., a xylitol-producing yeast species isolated from lignocellulosic materials
Authors: Cadete Raquel M. , Cheab Monaliza A. M. , Santos Renata O. , Safar Silvana V. B. , Zilli Jerri E. , Vital Marcos J. S. , Basso Luiz C. , Lee Ching-Fu , Kurtzman Cletus P. , Lachance Marc-André , Rosa Carlos A.
Published: May 2015

Independent surveys of yeasts associated with lignocellulosic-related materials led to the discovery of a novel yeast species belonging to theCyberlindneraclade (Saccharomycotina, Ascomycota). Analysis of the sequences of the internal transcribed spacer (ITS) region and the D1/D2 domains of the large subunit rRNA gene showed that this species is related toC. japonica,C. maesaandC. easanensis. Six isolates were obtained from different sources, including rotting wood, tree bark and sugar cane filter cake in Brazil, frass from white oak in the USA and decayed leaf in Taiwan. A novel species is suggested to accommodate these isolates, for which the nameC. xylosilyticasp. nov. is proposed. The type strain ofC. xylosilyticasp. nov. is NRRL YB-2097T( = CBS 13984T = UFMG-CM-Y347T) and the allotype is UFMG-CM-Y409 ( = CBS 14083). The novel species is heterothallic and complementary mating types are represented by the type and allotype strains. The MycoBank number is MB 811428.
Allochromatium humboldtianum sp. nov., isolated from soft coastal sediments
Authors: Serrano Wilbert , Schrübbers Jan , Amann Rudolf , Fischer Ulrich
Published: May 2015

A novel purple sulfur bacterium, strain AX1YPET, was isolated from marine sediments sampled at 47 m depth in Callao Bay, Perú. Strain AX1YPE grew anaerobically, synthesizing bacteriochlorophyll a and carotenoid pigments of the spirilloxanthin series. Cells were Gram-stain-negative rods and actively motile by a polar flagellum. Strain AX1YPE was able to grow photolithoautotrophically with sulfide and thiosulfate as electron donors. This new phototrophic organism utilized ammonium salt, N2, urea and glutamate as nitrogen sources. Strain AX1YPE had a DNA base composition of 63.9 mol% G+C. Analysis of the 16S rRNA gene sequence indicated that strain AX1YPE clusters in a separate branch within the genus Allochromatium of the family Chromatiaceae. Strain AX1YPE showed 16S rRNA gene sequence similarities of 98.2 % with Allochromatium vinosum DSM 180T and Allochromatium minutissimum DSM 1376T, 98.1 % with Allochromatium phaeobacterium JA144T, 97.3 % with Allochromatium renukae DSM 18713T and 96.8 % with Allochromatium warmingiiDSM 173T. DNA–DNA hybridization values to the type strains of its closest relatives, A. vinosum and A. minutissimum, were 59 and 64 %, respectively. The predominant fatty acid of strain AX1YPET was C18 : 1ω;7c and it notably possessed C20 : 1 as a minor component. PCR-based molecular typing (Box A1R and randomly amplified polymorphic DNA) produced a unique banding pattern for strain AX1YPET in comparison with the type strains of A. vinosum and A. minutissimum. Based on data from this polyphasic taxonomic study, which also includes average nucleotide identity comparison of five concatenated housekeeping genes, strain AX1YPET is considered to represent a novel species of the genus Allochromatium for which the name Allochromatium
humboldtianum sp. nov. is proposed. The type strain is AX1YPET ( = DSM 21881T = KCTC 15448T).
Rhizobium anhuiense sp. nov., isolated from effective nodules of Vicia faba and Pisum sativum
Authors: Zhang Yu Jing , Zheng Wen Tao , Everall Isobel , Young J. Peter W. , Zhang Xiao Xia , Tian Chang Fu , Sui Xin Hua , Wang En Tao , Chen Wen Xin
Published: May 2015

Four rhizobia-like strains, isolated from root nodules of Pisum sativum and Vicia faba grown in Anhui and Jiangxi Provinces of China, were grouped into the genus Rhizobium but were distinct from all recognized species of the genus Rhizobium by phylogenetic analysis of 16S rRNA and housekeeping genes. The combined sequences of the housekeeping genes atpD, recA and glnII for strain CCBAU 23252T showed 86.9 to 95 % similarity to those of known species of the genus Rhizobium. All four strains had nodC and nifH genes and could form effective nodules with Pisum sativum and Vicia faba, and ineffective nodules with Phaseolus vulgaris, but did not nodulate Glycine max, Arachis hypogaea, Medicago sativa, Trifolium repens or Lablab purpureus in cross-nodulation tests. Fatty acid composition, DNA–DNA relatedness and a series of phenotypic tests also separated these strains from members of closely related species. Based on all the evidence, we propose a novel species, Rhizobium anhuiense sp. nov., and designate CCBAU 23252T ( = CGMCC 1.12621T = LMG 27729T) as the type strain. This strain was isolated from a root nodule of Vicia faba and has a DNA G+C content of 61.1 mol% (T
m).
Eionea flava sp. nov., isolated from coastal seawater, and emended description of the genus Eionea
Authors: Baek Kiwoon , Choi Ahyoung , Cho Jang-Cheon
Published: May 2015

A Gram-staining-negative, non-motile, catalase- and oxidase-positive, facultatively aerobic bacterium, designated IMCC1962T was isolated from a surface seawater sample from the Yellow Sea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain IMCC1962T belonged to the genus Eionea, forming a robust clade with members of the genus, and was most closely related to Eionea nigra (97.3  % similarity). DNA–DNA relatedness between strain IMCC1962T and Eionea nigra DSM 19752T was 21.8–26.3  %, which indicated strain IMCC1962T represents a novel genomic species of the genus Eionea. The G+C content of the DNA of strain IMCC1962T was 48.7 mol%. The major isoprenoid quinone was ubiquinone Q-8 and major fatty acids were C16 : 1ω7c and/or C16 : 1ω6c (43.4  %), C18 : 1ω7c and/or C18 : 1ω6c (19.3  %) and C16 : 0 (17.2  %). The polar lipids found in strain IMCC1962T were phosphatidylethanolamine, phosphatidylglycerol, aminophospholipid, unknown phospholipid, and four unknown polar lipids. Strain IMCC1962T and Eionea nigra DSM 19752T differed from each other in diverse phenotypic characteristics including motility, colony colour and enzyme activities. On the basis of phenotypic and genotypic data, strain IMCC1962T ( = KACC 17481T = NBRC 109703T) represents a novel species of the genus Eionea, for which the name Eionea flava sp. nov. is proposed. An emended description of the genus Eionea is also provided.
On the valid publication of names and combinations
Authors: Tindall Brian J.
Published: May 2015

The valid publication of names and combinations in a single journal was one of the innovations in the 1975 revision of the International Code of Nomenclature of Bacteria. A number of assumptions are often made with regards the way names or combinations are evaluated as being validly published. A re-examination of the process of valid publication is appropriate.
Mirror bisulfite sequencing — a method for single-base resolution of hydroxymethylcytosine
Authors: Tan Darany , Chung Tzu Hung , Sun Xueguang , Jia Xi-Yu
Published: May 2015

While the role of 5-methylcytosine has been well studied, the biological role of 5- hydroxymethylcytosine still remains unclear due to the limited methods available for single-base detection of 5-hydroxymethylcytosine (5hmC). Here, we present Mirror bisulfite sequencing detects 5-hydroxymethylcytosines at a single CpG site by synthesizing a DNA strand to mirror the parental strand. This semi-conservative duplex is sequentially treated with β- glucosyltransferase and M.SssI methylase. A glucosyl-5hmCpG in the parental strand inhibits methylation of the mirroring CpG site, and after bisulfite conversion, a thymine in the mirroring strand indicates a 5hmCpG site in the parental strand whereas a cytosine indicates a non-5hmC site. Using this method, the 5hmC levels of various human tissues and paired liver tissues were mapped genome-wide.
Environmental complexity favors the evolution of learning
Authors: Dridi Slimane , Lehmann Laurent
Published: May 2015

Learning is a fundamental biological adaptation that is widespread throughout the animal kingdom. According to previous research, two conditions are necessary for learning to be adaptive: between-generation environmental variability and within-generation environmental predictability. In this paper, we show that between-generation variability is not necessary, and that instrumental learning can provide a selective advantage in complex environments, where an individual is exposed to a large number of different challenges during its lifespan. We construct an evolutionary model where individuals have a memory with limited storage capacity, and an evolving trait determines the fraction of that memory that should be allocated to innate responses to the environment versus learning these responses. The evolutionarily stable level of learning depends critically on the environmental process, but generally increases with environmental complexity. Overall, our work sheds light on the importance of global structural properties of the environment in shaping the evolution of learning.
Expression ofE. coliglycogen branching enzyme in anArabidopsismutant devoid of endogenous starch branching enzymes induces the synthesis of starch-like polyglucans
Authors: Boyer Laura , Roussel Xavier , Courseaux Adeline , Ndjindji Ofilia Mvundza , Lancelon-Pin Christine , Putaux Jean-Luc , Tetlow Ian , Emes Michael , Pontoire Bruno , D’Hulst Christophe , Wattebled Fabrice
Published: May 2015

Starch synthesis requires several enzymatic activities including branching enzymes (BEs) responsible for the formation ofα(1→6) linkages. Distribution and number of these linkages are further controlled by debranching enzymes (DBEs) that cleave some of them, rendering the polyglucan water-insoluble and semi-crystalline. Although the activity of BEs and DBEs is mandatory to sustain normal starch synthesis, the relative importance of each in the establishment of the plant storage polyglucan (i.e. water-insolubility, crystallinity, presence of amylose) is still debated. Here, we have substituted the activity of BEs inArabidopsiswith that of theEscherichia coliglycogen branching enzyme (GlgB). The latter is the BE counterpart in the metabolism of glycogen, a highly branched water-soluble and amorphous storage polyglucan. GlgB was expressed in thebe2 be3double mutant ofArabidopsisthat is devoid of BE activity and consequently free of starch. The synthesis of a water-insoluble, partly crystalline, amylose-containing starch-like polyglucan was restored in GlgB-expressing plants, suggesting that BEs origin only have a limited impact on establishing essential characteristics of starch. Moreover, the balance between branching and debranching is crucial for the synthesis of starch, as an excess of branching activity results in the formation of highly branched, water-soluble, poorly crystalline polyglucan.
The Moose of Isle Royale: An Unnatural Condition?
Authors: Scarpino Samuel V. , Guerrero Rafael F. , Scarpino Philip V.
Published: May 2015

The now iconic moose of Isle Royale National Park arrived on the island sometime between 1910 and 1915 (Hickie, 1936; Murie, 1934). Prior to that period there is no evidence of moose in either naturalist reports or in the archaeological history of the island (Murie, 1934; Scarpino, 2011). Early naturalists–while observing the moose during their first 20 years on the island—noted both their dramatic expansion, and equally dramatic population crash in the 1930s, see Figure 1. Around 1950, and just as the moose were rebounding, wolves crossed a frozen Lake Superior and began what is now one of our most emblematic predator/prey systems (Peterson, 1995). Recently, the wolves on Isle Royale appear headed for local extinction (Mlot, 2015). Calls to repopulate the island have renewed the vigorous debate surrounding what is and what is not wild about Isle Royale (Scarpino, 2011; Cronon, 1996; Nelson & Callicott, 2008; Cronon, 2003; Peterson, 1999).
The GL Service: Web Service to Exchange GL String Encoded HLA & KIR Genotypes With Complete and Accurate Allele and Genotype Ambiguity
Authors: Milius Robert P. , Heuer Michael , George Mike , Pollack Jane , Hollenbach Jill A. , Mack Steven J. , Maiers Martin
Published: May 2015

Genotype List (GL) Strings use a set of hierarchical character delimiters to represent allele and genotype ambiguity in HLA and KIR genotypes in a complete and accurate fashion. A RESTful web service called Genotype List Service was created to allow users to register a GL String and receive a unique identifier for that string in the form of a URI. By exchanging URIs and dereferencing them through the GL Service, users can easily transmit HLA genotypes in a variety of useful formats. The GL Service was developed to be secure, scalable, and persistent. An instance of the GL Service is configured with a nomenclature and can be run in strict or non-strict modes. Strict mode requires alleles used in the GL String to be present in the allele database using the fully qualified nomenclature. Non-strict mode allows any GL String to be registered as long as it is syntactically correct. The GL Service source code is free and open source software, distributed under the GNU Lesser General Public License (LGPL) version 3 or later.

Abbreviations

API

Application Program Interface

AWS

Amazon Web Services

CDISC

Clinical Data Interchange Standards Consortium

DaSH

Data Standard Hackathon

EMBL

European Molecular Biology Laboratory

EMDIS

European Marrow Donor Information System

ENA

European Nucleotide Archive

FDA

Food and Drug Administration

FHIR

Fast Healthcare Interoperability Resources

GL

Genotype List

GNU

GNU’s Not Unix

HL7

Health Level Seven, International

HLA

Human Leucocyte Antigen

HML

Histoimmunogenetics Markup Language

HTML

Hypertext Markup Language

HTTP

Hypertext Transfer Protocol

IMGT

ImMunoGeneTics

ISO

International Organization for Standardization

JDBC

Java Database Connectivity

JSON

Javascript Object Notation

KIR

Killer-cell Immunoglobulin-like Receptor

LGPL

Lesser General Public License

LSDAM

Life Sciences Domain Analysis Model

MHC

Major Histocompatibility Complex

MIRING

Minimum Information for Reporting Immunogenomic NGS Genotyping

MUG

Multilocus Unphased Genotype

N3

Notation 3

NCI

National Cancer Institute

NGS

Next Generation Sequencing

NMDP

National Marrow Donor Program

OID

Object Identifier

OWL

Web Ontology Language

PNG

Portable Network Graphics

QR Code

Quick Response Code

RAM

Random Access Memory

RDBMS

Relational Database Management System

RDF

Resource Description Language

REST

Representational State Transfer

SBT

Sequence Based Typing

SDK

Software Development Kit

SQL

Structured Query Language

SSO

Sequence Specific Oligonucleotide

SSP

Sequence Specific Primer

URI

Uniform Resource Identifier

URL

Uniform Resource Locator

XML

Extensible Markup Language

Abbreviations

GL Service

A web service to exchange GL Strings
Mixed Models for Meta-Analysis and Sequencing
Authors: Bulik-Sullivan Brendan
Published: May 2015

Mixed models are an effective statistical method for increasing power and avoiding confounding in genetic association studies. Existing mixed model methods have been designed for “pooled” studies where all individual-level genotype and phenotype data are simultaneously visible to a single analyst. Many studies follow a “meta-analysis” design, wherein a large number of independent cohorts share only summary statistics with a central meta-analysis group, and no one person can view individual-level data for more than a small fraction of the total sample. When using linear regression for GWAS, there is no difference in power between pooled studies and meta-analyses [1]; however, we show that when using mixed models, standard meta-analysis is much less powerful than mixed model association on a pooled study of equal size. We describe a method that allows meta-analyses to capture almost all of the power available to mixed model association on a pooled study without sharing individual-level genotype data. The added computational cost and analytical complexity of this method is minimal, but the increase in power can be large: based on the predictive performance of polygenic scoring reported in [2] and [3], we estimate that the next height and BMI studies could see increases in effective sample size of ≈15% and ≈8%, respectively. Last, we describe how a related technique can be used to increase power in sequencing, targeted sequencing and exome array studies.

Note that these techniques are presently only applicable to randomly ascertained studies and will sometimes result in loss of power in ascertained case/control studies. We are developing similar methods for case/control studies, but this is more complicated.
Optimizing error correction of RNAseq reads
Authors: MacManes Matthew D.
Published: May 2015

Motivation:

The correction of sequencing errors contained in Illumina reads derived from genomic DNA is a common pre-processing step in manyde novogenome assembly pipelines, and has been shown to improved the quality of resultant assemblies. In contrast, the correction of errors in transcriptome sequence data is much less common, but can potentially yield similar improvements in mapping and assembly quality. This manuscript evaluates several popular read-correction tool’s ability to correct sequence errors commonplace to transcriptome derived Illumina reads.

Results:

I evaluated the efficacy of correction of transcriptome derived sequencing reads using using several metrics across a variety of sequencing depths. This evaluation demonstrates a complex relationship between the quality of the correction, depth of sequencing, and hardware availability which results in variable recommendations depending on the goals of the experiment, tolerance for false positives, and depth of coverage. Overall, read error correction is an important step in read quality control, and should become a standard part of analytical pipelines.

Availability:

Results are non-deterministically repeatable using AMI:ami-3dae4956 (MacManes_EC_2015) and the Makefile available here:https://goo.gl/oVIuE0

Contact:

matthew.macmanes@unh.eduand @PeroMHC
Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators
Authors: Polstein Lauren R. , Perez-Pinera Pablo , Kocak D. Dewran , Vockley Christopher M. , Bledsoe Peggy , Song Lingyun , Safi Alexias , Crawford Gregory E. , Reddy Timothy E. , Gersbach Charles A.
Published: May 2015

Genome engineering technologies based on the CRISPR/Cas9 and TALE systems are enabling new approaches in science and biotechnology. However, the specificity of these tools in complex genomes and the role of chromatin structure in determining DNA binding are not well understood. We analyzed the genome-wide effects of TALE- and CRISPR-based transcriptional activators in human cells using ChIP-seq to assess DNA-binding specificity and RNA-seq to measure the specificity of perturbing the transcriptome. Additionally, DNase-seq was used to assess genome-wide chromatin remodeling that occurs as a result of their action. Our results show that these transcription factors are highly specific in both DNA binding and gene regulation and are able to open targeted regions of closed chromatin independent of gene activation. Collectively, these results underscore the potential for these technologies to make precise changes to gene expression for gene and cell therapies or fundamental studies of gene function.