bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of clam rake harvesting on the intertidal Ruditapes habitat of the English Channel
Authors: Beck Florence , Pezy Jean-Philippe , Baffreau Alexandrine , Dauvin Jean-Claude
Published: August 2015

Recreational and professional clam fishing was an important activity on the extensive intertidal zone of the western Cotentin coast (western English Channel). A variety of fishing gear was used to harvest the target species: the European clam Ruditapes decussatus (Linnaeus, 1758) and the introduced Manila clam R. philippinarum (Adams and Reeve, 1850). In this study, we studied the effect of rake harvesting during the spring tides of February–March 2014, following an experimental design with a control station and three stations impacted by rake harvesting in three sediment types: sandy, gravelly, and mixed gravelly rocky habitats. No significant sediment and macrofauna changes occurred at the three sites after rake harvesting. Nevertheless, the number of clams decreased significantly after raking on the gravelly habitat, whereas in the other two habitats, sediment transport in this high-energy hydrodynamic environment was able to transfer clams and other macrofauna species across the fishing sites, thus minimizing the effects of rake harvesting. Therefore, although the effect of rake harvesting appeared limited during winter, the regional impact (high fishing pressure along 60 km of coast) and increase of recreational fishers during summer needed to be studied in the future.
Historical discarding in Mediterranean fisheries: a fishers' perception
Authors: Damalas Dimitrios , Maravelias Christos D. , Osio Giacomo C. , Maynou Francesc , Sbrana Mario , Sartor Paolo , Casey John
Published: August 2015

Discarding of commercially important fish species in the bottom trawl fisheries in the northern Mediterranean Sea was investigated by soliciting the long-term recollections of fishers engaged or formerly engaged in such fisheries. The main aim of our investigation was to describe the prevalence of discarding and its evolution over the past 70 years using information gathered through individual questionnaire-based interviews with fishers from ports in Spain, Italy, and Greece, following a standardized sampling protocol. Although it proved impossible to derive absolute estimates of the volume of discarded catches over the period investigated, we conclude that over the past 70 years, discarding as a practice has gradually increased in the northern Mediterranean trawl fisheries and has been accompanied by a shift in the species composition of the discarded catch. While discarding can occur for a number of reasons, our investigations indicate that discarding in the past was mostly driven by market demand, but recent legal and regulatory constraints have led to changes in fishing strategies and became a significant reason for discards.
Rotation-induced deep crustal heating of millisecond pulsars
Authors: Gusakov M. E. , Kantor E. M. , Reisenegger A.
Published: August 2015

The spin-down of a neutron star, e.g. due to magneto-dipole losses, results in compression of the stellar matter and induces nuclear reactions at phase transitions between different nuclear species in the crust. We show that this mechanism is effective in heating recycled pulsars, in which the previous accretion process has already been compressing the crust, so it is not in nuclear equilibrium. We calculate the corresponding emissivity and confront it with available observations, showing that it might account for the likely thermal ultraviolet emission of PSR J0437−4715.
A Phase 1, Dose-escalation, Double-blind, Block-randomized, Controlled Trial of Safety and Efficacy of Neosaxitoxin Alone and in Combination with 0.2% Bupivacaine, with and without Epinephrine, for Cutaneous Anesthesia
Authors: Lobo Kimberly , Donado Carolina , Cornelissen Laura , Kim Joseph , Ortiz Rebeca , Peake Roy W. A. , Kellogg Mark , Alexander Mark E. , Zurakowski David , Kurgansky Katherine E. , Peyton James , Bilge Aykut , Boretsky Karen , McCann Mary Ellen , Berde Charles B. , Cravero Joseph
Published: August 2015

AbstractAbstract

In a first-in-human Food and Drug Administration–regulated phase 1 safety study in 84 male volunteers, subcutaneous infiltration of Neosaxitoxin with bupivacaine produced long-lasting anesthesia but no serious adverse events although perioral numbness and tingling were noted at high doses. Addition of epinephrine reduced circulating Neosaxitoxin concentrations and perioral tingling and numbness and further prolonged sensory block.

Supplemental Digital Content is available in the text.

Background:

Neosaxitoxin (NeoSTX) is a site-1 sodium channel blocker that produces prolonged local anesthesia in animals and humans. Under a Food and Drug Administration–approved phase 1 Investigational New Drug trial, the authors evaluated safety and efficacy of NeoSTX alone and combined with 0.2% bupivacaine (Bup) with and without epinephrine.

Methods:

The authors conducted a double-blind, randomized, controlled trial involving healthy male volunteers aged 18 to 35 yr receiving two 10-ml subcutaneous injections. Control sites received Bup. In part 1, active sites received (1) 5 to 40 μg NeoSTX+Saline (NeoSTX-Saline), (2) 5 to 40 μg NeoSTX+Bup (NeoSTX-Bup), or (3) placebo (Saline). In part 2, active sites received 10 or 30 μg NeoSTX+Bup+Epinephrine (NeoSTX-Bup-Epi) or placebo. Primary outcome measures were safety and adverse events associated with NeoSTX. Secondary outcomes included clinical biochemistry, NeoSTX pharmacokinetics, and cutaneous hypoesthesia.

Results:

A total of 84 subjects were randomized and completed the two-part trial with no serious adverse events or clinically significant physiologic impairments. Perioral numbness and tingling increased with NeoSTX dose for NeoSTX-Saline and NeoSTX-Bup. All symptoms resolved without intervention. NeoSTX-Bup-Epi dramatically reduced symptoms compared with other NeoSTX combinations (tingling: 0 vs. 70%, P = 0.004; numbness: 0 vs. 60%, P = 0.013) at the same dose. Mean peak plasma NeoSTX concentration for NeoSTX-Bup-Epi was reduced at least two-fold compared with NeoSTX-Saline and NeoSTX-Bup (67 ± 14, 134 ± 63, and 164 ± 81 pg/ml, respectively; P = 0.016). NeoSTX-Bup showed prolonged cutaneous block duration compared with Bup, NeoSTX-Saline, or placebo, at all doses. Median time to near-complete recovery for 10 μg NeoSTX-Bup-Epi was almost five-fold longer compared with Bup (50 vs. 10 h, P = 0.007).

Conclusion:

NeoSTX combinations have a tolerable side effect profile and appear promising for prolonged local anesthesia.
Neosaxitoxin in Rat Sciatic Block
Authors: Templin Jay S. , Wylie Matthew C. , Kim Joseph D. , Kurgansky Katherine E. , Gorski Grzegorz , Kheir John , Zurakowski David , Corfas Gabriel , Berde Charles
Published: August 2015

AbstractAbstract

In rats, combination of Neosaxitoxin with bupivacaine for sciatic nerve block resulted in motor and sensory block, which was longer than either agent alone, and was up to 48 h when epinephrine was added. Histologic examination showed no evidence of neural toxicity, and intravenous injection of Neosaxitoxin resulted in cardiotoxicity with longer delays than bupivacaine.

Background:

Neosaxitoxin (NeoSTX) is a site-1 sodium channel blocker undergoing clinical trials as a prolonged-duration local anesthetic. Rat sciatic block and intravenous infusion models were used to assess efficacy and local and systemic toxicities for NeoSTX in saline (NeoSTX-Saline), bupivacaine (Bup), and their combination (NeoSTX-Bup). Exploratory studies evaluated the effects of addition of epinephrine to NeoSTX-Bup (NeoSTX-Bup-Epi).

Methods:

Rats received percutaneous sciatic blocks with escalating doses of NeoSTX-Saline or NeoSTX-Bup. Sensory-nocifensive block was assessed using modified hotplate and Von Frey filaments. Motor-proprioceptive function was assessed by extensor postural thrust. Nerves were examined histologically after 7 days and scored on the Estebe–Myers scale. Median lethal dose was estimated for NeoSTX-Saline and in combinations. Accidental intravenous overdose was simulated in isoflurane-anesthetized, spontaneously breathing rats receiving NeoSTX-Saline (n = 6), Bup (n = 7), or NeoSTX-Bup (n = 13), with respiratory, hemodynamic, and electrocardiographic endpoints. Additional groups received blocks with NeoSTX-Bup-Epi (n = 80). Investigators were blinded for behavioral and histologic studies.

Results:

NeoSTX-Bup produced more prolonged sensory and motor block compared with NeoSTX-Saline or Bup. NeoSTX-Bup-Epi further prolonged median time to near-complete recovery for 3 μg/kg NeoSTX-Bup (hotplate: 48 vs. 6 h, P < 0.001). With sciatic injections, addition of Bup did not worsen the systemic toxicity (median lethal dose) compared with NeoSTX-Saline. Intravenous NeoSTX-Saline infusion had significantly longer times to apnea, first arrhythmia, and asystole compared with Bup (P < 0.001 for each). Histologic injury scores overall were low for all groups, with median scores of 0 (interquartile range, 0 to 0) on a 5-point scale.

Conclusion:

NeoSTX-Bup and NeoSTX-Bup-Epi hold promise for prolonged-duration local anesthesia.
Clinical Electroencephalography for Anesthesiologists
Authors: Purdon Patrick L. , Sampson Aaron , Pavone Kara J. , Brown Emery N.
Published: August 2015

AbstractAbstract

The widely used electroencephalogram-based indices for depth-of-anesthesia monitoring assume that the same index value defines the same level of unconsciousness for all anesthetics. In contrast, we show that different anesthetics act at different molecular targets and neural circuits to produce distinct brain states that are readily visible in the electroencephalogram. We present a two-part review to educate anesthesiologists on use of the unprocessed electroencephalogram and its spectrogram to track the brain states of patients receiving anesthesia care. Here in part I, we review the biophysics of the electroencephalogram and the neurophysiology of the electroencephalogram signatures of three intravenous anesthetics: propofol, dexmedetomidine, and ketamine, and four inhaled anesthetics: sevoflurane, isoflurane, desflurane, and nitrous oxide. Later in part II, we discuss patient management using these electroencephalogram signatures. Use of these electroencephalogram signatures suggests a neurophysiologically based paradigm for brain state monitoring of patients receiving anesthesia care.

The authors review the neurophysiology of the electroencephalogram signatures of the anesthetics: propofol, dexmedetomidine, ketamine, sevoflurane, isoflurane, desflurane, and nitrous oxide. These signatures provide a neurophysiologically based paradigm for brain state monitoring of patients receiving anesthesia care.
The Neurobiology of Anesthetic Emergence
Authors: Tarnal Vijay , Vlisides Phillip E. , Mashour George A.
Published: August 2015

Achieving a smooth and rapid emergence from general anesthesia is of particular importance for neurosurgical patients and is a clinical goal for neuroanesthesiologists. Recent data suggest that the process of emergence is not simply the mirror image of induction, but rather controlled by distinct neural circuits. In this narrative review, we discuss (1) hysteresis, (2) the concept of neural inertia, (3) the asymmetry between the neurobiology of induction and emergence, and (4) recent attempts at actively inducing emergence.
Outcomes of Orbital Blow-Out Fracture Repair Performed Beyond 6 Weeks After Injury
Authors: Scawn Richard L. , Lim Lee Hooi , Whipple Katherine M. , Dolmetsch Angela , Priel Ayelet , Korn Bobby , Kikkawa Don O.
Published: August 2015

Purpose:

Blow-out fractures cause expansion of the bony orbital walls and prolapse of orbital contents in the sinuses. This can result in diplopia, enophthalmos, and hypoglobus. Early surgical repair has been previously recommended, however, recent reports show that delayed surgery can also be effective. In this study, the clinical and functional outcome of patients with delayed presentation and blow-out fracture repair beyond 6 weeks after injury are described.

Methods:

This is a noncomparative retrospective study. Medical records of adult patients with late orbital floor fracture repair performed by 4 surgeons from April 2008 to January 2014 at 3 tertiary referral centers were reviewed. All repairs were performed more than 6 weeks from the time of injury. Patients with prior orbital fracture repair surgery were excluded.

Results:

Twenty patients were included in the study. The duration from time of injury to surgery ranged from 7 weeks to 21 years with a mean of 19 months. Follow up ranged from 6 weeks to 56 months (mean 8 months). Mean age was 48 years (range, 25–80). Male to female ratio was 11:9. Surgery was performed on 10 right eyes and 10 left eyes. CT imaging demonstrated 10 patients had isolated floor fractures, while the remaining 10 patients had combined floor and medial wall fractures. Four patients also had associated facial fractures that did not require surgery. Indications for surgery included enophthalmos of 2 mm or more (18 of 20) and/or significant diplopia within 30° of primary gaze (6 of 20). Mean pre- and postoperative enophthalmos was 2.4 ± 0.9 mm and 0.3 ± 0.2 mm, respectively, corresponding to a mean reduction in enophthalmos of 2.1 ± 1.2 mm (range, 1–5 mm). Four of 7 patients with hypoglobus ranging from 1.5 mm to 8 mm preoperatively had complete resolution postoperatively, the remaining 3 patients showed reduced hypoglobus. Of the 12 patients that had diplopia preoperatively in any position of gaze, 6 patients had complete resolution of diplopia postoperatively, 4 patients had reduced but residual diplopia in extreme gaze, and 2 patients had persistent diplopia, in primary position and down gaze, respectively. Two patients had poor vision that precluded the manifestation of diplopia. None of the 6 patients without preoperative diplopia developed symptoms post operatively.

Conclusion:

Surgical repair of blow-out fractures of the orbit occurring more than 6 weeks or more from injury can achieve marked improvement in both the functional and cosmetic aspects. The likelihood of induced diplopia is low. Orbital floor fracture repair should be considered to successfully treat enophthalmos or diplopia in patients with delayed clinical presentation, even decades postinjury.
Preadmission Use of Calcium Channel Blockers and Outcomes After Hospitalization With Pneumonia: A Retrospective Propensity-Matched Cohort Study
Authors: Zheng Lin , Hunter Krystal , Gaughan John , Poddar Sameer
Published: August 2015

In sepsis, an overwhelming immune response, as mediated by the release of various inflammatory mediators, can lead to shock, multiple organ damage, and even death. Pneumonia is the leading cause of sepsis. In animal septic models, sepsis could induce uncontrolled calcium (Ca2+) leaking, raising cytosolic Ca2+ to a toxic level, causing irreversible cellular injuries and organ failure. All types of calcium channel blockers (CCBs), by inhibiting Ca2+ influx, have been shown to decrease overall mortality in various septic animal models. However, to our best knowledge, no clinical study had been conducted to investigate the beneficial effect(s) of CCBs in sepsis. We conducted a retrospective propensity-matched cohort study after screening 2214 patients hospitalized for pneumonia from year 2012 to 2014 at our institution. We identified 387 preadmission CCB users and 387 nonusers by propensity score matching. Logistic regression analysis was then used to determine the association between preadmission CCB use and outcomes in pneumonia. Our study showed that the odds for development of severe sepsis was significantly lower in the CCB user group [odds ratio (OR), 0.466; 95% confidence interval (CI), 0.311–0.697; P = 0.002]. Preadmission CCB use was associated with a lower risk of contracting bacteremia (OR, 0.498; 95% CI, 0.262–0.99; P = 0.0327), lower risk of acute respiratory insufficiency (OR, 0.573; 95% CI, 0.412–0.798; P = 0.001), lower risk of intensive care unit admission (OR, 0.602; 95% CI, 0.432–0.840; P = 0.0028). In conclusion, our study suggested preadmission CCB use was associated with a reduction in the risks of development of respiratory insufficiency, bacteremia, and severe sepsis in patients admitted to the hospital with pneumonia.
Pseudomonas alkylphenolica sp. nov., a bacterial species able to form special aerial structures when grown on p-cresol
Authors: Mulet Magdalena , Sánchez David , Lalucat Jorge , Lee Kyoung , García-Valdés Elena
Published: August 2015

Pseudomonassp. KL28Tis an aerobic, rod-shaped bacterium that was isolated from the soil of Changwon, South Korea, based on its ability to grow in the presence of linear alkylphenols (C1–C5). Despite several studies on strain KL28T, it could not be assigned to any known species in the genusPseudomonas. The name ‘Pseudomonas alkylphenolia’was proposed for KL28T, but the strain had not until now been characterized taxonomically and the name currently has no standing in the bacterial nomenclature. A 16S rRNA gene sequence based phylogenetic analysis suggested an affiliation of strain KL28Twith thePseudomonas putidagroup, withPseudomonas vranovensisDSM 16006Tas the most closely related type strain (99.1 % similarity). A multilocus phylogenetic sequence analysis performed by concatenating 16S rRNA,gyrB,rpoDandrpoBpartial gene sequences showed that isolate KL28Tcould be differentiated fromP. vranovensisDSM 16006T(sequence similarity 93.7 %). Genomic comparisons of strain KL28Twith the type strains of the species in theP. putidagroup using average nucleotide index based onblast(ANIb) and genome-to genome distances (GGDC) revealed 87.06 % and 32.20 % similarities withP. vranovensisDSM 16006T, respectively, as the closest type strain. Both values are far from the thresholds established for species differentiation. These results, together with differences in phenotypic features and chemotaxonomic analyses [fatty acids and whole-cell matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS], support the proposal of strain KL28T( = JCM 16553T = KCTC 22206T) as the type strain of a novel species, for which the formerly proposed name, ‘P. alkylphenolia’, is correctly latinized asPseudomonas alkylphenolicasp. nov.
Complete absence of thebaine biosynthesis under home-brew fermentation conditions
Authors: Endy Drew , Galanie Stephanie , Smolke Christina D.
Published: August 2015

Yeast-based biosynthesis of medicinal compounds traditionally derived from plant materials is improving. Both concerns and hopes exist for the possibility that individual small volume batch fermentations could provide distributed and independent access to a diversity of compounds some of which are now abused, illegal, or unavailable to many who need for genuine medical purposes. However, there are differences between industrial bioreactors and ‘home-brew’ fermentation. We used engineered yeast that make thebaine, a morphinan opiate, to quantify if differences in fermentation conditions impact biosynthesis yields. We used yeast that make an English ale as a positive fermentation control. We observed no production of thebaine and miniscule amounts of reticuline, an upstream biosynthetic intermediate, in home-brew fermentations; the positive control was palatable. We suggest that additional technical challenges, some of which are unknown and likely unrelated to optimized production in large-volume bioreactors, would need to be addressed for engineered yeast to ever realize home-brew biosynthesis of medicinal opiates at meaningful yields.
Fasta-O-Matic: a tool to sanity check and if needed reformat FASTA files
Authors: Shelton Jennifer Marie , Brown Susan J
Published: August 2015

As the shear volume of bioinformatic sequence data increases the only way to take advantage of this content is to more completely automate robust analysis workflows. Analysis bottlenecks are often mundane and overlooked processing steps. Idiosyncrasies in reading and/or writing bioinformatics file formats can halt or impair analysis workflows by interfering with the transfer of data from one informatics tools to another. Fasta-O-Matic automates handling of common but minor format issues that otherwise may halt pipelines. The need for automation must be balanced by the need for manual confirmation that any formatting error is actually minor rather than indicative of a corrupt data file. To that end Fasta-O-Matic reports any issues detected to the user with optionally color coded and quiet or verbose logs. Fasta-O-Matic can be used as a general pre-processing tool in bioinformatics workflows (e.g. to automatically wrap FASTA files so that they can be read by BioPerl). It was also developed as a sanity check for bioinformatic core facilities that tend to repeat common analysis steps on FASTA files received from disparate sources. Fasta-O-Matic can be set with format requirements specific to downstream tools as a first step in a larger analysis workflow. Fasta-O-Matic is available free of charge to academic and non-profit institutions at https://github.com/i5K-KINBRE-script-share/read-cleaning-format-conversion/tree/master/KSU_bioinfo_lab/fasta-o-matic.
BRAINformat: A Data Standardization Framework for Neuroscience Data
Authors: Rübel Oliver , Prabhat  , Denes Peter , Conant David , Chang Edward , Bouchard Kristofer
Published: August 2015

Neuroscience is entering the era of ‘extreme data’ with little experience and few plans for the associated volume, velocity, variety, and veracity challenges. This is a serious impediment for both the sharing of data across labs, as well as the utilization of modern and high-performance computing capabilities to enable data driven discovery. Here, we introduce BRAINformat, a novel file format and model for management and storage of neuroscience data. The BRAINformat library defines application-independent design concepts and modules that together create a general framework for standardization of scientific data.

We describe the formal specification of scientific data standards, which facilitates sharing and verification of data and formats. We introduce the concept ofManaged Objects, enabling semantic components of data formats to be specified as self-contained units, supporting modular and reusable design of data format components and file storage. The BRAINformat is built off of HDF5, enabling portable, scalable, and self-describing data storage. We introduce the novel concept ofRelationship Attributesfor modeling and use of semantic relationships between data objects, and discuss the annotation of data using dedicated data annotation modules provided by the BRAINformat library. Based on these concepts we implement dedicated, application-oriented modules and design a data standard for neuroscience data. The BRAINformat software library is open source, easy-to-use, and provides detailed user and developer documentation and is freely available at:https://bitbucket.org/oruebel/brainformat.
Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry
Authors: Flegontov Pavel , Changmai Piya , Zidkova Anastassiya , Logacheva Maria D. , Altimşik N. Ezgi , Flegontova Olga , Gelfand Mikhail S. , Gerasimov Evgeny S. , Khrameeva Ekaterina E. , Konovalova Olga P. , Neretina Tatiana , Nikolsky Yuri V. , Starostin George , Stepanova Vita V. , Travinsky Igor V. , Tříska Martin , Tříska Petr , Tatarinova Tatiana V.
Published: August 2015

The Kets, an ethnic group in the Yenisei River basin, Russia, are considered the last nomadic hunter-gatherers of Siberia, and Ket language has no transparent affiliation with any language family. We investigated connections between the Kets and Siberian and North American populations, with emphasis on the Mal’ta and Paleo-Eskimo ancient genomes, using original data from 46 unrelated samples of Kets and 42 samples of their neighboring ethnic groups (Uralic-speaking Nganasans, Enets, and Selkups). We genotyped over 130,000 autosomal SNPs, identified mitochondrial and Y-chromosomal haplogroups, and performed high-coverage genome sequencing of two Ket individuals. We established that Nganasans, Kets, Selkups, and Yukaghirs form a cluster of populations most closely related to Paleo-Eskimos in Siberia (not considering indigenous populations of Chukotka and Kamchatka). Kets are closely related to modern Selkups and to some Bronze and Iron Age populations of the Altai region, with all these groups sharing a high degree of Mal’ta ancestry. Implications of these findings for the linguistic hypothesis uniting Ket and Na-Dene languages into a language macrofamily are discussed.
Robust Estimates of Overall Immune-Repertoire Diversity from High-Throughput Measurements on Samples
Authors: Kaplinsky Joseph , Arnaout Ramy
Published: August 2015

The diversity of a person’s B- and T-cell repertoires is both clinically important and a key measure of immunological complexity. However, diversity is hard to estimate by current methods, due to inherent uncertainty in the number of B- and T-cell clones that will be missing from a blood or tissue sample by chance (the missing-species problem), inevitable sampling bias, and experimental noise. To solve this problem we developed Recon, a modified maximum-likelihood method that outputs the overall diversity of a repertoire from measurements on a sample. Recon outputs accurate, robust estimates by any of a vast set of complementary diversity measures, including species richness and entropy, at fractional repertoire coverage. It also outputs error bars and power tables, allowing robust comparisons of diversity between individuals and over time. We apply Recon toin silicoand experimental immune-repertoire sequencing datasets as proof of principle for measuring diversity in large, complex systems.
Neurofibromatosis-1 regulation of neural stem cell proliferation and multilineage differentiation operates through distinct RAS effector pathways
Authors: Chen Yi-Hsien , Gianino Scott M. , Gutmann David H.
Published: August 2015

Neurofibromatosis type 1 (NF1) is a common neurodevelopmental disorder caused by impaired function of the neurofibromin RAS regulator. Using a combination of Nf1 genetically engineered mice and pharmacological/genetic inhibition approaches, we report that neurofibromin differentially controls neural stem cell (NSC) proliferation and multilineage differentiation through the selective use of the PI3K/AKT and RAF/MEK pathways. While PI3K/AKT governs neurofibromin-regulated NSC proliferation, multilineage differentiation is MEK-dependent. Moreover, whereas MEK-regulated multilineage differentiation requires Smad3-induced Jagged-1 expression and Notch activation, MEK/Smad3-regulated Hes1 induction is only responsible for astrocyte and neuronal differentiation. Collectively, these findings establish distinct roles for the RAS effector pathways in regulating brain NSC function.
Room-temperature serial crystallography using a kinetically optimized microfluidic device for protein crystallization and on-chip X-ray diffraction. Corrigendum
Authors: Heymann Michael , Opathalage Achini , Wierman Jennifer L. , Akella Sathish , Szebenyi Doletha M. E. , Gruner Sol M. , Fraden Seth
Published: August 2015

The name of one of the authors in the article by Heymannet al.[(2014),IUCrJ,1, 349–360] is corrected.
Crystal structure of 1-isopropyl-4,7-dimethyl-3-nitronaphthalene
Authors: Benharref Ahmed , Elkarroumi Jamal , El Ammari Lahcen , Saadi Mohamed , Berraho Moha
Published: August 2015

The title compound, C15H17NO2, was synthesized from a mixture of α-himachalene (2-methylene-6,6,9-trimethylbicyclo[5.4.01,7]undec-8-ene) and β-himachalene (2,6,6,9-tetramethylbicyclo[5.4.01,7]undeca-1,8-diene), which were isolated from an oil of the Atlas cedar (Cedrus Atlantica). The naphthalene ring system makes dihedral angles of 68.6 (2) and 44.3 (2)°, respectively, with its attached isopropyl C/C/C plane and the nitro group. In the crystal, molecules held together by a C—H...O interaction, forming a chain along [-101].
Crystal structure of 2-methoxy-2-[(4-methoxyphenyl)sulfanyl]-1-phenylethanone
Authors: Caracelli Ignez , Olivato Paulo R. , Traesel Henrique J. , Valença Jéssica , Rodrigues Daniel N. S. , Tiekink Edward R. T.
Published: August 2015

In the title β-thiocarbonyl compound, C16H16O3S, the adjacent methoxy and carbonyl O atoms are synperiplanar [the O—C—C—O torsion angle is 19.8 (4)°] and are separated by 2.582 (3) Å. The dihedral angle between the rings is 40.11 (16)°, and the methoxy group is coplanar with the benzene ring to which it is connected [the C—C—O—C torsion angle is 179.1 (3)°]. The most notable feature of the crystal packing is the formation of methine and methyl C—H...O(carbonyl) interactions that lead to a supramolecular chain with a zigzag topology along thecaxis. Chains pack with no specific intermolecular interactions between them.
Crystal structure ofL-tryptophan–fumaric acid–water (1/1/1)
Authors: Caroline M. Lydia , Kumaresan S. , Aravindan P. G. , Mohamed M. Peer , Mani G.
Published: August 2015

In the title compound, C11H12N2O2·C4H4O4·H2O, the L-tryptophan molecule crystallized as a zwitterion, together with a neutral fumaric acid molecule and a water solvent molecule. In the crystal, the three components are linked by a series of N—H...O, O—H...O and C—H...O hydrogen bonds, forming slabs lying parallel to (001). The slabs are connected by O—H...O hydrogen bonds, involving inversion-related fumaric acid groups, leading to the formation of a three-dimensional structure.
Crystal structure of [N,N′-bis(4-methylphenyl)-1,2-diphenylethane-1,2-diimine-κ2N,N′]dichloridopalladium(II) methanol monosolvate
Authors: Peñaloza Alfredo , Fronczek Frank R. , Isovitsch Ralph
Published: August 2015

The title compound, [PdCl2(C28H24N2)]·CH3OH, was prepared from the reaction of PdCl2(DMSO)2(DMSO is dimethyl sulfoxide) andN,N′-bis(4-methylphenyl)-1,2-diphenylethane-1,2-diimine in methanol. The chelating diimine core of the title compound deviates slightly from planarity, with an N—C—C—N torsion angle of 5.3 (3)°. Delocalization in the diimine core is indicated by N—C and C—C bonds that are, respectively, longer and shorter than those found in related nonchelating diimines. The distorted square-planar coordination environment around the PdIIatom is manifested as bond angles that are smaller and larger than 90°, and palladacycle torsion angles of −173.22 (16) and 167.06 (16)°. These deviations are attributed to the small bite angle of 79.13 (8)° of the diimine chelate. The crystal packing exhibits weak intermolecular hydrogen-bonding interactions involving aromatic H atoms, Cl atoms and intercalated methanol solvent molecules, defining layers parallel to (010).
Crystal structure of 5-benzoyl-2,4-diphenyl-4,5-dihydrofuran-3-carbonitrile
Authors: Rajni Swamy V. , Krishnakumar R.V. , Sivakumar S. , Srinivasan N. , Ranjith Kumar R.
Published: August 2015

In the title compound, C24H17NO2, the carbonyl O atom of the benzoyl group isciswith respect to the furanyl O atom, and the associated O—C—C—O torsion angle is 4.62 (19)°. The puckering of the dihydrofuran ring is close to twisted (4T5), with parametersQ= 0.1856 (16) Å and φ = 313.5 (5)°. Molecules are interconnectedviaa C—H...N and a C—H...O hydrogen bond, leading to layers parallel to the (200) plane and characterized byR44(28) andR44(36) graph-set motifs. The furan O atom does not participate in intermolecular hydrogen bonding. The crystal lattice encompasses a solvent-accessible void of 24.7 (8) Å3.
Crystal structures of three indole derivatives: 3-ethnyl-2-methyl-1-phenylsulfonyl-1H-indole, 4-phenylsulfonyl-3H,4H-cyclopenta[b]indol-1(2H)-one and 1-{2-[(E)-2-(5-chloro-2-nitrophenyl)ethenyl]-1-phenylsulfonyl-1H-indol-3-yl}ethan-1-one chloroform monosolvate
Authors: Gopinath S. , Sethusankar K. , Ramalingam Bose Muthu , Mohanakrishnan Arasambattu K.
Published: August 2015

The title compounds, C17H13NO2S, (I), C17H13NO3S, (II), and C24H17ClN2O5S·CHCl3, (III), are indole derivatives. Compounds (I) and (II) crystalize with two independent molecules in the asymmetric unit. The indole ring systems in all three structures deviate only slightly from planarity, with dihedral angles between the planes of the pyrrole and benzene rings spanning the tight range 0.20 (9)–1.65 (9)°. These indole ring systems, in turn, are almost orthogonal to the phenylsulfonyl rings [range of dihedral angles between mean planes = 77.21 (8)–89.26 (8)°]. In the three compounds, the molecular structure is stabilized by intramolecular C—H...O hydrogen bonds, generatingS(6) ring motifs with the sulfone O atom. In compounds (I) and (II), the two independent molecules are linked by C—H...O hydrogen bonds and C—H...π interactions, while in compound (III), the molecules are linked by C—H...O hydrogen bonds, generatingR22(22) inversion dimers.
Crystal structure of poly[[hexaqua-1κ4O,2κ2O-bis(μ3-pyridine-2,4-dicarboxylato-1κO2:2κ2N,O2′;1′κO4)cobalt(II)strontium(II)] dihydrate]
Authors: Yu Zhaojun , Jiang Peng , Chen Yanmei
Published: August 2015

In the title polymeric complex, {[CoSr(C7H3NO4)2(H2O)6]·2H2O}n, the CoIIion, which is situated on a crystallographic centre of inversion, is six-coordinated by two O atoms and two N atoms from two pyridine-2,4-dicarboxylate (pydc2−) ligands and two terminal water molecules in a slightly distorted octahedral geometry, to form atrans-[Co(pydc)2(H2O)2]2−unit. The SrIIion, situated on aC2axis, is coordinated by four O atoms from four pydc2−ligands and four water molecules. The coordination geometry of the SrIIatom can be best described as a distorted dodecahedron. Each SrIIion bridges four [Co(pydc)2(H2O)2]2−units by four COO−groups of four pydc2−ligands to form a three-dimensional network structure. Two additional solvent water molecules are observed in the crystal structure and are connected to the three-dimensional coordination polymer by O—H...O hydrogen bonds. Further intra- and intermolecular O—H...O hydrogen bonds consolidate the overall structure.
Crystal structure of (piperidine-1-carbodithioato-κ2S,S)[2-(pyridin-2-yl)phenyl-κ2C1,N]palladium(II)
Authors: Kondrashov Mikhail , Fleckhaus André , Gritcenko Roman , Wendt Ola F.
Published: August 2015

The title compound, [Pd(C11H8N)(C6H10NS2)], crystallizes with three similar and discrete molecules in the asymmetric unit. The CNS2donor set defines a distorted square-planar geometry around the PdIIatom, with very small deviations from planarity. The bidentate nature of the ligands gives fairly large deviations from the ideal 90° angles; the C—Pd—N angles are all around 81° and the S—Pd—S angles are around 75°. Molecules packviadispersion interactions.
Water use by Swedish boreal forests in a changing climate
Authors: Hasper Thomas B. , Wallin Göran , Lamba Shubhangi , Hall Marianne , Jaramillo Fernando , Laudon Hjalmar , Linder Sune , Medhurst Jane L. , Räntfors Mats , Sigurdsson Bjarni D. , Uddling Johan
Published: August 2015

The rising levels of atmospheric carbon dioxide concentration ([CO2]) and temperature have the potential to substantially affect the terrestrial water and energy balance by altering the stomatal conductance and transpiration of trees.

Many models assume decreases in stomatal conductance and plant water use under rising [CO2], which has been used as a plausible explanation for the positive global trend in river run‐off over the past century. Plant water use is, however, also affected by changes in temperature, precipitation and land use, and there is yet no consensus about the contribution of different drivers to temporal trends of evapotranspiration (ET) and river run‐off.

In this study, we assessed water‐use responses to climate change by using both long‐term monitoring and experimental data in Swedish boreal forests. Historical trends and patterns in ET of large‐scale boreal landscapes were determined using climate and run‐off data from the past 50 years, while explicit tree water‐use responses to elevated [CO2] and/or air temperature were examined in a whole‐tree chamber experiment using mature Norway spruce (Picea abies (L.) Karst.) trees.

The results demonstrated that ET estimated from water budgets at the catchment scale increased by 18% over the past 50 years while run‐off did not significantly change. The increase in ET was related to increasing precipitation and a steady increase in forest standing biomass over time. The whole‐tree chamber experiment showed that Norway spruce trees did not save water under elevated [CO2] and that experimentally elevated air temperature did not increase transpiration as decreased stomatal conductance cancelled the effect of higher vapour pressure deficit in warmed air.

Our findings have important implications for projections of future water use of European boreal coniferous forests, indicating that changes in precipitation and standing biomass are more important than the effects of elevated [CO2] or temperature on transpiration rates.
Surface nuclear magnetic resonance signals recovery by integration of a non‐linear decomposition method with statistical analysis
Authors: Ghanati Reza , Hafizi Mohammad Kazem , Fallahsafari Mahdi
Published: August 2015

Presence of noise in the acquisition of surface nuclear magnetic resonance data is inevitable. There are various types of noise, including Gaussian noise, spiky events, and harmonic noise that affect the signal quality of surface nuclear magnetic resonance measurements. In this paper, we describe an application of a two‐step noise suppression approach based on a non‐linear adaptive decomposition technique called complete ensemble empirical mode decomposition in conjunction with a statistical optimization process for enhancing the signal‐to‐noise ratio of the surface nuclear magnetic resonance signal. The filtering procedure starts with applying the complete ensemble empirical mode decomposition method to decompose the noisy surface nuclear magnetic resonance signal into a finite number of intrinsic mode functions. Afterwards, a threshold region based on de‐trended fluctuation analysis is defined to identify the noisy intrinsic mode functions, and then the no‐noise intrinsic mode functions are used to recover the partially de‐noised signal. In the second stage, we applied a statistical method based on the variance criterion to the signal obtained from the initial phase to mitigate the remaining noise. To demonstrate the functionality of the proposed strategy, the method was evaluated on an added‐noise synthetic surface nuclear magnetic resonance signal and on field data. The results show that the proposed procedure allows us to improve the signal‐to‐noise ratio significantly and, consequently, extract the signal parameters (i.e., and V0) from noisy surface nuclear magnetic resonance data efficiently.
Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples
Authors: Parada Alma E. , Needham David M. , Fuhrman Jed A.
Published: August 2015

Microbial community analysis via high‐throughput sequencing of amplified 16S rRNA genes is an essential microbiology tool. We found the popular primer pair 515F (515F‐C) and 806R greatly underestimated (e.g. SAR11) or overestimated (e.g. Gammaproteobacteria) common marine taxa. We evaluated marine samples and mock communities (containing 11 or 27 marine 16S clones), showing alternative primers 515F‐Y (5′‐GTGYCAGCMGCCGCGGTAA) and 926R (5′‐CCGYCAATTYMTTTRAGTTT) yield more accurate estimates of mock community abundances, produce longer amplicons that can differentiate taxa unresolvable with 515F‐C/806R, and amplify eukaryotic 18S rRNA. Mock communities amplified with 515F‐Y/926R yielded closer observed community composition versus expected (r2 = 0.95) compared with 515F‐Y/806R (r2 ∼ 0.5). Unexpectedly, biases with 515F‐Y/806R against SAR11 in field samples (∼4–10‐fold) were stronger than in mock communities (∼2‐fold). Correcting a mismatch to Thaumarchaea in the 515F‐C increased their apparent abundance in field samples, but not as much as using 926R rather than 806R. With plankton samples rich in eukaryotic DNA (> 1 μm size fraction), 18S sequences averaged ∼17% of all sequences. A single mismatch can strongly bias amplification, but even perfectly matched primers can exhibit preferential amplification. We show that beyond in silico predictions, testing with mock communities and field samples is important in primer selection.
Mobilization of horizontally acquired island 2 is induced in planta in the phytopathogen Pectobacterium atrosepticum SCRI1043 and involves the putative relaxase ECA0613 and quorum sensing
Authors: Vanga Bhanupratap R. , Ramakrishnan Pavithra , Butler Ruth C. , Toth Ian K. , Ronson Clive W. , Jacobs Jeanne M. E. , Pitman Andrew R.
Published: August 2015

Integrative and conjugative elements (ICEs) contribute to the rapid evolution of bacterial pathogens via horizontal gene transfer of virulence determinants. ICEs have common mechanisms for transmission, yet the cues triggering this process under natural environmental or physiological conditions are largely unknown. In this study, mobilization of the putative ICE horizontally acquired island 2 (HAI2), present in the chromosome of the phytopathogen Pectobacterium atrosepticum SCRI1043, was examined during infection of the host plant potato. Under these conditions, mobilization of HAI2 increased markedly compared with in vitro cultures. In planta‐induced mobilization of HAI2 was regulated by quorum sensing and involved the putative ICE‐encoded relaxase ECA0613. Disruption of ECA0613 also reduced transcription of genes involved in production of coronafacic acid (Cfa), the major virulence factor harboured on HAI2, whereas their expression was unaffected in the quorum‐sensing (expI) mutant. Thus, suppression of cfa gene expression was not regulated by the mobilization of the ICE per se, but was due directly to inactivation of the relaxase. The identification of genetic factors associated solely with in planta mobilization of an ICE demonstrates that this process is highly adapted to the natural environment of the bacterial host and can influence the expression of virulence determinants.
On integrating Jungian and other theories
Authors: Sedgwick David
Published: August 2015

This paper consists of reflections on some of the processes, subtleties, and ‘eros’ involved in attempting to integrate Jungian and other analytic perspectives. Assimilation of other theoretical viewpoints has a long history in analytical psychology, beginning when Jung met Freud. Since its inception, the Journal of Analytical Psychology has provided a forum for theoretical syntheses and comparative psychoanalysis. Such attempts at synthesizing other theories represent analytical psychology itself trying to individuate.
The Effect of Soft Tissue on Temperature Estimation from Burnt Bone Using Fourier Transform Infrared Spectroscopy
Authors: Ellingham Sarah T.D. , Thompson Tim J.U. , Islam Meez
Published: August 2015

This study investigated the effect of soft tissue and different exposure times on the prediction of burning temperatures of bone when using Fourier transform infrared spectroscopy (FTIR). Ovis aries rib bones were burnt at different temperatures and for varying time intervals. Results of a linear regression analysis indicated that burn temperatures can be predicted with a standard error of ±70°C from defleshed bone spectra. Exposure time does not have a significant impact on prediction accuracy. The presence of soft tissue has a significant impact on heat‐induced changes of the bone matrix in low (<300°C) as well as high temperatures (>800°C), slowing down combustion in the former and accelerating it in the latter (p < 0.05). At medium temperatures, no significant difference was noted. These results provide forensic investigators a new perspective with which to interpret the results of crystallinity measures derived from burnt bone.
Chemical Analysis in the Corpus Callosum Following Traumatic Axonal Injury using Fourier Transform Infrared Microspectroscopy: A Pilot Study
Authors: Zhang Ji , Liu Liang , Mu Jiao , Yang Tiantong , Zheng Na , Dong Hongmei
Published: August 2015

Evaluating traumatic axonal injury remains challenging in clinical and forensic sciences as its identification is difficult using routine diagnostic methods. This study used Fourier transform infrared microspectroscopy to detect TAI within the corpus callosum in an animal model. Protein conformational analysis revealed significantly increased β‐sheet and β‐turn contents paralleled by a decrease in α‐helix content at 24 h postinjury, while the antiparallel β‐sheet content was decreased at 12 h postinjury. Compared with the control group, the lipid/protein ratio was significantly reduced in all of the injured groups. At 24 h postinjury, there were increases in the olefinic=CH and CH3 group of lipids accompanied by the decreased CH2 group, but the results at 12 and 72 h were contrary to that at 24 h. Our study showed that FTIRM could differentiate injured from normal white matter at different time points following TBI via examination of these infrared spectral parameters.
Validity Comparison of Three Dental Methods for Age Estimation Based on Tooth Root Translucency
Authors: Santoro Valeria , Fiandaca Chiara , Roca Roberta , Marini Chiara , De Donno Antonio , Introna Francesco
Published: August 2015

Age estimation of nonliving subjects plays a very important role in identifying human remains. When adult remains are in question, this process becomes even more complex. Among the numerous dental methods that exist for adults aging, the evaluation of root translucency is one of the most useful. This study studies the correlation between age and root translucency by investigating monoradicular teeth affected by pathological processes using the equations proposed by Lamendin, Prince & Ubelaker and from Singhal et al. The average age values calculated according to the three methods were compared with the values of known age. Age estimation using the Student's t‐test resulted as more accurate in the methods by Singhal et al. and by Prince & Ubelaker, with respect to that of Lamendin. Age estimation based solely on the percentage of radicular dentinal translucency has been found to be more accurate when diseased teeth are involved.
Computerized Dental Comparison: A Critical Review of Dental Coding and Ranking Algorithms Used in Victim Identification
Authors: Adams Bradley J. , Aschheim Kenneth W.
Published: August 2015

Comparison of antemortem and postmortem dental records is a leading method of victim identification, especially for incidents involving a large number of decedents. This process may be expedited with computer software that provides a ranked list of best possible matches. This study provides a comparison of the most commonly used conventional coding and sorting algorithms used in the United States (WinID3) with a simplified coding format that utilizes an optimized sorting algorithm. The simplified system consists of seven basic codes and utilizes an optimized algorithm based largely on the percentage of matches. To perform this research, a large reference database of approximately 50,000 antemortem and postmortem records was created. For most disaster scenarios, the proposed simplified codes, paired with the optimized algorithm, performed better than WinID3 which uses more complex codes. The detailed coding system does show better performance with extremely large numbers of records and/or significant body fragmentation.