bluuebunny/crossref_metadata_2025_split huggingface dataset:
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.
Complete absence of thebaine biosynthesis under home-brew fermentation conditions
Authors: Endy Drew , Galanie Stephanie , Smolke Christina D. 
Published: August 2015

AbstractYeast-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.
BRAINformat: A Data Standardization Framework for Neuroscience Data
Authors: Rübel Oliver , Prabhat  , Denes Peter , Conant David , Chang Edward , Bouchard Kristofer 
Published: August 2015

ABSTRACTNeuroscience 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

AbstractThe 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

AbstractThe 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.
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

Summary

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

ABSTRACTPresence 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

SummaryMicrobial 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

SummaryIntegrative 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

AbstractThis 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

AbstractThis 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

AbstractEvaluating 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

AbstractAge 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

AbstractComparison 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.
Transforming cross‐cultural water research through trust, participation and place
Authors: Woodward Emma , Marrfurra McTaggart Patricia 
Published: August 2015

AbstractIndigenous voices in government‐led natural resource management planning processes are often marginalised, misinterpreted, or excluded. Third parties, including government‐employed geographers, can act as knowledge brokers in defining Indigenous values and interests so they might be included in government planning processes. This paper reviews and assesses a research partnership that evolved to document the complex and diverse ecological and hydrological values held by Ngan'gi speakers about the Daly River and connected water places in the Northern Territory, Australia. The development of trust through the slow building of a relationship based on place‐based dialogue, a key aspect of participatory action research (PAR), created the foundation from which a mutually beneficial and respectful research partnership was able to, and continues to, evolve. Both research partners' perspectives are revealed here to articulate why the research partnership was deemed a success. Key lessons learned from the research partnership include the importance of trust, respect for place‐based learning, researcher and institutional flexibility, and awareness of the intricacies of relationship building and the benefits that research engagement can bring to Indigenous people and communities. We aim to further dialogue among geographers and interested disciplines as to the potential for PAR methods to foster mutually beneficial Indigenous–non‐Indigenous research partnerships.