bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quality of life and pruritus in patients with severe sepsis resuscitated with hydroxyethyl starch long-term follow-up of a randomised trial
Authors: Wittbrodt Piotr , Haase Nicolai , Butowska Dominika , Winding Robert , Poulsen Jesper B , Perner Anders ,   the 6S trial group and the Scandinavian Critical Care Trials Group
Published: March 2013

Abstract
Introduction
The effects of hydroxyethyl starch (HES) on patient-centered outcome measures have not been fully described in patients with severe sepsis. We assessed health-related quality of life (HRQoL) and the occurrence of pruritus in patients with severe sepsis randomized to resuscitation with HES 130/0.42 or Ringer's acetate.

Methods
We did post hoc analyses of the Danish survivors (n = 295) of the 6S trial using mailed questionnaires on self-perceived HRQoL (Short Form (SF) - 36) and pruritus.

Results
Median 14 months (interquartile range 10 to 18) after randomization, 182 (61%) and 185 (62%) completed questionnaires were obtained for the assessment of HRQoL and pruritus, respectively. Responders were older than nonresponders, but characteristics at randomization of the responders in the HES vs. Ringer's groups were comparable. At follow-up, the patients in the HES group had lower mental component summary scores than those in the Ringer's group (median 45 (interquartile range 36 to 55) vs. 53 (39 to 60), P = 0.01). The group differences were mainly in the scales of vitality and mental health. There was no difference in the physical component summary scores between groups, but patients in the HES group scored worse in bodily pain. Forty-nine percent of patients allocated to HES had experienced pruritus at any time after ICU discharge compared to 43% of those allocated to Ringer's (relative risk 1.13, 95% confidence interval 0.83 to 1.55, P = 0.43).

Conclusions
At long-term follow-up patients with severe sepsis assigned to resuscitation with HES 130/0.42 had worse self-perceived HRQoL than those assigned to Ringer's acetate whereas there were no statistically significant differences in the occurrence of pruritus.
Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing
Authors: O'Rawe Jason , Jiang Tao , Sun Guangqing , Wu Yiyang , Wang Wei , Hu Jingchu , Bodily Paul , Tian Lifeng , Hakonarson Hakon , Johnson W Evan , Wei Zhi , Wang Kai , Lyon Gholson J 
Published: March 2013

Abstract
Background
To facilitate the clinical implementation of genomic medicine by next-generation sequencing, it will be critically important to obtain accurate and consistent variant calls on personal genomes. Multiple software tools for variant calling are available, but it is unclear how comparable these tools are or what their relative merits in real-world scenarios might be.

Methods
We sequenced 15 exomes from four families using commercial kits (Illumina HiSeq 2000 platform and Agilent SureSelect version 2 capture kit), with approximately 120X mean coverage. We analyzed the raw data using near-default parameters with five different alignment and variant-calling pipelines (SOAP, BWA-GATK, BWA-SNVer, GNUMAP, and BWA-SAMtools). We additionally sequenced a single whole genome using the sequencing and analysis pipeline from Complete Genomics (CG), with 95% of the exome region being covered by 20 or more reads per base. Finally, we validated 919 single-nucleotide variations (SNVs) and 841 insertions and deletions (indels), including similar fractions of GATK-only, SOAP-only, and shared calls, on the MiSeq platform by amplicon sequencing with approximately 5000X mean coverage.

Results
SNV concordance between five Illumina pipelines across all 15 exomes was 57.4%, while 0.5 to 5.1% of variants were called as unique to each pipeline. Indel concordance was only 26.8% between three indel-calling pipelines, even after left-normalizing and intervalizing genomic coordinates by 20 base pairs. There were 11% of CG variants falling within targeted regions in exome sequencing that were not called by any of the Illumina-based exome analysis pipelines. Based on targeted amplicon sequencing on the MiSeq platform, 97.1%, 60.2%, and 99.1% of the GATK-only, SOAP-only and shared SNVs could be validated, but only 54.0%, 44.6%, and 78.1% of the GATK-only, SOAP-only and shared indels could be validated. Additionally, our analysis of two families (one with four individuals and the other with seven), demonstrated additional accuracy gained in variant discovery by having access to genetic data from a multi-generational family.

Conclusions
Our results suggest that more caution should be exercised in genomic medicine settings when analyzing individual genomes, including interpreting positive and negative findings with scrutiny, especially for indels. We advocate for renewed collection and sequencing of multi-generational families to increase the overall accuracy of whole genomes.
Clinical Relevance of Combined FSH and AMH Observations in Infertile Women
Authors: Gleicher Norbert , Kim Ann , Kushnir Vitaly , Weghofer Andrea , Shohat-Tal Aya , Lazzaroni Emanuela , Lee Ho-Joon , Barad David H. 
Published: March 2013

Context:
FSH and anti-Müllerian hormone (AMH) are, individually, widely used to assess functional ovarian reserve (FOR) but demonstrate discrepancies in efficacy. How predictive they are combined is unknown.

Objective:
The purpose of this study was to assess predictive values of different FSH and AMH combinations on in vitro fertilization (IVF).

Design and Setting:
FSH and AMH levels in patients were categorized as low, normal, and high, based on age-specific 95% confidence intervals. This allowed for establishment of nine combinations of low, normal, or high FSH/AMH patient categories. With use of various statistical methods, patients in individual categories were then compared in outcomes.

Patients:
We investigated 544 consecutive infertility patients in their first IVF cycles.

Interventions:
IVF cycles were managed.

Main Outcome Measures:
Oocyte yields and implantation and pregnancy rates, adjusted for age and fragile X mental retardation 1 (FMR1) genotypes/subgenotypes, were measured.

Results:
The most notable repeated finding was a strong statistical association of the FSH/AMH high/high category (characterized by abnormally high FSH and AMH levels) with favorable IVF outcomes compared with outcomes for other FSH/AMH variations (4.34 times odds of high oocyte yields and 1.93 times odds of clinical pregnancy). Addition of age to the model only minimally further improved the odds of pregnancy to 2.03 times. The positive association with high oocyte yields, however, turned negative (0.75 times lower yields) with addition of FMR1 to the model for women with FSH/AMH high/high and the het-norm/low FMR1 subgenotype compared with women with the norm FMR1 genotype and other FSH/AMH categories.

Conclusions:
In the absence of het-norm/low FMR1, abnormally high FSH and AMH, a seemingly contradictory combination, reflects highly beneficial outcomes in IVF compared with the other FSH/AMH categories, suggesting greater importance of FSH in early follicle maturation than currently recognized. The study also confirms adverse outcome effects of het-norm/low FMR1 and, therefore, the gene's importance for reproductive success.
The effects of hibernation on the contractile and biochemical properties of skeletal muscles in the thirteen-lined ground squirrel, Ictidomys tridecemlineatus
Authors: James Rob S. , Staples James F. , Brown Jason C. L. , Tessier Shannon N. , Storey Kenneth B. 
Published: March 2013

Summary
Hibernation is a crucial strategy of winter survival used by many mammals. During hibernation, thirteen-lined ground squirrels, Ictidomys tridecemlineatus, cycle through a series of torpor bouts, each lasting more than a week, during which the animals are largely immobile. Previous hibernation studies have demonstrated that such natural models of skeletal muscle disuse cause limited or no changes in either skeletal muscle size or mechanical performance. However, work loop analysis of skeletal muscle, which provides a realistic assessment of in vivo power output, has not previously been undertaken in mammals that undergo prolonged torpor during hibernation. In the present study, our aim was to assess the effects of 3 months of hibernation on mechanical performance (using the work loop technique) and several biochemical properties that may affect performance. There was no significant difference in soleus muscle power output-cycle frequency curves between winter (torpid) and summer animals. Total antioxidant capacity of gastrocnemius muscle was 156% higher in torpid than summer animals, suggesting one potential mechanism for maintenance of acute muscle performance. Soleus muscle fatigue resistance was significantly lower in torpid than summer animals. Gastrocnemius muscle glycogen content was unchanged. However, state 3 and state 4 mitochondrial respiration rates were significantly suppressed, by 59% and 44% respectively, in mixed hind-limb skeletal muscle from torpid animals compared with summer controls. These findings in hind-limb skeletal muscles suggest that, although maximal mechanical power output is maintained in torpor, there is both suppression of ATP production capacity and reduced fatigue resistance.
High frequency electrical stimulation reveals a p38-mTOR signaling module correlated with force-time integral
Authors: Rahnert Jill A. , Burkholder Thomas J. 
Published: March 2013

Summary
High frequency electrical stimulation (HFES) leads to muscle hypertrophy, and attention has been drawn to the high forces involved. However, both mechanical and metabolic stresses occur simultaneously, and both stimuli influence signaling cascades related to protein synthesis. This study aimed to identify the immediate signaling correlates of contraction-induced force and metabolic stresses under the hypothesis that HFES induces growth-related signaling through mechanical stimulation. Force-time integral (FTI) signaling in mouse tibialis anterior muscle was examined by separately manipulating the time of contraction to emphasize the metabolic aspect or the force of contraction to emphasize the mechanical aspect. When FTI was manipulated by changing the total time of activation, phosphorylation of p54 JNK, ERK and p70S6kT421/S424 was independent of FTI, while phosphorylation of ACC and p38 correlated with FTI. When FTI was manipulated by changing the force of contraction, p54 JNK, ERK, and p70S6kT421/S424 were again independent of FTI, while phosphorylation of p38 and FAK correlated with FTI. Factor analysis identified a p38-mTOR signaling module that correlated with FTI in both experiments. The consistent link among p38, mTOR and FTI suggests that they form a connected signaling module sensitive to the mechanical aspects of FTI, separate from markers of metabolic load.
Meal consumption is ineffective at maintaining or correcting water balance in a desert lizard, Heloderma suspectum
Authors: Wright Christian D. , Jackson Marin L. , DeNardo Dale F. 
Published: March 2013

SUMMARY
Many xeric organisms maintain water balance by relying on dietary and metabolic water rather than free water, even when free water may be available. For such organisms, hydric state may influence foraging decisions, since meal consumption is meeting both energy and water demands. To understand foraging decisions it is vital to understand the role of dietary water in maintaining water balance. We investigated whether meal consumption was sufficient to maintain water balance in captive Gila monsters (Heloderma suspectum) at varying levels of dehydration. Gila monsters could not maintain water balance over long time scales through meal consumption alone. Animals fed a single meal took no longer to dehydrate than controls when both groups were deprived of free water. Additionally, meal consumption imparts an acute short-term hydric cost regardless of hydration state. Meal consumption typically resulted in a significant elevation in osmolality at 6 h post-feeding, and plasma osmolality never fell below pre-feeding levels despite high water content (~70%) of meals. These results failed to support our hypothesis that dietary water is valuable to Gila monsters during seasonal drought. When considered in conjunction with previous research, these results demonstrate that Gila monsters, unlike many xeric species, are heavily reliant on seasonal rainfall and the resulting free-standing water to maintain water balance.
Gait transitions and modular organization of mammal locomotion
Authors: Maes Ludovic , Abourachid Anick 
Published: March 2013

Summary
Quadrupedal locomotion is the result of complex interactions between biomechanical and neural systems. During steady gaits both systems are in stable states. When the animal changes its speed, transitions between gaits can occur where the different coordination parameters are dissociated. Consequently, transitions are the periods where it is possible to detect and identify those parameters involved in the mechanical or neural control of locomotion. We study the interlimb coordination using a sequential method (APS) to measure the footfall patterns of dogs when accelerating and decelerating from 1.5ms-1 to more than 6ms-1 and conversely. We obtained 383 transitions between all the symmetrical and asymmetrical gaits used by the dogs. The analysis of the interlimb coordination modifications and of each foot parameter showed that mechanics drive the stance phase whereas the coordination is controlled during the swing phase. Furthermore, the comparison of the transition patterns between all gaits reveals the modular organization of locomotion: a pectoral module coordinates the two fore limbs, a pelvic module coordinates the two hind limbs and an axial module coordinates the two pairs and the trunk motion. The three modules cooperate to give rise to template of stable inter-limb coordination pattern, such as the walks, the trot or the gallop.
Biostratigraphic correlation in the Karoo: The case of the Middle Permian parareptile Eunotosaurus
Authors: Day Mike , Rubidge Bruce , Almond John , Jirah Sifelani 
Published: March 2013

The richness of fossil tetrapods from the Beaufort Group of South Africa has enabled biostratigraphic subdivision of this Permo-Triassic succession, with global applicability. Despite being the thickest of the seven biozones recognised, attempts at further subdivision of the Middle Permian Tapinocephalus Assemblage Zone (Abrahamskraal Formation) have not been successful, largely because the exact stratigraphic ranges of fossil taxa are unknown. This gap in knowledge has limited stratigraphic correlation of the Abrahamskraal Formation and hindered understanding of Middle Permian Karoo basin development. Currently, the lowermost Beaufort Group is split between an eastern and a western stratigraphic scheme and, because of poor outcrop and the relative paucity of fossils in the east, stratigraphic correlation between the two areas has been uncertain. Recent fossil discoveries of the parareptile Eunotosaurus africanus in the Eastern Cape and Free State provinces have extended its known geographic range in the east. An additional specimen from the lower Middleton Formation in the Eastern Cape has, for the first time, enabled the biostratigraphic correlation of this unit with the Poortjie Member of the Teekloof Formation in the west. These finds confirm the diachroneity of the boundary between the marine Ecca Group and the terrestrial Beaufort Group.
Large Scale Composting as a Means of Managing Water Hyacinth (Eichhornia crassipes)
Authors: Montoya John E. , Waliczek Tina M. , Abbott Michael L. 
Published: March 2013

AbstractThe intent of this study was to determine if composting is an effective means of managing water hyacinth while producing a quality horticultural compost product. Preliminary tests for the study included germination and seed mortality tests. Germination tests found that water hyacinth seeds germinated on filter paper media soaked in distilled water while placed in petri dishes held at a constant temperature of 27 C for 14 d. Seed mortality test results found that seeds of water hyacinth were rendered inviable at temperatures equal to or above 57 C. The study successfully developed a large-scale composting system that used water hyacinth as a primary feedstock. Eleven compost piles were derived from 10,000 kg of water hyacinth, 9,000 kg of food waste, 11,300 kg of poultry litter, and 17,200 kg of wood chips. Results indicated that the composting process reached and sustained sufficiently high enough temperatures to inactivate and fully decompose seeds and other propagules of water hyacinth. Therefore, water hyacinth can be composted without the potential danger of it spreading. Compost quality tests found that the compost produced was within acceptable to ideal ranges of accepted industry quality standards, though there was a learning curve by student workers in the preparation of the piles using the large equipment.
Change in Leafy Spurge (Euphorbia esula) Density and Soil Seedbank Composition 10 Years following Release of Aphthona spp. Biological Control Agents
Authors: Setter Cassandra M. , Lym Rodney G. 
Published: March 2013

AbstractFlea beetles (Aphthona spp.) were released in the Little Missouri National Grasslands (LMNG) in western North Dakota in 1999 to control leafy spurge. The changes in leafy spurge density and soil seedbank composition were evaluated on two ecological sites 10 yr (2009) after Aphthona spp. release to monitor the effectiveness of the insects on weed control and the associated changes in plant communities. In 2009, leafy spurge stem density averaged 2 and 9 stems m−2 (0.19 to 0.84 ft−2) in the loamy overflow and loamy sites, respectively, compared with 110 and 78 stems m−2, respectively, in 1999. Leafy spurge constituted nearly 67% of the loamy overflow seedbank in 1999, compared with 2% in 2009. In the loamy seedbank, the weed represented nearly 70% in 1999, compared with approximately 15% in 2009. As leafy spurge abundance was reduced, native species richness and seed count increased 10 yr after Aphthona spp. release. Late seral species represented 17% of the loamy overflow seedbank in 2009, an increase from 5% in 1999. However, Kentucky bluegrass, a nontarget weedy species, increased more than 250% in the loamy overflow seedbank. Late seral species were 38% of the loamy seedbank in 2009, compared with 13% in 1999. The number of native species increased from 31 in 1999 to 39 in 2009 in the loamy overflow seedbank, but only changed from 32 to 34 species in the loamy site during the same period. The reestablishment of native species has been slow, but seedbank analysis indicates the number and type of species found before the leafy spurge infestation have increased. Planting native species in selected areas may have reduced the lag time in these species return to the seedbank and reduced invasion from other nondesirable species, such as Kentucky bluegrass.
Improved Understanding of Weed Biological Control Safety and Impact with Chemical Ecology: A Review
Authors: Wheeler Gregory S. , Schaffner Urs 
Published: March 2013

AbstractWe review chemical ecology literature as it relates to biological control of weeds and discuss how this means of controlling invasive plants could be enhanced by the consideration of several well-established research approaches. The interface between chemical ecology and biological control of weeds presents a rich opportunity to exploit potentially coevolved relationships between agents and plants where chemical factors mediating interactions are important. Five topics seem relevant, which if implemented could improve the predictability of host range determination, agent establishment, and impact on the target weed. (1) The host secondary plant chemistry and a potential biological control agent's response to that chemistry can be exploited to improve predictability of potential agent host range. (2) Evolutionary changes may occur in secondary plant chemistry of invasive weeds that have been introduced to novel environments and exposed to a new set of biotic and abiotic stressors. Further, such a scenario facilitates rapid evolutionary changes in phenotypic traits, which in turn may help explain one mechanism of invasiveness and affect the outcome of biological control and other management options. (3) Herbivores can induce production of secondary plant compounds. (4) Variability of weed secondary chemistry which, either constitutive or inducible, can be an important factor that potentially influences the performance of some biological control agents and their impact on the target weed. (5) Finally, sequestration of secondary plant chemistry may protect herbivores against generalist predators, which might improve establishment of a biological control agent introduced to a new range and eventually impact on the target weed. Recognition of these patterns and processes can help identify the factors that impart success to a biological control program.
Role of Size and Nitrogen in Competition between Annual and Perennial Grasses
Authors: Orloff L. Noelle , Mangold Jane M. , Menalled Fabian D. 
Published: March 2013

AbstractDiffering life histories contribute to difficulties establishing perennial grasses on lands dominated by exotic annual grasses. In a greenhouse study, we investigated to what extent allowing the perennial grass bluebunch wheatgrass to emerge before the exotic annual grass downy brome would increase its competitive ability and whether modifying nitrogen (N) would affect competition. We conducted an addition-series factorial experiment. In three cohort treatments, the two species were seeded concurrently or bluebunch wheatgrass was at the two- or four-leaf stage when downy brome was planted. N treatments were low (ambient) or high (N added to maintain 10 mg kg−1 [0.1286 oz lb−1]). Larger bluebunch wheatgrass avoided suppression by downy brome regardless of N. Under concurrent sowing, doubling downy brome density decreased bluebunch wheatgrass biomass by 22.6% ± 2.38 SE. In contrast, when bluebunch wheatgrass had a four-leaf size advantage, the same increase in downy brome density decreased bluebunch wheatgrass biomass by 4.14% ± 2.31. Larger bluebunch wheatgrass also suppressed downy brome more effectively, but N enrichment decreased the suppressive ability of bluebunch wheatgrass.
Is Pyrenophora semeniperda the Cause of Downy Brome (Bromus tectorum) Die-offs?
Authors: Baughman Owen W. , Meyer Susan E. 
Published: March 2013

AbstractDowny brome (cheatgrass) is a highly successful, exotic, winter annual invader in semi-arid western North America, forming near-monocultures across many landscapes. A frequent but poorly understood phenomenon in these heavily invaded areas is periodic ‘die-off’ or complete stand failure. The fungal pathogen Pyrenophora semeniperda is abundant in cheatgrass seed banks and causes high mortality. To determine whether this pathogen could be responsible for stand failure, we quantified late spring seed banks in die-off areas and adjacent cheatgrass stands at nine sites. Seed bank analysis showed that this pathogen was not a die-off causal agent at those sites. We determined that seed bank sampling and litter data could be used to estimate time since die-off. Seed bank patterns in our recent die-offs indicated that the die-off causal agent does not significantly impact seeds in the persistent seed bank.