bluuebunny/crossref_metadata_2025_split huggingface dataset:
Turbulent structure of high-amplitude pressure peaks within the turbulent boundary layer
Authors: Ghaemi S. , Scarano F. 
Published: October 2013

AbstractThe positive and negative high-amplitude pressure peaks (HAPP) are investigated in a turbulent boundary layer at $R{e}_{\theta } = $ 1900 in order to identify their turbulent structure. The three-dimensional velocity field is measured within the inner layer of the turbulent boundary layer using tomographic particle image velocimetry (tomo-PIV). The measurements are performed at an acquisition frequency of 10 000 Hz and over a volume of $418\times 149\times 621$ wall units in the streamwise, wall-normal and spanwise directions, respectively. The time-resolved velocity fields are applied to obtain the material derivative using the Lagrangian method followed by integration of the Poisson pressure equation to obtain the three-dimensional unsteady pressure field. The simultaneous volumetric velocity, acceleration, and pressure data are conditionally sampled based on local maxima and minima of wall pressure to analyse the three-dimensional turbulent structure of the HAPPs. Analysis has associated the positive HAPPs to the shear layer structures formed by an upstream sweep of high-speed flow opposing a downstream ejection event. The sweep event is initiated in the outer layer while the ejection of near-wall fluid is formed by the hairpin category of vortices. The shear layers were observed to be asymmetric in the instantaneous visualizations of the velocity and acceleration fields. The asymmetric pattern originates from the spanwise component of temporal acceleration of the ejection event downstream of the shear layer. The analysis also demonstrated a significant contribution of the pressure transport term to the budget of the turbulent kinetic energy in the shear layers. Investigation of the conditional averages and the orientation of the vortices showed that the negative HAPPs are linked to both the spanwise and quasi-streamwise vortices of the turbulent boundary layer. The quasi-streamwise vortices can be associated with the hairpin category of vortices or the isolated quasi-streamwise vortices of the inner layer. A bi-directional analysis of the link between the HAPPs and the hairpin paradigm is also conducted by conditionally averaging the pressure field based on the detection of hairpin vortices using strong ejection events. The results demonstrated positive pressure in the shear layer region of the hairpin model and negative pressure overlapping with the vortex core.
On the measurement of turbulent magnetic diffusivities: the three-dimensional case
Authors: Cattaneo F. , Tobias S. M. 
Published: October 2013

AbstractIt has been shown that it is possible to measure the turbulent diffusivity of a magnetic field by a method involving oscillatory sources. So far the method has only been tried in the special case of two-dimensional fields and flows. Here we extend the method to three dimensions and consider the case where the flow is thermally driven convection in a large-aspect-ratio domain. We demonstrate that if the diffusing field is horizontal the method is successful even if the underlying flow can sustain dynamo action. We show that the resulting turbulent diffusivity is comparable with, although not exactly the same as, that of a passive scalar. We were not able to measure unambiguously the diffusivity if the diffusing field is vertical, but argue that such a measurement is possible if enough resources are utilized on the problem.
Diverse capacity for 2-methylhopanoid production correlates with a specific ecological niche
Authors: Ricci Jessica N , Coleman Maureen L , Welander Paula V , Sessions Alex L , Summons Roger E , Spear John R , Newman Dianne K 
Published: October 2013

Abstract
Molecular fossils of 2-methylhopanoids are prominent biomarkers in modern and ancient sediments that have been used as proxies for cyanobacteria and their main metabolism, oxygenic photosynthesis. However, substantial culture and genomic-based evidence now indicates that organisms other than cyanobacteria can make 2-methylhopanoids. Because few data directly address which organisms produce 2-methylhopanoids in the environment, we used metagenomic and clone library methods to determine the environmental diversity of hpnP, the gene encoding the C-2 hopanoid methylase. Here we show that hpnP copies from alphaproteobacteria and as yet uncultured organisms are found in diverse modern environments, including some modern habitats representative of those preserved in the rock record. In contrast, cyanobacterial hpnP genes are rarer and tend to be localized to specific habitats. To move beyond understanding the taxonomic distribution of environmental 2-methylhopanoid producers, we asked whether hpnP presence might track with particular variables. We found hpnP to be significantly correlated with organisms, metabolisms and environments known to support plant–microbe interactions (P-value&lt;10−6); in addition, we observed diverse hpnP types in closely packed microbial communities from other environments, including stromatolites, hot springs and hypersaline microbial mats. The common features of these niches indicate that 2-methylhopanoids are enriched in sessile microbial communities inhabiting environments low in oxygen and fixed nitrogen with high osmolarity. Our results support the earlier conclusion that 2-methylhopanoids are not reliable biomarkers for cyanobacteria or any other taxonomic group, and raise the new hypothesis that, instead, they are indicators of a specific environmental niche.
Metabolic and protein interaction sub-networks controlling the proliferation rate of cancer cells and their impact on patient survival
Authors: Feizi Amir , Bordel Sergio 
Published: October 2013

AbstractCancer cells can have a broad scope of proliferation rates. Here we aim to identify the molecular mechanisms that allow some cancer cell lines to grow up to 4 times faster than other cell lines. The correlation of gene expression profiles with the growth rate in 60 different cell lines has been analyzed using several genome-scale biological networks and new algorithms. New possible regulatory feedback loops have been suggested and the known roles of several cell cycle related transcription factors have been confirmed. Over 100 growth-correlated metabolic sub-networks have been identified, suggesting a key role of simultaneous lipid synthesis and degradation in the energy supply of the cancer cells growth. Many metabolic sub-networks involved in cell line proliferation appeared also to correlate negatively with the survival expectancy of colon cancer patients.
Codon optimisation improves the expression of Trichoderma viride sp. endochitinase in Pichia pastoris
Authors: Yu Ping , Yan Yuan , Gu Qing , Wang Xiangyang 
Published: October 2013

AbstractThe mature cDNA of endochitinase from Trichoderma viride sp. was optimised based on the codon bias of Pichia pastoris GS115 and synthesised by successive PCR; the sequence was then transformed into P. pastoris GS115 via electroporation. The transformant with the fastest growth rate on YPD plates containing 4 mg/mL G418 was screened and identified. This transformant produced 23.09 U/mL of the recombinant endochitinase, a 35% increase compared to the original strain bearing the wild-type endochitinase cDNA. The recombinant endochitinase was sequentially purified by ammonia sulphate precipitation, DE-52 anion-exchange chromatography and Sephadex G-100 size-exclusion chromatography. Thin-layer chromatography indicated that the purified endochitinase could hydrolyse chito-oligomers or colloidal chitin to generate diacetyl-chitobiose (GlcNAc)2 as the main product. This study demonstrates (1) a means for high expression of Trichoderma viride sp. endochitinase in P. pastoris using codon optimisation and (2) the preparation of chito-oligomers using endochitinase.
SLC22A13 catalyses unidirectional efflux of aspartate and glutamate at the basolateral membrane of type A intercalated cells in the renal collecting duct
Authors: Schulz Christian , Fork Christian , Bauer Tim , Golz Stefan , Geerts Andreas , Schömig Edgar , Gründemann Dirk 
Published: October 2013

In vertebrates, SLC22A13 is an evolutionarily conserved transport protein of the plasma membrane. In humans and rat, it is principally expressed in the kidney. The precise localization and physiological function are unknown. In the present study, immunohistochemistry revealed that expression of SLC22A13 is confined to the basolateral membrane of type A intercalated cells in rat kidney. Double-staining confirmed that SLC22A13 co-localizes with anion exchanger 1. LC–MS difference shading showed that heterologous expression of human and rat SLC22A13 in HEK (human embryonic kidney)-293 cells stimulates efflux of guanidinosuccinate, aspartate, glutamate and taurine. Time courses of uptake of [3H]aspartate and [3H]glutamate revealed that SLC22A13 counteracted endogenous uptake. By contrast, OAT2 (organic anion transporter 2), a bidirectional glutamate transporter, increased accumulation of [3H]glutamate. Thus SLC22A13 catalyses unidirectional efflux. Velocity of efflux of standard amino acids was measured by LC–MS/MS. Expression of SLC22A13 strongly stimulated efflux of aspartate, taurine and glutamate. When the intracellular concentrations of aspartate and taurine were increased by pre-incubation, velocities of efflux increased linearly. We propose that in type A intercalated cells, SLC22A13 compensates luminal exit of protons by mediating the basolateral expulsion of the anions aspartate and glutamate. In this context, unidirectional efflux is essential to avoid anion re-entering. Loss of SLC22A13 function could cause distal tubular acidosis.
IFI16 senses DNA forms of the lentiviral replication cycle and controls HIV-1 replication
Authors: Jakobsen Martin R. , Bak Rasmus O. , Andersen Annika , Berg Randi K. , Jensen Søren B. , Jin Tengchuan , Laustsen Anders , Hansen Kathrine , Østergaard Lars , Fitzgerald Katherine A. , Xiao T. Sam , Mikkelsen Jacob G. , Mogensen Trine H. , Paludan Søren R. 
Published: October 2013

Significance
HIV-1 is a lentivirus and replicates through a replication cycle involving several DNA forms including ssDNA. Here we report that synthetic DNA oligos corresponding to DNA forms of the lentivirus replication cycle as well as viral DNA are detected by the immunological DNA sensor IFN-inducible protein 16 (IFI16) and stimulate innate immune responses through a pathway dependent on stimulator of IFN genes (STING). Moreover, we show that replication of HIV-1 is elevated in cells with decreased expression of IFI16 or STING. We suggest IFI16 is a sensor for lentivirus DNA in macrophages stimulating innate immune responses, which contribute to early control of the virus.
Delayed star formation in high-redshift stream-fed galaxies
Authors: Gabor J. M. , Bournaud Frédéric 
Published: October 2013

Abstract
We propose that star formation (SF) is delayed relative to the inflow rate in rapidly accreting galaxies at very high redshift (z &gt; 2) because of the energy conveyed by the accreting gas. Accreting gas streams provide fuel for SF, but they stir the disc and increase turbulence above the usual levels compatible with gravitational instability, reducing the SF efficiency in the available gas. After the specific inflow rate has sufficiently decreased – typically at z &lt; 3 – galaxies settle in a self-regulated regime with efficient SF. An analytic model shows that this interaction between infalling gas and young galaxies can significantly delay SF and maintain high gas fractions (&gt;40 per cent) down to z ≈ 2, in contrast to other galaxy formation models. Idealized hydrodynamic simulations of infalling gas streams on to primordial galaxies confirm the efficient energetic coupling at z &gt; 2 and suggest that this effect is largely under-resolved in existing cosmological simulations.
The deleterious effect of red blood cell storage on microvascular response to transfusion
Authors: Weinberg Jordan A. , MacLennan Paul A. , Vandromme-Cusick Marianne J. , Magnotti Louis J. , Kerby Jeffrey D. , Rue Loring W. , Angotti Jonathan M. , Garrett Cristen A. , Hendrick Leah E. , Croce Martin A. , Fabian Timothy C. , Barnum Scott R. , Patel Rakesh P. 
Published: October 2013

BACKGROUND
The transfusion of relatively older red blood cells (RBCs) has been associated with both morbidity and mortality in trauma patients in observational studies. Although the mechanisms responsible for this phenomenon remain unclear, alterations in the microcirculation as a result of the transfusion of relatively older blood may be a causative factor. To assess this hypothesis, we evaluated microvascular perfusion in trauma patients during RBC transfusion.

METHODS
Anemic but otherwise stable trauma intensive care unit patients with orders for transfusion were identified. Thenar muscle tissue oxygen saturation (StO2) was measured continuously by near-infrared spectroscopy during the course of transfusion of one RBC unit. Sublingual microcirculation was observed by sidestream dark-field illumination microscopy before and after transfusion of one RBC unit. Thenar muscle StO2 was recorded during the course of transfusion. Pretransfusion and posttransfusion perfused capillary vascular density (PCD) was determined by semiquantitative image analysis. Changes in StO2 and PCD relative to age of RBC unit were evaluated using mixed models that adjusted for baseline StO2 and Spearman correlation, respectively.

RESULTS
Overall, 93 patients were recruited for study participation, 69% were male, and average Injury Severity Score (ISS) was 26.4. The average pretransfusion hemoglobin was 7.5 mg/dL, and the average age of RBC unit transfused was 29.4 days. The average peritransfusion StO2 was negatively associated with increasing RBC age (slope, −0.11; p = 0.0014). Change in PCD from pretransfusion to posttransfusion period was found to correlate negatively with RBC storage age (Spearman correlation, −0.27; p = 0.037).

CONCLUSION
The transfusion of relatively older RBC units was associated with a decline in both StO2 and PCD. Collectively, these observations demonstrate that transfusions of older RBC units are associated with the inhibition of regional microvascular perfusion. In patients requiring multiple units of RBCs, alteration of the microcirculation by relatively older units could potentially contribute to adverse outcomes.

LEVEL OF EVIDENCE
Prognostic study, level III.
Vancomycin and nephrotoxicity
Authors: Davies Stephen W. , Guidry Christopher A. , Petroze Robin T. , Hranjec Tjasa , Sawyer Robert G. 
Published: October 2013

BACKGROUND
Vancomycin is considered the drug of choice for methicillin-resistant Staphylococcus aureus infection; however, it has also been linked with nephrotoxicity in the past, sometimes leading to its substitution with linezolid. We hypothesized that patients treated with vancomycin for gram-positive (GP) infections would have an increased incidence of rise in creatinine and need for hemodialysis (HD) compared with patients receiving linezolid.

METHODS
This was a retrospective cohort study of a prospectively maintained database of all surgical patients treated with either vancomycin or linezolid for GP infections in a single intensive care unit from 2001 to 2008 and managed under a cycling antibiotic protocol. Patients were followed up until hospital discharge. Categorical and continuous variables were evaluated. Multivariable logistic regression was performed.

RESULTS
A total of 545 patients were treated for 1,046 GP infections (571 with vancomycin, 475 with linezolid) over 7 years. Patient demographics were similar between groups; however, the vancomycin group was associated with a longer treatment course (16.2 [0.5] days vs. 14.3 [0.5] days; p = 0.022). Unadjusted outcomes were similar between groups. Multivariable analysis revealed that Acute Physiology and Chronic Health Evaluation II score predicted an increase in creatinine levels greater than 1.0 following antibiotic therapy (relative risk [RR], 3.01; 95% confidence interval [CI], 1.22–7.42) and subsequent need for HD (RR, 3.07; 95% CI, 1.23–7.62). In addition, initial creatinine level predicted an increase in creatinine levels greater than 1.0 following antibiotic therapy (RR, 4.36; 95% CI, 1.46–12.99) and subsequent need for HD (RR, 10.83; 95% CI, 3.19–36.77). Linezolid was found to be protective regarding rise in creatinine levels greater than 1.0 following antibiotic therapy; however, this was only experienced when vancomycin trough levels greater than 20 were encountered (RR, 5.4;95% CI, 1.19–24.51).

CONCLUSION
These data suggest that vancomycin is minimally nephrotoxic and has a similar nephrotoxic profile as compared with linezolid when appropriate dosing is used, even among critically ill patients with complex infections.

LEVEL OF EVIDENCE
Therapeutic/care management, level II.
Brain-type natriuretic peptide and right ventricular end-diastolic volume index measurements are imprecise estimates of circulating blood volume in critically ill subjects
Authors: Takahashi Edwin A. , Moran Sharon E. , Hayashi Michael S. , Inouye David S. , Takanishi Danny M. , Yu Mihae 
Published: October 2013

BACKGROUND
Surrogate indicators have often been used to estimate intravascular volume to guide fluid management. Brain-type natriuretic peptide (BNP) has been used as a noninvasive adjunct in the diagnosis of fluid overload and as a marker of response to therapy, especially in individuals with congestive heart failure. Similarly, right ventricular end-diastolic volume index (RVEDVI) measurements represent another parameter used to guide fluid resuscitation. The aim of this study was to evaluate whether BNP and RVEDVI are clinically valuable parameters that can distinguish among hypovolemia, euvolemia, and hypervolemia, as measured by blood volume (BV) analysis in critically ill surgical subjects.

METHODS
This observational study was part of a prospective, randomized controlled trial. Subjects with pulmonary artery catheters for the treatment of traumatic injuries, severe sepsis/septic shock, cardiovascular collapse, adult respiratory distress syndrome, and postsurgical care were studied. Circulating BV was measured by a radioisotope dilution technique using the BVA-100 Analyzer (Daxor Corporation, New York, NY) within the first 24 hours of acute resuscitation. BV results were reported as percent deviation from the patient’s ideal BV based on height and percent deviation from optimum weight. Hypovolemia was defined as less than 0%, euvolemia was defined as 0% to +16%, and hypervolemia was defined as greater than +16% deviation from ideal BV. RVEDVI was measured by continuous cardiac output pulmonary artery catheters (Edwards Lifesciences, Irvine, CA). BNP and RVEDVI measurements obtained with BV analysis were evaluated with Fisher’s exact test and regression analysis.

RESULTS
In 81 subjects, there was no difference in BV status between those with BNP of 500 pg/mL or greater and BNP of less than 500 pg/mL (p = 0.82) or in those with RVEDVI of 140 mL/m2 or greater and RVEDVI of less than 140 mL/m2 (p = 0.43). No linear relationship existed between BV and these parameters.

CONCLUSION
In critically ill surgical patients, BNP and RVEDVI were not associated with intravascular volume status, although they may be useful as indices that reflect increased cardiac preload.

LEVEL OF EVIDENCE
Diagnostic study, level III.
Early abdominal closure improves long-term outcomes after damage-control laparotomy
Authors: Fox Nicole , Crutchfield Melanie , LaChant Mary , Ross Steven E. , Seamon Mark J. 
Published: October 2013

BACKGROUND
The impact of initial clinical decisions on the long-term quality of life and functional outcome of patients who undergo damage-control laparotomy (DCL) is unknown. We hypothesized that early abdominal closure after DCL improves long-term outcomes.

METHODS
Patients (2005–2011) who underwent DCL (n = 140) at our Level I trauma center were identified. A total of 108 patients survived their hospitalization, and 15 died following discharge. Of the remaining 93 survivors, 59 were unreachable and not present in the social security death index. Our final study population of 34 survivors prospectively completed a standardized study questionnaire, the SF-36 health survey, and inpatient and outpatient records were reviewed. Survivors were compared on the basis of time with final abdominal closure (early, <7 days vs. late, >7 days; either primary closure or Vicryl mesh), and study variables were analyzed. A p < 0.05 was considered significant.

RESULTS
Our study population was primarily male (82%) of varying age (36 [13]) and mechanism (blunt 56%, penetrating 44%) with severe injuries (mean [SD] Injury Severity Score [ISS], 17 [8]). Despite no differences in age, sex, mechanism, ISS, admission Glasgow Coma Scale (GCS) score, or admission systolic blood pressure, early-closure patients (n = 13) had shorter hospital (25 days vs. 57 days) and intensive care unit (12 days vs. 20 days) stays and, upon long-term follow-up, higher physical (54 vs. 18), emotional (86 vs. 44), and general health (66 vs. 50) SF-36 scores than late-closure patients (n = 21) (all p < 0.05). Early-closure patients had less daily pain (38% vs. 95%), had higher overall SF-36 scores (66 vs. 46), and were more likely to return to work (54% vs. 10%) than late-closure patients (all p < 0.05).

CONCLUSION
Early clinical decisions impact the lives of critically injured patients. Abdominal closure within 7 days of DCL improves long-term quality of life and functional outcome.

LEVEL OF EVIDENCE
Therapeutic study, level IV.
Incidental findings in patients with multiple injuries
Authors: Ruesseler Miriam , Schill Anna , Lehnert Thomas , Wyen Hendrik , Wutzler Sebastian , Marzi Ingo , Walcher Felix 
Published: October 2013

BACKGROUND
Multislice computed tomography (MSCT) is the diagnostic criterion standard for the initial evaluation of patients with suspected multiple injuries. Besides scanning for injuries directly related to the initial trauma, MSCT scans can reveal pathologies unrelated to the trauma of clinical relevance.
The aim of the present study was to determine the frequency and follow-up course of incidental findings in patients with multiple injuries.

METHODS
This is a retrospective analysis of prospectively collected data on 2,242 patients with suspected multiple injuries at a Level I trauma center from 2006 to 2010.
The MSCT reports were retrospectively reviewed regarding abnormal findings not related to trauma. These incidental findings were classified on a four-point level scoring system with respect to clinical importance and urgency for further diagnostic and therapeutic procedures.

RESULTS
During initial trauma center evaluation in the emergency department, 2,246 patients met our inclusion criteria. A total of 2,036 patients (90.7%) underwent MSCT; 1,142 (50.9%) of the patients had one or more incidental findings. A total of 2,844 incidental findings were detected. Overall, 349 tumor findings were noted (12.3% of all incidental findings); 113 findings were suspicious for malignant processes or metastasis. According to our classification, 168 (5.9%) of the incidental findings required urgent follow-up (Level 4), and 527 (18.5%) of the incidental findings required a follow-up before discharge (Level 3).

CONCLUSION
MSCT in patients with multiple injuries reveals one or more incidental findings in more than one of two patients. A scoring system classifying for relevance of incidental findings was introduced and could be applied in routine trauma care in the future.

LEVEL OF EVIDENCE
Epidemiologic study, level III.