bluuebunny/crossref_metadata_2025_split huggingface dataset:
How to decompose a permutation into a pair of labeled Dyck paths by playing a game
Authors: Billera Louis , Levine Lionel , Mészáros Karola 
Published: January 2015

We give a bijection between permutations of

1
,
…
,
2
n

1,\ldots ,2n

and certain pairs of Dyck paths with labels on the down steps. The bijection arises from a game in which two players alternate selecting from a set of

2
n

2n

items: the permutation encodes the players’ preference ordering of the items, and the Dyck paths encode the order in which items are selected under optimal play. We enumerate permutations by certain new statistics, AA inversions and BB inversions, which have natural interpretations in terms of the game. We derive identities such as
\[

∑

p

∏

i
=
1

n

q

h
i

−
1

[

h
i

]
q

=
[
1

]
q

[
3

]
q

⋯
[
2
n
−
1

]
q

\sum _{p} \prod _{i=1}^n q^{h_i -1} [h_i]_q = [1]_q [3]_q \cdots [2n-1]_q

\]
where the sum is over all Dyck paths

p
p

of length

2
n

2n

, and

h
1

,
…
,

h
n

h_1,\ldots ,h_n

are the heights of the down steps of

p
p

.
Interpretation and design of ocean acidification experiments in upwelling systems in the context of carbonate chemistry co-variation with temperature and oxygen
Authors: Reum Jonathan C. P. , Alin Simone R. , Harvey Chris J. , Bednaršek Nina , Evans Wiley , Feely Richard A. , Hales Burke , Lucey Noelle , Mathis Jeremy T. , McElhany Paul , Newton Jan , Sabine Christopher L. 
Published: January 2015

AbstractCoastal upwelling regimes are some of the most productive ecosystems in the ocean but are also among the most vulnerable to ocean acidification (OA) due to naturally high background concentrations of CO2. Yet our ability to predict how these ecosystems will respond to additional CO2 resulting from anthropogenic emissions is poor. To help address this uncertainty, researchers perform manipulative experiments where biological responses are evaluated across different CO2 partial pressure (pCO2) levels. In upwelling systems, however, contemporary carbonate chemistry variability remains only partly characterized and patterns of co-variation with other biologically important variables such as temperature and oxygen are just beginning to be explored in the context of OA experimental design. If co-variation among variables is prevalent, researchers risk performing OA experiments with control conditions that are not experienced by the focal species, potentially diminishing the ecological relevance of the experiment. Here, we synthesized a large carbonate chemistry dataset that consists of carbonate chemistry, temperature, and oxygen measurements from multiple moorings and ship-based sampling campaigns from the California Current Ecosystem (CCE), and includes fjord and tidal estuaries and open coastal waters. We evaluated patterns of pCO2 variability and highlight important co-variation between pCO2, temperature, and oxygen. We subsequently compared environmental pCO2–temperature measurements with conditions maintained in OA experiments that used organisms from the CCE. By drawing such comparisons, researchers can gain insight into the ecological relevance of previously published OA experiments, but also identify species or life history stages that may already be influenced by contemporary carbonate chemistry conditions. We illustrate the implications co-variation among environmental variables can have for the interpretation of OA experimental results and suggest an approach for designing experiments with pCO2 levels that better reflect OA hypotheses while simultaneously recognizing natural co-variation with other biologically relevant variables.
Effects of ghost fishing lobster traps in the Florida Keys
Authors: Butler Casey B. , Matthews Thomas R. 
Published: January 2015

AbstractGhost fishing is the capacity of lost traps to continue to catch and kill animals. In the spiny lobster (Panulirus argus) fishery in Florida, the effects of ghost fishing are of particular concern, given the estimated 10s of 1000s of traps lost annually. We distributed 40 each of the three types of lobster traps (wire, wood–wire hybrid, and wood slat) at three locations in the Florida Keys to simulate ghost fishing. Divers monitored these traps biweekly for 1 year then monthly for two additional years, recording the time ghost traps remained intact and continued to fish, as well as the number of live and dead lobsters and other animals in each trap. Wood slat and hybrid traps remained intact and fished for 509 ± 97 (median ± median absolute deviation) and 480 ± 142 d, respectively. Wire traps fished significantly longer (779.5 ± 273.5 d, p &lt; 0.001), and several fished until the end of the experiment (1071 d). Traps in Florida Bay fished longer (711.5 ± 51.5 d) than traps inshore (509 ± 94.5 d) and offshore (381 ± 171 days; p &lt; 0.001) in the Atlantic Ocean. More lobsters were observed in hybrid traps (mean = 4.81 ± 0.03 s.e.) than in wood slat (3.85 ± 0.16) or wire traps (3.17 ± 0.03; F = 40.15, d.f. = 2, p &lt; 0.001). Wire traps accounted for 83% of fish confined overall and 74% of the dead fish observed in traps. Ghost traps in Florida Bay and Atlantic inshore killed 6.8 ± 1.0 and 6.3 ± 0.88 lobsters per trap annually, while Atlantic offshore traps killed fewer (3.0 ± 0.69) lobsters, likely as a result of lower lobster abundance in traps. The combined effects of greater lobster mortality and greater abundance of lost traps in inshore areas account for the majority of the estimated 637 622 ± 74 367 (mean ± s.d.) lobsters that die in ghost traps annually.
Basin-wide mechanisms for spring bloom initiation: how typical is the North Atlantic?
Authors: Cole Harriet S. , Henson Stephanie , Martin Adrian P. , Yool Andrew 
Published: January 2015

AbstractThe annual phytoplankton bloom is a key event in pelagic ecosystems. Variability in the timing, or phenology, of these blooms affects ecosystem dynamics with implications for carbon export efficiency and food availability for higher trophic levels. Furthermore, interannual variability in phytoplankton bloom timing may be used to monitor changes in the pelagic ecosystem that are either naturally or anthropogenically forced. The onset of the spring bloom has traditionally been thought to be controlled by the restratification of the water column and shoaling of the mixed layer, as encapsulated in Sverdrup's critical depth hypothesis. However, this has been challenged by recent studies which have put forward different mechanisms. For example, the critical turbulence hypothesis attributes bloom initiation to a reduction in turbulent mixing associated with the onset of positive net heat fluxes (NHFs). To date, the majority of studies on bloom initiation mechanisms have concentrated on North Atlantic datasets leaving their validity in other subpolar regions unknown. Here, we use chlorophyll output from a model that assimilates satellite ocean colour data to calculate bloom initiation timing and examine the basin-wide drivers of spatial and interannual variability. We find that the date that the NHF turns positive is a stronger predictor for the date of bloom initiation, both spatially and interannually, across the North Atlantic than changes in the mixed layer depth. However, results obtained from the North Pacific and Southern Ocean show no such basin-wide coherency. The lack of consistency in the response of the subpolar basins indicates that other drivers are likely responsible for variability in bloom initiation. This disparity between basins suggests that the North Atlantic bloom initiation processes are unique and therefore that this region may not be a suitable model for a global, theoretical understanding of the mechanisms leading to the onset of the spring bloom.
Analysis of IL-22 contribution to hepcidin induction and hypoferremia during the response to LPS in vivo
Authors: Wallace Daniel F. , Subramaniam V. Nathan 
Published: January 2015

Abstract
The anaemia of chronic disease (ACD) results from inflammation-mediated up-regulation of the iron regulatory hormone hepcidin, with the consequent sequestration of iron limiting its availability for erythropoiesis. The inflammatory cytokine IL-6, a regulator of hepcidin, has been implicated in this process. Recent in vivo and in vitro studies indicate that IL-22 is also able to stimulate hepcidin expression. We aimed to determine if IL-22 had a role in causing the hypoferremia associated with the inflammatory response. Wild-type and Il22-knockout mice were subjected to an acute inflammatory stimulus via administration of LPS and the response of hepcidin and iron homeostasis was analysed. In the absence of IL-22, there was a response of hepcidin, resulting in a reduction in serum iron levels. However, the hypoferremic response to LPS was slightly blunted in mice lacking IL-22, suggesting that, during LPS-mediated inflammation, IL-22 may play a minor role in mediating the hypoferremic response. These results may have implications for the treatment and management of the ACD.
Drak2 is not required for tumor surveillance and suppression
Authors: Edwards Benjamin A. , Harris Tarsha L. , Floersh Helen , Lukens John R. , Zaki Md. Hasan , Vogel Peter , Kanneganti Thirumala-Devi , Bui Jack D. , McGargill Maureen A. 
Published: January 2015

Abstract
Drak2 is a promising therapeutic target to treat organ-specific autoimmune diseases such as type 1 diabetes and multiple sclerosis without causing generalized immune suppression. Inhibition of Drak2 may also prevent graft rejection following organ transplantation. However, Drak2 may function as a critical tumor suppressor, which would challenge the prospect of targeting Drak2 for therapeutic treatment. Thus, we examined the susceptibility of Drak2−/− mice in several tumor models. We show that Drak2 is not required to prevent tumor formation in a variety of settings. Therefore, Drak2 does not function as an essential tumor suppressor in in vivo tumor models. These data further validate Drak2 as a viable therapeutic target to treat autoimmune disease and graft rejection. Importantly, these data also indicate that while Drak2 may induce apoptosis when overexpressed in cell lines, it is not an essential tumor suppressor.
Silver resistance in Gram-negative bacteria: a dissection of endogenous and exogenous mechanisms
Authors: Randall Christopher P. , Gupta Arya , Jackson Nicole , Busse David , O'Neill Alex J. 
Published: January 2015

Abstract

Objectives
To gain a more detailed understanding of endogenous (mutational) and exogenous (horizontally acquired) resistance to silver in Gram-negative pathogens, with an emphasis on clarifying the genetic bases for resistance.

Methods
A suite of microbiological and molecular genetic techniques was employed to select and characterize endogenous and exogenous silver resistance in several Gram-negative species.

Results
In Escherichia coli, endogenous resistance arose after 6 days of exposure to silver, a consequence of two point mutations that were both necessary and sufficient for the phenotype. These mutations, in ompR and cusS, respectively conferred loss of the OmpC/F porins and derepression of the CusCFBA efflux transporter, both phenotypic changes previously linked to reduced intracellular accumulation of silver. Exogenous resistance involved derepression of the SilCFBA efflux transporter as a consequence of mutation in silS, but was additionally contingent on expression of the periplasmic silver-sequestration protein SilE. Silver resistance could be selected at high frequency (&gt;10−9) from Enterobacteriaceae lacking OmpC/F porins or harbouring the sil operon and both endogenous and exogenous resistance were associated with modest fitness costs in vitro.

Conclusions
Both endogenous and exogenous silver resistance are dependent on the derepressed expression of closely related efflux transporters and are therefore mechanistically similar phenotypes. The ease with which silver resistance can become selected in some bacterial pathogens in vitro suggests that there would be benefit in improved surveillance for silver-resistant isolates in the clinic, along with greater control over use of silver-containing products, in order to best preserve the clinical utility of silver.
Multilayered genetic safeguards limit growth of microorganisms to defined environments
Authors: Gallagher Ryan R. , Patel Jaymin R. , Interiano Alexander L. , Rovner Alexis J. , Isaacs Farren J. 
Published: January 2015

Abstract
Genetically modified organisms (GMOs) are commonly used to produce valuable compounds in closed industrial systems. However, their emerging applications in open clinical or environmental settings require enhanced safety and security measures. Intrinsic biocontainment, the creation of bacterial hosts unable to survive in natural environments, remains a major unsolved biosafety problem. We developed a new biocontainment strategy containing overlapping ‘safeguards’—engineered riboregulators that tightly control expression of essential genes, and an engineered addiction module based on nucleases that cleaves the host genome—to restrict viability of Escherichia coli cells to media containing exogenously supplied synthetic small molecules. These multilayered safeguards maintain robust growth in permissive conditions, eliminate persistence and limit escape frequencies to &lt;1.3 × 10−12. The staged approach to safeguard implementation revealed mechanisms of escape and enabled strategies to overcome them. Our safeguarding strategy is modular and employs conserved mechanisms that could be extended to clinically or industrially relevant organisms and undomesticated species.
Postoperative Opioid-induced Respiratory Depression
Authors: Lee Lorri A. , Caplan Robert A. , Stephens Linda S. , Posner Karen L. , Terman Gregory W. , Voepel-Lewis Terri , Domino Karen B. 
Published: January 2015

AbstractAbstract
In a review of 357 acute pain claims from the Anesthesia Closed Claims Project database, 92 cases involved likely opioid-related respiratory depression. The vast majority of these injuries occurred within 24 h of surgery, and 97% were judged as preventable with better monitoring and response.

Background:
Postoperative opioid-induced respiratory depression (RD) is a significant cause of death and brain damage in the perioperative period. The authors examined anesthesia closed malpractice claims associated with RD to determine whether patterns of injuries could guide preventative strategies.

Methods:
From the Anesthesia Closed Claims Project database of 9,799 claims, three authors reviewed 357 acute pain claims that occurred between 1990 and 2009 for the likelihood of RD using literature-based criteria. Previously cited patient risk factors for RD, clinical management, nursing assessments, and timing of events were abstracted from claim narratives to identify recurrent patterns.

Results:
RD was judged as possible, probable, or definite in 92 claims (κ = 0.690) of which 77% resulted in severe brain damage or death. The vast majority of RD events (88%) occurred within 24 h of surgery, and 97% were judged as preventable with better monitoring and response. Contributing and potentially actionable factors included multiple prescribers (33%), concurrent administration of nonopioid sedating medications (34%), and inadequate nursing assessments or response (31%). The time between the last nursing check and the discovery of a patient with RD was within 2 h in 42% and within 15 min in 16% of claims. Somnolence was noted in 62% of patients before the event.

Conclusions:
This claims review supports a growing consensus that opioid-related adverse events are multifactorial and potentially preventable with improvements in assessment of sedation level, monitoring of oxygenation and ventilation, and early response and intervention, particularly within the first 24 h postoperatively.
Up-regulation of MicroRNA-21 Mediates Isoflurane-induced Protection of Cardiomyocytes
Authors: Olson Jessica M. , Yan Yasheng , Bai Xiaowen , Ge Zhi-Dong , Liang Mingyu , Kriegel Alison J. , Twaroski Danielle M. , Bosnjak Zeljko J. 
Published: January 2015

AbstractAbstract
Isoflurane directly affects microRNA expression profiles in cardiomyocytes and that miR-21 is acting to protect cardiomyocytes after isoflurane exposure, most likely through its actions on programmed cell death protein 4.
Supplemental Digital Content is available in the text.

Background:
Anesthetic cardioprotection reduces myocardial infarct size after ischemia–reperfusion injury. Currently, the role of microRNA in this process remains unknown. MicroRNAs are short, noncoding nucleotide sequences that negatively regulate gene expression through degradation or suppression of messenger RNA. In this study, the authors uncovered the functional role of microRNA-21 (miR-21) up-regulation after anesthetic exposure.

Methods:
MicroRNA and messenger RNA expression changes were analyzed by quantitative real-time polymerase chain reaction in cardiomyocytes after exposure to isoflurane. Lactate dehydrogenase release assay and propidium iodide staining were conducted after inhibition of miR-21. miR-21 target expression was analyzed by Western blot. The functional role of miR-21 was confirmed in vivo in both wild-type and miR-21 knockout mice.

Results:
Isoflurane induces an acute up-regulation of miR-21 in both in vivo and in vitro rat models (n = 6, 247.8 ± 27.5% and 258.5 ± 9.0%), which mediates protection to cardiomyocytes through down-regulation of programmed cell death protein 4 messenger RNA (n = 3, 82.0 ± 4.9% of control group). This protective effect was confirmed by knockdown of miR-21 and programmed cell death protein 4 in vitro. In addition, the protective effect of isoflurane was abolished in miR-21 knockout mice in vivo, with no significant decrease in infarct size compared with nonexposed controls (n = 8, 62.3 ± 4.6% and 56.2 ± 3.2%).

Conclusions:
The authors demonstrate for the first time that isoflurane mediates protection of cardiomyocytes against oxidative stress via an miR-21/programmed cell death protein 4 pathway. These results reveal a novel mechanism by which the damage done by ischemia/reperfusion injury may be decreased.
Effects of Acute Respiratory and Metabolic Acidosis on Diaphragm Muscle Obtained from Rats
Authors: Michelet Pierre , Carreira Serge , Demoule Alexandre , Amour Julien , Langeron Olivier , Riou Bruno , Coirault Catherine 
Published: January 2015

AbstractAbstract
Diaphragm strips were exposed to a pH of 7.0 using carbon dioxide or strips exposed to low bicarbonate and both compared with strips exposed to a pH of 7.4. The strips exposed to high carbon dioxide had impairment in contraction and even more impairment in relaxation–contraction coupling. In contrast, diaphragmatic strips exposed to lower bicarbonate had no significant differences in diaphragmatic contraction, relaxation, or contraction–relaxation coupling.

Background:
Acute respiratory acidosis is associated with alterations in diaphragm performance. The authors compared the effects of respiratory acidosis and metabolic acidosis in the rat diaphragm in vitro.

Methods:
Diaphragmatic strips were stimulated in vitro, and mechanical and energetic variables were measured, cross-bridge kinetics calculated, and the effects of fatigue evaluated. An extracellular pH of 7.00 was obtained by increasing carbon dioxide tension (from 25 to 104 mmHg) in the respiratory acidosis group (n = 12) or lowering bicarbonate concentration (from 24.5 to 5.5 mM) in the metabolic acidosis group (n = 12) and the results compared with a control group (n = 12, pH = 7.40) after 20-min exposure.

Results:
Respiratory acidosis induced a significant decrease in maximum shortening velocity (−33%, P < 0.001), active isometric force (−36%, P < 0.001), and peak power output (−59%, P < 0.001), slowed relaxation, and decreased the number of cross-bridges (−35%, P < 0.001) but not the force per cross-bridge, and impaired recovery from fatigue. Respiratory acidosis impaired more relaxation than contraction, as shown by impairment in contraction–relaxation coupling under isotonic (−26%, P < 0.001) or isometric (−44%, P < 0.001) conditions. In contrast, no significant differences in diaphragmatic contraction, relaxation, or contraction–relaxation coupling were observed in the metabolic acidosis group.

Conclusions:
In rat diaphragm, acute (20 min) respiratory acidosis induced a marked decrease in the diaphragm contractility, which was not observed in metabolic acidosis.
Feasibility of Closed-loop Titration of Propofol and Remifentanil Guided by the Bispectral Monitor in Pediatric and Adolescent Patients
Authors: Orliaguet Gilles A. , Benabbes Lambert Fatema , Chazot Thierry , Glasman Pauline , Fischler Marc , Liu Ngai 
Published: January 2015

AbstractAbstract
Bispectral index–guided automated control of propofol hypnosis and remifentanil analgesia is feasible and maintains bispectral index in the range of 40 to 60 in 6- to 16-yr-old old patients better than skilled manual control. Propofol consumption during maintenance of anesthesia was similar in the two groups, but remifentanil consumption was higher in the automated control group.

Background:
This study was designed to assess the feasibility of dual closed-loop titration of propofol and remifentanil guided solely by the Bispectral Index (BIS) monitor in pediatric and adolescent patients during anesthesia.

Methods:
Children undergoing elective surgery in this single-blind randomized study were allocated into the closed-loop (auto) or manual (manual) group. Primary outcome was the percentage of time with the BIS in the range 40 to 60 (BIS40–60). Secondary outcomes were the percentage of deep (BIS<40) anesthesia and drug consumption. Data are presented as median (interquartile range) or number (%).

Results:
Twenty-three patients (12 [10 to 14] yr) were assigned to the auto group and 19 (14 [7 to 14] yr) to the manual group. The closed-loop controller was able to provide induction and maintenance for all patients. The percentage of time with BIS40–60 was greater in the auto group (87% [75 to 96] vs. 72% [48 to 79]; P = 0.002), with a decrease in the percentage of BIS<40 (7% [2 to 17] vs. 21% [11 to 38]; P = 0.002). Propofol (2.4 [1.9 to 3.3] vs. 1.7 [1.2 to 2.8] mg/kg) and remifentanil (2.3 [2.0 to 3.0] vs. 2.5 [1.2 to 4.3] μg/kg) consumptions were similar in auto versus manual groups during induction, respectively. During maintenance, propofol consumption (8.2 [6.0 to 10.2] vs. 7.9 [7.2 to 9.1] mg kg−1 h−1; P = 0.89) was similar between the two groups, but remifentanil consumption was greater in the auto group (0.39 [0.22 to 0.60] vs. 0.22 [0.17 to 0.32] μg kg−1 min−1; P = 0.003). Perioperative adverse events and length of stay in the postanesthesia care unit were similar.

Conclusion:
Intraoperative automated control of hypnosis and analgesia guided by the BIS is clinically feasible in pediatric and adolescent patients and outperformed skilled manual control.