bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic correlations, fluctuation-dissipation relations, and effective temperatures after a quantum quench of the transverse field Ising chain
Authors: Foini Laura , Cugliandolo Leticia F , Gambassi Andrea 
Published: September 2012

Abstract
Fluctuation-dissipation relations, i.e., the relation between two-time correlation and linear response functions, were successfully used to search for signs of equilibration and to identify effective temperatures in the non-equilibrium behavior of a number of macroscopic classical and quantum systems in contact with thermal baths. Among the most relevant cases in which the effective temperatures thus defined were shown to have a thermodynamic meaning one finds the stationary dynamics of driven super-cooled liquids and vortex glasses, and the relaxation of glasses. Whether and under which conditions an effective thermal behavior can be found in quantum isolated many-body systems after a global quench is a question of current interest. We propose to study the possible emergence of thermal behavior long after the quench by studying fluctuation-dissipation relations in which (possibly time- or frequency-dependent) parameters replace the equilibrium temperature. If thermalization within the Gibbs ensemble eventually occurs these parameters should be constant and equal for all pairs of observables in ‘partial’ or ‘mutual’ equilibrium. We analyze these relations in the paradigmatic quantum system, i.e., the quantum Ising chain, in the stationary regime after a quench of the transverse field. The lack of thermalization to a Gibbs ensemble becomes apparent within this approach.
Generalized analyticity on the 𝑁-torus
Authors: Shapiro Victor 
Published: September 2012

In dimension

N
=
2
,

N=2,

let

v
v

be a unit vector of irrational slope. With

T

2

T_{2}

the 2-torus, say

f
∈

A

v

+

f\in \mathcal {A}_{v}^{+}

if

f
∈

L

1

(

T

2

)

f\in L^{1}(\mathbf {T}_{2})

and

m
⋅
v
>
0

m\cdot v>0

⇒

f
^

(
m
)

=
0

\Rightarrow \widehat {f}\left (m\right ) =0

for

m
m

an integral lattice point. Let

G

v

G_{v}

be the one-parameter group generated by

v
v

on

T

2

,

T_{2},

and let

E
⊂

G

v

E\subset G_{v}

be a closed and bounded set. Call

E
E

a set of uniqueness for

A

v

+

∩
C

(

T

2

)

\mathcal {A}_{v}^{+}\cap C\left (T_{2}\right )

if

f
∈

A

v

+

∩
C

(

T

2

)

f\in \mathcal {A}_{v}^{+}\cap C\left (T_{2}\right )

and if

f

(
x
)

=
0

\ f\left (x\right ) =0

for

x
∈
E

x\in E

implies

f
≡
0

f\equiv 0

on

T

2

.

T_{2}.

The following result is established

:
:

A necessary and sufficient condition that E be a set of uniqueness for

A

v

+

∩
C

(

T

2

)

\mathcal {A} _{v}^{+}\cap C\left (T_{2}\right )

is that E is a set of positive linear measure.
SGNS2: a compartmentalized stochastic chemical kinetics simulator for dynamic cell populations
Authors: Lloyd-Price Jason , Gupta Abhishekh , Ribeiro Andre S. 
Published: September 2012

Abstract
Motivation: Cell growth and division affect the kinetics of internal cellular processes and the phenotype diversity of cell populations. Since the effects are complex, e.g. different cellular components are partitioned differently in cell division, to account for them in silico, one needs to simulate these processes in great detail.
Results: We present SGNS2, a simulator of chemical reaction systems according to the Stochastic Simulation Algorithm with multi-delayed reactions within hierarchical, interlinked compartments which can be created, destroyed and divided at runtime. In division, molecules are randomly segregated into the daughter cells following a specified distribution corresponding to one of several partitioning schemes, applicable on a per-molecule-type basis. We exemplify its use with six models including a stochastic model of the disposal mechanism of unwanted protein aggregates in Escherichia coli, a model of phenotypic diversity in populations with different levels of synchrony, a model of a bacteriophage’s infection of a cell population and a model of prokaryotic gene expression at the nucleotide and codon levels.
Availability: SGNS2, instructions and examples available at www.cs.tut.fi/~lloydpri/sgns2/ (open source under New BSD license).
Contact: jason.lloyd-price@tut.fi
Supplementary information: Supplementary data are available at Bioinformatics online.
Evaluating health systems strengthening interventions in low-income and middle-income countries: are we asking the right questions?
Authors: Adam Taghreed , Hsu Justine , de Savigny Don , Lavis John N , Røttingen John-Arne , Bennett Sara 
Published: September 2012

Abstract
In recent years, there have been several calls for rigorous health policy and systems research to inform efforts to strengthen health systems (HS) in low- and middle-income countries (LMICs), including the use of systems thinking concepts in designing and evaluating HS strengthening interventions. The objectives of this paper are to assess recent evaluations of HS strengthening interventions to examine the extent to which they ask a broader set of questions, and provide an appropriately comprehensive assessment of the effects of these interventions across the health system. A review of evaluations conducted in 2009–10 was performed to answer these questions.
Out of 106 evaluations, less than half (43%) asked broad research questions to allow for a comprehensive assessment of the intervention’s effects across multiple HS building blocks. Only half of the evaluations referred to a conceptual framework to guide their impact assessment. Overall, 24% and 9% conducted process and context evaluations, respectively, to answer the question of whether the intervention worked as intended, and if so, for whom, and under what circumstances. Almost half of the evaluations considered HS impact on one building block, while most interventions were complex targeting two or more building blocks. None incorporated evaluation designs that took into account the characteristics of complex adaptive systems such as non-linearity of effects or interactions between the HS building blocks.
While we do not argue that all evaluations should be comprehensive, there is a need for more comprehensive evaluations of the wider range of the intervention’s effects, when appropriate. Our findings suggest that the full range of barriers to more comprehensive evaluations need to be examined and, where appropriate, addressed. Possible barriers may include limited capacity, lack of funding, inadequate time frames, lack of demand from both researchers and research funders, or difficulties in undertaking this type of evaluation.
First Report of the Root-Knot Nematode Meloidogyne artiellia in Belgium
Authors: Damme N. , Waeyenberge L. , Viaene N. , van Hoenselaar T. , Karssen G. 
Published: September 2012

In 2011, second-stage juveniles (J2) of an unknown root-knot nematode (Meloidogyne spp.) were detected during a routine survey for root-knot nematodes on arable land in Harveng, Belgium, after a crop of wheat. Most of the loamy soil samples (36 out of 42) contained J2 of the common root-knot nematode M. naasi Franklin, 1965 (1), while 15 of these also contained the unknown species, albeit in lower densities (22 J2/100 ml vs. 157 J2/100 ml soil). After detailed morphological observation of the unknown J2, they were until further notice identified as Meloidogyne artiellia Franklin, 1961 (2), the British root-knot nematode. To confirm the identification, a pure culture of M. artiellia was established by adding nematode suspensions to pots planted with kale (Brassica oleracea var. laciniata), a non-host for M. naasi (3). After 2 months, Meloidogyne spp. females, males, and J2 were isolated from galled kale roots. Morphological characteristics (n = 25) from the perineal pattern (rounded with fine striae, lateral area with coarse ridges, angular dorsal arch) and stylet knobs (small, ovoid, and backwardly sloping) for the females, the head shape (set off with distinct head cap) and stylet knobs (small, ovoid and backwardly sloping) for the males, the hemizonid position (anterior, adjacent to S to E pore), tail shape (conical), and short tail length (18 to 27 μm) for the J2, fit with previous observed populations of M. artiellia (3). Young egg-laying females were used for isozyme electrophoresis, and showed typical malate dehydrogenase (N1b) and esterase (M2-VF1) patterns (3). Additionally, DNA was extracted from single juveniles by incubating them in a lysis buffer (200 mM NaCl, 200 mM Tris-HCl (pH 8), 1% β-mercaptoethanol and 800 μg/ml Proteinase K) during 1.5 h at 65°C and 5 min at 99°C in a thermocycler. One microliter of crude DNA extract was used for PCR. ITS-rDNA sequencing (GenBank Accession Numbers JX393299 and JX393300) confirmed the identity, showing a 98 to 100% homology with other M. artiellia sequences (AY150368 and AF248478). To our knowledge, this is the first report of the root-knot nematode, M. artiellia, in Belgium. This nematode has been reported from the Mediterranean area, where it causes damage on chickpea and wheat (4), as well as from the U.K. Its finding in Harveng, close to the French border, suggests a more extensive geographical distribution. References: (1) M. T. Franklin. Nematologica 11:79, 1965. (2) M. T. Franklin et al. Suppl.:85, 1961. (3) G. Karssen. Pages 93-97 in: The Plant-Parasitic Nematode Genus Meloidogyne Göldi, 1892 (Tylenchida) in Europe, Brill Leiden, The Netherlands, 2002. (4) M. Di Vito and N. Greco. Revue Nématol. 11:223, 1988.
Recession and job satisfaction of Indian information technology professionals
Authors: Menon Praseeda , Thingujam Nutankumar S. 
Published: September 2012

PurposeThe purpose of this paper is to replicate the dispositional source of job satisfaction (JS) in a different cultural setting on the backdrop of the recession of 2008‐2009 and to investigate the specific subjective job‐related aspects that influenced Indian IT professionals' overall evaluation of JS.Design/methodology/approachData were collected from 221 IT employees. Pearson's correlation, partial correlation and stepwise regression analyses were used to test hypotheses.FindingsApart from confirming the dispositional source of JS, satisfaction with nature of work, as well as relations with one's supervisor, emerged as the most important situational contributors over and above that of personality factors during recession in the Indian IT sector.Practical implicationsAs the personality factors of Neuroticism, Extraversion and Agreeableness showed a key role in JS of Indian software employees in adverse conditions, selection and recruitment of IT personnel should lay emphasis on these factors. Also, paying attention to making the nature of work more satisfying, as well as promoting positive relationships between team members and leaders could serve as a buffer during economic downturns in maintaining the JS of Indian IT employees.Originality/valueAlthough previous studies have looked at how personality plays an essential role in JS, they have hardly looked at the person‐situation interaction with respect to type of industry and status of economy. The paper reveals that specific personality and job factors can matter more in a certain type of industry, particularly during a rough economic patch.
Novel cooperation between CX3CL1 and CCL26 inducing NK cell chemotaxis via CX3CR1: a possible mechanism for NK cell infiltration of the allergic nasal tissue
Authors: El‐Shazly A. E. , Doloriert H. C. , Bisig B. , Lefebvre P. P. , Delvenne P. , Jacobs N. 
Published: September 2012

SummaryBackgroundRecent data indicated that natural killer (NK) cells and chemokines could play a pivotal role in nasal inflammation. CX3CR1, the only receptor for fractalkine/CX3CL1, is abundantly expressed by NK cells, and was recently shown to also be a receptor for eotaxin‐3/CCL26. However, no reports explored the NK cells‐CX3CL1‐CCL26 axis via CX3CR1 in allergy.ObjectiveOur goals were first to determine specifically NK cell recruitment pattern in nasal tissue of allergic chronic rhinosinusitis (ACRS) and non‐allergic chronic rhinosinusitis (NACRS) patients in comparison with healthy controls, and secondly, to investigate the function of CX3CR1 in NK cell migration.MethodsImmunohistochemistry, microchemotaxis chambers, flow cytometry and confocal microscopy were used in this study.ResultsHerein, we showed that NK cells infiltrated the epithelial layers of nasal tissue only in ACRS patients and not in NACRS patients or controls. NK cells were also more numerous in the stroma of the nasal tissue from ACRS patients compared with NACRS patients or controls. This migration could be mediated by both CX3CL1 and CCL26, as these two chemokines induced NK cell migration. Moreover, both molecules also stimulated cytoskeleton changes and F‐actin reorganisation in NK cells. Chemotaxis and cytoskeleton changes were sensitive to genistein, a tyrosine kinase inhibitor. By flow cytometry, we demonstrated that a single antigen nasal provocation challenge increased the expression of CX3CR1 on NK cells in allergic rhinitis (AR) patients. The function of this receptor was associated with a significant augmentation of NK cell chemotaxis against the optimal doses of CX3CL1 and CCL26.Conclusions and Clinical RelevanceOur results highlight a novel role for CX3CR1 in NK cell migration that may contribute to the NK cell trafficking to the allergic upper airway. This could be mediated largely by CX3CL1 and CCL26 stimulation of the tyrosine kinase pathway.
Peamaclein – A new peach allergenic protein: similarities, differences and misleading features compared to Pru p 3
Authors: Tuppo L. , Alessandri C. , Pomponi D. , Picone D. , Tamburrini M. , Ferrara R. , Petriccione M. , Mangone I. , Palazzo P. , Liso M. , Giangrieco I. , Crescenzo R. , Bernardi M. L. , Zennaro D. , Helmer‐Citterich M. , Mari A. , Ciardiello M. A. 
Published: September 2012

SummaryBackgroundAmong the peach‐derived allergens which are already known, the lipid transfer protein (Pru p 3) seems to be the one to exert severe allergic reactions.ObjectiveTo identify and characterize a new peach allergen causing a clinical picture similar to that of Pru p 3.MethodsPatients were selected on the basis of their severe clinical reactivity and negative results to a panel of peach allergens available on the ISAC103 microarray. Several in‐house and commercial preparations were compared. Several methods were used to characterize the newly identified molecule. Specific IgE and inhibition assays were performed using the Allergen micro‐Beads Array (ABA) assay.ResultsNegative ISAC results to Pru p 3 were confirmed by additional testing in contrast with the positive results obtained by commercial Pru p 3‐enriched peach peel extracts. The analyses of one of these preparations led to the identification of Peamaclein, a new allergenic protein. It is a small, basic, cysteine‐rich, heat‐stable, digestion‐resistant protein, homologous to a potato antimicrobial peptide. Peamaclein was able to trigger positive skin test reactions and to bind IgE in the ABA assay. It displays an electrophoretic mobility and chromatographic behaviour similar to that of Pru p 3; therefore, it can be hidden in Pru p 3 preparations. In fact, Pru p 3‐enriched peach peel extracts were found to contain both Pru p 3 and Peamaclein by means of comparative in vivo testing, and by biochemical and immunochemical assays. Commercially available anti‐Pru p 3 polyclonal antibodies were found to have a double specificity for the two molecules.Conclusions and Clinical RelevanceA new allergen from peach belonging to a new family of allergenic proteins has been identified and characterized. This knowledge on Peamaclein will improve our understanding on the clinical aspects of the peach allergy and the quality of diagnostic reagents.
Downregulation of miR‐101 in gastric cancer correlates with cyclooxygenase‐2 overexpression and tumor growth
Authors: He Xiao‐Pu , Shao Yun , Li Xiao‐Lin , Xu Wei , Chen Guo‐Sheng , Sun Huan‐Huan , Xu Hai‐Chen , Xu Xian , Tang Dan , Zheng Xi‐Feng , Xue Yi‐Ping , Huang Guo‐Chang , Sun Wei‐Hao 
Published: September 2012

Cyclooxygenase‐2 (COX‐2) plays an important role in the carcinogenesis and progression of gastric cancer. It has been demonstrated that COX‐2 overexpression depends on different cellular pathways, involving both transcriptional and post‐transcriptional regulation. MicroRNAs (miRNAs) are small, noncoding RNAs that function as post‐transcriptional regulators. Here, we characterize miR‐101 expression and its role in the regulation of COX‐2 expression, which in turn, will provide us with additional insights into the potential therapeutic benefits of exogenous miR‐101 for treatment of gastric cancer. Our results showed that miR‐101 levels in gastric cancer tissues were significantly lower than those in the matched normal tissue (P < 0.01). Furthermore, lower levels of miR‐101 were associated with increased tumor invasion and lymph node metastasis (P < 0.05). We also found an inverse correlation between miR‐101 and COX‐2 expression in both gastric cancer specimens and cell lines. Significant decreases in COX‐2 mRNA and COX‐2 levels were observed in the pre‐miR‐101‐infected gastric cancer cells. One possible mechanism of interaction is that miR‐101 inhibited COX‐2 expression by directly binding to the 3′‐UTR of COX‐2 mRNA. Overexpression of miR‐101 in gastric cancer cell lines also inhibited cell proliferation and induced apoptosis in vitro, as well as inhibiting tumor growth in vivo. These results collectively indicate that miR‐101 may function as a tumor suppressor in gastric cancer, with COX‐2 as a direct target.
Accumulation of squalene is associated with the clustering of lipid droplets
Authors: Ta Minh T. , Kapterian Tamar S. , Fei Weihua , Du Ximing , Brown Andrew J. , Dawes Ian W. , Yang Hongyuan 
Published: September 2012

The isoprenoid squalene is an important precursor for the biosynthesis of sterols. The cellular storage of squalene and its impact on membrane properties have been the subject of recent investigations. In a screen for abnormal lipid droplet morphology and distribution in the yeast Saccharomyces cerevisiae, we found significant lipid droplet clustering (arbitrarily defined as an aggregation of six or more lipid droplets) in a number of mutants (e.g. erg1) that are defective in sterol biosynthesis. Interestingly, these mutants are also characterized by accumulation of large amounts of squalene. Reducing the level of squalene in these mutants restored normal lipid droplet distribution. Moreover, inhibition of squalene monooxygenase in two mammalian cell lines (CHO‐K1 and 3T3‐L1) by terbinafine also resulted in lipid droplet clustering. These results indicate that the level of squalene may affect the growth and distribution of lipid droplets.
Emerging aquatic insects as predators in terrestrial systems across a gradient of stream temperature in North and South America
Authors: WESNER JEFF S. 
Published: September 2012

Summary1. Empirical and theoretical research over the past decade has demonstrated the widespread importance of aquatic subsidies to terrestrial food webs. In particular, adult aquatic insects that emerge from streams and lakes are prey for terrestrial predators. While variation in the magnitude of this subsidy is clearly important, the potential top‐down effects of the predatory adults of some aquatic insects in terrestrial food webs are largely unknown.2. I used published data on benthic insect density (as a proxy for emergence) in North and South America to explore how the proportion of benthic insects that are predatory as adults varies across a gradient of mean annual stream temperature.3. The proportion of benthic insects that are predatory as adults varied widely across sites (0–12% by abundance; 0–86% by biomass). There was a positive relationship between mean annual stream temperature and the proportion of predatory adults across all sites, driven largely by the greater abundance/biomass of predatory taxa (e.g. odonates), relative to non‐predators (e.g. midges, mayflies, caddisflies), in tropical than in temperate streams.4. The ‘trophic structure’ (i.e. the proportion of predators) of emerging adult aquatic insects is an understudied source of variation in aquatic–terrestrial interactions. Incorporation of trophic structure in future studies is needed to understand how future modification of fresh waters may affect adjacent terrestrial food webs through both bottom‐up and top‐down effects.
Pharmacokinetics of 450 mg ropivacaine with and without epinephrine for combined femoral and sciatic nerve block in lower extremity surgery. A pilot study
Authors: Schoenmakers Karin P. W. , Vree Tom B. , Jack Nigel T. M. , van den Bemt Bart , van Limbeek Jacques , Stienstra Rudolf 
Published: September 2012

AimsNo pharmacokinetic data exist on doses of ropivacaine larger than 300 mg for peripheral nerve block in man, although in clinical practice higher doses are frequently used. The purpose of the present study was to describe the pharmacokinetic profile in serum of 450 mg ropivacaine with and without epinephrine in patients undergoing anterior cruciate ligament reconstruction.MethodsTwelve patients were randomly allocated to receive a single shot combined sciatic/femoral nerve block with 60 ml of either ropivacaine 0.75% alone (group R, n = 6) or ropivacaine 0.75% plus epinephrine 5 μg ml−1 (group RE, n = 6). Venous blood samples for total and free ropivacaine serum concentrations were obtained during 48 h following block placement. Pharmacokinetic parameters were calculated using a non‐compartmental approach.ResultsResults are given as mean (SD) for group R vs. group RE (95% CI of the difference). Total Cmax was 2.81 (0.94) μg ml−1 vs. 2.16 (0.21) μg ml−1 (95% CI −0.23, 1.53). tmax was 1.17 (0.30) h vs. 1.67 (0.94) h (95% CI −1.40, 0.40). The highest free ropivacaine concentration per patient was 0.16 (0.08) μg ml−1 vs. 0.12 (0.04) μg ml−1 (95% CI −0.04, 0.12). t1/2 was 6.82 (2.26) h vs. 5.48 (1.69) h (95% CI −1.23, 3.91). AUC was 28.35 (5.92) μg ml−1 h vs. 29.12 (7.34) μg ml−1 h (95% CI −9.35, 7.81).ConclusionsFree serum concentrations of ropivacaine with and without epinephrine remained well below the assumed threshold of 0.56 μg ml−1 for systemic toxicity. Changes in pharmacokinetics with epinephrine co‐administration did not reach statistical significance.
Decreased levels of serum complement C3 and natural killer cells add to the predictive value of total immunoglobulin G for severe infection in heart transplant recipients
Authors: Sarmiento E. , del Pozo N. , Gallego A. , Fernández‐Yañez J. , Palomo J. , Villa A. , Ruiz M. , Muñoz P. , Rodríguez C. , Rodríguez‐Molina J. , Navarro J. , Kotsch K. , Fernandez‐Cruz E. , Carbone J. 
Published: September 2012

AbstractBackgroundInfection remains a source of mortality in heart recipients. We previously reported that post‐transplant immunoglobulin G (IgG) quantification can help identify the risk for infection. We assessed whether other standardized parameters of humoral and cellular immunity could prove useful when identifying patients at risk of infection.MethodsWe prospectively studied 133 heart recipients over a 12‐month period. Forty‐eight patients had at least one episode of severe infection. An event was defined as an infection requiring intravenous antimicrobial therapy.ResultsCox regression analysis revealed an association between the risk of developing infection and the following: lower IgG2 subclass levels (day 7: relative hazard [RH] 1.71; day 30: RH 1.76), lower IgA levels (day 7: RH 1.61; day 30: RH 1.91), lower complement C3 values (day 7: RH 1.25), lower CD3 absolute counts (day 30: RH 1.10), lower absolute natural killer [NK] cell count (day 7: RH 1.24), and lower IgG concentrations (day 7: RH 1.31; day 30: RH 1.36). Cox regression bivariate analysis revealed that lower day 7 C3 levels, IgG2 concentration, and absolute NK cell count remained significant after adjustment for total IgG levels.ConclusionsData suggest that early immune monitoring including C3, IgG2, and NK cell testing in addition to IgG concentrations is useful when attempting to identify the risk of infection in heart transplant recipients.