bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversification of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution
Authors: Oh Phaik Lyn , Benson Andrew K , Peterson Daniel A , Patil Prabhu B , Moriyama Etsuko N , Roos Stefan , Walter Jens 
Published: November 2009

Abstract
The vertebrate digestive tract, including that of humans, is the habitat to trillions of bacteria that are of significant importance to host biology and health. Although these communities are often postulated to have coevolved with their hosts, evidence is lacking, yet critical for our understanding of microbial symbiosis in vertebrates. To gain insight into the evolution of a gut symbiont, we have characterized the population genetic structure and phylogeny of Lactobacillus reuteri strains isolated from six different host species (human, mouse, rat, pig, chicken and turkey) using Amplified-Fragment Length Polymorphism (AFLP) and Multi-Locus Sequence Analysis (MLSA). The results revealed considerable genetic heterogeneity within the L. reuteri population and distinct monophyletic clades reflecting host origin but not provenance. The evolutionary patterns detected indicate a long-term association of L. reuteri lineages with particular vertebrate species and host-driven diversification. Results from a competition experiment in a gnotobiotic mouse model revealed that rodent isolates showed elevated ecological performance, indicating that evolution of L. reuteri lineages was adaptive. These findings provide evidence that some vertebrate gut microbes are not promiscuous, but have diversified into host-adapted lineages by a long-term evolutionary process, allowing the development of a highly specialized symbiosis.
Gut wall bacteria of earthworms: a natural selection process
Authors: Thakuria Dwipendra , Schmidt Olaf , Finan Dillon , Egan Damian , Doohan Fiona M 
Published: November 2009

Abstract
Earthworms and microorganisms are interdependent and their interactions regulate the biogeochemistry of terrestrial soils. Investigating earthworm–microorganism interactions, we tested the hypothesis that differences in burrowing and feeding habits of anecic and endogeic earthworms are reflected by the existence of ecological group-specific gut wall bacterial communities. Bacterial community was detected using automated ribosomal intergenic spacer analysis of 16S and 23S genes and ribotype data was used to assess diversity and community composition. Using soil and earthworm samples collected from adjacent wheat–barley and grass–clover fields, we found that the anecic Lumbricus terrestris and L. friendi, the endogeic Aporrectodea caliginosa and A. longa (classically defined as anecic, but now known to possess endogeic characteristics) contain ecological group-specific gut wall-associated bacterial communities. The abundance of specific gut wall-associated bacteria (identified by sequence analysis of ribotype bands), including Proteobacteria, Firmicutes and an actinobacterium, was ecological group dependent. A microcosm study, conducted using A. caliginosa and L. terrestris and five different feeding regimes, indicated that food resource can cause shifts in gut wall-associated bacterial community, but the magnitude of these shifts did not obscure the delineation between ecological group specificity. Using A. caliginosa and A. longa samples collected in six different arable fields, we deduced that, within an ecological group, habitat was a more important determinant of gut wall-associated bacterial community composition than was host species. Hence, we conclude that the selection of bacteria associated with the gut wall of earthworms is a natural selection process and the strongest determinant of this process is in the order ecological group&gt;habitat&gt;species.
Rapid dendritic and axonal responses to neuronal insults
Authors: Mizielinska Sarah M. , Greenwood Sam M. , Tummala Hemanth , Connolly Christopher N. 
Published: November 2009

Glutamate is the major excitatory neurotransmitter in the mammalian central nervous system playing critical roles in basal synaptic transmission and mechanisms of learning and memory. Under normal conditions, glutamate is sequestered within synaptic vesicles (~100 mM) with extracellular glutamate concentrations being limited (&lt;1 μM), via retrieval by plasma-membrane transporters on neuronal and glial cells. In the case of central nervous system trauma, stroke, epilepsy, and in certain neurodegenerative diseases, increased concentrations of extracellular glutamate (by vesicular release, cell lysis and/or decreased glutamate transporter uptake/reversal) stimulate the overactivation of local ionotropic glutamate receptors that trigger neuronal cell death (excitotoxicity). Other natural agonists, such as domoic acid, alcohol and auto-antibodies, have also been reported to induce excitotoxicity.
Arms and Letters: Julius Caesar, theCommentariesof Pope Pius II, and the Politicization of Papal Imagery*
Authors: O'Brien Emily 
Published: November 2009

AbstractIn their title, theCommentariesof Pope Pius II recall the works of Julius Caesar by the same name. The connections between these ancient and humanist histories, however, run much deeper. This article explores this relationship in detail and in the broader historical and historiographical contexts of fifteenth-century Italy. It argues that in both Caesar's histories and in his career more generally, Pius found much that resonated with his own experiences, challenges, and goals. More importantly, he found in these ancientCommentariesvaluable apologetic strategies for constructing his own textual self-portrait as both pope and prince. In choosing Caesar's histories as his models, Pius was following a recent historiographical precedent. Several Italian Renaissance humanists had also turned to Caesar's works as guides for writing histories about leaders of contemporary temporal politics. This article argues that by adopting the same models when shaping his own image, Pius was effectively politicizing his self-portrait in hisCommentaries.
(e, 2e) triple differential cross sections of Ca atoms at low energies
Authors: Purohit G , Patidar Vinod , Sud K K 
Published: November 2009

Recently, several theoretical studies (Hitawala et al 2008 J. Phys. B: At. Mol. Opt. Phys.
41 035205; Khajuria and Deshmukh 2008 Phys. Rev. A 78 024702; Chauhan et al 2005 Phys. Rev. A 71 032708) have been reported to analyze the measurements of triple differential cross section (TDCS) for (e, 2e) processes on Ca (4s2) atom in coplanar geometry (Murray 2005 Phys. Rev. A 72 062711). In this paper, the (e, 2e) TDCS of the Ca atom has been revisited with the inclusion of correlation-polarization potential and post-collision interaction in the distorted wave Born approximation formalism. We note that the present attempt significantly improves the understanding of (e, 2e) processes at low energies on Ca atom. Still there are several discrepancies between the experimental and theoretical results that require more theoretical attempts to explain them properly.
SCAN: SNP and copy number annotation
Authors: Gamazon Eric R. , Zhang Wei , Konkashbaev Anuar , Duan Shiwei , Kistner Emily O. , Nicolae Dan L. , Dolan M. Eileen , Cox Nancy J. 
Published: November 2009

Abstract
Motivation: Genome-wide association studies (GWAS) generate relationships between hundreds of thousands of single nucleotide polymorphisms (SNPs) and complex phenotypes. The contribution of the traditionally overlooked copy number variations (CNVs) to complex traits is also being actively studied. To facilitate the interpretation of the data and the designing of follow-up experimental validations, we have developed a database that enables the sensible prioritization of these variants by combining several approaches, involving not only publicly available physical and functional annotations but also multilocus linkage disequilibrium (LD) annotations as well as annotations of expression quantitative trait loci (eQTLs).
Results: For each SNP, the SCAN database provides: (i) summary information from eQTL mapping of HapMap SNPs to gene expression (evaluated by the Affymetrix exon array) in the full set of HapMap CEU (Caucasians from UT, USA) and YRI (Yoruba people from Ibadan, Nigeria) samples; (ii) LD information, in the case of a HapMap SNP, including what genes have variation in strong LD (pairwise or multilocus LD) with the variant and how well the SNP is covered by different high-throughput platforms; (iii) summary information available from public databases (e.g. physical and functional annotations); and (iv) summary information from other GWAS. For each gene, SCAN provides annotations on: (i) eQTLs for the gene (both local and distant SNPs) and (ii) the coverage of all variants in the HapMap at that gene on each high-throughput platform. For each genomic region, SCAN provides annotations on: (i) physical and functional annotations of all SNPs, genes and known CNVs within the region and (ii) all genes regulated by the eQTLs within the region.
Availability: http://www.scandb.org
Contact: ncox@medicine.bsd.uchicago.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
CYSTM, a novel cysteine-rich transmembrane module with a role in stress tolerance across eukaryotes
Authors: Venancio Thiago M. , Aravind L. 
Published: November 2009

Abstract
Using sensitive sequence profile analysis, we identify a hitherto uncharacterized cysteine-rich, transmembrane (TM) module, CYSTM, found in a wide range of tail-anchored membrane proteins across eukaryotes. This superfamily includes Schizosaccharomyces Uvi15, Arabidopsis PCC1, Digtaria CDT1 and Saccharomyces proteins YDL012C and YDR210W, which have all been implicated in resistance/response to stress or pathogens. Based on the pattern of conserved cysteines and data from different chemical genetics studies, we suggest that CYSTM proteins might have critical role in responding to deleterious compounds at the plasma membrane via chelation or redox-based mechanisms. Thus, CYSTM proteins are likely to be part of a novel cellular protective mechanism that is widely active in eukaryotes, including humans.
Contact: aravind@ncbi.nih.gov
Supplementary Information: Supplementary data are available at Bioinformatics online.
Differential Effects of Buffered Hypercapnia versus Hypercapnic Acidosis on Shock and Lung Injury Induced by Systemic Sepsis
Authors: Higgins Brendan D. , Costello Joseph , Contreras Maya , Hassett Patrick , O' Toole Daniel , Laffey John G. 
Published: November 2009

Background
Acute hypercapnic acidosis protects against lung injury caused by nonseptic insults and after both pulmonary and systemic sepsis. The authors wished to dissect the contribution of the acidosis versus hypercapnia per se to the effects of hypercapnic acidosis on the hemodynamic profile and severity of lung injury induced by systemic sepsis.

Methods
In the hypercapnic acidosis series, adult male Sprague-Dawley rats were randomized to normocapnia or hypercapnic acidosis-produced by adding 5% carbon dioxide to the inspired gas-and cecal ligation and puncture performed. In the buffered hypercapnia series, animals were first randomized to housing under conditions of environmental normocapnia or hypercapnia-produced by exposure to 8% carbon dioxide-to allow renal buffering. After 96 h, cecal ligation and puncture was performed. In both series, the animals were ventilated for 6 h, and the severity of the lung injury and hemodynamic deterioration were assessed.

Results
Both hypercapnic acidosis and buffered hypercapnia attenuated the development and severity of hypotension and reduced lactate accumulation compared to normocapnia. Hypercapnic acidosis reduced lung injury and inflammation, decreased mean (+ or - SD) bronchoalveolar lavage protein concentration (232 + or - 50 versus 279 + or - 27 microg x ml(-1)) and median neutrophil counts (3,370 versus 9,120 cells x ml(-1)), and reduced histologic lung injury. In contrast, buffered hypercapnia did not reduce the severity of systemic sepsis induced lung injury.

Conclusions
Both hypercapnic acidosis and buffered hypercapnia attenuate the hemodynamic consequences of systemic sepsis. In contrast, hypercapnic acidosis, but not buffered hypercapnia, reduced the severity of sepsis-induced lung injury.
Opioid-induced Decreases in Rat Brain Adenosine Levels Are Reversed by Inhibiting Adenosine Deaminase
Authors: Nelson Ariana M. , Battersby Alanna S. , Baghdoyan Helen A. , Lydic Ralph 
Published: November 2009

Background
Opioids disrupt sleep and adenosine promotes sleep, but no studies have characterized the effects of opioids on adenosine levels in brain regions known to regulate states of arousal. Delivering opioids to the pontine reticular formation (PRF) and substantia innominata (SI) region of the basal forebrain disrupts sleep. In contrast, administering adenosine agonists to the PRF or SI increases sleep. These findings encouraged the current study testing the hypothesis that microdialysis delivery of opioids to the PRF or SI decreases adenosine levels in the PRF or SI, respectively.

Methods
A microdialysis probe was placed in the PRF of isoflurane anesthetized rats and perfused with Ringer's solution (control) followed by Ringer's solution containing morphine (0, 10, 30, 100, or 300 microm), fentanyl (100 microm), morphine (100 microm) and the adenosine deaminase inhibitor EHNA (100 microm), or naloxone (10 microm) and morphine (100 microm). Additional experiments measured adenosine levels in the SI before and during microdialysis delivery of morphine, fentanyl, and morphine plus EHNA.

Results
Morphine caused a significant (P < 0.05) concentration-dependent decrease in PRF adenosine levels. The significant decrease (-20%) in adenosine caused by 100 microm morphine was blocked by coadministration of naloxone. Fentanyl also significantly decreased (-13.3%) PRF adenosine. SI adenosine levels were decreased by morphine (-26.8%) and fentanyl (-27.4%). In both PRF and SI, coadministration of morphine and EHNA prevented the significant decrease in adenosine levels caused by morphine alone.

Conclusions
These data support the interpretation that decreased adenosine levels in sleep-regulating brain regions may be one of the mechanisms by which opioids disrupt sleep.
Modulation of Morphine-induced Antinociception in Acute and Chronic Opioid Treatment by Ibudilast
Authors: Lilius Tuomas O. , Rauhala Pekka V. , Kambur Oleg , Kalso Eija A. 
Published: November 2009

Background
Opioid analgesics are effective in relieving chronic pain, but they have serious adverse effects, including development of tolerance and dependence. Ibudilast, an inhibitor of glial activation and cyclic nucleotide phosphodiesterases, has shown potential in the treatment of neuropathic pain and opioid withdrawal. Because glial cell activation could also be involved in the development of opioid tolerance in rats, the authors studied the antinociceptive effects of ibudilast and morphine in different models of coadministration.

Methods
Antinociception was assessed using male Sprague- Dawley rats in hot plate and tail-flick tests. The effects of ibudilast on acute morphine-induced antinociception, induction of morphine tolerance, and established morphine tolerance were studied.

Results
Systemic ibudilast produced modest dose-related antinociception and decreased locomotor activity at the studied doses of 2.5-22.5 mg/kg. The highest tested dose of 22.5 mg/kg produced 52% of the maximum possible effect in the tail-flick test. It had an additive antinociceptive effect when combined with systemic morphine. Coadministration of ibudilast with morphine did not attenuate the development of morphine tolerance. However, in morphine-tolerant rats, ibudilast partly restored morphine-induced antinociception.

Conclusions
Ibudilast produces modest antinociception, and it is effective in restoring but not in preventing morphine tolerance. The mechanisms of the effects of ibudilast should be better understood before it is considered for clinical use.
Pronociceptive Effects of Remifentanil in a Mouse Model of Postsurgical Pain
Authors: Cabañero David , Campillo Ana , Célérier Evelyne , Romero Asunción , Puig Margarita M. 
Published: November 2009

Background
Remifentanil anesthesia enhances postoperative pain in animals and humans. The authors evaluated the impact of the dose (microg x kg(-1) x min(-1)) and duration of remifentanil infusion, and the effects of a second surgery on postoperative pain sensitization.

Methods
Mice received different doses of remifentanil over 30 or 60 min. The authors assessed thermal (Hargreaves) and mechanical hyperalgesia (von Frey) at 2, 4, 7, and 10 days. In other experiments, mice had a plantar incision during sevoflurane with or without remifentanil anesthesia that was repeated 27 days later, when nociceptive thresholds returned to baseline. Linear mixed models were used for statistical analysis.

Results
Remifentanil induced dose-dependent pronociceptive effects with calculated ED(50)s of 1.7 (95% confidence interval, 1.3-2.1) and 1.26 (1.0-1.6) microg x kg(-1) x min(-1) for thermal and mechanical hyperalgesia, respectively, which lasted longer with higher doses (P < 0.001). The duration of infusion did not alter the pronociceptive effects of remifentanil when administered at a constant dose of infusion. When given during surgery, high (2.66 microg x kg(-1) x min(-1)) or low (0.66 microg x kg(-1) x min(-1)) remifentanil increased the extent (P < 0.05) and duration (P < 0.01) of thermal and mechanical hyperalgesia. The latter was further enhanced after a second surgery performed in the same experimental conditions (P < 0.05). Surgery or remifentanil infusion, each one individually, induced significant mechanical hyperalgesia, which was greater when repeated (P < 0.05).

Conclusions
In this model of incisional pain, remifentanil induces pronociceptive effects, which are dose dependent but unaltered by the duration of administration. A second surgery performed on the same site and experimental conditions induces greater postoperative hyperalgesia that is enhanced when remifentanil is used as an anesthetic.
Perioperative Outcomes after Unilateral and Bilateral Total Knee Arthroplasty
Authors: Memtsoudis Stavros G. , Ma Yan , González Della Valle Alejandro , Mazumdar Madhu , Gaber-Baylis Licia K. , MacKenzie C Ronald , Sculco Thomas P. 
Published: November 2009

Background
The safety of bilateral total knee arthroplasties (BTKAs) during the same hospitalization remains controversial. The authors sought to study differences in perioperative outcomes between unilateral and BTKA and to further compare BTKAs performed during the same versus different operations during the same hospitalization.

Methods
Nationwide Inpatient Sample data from 1998 to 2006 were analyzed. Entries for unilateral and BTKA procedures performed on the same day (simultaneous) and separate days (staged) during the same hospitalization were identified. Patient and healthcare system-related demographics were determined. The incidences of in-hospital mortality and procedure-related complications were estimated and compared between groups. Multivariate regression was used to identify independent risk factors for morbidity and mortality.

Results
Despite younger average age and lower comorbidity burden, procedure-related complications and in-hospital mortality were more frequent after BTKA than after unilateral procedures (9.45% vs. 7.07% and 0.30% vs. 0.14%; P < 0.0001 each). An increased rate of complications was associated with a staged versus simultaneous approach with no difference in mortality (10.30% vs. 9.15%; P < 0.0001 and 0.29% vs. 0.26%; P = 0.2875). Independent predictors for in-hospital mortality included BTKA (simultaneous: odds ratio, 2.23 [95% confidence interval, 1.69-2.95]; P < 0.0001; staged: odds ratio, 2.01 [confidence interval, 1.28-3.41]; P = 0.0031), male sex (odds ratio, 2.02 [confidence interval, 1.75-2.34]; P < 0.0001), age older than 75 yr (odds ratio, 3.96 [confidence interval, 2.77-5.66]; P < 0.0001), and the presence of a number of comorbidities and complications.

Conclusion
BTKAs carry increased risk of perioperative morbidity and mortality compared with unilateral procedures. Staging BTKA procedures during the same hospitalization offers no mortality benefit and may even expose patients to increased morbidity.
Serious Complications Associated with External Intrathecal Catheters Used in Cancer Pain Patients
Authors: Aprili Daniel , Bandschapp Oliver , Rochlitz Christoph , Urwyler Albert , Ruppen Wilhelm 
Published: November 2009

Background
Potential risks of intrathecal catheters in cancer patients include infection, bleeding, and neurologic injury.

Methods
A systematic review and a pooled analysis of observational studies were performed. Articles reporting on adverse events (infections, bleeding, granuloma, and death) associated with intrathecal catheters and external pumps in cancer patients were identified. Electronic searches of PubMed, MEDLINE, and EMBASE were conducted. Observations from different studies were pooled using a generalized mixed-effect model. Model estimates and their standard errors (SEs) were used for calculating 95% confidence intervals (CIs) on the overall proportion.

Results
The analysis identified 10 articles, including a total of 821 patients. Twenty catheter-related infections were identified. Of these, 10 were superficial and 10 were deep infections, with rates of 2.3% (95% CI, 0.8-6.1) and 1.4% (95% CI, 0.5-3.8), respectively. Furthermore, the authors calculated that every 71st patient had a deep infection after an average catheter duration of 54 days. The risk of bleeding was found to be 0.9% (95% CI, 0-2.0), and for neurologic injury 0.4% (95% CI, 0-1.0). The infection rates are comparable to other intrathecal catheter techniques.

Conclusions
Serious complications are rare in both hospitalized and homebound patients with intrathecal catheters. This analysis supports the reasoning that the potential benefit of intrathecal catheters in the treatment of severe cancer pain is likely to outweigh the potential for serious complications associated with this technique. Therefore, an external intrathecal catheter can be considered an effective and low-cost solution for the control of pain in such patients.