bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extensive recombination events and horizontal gene transfer shaped the Legionella pneumophila genomes
Authors: Gomez-Valero Laura , Rusniok Christophe , Jarraud Sophie , Vacherie Benoit , Rouy Zoé , Barbe Valerie , Medigue Claudine , Etienne Jerome , Buchrieser Carmen 
Published: November 2011

Abstract

Background

Legionella pneumophila is an intracellular pathogen of environmental protozoa. When humans inhale contaminated aerosols this bacterium may cause a severe pneumonia called Legionnaires' disease. Despite the abundance of dozens of Legionella species in aquatic reservoirs, the vast majority of human disease is caused by a single serogroup (Sg) of a single species, namely L. pneumophila Sg1. To get further insights into genome dynamics and evolution of Sg1 strains, we sequenced strains Lorraine and HL 0604 1035 (Sg1) and compared them to the available sequences of Sg1 strains Paris, Lens, Corby and Philadelphia, resulting in a comprehensive multigenome analysis.

Results
We show that L. pneumophila Sg1 has a highly conserved and syntenic core genome that comprises the many eukaryotic like proteins and a conserved repertoire of over 200 Dot/Icm type IV secreted substrates. However, recombination events and horizontal gene transfer are frequent. In particular the analyses of the distribution of nucleotide polymorphisms suggests that large chromosomal fragments of over 200 kbs are exchanged between L. pneumophila strains and contribute to the genome dynamics in the natural population. The many secretion systems present might be implicated in exchange of these fragments by conjugal transfer. Plasmids also play a role in genome diversification and are exchanged among strains and circulate between different Legionella species.

Conclusion
Horizontal gene transfer among bacteria and from eukaryotes to L. pneumophila as well as recombination between strains allows different clones to evolve into predominant disease clones and others to replace them subsequently within relatively short periods of time.
Characteristics of the aberrant pyramidal tract in comparison with the pyramidal tract in the human brain
Authors: Kwon Hyeok Gyu , Son Su Min , Chang Min Cheol , Kim Saeyoon , Kwon Yong Hyun , Jang Sung Ho 
Published: November 2011

Abstract

Background
The aberrant pyramidal tract (APT) refers to the collateral pathway of the pyramidal tract (PT) through the medial lemniscus in the midbrain and pons. Using diffusion tensor tractography (DTT), we investigated the characteristics of the APT in comparison with the PT in the normal human brain.

Results
In thirty-four (18.3%, right hemisphere: 20, left hemisphere: 14) of the 186 hemispheres, the APTs separated from the PT at the upper midbrain level, descended through the medial lemniscus from the midbrain to the pons, and then rejoined with the PT at the upper medulla. Nine (26.5%) of the 34 APTs were found to originate from the primary somatosensory cortex without a primary motor cortex origin. Values of fractional anisotropy (FA) and tract volume of the APT were lower than those of the PT (P < 0.05); however, no difference in mean diffusivity (MD) value was observed (P > 0.05).

Conclusion
We found that the APT has different characteristics, including less directionality, fewer neural fibers, and less origin from the primary motor cortex than the PT.
Predictors of long-term pain and disability in patients with low back pain investigated by magnetic resonance imaging: A longitudinal study
Authors: McNee Philip , Shambrook James , Harris E Clare , Kim Miranda , Sampson Madeleine , Palmer Keith T , Coggon David 
Published: November 2011

Abstract

Background
It is possible that clinical outcome of low back pain (LBP) differs according to the presence or absence of spinal abnormalities on magnetic resonance imaging (MRI), in which case there could be value in using MRI findings to refine case definition of LBP in epidemiological research. We therefore conducted a longitudinal study to explore whether spinal abnormalities on MRI for LBP predict prognosis after 18 months.

Methods
A consecutive series of patients aged 20-64 years, who were investigated by MRI because of mechanical LBP (median duration of current episode 16.2 months), were identified from three radiology departments, and those who agreed completed self-administered questionnaires at baseline and after a mean follow-up period of 18.5 months (a mean of 22.2 months from MRI investigation). MRI scans were assessed blind to other clinical information, according to a standardised protocol. Associations of baseline MRI findings with pain and disability at follow-up, adjusted for treatment and for other potentially confounding variables, were assessed by Poisson regression and summarised by prevalence ratios (PRs) with their 95% confidence intervals (CIs).

Results
Questionnaires were completed by 240 (74%) of the patients who had agreed to be followed up. Among these 111 men and 129 women, 175 (73%) reported LBP in the past four weeks, 89 (37%) frequent LBP, and 72 (30%) disabling LBP. In patients with initial disc degeneration there was an increased risk of frequent (PR 1.3, 95%CI 1.0-1.9) and disabling LBP (PR 1.7, 95%CI 1.1-2.5) at follow-up. No other associations were found between MRI abnormalities and subsequent outcome.

Conclusions
Our findings suggest that the MRI abnormalities examined are not major predictors of outcome in patients with LBP. They give no support to the use of MRI findings as a way of refining case definition for LBP in epidemiological research.
Predicting recovery at home after Ambulatory Surgery
Authors: Viñoles Juan , Ibáñez Maía V , Ayala Guillermo 
Published: November 2011

Abstract
The correct implementation of Ambulatory Surgery must be accompanied by an accurate monitoring of the patient post-discharge state. We fit different statistical models to predict the first hours postoperative status of a discharged patient. We will also be able to predict, for any discharged patient, the probability of needing a closer follow-up, or of having a normal progress at home.

Background

The status of a discharged patient is predicted during the first 48 hours after discharge by using variables routinely used in Ambulatory Surgery. The models fitted will provide the physician with an insight into the post-discharge progress. These models will provide valuable information to assist in educating the patient and their carers about what to expect after discharge as well as to improve their overall level of satisfaction.

Methods

A total of 922 patients from the Ambulatory Surgery Unit of the Dr. Peset University Hospital (Valencia, Spain) were selected for this study. Their post-discharge status was evaluated through a phone questionnaire. We pretend to predict four variables which were self-reported via phone interviews with the discharged patient: sleep, pain, oral tolerance of fluid/food and bleeding status. A fifth variable called phone score will be built as the sum of these four ordinal variables. The number of phone interviews varies between patients, depending on the evolution. The proportional odds model was used. The predictors were age, sex, ASA status, surgical time, discharge time, type of anaesthesia, surgical specialty and ambulatory surgical incapacity (ASI). This last variable reflects, before the operation, the state of incapacity and severity of symptoms in the discharged patient.

Results

Age, ambulatory surgical incapacity and the surgical specialty are significant to explain the level of pain at the first call. For the first two phone calls, ambulatory surgical incapacity is significant as a predictor for all responses except for sleep at the first call.

Conclusions

The variable ambulatory surgical incapacity proved to be a good predictor of the patient's status at home. These predictions could be used to assist in educating patients and their carers about what to expect after discharge, as well as to improve their overall level of satisfaction.
Regulation of mtl operon promoter of Bacillus subtilis: requirements of its use in expression vectors
Authors: Morabbi Heravi Kambiz , Wenzel Marian , Altenbuchner Josef 
Published: November 2011

Abstract

Background
Several vector systems have been developed to express any gene desired to be studied in Bacillus subtilis. Among them, the transcriptionally regulated promoters involved in carbohydrate utilization are a research priority. Expression systems based on Bacillus promoters for xylose, maltose, and mannose utilization, as well as on the heterologous E. coli lactose promoter, have been successfully constructed. The promoter of the mtlAFD operon for utilization of mannitol is another promising candidate for its use in expression vectors. In this study, we investigated the regulation of the mtl genes in order to identify the elements needed to construct a strong mannitol inducible expression system in B. subtilis.

Results
Regulation of the promoters of mtlAFD operon (P

mtlA
) and mtlR (P

mtlR
) encoding the activator were investigated by fusion to lacZ. Identification of the P

mtlA
and P

mtlR
transcription start sites revealed the σA like promoter structures. Also, the operator of P

mtlA
was determined by shortening, nucleotide exchange, and alignment of P

mtlA
and P

mtlR
operator regions. Deletion of the mannitol-specific PTS genes (mtlAF) resulted in P

mtlA
constitutive expression demonstrating the inhibitory effect of EIICBMtl and EIIAMtl on MtlR in the absence of mannitol. Disruption of mtlD made the cells sensitive to mannitol and glucitol. Both P

mtlA
and P

mtlR
were influenced by carbon catabolite repression (CCR). However, a CcpA deficient mutant showed only a slight reduction in P

mtlR
catabolite repression. Similarly, using P

groE
as a constitutive promoter, putative cre sites of P

mtlA
and P

mtlR
slightly reduced the promoter activity in the presence of glucose. In contrast, glucose repression of P

mtlA
and P

mtlR
was completely abolished in a ΔptsG mutant and significantly reduced in a MtlR (H342D) mutant.

Conclusions
The mtl operon promoter (P

mtlA
) is a strong promoter that reached a maximum of 13,000 Miller units with lacZ as a reporter on low copy plasmids. It is tightly regulated by just one copy of the mtlR gene on the chromosome and subject to CCR. CCR can be switched off by mutations in MtlR and the glucose transporter. These properties and the low costs of the inducers, i.e. mannitol and glucitol, make the promoter ideal for designing regulated expression systems.
LPS preconditioning redirects TLR signaling following stroke: TRIF-IRF3 plays a seminal role in mediating tolerance to ischemic injury
Authors: Vartanian Keri B , Stevens Susan L , Marsh Brenda J , Williams-Karnesky Rebecca , Lessov Nikola S , Stenzel-Poore Mary P 
Published: November 2011

Abstract

Background
Toll-like receptor 4 (TLR4) is activated in response to cerebral ischemia leading to substantial brain damage. In contrast, mild activation of TLR4 by preconditioning with low dose exposure to lipopolysaccharide (LPS) prior to cerebral ischemia dramatically improves outcome by reprogramming the signaling response to injury. This suggests that TLR4 signaling can be altered to induce an endogenously neuroprotective phenotype. However, the TLR4 signaling events involved in this neuroprotective response are poorly understood. Here we define several molecular mediators of the primary signaling cascades induced by LPS preconditioning that give rise to the reprogrammed response to cerebral ischemia and confer the neuroprotective phenotype.

Methods
C57BL6 mice were preconditioned with low dose LPS prior to transient middle cerebral artery occlusion (MCAO). Cortical tissue and blood were collected following MCAO. Microarray and qtPCR were performed to analyze gene expression associated with TLR4 signaling. EMSA and DNA binding ELISA were used to evaluate NFκB and IRF3 activity. Protein expression was determined using Western blot or ELISA. MyD88-/- and TRIF-/- mice were utilized to evaluate signaling in LPS preconditioning-induced neuroprotection.

Results
Gene expression analyses revealed that LPS preconditioning resulted in a marked upregulation of anti-inflammatory/type I IFN-associated genes following ischemia while pro-inflammatory genes induced following ischemia were present but not differentially modulated by LPS. Interestingly, although expression of pro-inflammatory genes was observed, there was decreased activity of NFκB p65 and increased presence of NFκB inhibitors, including Ship1, Tollip, and p105, in LPS-preconditioned mice following stroke. In contrast, IRF3 activity was enhanced in LPS-preconditioned mice following stroke. TRIF and MyD88 deficient mice revealed that neuroprotection induced by LPS depends on TLR4 signaling via TRIF, which activates IRF3, but does not depend on MyD88 signaling.

Conclusion
Our results characterize several critical mediators of the TLR4 signaling events associated with neuroprotection. LPS preconditioning redirects TLR4 signaling in response to stroke through suppression of NFκB activity, enhanced IRF3 activity, and increased anti-inflammatory/type I IFN gene expression. Interestingly, this protective phenotype does not require the suppression of pro-inflammatory mediators. Furthermore, our results highlight a critical role for TRIF-IRF3 signaling as the governing mechanism in the neuroprotective response to stroke.
Is decreased bone mineral density associated with development of scoliosis? A bipedal osteopenic rat model
Authors: Dede Ozgur , Akel Ibrahim , Demirkiran Gokhan , Yalcin Nadir , Marcucio Ralph , Acaroglu Emre 
Published: November 2011

Abstract

Background
An association between adolescent idiopathic scoliosis and osteopenia has been proposed to exist. It is still not clear whether there is such an association and if so, whether osteopenia is a causative factor or a consequence. Our previous pilot studies have suggested the presence of osteopenia in scoliotic animals. The aim of this study was to investigate the development of scoliosis in an unpinealectomized bipedal osteopenic rat model, implementing osteoporosis as a causative factor.

Methods
Fifty Sprague-Dawley rats were rendered bipedal at the 3rd postnatal week and separated into control (25 rats) and heparin (25 rats receiving 1 IU/gr body weight/day) groups. DEXA scans after 4 weeks of heparin administration showed low bone mass in the heparin group. Anteroposterior and lateral x-rays of the surviving 42 animals (19 in heparin and 23 in control groups) were taken under anesthesia at the 40th week to evaluate for spinal deformity. Additional histomorphometric analysis was done on spine specimens to confirm the low bone mass in heparin receiving animals. Results of the DEXA scans, histomorphometric analysis and radiological data were compared between the groups.

Results
Bone mineral densities of rats in the heparin group were significantly lower than the control group as evidenced by both the DEXA scans and histomorphometric analyses. However, the incidence of scoliosis (82% in heparin and 65% in control; p > 0.05) as well as the curve magnitudes (12.1 ± 3.8 in heparin versus 10.1 ± 4.3 degrees in control; p > 0.05) were not significantly different. Osteopenic rats were significantly less kyphotic compared to control specimens (p = 0.001).

Conclusions
This study has revealed two important findings. One is that bipedality (in the absence of pinealectomy) by itself may be a cause of scoliosis in this animal model. Further studies on animal models need to consider bipedality as an independent factor. Secondly, relative hypokyphosis in osteopenic animals may have important implications. The absence of sagittal plane analyses in previous studies makes comparison impossible, but nonetheless these findings suggest that osteopenia may be important in the development of 3D deformity in adolescent idiopathic scoliosis.
Castleman's disease in childhood: report of three cases and review of the literature
Authors: Farruggia Piero , Trizzino Antonino , Scibetta Nunzia , Cecchetto Giovanni , Guerrieri Patrizia , D'Amore Emanuele SG , D'Angelo Paolo 
Published: November 2011

Abstract
Castleman's disease (CD) is a rare, localized or generalized, lymphoproliferative disorder with a frequent mediastinal location, but possible in any lymph node or extra nodal site. It usually appears in young adults whilst it rarely occurs in childhood. There are only about 100 pediatric cases published, five of them in Italy. We report 3 cases of localized Castleman's disease, investigated in our Department in a 3 years period and reviewed the literature.
Glucose deprivation in tuberous sclerosis complex-related tumors
Authors: Jiang Xiuyun , Kenerson Heidi L , Yeung Raymond S 
Published: November 2011

Abstract

Background
Cancer cells possess unique metabolic phenotypes that are determined by their underlying oncogenic pathways. Activation of the PI3K/Akt/mTOR signaling cascade promotes glycolysis and leads to glucose-dependence in tumors. In particular, cells with constitutive mTORC1 activity secondary to the loss of TSC1/TSC2 function are prone to undergo apoptosis upon glucose withdrawal in vitro, but this concept has not been tested in vivo. This study examines the effects of restricting glucose metabolism by pharmacologic and dietary means in a tuberous sclerosis complex (TSC) tumor xenograft model.

Results
Tumor-bearing mice were randomly assigned to receive unrestricted carbohydrate-free ("Carb-free") or Western-style diet in the absence or presence of 2-deoxyglucose (2-DG) in one of four treatment groups. After 14 weeks, tumor sizes were significantly different among the four treatment groups with those receiving 2-DG having the smallest tumors. Unexpectedly, the "Carb-free" diet was associated with the largest tumors but they remained responsive to 2-DG. PET imaging showed significant treatment-related changes in tumor 18fluorodeoxyglucose-uptake but the standard uptake values did not correlate with tumor size. Alternative energy substrates such as ketone bodies and monounsaturated oleic acid supported the growth of the Tsc2-/- cells in vitro, whereas saturated palmitic acid was toxic. Correspondingly, tumors in the high-fat, "Carb-free" group showed greater necrosis and liquefaction that contributed to their larger sizes. In contrast, 2-DG treatment significantly reduced tumor cell proliferation, increased metabolic stress (i.e., ketonemia) and AMPK activity, whereas rapamycin primarily reduced cell size.

Conclusions
Our data support the concept of glycolytic inhibition as a therapeutic approach in TSC whereas dietary withdrawal of carbohydrates was not effective.
Urinary Bisphenol A (BPA) Concentration Associates with Obesity and Insulin Resistance
Authors: Wang Tiange , Li Mian , Chen Bing , Xu Min , Xu Yu , Huang Yun , Lu Jieli , Chen Yuhong , Wang Weiqing , Li Xiaoying , Liu Yu , Bi Yufang , Lai Shenghan , Ning Guang 
Published: November 2011

Context:Bisphenol A (BPA) is one of the world's highest-volume chemicals in use today. Previous studies have suggested BPA disturbs body weight regulation and promotes obesity and insulin resistance. But epidemiological data in humans were limited.Objective:Our objective was to determine whether BPA associates with obesity and insulin resistance.Design, Setting, and Participants:This cross-sectional study included 3390 adults aged 40 yr or older, in Songnan Community, Baoshan District, Shanghai, China.Main Outcome Measures:Questionnaire, clinical and biochemical measurements, and urinary BPA concentration were determined. Generalized overweight was defined as body mass index (BMI) of 24 to less than 28 kg/m2 and obesity was defined as BMI of 28 kg/m2 or higher. Abdominal obesity was defined as waist circumference at least 90 cm for men and at least 85 cm for women. Insulin resistance was defined as the index of homeostasis model assessment of insulin resistance higher than 2.50.Results:The participants in the highest quartile of BPA had the highest prevalence of generalized obesity [odds ratio (OR) = 1.50; 95% confidence interval (CI) = 1.15–1.97], abdominal obesity (OR = 1.28; 95% CI = 1.03–1.60), and insulin resistance (OR = 1.37; 95% CI = 1.06–1.77). In participants with BMI under 24 kg/m2, compared with the lowest quartile, the highest quartile of BPA increased the prevalence of insulin resistance by 94% (OR = 1.94; 95% CI = 1.20–3.14), but this association was not observed in those with BMI of 24 kg/m2 or higher.Conclusions:BPA was positively associated with generalized obesity, abdominal obesity, and insulin resistance in middle-aged and elderly Chinese adults.
Acute hepatitis B: the limits of maintaining patient confidentiality
Authors: Quinn K J , Mccarty E J , Quah S P 
Published: November 2011

Summary Household contacts of hepatitis B (HBV) are at risk of infection, and guidelines advise vaccination of these contacts in addition to sexual partners (along with traditional high-risk groups). We present a case of intrafamilial transmission of acute hepatitis B virus (HBV) following failure to self-disclose status to family members. Complex confidentiality issues can arise following a diagnosis of HBV infection.
Factors associated with repeat visits among clients attending a clinic for sexually transmitted infections in Kisumu, Kenya
Authors: Pultorak E , Odoyo-June E , Hayombe J , Opiyo F , Odongo W , Ogollah J A , Moses S , Bailey R C , Mehta S D 
Published: November 2011

Summary To identify factors associated with repeat visits among patients attending a clinic for sexually transmitted infections (STIs) in Kisumu, Kenya, we examined records of clinic visits from March 2009 to May 2010. Multivariable logistic regression identified factors associated with repeat visits occurring >30 days after the initial visit. Among 1473 clients (1296 single-visit individuals versus 177 individuals with repeat visits), the median age was 24 years, 67% were men and 8.6% self-reported being HIV-positive. In adjusted analyses, men with repeat visits were more likely to report ≥2 recent sexual partners (adjusted odds ratio [aOR] = 1.60) and being HIV-positive (aOR = 2.35). They were less likely to have been referred from other health facilities (aOR = 0.14) and more likely to have urethral discharge at their initial visit (aOR = 2.46). Among women, repeat visits were associated with vaginal discharge (aOR = 2.22), but attending the clinic with a partner was protective (aOR = 0.38). The association between sexual risk, HIV positivity and repeat visits among male clients highlights the need to focus intervention efforts on this group. For women, attending with a partner may reflect a decreased risk of re-infection if both partners are treated and counselled together.