bluuebunny/crossref_metadata_2025 huggingface dataset:
Whole genome sequencing of the fish pathogen Francisella noatunensis subsp. orientalis Toba04 gives novel insights into Francisella evolution and pathogenecity
Authors: Sridhar Settu , Sharma Animesh , Kongshaug Heidi , Nilsen Frank , Jonassen Inge
Published: December 2012

Background

Francisella is a genus of gram-negative bacterium highly virulent in fishes and human where F. tularensis is causing the serious disease tularaemia in human. Recently Francisella species have been reported to cause mortality in aquaculture species like Atlantic cod and tilapia. We have completed the sequencing and draft assembly of the Francisella noatunensis subsp. orientalisToba04 strain isolated from farmed Tilapia. Compared to other available Francisella genomes, it is most similar to the genome of Francisella philomiragia subsp. philomiragia, a free-living bacterium not virulent to human.

Results

The genome is rearranged compared to the available Francisella genomes even though we found no IS-elements in the genome. Nearly 16% percent of the predicted ORFs are pseudogenes. Computational pathway analysis indicates that a number of the metabolic pathways are disrupted due to pseudogenes. Comparing the novel genome with other available Francisella genomes, we found around 2.5% of unique genes present in Francisella noatunensis subsp. orientalis Toba04 and a list of genes uniquely present in the human-pathogenic Francisella subspecies. Most of these genes might have transferred from bacterial species through horizontal gene transfer. Comparative analysis between human and fish pathogen also provide insights into genes responsible for pathogenecity. Our analysis of pseudogenes indicates that the evolution of Francisella subspecies’s pseudogenes from Tilapia is old with large number of pseudogenes having more than one inactivating mutation.

Conclusions

The fish pathogen has lost non-essential genes some time ago. Evolutionary analysis of the Francisella genomes, strongly suggests that human and fish pathogenic Francisella species have evolved independently from free-living metabolically competent Francisella species. These findings will contribute to understanding the evolution of Francisella species and pathogenesis.
Whole genome HBV deletion profiles and the accumulation of preS deletion mutant during antiviral treatment
Authors: Zhang Dake , Dong Peiling , Zhang Ke , Deng Libin , Bach Christian , Chen Wei , Li Feifei , Protzer Ulrike , Ding Huiguo , Zeng Changqing
Published: December 2012

Background

Hepatitis B virus (HBV), because of its error-prone viral polymerase, has a high mutation rate leading to widespread substitutions, deletions, and insertions in the HBV genome. Deletions may significantly change viral biological features complicating the progression of liver diseases. However, the clinical conditions correlating to the accumulation of deleted mutants remain unclear. In this study, we explored HBV deletion patterns and their association with disease status and antiviral treatment by performing whole genome sequencing on samples from 51 hepatitis B patients and by monitoring changes in deletion variants during treatment. Clone sequencing was used to analyze preS regions in another cohort of 52 patients.

Results

Among the core, preS, and basic core promoter (BCP) deletion hotspots, we identified preS to have the highest frequency and the most complex deletion pattern using whole genome sequencing. Further clone sequencing analysis on preS identified 70 deletions which were classified into 4 types, the most common being preS2. Also, in contrast to the core and BCP regions, most preS deletions were in-frame. Most deletions interrupted viral surface epitopes, and are possibly involved in evading immuno-surveillance. Among various clinical factors examined, logistic regression showed that antiviral medication affected the accumulation of deletion mutants (OR = 6.81, 95% CI = 1.296 ~ 35.817, P = 0.023). In chronic carriers of the virus, and individuals with chronic hepatitis, the deletion rate was significantly higher in the antiviral treatment group (Fisher exact test, P = 0.007). Particularly, preS2 deletions were associated with the usage of nucleos(t)ide analog therapy (Fisher exact test, P = 0.023). Dynamic increases in preS1 or preS2 deletions were also observed in quasispecies from samples taken from patients before and after three months of ADV therapy. In vitro experiments demonstrated that preS2 deletions alone were not responsible for antiviral resistance, implying the coordination between wild type and mutant strains during viral survival and disease development.

Conclusions

We present the HBV deletion distribution patterns and preS deletion substructures in viral genomes that are prevalent in northern China. The accumulation of preS deletion mutants during nucleos(t)ide analog therapy may be due to viral escape from host immuno-surveillance.
Altered serum microRNAs as biomarkers for the early diagnosis of pulmonary tuberculosis infection
Authors: Qi Yuhua , Cui Lunbiao , Ge Yiyue , Shi Zhiyang , Zhao Kangchen , Guo Xiling , Yang Dandan , Yu Hao , Cui Lan , Shan Yunfeng , Zhou Minghao , Wang Hua , Lu Zuhong
Published: December 2012

Background

Pulmonary tuberculosis (TB) is a highly lethal infectious disease and early diagnosis of TB is critical for the control of disease progression. The objective of this study was to profile a panel of serum microRNAs (miRNAs) as potential biomarkers for the early diagnosis of pulmonary TB infection.

Methods

Using TaqMan Low-Density Array (TLDA) analysis followed by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) validation, expression levels of miRNAs in serum samples from 30 patients with active tuberculosis and 60 patients with Bordetella pertussis (BP), varicella-zoster virus (VZV) and enterovirus (EV) were analyzed.

Results

The Low-Density Array data showed that 97 miRNAs were differentially expressed in pulmonary TB patient sera compared with healthy controls (90 up-regulated and 7 down-regulated). Following qRT-PCR confirmation and receiver operational curve (ROC) analysis, three miRNAs (miR-361-5p, miR-889 and miR-576-3p) were shown to distinguish TB infected patients from healthy controls and other microbial infections with moderate sensitivity and specificity (area under curve (AUC) value range, 0.711-0.848). Multiple logistic regression analysis of a combination of these three miRNAs showed an enhanced ability to discriminate between these two groups with an AUC value of 0.863.

Conclusions

Our study suggests that altered levels of serum miRNAs have great potential to serve as non-invasive biomarkers for early detection of pulmonary TB infection.
Prognostic value of stromal and epithelial periostin expression in human prostate cancer: correlation with clinical pathological features and the risk of biochemical relapse or death
Authors: Nuzzo Pier Vitale , Rubagotti Alessandra , Zinoli Linda , Ricci Francesco , Salvi Sandra , Boccardo Simona , Boccardo Francesco
Published: December 2012

Background

The purpose of the present study was to evaluate the prognostic value of POSTN expression following prostatectomy.

Methods

Periostin (POSTN) expression in prostate cancer (PCa) and in normal specimens was evaluated in 90 patients by an immuno-reactive score(IRS) based on the intensity of immunostaining and on the quantity of stained cells. The t-test was applied to compare IRS values in cancer specimens to values in normal specimens. Pearson’s test was used to correlate POSTN expression to clinical pathologic features. PSA progression-free and survival curves were constructed by the Kaplan–Meier method and compared using the log-rank test. Multi-parametric models were constructed according to the Cox technique adding all the covariates predicting for either PSA progression or death into the models after univariate analysis.

Results

Both stromal and epithelial POSTN expression were significantly increased in tumor tissues.In particular, we found stromal expression to be significantly higher than epithelial expression as compared to normal tissues (p<0.000 and p=0.001).A significant correlation between POSTN epithelial expression and extra-prostatic extension was found (p=0.03). While high stromal expression was significantly associated with shorter survival (p=0.008), a low epithelial score significantly correlated with shorter PSA-free survival (p=0.04), suggesting that POSTN plays an apparently opposing biological role depending on its compartmentalization.Regardless of the mechanism that is involved, patients showing both high stromal and low epithelial expression made up a subgroup with a very bleak prognosis.

Conclusions

Although requiring further validation through larger studies, our findings show that POSTN might represent a novel prognostic marker for PCa.
Outcome at two years of age in a Swiss national cohort of extremely preterm infants born between 2000 and 2008
Authors: Schlapbach Luregn J , Adams Mark , Proietti Elena , Aebischer Maude , Grunt Sebastian , Borradori-Tolsa Cristina , Bickle-Graz Myriam , Bucher Hans Ulrich , Latal Beatrice , Natalucci Giancarlo ,   for the Swiss Neonatal Network & Follow-up Group
Published: December 2012

Background

While survival rates of extremely preterm infants have improved over the last decades, the incidence of neurodevelopmental disability (ND) in survivors remains high. Representative current data on the severity of disability and of risk factors associated with poor outcome in this growing population are necessary for clinical guidance and parent counselling.

Methods

Prospective longitudinal multicentre cohort study of preterm infants born in Switzerland between 240/7and 276/7weeks gestational age during 2000–2008. Mortality, adverse outcome (death or severe ND) at two years, and predictors for poor outcome were analysed using multilevel multivariate logistic regression. Neurodevelopment was assessed using Bayley Scales of Infant Development II. Cerebral palsy was graded after the Gross Motor Function Classification System.

Results

Of 1266 live born infants, 422 (33%) died. Follow-up information was available for 684 (81%) survivors: 440 (64%) showed favourable outcome, 166 (24%) moderate ND, and 78 (11%) severe ND. At birth, lower gestational age, intrauterine growth restriction and absence of antenatal corticosteroids were associated with mortality and adverse outcome (p < 0.001). At 360/7weeks postmenstrual age, bronchopulmonary dysplasia, major brain injury and retinopathy of prematurity were the main predictors for adverse outcome (p < 0.05). Survival without moderate or severe ND increased from 27% to 39% during the observation period (p = 0.02).

Conclusions

In this recent Swiss national cohort study of extremely preterm infants, neonatal mortality was determined by gestational age, birth weight, and antenatal corticosteroids while neurodevelopmental outcome was determined by the major neonatal morbidities. We observed an increase of survival without moderate or severe disability.
Methadone treatments in a Swiss Region, 2001–2008: a registry-based analysis
Authors: Huissoud Thérèse , Rousson Valentin , Dubois-Arber Françoise
Published: December 2012

Background

To determine, in a region of Switzerland, the duration of retention in opioid substitution treatments with methadone (OSTM), duration of treatment interruptions, probability of re-entry to treatment after a treatment interruption, and associated factors.

Methods

A secondary analysis of registry-based data was performed with patients (n = 2880) registered in the methadone treatment register database of the Public Health Service of the canton of Vaud between January 1, 2001 and June 30, 2008. Survival analysis and multivariate analysis was conducted.

Results

The probability of remaining on treatment was 69% at 1 year and 45% at 3 years (n =1666). One-third of patients remained on treatment beyond 5 years. The estimated hazard of leaving treatment was increased by a ratio of 1.31 in the case of a first treatment (P = 0.001), 1.83 for those without a fixed home (P < 0.001), and 1.29 for those younger than 30 years old (P < 0.001). The probability of having begun a new treatment after a first interruption was 21% at one year, 38% at 3 years, and 43% at 5 years (n = 1581). Factors at the interruption of treatment associated with a higher probability of re-entering were: interruption not due to methadone withdrawal, bad physical health, and higher methadone dose.

Conclusions

OSTM are long-term (maintenance) treatments in Switzerland. Younger age, bad living conditions at entry, and first treatment are predictors of lower retention. Approximately one-half of patients who interrupt treatment will re-enter treatment within 5 years.
An analysis of potential barriers and enablers to regulating the television marketing of unhealthy foods to children at the state government level in Australia
Authors: Chung Alexandra , Shill Jane , Swinburn Boyd , Mavoa Helen , Lawrence Mark , Loff Bebe , Crammond Bradley , Sacks Gary , Allender Steven , Peeters Anna
Published: December 2012

Background

In Australia there have been many calls for government action to halt the effects of unhealthy food marketing on children's health, yet implementation has not occurred. The attitudes of those involved in the policy-making process towards regulatory intervention governing unhealthy food marketing are not well understood. The objective of this research was to understand the perceptions of senior representatives from Australian state and territory governments, statutory authorities and non-government organisations regarding the feasibility of state-level government regulation of television marketing of unhealthy food to children in Australia.

Method

Data from in-depth semi-structured interviews with senior representatives from state and territory government departments, statutory authorities and non-government organisations (n=22) were analysed to determine participants' views about regulation of television marketing of unhealthy food to children at the state government level. Data were analysed using content and thematic analyses.

Results

Regulation of television marketing of unhealthy food to children was supported as a strategy for obesity prevention. Barriers to implementing regulation at the state level were: the perception that regulation of television advertising is a Commonwealth, not state/territory, responsibility; the power of the food industry and; the need for clear evidence that demonstrates the effectiveness of regulation. Evidence of community support for regulation was also cited as an important factor in determining feasibility.

Conclusions

The regulation of unhealthy food marketing to children is perceived to be a feasible strategy for obesity prevention however barriers to implementation at the state level exist. Those involved in state-level policy making generally indicated a preference for Commonwealth-led regulation. This research suggests that implementation of regulation of the television marketing of unhealthy food to children should ideally occur under the direction of the Commonwealth government. However, given that regulation is technically feasible at the state level, in the absence of Commonwealth action, states/territories could act independently. The relevance of our findings is likely to extend beyond Australia as unhealthy food marketing to children is a global issue.
In the face of war: examining sexual vulnerabilities of Acholi adolescent girls living in displacement camps in conflict-affected Northern Uganda
Authors: Patel Sheetal H , Muyinda Herbert , Sewankambo Nelson K , Oyat Geoffrey , Atim Stella , Spittal Patricia M
Published: December 2012

Background

Adolescent girls are an overlooked group within conflict-affected populations and their sexual health needs are often neglected. Girls are disproportionately at risk of HIV and other STIs in times of conflict, however the lack of recognition of their unique sexual health needs has resulted in a dearth of distinctive HIV protection and prevention responses. Departing from the recognition of a paucity of literature on the distinct vulnerabilities of girls in time of conflict, this study sought to deepen the knowledge base on this issue by qualitatively exploring the sexual vulnerabilities of adolescent girls surviving abduction and displacement in Northern Uganda.

Methods

Over a ten-month period between 2004–2005, at the height of the Lord’s Resistance Army insurgency in Northern Uganda, 116 in-depth interviews and 16 focus group discussions were held with adolescent girls and adult women living in three displacement camps in Gulu district, Northern Uganda. The data was transcribed and key themes and common issues were identified. Once all data was coded the ethnographic software programme ATLAS was used to compare and contrast themes and categories generated in the in-depth interviews and focus group discussions.

Results

Our results demonstrated the erosion of traditional Acholi mentoring and belief systems that had previously served to protect adolescent girls’ sexuality. This disintegration combined with: the collapse of livelihoods; being left in camps unsupervised and idle during the day; commuting within camp perimeters at night away from the family hut to sleep in more central locations due to privacy and insecurity issues, and; inadequate access to appropriate sexual health information and services, all contribute to adolescent girls’ heightened sexual vulnerability and subsequent enhanced risk for HIV/AIDS in times of conflict.

Conclusions

Conflict prevention planners, resettlement programme developers, and policy-makers need to recognize adolescent girls affected by armed conflict as having distinctive needs, which require distinctive responses. More adaptive and sustainable gender-sensitive reproductive health strategies and HIV prevention initiatives for displaced adolescent girls in conflict settings must be developed.
Optimization of dye adsorption time and film thickness for efficient ZnO dye-sensitized solar cells with high at-rest stability
Authors: Chang Wei-Chen , Lee Chia-Hua , Yu Wan-Chin , Lin Chun-Min
Published: December 2012

Photoelectrodes for dye-sensitized solar cells were fabricated using commercially available zinc oxide (ZnO) nanoparticles and sensitized with the dye N719. This study systematically investigates the effects of two fabrication factors: the ZnO film thickness and the dye adsorption time. Results show that these two fabrication factors must be optimized simultaneously to obtain efficient ZnO/N719-based cells. Different film thicknesses require different dye adsorption times for optimal cell performance. This is because a prolonged dye adsorption time leads to a significant deterioration in cell performance. This is contrary to what is normally observed for titanium dioxide-based cells. The highest overall power conversion efficiency obtained in this study was 5.61%, which was achieved by 26-μm-thick photoelectrodes sensitized in a dye solution for 2 h. In addition, the best-performing cell demonstrated remarkable at-rest stability despite the use of a liquid electrolyte. Approximately 70% of the initial efficiency remained after more than 1 year of room-temperature storage in the dark. To better understand how dye adsorption time affects electron transport properties, this study also investigated cells based on 26-μm-thick films using electrochemical impedance spectroscopy (EIS). The EIS results show good agreement with the measured device performance parameters.
Best proximity point results in geodesic metric spaces
Authors: Alghamdi Maryam A , Alghamdi Mohammed A , Shahzad Naseer
Published: December 2012

In this paper, the existence of a best proximity point for relatively u-continuous mappings is proved in geodesic metric spaces. As an application, we discuss the existence of common best proximity points for a family of not necessarily commuting relatively u-continuous mappings.
Classifications of solutions of second-order nonlinear neutral differential equations of mixed type
Authors: Thandapani E , Padmavathi S , Pinelas S
Published: December 2012

In this paper the authors classified all solutions of the second-order nonlinear neutral differential equations of mixed type,

(a(t)(x(t)+bx(t−τ1)+cx(t+τ2))′)′+p(t)xα(t−σ1)+q(t)xβ(t+σ2)=0,

into four classes and obtained conditions for the existence/non-existence of solutions in these classes. Examples are provided to illustrate the main results.

MSC:34C15.
Stabilization of Lur’e-type nonlinear control systems by Lyapunov-Krasovskii functionals
Authors: Shatyrko Andrei , Diblík Josef , Khusainov Denys , Růžičková Miroslava
Published: December 2012

The paper deals with the stabilization problem of Lur’e-type nonlinear indirect control systems with time-delay argument. The sufficient conditions for absolute stability of the control system are established in the form of matrix algebraic inequalities and are obtained by the direct Lyapunov method.

MSC:34H15, 34K20, 93C10, 93D05.
Computing center conditions for non-analytic ninth degree vector fields with constant angular speed
Authors: Ren Qingjun , Huang Yikun , Li Feng
Published: December 2012

We investigate the planar ninth degree non-analytic Poincare systems which have center-focus equilibriums at the origins. Those systems could be changed into analytic systems by two transformations with the help of computer algebra system MATHEMATICA. The conditions of uniform isochronous center are obtained. Furthermore, we prove that five limit cycles could be bifurcated from the origin.

MSC:34C05, 34C07.
The InterHerz project - a web-based psychological treatment for cardiac patients with depression: study protocol of a randomized controlled trial
Authors: Messerli-Bürgy Nadine , Barth Jürgen , Berger Thomas
Published: December 2012

Background

Patients with heart disease often suffer from difficulties in psychological adaptation during cardiac rehabilitation. Mood disorders such as depression are known to be highly prevalent in cardiac patients and to have a negative impact on the progression of coronary heart disease. However, cardiac patients have difficulties to get psychological treatments due to low availability and motivational difficulties. Web-based interventions have been proven to be effective in treating depressive symptoms. Deprexis is a promising web-based psychological treatment which was devised for depressed patients. The aim of the study InterHerz is to examine if Deprexis is an effective psychological treatment to reduce stress and depression in cardiac patients.

Methods/Design

The sample will consist of 80 depressed patients randomized to an intervention group or a waitlist (10 weeks). Patients are recruited via cardiologists, cardiac rehabilitation units and the website of the Swiss Heart Foundation. Patients have access to a guided self-help program in which they work themselves through several modules and receive feedback from a clinical psychologist. Pre- and post-assessments, and a six-month follow-up, are conducted using online questionnaires and diagnostic interviews.

Discussion

Deprexis is a new web-based treatment which has the potential to help depressed cardiac patients with limited access to psychological treatment to increase their mental health.

Trial registration

Current Controlled Trials ISRCTN45945396
Intravesical colistin irrigation to treat multidrug-resistant Acinetobacter baumannii urinary tract infection: a case report
Authors: Volkow-Fernández Patricia , Rodríguez Cecilia Franco , Cornejo-Juárez Patricia
Published: December 2012

Introduction

Acinetobacter baumannii is a Gram-negative bacteria and a significant nosocomial pathogen in hospitals. Multidrug-resistant A. baumannii have emerged as a cause of nosocomial infections in critically ill patients. This microorganism has the ability to produce biofilms on different surfaces, which could explain their ability to persist in clinical environments and their role in device-related infections.

Case presentation

We present the case of a 33-year-old Hispanic man with local invasive retroperitoneal leiomyosarcoma and right kidney exclusion along with femoral venous thrombosis, who was admitted for tumor resection. He had been receiving multiple nephrotoxic antibiotics for a long time (including tigecycline and colistimethate sodium) and had a persistent urinary infection related to multidrug-resistant A. baumannii (with susceptibility to colistimethate). Colistimethate was administered through a three-lumen urinary device for continuous urinary irrigation over seven days. Our patient did not refer to any adverse effects. A urine culture control taken at the end of the irrigation and another taken 10 days later were negative.

Conclusion

Colistimethate sodium and other antimicrobials infused by urinary irrigation can be a good option in patients in whom parenteral administration could be toxic.
Spontaneous coronary artery dissection causing acute myocardial infarction in a 62-year-old postmenopausal woman without co-morbidities: a case report
Authors: Mujtaba Sobia , Srinivas Vankeepuram S , Taub Cynthia C
Published: December 2012

Introduction

Spontaneous coronary artery dissection is an important yet rare cause of acute coronary syndrome. The available literature shows a higher risk factor for women, notably during pregnancy and puerperium. The incidence in postmenopausal women is exceedingly rare, and is more commonly seen in association with concurrent predisposing factors.

We illustrate an extremely rare case of a 62-year-old post-menopausal woman presenting with an acute myocardial infarction secondary to spontaneous dissection of the left anterior descending artery. Subsequent investigations did not reveal the presence of any co-morbidities.

To the best of our knowledge, our patient is one of the oldest documented cases of spontaneous coronary artery dissection on record, and is notable for having no known underlying risk factors for development of spontaneous coronary artery dissection.

Given the paucity of literature on spontaneous coronary artery dissection, particularly in postmenopausal women, we believe this case will provide further insight into the clinical presentation and management of this rare entity.

Case presentation

A 62-year-old previously healthy postmenopausal Hispanic woman presented with chest pain and was found to have an ST elevation myocardial infarction. Cardiac catheterization revealed a dissection in her left anterior descending artery. Revascularization was deferred; our patient received appropriate medical management and remained asymptomatic. A full panel of tests was done to exclude underlying connective tissue disorders and vasculitis. On subsequent follow-up, our patient continued to do well and all work-up was reported as negative.

Conclusion

We describe the varied presentation and subsequent management of a case of spontaneous coronary artery dissection and highlight the importance of considering spontaneous coronary artery dissection as a differential diagnosis even in older, postmenopausal women.

The consequences of a delay in diagnosis and appropriate management are associated with a high mortality and morbidity; hence we believe that reporting all cases of spontaneous coronary artery dissection, particularly in postmenopausal women, will add invaluable information to the limited literature on this rare condition.
Intracranial cystic chondroma: a case report
Authors: Uddin Muhammad Muzaffer , Ashraf Junaid , Memon Akhtar Amin , Ali Jamshed
Published: December 2012

Introduction

Intracranial chondromas are rare benign tumors with an incidence of 0.2% to 0.3% of all intracranial tumors. This is the first case of an intracranial chondroma reported from Pakistan.

Case presentation

We report a case of a 23-year-old Asian man presenting with intracerebral chondroma of the left frontal lobe, which was eroding the dura matter. The intracranial chondroma was completely removed by surgery.

Conclusion

Intracranial chondromas are rare benign cartilaginous tumors. Through this case presentation we have discussed the diagnostic procedures, radiological and pathological findings. The purpose of presenting such a rare case is to develop awareness among clinicians and medical students and to highlight the requirement of immediate actions to ensure proper management of such cases.
Orofacial neuropathic pain mouse model induced by Trigeminal Inflammatory Compression (TIC) of the infraorbital nerve
Authors: Ma Fei , Zhang Liping , Lyons Danielle , Westlund Karin N
Published: December 2012

Background

Trigeminal neuropathic pain attacks can be excruciating for patients, even after being lightly touched. Although there are rodent trigeminal nerve research models to study orofacial pain, few models have been applied to studies in mice. A mouse trigeminal inflammatory compression (TIC) model is introduced here which successfully and reliably promotes vibrissal whisker pad hypersensitivity.

Results

The chronic orofacial neuropathic pain model is induced after surgical placement of chromic gut suture in the infraorbital nerve fissure in the maxillary bone. Slight compression and chemical effects of the chromic gut suture on the portion of the infraorbital nerve contacted cause mild nerve trauma. Nerve edema is observed in the contacting infraorbital nerve bundle as well as macrophage infiltration in the trigeminal ganglia. Centrally in the spinal trigeminal nucleus, increased immunoreactivity for an activated microglial marker is evident (OX42, postoperative day 70). Mechanical thresholds of the affected whisker pad are significantly decreased on day 3 after chromic gut suture placement, persisting at least 10 weeks. The mechanical allodynia is reversed by suppression of microglial activation. Cold allodynia was detected at 4 weeks.

Conclusions

A simple, effective, and reproducible chronic mouse model mimicking clinical orofacial neuropathic pain (Type 2) is induced by placing chromic gut suture between the infraorbital nerve and the maxillary bone. The method produces mild inflammatory compression with significant continuous mechanical allodynia persisting at least 10 weeks and cold allodynia measureable at 4 weeks.
Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection
Authors: Zhang Zhao , Theurkauf William E , Weng Zhiping , Zamore Phillip D
Published: December 2012

Background

High throughput DNA sequencing technology has enabled quantification of all the RNAs in a cell or tissue, a method widely known as RNA sequencing (RNA-Seq). However, non-coding RNAs such as rRNA are highly abundant and can consume >70% of sequencing reads. A common approach is to extract only polyadenylated mRNA; however, such approaches are blind to RNAs with short or no poly(A) tails, leading to an incomplete view of the transcriptome. Another challenge of preparing RNA-Seq libraries is to preserve the strand information of the RNAs.

Design

Here, we describe a procedure for preparing RNA-Seq libraries from 1 to 4 μg total RNA without poly(A) selection. Our method combines the deoxyuridine triphosphate (dUTP)/uracil-DNA glycosylase (UDG) strategy to achieve strand specificity with AMPure XP magnetic beads to perform size selection. Together, these steps eliminate gel purification, allowing a library to be made in less than two days. We barcode each library during the final PCR amplification step, allowing several samples to be sequenced in a single lane without sacrificing read length. Libraries prepared using this protocol are compatible with Illumina GAII, GAIIx and HiSeq 2000 platforms.

Discussion

The RNA-Seq protocol described here yields strand-specific transcriptome libraries without poly(A) selection, which provide approximately 90% mappable sequences. Typically, more than 85% of mapped reads correspond to protein-coding genes and only 6% derive from non-coding RNAs. The protocol has been used to measure RNA transcript identity and abundance in tissues from flies, mice, rats, chickens, and frogs, demonstrating its general applicability.
Pharmacokinetic and pharmacodynamic characterization of a new formulation containing synergistic proportions of interferons alpha-2b and gamma (HeberPAG®) in patients with mycosis fungoides: an open-label trial
Authors: García-Vega Yanelda , García-García Idrian , Collazo-Caballero Sonia E , Santely-Pravia Egla E , Cruz-Ramírez Alieski , Tuero-Iglesias Ángela D , Alfonso-Alvarado Cristian , Cabrera-Placeres Mileidys , Castro-Basart Nailet , Duncan-Roberts Yaquelín , Carballo-Treto Tania I , Soto-Matos Josanne , Izquierdo-Toledo Yoandy , Vázquez-Blomquist Dania , García-Iglesias Elizeth , Bello-Rivero Iraldo
Published: December 2012

Background

The synergistic combination of interferon (IFN) alpha-2b and IFN gamma results in more potentin vitrobiological effects mediated by both IFNs. The aim of this investigation was to evaluate by first time the pharmacokinetics and pharmacodynamics of this combination in patients with mycosis fungoides.

Methods

An exploratory, prospective, open-label clinical trial was conducted. Twelve patients, both genders, 18 to 75 years-old, with mycosis fungoides at stages IB to III, were eligible for the study. All of them received intramuscularly a single high dose (23 × 106 IU) of a novel synergistic IFN mixture (HeberPAG®) for pharmacokinetic and pharmacodynamic studies. Serum IFN alpha-2b and IFN gamma concentrations were measured during 96 hours by commercial enzyme immunoassays (EIA) specific for each IFN. Other blood IFN-inducible markers and laboratory variables were used as pharmacodynamics and safety criteria.

Results

The pharmacokinetic evaluation by EIA yielded a similar pattern for both IFNs that are also in agreement with the well-known described profiles for these molecules when these are administered separately. The average values for main parameters were: Cmax: 263 and 9.3 pg/mL; Tmax: 9.5 and 6.9 h; AUC: 4483 and 87.5 pg.h/mL, half-life (t1/2): 4.9 and 13.4 h; mean residence time (MRT): 13.9 and 13.5 h, for serum IFN alpha-2b and IFN gamma, respectively. The pharmacodynamic variables were strongly stimulated by simultaneous administration of both IFNs: serum neopterin and beta-2 microglobulin levels (β2M), and stimulation of 2’-5’ oligoadenylate synthetase (OAS1) mRNA expression. The most encouraging data was the high increment of serum neopterin, 8.0 ng/mL at 48 h, not been described before for any unmodified or pegylated IFN. Additionally, β2M concentration doubled the pre-dose value at 24–48 hours. For both variables the values remained clearly upper baseline levels at 96 hours.

Conclusions

HeberPAG®possesses improved pharmacodynamic properties that may be very useful in the oncologic setting. Efficacy trials can be carried out to confirm these findings.

Trial registration

Registro Público Cubano de Ensayos ClínicosRPCEC00000130
Differences in employment outcomes for college town stayers and leavers
Authors: Winters John V
Published: December 2012

New college graduates must choose whether to stay in the geographic area where they completed their degree or move to a new location to begin their careers. This paper classifies 41 U.S. metropolitan areas as “college towns” and investigates differences in employment outcomes between college graduates who stay in the college town where they obtained their degree and college graduates who leave after completing their degree. We find that college town stayers experience less favorable employment outcomes along multiple dimensions. On average, stayers earn lower annual and hourly wages and work in less educated occupations.

JEL codes

J61, R23
Induction of BAFF expression by IFN-γ via JAK/STAT signaling pathways in human intestinal epithelial cells
Authors: Woo Sun-Je , Im Jintaek , Jeon Jun Ho , Kang Seok-Seong , Lee Mi-Hee , Yun Cheol-Heui , Moon Eun-Yi , Song Man Ki , Kim Hong-Hee , Han Seung Hyun
Published: December 2012

In human intestinal epithelial cells, IFN-γ induces BAFF expression through the signaling pathway of JAK/STAT and GAS, in the promoter region of the BAFF gene.

BAFF plays an important role in the development of B cells. Here, we investigated the effect of IFN-γ on BAFF expression in human intestinal epithelial cells. IFN-γ induced soluble and membrane-bound BAFF production in a dose- and time-dependent manner. IFN-γ-induced BAFF release from polarized intestinal epithelial cells was observed in apical and basolateral compartments. JAK I inhibitor suppressed IFN-γ-induced BAFF expression. Moreover, IFN-γ enhanced STAT1 phosphorylation and expression of IRF-1. Transient transfection and reporter gene assay showed that the BAFF promoter region spanning −750 to −500 bp from the translation initiation site was crucial for IFN-γ-induced BAFF expression. Nucleotide sequence analysis revealed a GAS element in the promoter region. ChIP assay confirmed the enhanced binding of phosphorylated STAT1 to the BAFF promoter region at −800 to −601 bp. Furthermore, IFN-γ enhanced DNA binding to GAS and its transcriptional activation, as determined by the EMSA and reporter gene assay. Collectively, these results suggest that IFN-γ induces BAFF expression in human intestinal epithelial cells through JAK/STAT signaling pathways that might activate the GAS and IRF-1-binding element in the BAFF promoter.
Correlates of relative resistance against low-dose rectal simian immunodeficiency virus challenges in peripheral blood mononuclear cells of vaccinated rhesus macaques
Authors: Kurupati Raj , Tuyishime Steve , Kossenkov Andrew V , Sazanovich Marina , Haut Larissa H , Lasaro Marcio O , Ratcliffe Sarah J , Bosinger Steven E , Carnathan Diane G , Lewis Mark , Showe Louise C , Silvestri Guido , Ertl Hildegund C J
Published: December 2012

Vaccine-induced molecular correlates of protection against repeated low-dose rectal SIVmac251 challenges of rhesus macaques, in peripheral blood mononuclear cells.

In this study, we compared the immunogenicity and protection from repeated low-dose intrarectal SIVmac251 challenge in two groups of vaccinated RMs. Animals were immunized with live SIVmac239, which had been attenuated by a deletion of the nef sequence, or they were vaccinated twice with an E1-deleted AdHu5, expressing SIVmac239gag. The vaccinated animals and a cohort of unvaccinated control animals were then challenged 10 times in weekly intervals with low doses of SIVmac251 given rectally. Our results confirm previous studies showing that whereas SIVΔnef provides some degree of protection against viral acquisition after repeated low-dose rectal SIVmac251 challenges, vaccination with an AdHu5gag vaccine designed to induce only antiviral T cell responses is ineffective. As immunological analyses of prechallenge, vaccine-induced T and B cell responses failed to reveal correlates of protection that distinguished the more susceptible from the more resistant vaccinated animals, we carried out RNA-Seq studies of paired pre- and postvaccination samples to identify transcriptional patterns that correlated with the differences in response. We show that gene expression signatures associated with the delayed SIV infection seen in some AdHu5gag recipients were largely present in prevaccination samples of those animals. In contrast, the responding SIVΔnef-immunized animals showed a predominance of vaccine-induced changes, thus enabling us to define inherited and vaccine-induced gene expression signatures and their associated pathways that may play a role in preventing SIV acquisition.
Systemic administration of TLR3 agonist induces IL-7 expression and IL-7-dependent CXCR3 ligand production in the lung
Authors: Jin Jun-O , Yu Qing
Published: December 2012

Delineate a new mechanism where systemic poly I:C administration boosts local T cell immunity, and how IL-7 bridges TLR3 signal to adaptive immunity.

In this study, we tested the hypothesis that systemic administration of TLR3 agonist poly I:C can enhance T cell infiltration of lung through up-regulating IL-7 expression. poly I:C, a synthetic analog of viral dsRNA and a TLR3 agonist, is studied extensively as vaccine adjuvant as a result of its pleotropic immune-stimulatory effects. Here, we show that systemic poly I:C administration induces substantial IL-7 production in the lung in a type 1 IFN- and IFN-γ-dependent fashion. Blockade of the IL-7Rα signal with a neutralizing antibody abrogated poly I:C-induced MCP-1 up-regulation, macrophage recruitment, and CXCR3 ligand expression in the lung. Conversely, administration of IL-7 enhances these events, and it does so by enhancing T cell IFN-γ production. We also show that the initial up-regulation of CXCR3 ligands and infiltration of T cells in the lung are mediated by poly I:C-induced IFN-γ from NK cells; however, the sustained and optimal CXCR3 ligand expression and T cell infiltration require poly I:C-induced IL-7 and T cell-derived IFN-γ. In a model of multiorgan inflammation elicited by adoptive transfer of immune cells into RAG1−/− mice, we show that poly I:C enhances IL-7 production in the lung and promotes expression of CXCR3 ligands and recruitment of IFN-γ+ T cells in an IL-7-dependent fashion. Collectively, these results strongly support our hypothesis and delineate a new mechanism by which poly I:C boosts the T cell immune response in the lung by inducing local IL-7 production, which in turn, enhances T cell-derived IFN-γ to promote macrophage recruitment, CXCR3 ligand expression, and T cell infiltration.
Self-eating and self-defense: autophagy controls innate immunity and adaptive immunity
Authors: Liu Guangwei , Bi Yujing , Wang Ruoning , Wang Xianghui
Published: December 2012

Review on how the self-eating (autophagy) process could regulate the self-defense (immune) system.

Autophagy (macroautophagy; “self-eating”) is a degradation process, in which cytoplasmic content is engulfed and degraded by the lysosome. And, immunity is an important mechanism of the “self-defense” system. Autophagy has long been recognized as a stress response to nutrient deprivation. This will provide energy and anabolic building blocks to maintain cellular bioenergetic homeostasis. Thus, autophagy plays critical roles in regulating a wide variety of pathophysiological processes, including tumorigenesis, embryo development, tissue remodeling, and most recently, immunity. The latter shows that a self-eating (autophagy) process could regulate a self-defense (immune) system. In this review, we summarize the recent findings regarding the regulatory and mechanistic insights of the autophagy pathway in immunity.
Identification of a region in p47phox/NCF1 crucial for phagocytic NADPH oxidase (NOX2) activation
Authors: Sareila Outi , Jaakkola Noora , Olofsson Peter , Kelkka Tiina , Holmdahl Rikard
Published: December 2012

The p47phox (NCF1) variant expressed in Ncf1m1J mice is defective in activating the NOX2 complex to produce ROS.

A point mutation in the mouse Ncf1m1J gene decreases production of ROS by the phagocytic NOX2 complex. Three mRNA splice variants are expressed, but only one is expressed as a protein, although at lower levels than the WT NCF1 (also known as p47phox). Our aim was to investigate whether the mutant p47phox, lacking 8 aa, is active, but as a result of its low expression, ROS production is decreased in Ncf1m1J mice, or whether the mutant p47phox completely lacks the capability to activate the NOX2 complex. The p47phox mutant (Δ228–235), which was equal to the protein in Ncf1m1J mice, failed to activate the NOX2 complex. When the deleted region was narrowed down to 2 aa, the p47phox protein remained inactive and failed to translocate to the membrane upon activation. Single amino acid substitutions revealed Thr233 to be vital for ROS production. Residues Tyr231 and Val232 also seemed to be important for p47phox function, as p47phox_Y231G and p47phox_V232G resulted in a >50% decrease in ROS production by the NOX2 complex. In addition, we identified the epitope of the D-10 anti-p47phox mAb. In conclusion, the p47phox protein variant expressed in Ncf1m1J mice is completely defective in activating the NOX2 complex to produce ROS, and the effect is dependent on SH3 region amino acids at positions 231–233, which are vital for the proper assembly of the NOX2 complex.
Coming Full Circle: Contributions of Central and Peripheral Oxytocin Actions to Energy Balance
Authors: Ho Jacqueline M. , Blevins James E.
Published: December 2012

The neuropeptide oxytocin has emerged as an important anorexigen in the regulation of energy balance. Its effects on food intake have largely been attributed to limiting meal size through interactions in key regulatory brain regions such as the hypothalamus and hindbrain. Pharmacologic and pair-feeding studies indicate that its ability to reduce body mass extends beyond that of food intake, affecting multiple factors that determine energy balance such as energy expenditure, lipolysis, and glucose regulation. Systemic administration of oxytocin recapitulates many of its effects when administered centrally, raising the questions of whether and to what extent circulating oxytocin contributes to energy regulation. Its therapeutic potential to treat metabolic conditions remains to be determined, but data from diet-induced and genetically obese rodent models as well as application of oxytocin in humans in other areas of research have revealed promising results thus far.
Structure of Concentrated Aqueous Urea Solutions Involving Alkali Metal Salts Studied by Neutron Diffraction with 14N/15N, 6Li/7Li, and 35Cl/37Cl Isotopic Substitution Methods
Authors: Miyazaki Takuya , Kameda Yasuo , Amo Yuko , Usuki Takeshi
Published: December 2012

Neutron diffraction with 14N/15N, 35Cl/37Cl, and 6Li/7Li isotopic substitution methods have been applied to aqueous 10 mol % urea solutions involving 5 mol % NaCl and 10 mol % LiCl, in order to obtain information on the hydration structure around the amino group of urea which is affected by coexisting ions, Cl− and Li+. Observed first-order difference functions, ΔNinter(Q), ΔCl(Q), and ΔLi(Q), were respectively analyzed using least-squares fitting. The nearest neighbor intermolecular N···Ow (Ow: oxygen atom in D2O) distance was determined to be 3.09(1) and 3.19(1) Å, from the analyses for sample solutions involving NaCl and LiCl, respectively. These intermolecular N···Ow distances are slightly longer than those reported for aqueous urea solutions of similar concentrations. These results suggest that hydrogen bonds among amino groups of urea and neighboring water molecules are weakened by coexisting alkali metal salts. The structural parameters concerning the first hydration shell of Cl− and Li+, have been determined to be r(Cl−···Dw) = 2.27(1) Å (Dw: deuterium atom in D2O) and r(Li+···Ow) = 1.95(1) Å, respectively. The results indicate that the structure of the first hydration shell around Cl− and Li+ is not affected by the presence of urea molecules in the aqueous solution.
Simple Observation of the Interaction between Nanoparticles and Cells by Scanning Electron Microscopy Employing Ionic Liquid
Authors: Shima Fumiaki , Kawakami Koshi , Akagi Takami , Mochizuki Eiko , Tsuda Tetsuya , Kuwabata Susumu , Akashi Mitsuru
Published: December 2012

The cellular uptake of nanoparticles (NPs) was clearly observed by scanning electron microscopy (SEM) employing an ionic liquid for the first time. The samples did not show charge-up effect without staining, and high contrast images were achieved. Because of these unique properties of the ionic liquid, we could finely observe the cellular uptake of NPs compared with conventional SEM observation method. Moreover, the cells became transparent as the accelerating voltage increased, and the internalized NPs composed of heavy atoms were easily determined. This ionic liquid method provides a simple and short pretreatment procedure and thus is a promising technique for evaluating the cellular uptake of NPs and the intracellular fate of NPs. This method also gives a strategy to observe NPs which are unstable in the dry condition by choosing a suitable ionic liquid.