bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic analysis of torque teno virus genome from Pakistani isolate and incidence of co-infection among HBV/HCV infected patients
Authors: Hussain Tabinda , Manzoor Sobia , Waheed Yasir , Tariq Huma , Hanif Khushbakht 
Published: December 2012

Abstract

Background
Torque Teno Virus (TTV) was the first single stranded circular DNA virus to be discovered that infects humans. Although there have been numerous reports regarding the prevalence of TTV from other countries of South Asia, there is severe lack of information regarding its prevalence in Pakistan. Thus the present study compiles the first indigenous report to comprehensively illustrate the incidence of the virus in uninfected and hepatitis infected population from Pakistan. Another aim of the study was to present the sequence of full length TTV genome from a local isolate and compare it with the already reported genome sequences from other parts of the world.

Methods
TTV DNA was screened in the serum of 116, 100 and 40 HBV infected, HCV infected and uninfected individuals respectively. Nearly full length genome of TTV was cloned from a HBV patient. The genome sequence was subjected to in-silico analysis using CLC Workbench, ClustalW, ClustalX and TreeView. Statistical analysis was carried out in SPSS v17.0.

Results
Our results report that 89.7%, 90.0% and 92.5% of HBV, HCV patients and healthy control population were positive for TTV infection. TTV genome of 3603 bp was also cloned from a local isolate and given the identity of TPK01. The TTV genome sequence mentioned in this paper is submitted in the GenBank/EMBL/DDBJ under the accession number JN980171. Phylogenetic analysis of TPK01 revealed that the Pakistani isolate has sequence similarities with genotype 23 and 22 (Genogroup 2).

Conclusion
The results of the current study indicate that the high frequency of TTV viremia in Pakistan conforms to the reports from other areas of the world, wherever screening of TTV DNA was performed against 5′-UTR of the genome. The high sequence diversity among TTV genome sequences and the high frequency of prevalence makes it harder to study this virus in cellular systems.
Dietary patterns and odds of Type 2 diabetes in Beirut, Lebanon: a case–control study
Authors: Naja Farah , Hwalla Nahla , Itani Leila , Salem Maya , Azar Sami T , Zeidan Maya Nabhani , Nasreddine Lara 
Published: December 2012

Abstract

Background
In Lebanon, Type 2 diabetes (T2D) has a major public health impact through high disease prevalence, significant downstream pathophysiologic effects, and enormous financial liabilities. Diet is an important environmental factor in the development and prevention of T2D. Dietary patterns may exert greater effects on health than individual foods, nutrients, or food groups. The objective of this study is to examine the association between dietary patterns and the odds of T2D among Lebanese adults.

Methods
Fifty-eight recently diagnosed cases of T2D and 116 population-based age, sex, and place of residence matched control participants were interviewed. Data collection included a standard socio-demographic and lifestyle questionnaire. Dietary intake was evaluated by a semi-quantitative 97-item food frequency questionnaire. Anthropometric measurements including weight, height, waist circumference, and percent body fat were also obtained. Dietary patterns were identified by factor analysis. Multivariate logistic regression analysis was used to evaluate the associations of extracted patterns with T2D. Pearson correlations between these patterns and obesity markers, energy, and nutrient intakes were also examined.

Results
Four dietary patterns were identified: Refined Grains & Desserts, Traditional Lebanese, Fast Food and Meat & Alcohol. While scores of the “Refined Grains & Desserts” had the highest correlations with energy (r = 0.74) and carbohydrates (r = 0.22), those of the “Fast Food” had the highest correlation with fat intake (r = 0.34). After adjustment for socio-demographic and lifestyle characteristics, scores of the Refined Grains & Desserts and Fast Food patterns were associated with higher odds of T2D (OR: 3.85, CI: 1.13-11.23 and OR: 2.80, CI: 1.14-5.59; respectively) and scores of the Traditional Lebanese pattern were inversely associated with the odds of T2D (OR: 0.46, CI: 0.22-0.97).

Conclusions
The findings of this study demonstrate direct associations of the Refined Grains & Desserts and Fast Food patterns with T2D and an inverse association between the Traditional Lebanese pattern and the disease among Lebanese adults. These results may guide the development of nutrition interventions for the prevention and management of T2D among Lebanese adults.
Jerusalem artichoke and chungkookjang additively improve insulin secretion and sensitivity in diabetic rats
Authors: Yang Hye Jeong , Kwon Dae Young , Kim Min Jung , Kang Suna , Kim Da Sol , Park Sunmin 
Published: December 2012

Abstract
Jerusalem artichoke (Helianthus tuberosus Linne, HTL) and chungkookjang (CKJ; fermented soybeans) both modulate energy and glucose metabolism. However, the mechanism and their additive effects are unknown. We investigated whether the consumption of HTL and CKJ altered insulin sensitivity, insulin secretion capacity and β-cell survival in type 2 diabetic animals. Rats were divided into partially pancreatectomized (Px) diabetic rats, and sham operated non-diabetic control rats and all fed high fat diets. Diabetic rats were sub-divided into an untreated diabetic control group and those fed 5% HTL, 5% CKJ or 5% HTL+5% CKJ for 8 weeks. HTL+CKJ treatment reduced visceral fat without modulating energy intake compared to the diabetic-control. Glucose tolerance was improved in an ascending order of diabetic-control, CKJ, HTL, HTL+CKJ, and normal-control, but by different mechanisms. CKJ and CKJ+HTL, but not HTL, increased first and second phase insulin secretion in comparison to the diabetic-control at hyperglycemic clamp. However, glucose infusion rates (mg/kg bw/min) were increased by and CKJ+HTL (13.5), but not HTL (9.4) or CKJ (9.5) alone, and HTL and CKJ+ HTL decreased hepatic glucose compared to diabetic-control during the hyperinsulinemic euglycemic study and were associated with decreased triglyceride accumulation and increased glycogen storage. The improved hepatic insulin sensitivity by HTL and CKJ+HTL was explained by potentiated insulin signaling (tyrosine phosphorylation of insulin receptor substrate 2→phosphorylation of Akt) and phosphorylation of AMPK→phosphorykation of acetyl Co carboxlase in comparison to diabetic-control and decreased PEPCK expression. Absolute β-cell mass was increased by CKJ (23.4mg) and CKJ+HTL (26.3 mg) by increasing proliferation compared to the diabetic-control (21.26 mg). Although HTL lowered β-cell apoptosis, it did not increase β-cell mass (20.8 mg). In conclusions, HTL and CKJ enhanced glucose tolerance in different manners, and exhibited partially additive and complementary effects by reversing insulin resistance and enhancing β-cell function in diabetic rats.
Effects of different chlorhexidine pretreatments on adhesion of metal brackets in vitro
Authors: Frey Corinne , Yetkiner Enver , Stawarczyk Bogna , Attin Thomas , Attin Rengin 
Published: December 2012

Abstract

Objective
To investigate the effect of chlorhexidine applications in various forms and concentrations on adhesion and failure modes of metal brackets in vitro.

Material and methods
Ninety bovine enamel specimens were allocated to six groups (n=15). Metal brackets were bonded on all specimens after chlorhexidine pre-treatments forming the following groups: (1) untreated specimens (control); (2) 40% varnish (EC40, Biodent BV, Netherlands), remnants removed with brushing mimicking patient cleaning; (3) 40% varnish (EC40), remnants removed with brushing mimicking professional cleaning; (4) 1% varnish (Cervitec Plus, Ivoclar vivadent, Schaan, Liechtenstein), remnants not removed; (5) brushed with% 1 gel (Corsodyl, GlaxoSmithKline, Münchenbuchsee, Germany), remnants not removed; (6) immersed in 0.07% mouthrinse (Corsodyl, GlaxoSmithKline, Münchenbuchsee, Germany), remnant not rinsed. Debonding of brackets was performed using a universal testing machine. Data were analysed using one-way ANOVA and post-hoc Scheffé test.

Results
Group 4 performed significantly inferior than all the other groups and the control. Group 4 presented the highest number of adhesive failures at the enamel-resin interface whereas in other groups no failures at adhesive-resin interface was observed.

Conclusion
Presence of chlorhexidine varnish prior to bracket bonding adversely affects adhesion. Concentration of chlorhexidine pre-treatment has no influence on shear bond strength.
Urine neutrophil gelatinase-associated lipocalin (NGAL) as a biomarker for acute canine kidney injury
Authors: Lee Ya-Jane , Hu Yu-Yen , Lin Yi-Shan , Chang Chun-Ting , Lin Fong-Yuan , Wong Min-Liang , Kuo-Hsuan Hsu , Hsu Wei-Li 
Published: December 2012

AbstractBackgroundBiomarkers for the early prediction of canine acute kidney injury (AKI) are clinically important. Recently, neutrophil gelatinase-associated lipocalin (NGAL) was found to be a sensitive biomarker for the prediction of human AKI at a very early stage and the development of AKI after surgery. However, NGAL has not yet been studied with respect to dog kidney diseases. The application of NGAL canine AKI was investigated in this study.ResultsThe canine NGAL gene was successfully cloned and expressed. Polyclonal antibodies against canine NGAL were generated and used to develop an ELISA for measuring NGAL protein in serum and urine samples that were collected from 39 dogs at different time points after surgery.AKI was defined by the standard method, namely a serum creatinine increase of greater than or equal to 26.5 μmol/L from baseline within 48 h. At 12 h after surgery, compared to the group without AKI (12 dogs), the NGAL level in the urine of seven dogs with AKI was significantly increased (median 178.4 pg/mL vs. 88.0 pg/mL), and this difference was sustained to 72 h.ConclusionAs the increase in NGAL occurred much earlier than the increase in serum creatinine, urine NGAL seems to be able to serve as a sensitive and specific biomarker for the prediction of AKI in dogs.
Four new loci associations discovered by pathway-based and network analyses of the genome-wide variability profile of Hirschsprung’s disease
Authors: Fernández Raquel Ma , Bleda Marta , Núñez-Torres Rocío , Medina Ignacio , Luzón-Toro Berta , García-Alonso Luz , Torroglosa Ana , Marbà Martina , Enguix-Riego Ma Valle , Montaner David , Antiñolo Guillermo , Dopazo Joaquín , Borrego Salud 
Published: December 2012

AbstractFinding gene associations in rare diseases is frequently hampered by the reduced numbers of patients accessible. Conventional gene-based association tests rely on the availability of large cohorts, which constitutes a serious limitation for its application in this scenario. To overcome this problem we have used here a combined strategy in which a pathway-based analysis (PBA) has been initially conducted to prioritize candidate genes in a Spanish cohort of 53 trios of short-segment Hirschsprung’s disease. Candidate genes have been further validated in an independent population of 106 trios. The study revealed a strong association of 11 gene ontology (GO) modules related to signal transduction and its regulation, enteric nervous system (ENS) formation and other HSCR-related processes. Among the preselected candidates, a total of 4 loci,RASGEF1A,IQGAP2,DLC1andCHRNA7, related to signal transduction and migration processes, were found to be significantly associated to HSCR. Network analysis also confirms their involvement in the network of already known disease genes. This approach, based on the study of functionally-related gene sets, requires of lower sample sizes and opens new opportunities for the study of rare diseases.
Microtubule asters as templates for nanomaterials assembly
Authors: Verma Vivek , Catchmark Jeffrey M , Brown Nicole R , Hancock William O 
Published: December 2012

Abstract
Self organization of the kinesin-microtubule system was implemented as a novel template to create percolated nanofiber networks. Asters of microtubule seeds were immobilized on glass surfaces and their growth was recorded over time. The individual aster islands became interconnected as microtubules grew and overlapped, resulting in a highly percolated network. Cellulose nanowhiskers were used to demonstrate the application of this system to nanomaterials organization. The size distribution of the cellulose nanowhiskers was comparable to that of microtubules. To link cellulose nanowhiskers to microtubules, the nanowhiskers were functionalized by biotin using cellulose binding domains. Fluorescence studies confirmed biotinylation of cellulose nanowhiskers and binding of cellulose nanowhiskers to biotinylated microtubules.
Diabetic muscle infarction in a 57 year old male: a case report
Authors: Litvinov Ivan V , Radu Arnold , Garfield Natasha 
Published: December 2012

Abstract

Background
Diabetic muscle infarction is a rare complication of diabetes mellitus (DM) and is often misdiagnosed as cellulitis. This complication is usually associated with poor disease prognosis and high mortality with previous studies reporting a risk of 50% recurrence or another macrovascular complication occurring within one year. Thus, there needs to be greater awareness of this complication of diabetes.

Case presentation
In the current work, we present a case report and literature review of DMI occurring in a calf of a 57 year old male. However, unlike the suspected trend, our patient has performed well after this incident and has not sustained another macrovascular event now > 15 month since his original diabetic muscle infarction.

Conclusion
Even though diabetic muscle infarction is an uncommon condition, it is important to consider this diagnosis in a diabetic patient. We hope that our findings and literature review will aid clinicians to better diagnose and manage this condition.
Zoonotic pathogens associated with Hyalomma aegyptium in endangered tortoises: evidence for host-switching behaviour in ticks?
Authors: Paștiu Anamaria I , Matei Ioana A , Mihalca Andrei D , D’Amico Gianluca , Dumitrache Mirabela O , Kalmár Zsuzsa , Sándor Attila D , Lefkaditis Menelaos , Gherman Călin M , Cozma Vasile 
Published: December 2012

Abstract

Background

Hyalomma aegyptium is a hard-tick with a typical three-host life cycle. The main hosts are Palearctic tortoises of genus Testudo. However, other hosts can be used by immature ticks for feeding in natural conditions. Given this complex ecology and multiple host use, the circulation of pathogens by H. aegyptium between various hosts can be important from epidemiological point of view. The aim of this study was to evaluate the role of H. aegyptium as natural carrier of four important zoonotic pathogens.

Methods
From 2008 to 2011, 448 H. aegyptium ticks were collected from 45 Spur-thighed tortoises, Testudo graeca in Romania. DNA was extracted individually from each tick using a commercial kit. DNA was examined for the presence of specific sequences of Borrelia burgdorferi s.l., Anaplasma phagocytophilum, Ehrlichia canis and Coxiella burnetii by PCR, according to previously described protocols.

Results
PCR analysis of H. aegyptium revealed the presence of A. phagocytophilum (18.8%), E. canis (14.1%) and C. burnetii (10%). 32.4% of the ticks were infected with at least one pathogen and 9.8% had co-infections. The stages most frequently infected were nymphs (50%) followed by males (33.9%) and females (27%). The number of tortoises which harboured infected ticks was 27/45 examined (60%). From all tested T. graeca, 40% harboured ticks infected with A. phagocytophilum, 46.7% had ticks infected with E. canis and 33.3% had ticks with C. burnetii. This study reports for the first time the presence of A. phagocytophilum and E. canis in H. aegyptium.

Conclusions
The presence and relatively high prevalence of three important zoonotic pathogens in H. aegyptium raises the question of their epidemiologic importance in disease ecology. As tortoises are unlikely to be reservoir hosts for A. phagocytophilum and E. canis and both these pathogens are common in H. aegyptium, this is an important indication for (1) a possible increased host-switching behaviour of these ticks to competent reservoir hosts (i.e. hedgehogs) and (2) transstadial transmission. Furthermore, if we consider also the presence of C. burnetii, we conclude that T. graeca and its ticks should be evaluated more seriously when assessing the eco-epidemiology of zoonotic diseases.
Oxidative damage to macromolecules in the thyroid - experimental evidence
Authors: Karbownik-Lewińska Małgorzata , Kokoszko-Bilska Agnieszka 
Published: December 2012

AbstractWhereas oxidative reactions occur in all tissues and organs, the thyroid gland constitutes such an organ, in which oxidative processes are indispensable for thyroid hormone synthesis. It is estimated that huge amount of reactive oxygen species, especially of hydrogen peroxide (H2O2), are produced in the thyroid under physiological conditions, justifying the statement that the thyroid gland is an organ of “oxidative nature”. Apart from H2O2, also other free radicals or reactive species, formed from iodine or tyrosine residues, participate in thyroid hormone synthesis. Under physiological conditions, there is a balance between generation and detoxification of free radicals. Effective protective mechanisms, comprising antioxidative molecules and the process of compartmentalization of potentially toxic molecules, must have been developed in the thyroid to maintain this balance. However, with additional oxidative abuse caused by exogenous or endogenous prooxidants (ionizing radiation being the most spectacular), increased damage to macromolecules occurs, potentially leading to different thyroid diseases, cancer included.
Role of metallothioneins in benign and malignant thyroid lesions
Authors: Pula Bartosz , Domoslawski Pawel , Podhorska-Okolow Marzena , Dziegiel Piotr 
Published: December 2012

Abstract
Recent findings in the past two decades have brought many insights into the biology of thyroid benign and malignant lesions, in particular the papillary and follicular thyroid cancers. Although, much progress have been made, thyroid cancers still pose diagnostic problems regarding differentiation of follicular lesions in relation to their aggressiveness and the treatment of advanced and undifferentiated thyroid cancers. Metallothioneins (MTs) were shown to induce cancer cells proliferation, mediate resistance to apoptosis, certain chemotherapeutics and radiotherapy. Therefore, MTs may be of utility in diagnosis and management of patients with benign and malignant lesions of the thyroid.
KCNA5 gene is not confirmed as a systemic sclerosis-related pulmonary arterial hypertension genetic susceptibility factor
Authors: Bossini-Castillo Lara , Simeon Carmen P , Beretta Lorenzo , Broen Jasper , Vonk Madelon C , Callejas José Luis , Carreira Patricia , Rodríguez-Rodríguez Luis , García-Portales Rosa , González-Gay Miguel A , Castellví Ivan , Camps María Teresa , Tolosa Carlos , Vicente-Rabaneda Esther , Egurbide María Victoria ,   the Spanish Scleroderma Group, Schuerwegh Annemie J , Hesselstrand Roger , Lunardi Claudio , van Laar Jacob M , Shiels Paul , Herrick Ariane , Worthington Jane , Denton Christopher , Radstake Timothy RDJ , Fonseca Carmen , Martin Javier 
Published: December 2012

Abstract
Introduction
Potassium voltage-gated channel shaker-related subfamily member 5 (KCNA5) is implicated in vascular tone regulation, and its inhibition during hypoxia produces pulmonary vasoconstriction. Recently, a protective association of the KCNA5 locus with systemic sclerosis (SSc) patients with pulmonary arterial hypertension (PAH) was reported. Hence, the aim of this study was to replicate these findings in an independent multicenter Caucasian SSc cohort.

Methods
The 2,343 SSc cases (179 PAH positive, confirmed by right-heart catheterization) and 2,690 matched healthy controls from five European countries were included in this study. Rs10744676 single-nucleotide polymorphism (SNP) was genotyped by using a TaqMan SNP genotyping assay.

Results
Individual population analyses of the selected KCNA5 genetic variant did not show significant association with SSc or any of the defined subsets (for example, limited cutaneous SSc, diffuse cutaneous SSc, anti-centromere autoantibody positive and anti-topoisomerase autoantibody positive). Furthermore, pooled analyses revealed no significant evidence of association with the disease or any of the subsets, not even the PAH-positive group. The comparison of PAH-positive patients with PAH-negative patients showed no significant differences among patients.

Conclusions
Our data do not support an important role of KCNA5 as an SSc-susceptibility factor or as a PAH-development genetic marker for SSc patients.
Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus
Authors: Castillo-Ramírez Santiago , Corander Jukka , Marttinen Pekka , Aldeljawi Mona , Hanage William P , Westh Henrik , Boye Kit , Gulay Zeynep , Bentley Stephen D , Parkhill Julian , Holden Matthew T , Feil Edward J 
Published: December 2012

Abstract
Background
Next-generation sequencing (NGS) is a powerful tool for understanding both patterns of descent over time and space (phylogeography) and the molecular processes underpinning genome divergence in pathogenic bacteria. Here, we describe a synthesis between these perspectives by employing a recently developed Bayesian approach, BRATNextGen, for detecting recombination on an expanded NGS dataset of the globally disseminated methicillin-resistant Staphylococcus aureus (MRSA) clone ST239.

Results
The data confirm strong geographical clustering at continental, national and city scales and demonstrate that the rate of recombination varies significantly between phylogeographic sub-groups representing independent introductions from Europe. These differences are most striking when mobile non-core genes are included, but remain apparent even when only considering the stable core genome. The monophyletic ST239 sub-group corresponding to isolates from South America shows heightened recombination, the sub-group predominantly from Asia shows an intermediate level, and a very low level of recombination is noted in a third sub-group representing a large collection from Turkey.

Conclusions
We show that the rapid global dissemination of a single pathogenic bacterial clone results in local variation in measured recombination rates. Possible explanatory variables include the size and time since emergence of each defined sub-population (as determined by the sampling frame), variation in transmission dynamics due to host movement, and changes in the bacterial genome affecting the propensity for recombination.