bluuebunny/crossref_metadata_2025_split huggingface dataset:
Weight change associated with antiepileptic drugs
Authors: Pickrell William Owen , Lacey Arron S , Thomas Rhys H , Smith Philip E M , Rees Mark I 
Published: December 2012

AimTo investigate antiepileptic drug (AED)-related weight changes in patients with epilepsy through a retrospective observational study.MethodWe analysed the anonymised electronic primary care records of 1.1 million adult patients in Wales. We included patients aged 18 years and over with a diagnosis of epilepsy, whose body weight had been measured up to 12 months before starting, and between 3 and 12 months after starting, one of five AEDs. We calculated the weight difference after starting the AED for each patient.Results1423 patients were identified in total. The mean difference between body weight after and before starting each AED (together with 95% CI and p values for no difference) were: carbamazepine (CBZ) 0.43 (−0.19 to 1.05) p=0.17; lamotrigine (LTG) 0.31 (−0.38 to 1.00) p=0.38; levetiracetam (LEV) 1.00 (0.16 to 1.84) p=0.02; sodium valproate (VPA) 0.74 (0.10 to 1.38) p=0.02; topiramate (TPM) −2.30 (−4.27 to −0.33) p=0.02.ConclusionsLEV and VPA were associated with significant weight gain, TPM was associated with significant weight loss, and LTG and CBZ were not associated with significant weight change.
APPLYING COMBINATORIAL OPTIMIZATION HEURISTICS FOR ENHANCING THE PERFORMANCE OF TH-PPM UWB SYSTEMS: CHAOTIC VERSUS CLASSICAL CODE SEQUENCES
Authors: NAANAA ANIS , BELGHITH SAFYA 
Published: December 2012

In this article, we propose a process to minimize the Multi-User Interference (MUI) caused by Multiple Access (MA) in a Time Hopping Ultra Wide Band (TH-UWB) system with No Line-Of-Sight (NLOS) multipath channel in a residential environment IEEE 802.15.4a Channel Model 2 (CM2). We discuss both synchronous and asynchronous channels with an Additive White Gaussian Noise (AWGN). The choice of codes allowing multiple access is crucial for minimizing the MUI and to improve the system performance. Recently much works has been done in order to optimize performance by code selection [Bravo et al., 1999; Moreno & Marić, 2000; Guvenc & Arslan, 2004]. This paper is a contribution to this research axis. The minimization of the MUI is formulated as a Combinatorial Optimization Problem (COP) and solved by means of an efficient generic optimization method called Guided Local Search (GLS) [Voudouris, 1997]. In this context, we exploit the richness of chaotic sequences with respect to topologic properties. Simulation results based on the Binary Error Rate (BER) show that optimized chaotic sequences outperforms the classical code sequences.
Assessment of trace elements concentrations in Western reef heron (Egretta gularis) from southern Iran
Authors: Hoshyari Ebrahim , Pourkhabbaz Alireza , Mansouri Borhan 
Published: December 2012

The purpose of this article was to investigate the levels of metals, cadmium, lead, and zinc, in Western reef heron ( Egretta gularis) ( n = 15) in order to (1) examine the sex-related variation in trace metal accumulation and (2) determine the significant differences between the metal concentrations in the kidney, liver, and pectoral muscle. Bird samples were collected from throughout the Hara biosphere reserve of southern Iran, during November and December 2010 and the concentration of metals were measured using a Shimadzu AA 680 flame atomic absorption spectrophotometer. The overall cadmium, lead and zinc concentrations means were measured as 0.8 ± 0.1, 3.4 ± 1.1, and 29.4 ± 12.9 μg/g for kidney; 0.7 ± 0.1, 2.2 ± 0.5, and 65.9 ± 20.7 μg/g for liver; and 0.2 ± 0.1, 2.2 ± 0.7, and 17.6 ± 12.9 μg/g for pectoral muscle, respectively. The results showed that with the exception of cadmium in liver, there were no significant differences between males and females ( t test, p > 0.05). In the contrast, the results indicated metal concentrations differed significantly in kidneys, livers, and pectoral muscles among tissues in Western reef heron (one-way analysis of variance, p < 0.001).
A nosological review of depressive disorders based on observations in clinical practice, Part 2: a working typology for clinicians
Authors: Restifo Sam 
Published: December 2012

Objective: The purpose of this paper is to examine the essential nosological differentiation between melancholic and non-melancholic forms of depression with a view to promoting a meaningful, working typology for clinicians. The paper primarily comprises observations and reflections drawn from clinical practice. Conclusions: The most specific symptoms of melancholic depression are described, as are the main varieties of non-melancholic ‘depression’, including demoralisation, grief, loneliness, existential depression and depressive personality.
Perspectives on the EdD from academics at English universities
Authors: Poole Brian 
Published: December 2012

Since first appearing in British universities during the early 1990s, the Doctor of Education (EdD) degree has spread rapidly through the UK higher education sector. However, despite the existence of a single set of Quality Assurance Agency (QAA) descriptors for doctoral-level achievement, some in academia have always been willing to describe the EdD, either openly or in private, as inferior to the PhD. This thesis endeavours (through a wide-ranging questionnaire completed anonymously by 27 academics from a total of 16 English universities, and follow-up interviews with seven individuals selected from the original sample) to discover how a sample of those who teach on such programmes (EdD academics) view the EdD, in general terms. For instance, it seeks to ascertain how widespread among EdD academics is the notion that the EdD does not reach the ‘gold standard’ represented by the PhD in Education. As data collection proceeds from the questionnaire to the interviews, the focus narrows to three key topics: specific characteristics of the EdD as compared with the PhD in Education (in terms, for example, of learning experience, programme aims, and modes of assessment); strengths, weaknesses and purposes of the EdD viva voce examination; and the concept of ‘originality’ as operationalized by EdD academics/examiners in deciding whether or not an EdD candidate/thesis displays ‘doctorateness’. A range of informed and sometimes forthright views from EdD academics on these matters is recorded. On the basis of data analysis and interpretation, the thesis concludes with proposals for further, more extensive research, and a call for one of two courses of action: either the abolition of the EdD, or the appointment of a committee to review EdD practices nationally, and to recommend ways of strengthening EdD rigour and reputation.
Multiplexed mAbs: a new strategy in preclinical time-domain imaging of acute myeloid leukemia
Authors: McCormack Emmet , Mujić Maja , Osdal Tereza , Bruserud Øystein , Gjertsen Bjørn Tore 
Published: December 2012

Key Points
Multiplexing antibodies against common human epitopes all labeled with the same fluorophore facilitates optical imaging of heterogenous AML. Multiplexing fluorescently labeled monoclonal antibodies permits optical imaging of primary patient xenograft pathology/therapy response.
Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study
Authors: Sun Lei , Zhang Zhihua , Bailey Timothy L , Perkins Andrew C , Tallack Michael R , Xu Zhao , Liu Hui 
Published: December 2012

AbstractBackgroundStudy on long non-coding RNAs (lncRNAs) has been promoted by high-throughput RNA sequencing (RNA-Seq). However, it is still not trivial to identify lncRNAs from the RNA-Seq data and it remains a challenge to uncover their functions.ResultsWe present a computational pipeline for detecting novel lncRNAs from the RNA-Seq data. First, the genome-guided transcriptome reconstruction is used to generate initially assembled transcripts. The possible partial transcripts and artefacts are filtered according to the quantified expression level. After that, novel lncRNAs are detected by further filtering known transcripts and those with high protein coding potential, using a newly developed program called lncRScan. We applied our pipeline to a mouseKlf1knockout dataset, and discussed the plausible functions of the novel lncRNAs we detected by differential expression analysis. We identified 308 novel lncRNA candidates, which have shorter transcript length, fewer exons, shorter putative open reading frame, compared with known protein-coding transcripts. Of the lncRNAs, 52 large intergenic ncRNAs (lincRNAs) show lower expression level than the protein-coding ones and 13 lncRNAs represent significant differential expression between the wild-type andKlf1knockout conditions.ConclusionsOur method can predict a set of novel lncRNAs from the RNA-Seq data. Some of the lncRNAs are showed differentially expressed between the wild-type andKlf1knockout strains, suggested that those novel lncRNAs can be given high priority in further functional studies.
A linear-time algorithm for reconstructing zero-recombinant haplotype configuration on a pedigree
Authors: Lai En-Yu , Wang Wei-Bung , Jiang Tao , Wu Kun-Pin 
Published: December 2012

Abstract

Background
When studying genetic diseases in which genetic variations are passed on to offspring, the ability to distinguish between paternal and maternal alleles is essential. Determining haplotypes from genotype data is called haplotype inference. Most existing computational algorithms for haplotype inference have been designed to use genotype data collected from individuals in the form of a pedigree. A haplotype is regarded as a hereditary unit and therefore input pedigrees are preferred that are free of mutational events and have a minimum number of genetic recombinational events. These ideas motivated the zero-recombinant haplotype configuration (ZRHC) problem, which strictly follows the Mendelian law of inheritance, namely that one haplotype of each child is inherited from the father and the other haplotype is inherited from the mother, both without any mutation. So far no linear-time algorithm for ZRHC has been proposed for general pedigrees, even though the number of mating loops in a human pedigree is usually very small and can be regarded as constant.

Results
Given a pedigree with n individuals, m marker loci, and k mating loops, we proposed an algorithm that can provide a general solution to the zero-recombinant haplotype configuration problem in O(kmn + k
2
m) time. In addition, this algorithm can be modified to detect inconsistencies within the genotype data without loss of efficiency. The proposed algorithm was subject to 12000 experiments to verify its performance using different (n, m) combinations. The value of k was uniformly distributed between zero and six throughout all experiments. The experimental results show a great linearity in terms of execution time in relation to input size when both n and m are larger than 100. For those experiments where n or m are less than 100, the proposed algorithm runs very fast, in thousandth to hundredth of a second, on a personal desktop computer.

Conclusions
We have developed the first deterministic linear-time algorithm for the zero-recombinant haplotype configuration problem. Our experimental results demonstrated the linearity of its execution time in relation to the input size. The proposed algorithm can be modified to detect inconsistency within the genotype data without loss of efficiency and is expected to be able to handle recombinant and missing data with further extension.
Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets
Authors: Chiu Yi-Yuan , Lin Chun-Yu , Lin Chih-Ta , Hsu Kai-Cheng , Chang Li-Zen , Yang Jinn-Moon 
Published: December 2012

Abstract

Background
To discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). In general, the polypharmacological proteins often share similar local binding environments and motifs. As the exponential growth of the number of protein structures, to find the similar structural binding motifs (pharma-motifs) is an emergency task for drug discovery (e.g. side effects and new uses for old drugs) and protein functions.

Results
We have developed a Space-Related Pharmamotifs (called SRPmotif) method to recognize the binding motifs by searching against protein structure database. SRPmotif is able to recognize conserved binding environments containing spatially discontinuous pharma-motifs which are often short conserved peptides with specific physico-chemical properties for protein functions. Among 356 pharma-motifs, 56.5% interacting residues are highly conserved. Experimental results indicate that 81.1% and 92.7% polypharmacological targets of each protein-ligand complex are annotated with same biological process (BP) and molecular function (MF) terms, respectively, based on Gene Ontology (GO). Our experimental results show that the identified pharma-motifs often consist of key residues in functional (active) sites and play the key roles for protein functions. The SRPmotif is available at http://gemdock.life.nctu.edu.tw/SRP/.

Conclusions
SRPmotif is able to identify similar pharma-interfaces and pharma-motifs sharing similar binding environments for polypharmacological targets by rapidly searching against the protein structure database. Pharma-motifs describe the conservations of binding environments for drug discovery and protein functions. Additionally, these pharma-motifs provide the clues for discovering new sequence-based motifs to predict protein functions from protein sequence databases. We believe that SRPmotif is useful for elucidating protein functions and drug discovery.
In silico engineering of aggregation-prone recombinant proteins for substrate recognition by the chaperonin GroEL
Authors: Kumar Vipul , Punetha Ankita , Sundar Durai , Chaudhuri Tapan K 
Published: December 2012

Abstract

Background
Molecular chaperones appear to have been evolved to facilitate protein folding in the cell through entrapment of folding intermediates on the interior of a large cavity formed between GroEL and its co-chaperonin GroES. They bind newly synthesized or non-native polypeptides through hydrophobic interactions and prevent their aggregation. Some proteins do not interact with GroEL, hence even though they are aggregation prone, cannot be assisted by GroEL for their folding.

Results
In this study, we have attempted to engineer these non-substrate proteins to convert them as the substrate for GroEL, without compromising on their function. We have used a computational biology approach to generate mutants of the selected proteins by selectively mutating residues in the hydrophobic patch, similar to GroES mobile loop region that are responsible for interaction with GroEL, and compared with the wild counterparts for calculation of their instability and aggregation propensities. The energies of the newly designed mutants were computed through molecular dynamics simulations. We observed increased aggregation propensity of some of the mutants formed after replacing charged amino acid residues with hydrophobic ones in the well defined hydrophobic patch, raising the possibility of their binding ability to GroEL.

Conclusions
The newly generated mutants may provide potential substrates for Chaperonin GroEL, which can be experimentally generated and tested for their tendency of aggregation, interactions with GroEL and the possibility of chaperone-assisted folding to produce functional proteins.
The influence of carbapenem resistance on mortality in solid organ transplant recipients with Acinetobacter baumanniiinfection
Authors: de Gouvêa Erika Ferraz , Martins Ianick Souto , Halpern Marcia , Ferreira Adriana Lúcia Pires , Basto Samanta Teixeira , Gonçalves Renato Torres , Moreira Beatriz Meurer , Santoro-Lopes Guilherme 
Published: December 2012

Abstract

Background
Infection with carbapenem-resistant Acinetobacter baumannii has been associated with high morbidity and mortality in solid organ transplant recipients. The main objective of this study was to assess the influence of carbapenem resistance and other potential risk factors on the outcome of A. baumannii infection after kidney and liver transplantation.

Methods
Retrospective study of a case series of A. baumannii infection among liver and renal transplant recipients. The primary outcome was death associated with A. baumannii infection. Multivariate logistic regression was used to assess the influence of carbapenem resistance and other covariates on the outcome.

Results
Forty-nine cases of A. baumannii infection affecting 24 kidney and 25 liver transplant recipients were studied. Eighteen cases (37%) were caused by carbapenem-resistant isolates. There were 17 (35%) deaths associated with A. baumannii infection. In unadjusted analysis, liver transplantation (p = 0.003), acquisition in intensive care unit (p = 0.001), extra-urinary site of infection (p < 0.001), mechanical ventilation (p = 0.001), use of central venous catheter (p = 0.008) and presentation with septic shock (p = 0.02) were significantly related to a higher risk of mortality associated with A. baumannii infection. The number of deaths associated with A. baumannii infection was higher among patients infected with carbapenem-resistant isolates, but the difference was not significant (p = 0.28). In multivariate analysis, the risk of A. baumannii-associated mortality was higher in patients with infection acquired in the intensive care unit (odds ratio [OR] = 34.8, p = 0.01) and on mechanical ventilation (OR = 15.2, p = 0.04). Appropriate empiric antimicrobial therapy was associated with significantly lower mortality (OR = 0.04, p = 0.03), but carbapenem resistance had no impact on it (OR = 0.73, p = 0.70).

Conclusion
These findings suggest that A. baumannii-associated mortality among liver and kidney transplant recipients is influenced by baseline clinical severity and by the early start of appropriate therapy, but not by carbapenem resistance.
Overexpression of SERBP1 (Plasminogen activator inhibitor 1 RNA binding protein) in human breast cancer is correlated with favourable prognosis
Authors: Serce Nuran Bektas , Boesl Andreas , Klaman Irina , von Serényi Sonja , Noetzel Erik , Press Michael F , Dimmler Arno , Hartmann Arndt , Sehouli Jalid , Knuechel Ruth , Beckmann Matthias W , Fasching Peter A , Dahl Edgar 
Published: December 2012

Abstract

Background
Plasminogen activator inhibitor 1 (PAI-1) overexpression is an important prognostic and predictive biomarker in human breast cancer. SERBP1, a protein that is supposed to regulate the stability of PAI-1 mRNA, may play a role in gynaecological cancers as well, since upregulation of SERBP1 was described in ovarian cancer recently. This is the first study to present a systematic characterisation of SERBP1 expression in human breast cancer and normal breast tissue at both the mRNA and the protein level.

Methods
Using semiquantitative realtime PCR we analysed SERBP1 expression in different normal human tissues (n = 25), and in matched pairs of normal (n = 7) and cancerous breast tissues (n = 7). SERBP1 protein expression was analysed in two independent cohorts on tissue microarrays (TMAs), an initial evaluation set, consisting of 193 breast carcinomas and 48 normal breast tissues, and a second large validation set, consisting of 605 breast carcinomas. In addition, a collection of benign (n = 2) and malignant (n = 6) mammary cell lines as well as breast carcinoma lysates (n = 16) were investigated for SERBP1 expression by Western blot analysis. Furthermore, applying non-radioisotopic in situ hybridisation a subset of normal (n = 10) and cancerous (n = 10) breast tissue specimens from the initial TMA were analysed for SERBP1 mRNA expression.

Results
SERBP1 is not differentially expressed in breast carcinoma compared to normal breast tissue, both at the RNA and protein level. However, recurrence-free survival analysis showed a significant correlation (P = 0.008) between abundant SERBP1 expression in breast carcinoma and favourable prognosis. Interestingly, overall survival analysis also displayed a tendency (P = 0.09) towards favourable prognosis when SERBP1 was overexpressed in breast cancer.

Conclusions
The RNA-binding protein SERBP1 is abundantly expressed in human breast cancer and may represent a novel breast tumour marker with prognostic significance. Its potential involvement in the plasminogen activator protease cascade warrants further investigation.
Household food access and child malnutrition: results from the eight-country MAL-ED study
Authors: Psaki Stephanie , Bhutta Zulfiqar A , Ahmed Tahmeed , Ahmed Shamsir , Bessong Pascal , Islam Munirul , John Sushil , Kosek Margaret , Lima Aldo , Nesamvuni Cebisa , Shrestha Prakash , Svensen Erling , McGrath Monica , Richard Stephanie , Seidman Jessica , Caulfield Laura , Miller Mark , Checkley William ,   and MALED Network Investigators
Published: December 2012

Abstract

Background
Stunting results from decreased food intake, poor diet quality, and a high burden of early childhood infections, and contributes to significant morbidity and mortality worldwide. Although food insecurity is an important determinant of child nutrition, including stunting, development of universal measures has been challenging due to cumbersome nutritional questionnaires and concerns about lack of comparability across populations. We investigate the relationship between household food access, one component of food security, and indicators of nutritional status in early childhood across eight country sites.

Methods
We administered a socioeconomic survey to 800 households in research sites in eight countries, including a recently validated nine-item food access insecurity questionnaire, and obtained anthropometric measurements from children aged 24 to 60 months. We used multivariable regression models to assess the relationship between household food access insecurity and anthropometry in children, and we assessed the invariance of that relationship across country sites.

Results
Average age of study children was 41 months. Mean food access insecurity score (range: 0–27) was 5.8, and varied from 2.4 in Nepal to 8.3 in Pakistan. Across sites, the prevalence of stunting (42%) was much higher than the prevalence of wasting (6%). In pooled regression analyses, a 10-point increase in food access insecurity score was associated with a 0.20 SD decrease in height-for-age Z score (95% CI 0.05 to 0.34 SD; p = 0.008). A likelihood ratio test for heterogeneity revealed that this relationship was consistent across countries (p = 0.17).

Conclusions
Our study provides evidence of the validity of using a simple household food access insecurity score to investigate the etiology of childhood growth faltering across diverse geographic settings. Such a measure could be used to direct interventions by identifying children at risk of illness and death related to malnutrition.