bluuebunny/crossref_metadata_2025_split huggingface dataset:
The empirical codon mutation matrix as a communication channel
Authors: Nigatu Dawit , Mahmood Attiya , Henkel Werner 
Published: March 2014

Abstract

Background
A number of evolutionary models have been widely used for sequence alignment, phylogenetic tree reconstruction, and database searches. These models focus on how sets of independent substitutions between amino acids or codons derive one protein sequence from its ancestral sequence during evolution. In this paper, we regard the Empirical Codon Mutation (ECM) Matrix as a communication channel and compute the corresponding channel capacity.

Results
The channel capacity of 4.1875 bit, which is needed to preserve the information determined by the amino acid distribution, is obtained with an exponential factor of 0.26 applied to the ECM matrix. Additionally, we have obtained the optimum capacity achieving codon distribution. Compared to the biological distribution, there is an obvious difference, however, the distribution among synonymous codons is preserved. More importantly, the results show that the biological codon distribution allows for a “transmission” at a rate very close to the capacity.

Conclusion
We computed an exponential factor for the ECM matrix that would still allow for preserving the genetic information given the redundancy that is present in the codon-to-amino acid mapping. This gives an insight how such a mutation matrix relates to the preservation of a species in an information-theoretic sense.
H ip joint pain in children with cerebral palsy and developmental dysplasia of the hip: why are the differences so huge?
Authors: Grzegorzewski Andrzej , Jóźwiak Marek , Pawlak Maciej , Modrzewski Tadeusz , Buchcic Piotr , Masłoń Adrian 
Published: March 2014

Abstract

Backgrounds
Non-traumatic hip dislocation in children is most often observed in the course of developmental dysplasia of the hip (DDH) and infantile cerebral palsy. The risk of pain sensations from dislocated hip joint differentiates the discussed groups of patients. Will every painless hip joint in children with cerebral palsy painful in the future?

Methods
Material included 34 samples of joint capsule and 34 femoral head ligaments, collected during open hip joint reduction from 19 children with CP, GMFCS level V and from 15 children with DDH and unilateral hip dislocation. All the children were surgically treated.
The density of nociceptive fibres was compared between the children with CP and DDH, using S-100 and substance P monoclonal antibodies.

Results
More frequent positive immunohistochemical reaction to S-100 protein concerned structures of the femoral head ligaments in children with CP and cartilage losses on the femoral head, when compared to the same structures in children with DDH (p = 0.010). More frequent were found positive immunohistochemical reactions for S-100 protein in the joint capsules of children with cartilage losses (p = 0.031) and pain ailments vs. the children with DDH (p = 0.027). More frequent positive reaction to substance P concerned in femoral head ligaments in CP children and cartilage lesions (p = 0.002) or with pain ailments (p = 0.001) vs. the DDH children.

Conclusions
Surgical treatment of hip joint dislocation should be regarded as a prophylactics of pain sensations, induced by tissue sensitisation, inflammatory process development or articular cartilage defects.
Choroidal atrophy and loss of choriocapillaris in convalescent stage of Vogt-Koyanagi-Harada disease: in vivo documentation
Authors: Nazari Hossein , Hariri Amirhossein , Hu Zhihong , Ouyang Yanwei , Sadda SiriniVas , Rao Narsing A 
Published: March 2014

Abstract

Background
The aim of this study was to determine the clinical significance of posterior choroidal thickness and vascular changes in the convalescent stage of Vogt-Koyanagi-Harada disease (VKH). Macular spectral domain optical coherence tomography (SD-OCT) images of 22 eyes of 13 consecutive patients with VKH at the convalescent stage were compared to 17 eyes of 9 age/sex/refraction-matched normal subjects. The choriocapillaris layer, medium choroidal vessels (Sattler's layer), and large choroidal vessels (Haller's layer) were assessed in foveal SD-OCT scans. The presence and the extent of disruption of outer retinal structures were also noted. Inner and outer choroid boundaries were manually drawn on horizontal raster SD-OCT scans, and choroidal thickness and volume maps were generated. Correlation analysis was run to assess the association of the above parameters in the VKH patients compared to the normal subjects.

Results
In the eyes with convalescent stage of VKH, mean choroidal thickness in the foveal central subfield (200 ± 60 μm) was lower than in matched controls (288 ± 40 μm) (P < 0.0001). A thinner sub-macular choroid correlated with a lower visual acuity in uveitis eyes (Pearson correlation, r = -0.5089, P = 0.005). While the choriocapillaris layer was continuous and intact in all control eyes, various degrees of choriocapillaris loss were observed in 11 eyes (50%) with VKH (P < 0.0001). In these patients, the presence of outer retinal disruption was associated with a lower visual acuity (Spearman correlation, P < 0.001).

Conclusions
The choroid is significantly thinner and the choriocapillaris layer is disrupted in the eyes with convalescent stage of VKH. Evaluation of the choriocapillaris in SD-OCT scans may be a useful surrogate marker for visual function in the convalescent stage of VKH.
At the Bench: Adoptive cell therapy for melanoma
Authors: Urba Walter J 
Published: March 2014

AbstractThe cellular and molecular principles that furnish the foundation for ACT of melanoma and their implications for further clinical research are reviewed. The parallel advances in basic immunology, preclinical animal studies, and clinical trials over the last two decades have been integrated successfully with improvements in technology to produce an effective ACT strategy for patients with melanoma. From the initial observation that tumors could be treated effectively by the transfer of immune cells to current strategies using preconditioning with myeloablative therapy before adoptive transfer of native or genetically altered T cells, the role of preclinical animal models is discussed. The importance of the pmel transgenic mouse model in the determination of the mechanisms of lymphodepletion, the ongoing work to identify the optimal T cells for adoptive immunotherapy, and the early impact of the emerging discipline of synthetic biology are highlighted. The clinical consequences of the research described herein are reviewed in the companion manuscript.
Hepatitis C virus (HCV)-induced suppressor of cytokine signaling (SOCS) 3 regulates proinflammatory TNF-α responses
Authors: Collins Aideen S , Ahmed Suaad , Napoletano Silvia , Schroeder Martina , Johnston James A , Hegarty John E , O'Farrelly Cliona , Stevenson Nigel J 
Published: March 2014

AbstractTNF-α is a proinflammatory cytokine, dramatically elevated during pathogenic infection and often responsible for inflammation-induced disease pathology. SOCS proteins are inhibitors of cytokine signaling and regulators of inflammation. In this study, we found that both SOCS1 and SOCS3 were transiently induced by TNF-α and negatively regulate its NF-κB-mediated signal transduction. We discovered that PBMCs from HCV-infected patients have elevated endogenous SOCS3 expression but less TNF-α-mediated IκB degradation and proinflammatory cytokine production than healthy controls. HCV protein expression in Huh7 hepatocytes also induced SOCS3 and directly inhibited TNF-α-mediated IL-8 production. Furthermore, we found that SOCS3 associates with TRAF2 and inhibits TRAF2-mediated NF-κB promoter activity, suggesting a mechanism by which SOCS3 inhibits TNF-α-mediated signaling. These results demonstrate a role for SOCS3 in regulating proinflammatory TNF-α signal transduction and reveal a novel immune-modulatory mechanism by which HCV suppresses inflammatory responses in primary immune cells and hepatocytes, perhaps explaining mild pathology often associated with acute HCV infection.
Coilin association with Box C/D scaRNA suggests a direct role for the Cajal body marker protein in scaRNP biogenesis
Authors: Enwerem Isioma I. , Velma Venkatramreddy , Broome Hanna J. , Kuna Marija , Begum Rowshan A. , Hebert Michael D. 
Published: March 2014

ABSTRACT
Spliceosomal small nuclear ribonucleoproteins (snRNPs) are enriched in the Cajal body (CB). Guide RNAs, known as small Cajal body-specific RNAs (scaRNAs), direct modification of the small nuclear RNA (snRNA) component of the snRNP. The protein WRAP53 binds a sequence motif (the CAB box) found in many scaRNAs and the RNA component of telomerase (hTR) and targets these RNAs to the CB. We have previously reported that coilin, the CB marker protein, associates with certain non-coding RNAs. For a more comprehensive examination of the RNAs associated with coilin, we have sequenced the RNA isolated from coilin immunocomplexes. A striking preferential association of coilin with the box C/D scaRNAs 2 and 9, which lack a CAB box, was observed. This association varied by treatment condition and WRAP53 knockdown. In contrast, reduction of WRAP53 did not alter the level of coilin association with hTR. Additional studies showed that coilin degrades/processes scaRNA 2 and 9, associates with active telomerase and can influence telomerase activity. These findings suggest that coilin plays a novel role in the biogenesis of box C/D scaRNPs and telomerase.
Various applications of TALEN- and CRISPR/Cas9-mediated homologous recombination to modify the Drosophila genome
Authors: Yu Zhongsheng , Chen Hanqing , Liu Jiyong , Zhang Hongtao , Yan Yan , Zhu Nannan , Guo Yawen , Yang Bo , Chang Yan , Dai Fei , Liang Xuehong , Chen Yixu , Shen Yan , Deng Wu-Min , Chen Jianming , Zhang Bo , Li Changqing , Jiao Renjie 
Published: March 2014

ABSTRACT
Modifying the genomes of many organisms is becoming as easy as manipulating DNA in test tubes, which is made possible by two recently developed techniques based on either the customizable DNA binding protein, TALEN, or the CRISPR/Cas9 system. Here, we describe a series of efficient applications derived from these two technologies, in combination with various homologous donor DNA plasmids, to manipulate the Drosophila genome: (1) to precisely generate genomic deletions; (2) to make genomic replacement of a DNA fragment at single nucleotide resolution; and (3) to generate precise insertions to tag target proteins for tracing their endogenous expressions. For more convenient genomic manipulations, we established an easy-to-screen platform by knocking in a white marker through homologous recombination. Further, we provided a strategy to remove the unwanted duplications generated during the “ends-in” recombination process. Our results also indicate that TALEN and CRISPR/Cas9 had comparable efficiency in mediating genomic modifications through HDR (homology-directed repair); either TALEN or the CRISPR/Cas9 system could efficiently mediate in vivo replacement of DNA fragments of up to 5 kb in Drosophila, providing an ideal genetic tool for functional annotations of the Drosophila genome.
Novel apprehensions and hybrid utterances: Practice, research, language
Authors: Kill Rebekka 
Published: March 2014

Abstract
This article explores current debates on the role of writing in artistic research. This discussion has been in train for several decades, and yet we are still not clear, as an academic community, in regards to a number of issues related to the status of, role and purpose writing in research by practice. In order to explore this I initially look at some of the discussion, and confusion, surrounding the regulations on, and support for, Ph.D.s in practice in universities in the United Kingdom. I will also explore disciplinary notions of research and then the final part of the article digs a little deeper into the effect of language and logobias in the university.
Practice what you teach? Examining the significance and complexities of textile designer educator creative practice
Authors: Britt Helena 
Published: March 2014

Abstract
Learning to practice is central to undergraduate and the majority of taught postgraduate art and design programmes in the United Kingdom. Therefore, the creative practice of educators employed to teach, including part-time and visiting lecturers, has long been recognized as contributing to student learning. An emphasis on undertaking research has prompted educators, initially employed due to their expertise as creative practitioners, to formulate and adopt practice-led and practice-based approaches to research. The benefits of educator research to learning and teaching are also recognized. The higher education (HE) system is in a continual state of change, higher education institutions (HEIs) and educators respond to government policy and initiatives. Operating in the United Kingdom HE system together with pressures encountered can be counterproductive to educator creative practice. While research can involve creative practice activity there are issues, for example, with adoption of appropriate methodologies and difficulties with explicating tacit knowledge through writing. As a discipline, textile design exists on the periphery of design and design research discourse. The research project featured in this article responds to the context described and the deficit of literature surrounding contemporary textile design HE and educator creative practice and teaching linkages. The focus is on the textile designer educator role in the United Kingdom and examination of creative practice activity, to establish the means by which educator creative practice informs teaching and therefore influences student learning. The investigation used a combination of self-case study, survey, interview and case study methods. Findings indicate that textile designer educator creative practice is important to HE due to the positive impact that engagement has on teaching. However, issues are encountered and these are discussed in order to propose suggestions to improve the existent situation and to highlight areas for further investigation.
Medium of ‘Curiosità’: An innovative studio environment for design education
Authors: Yurtkuran Selay , Taneli Yavuz 
Published: March 2014

Abstract
Basic Design is a studio course in architectural education that requires creative problem-solving and critical thinking skills, a non-ending appetite for knowledge, and non-diminishing curiosity. This article describes an innovative studio environment that allows for this particular mentality to flourish and appropriate professional skills to be strengthened. The manuscript further outlines a studio project that utilizes an olfactory stimulus to rekindle curiosity. The project is an introductory exercise, using line as a conceptual design element, and a tool for communication. Through subsequent content analysis, the qualitative case study methodologically records this two-week exercise, and uses verbal and visual data, as well as written student responses to assess the benefits of this altered learning experience. The authors argue that, only through curiosity will the studio environment become the catalyst to foster innovative design ideas.
Inferring a collective concept of research from the actions of the art and design research community
Authors: Biggs Michael , Büchler Daniela 
Published: March 2014

Abstract
This article examines output types as manifestations of different concepts of research. We compare the UK academic scene to that of Brazil, identifying the former as responding ‘bottom-up’ to researcher needs and the latter determining ‘top-down’ what researchers can do. Taking the UK model as indicative of what researchers think they need, we undertook a detailed analysis of the output types used in RAE2008 across all subjects in order to see which types were used and by whom. We also undertook a further analysis of the use of traditional, text-based formats in art and design, and the use of non-traditional, non-textual output types in other subjects. We conclude that both the journal format and the exhibition format are expressive of the understanding each community has of the meaning of research as an activity. This is further reinforced by the national structures within which research is undertaken and evaluated.
Screening for diabetic complications as a tool for the evaluation of medical and preventive aid to patients
Authors: Suntsov Iu I , Maslova O V , Dedov I I 
Published: March 2014

The objective of this work was to study the actual prevalence of diabetes mellitus complications and evaluate the quality of health care provided to the patients with these problems in different regions of Russia. A random sample of 11 240 patients with diabetes mellitus (DM) was obtained from a total of 20 regions of the Russian Federation. The study protocol included evaluation of visual function, the state of peripheral nervous system and lower extremities, renal and cardiovascular functions; in addition, HbA1c, creatinine, total cholesterol and triglyceride levels were measured along with albuminuria. It was found that the actual prevalence of major diabetic complications is 20-50% higher than the registered one. The overwhelming majority of the patients were shown to be chronically decompensated. This finding holds for 85.5% of the children, 92.6% of the adolescents, 83.9% and 74.8% of the adult patients with types 1 and 2 DM respectively. The HbA1c level in patients living in rural areas was 33.7-42.1% higher than in residents of regional urban centres. Fewer than 14.4% and 0.6% of the patients with type 2 DM used insulin and its analogs respectively. Overall, the study demonstrated rather poor quality of medical and preventive aid provided to diabetic patients and the necessity of its improvement.
Emotional-volitional disorders in patients with type 2 diabetes mellitus, concomitant arterial hypertension and diabetic polyneuropathy
Authors: Petrova M M , Kurumchina O B , Pronina E A 
Published: March 2014

The objective of the present work was to evaluate effects of type 2 diabetes mellitus (DM2) combined with arterial hypertension (AH) and diabetic polyneuropathy (DPN) on the development of alterations in the emotional-volitional sphere. The work was comprised of two prospective studies; one of them (study 1) included 140 women presenting with DM2, the other (study 2) enrolled 80 patients with DM2 hospitalized at the Endocrinological Department of N.S. Karpovich City Clinical Hospital No 6, Krasnoyarsk. Disturbances in the emotional-volitional sphere were evaluated based on the hospital anxiety and depression scale (HADS). Their frequency proved to be as high as 67.9 and 70.7% in studies 1 and 2 respectively. The number of anxiety disorders was on the whole greater than that of depressive ones. The latter disorders in patients with AH occurred twice as often as in DM2 patients without AH (50.5 and 25.9% respectively). The frequency of anxiety disorders was not significantly different in the two groups, but they were found to be more severe in patients presenting with combination of DM2 and AH. It is concluded that DM2 is associated with frequent clinically significant anxiety and depressive symptoms depending on the duration of the disease and insulinotherapy. Patients presenting with a combination of DM2 and AH or DPN suffer significantly more pronounced anxiety and depression disordered.
About informative value of very high prolactin levels in patients presenting with prolactin-secreting pituitary macroadenomas (clinical observations)
Authors: Astaf'eva L I , Kadashev B A , Tenedieva V D , Moshkin A V , Shifrin M A 
Published: March 2014

The mean blood prolactin level in patients with microprolactinomas is usually 3000-4000 mU/l compared with 10 000-20 000 mU/l in cases presenting with macroprolactinomas. It may be as high as 1 mln mU/l and more in patients with a giant tumour. The measurement of prolactin levels requires laboratory studies of strongly diluted plasma samples. Significant dilution is fraught with erroneous prolactin levels: nevertheless, this approach allows a tendency toward decreasing concentration of prolactin to be revealed which may be important for taking rapid decision concerning the choice of the treatment strategy (either surgical or medicamental) especially in critical situations. A few clinical cases of giant prolactinomas with an unusually high blood prolactin level are described with reference to its dynamics during treatment with cabergoline.
Papillon‐Lefèvre or Haim‐Munk Syndrome? Report on Two Sisters in a Consanguineous Family
Authors: Dababneh Reem H. , Jebrin Sami E. , Khouri Antwan T. , Bissada Nabil F. 
Published: March 2014

Introduction: Papillon‐Lefèvre (PLS) and Haim‐Munk (HMS) syndromes are rare autosomal recessive type IV palmar plantar keratosis (PPK), which are clinically different from other types of PPK by their association with aggressive periodontitis and genetically by the mode of transmission.Case Presentation: Two Jordanian sisters, aged 10 and 13 years, from a consanguineous family were preliminarily diagnosed as having PLS by a pediatric dentist who referred them to the periodontal clinic in May 2010 because of the presence of loose teeth and to a dermatologist for the management of existing skin lesions. Physical examination of the two sisters revealed severe bilateral hyperkeratotic lesions on the palms and soles extending to the lateral and dorsal aspects; bilateral pes planus; scaly patches on the knees and elbows; overgrown fingernails and toenails that were curved inward; and range of movement limitations in the fingers. The patients were treated with topical emollients and keratolytic preparations containing salicylic acid for the skin lesions. Oral radiographs showed generalized severe bone loss around the remaining primary and permanent teeth. Oral treatment included dental prophylaxis, chlorhexidine mouthrinse, amoxicillin syrup, and extraction of several teeth.Conclusions: The two patients in this case report presented atypical symptoms of PLS. Mutational genetic analysis is proposed to confirm whether PLS and HMS are the same or two different symptoms.