bluuebunny/crossref_metadata_2025_split huggingface dataset:
Controlling DNA degradation from a distance: a new role for the Mu transposition enhancer
Authors: Choi Wonyoung , Saha Rudra P. , Jang Sooin , Harshey Rasika M. 
Published: September 2014

SummaryPhage Mu is unique among transposable elements in employing a transposition enhancer. The enhancer DNA segment is the site where the transposase MuA binds and makes bridging interactions with the two Mu ends, interwrapping the ends with the enhancer in a complex topology essential for assembling a catalytically active transpososome. The enhancer is also the site at which regulatory proteins control divergent transcription of genes that determine the phage lysis‐lysogeny decision. Here we report a third function for the enhancer – that of regulating degradation of extraneous DNA attached to both ends of infecting Mu. This DNA is protected from nucleases by a phage protein until Mu integrates into the host chromosome, after which it is rapidly degraded. We find that leftward transcription at the enhancer, expected to disrupt its topology within the transpososome, blocks degradation of this DNA. Disruption of the enhancer would lead to the loss or dislocation of two non‐catalytic MuA subunits positioned in the transpososome by the enhancer. We provide several lines of support for this inference, and conclude that these subunits are important for activating degradation of the flanking DNA. This work also reveals a role for enhancer topology in phage development.
Identification of Trypanosoma brucei components involved in trypanolysis by normal human serum
Authors: Lecordier Laurence , Uzureau Pierrick , Tebabi Patricia , Pérez‐Morga David , Nolan Derek , Schumann Burkard Gabriela , Roditi Isabel , Pays Etienne 
Published: September 2014

SummaryNormal human serum (NHS) confers human resistance to infection by the parasite Trypanosoma brucei owing to the trypanolytic activity of apolipoprotein L1 (APOL1), present in two serum complexes termed Trypanolytic Factors (TLF‐1 and ‐2). In order to identify parasite components involved in the intracellular trafficking and activity of TLFs, an inducible RNA interference (RNAi) genomic DNA library constructed in bloodstream form T. brucei was subjected to RNAi induction and selection for resistant parasites under NHS conditions favouring either TLF‐1 or TLF‐2 uptake. While TLF‐1 conditions readily selected the haptoglobin‐haemoglobin (HP‐HB) surface receptor TbHpHbR as expected, given its known ability to bind TLF‐1, under TLF‐2 conditions no specific receptor for TLF‐2 was identified. Instead, the screen allowed the identification of five distinct factors expected to be involved in the assembly of the vacuolar proton pump V‐ATPase and consecutive endosomal acidification. These data confirm that lowering the pH during endocytosis is required for APOL1 toxic activity.
Rapid recovery of Dutch gray seal colonies fueled by immigration
Authors: Brasseur Sophie M. J. M. , van Polanen Petel Tamara D. , Gerrodette Tim , Meesters Erik H.W.G. , Reijnders Peter J. H. , Aarts Geert 
Published: September 2014

AbstractGray seals were first observed breeding in the Dutch Wadden Sea in 1985, after centuries of absence. The breeding colony there is now the largest on the European continent. We describe the changes in gray seal numbers and their geographical expansion, and estimate how these processes were influenced by immigration from other colonies. Counts of hauled out animals were carried out between 1985 and 2013, monitoring three different periods of the seals' annual cycle. Using priors determined for the UK population, a Bayesian demographic model was fitted to pup numbers to estimate the population parameters driving the growth. This included immigration of subadults into the breeding population, which contributed to an average growth rate in the pup counts of 19%/yr, much higher than expected in a closed population. This immigration may account for approximately 35% of the total annual growth. In addition, at least 200 gray seals from the UK visit the area temporarily. Recovery of the population in the Netherlands occurred more than 50 yr after gray seals were protected in the UK. These time scales should be taken into account when studying long living marine mammals, e.g., in impact and conservation studies.
Host‐iron assimilation: pathogenesis and novel therapies of mucormycosis
Authors: Ibrahim Ashraf S. 
Published: September 2014

SummaryMucormycosis is a fungal infection caused by organisms belonging to the orderMucorales. Although considered uncommon, mucormycosis has been steadily increasing in incidents for the last two decades. Mortality of the disease is unacceptably high despite antifungal therapy and surgical interventions. The lack of understanding of the pathogenesis of the disease and the absence of rapid diagnostic assay contribute to the poor prognosis of mucormycosis. The hyper susceptibility of patients with elevated available serum iron points to the critical role of the ability ofMucoralesto acquire host iron as a critical virulence factor. Specifically patients with deferoxamine‐therapy, hyperglycaemic with or without ketoacidosis, or other forms of acidosis are uniquely predisposed to mucormycosis. In this review, we discuss the molecular mechanisms of infection in these patient categories in an attempt to identify novel therapies for a disease with poor prognosis. Emphasis on the effect of glucose and free iron on host–pathogen interactions are also covered.
Effectiveness of zonisamide in a patient with Parkinson's disease and various levodopa‐induced psychotic symptoms
Authors: Yabe Ichiro , Ohta Midori , Egashira Toshiaki , Sato Kazunori , Kano Takahiro , Hirotani Makoto , Kunieda Yasuyuki , Sasaki Hidenao 
Published: September 2014

AbstractLevodopa and dopamine agonists are useful as Parkinson's disease medications. However, they often induce persistent psychotic symptoms and motor complications, which make Parkinson's disease treatment difficult. This is a case report of a patient with advanced Parkinson's disease accompanied by exacerbation of motor symptoms and psychotic symptoms derived from prolonged use of conventional anti‐Parkinson's disease drugs, and in whom adjunctive therapy with a new anti‐Parkinson's disease drug, zonisamide, was shown to improve motor symptoms with no exacerbation of psychotic symptoms.
Potentially malignant oral disorders and high‐risk habits in liver cirrhosis and lung cancer patients
Authors: Salarić I , Povrzanović I , Brajdić D , Lukšić I , Macan D 
Published: September 2014

ObjectivesTo analyze the role of smoking, drinking, and their synergistic effect in the occurrence of potentially malignant oral disorders (PMOD).Subjects and methodsWe examined three groups: 50 patients with lung cancer, 50 patients with liver cirrhosis, and 50 patients with clear medical history. Scores were developed for drinking, smoking, drinking & smoking, and PMOD.ResultsAll four scores were the lowest in the control group. The lung cancer group showed the highest Smoking, Alcohol & Smoking and Lesions score, while the liver cirrhosis group had the Alcohol score the highest. Compared with the control group, lung cancer group is more likely to develop a PMOD than the liver cirrhosis group (OR = 12.31/OR = 6.71). Statistical significance between the groups was found in the Lesions score (χ2 = 15.34; P = 0.001).ConclusionsThe patients with lung cancer and liver cirrhosis represent a high‐risk group for PMOD. Patients with lung cancer and liver cirrhosis have never, to our knowledge, been categorized as high‐risk patients for PMOD. After diagnosed, patients with lung cancer and liver cirrhosis should have a routine oral cavity examination, as they present a high‐risk group for PMOD and oral cancer.
‘To me, it's like a little box of tricks’: Breaking the depressive interlock as a programme participant in mindfulness‐based cognitive therapy
Authors: Murphy Helen , Lahtinen Marika 
Published: September 2014

ObjectivesMindfulness meditation practices have become increasingly popular in clinical therapies, changing patterns of depressogenic thinking for individuals who experience consecutive episodes of depression. We were interested in finding out how mindfulness‐based cognitive therapy (MBCT) worked for programme participants by focussing on how meditative practices changed their relationships with their thoughts.DesignData for the study came from six semi‐structured research interviews carried out with individuals who had taken part in an 8‐week MBCT programme.MethodsWe used interpretative phenomenological analysis to analyse the experiential accounts.ResultsWe report on two superordinate themes – Engaging the Neutral Mind (with subordinate themes ‘breaking the paralysis of worry’ and ‘choosing to think differently’) and Experiencing the Neutral Mind (with subordinate themes of ‘reflection on previous thinking styles’ and ‘becoming psychologically self‐reliant’).ConclusionsThemes from the present study offer support to the assertion that mindfulness meditation helps facilitate a different mode of meta‐cognitive processing with which to handle depression‐related cognitions.Practitioner points

Participants reported that they experienced an enhanced capacity to differentiate between their thought processes, experiencing an ability to tolerate some more uncomfortable thoughts, and experiencing a/more choice in how to respond to thoughts.

Participants recognized that ruminating over negative thoughts was related to depressive states and experienced a shift in meta‐cognitive processes that actively challenged depressogenic cognitions.

Participants became more psychologically self‐reliant and therapeutically independent following MBCT.

Integrating mindfulness‐based practices in therapy may be a mediating factor in sustaining psychological well‐being and may help clients develop self‐compassion.

Future research looks to examining exit cases to understand elements of MBCT which are experienced as less successful by clients.
Health‐related quality of life in pediatric intestinal transplantation
Authors: Andres A. M. , Alameda A. , Mayoral O. , Hernandez F. , Dominguez E. , Martinez Ojinaga E. , Ramos E. , Prieto G. , Lopez Santamaría M. , Tovar J. A. 
Published: September 2014

AbstractTo determine HRQOL after pediatric intestinal transplantation. Thirty‐four IT survivors from 1999 to 2012 were asked to complete age‐specific HRQOL non‐disease‐specific questionnaires: TAPQOL (0–4 yr), KINDL‐R (5–7 yr; 8–12 yr; 13–17 yr), and SF‐36v2 (>18 yr), all validated with Spanish population. Primary caregiver completed a SF‐36 questionnaire and CBI. Thirty‐one participants were included. Median age was 10.2 yr (1–29) and time after transplant 4.4 yr (0–13). Overall patient scores were 78.2 ± 10.6 (n = 8), 83.3 ± 9.7 (n = 6), 72.2 ± 9.21 (n = 6), 80.5 ± 12.4 (n = 7), and 82.2 ± 12.4 (n = 4) for each age group. Highest scores were obtained for vitality (group I), self‐esteem (group IV), and physical and social functioning and emotions (group V). Lowest scores were obtained in appetite and behavior (I), family and school (III), and chronic disease perception (III, IV). No significant differences were found between caregivers and their children. CBI showed stress in 52%. SF‐36 for caregivers was lower than general population. No significant differences were found depending on relevant clinical and sociodemographic data. HRQOL was acceptable and improved with age and time since transplantation. Parents had a slighter own QOL and worse perception of health than their children. When successful, intestinal transplantation allows a normal life in most patients and can be offered as an attractive option.
Network Governance and Programme Steering – Rationales and Tensions in Planning Child and Youth Policies
Authors: Määttä Mirja , Eriksson Kai 
Published: September 2014

AbstractThis article examines the underlying rationales and tensions of network governance and programme steering in policy planning processes by closely examining their practical implementation in the national and municipal child and youth welfare planning. It is asserted that a fundamental gap exists not only between the ideals and actual practices of networked planning, but also (despite being seen as forming a natural alliance) between network governance and programme steering. This gap is mainly because the former emphasizes governmental openness, whereas the latter tends to be connected to administrative centralization and control. In order to be successful, the article concludes, both need elements of political exclusion albeit for different reasons.
A cross‐sectional study of tetanus and diphtheria antibody concentrations post vaccination among lung transplant patients compared with healthy individuals
Authors: Rohde K.A. , Cunningham K.C. , Henriquez K.M. , Nielsen A.R. , Worzella S.L. , Hayney M.S. 
Published: September 2014

AbstractBackgroundLung transplant (LuTx) patients are routinely immunized against tetanus and diphtheria. However, few studies have been done to measure serologic immunity in the transplant population.ObjectivesThe primary objective of this study was to compare tetanus and diphtheria antibody concentrations in LuTx vs. healthy subjects.MethodsSerum was used from an available sample of 111 total individuals (n = 36 healthy;n = 75 LuTx). Tetanus and diphtheria antibody concentrations were measured using an enzyme‐linked immunosorbant assay method.ResultsA statistically significant difference in both tetanus and diphtheria antibody concentrations was found between the groups. The median concentration of tetanus antibody was higher for healthy individuals compared with the LuTx group (3.2 IU/mL [1.2–5.2 interquartile range {IQR}] vs. 1.3 IU/mL [0.4–2.6IQR], respectively;P = 0.0001). No difference in time was found since the last tetanus‐diphtheria vaccine or tetanus‐diphtheria‐pertussis vaccine dose between the groups (healthy 76.5 months [16–114IQR] vs. LuTx 74.5 months [45–118IQR];P = 0.44).ConclusionsTetanus and diphtheria immunizations are recommended for LuTx patients to reduce the risk of infection. Because the LuTx group has lower antibody concentrations, further studies should investigate the possible need for more frequent tetanus and diphtheria boosters.
Production of human monoclonal anti‐Jk3, recognising an epitope including the Jka/Jkb polymorphic site of the Kidd glycoprotein
Authors: Toyoda C. , Suzuki Y. , Tsuneyama H. , Onodera T. , Masuno A. , Yabe R. , Ogasawara K. , Okuda M. , Nakajima K. , Uchikawa M. 
Published: September 2014

SUMMARYBackground and objectivesThe Kidd blood group system consists of polymorphic antigens, Jka (JK1) and Jkb (JK2), and a high‐incidence antigen, Jk3. Anti‐Jk3 is often observed in immunised Jk(a−b−) individuals. In this study, we aimed to establish a human hybridoma cell line secreting monoclonal anti‐Jk3 (HIRO‐294).Materials and methodsPeripheral blood lymphocytes of a Filipino woman with the Jk(a−b−) phenotype having anti‐Jk3 were transformed with Epstein‐Barr virus and then hybridised with the myeloma cell line JMS‐3 using the polyethylene glycol (PEG) method. The reactivity and specificity of the anti‐Jk3 were examined by serology and flow cytometry.ResultsFour hybridoma clones secreting anti‐Jk3 were established and the antibody from one of these clones, HIRO‐294, was examined. The reactivity of HIRO‐294 was positive with 227 Jk(a+b−) red blood cells (RBCs), 298 Jk(a−b+) RBCs, and 1043 Jk(a+b+) RBCs, but was negative with 21 Jk(a−b−) RBCs. Eluates from Jk(a+b−) RBCs and Jk(a−b+) RBCs sensitised with the anti‐Jk3 were cross‐reacted with Jk(a−b+) RBCs and Jk(a+b−) RBCs, respectively. The reactivity of HIRO‐294 was enhanced by the treatment of RBCs with ficin, trypsin, pronase and α‐chymotrypsin, but was not changed by their treatment with neuraminidase, dithiothreitol and ethylenediaminetetraacetic acid (EDTA) glycine acid (GA). The RBCs sensitised by the anti‐Jk3 were not agglutinated with the commercial reagents of anti‐Jka and anti‐Jkb by saline test, whereas the nonsensitised RBCs or those sensitised by monoclonal anti‐D [HIRO‐3, immunoglobulin G (IgG) class] were agglutinated with those reagents.ConclusionsWe established a human hybridoma cell line secreting monoclonal anti‐Jk3 (HIRO‐294). This antibody had unique specificity, recognising the Kidd glycoprotein including the Jka/Jkb polymorphic site.
Young but not relatively old retrotransposons are preferentially located in gene‐rich euchromatic regions in tomato (Solanum lycopersicum) plants
Authors: Xu Yingxiu , Du Jianchang 
Published: September 2014

SummaryLong terminal repeat (LTR) retrotransposons are the major DNA components of flowering plants. They are generally enriched in pericentromeric heterochromatin regions of their host genomes, which could result from the preferential insertion of LTR retrotransposons and the low effectiveness of purifying selection in these regions. To estimate the relative importance of the actions of these two factors on their distribution pattern, the LTR retrotransposons in Solanum lycopersicum (tomato) plants were characterized at the genome level, and then the distribution of young elements was compared with that of relatively old elements. The current data show that old elements are mainly located in recombination‐suppressed heterochromatin regions, and that young elements are preferentially located in the gene‐rich euchromatic regions. Further analysis showed a negative correlation between the insertion time of LTR retrotransposons and the recombination rate. The data also showed there to be more solo LTRs in genic regions than in intergenic regions or in regions close to genes. These observations indicate that, unlike in many other plant genomes, the current LTR retrotransposons in tomatoes have a tendency to be preferentially located into euchromatic regions, probably caused by their severe suppression of activities in heterochromatic regions. These elements are apt to be maintained in heterochromatin regions, probably as a consequence of the pericentromeric effect in tomatoes. These results also indicate that local recombination rates and intensities of purifying selection in different genomic regions are largely responsible for structural variation and non‐random distribution of LTR retrotransposons in tomato plants.
Comparative expression profiling reveals gene functions in female meiosis and gametophyte development in Arabidopsis
Authors: Zhao Lihua , He Jiangman , Cai Hanyang , Lin Haiyan , Li Yanqiang , Liu Renyi , Yang Zhenbiao , Qin Yuan 
Published: September 2014

SummaryMegasporogenesis is essential for female fertility, and requires the accomplishment of meiosis and the formation of functional megaspores. The inaccessibility and low abundance of female meiocytes make it particularly difficult to elucidate the molecular basis underlying megasporogenesis. We used high‐throughput tag‐sequencing analysis to identify genes expressed in female meiocytes (FMs) by comparing gene expression profiles from wild‐type ovules undergoing megasporogenesis with those from the spl mutant ovules, which lack megasporogenesis. A total of 862 genes were identified as FMs, with levels that are consistently reduced in spl ovules in two biological replicates. Fluorescence‐assisted cell sorting followed by RNA‐seq analysis of DMC1:GFP‐labeled female meiocytes confirmed that 90% of the FMs are indeed detected in the female meiocyte protoplast profiling. We performed reverse genetic analysis of 120 candidate genes and identified four FM genes with a function in female meiosis progression in Arabidopsis. We further revealed that KLU, a putative cytochrome P450 monooxygenase, is involved in chromosome pairing during female meiosis, most likely by affecting the normal expression pattern of DMC1 in ovules during female meiosis. Our studies provide valuable information for functional genomic analyses of plant germline development as well as insights into meiosis.
Comparison of two platelet transfusion strategies to minimize ABO‐nonidentical transfusion, outdating, and shortages using a computer‐simulated “virtual blood bank”
Authors: Jackups Ronald , Kymes Steven 
Published: September 2014

BackgroundTransfusion of ABO‐incompatible platelets (PLTs) is associated with reduced PLT recovery and a risk of transfusion reactions. However, a policy of transfusing only ABO‐identical PLTs may increase wastage due to product outdating. A prospective study attempting to compare the effects of different ABO compatibility strategies could be costly and disruptive to a blood bank's operations.Study Design and MethodsWe designed a “virtual blood bank,” a stochastic computer program that models the stocking and release of products to meet demand for PLT transfusion in a simulated hospital population. ABO‐nonidentical transfusions (ABOni), outdates, and inventory shortages were recorded and compared under two different transfusion strategies: ABO‐First, a strategy that prioritizes transfusion of ABO‐identical PLTs, and Age‐First, a strategy that minimizes outdating by transfusing products closest to expiration.ResultsThe ABO‐First strategy resulted in fewer ABOni but more outdates than the Age‐First strategy. Under conditions that mimic a large hospital blood bank, the ABO‐First strategy was more cost‐effective overall than the Age‐First strategy if avoiding an ABOni is valued at more than $19 to $26. For a small blood bank, the ABO‐First strategy was more cost‐effective if avoiding an ABOni is valued at more than $104 to $123.ConclusionBased on a virtual blood bank computer simulation, the cost of avoiding an ABOni using the ABO‐First strategy varies greatly by size of institution. Individual blood banks must carefully consider these management strategies to determine the most cost‐effective solution.
Diverse Bacterial Microcompartment Organelles
Authors: Chowdhury Chiranjit , Sinha Sharmistha , Chun Sunny , Yeates Todd O. , Bobik Thomas A. 
Published: September 2014

SUMMARY
Bacterial microcompartments (MCPs) are sophisticated protein-based organelles used to optimize metabolic pathways. They consist of metabolic enzymes encapsulated within a protein shell, which creates an ideal environment for catalysis and facilitates the channeling of toxic/volatile intermediates to downstream enzymes. The metabolic processes that require MCPs are diverse and widely distributed and play important roles in global carbon fixation and bacterial pathogenesis. The protein shells of MCPs are thought to selectively control the movement of enzyme cofactors, substrates, and products (including toxic or volatile intermediates) between the MCP interior and the cytoplasm of the cell using both passive electrostatic/steric and dynamic gated mechanisms. Evidence suggests that specialized shell proteins conduct electrons between the cytoplasm and the lumen of the MCP and/or help rebuild damaged iron-sulfur centers in the encapsulated enzymes. The MCP shell is elaborated through a family of small proteins whose structural core is known as a bacterial microcompartment (BMC) domain. BMC domain proteins oligomerize into flat, hexagonally shaped tiles, which assemble into extended protein sheets that form the facets of the shell. Shape complementarity along the edges allows different types of BMC domain proteins to form mixed sheets, while sequence variation provides functional diversification. Recent studies have also revealed targeting sequences that mediate protein encapsulation within MCPs, scaffolding proteins that organize lumen enzymes and the use of private cofactor pools (NAD/H and coenzyme A [HS-CoA]) to facilitate cofactor homeostasis. Although much remains to be learned, our growing understanding of MCPs is providing a basis for bioengineering of protein-based containers for the production of chemicals/pharmaceuticals and for use as molecular delivery vehicles.