bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional profile of glucose‐shocked and acid‐adapted strains of Streptococcus mutans
Authors: Baker J.L. , Abranches J. , Faustoferri R.C. , Hubbard C.J. , Lemos J.A. , Courtney M.A. , Quivey R. 
Published: June 2015

SummaryThe aciduricity of Streptococcus mutans is an important virulence factor of the organism, required to both out‐compete commensal oral microorganisms and cause dental caries. In this study, we monitored transcriptional changes that occurred as a continuous culture of either an acid‐tolerant strain (UA159) or an acid‐sensitive strain (fabM::Erm) moved from steady‐state growth at neutral pH, experienced glucose‐shock and acidification of the culture, and transitioned to steady‐state growth at low pH. Hence, the timing of elements of the acid tolerance response (ATR) could be observed and categorized as acute vs. adaptive ATR mechanisms. Modulation of branched chain amino acid biosynthesis, DNA/protein repair mechanisms, reactive oxygen species metabolizers and phosphoenolpyruvate:phosphotransferase systems occurred in the initial acute phase, immediately following glucose‐shock, while upregulation of F1F0‐ATPase did not occur until the adaptive phase, after steady‐state growth had been re‐established. In addition to the archetypal ATR pathways mentioned above, glucose‐shock led to differential expression of genes suggesting a re‐routing of resources away from the synthesis of fatty acids and proteins, and towards synthesis of purines, pyrimidines and amino acids. These adjustments were largely transient, as upon establishment of steady‐state growth at acidic pH, transcripts returned to basal expression levels. During growth at steady‐state pH 7, fabM::Erm had a transcriptional profile analogous to that of UA159 during glucose‐shock, indicating that even during growth in rich media at neutral pH, the cells were stressed. These results, coupled with a recently established collection of deletion strains, provide a starting point for elucidation of the acid tolerance response in S. mutans.
Influence of age on IgE response in peanut‐allergic children and adolescents from the Mediterranean area
Authors: Garcia‐Blanca A. , Aranda A. , Blanca‐Lopez N. , Perez D. , Gomez F. , Mayorga C. , Torres M. J. , Diaz‐Perales A. , Perkins J. R. , Villalba M. , Blanca M. , Canto G. 
Published: June 2015

AbstractBackgroundPeanut allergens are common triggers of food allergy. Analyses of sensitization patterns, relationships with other allergens, clinical symptoms, and variation with age are needed. We studied sensitization to Ara h 2, Ara h 9, and Pru p 3 in a peanut allergic children/adolescents and the relationship with peach and pollen.MethodsPeanut allergic patients aged between 1 and 20 years old were classified into two groups: A) allergic to peanut only and B) allergic to peach and peanut. The IgE response was measured to Ara h 2, Ara h 9, and Pru p 3.ResultsOf 964 subjects evaluated, 28% were allergic to peanut. From this group, 68% were also sensitized to pollen. Urticaria was the most frequent entity followed by anaphylaxis and OAS. Fifty‐eight percent had Ara h 2‐ and/or Ara h 9‐specific IgE. More than half reported symptoms with peanut alone (Group A) and 35% to peanut and peach (Group B). We observed significant differences in sex, age, onset of symptoms, and sensitization to Artemisia between groups. IgE response to Ara h 2 was more frequent in Group A, and Ara h 9 and Pru p 3 in Group B. We observed a decrease in sensitization to Ara h 2 and an increase to Ara h 9 and Pru p 3 with increasing age.ConclusionPeanut allergy is frequent in subjects with allergy to plant foods, with Ara h 2 and Ara h 9 being two important allergens. In younger patients, Ara h 2 predominates over Ara h 9. The reverse was observed in older patients.
Long‐term tolerability of capnography and respiratory inductance plethysmography for respiratory monitoring in pediatric patients treated with patient‐controlled analgesia
Authors: Miller Karen M. , Kim Andrew Y. , Yaster Myron , Kudchadkar Sapna R. , White Elizabeth , Fackler James , Monitto Constance L. 
Published: June 2015

SummaryBackgroundThe Anesthesia Patient Safety Foundation has advocated the use of continuous electronic monitoring of oxygenation and ventilation to preemptively identify opioid‐induced respiratory depression. In adults, capnography is the gold standard in respiratory monitoring. An alternative technique used in sleep laboratories is respiratory inductance plethysmography (RIP). However, it is not known if either monitor is well tolerated by pediatric patients for prolonged periods of time.AimThe goal of this study was to determine whether capnography or RIP is better tolerated in nonintubated, spontaneously breathing pediatric patients being treated with intravenous patient‐controlled analgesia (IVPCA).MethodsNasal cannula capnography with oral sampling and thoracic and abdominal inductance plethysmography bands were placed along with the routine monitors on pediatric patients being treated for acute pain with IVPCA. Study monitors were left in place for as long as they were tolerated by the patient, up to a maximum of 24 consecutive hours. If the patient did not wear a particular study monitor for any reason, but tolerated the remaining monitor, participation in the study continued. If the patient would not wear either monitor, participation was terminated.ResultsTwenty‐six patients (18 female, eight male, average age 10.1 ± 5.5 years) consented to participate, but only 14 patients attempted to wear one or both the devices. Among those who wore either device, median time to device removal was 8.33 h (range 0.3–23.6 h) for capnography and 23.5 h (range 0.7–24 h) for RIP bands.ConclusionChildren did not tolerate wearing capnography cannulae for prolonged periods of time, limiting the usefulness of this device as a continuous monitor of ventilation in children. RIP bands were better tolerated; however, they require further assessment of their utility. Until more effective, child‐friendly monitors are developed and their utility is validated, guidelines recommended for adult patients cannot be extended to children.
Genetic variation among cocoa (Theobroma cacao L.) families for resistance to cocoa swollen shoot virus disease in relation to total phenolic content
Authors: Ofori Atta , Padi Francis Kwame , Ameyaw George Akumfi , Dadzie Abu Mustapha , Lowor Samuel 
Published: June 2015

AbstractPhenolic compounds have been suggested as one of the defence mechanisms to cocoa swollen shoot virus disease (CSSVD), but not well studied. Correlation and genetic variation of total phenolic content (TPC) and CSSVD resistance among 53 cocoa families were investigated. Three‐month‐old seedlings of 15 families obtained from an incomplete 6 × 3 NCII mating design, of 24 families from a 3 × 8 NCII mating design and of 14 other families were evaluated for CSSVD and TPC. Plants were inoculated with viruliferous mealybugs carrying the New Juaben CSSV strain (1A) in a gauze house facility. A single seedling randomization within blocks procedure was followed, using the gauze house units as blocks. There were six blocks with five seedlings of each family randomized within each block. Disease severity scores on leaf flushes at the first, second, third and seventh flushes after inoculation were recorded. The TPC before and 3 months after inoculation was also determined. Family effects were highly significant (P ≤ 0.01) for CSSVD severity scores and TPC. Narrow‐ and broad‐sense heritability estimates were low for CSSVD severity but moderate to high for TPC evaluations. Correlations between severity scores and TPC were weak (r = −0.22 to 0.40) suggesting that the TPC may be of little value in selecting CSSVD resistance varieties in cocoa. Additive effect in terms of significant GCA was important for CSSVD severity scores whereas both additive and non‐additive effects were important for TPC values when the 3 × 8 and 6 × 3 NCII mating designs were analysed. Only clones GU 239/H, GU 290/H and GU 225/V had favourable GCA effects for CSSVD symptom expression indicating their potential for developing progeny with high levels of resistance to CSSVD infection.
National risk factors and estimated costs for redo ureteroneocystostomy after pediatric renal transplant
Authors: Godebu Elana , Palazzi Kerrin , Bush Ruth , Marietti Sarah , Chiang George 
Published: June 2015

AbstractApproximately 800 pediatric renal transplants are performed annually in the United States. VUR or obstruction may cause graft failure requiring redo ureteroneocystostomy. We examined possible risk factors and cost using the PHIS national database. We examined the PHIS for 8.5 yr to determine the association between redo ureteroneocystostomy following pediatric renal transplant to demographics, comorbidities, GU conditions, insurance status, and hospital characteristics, and looked at relative costs using descriptive and comparative statistics. A total of 2390 pediatric renal transplants were identified, of which 69 (2.3%) underwent redo ureteroneocystostomy (median 11.6 months post‐transplant). Risk factors for redo ureteroneocystostomy are younger age (p = 0.048), PUVs (p < 0.001), female gender (p = 0.005), race (p = 0.014), insurance type (p < 0.027), region (p = 0.045), and transplant surgery volume (p = 0.048). Redo ureteroneocystostomy after transplant does not significantly increase the overall cost of transplant (p = 0.175). We confirmed previous findings that younger age and PUVs increase the risk of post‐transplant redo ureteroneocystostomy, with a five‐yr plateau. We found an association with gender, race, insurance status, and hospital characteristics. Redo ureteroneocystostomy, which increases costs, does not statistically significantly increase overall cost of individual treatment in this database, although costs may be underreported.
Improving the Budget Process in Fragile and Conflict‐Ridden States: Two Modest Lessons from Afghanistan
Authors: Guinn David E. , Straussman Jeffrey D. 
Published: June 2015

AbstractBoth the donor community and scholars have created a cottage industry studying “fragile” states. International nongovernmental organizations that have developed indexes measuring corruption or governance have been unkind to Afghanistan. One index suggests a different and more optimistic story. The International Budget Partnership measures transparency every two years with its Open Budget Index. Afghanistan demonstrated dramatic improvement on this index between 2008 and 2012. The authors use the improvement in Afghanistan's transparency score as an entry point to explore how donors try to intervene and promote transparency as part of broader efforts in public financial management development and how legislative strengthening has also contributed to budget reform. The analysis offers a modest corrective to the overly pessimistic assessments of fragile states by showing that a fragile state can improve its budgetary transparency and enhance governance by strengthening the legislature's involvement in the budget process.
The Distributional and Allocative Impacts of Virtual Labor Mobility across Time Zones through Communication Networks
Authors: Nakanishi Noritsugu , Long Ngo Van 
Published: June 2015

AbstractUsing a specific‐factors' model, with two goods (a shift‐working good and a non‐shift‐working good), three factors (capital specific to shift‐working, land specific to non‐shift‐working and labor) and two countries (Home and Foreign), which are located in different time zones, we highlight the impact of trade in labor services via communication networks on factor prices and production patterns. If two countries are identical in size, then under free trade in labor services, all workers work only in their local daytime, and night shift in each country is performed by imported labor services supplied by residents of the other country in their local daytime. Night‐time wage becomes the same as daytime wage (a wage equalization result). Other factor prices are also equalized. In both countries, capital rental rate increases, while land rent decreases. However, if two countries are different in size, trade in labor services does not equalize wages: in the large country, wages for night‐shift workers are higher than daytime wages and some residents work at night; in the small country, daytime wages become higher than night‐time wages and no one works at night, and night‐shift work is done by imported labor services from the large country. Land rent in the small country decreases. Land rent in the large country may or may not decrease, but it is always higher than in the small country. Capital rental rates in both countries are equalized and increase.
Genetic testing and human subjectivity
Authors: Arribas‐Ayllon Michael 
Published: June 2015

AbstractThis article offers a brief overview of how methods of DNA testing are reframing what it means to be a living being in a living world. It is no longer the case that genetic technologies objectify life in such a way as to deny something essential to human subjectivity. The style of reasoning of the life sciences today is characterised by complexity, dynamism and emergence. This requires rethinking the relationship between technology, society and subjectivity. Genetic testing is a social and symbolic practice through which notions of identity and relatedness are reconfigured in terms of being genetically at risk. Far from reducing subjectivity to one's biological destiny, genetic technologies have consequences in terms of not only governing others to govern their risk wisely, but also aligning conduct with Western liberal values of autonomy, responsibility and choice. New pastors and gatekeepers of genetic information have assembled around these technologies where psychology plays a key role in facilitating autonomy and instilling a sense of genetic responsibility. Nevertheless, the increasing capitalization of genomics is moving genetic testing beyond these clinical enclosures of control into the domain of consumer choice, creating new forms of subjectification, citizenship and community.
Effect of potassium present in stratum corneum during non‐invasive measurement of potassium in human subjects using reverse iontophoresis
Authors: Varadharaj E. K. , Jampana N. 
Published: June 2015

PurposeReverse iontophoresis (RI) is one of the potential techniques used to monitor the concentration of various analytes in body fluids non‐invasively. Transdermal extraction of potassium is investigated using RI. In the present work, the effect of potassium on stratum corneum (SC) during RI, feasibility of RI for continuous monitoring of potassium, and use of potassium as internal standard in RI, are investigated.MethodsTape stripping experiment is carried out to find potassium concentration in SC. RI is carried out continuously for 180 min without passive diffusion and after passive diffusion for 60 min. Skin impedance measurements are done at 20 Hz and 20 kHz.ResultsPotassium is found to be in the range 300–650 nmol/cm2 on SC by tape stripping experiment. Correlation coefficient between blood potassium and extracted potassium through RI after passive diffusion (R2 = 0.5870) is more than without passive diffusion (R2 = 0.5117). The skin impedance measurement shows that RI has more effect on SC than superficial layer of SC during RI.ConclusionThe present investigations conclude that it is possible to monitor potassium continuously through RI and using potassium as internal standard in RI.
Four decades of National Blood Service in Iran: outreach, prospect and challenges
Authors: Pourfathollah A. A. , Hosseini Divkolaye N. S. , Seighali F. 
Published: June 2015

SUMMARYObjectiveThis study aims to compare the changes and progress made to Iranian Blood Transfusion Organization (IBTO) during 1974–2014 in order to identify the shortcomings.BackgroundThe History of Blood transfusion in Iran can be traced back to the 1940s. IBTO was established in 1974 as a national centralised organisation, supported by Iranian government for its budget and supplies and provides its products free of charge to both public and private hospitals.MethodsThe statistics have been derived from IBTO Statistical Center. Also related literature has been reviewed.ResultsFrom 1974 to 2014, donation per population has been increased about eight times. IBTO reached 100% voluntary blood donation in 2007, but the number of female blood donors in Iran is six times lower than average global rate. On one hand, the prevalence rate of Hepatitis B virus (HBV) and Hepatitis C virus (HCV) in blood donors was dropped in to one fifth and one third, respectively during past 8 years. On the other hand, irrational blood usage and lack of integrated blood stock management systems and non self‐sufficiency on plasma‐derivedmedicines are considered as main challenges of IBTO.ConclusionForty years since the establishment, IBTO managed to achieve considerable improvements in different fields but many challenges still remain, which need to be addressed urgently. Great gap between the number of male and female blood donors in Iran has to be filled. The improvement of knowledge and practice on patient blood management and use of alternatives are on the agenda of IBTO in next coming years.
International survey on definitions and current practices in prevention, diagnosis, management and reporting of transfusion‐transmitted bacterial infections
Authors: Chew E. , Benjamin R. J. , McDonald C. P. , Wiersum‐Osselton J. C. , Wood E. M. ,   the International Society of Blood Transfusion Working Parties on Transfusion‐Transmitted Infectious Diseases (Bacterial subgroup) and Haemovigilance
Published: June 2015

Background and objectivesTransfusion‐transmitted bacterial infections (TTBI) remain a threat to safe blood transfusion. Currently, there is no consensus on the definition, presentation, management and prevention of TTBI. A common set of criteria would facilitate haemovigilance and benchmarking. An international survey to assess current practices in TTBI was performed as part of efforts in developing an accepted TTBI definition.Material and MethodsAfter a pilot study, the questionnaire was sent via a web‐based survey (www.surveymonkey.com) to members of the International Society of Blood Transfusion (ISBT) Working Parties on Transfusion‐Transmitted Infectious Diseases (bacterial subgroup) and Haemovigilance as well as members of the transfusion community with an interest in transfusion safety.ResultsResults from 58 respondents in 39 countries were available. Twenty‐seven countries had a haemovigilance programme. A TTBI definition was available from 27 respondents (17 countries). The reported clinical presentation and management of TTBI, and procedures to prevent bacterial contamination and screening of blood products varied amongst the respondents. The most frequently cited signs of a TTBI were fever, tachycardia, rigours and hypotension. Common methods to prevent bacterial contamination of blood products included donor health questionnaire, skin disinfection prior to blood collection and use of a diversion pouch. Routine bacterial screening of blood products was performed in 19 countries.ConclusionThis survey highlighted the different practices in TTBI globally and provides a baseline for ongoing endeavours to harmonize TTBI definitions and management.
High-Resolution Analysis by Whole-Genome Sequencing of an International Lineage (Sequence Type 111) of Pseudomonas aeruginosa Associated with Metallo-Carbapenemases in the United Kingdom
Authors: Turton Jane F. , Wright Laura , Underwood Anthony , Witney Adam A. , Chan Yuen-Ting , Al-Shahib Ali , Arnold Catherine , Doumith Michel , Patel Bharat , Planche Timothy D. , Green Jonathan , Holliman Richard , Woodford Neil 
Published: June 2015

ABSTRACT

Whole-genome sequencing (WGS) was carried out on 87 isolates of sequence type 111 (ST-111) of
Pseudomonas aeruginosa
collected between 2005 and 2014 from 65 patients and 12 environmental isolates from 24 hospital laboratories across the United Kingdom on an Illumina HiSeq instrument. Most isolates (73) carried VIM-2, but others carried IMP-1 or IMP-13 (5) or NDM-1 (1); one isolate had VIM-2 and IMP-18, and 7 carried no metallo-beta-lactamase (MBL) gene. Single nucleotide polymorphism analysis divided the isolates into distinct clusters; the NDM-1 isolate was an outlier, and the IMP isolates and 6/7 MBL-negative isolates clustered separately from the main set of 73 VIM-2 isolates. Within the VIM-2 set, there were at least 3 distinct clusters, including a tightly clustered set of isolates from 3 hospital laboratories consistent with an outbreak from a single introduction that was quickly brought under control and a much broader set dominated by isolates from a long-running outbreak in a London hospital likely seeded from an environmental source, requiring different control measures; isolates from 7 other hospital laboratories in London and southeast England were also included. Bayesian evolutionary analysis indicated that all the isolates shared a common ancestor dating back ∼50 years (1960s), with the main VIM-2 set separating approximately 20 to 30 years ago. Accessory gene profiling revealed blocks of genes associated with particular clusters, with some having high similarity (≥95%) to bacteriophage genes. WGS of widely found international lineages such as ST-111 provides the necessary resolution to inform epidemiological investigations and intervention policies.
Primer ID Validates Template Sampling Depth and Greatly Reduces the Error Rate of Next-Generation Sequencing of HIV-1 Genomic RNA Populations
Authors: Zhou Shuntai , Jones Corbin , Mieczkowski Piotr , Swanstrom Ronald 
Published: June 2015

ABSTRACT
Validating the sampling depth and reducing sequencing errors are critical for studies of viral populations using next-generation sequencing (NGS). We previously described the use of Primer ID to tag each viral RNA template with a block of degenerate nucleotides in the cDNA primer. We now show that low-abundance Primer IDs (offspring Primer IDs) are generated due to PCR/sequencing errors. These artifactual Primer IDs can be removed using a cutoff model for the number of reads required to make a template consensus sequence. We have modeled the fraction of sequences lost due to Primer ID resampling. For a typical sequencing run, less than 10% of the raw reads are lost to offspring Primer ID filtering and resampling. The remaining raw reads are used to correct for PCR resampling and sequencing errors. We also demonstrate that Primer ID reveals bias intrinsic to PCR, especially at low template input or utilization. cDNA synthesis and PCR convert ca. 20% of RNA templates into recoverable sequences, and 30-fold sequence coverage recovers most of these template sequences. We have directly measured the residual error rate to be around 1 in 10,000 nucleotides. We use this error rate and the Poisson distribution to define the cutoff to identify preexisting drug resistance mutations at low abundance in an HIV-infected subject. Collectively, these studies show that >90% of the raw sequence reads can be used to validate template sampling depth and to dramatically reduce the error rate in assessing a genetically diverse viral population using NGS.

IMPORTANCE
Although next-generation sequencing (NGS) has revolutionized sequencing strategies, it suffers from serious limitations in defining sequence heterogeneity in a genetically diverse population, such as HIV-1 due to PCR resampling and PCR/sequencing errors. The Primer ID approach reveals the true sampling depth and greatly reduces errors. Knowing the sampling depth allows the construction of a model of how to maximize the recovery of sequences from input templates and to reduce resampling of the Primer ID so that appropriate multiplexing can be included in the experimental design. With the defined sampling depth and measured error rate, we are able to assign cutoffs for the accurate detection of minority variants in viral populations. This approach allows the power of NGS to be realized without having to guess about sampling depth or to ignore the problem of PCR resampling, while also being able to correct most of the errors in the data set.