bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA Polymerase–I‐Dependent Transcription‐coupled Nucleotide Excision Repair of UV‐Induced DNA Lesions at Transcription Termination Sites, in Saccharomyces cerevisiae
Authors: Peyresaubes François , Zeledon Carlos , Guintini Laetitia , Charton Romain , Muguet Alexia , Conconi Antonio 
Published: December 2016

AbstractIf not repaired, ultraviolet light‐induced DNA damage can lead to genome instability. Nucleotide excision repair (NER) of UV photoproducts is generally fast in the coding region of genes, where RNA polymerase‐II (RNAP2) arrest at damage sites and trigger transcription‐coupled NER (TC‐NER). In Saccharomyces cerevisiae, there is RNA polymerase‐I (RNAP1)‐dependent TC‐NER, but this process remains elusive. Therefore, we wished to characterize TC‐NER efficiency in different regions of the rDNA locus: where RNAP1 are present at high density and start transcription elongation, where the elongation rate is slow, and in the transcription terminator where RNAP1 pause, accumulate and then are released. The Rpa12 subunit of RNAP1 and the Nsi1 protein participate in transcription termination, and NER efficiency was compared between wild type and cells lacking Rpa12 or Nsi1. The presence of RNAP1 was determined by chromatin endogenous cleavage and chromatin immunoprecipitation, and repair was followed at nucleotide precision with an assay that is based on the blockage of Taq polymerase by UV photoproducts. We describe that TC‐NER, which is modulated by the RNAP1 level and elongation rate, ends at the 35S rRNA gene transcription termination site.
Noninvasive red and near‐infrared wavelength‐induced photobiomodulation: promoting impaired cutaneous wound healing
Authors: Yadav Anju , Gupta Asheesh 
Published: December 2016

SummaryThe innumerable intricacies associated with chronic wounds have made the development of new painless, noninvasive, biophysical therapeutic interventions as the focus of current biomedical research. Red and near‐infrared light‐induced photobiomodulation therapy appears to emerge as a promising drug‐free approach for promoting wound healing, reduction in inflammation, pain and restoration of function owing to penetration power in conjunction with their ability to positively modulate the biochemical and molecular responses. This review will describe the physical properties of red and near‐infrared light and their interaction with skin and highlight their efficacy of wound repair and regeneration. Near‐infrared (800–830 nm) was found to be the most effective and widely studied wavelength range followed by red (630–680 nm) and 904 nm superpulsed light exhibiting beneficial photobiomodulatory effects on impaired dermal wound healing.
Photobiomodulation therapy in breast cancer‐related lymphedema: a randomized placebo‐controlled trial
Authors: Storz Maximilian Andreas , Gronwald Benjamin , Gottschling Sven , Schöpe Jakob , Mavrova Russalina , Baum Sascha 
Published: December 2016

SummaryBackgroundThe aim of our study was to examine the effects of photobiomodulation therapy (PBMT) in the treatment of breast cancer‐related lymphedema using a compactly designed treatment regime consisting of eight therapy sessions in combination with a cluster laser device covering a total area size of 78.54 cm² over the axillary.MethodsForty patients with unilateral lymphedema were enrolled in this double‐blind, placebo‐controlled trial in order to evaluate effects of PBMT on lymphedema‐related pain, quality of life, grip strength and limb volume difference. Subjects received irradiation for ten minutes per session using a cluster laser covering a beam area of 78.54 cm². The applied energy was 384 Joules resulting in an energy density of 4.89 J/cm².ResultsPost‐treatment, a 50% reduction in median pain scores and an increase in mean quality of life were observed. Mean grip strength was persistently higher after eight sessions of PBMT compared with pretreatment; however, no statistically significant intergroup differences (P > 0.05) were found over the time course.ConclusionPBMT using a compactly designed treatment regime in combination with a cluster laser device did not significantly improve quality of life, pain scores, grip strength and limb volume over the time course.
Photosynthetically active radiation and carbon gain drives the southern orientation of Myrtillocactus geometrizans fruits
Authors: Ponce‐Bautista A. , Valverde P. L. , Flores J. , Zavala‐Hurtado A. , Vite F. , López‐Ortega G. , Pérez‐Hernández M. A. 
Published: December 2016

Abstract

The equatorial orientation of reproductive structures is known in some columnar cacti from extratropical deserts. It has been hypothesised that photosynthetically active radiation (PAR) interception is the main reason for this orientation, because of its key effect on nocturnal CO2 uptake. However, there are no studies addressing both the effect of PAR and its consequence, carbon gain, on fruit orientation. Accordingly, we tested whether PAR and carbon gain could explain the southern fruit orientation of Myrtillocactus geometrizans, an inter‐tropical columnar cactus.

We studied three populations of M. geometrizans in Mexico. For each population, azimuth of fruits, total daily PAR, nocturnal acid accumulation (NAA) and fruit production were measured. The relationships between rib orientation and number of fruits, as well as total daily PAR, were evaluated using periodic regressions. The effect of total daily PAR and NAA on number of fruits was assessed using generalised linear models.

During spring, mean fruit orientation had a south azimuth for three populations. Likewise, rib orientation had a significant effect on fruit production, with the south‐facing ribs having the maximum number of fruits. Total daily PAR was highest in the south‐facing ribs, at least for those in the northern and central populations. Furthermore, during spring, there was a significant positive effect of total daily PAR and NAA on fruit production.

Our results provide strong evidence that the higher carbon gain in equatorial ribs, through a highest interception of PAR, would be the responsible factor for equatorial orientation of fruits in an inter‐tropical columnar cactus.
The Inflammation Induced by Lipopolysaccharide can be Mitigated by Short‐chain Fatty Acid, Butyrate, through Upregulation of IL‐10 in Septic Shock
Authors: Wang F. , Liu J. , Weng T. , Shen K. , Chen Z. , Yu Y. , Huang Q. , Wang G. , Liu Z. , Jin S. 
Published: December 2016

AbstractShort‐chain fatty acids (SCFAs) with the anti‐inflammatory capacity are produced by intestinal bacteria; however, their effect on the acute systematical inflammation remains unclear. This study aimed to investigate the effects of SCFAs, acetate, propionate and butyrate, on septic shock and the underlying mechanism. The LPS‐induced septic model was used to evaluate the function of SCFAs by survival rate observation. Only butyrate, but not acetate or propionate, significantly decrease the mortality of septic mice. At 2 h and 6 h of LPS administration, the levels of TNF‐α, IL‐6 and IL‐1β in plasma were measured by ELISA to estimate the effects of butyrate pretreatment on excessive inflammation. And the anti‐inflammatory mediators including TGF‐β, IL‐10 and LXT4 in plasma were detected for further mechanism study in septic mice. Moreover, the murine macrophage‐like RAW 264.7 cells were stimulated by LPS to further confirm the finding in vivo. Pretreatment with butyrate led to significant attenuation of the LPS‐induced elevation of TNF‐α, IL‐6 and IL‐1β levels. However, when detecting the anti‐inflammatory factors, a significant increase in IL‐10, but not TGF‐β or LXT4, was shown in butyrate‐pretreated group. Pretreatment of RAW 264.7 cells with butyrate led to downregulation of LPS‐induced pro‐inflammatory mediators, IL‐6 and IL‐1β, but did not affect the level of TNF‐α, and increased IL‐10 (P < 0.01). In conclusion, SCFA butyrate significantly attenuated the inflammation against sepsis through upregulation of anti‐inflammatory IL‐10.
In vitro Monocyte IL‐6 Secretion Levels Following Stimulation with Autologous Spheroids Derived from Tumour or Benign Mucosa Predict Long‐term Survival in Head and Neck Squamous Cell Carcinoma Patients
Authors: Aarstad H. J. , Aarstad H. H. , Vintermyr O. K. , Kross K. W. , Lybak S. , Heimdal J.‐H. 
Published: December 2016

AbstractMCP‐1/IL‐6 in vitro monocyte secretion upon coculture with autologous fragment spheroids was studied in relation to patient 5‐ and 10‐year overall survival rates in head and neck squamous cell carcinoma (HNSCC) patients (n = 65) diagnosed between 1998 and 2005, nine of whom had an human papilloma virus (HPV) tumour infection. The spheroids were harvested from malignant or benign tissue during primary surgery. Two weeks following surgery, freshly isolated autologous monocytes and benign or malignant spheroids were cocultured 24 h in vitro. The IL‐6 secretion was expressed as a fraction of the lipopolysaccharide (LPS) response from the same batch of monocytes. HPV status was obtained by employing PCR analyses of primary diagnostic blocks. IL‐6/MCP‐1 response levels were not found to be dependent on HPV infection status. MCP‐1 secretion did not predict prognosis, nor did in vitro IL‐6 monocyte background or LPS‐stimulated IL‐6 secretion. At 5‐year observation, dichotomized IL‐6 levels following monocyte coculture, with both malignant and benign spheroids, showed a strong trend towards predicting survival, that is a low monocyte malignant coculture response showed a survival of 31 ± 17 versus 58 ± 17% with a high such response (P = 0.057). When studying monocyte IL‐6 coculture responses evaluating benign and malignant spheroid results statistically together, a prediction of survival up to 10 years was found (hazard ratio = 0.48; confidence interval = 0.24–0.96; P < 0.05) with double low IL‐6 responses. This survival prediction was also present after an adjustment for HPV tumour infection status. In conclusion, monocyte IL‐6 in vitro secretion in cocultures with autologous spheroids/serum from HNSCCs predicted 5‐ and 10‐year survivals, both with and without tumour HPV tumour adjustment.
Treatment of hepatitis C virus recurrence after transplantation with sofosbuvir/ledipasvir: The role of ribavirin
Authors: Globke Brigitta , Raschzok Nathanael , Teegen Eva‐Maria , Pratschke Johann , Schott Eckart , Eurich Dennis 
Published: December 2016

AbstractBackgroundHepatitis C virus (HCV) recurrence after liver transplantation (LT) used to be a serious problem in the era of interferon‐based treatment. Since the introduction of modern directly acting antivirals, treatment has become easier and shorter. According to published data, in the natural course of hepatitis C infection the duration of antiviral treatment with sofosbuvir (SOF) and ledipasvir (LDV) may be shortened to 12 instead of 24 weeks, using ribavirin (RBV) in addition. Furthermore, the question of whether or not RBV is really necessary, in a 12‐week SOF/LDV treatment in the post‐transplant setting, is still unanswered.Patients and methodsAt our institution, 100 liver transplant patients with HCV recurrence underwent interferon‐free SOF‐based treatment. A total of 51 patients received SOF/LDV with or without RBV. Twenty‐nine HCV genotype 1 or 4 patients with histologically proven stage 0‐2 fibrosis were treated with SOF/LDV for 12 weeks; another 22 patients with advanced fibrosis (stage 3‐4) either received SOF/LDV plus weight‐adjusted RBV or prolonged treatment for 24 weeks.ResultsEnd of treatment response and sustained virological response (SVR) were achieved in 100% of the 51 patients, irrespective of the treatment group. Patients with prolonged treatment duration or with RBV developed significantly more adverse events (AEs) compared to the SOF/LDV group: 19 (86.4%) vs 8 (27.6%), P<.001. One of the predominant and most relevant AEs was the development of anemia in 43.1% of 10 patients receiving RBV, which was a significant result (P<.001). RBV co‐medication had to be reduced in 11 (55%) patients and then stopped in 8 (40%) patients because of AEs. No significant difference was observed among the groups regarding kidney function.ConclusionThe SOF/LDV combination is a reliable therapy of recurrent HCV infection after LT. It is easy to administer and to achieve SVR in immunocompromised patients without interactions with immunosuppressive medications. Considering the high rate of AEs, frequent discontinuation of RBV treatment, and the 100% SVR, the use of RBV as co‐medication in a 12‐week SOF/LDV regimen does not seem to be justified after LT.
Association between diabetes mellitus and active tuberculosis in Africa and the effect of HIV
Authors: Bailey S. L. , Ayles H. 
Published: December 2016

AbstractObjectiveTo determine current evidence for the association between diabetes and active tuberculosis in Africa, and how HIV modifies, or not, any association between diabetes and active tuberculosis.MethodsWe conducted a systematic review by searching the EMBASE, Global Health and MEDLINE databases. Studies were eligible for inclusion if they explored the association between diabetes mellitus prevalence and active tuberculosis incidence or prevalence, used a comparison group, were conducted in an African population and adjusted the analysis for at least age. Study characteristics were compared, and risk of bias was assessed. The range of effect estimates was determined for the primary association and for effect modification by HIV.ResultsThree eligible studies were identified: two investigated the primary association and two investigated HIV as a potential effect modifier. All studies were case–control studies, including a combined total of 1958 tuberculosis cases and 2111 non‐tuberculosis controls. Diabetes diagnostic methods and analysis strategies varied between studies. Individual study adjusted odds ratios of active tuberculosis for the effect of diabetes mellitus (unstratified) ranged from 0.88 (95% CI 0.17–4.58) to 10.7 (95% CI 4.5–26.0). Individual study P‐values for HIV interaction ranged from 0.01 to 0.83. Quantitative synthesis of individual study data was not performed due to heterogeneity between studies.ConclusionsFew data currently exist on the association between diabetes and active tuberculosis in Africa, and on the effect of HIV on this association. Existing data are disparate. More regional research is needed to guide policy and practice on the care and control of tuberculosis and diabetes in Africa.
Tobacco pollen tubes – a fast and easy tool for studying lipid droplet association of plant proteins
Authors: Müller Anna Ophelia , Blersch Katharina Franziska , Gippert Anna Lena , Ischebeck Till 
Published: December 2016

SummaryIn recent years, lipid droplets have emerged as dynamic organelles rather than inactive storage sites for triacylglycerol. The number of proteins known to be associated with lipid droplets has increased, but remains small in comparison with those found with other organelles. Also the mechanisms of how lipid droplets are recognized and bound by proteins need deeper investigation. Here, we present a fast, simple and inexpensive approach to assay proteins for their association with lipid droplets in vivo that can help to screen protein candidates or mutated variants of proteins for their association in an efficient manner. For this, a system to transiently transform Nicotiana tabacum pollen grains was used because these naturally contain lipid droplets. We designed vectors for fast cloning of genes as fusions with either mVenus or mCherry. This allowed us to assay colocalization with lipid droplets stained with Nile Red and Bodipy 505/515, respectively. We successfully tested our system not only for proteins from Arabidopsis thaliana, but also for proteins from the moss Physcomitrella patens and the alga Chlamydomonas reinhardtii. The small size of the vector used allows easy exchange of codons by site‐directed mutagenesis. We used this to show that two proline residues in the proline knot of a caleosin are not essential for the binding of lipid droplets. We also demonstrated that peroxisomes are not associated with the lipid droplets in tobacco pollen tubes, which reduces the risk of false interpretation of microscopic data in our system.
Cytogenetic features of rRNA genes across land plants: analysis of the Plant rDNA database
Authors: Garcia Sònia , Kovařík Ales , Leitch Andrew R. , Garnatje Teresa 
Published: December 2016

SummaryThe online resource http://www.plantrdnadatabase.com/ stores information on the number, chromosomal locations and structure of the 5S and 18S‐5.8S‐26S (35S) ribosomal DNAs (rDNA) in plants. This resource was exploited to study relationships between rDNA locus number, distribution, the occurrence of linked (L‐type) and separated (S‐type) 5S and 35S rDNA units, chromosome number, genome size and ploidy level. The analyses presented summarise current knowledge on rDNA locus numbers and distribution in plants. We analysed 2949 karyotypes, from 1791 species and 86 plant families, and performed ancestral character state reconstructions. The ancestral karyotype (2n = 16) has two terminal 35S sites and two interstitial 5S sites, while the median (2n = 24) presents four terminal 35S sites and three interstitial 5S sites. Whilst 86.57% of karyotypes show S‐type organisation (ancestral condition), the L‐type arrangement has arisen independently several times during plant evolution. A non‐terminal position of 35S rDNA was found in about 25% of single‐locus karyotypes, suggesting that terminal locations are not essential for functionality and expression. Single‐locus karyotypes are very common, even in polyploids. In this regard, polyploidy is followed by subsequent locus loss. This results in a decrease in locus number per monoploid genome, forming part of the diploidisation process returning polyploids to a diploid‐like state over time.
The functions of plant small RNAs in development and in stress responses
Authors: Li Shengjun , Castillo‐González Claudia , Yu Bin , Zhang Xiuren 
Published: December 2016

SummaryLike metazoans, plants use small regulatory RNAs (sRNAs) to direct gene expression. Several classes of sRNAs, which are distinguished by their origin and biogenesis, exist in plants. Among them, microRNAs (miRNAs) and trans‐acting small interfering RNAs (ta‐siRNAs) mainly inhibit gene expression at post‐transcriptional levels. In the past decades, plant miRNAs and ta‐siRNAs have been shown to be essential for numerous developmental processes, including growth and development of shoots, leaves, flowers, roots and seeds, among others. In addition, miRNAs and ta‐siRNAs are also involved in the plant responses to abiotic and biotic stresses, such as drought, temperature, salinity, nutrient deprivation, bacteria, virus and others. This review summarizes the roles of miRNAs and ta‐siRNAs in plant physiology and development.
High‐efficiency gene targeting in hexaploid wheat using DNA replicons and CRISPR/Cas9
Authors: Gil‐Humanes Javier , Wang Yanpeng , Liang Zhen , Shan Qiwei , Ozuna Carmen V. , Sánchez‐León Susana , Baltes Nicholas J. , Starker Colby , Barro Francisco , Gao Caixia , Voytas Daniel F. 
Published: December 2016

SummaryThe ability to edit plant genomes through gene targeting (GT) requires efficient methods to deliver both sequence‐specific nucleases (SSNs) and repair templates to plant cells. This is typically achieved using Agrobacterium T‐DNA, biolistics or by stably integrating nuclease‐encoding cassettes and repair templates into the plant genome. In dicotyledonous plants, such as Nicotinana tabacum (tobacco) and Solanum lycopersicum (tomato), greater than 10‐fold enhancements in GT frequencies have been achieved using DNA virus‐based replicons. These replicons transiently amplify to high copy numbers in plant cells to deliver abundant SSNs and repair templates to achieve targeted gene modification. In the present work, we developed a replicon‐based system for genome engineering of cereal crops using a deconstructed version of the wheat dwarf virus (WDV). In wheat cells, the replicons achieve a 110‐fold increase in expression of a reporter gene relative to non‐replicating controls. Furthermore, replicons carrying CRISPR/Cas9 nucleases and repair templates achieved GT at an endogenous ubiquitin locus at frequencies 12‐fold greater than non‐viral delivery methods. The use of a strong promoter to express Cas9 was critical to attain these high GT frequencies. We also demonstrate gene‐targeted integration by homologous recombination (HR) in all three of the homoeoalleles (A, B and D) of the hexaploid wheat genome, and we show that with the WDV replicons, multiplexed GT within the same wheat cell can be achieved at frequencies of ~1%. In conclusion, high frequencies of GT using WDV‐based DNA replicons will make it possible to edit complex cereal genomes without the need to integrate GT reagents into the genome.
A large national study of ferritin testing in Canadian blood donors
Authors: Goldman Mindy , Uzicanin Samra , Osmond Lori , Scalia Vito , O'Brien Sheila F. 
Published: December 2016

BACKGROUNDWe assessed risk groups for iron deficiency and the feasibility and efficacy of ferritin testing in a large blood center.STUDY DESIGN AND METHODSDonors were informed of possible testing in the predonation pamphlet. Plasma ferritin was measured on retention samples (n = 12,595) from representative clinics. Low‐ferritin donors (<25 µg/L) were sent a letter and information sheet and not called for 6 months. Ferritin testing was repeated on 25% of donors; donor return rate and frequency were monitored.RESULTSLow‐ferritin donors represented 2.9% of first‐time and reactivated (no donation in past 12 months) male donors, 32.2% of first‐time and reactivated female donors, 41.6% of repeat male donors, and 65.1% of repeat female donors. A mean of 11.7 months after index donation, the return rate was 76% for normal and 58% for low‐ferritin donors; returning low‐ferritin donors had made approximately one fewer donation. Ferritin increased by 16.3 and 12.1 µg/L in male and female low‐ferritin donors and decreased by 17 µg/L in male and female normal‐ferritin donors.CONCLUSIONThe minimum hemoglobin level will be increased to 130 g/L for male donors and the minimum interdonation interval changed to 84 days (four donations yearly) for female donors based on iron deficiency risk groups. Large‐scale ferritin testing was feasible. Donors informed of low‐ferritin results had a lower return rate, donated less often, and had an increase in ferritin on return, approximately 1 year after initial testing, compared to donors with normal ferritin results.
Rapid and durable response to intravenous immunoglobulin in delayed heparin‐induced thrombocytopenia: a case report
Authors: Lei Brandon Z. , Shatzel Joseph J. , Sendowski Merav 
Published: December 2016

BACKGROUNDHeparin‐induced thrombocytopenia (HIT) results in platelet consumption and a virulent thrombotic state, which generally responds to cessation of heparin and initiation of anticoagulation. Rarely, delayed HIT can occur and/or persist after heparin is discontinued.STUDY DESIGN AND METHODSA 47‐year‐old male developed delayed HIT with severe thrombocytopenia and thrombosis after cardiac surgery. Thrombocytopenia developed and persisted after heparin cessation and did not improve despite sequential use of argatroban followed by bivalirudin. Treatment with intravenous immunoglobulin (IVIg) was well tolerated and resulted in rapid resolution of thrombocytopenia.RESULTSThere are few case reports on the management of delayed HIT with severe and prolonged thrombocytopenia. The risk for thrombosis and bleeding in the setting of an undefined time course increases uncertainty in management.CONCLUSIONThis case, along with others accumulating in the literature, suggest that IVIg may be effective in treating delayed HIT with persistent thrombocytopenia.