bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phosphoenolpyruvate phosphotransferase system regulates detection and processing of the quorum sensing signal autoinducer‐2
Authors: Pereira Catarina S. , Santos António J. M. , Bejerano‐Sagie Michal , Correia Paulo B. , Marques Joao C. , Xavier Karina B. 
Published: March 2012

SummaryAutoinducer‐2 (AI‐2) a signal produced by a range of phylogenetically distant microorganisms, enables inter‐species cell–cell communication and regulates many bacterial phenotypes. Certain bacteria can interfere with AI‐2‐regulated behaviours of neighbouring species by internalizing AI‐2 using the Lsr transport system (encoded by the lsr operon). AI‐2 imported by the Lsr is phosphorylated by the LsrK kinase and AI‐2‐phosphate is the inducer of the lsr operon. Here we show that in Escherichia coli the phosphoenolpyruvate phosphotransferase system (PTS) is required for Lsr activation and is essential for AI‐2 internalization. Although the phosphorylation state of Enzyme I of PTS is important for this regulation, LsrK is necessary for the phosphorylation of AI‐2, indicating that AI‐2 is not phosphorylated by PTS. Our results suggest that AI‐2 internalization is initiated by a PTS‐dependent mechanism, which provides sufficient intracellular AI‐2 to relieve repression of the lsr operon and, thus induce depletion of AI‐2 from the extracellular environment. The fact that AI‐2 internalization is not only controlled by the community‐dependent accumulation of AI‐2, but also depends on the phosphorylation state of PTS suggests that E. coli can integrate information on the availability of substrates with external communal information to control quorum sensing and its interference.
Identification and characterization of a GDSL lipase‐like protein that catalyzes the ester‐forming reaction for pyrethrin biosynthesis in Tanacetum cinerariifolium– a new target for plant protection
Authors: Kikuta Yukio , Ueda Hirokazu , Takahashi Masafumi , Mitsumori Tomonori , Yamada Gen , Sakamori Koji , Takeda Kengo , Furutani Shogo , Nakayama Koji , Katsuda Yoshio , Hatanaka Akikazu , Matsuda Kazuhiko 
Published: March 2012

SummaryAlthough natural insecticides pyrethrins produced by Tanacetum cinerariifolium are used worldwide to control insect pest species, little information is known of their biosynthesis. From the buds of T. cinerariifolium, we have purified a protein that is able to transfer the chrysanthemoyl group from the coenzyme A (CoA) thioester to pyrethrolone to produce pyrethrin I and have isolated cDNAs that encode the enzyme. To our surprise, the active principle was not a member of a known acyltransferase family but a member of the GDSL lipase family. The recombinant enzyme (TcGLIP) was expressed in Escherichia coli and displayed the acyltransferase reaction with high substrate specificity, recognized the absolute configurations of three asymmetric carbons and also showed esterase activity. A S40A mutation in the Block I domain reduced both acyltransferase and esterase activities, which suggested an important role of this serine residue in these two activities. The signal peptide directed the localization of TcGLIP::enhanced green fluorescent protein (EGFP) fusion, as well as EGFP, to the extracellular space. High TcGLIP gene expression was observed in the leaves of mature plants and seedlings as well as in buds and flowers, a finding that was consistent with the pyrethrin I content in these parts. Expression was enhanced in response to wounding, which suggested that the enzyme plays a key role in the defense mechanism of T. cinerariifolium.
Evaluation of overnight storage conditions for autologous peripheral blood stem cell products: comparison of three different conditions
Authors: Seo J. Y. , Huh H.‐J. , Park H.‐K. , Choung H.‐K. , Kim D.‐W. , Koo H. H. , Sung K. W. , Kang E.‐S. 
Published: February 2012

Background  Overnight (ON) storage of peripheral blood stem cell (PBSC) occurs frequently in clinical settings. However, there are no standard guidelines for optimal storage conditions of freshly harvested PBSC. The aim of this study was to investigate the influence of storage temperatures on the quality of autologous PBSC and establish optimal storage conditions before cryopreservation.Methods  A retrospective analysis was performed on 260 PBSC harvests according to pre‐cryopreservation conditions: immediate processing or ON storage at room temperature (RT). For direct comparison, 30 autologous PBSC products were collected prospectively and prepared under three different pre‐cryopreservation conditions: immediate processing, ON storage at 4°C and ON storage at RT. The recovery of CD34+ cells, post‐thaw CFU‐GM count and viability were analysed.Results  Retrospective analysis revealed that post‐thaw CFU‐GM count was significantly lower when PBSC were stored ON at RT compared to when immediately processed (136·4 vs. 409·6/μl). Prospective analysis showed a mean recovery of CD34+ cells of 65·5 ± 25·1%, 70·5 ± 27·4% and 35·9 ± 25·1% for immediate processing, ON storage at 4°C and ON storage at RT, respectively. Similarly, mean viability and CFU‐GM counts were significantly reduced when stored ON at RT compared to when immediately processed or stored ON at 4°C (60·4 ± 25·6 vs. 84·1 ± 12·9 vs. 82·7 ± 12·6%, 15·7 ± 25·7 vs. 398·5 ± 906·2 vs. 350·0 ± 847·9/μl, respectively).Conclusions  ON storage of autologous PBSC at RT significantly decreased the quality of HPCs. These data indicate that ON storage of autologous PBSC at 4°C would be the most reasonable approach for maintaining the quality of HPCs when immediate processing is not possible.
Screening of core simple sequence repeat primer pairs and establishment of a multiplex polymerase chain reaction system for Brassica genomes A and C
Authors: Wei Lijuan , Zhao Chaoxian , Li Jiana , Qian Wei , Fu Donghui 
Published: March 2012

With 2 figures and 1 tableAbstractBrassica species are important industrial materials. Recently, simple sequence repeat (SSR) markers have become preferred molecular markers because of their simplicity, high levels of polymorphism and codominant nature. Numerous SSR markers have been developed in Brassica crops, but not every SSR marker has an equal value, and they must be tested individually for each application. To develop a set of standardized, highly efficient core SSR primers, we screened 190 primer pairs from among over 2353 SSR primer pairs that have been mapped for Brassica species. Ten different primer pairs were selected for each of the 19 linkage groups that corresponded with the chromosomes of Brassica genomes A and C. We also established 19 multiplex polymerase chain reaction (PCR) combinations, one per linkage group. Twenty accessions from six Brassica species were used to test these primer combinations, and an average of 15 clear bands were amplified successfully in each reaction. It is clear that multiplex PCR is a practical method for germplasm identification, genetic diversity analysis and backcross breeding in Brassica crops.
Changes in the Aral Sea ichthyofauna and fishery during the period of ecological crisis
Authors: Ermakhanov Z. K. , Plotnikov I. S. , Aladin N. V. , Micklin P. 
Published: February 2012

AbstractAboriginal ichthyofauna of the Aral Sea consisted of 20 generative‐freshwater species from seven families. After acclimatization in 1927–1963, the number of species increased to 34. The regulation of Syr Dar’ya and Amu Dar’ya river water flows, and increasing water withdrawals, primarily for irrigation, resulted in a declining lake water level, increasing salinization and changing habitat conditions, especially for reproduction. As a result, the spawning areas were greatly reduced, and because of worsening conditions for natural reproduction, fish catches in 1961–1976 decreased more than 4‐fold. The first signs of the negative impacts of salinization on fishes appeared in the mid‐1960s. Natural reproduction ceased by the mid‐1970s, and indigenous commercial fish fauna were lost by the end of the 1970s. Flounder‐gloss was introduced from the Black Sea in 1979–1987 to preserve the fishery, and it was the only commercial fish left by 1991–2000. Because of the water level decline, the Aral Sea became divided in 1989 into the Large and Small Seas. By the end of the 1990s, flounder became extinct in the Large Aral because of high salinity, as did other fishes. Decreasing agriculture activity has resulted in stabilized run‐off of the Syr Dar’ya to the Small Aral since 1988, creating a freshened water zone where indigenous ichthyofauna returned from lacustrine systems and the river. The ecological state of the Small Aral is improving, with some aboriginal valuable commercial fishes having reached numbers making their commercial catch possible once again.
Variations, trends and patterns of fish landings in large tropical reservoirs
Authors: Jutagate Tuantong , Srichareondham Boonsong , Lek Sovan , Amarasinghe Upali S. , De Silva Sena S. 
Published: February 2012

AbstractTemporal variations of fish yields in four major reservoirs in Thailand (Ubolratana; Sirindhorn; Srinakarin; Vajiralongkorn) were investigated with the use of long‐term fish landing data (≥20 years). The long‐term variations in fish yield, measured as the coefficient of variation of yearly yield, ranged mostly between 50% and 100%. For short‐term variations, the means of the relative variation (85%) were larger than the absolute variation (63%). This finding indicates that short‐term variations were inversely related to fish yield and that a higher uncertainty occurs when fish catches are low. The stocked exotic species exhibited higher variations than the indigenous species. The trend analyses indicated some species had sharply declined fish landings, while some species were quite stable (i.e. reservoir‐adapted species). Stocked species tended to increase in relatively shallow reservoirs, compared to the deep reservoir. Fish landing data for each reservoir were patternized, using the self‐organizing map, indicating temporal trends of chronological order. The differences among clusters in each reservoir were with respect to the weight of each species in the fish landings in each year, and temporal changes in species composition in the reservoirs, which would primarily be attributed to the environmental changes followed by anthropogenic pressures. The mean trophic level (τ) fluctuated, resulting from changes in species composition and weight of fish landing, as well as fish stocking programmes.
Bathymetric distribution of chironomid larvae (Diptera: Chironomidae) in Lake Saiko, Japan
Authors: Fu Zhenghai , Yoshizawa Kazuya , Yoshida Norihiko , Kazama Futaba , Hirabayashi Kimio 
Published: February 2012

AbstractThe distribution of benthic macroinvertebrate on 8 March 2009 was studied in Lake Saiko (73.2 m maximum depth). The average density of the benthic community for the entire lake was 19 583 individuals m−2, being comprised of oligochaetes and chironomid larvae, with densities of 18 163 (92.8%) and 1274 (6.5%), respectively. The average wet weights of oligochaetes and chironomid larvae were 15.96 and 1.67 g m−2, respectively. The oligochaetes inhabited the entire lake bottom, with their densities being higher in the transitional region (20–40 m) and deeper region (>40 m) than in the shallower region. However, the densities of chironomid larvae were low in the deeper region (>40 m), with only a few chironomid larvae being found in the centre of the lake (>60 m). The most abundant species (Micropsectra chuzeprima) exhibited the widest distribution (from 10.1 to 65.5 m depth), followed by Polypedilum nubeculosum. The results of this study also were compared to previous data on oligochaetes and chironomid larvae reported by Kitagawa (1973). The density of these animals increased throughout the whole lake in 2009. However, the chironomid species compositions did not changed. The larval distribution pattern of chironomid changed since Kitagawa’s study, being distributed from 11 to 68 m in 1973. In contrast, almost all chironomid larvae were found in the transitional (e.g. M. chuzeprima) and shallower (e.g. Procladius choreus and P. nubeculosum) regions in 2009, with only a few individuals being observed in the deeper regions (>60 m). In contrast, the oligochaete density increased in the deeper regions. Large environmental changes must have affected the oligochaetes and chironomids densities, especially in the deeper regions with low dissolved oxygen concentrations. Consequently, the distribution pattern of oligochaetes and chironomids in the lake has changed. These study findings suggest the lake is experiencing increasing eutrophication.
Solving the Light's criteria misclassification rate of cardiac and hepatic transudates
Authors: BIELSA SILVIA , PORCEL JOSÉ M. , CASTELLOTE JOSÉ , MAS ESTELA , ESQUERDA AURELI , LIGHT RICHARD W. 
Published: February 2012

ABSTRACTBackground and objective:  Pleural transudates are most commonly due to heart failure (HF) or hepatic hydrothorax (HH), but a number of these effusions are misclassified as exudates by standard (Light's) criteria. The aim of this study was to determine the prevalence of mislabelled transudates and to establish simple alternative parameters to correctly identify them.Methods:  We retrospectively analysed the pleural fluid and serum protein, lactate dehydrogenase and albumin concentrations from 364 cardiac effusions and 102 HH. The serum–to–pleural fluid protein and albumin gradients (serum concentration minus pleural fluid concentration), as well as the pleural fluid–to–serum albumin ratio (pleural fluid concentration divided by the serum concentration) were calculated for the mislabelled transudates.Results:  Light's criteria had misclassified more HF‐associated effusions than HH (29% vs 18%, P = 0.002). A serum–to–pleural fluid protein gradient >3.1 g/dL correctly identified 55% and 61% of the HF and HH false exudates, respectively. The figures for an albumin gradient >1.2 g/dL were 83% and 62%. Finally, a pleural fluid–to–serum albumin ratio <0.6 had identical accuracy for labelling miscategorized cardiac and liver‐related effusions (78% and 77%, respectively).Conclusions:  If the clinical picture is consistent with HF but the pleural fluid meets Light's exudative criteria, the measurement of the albumin rather than the protein gradient is recommended. In the context of cirrhosis, a potentially ‘false’ exudate is identified better by the pleural fluid–to–serum albumin ratio.
Reference values for airway resistance in newborns, infants and preschoolers from a Latin American population
Authors: GOCHICOA LAURA G. , THOMÉ‐ORTIZ LAURA P. , FURUYA MARÍA E. Y. , CANTO RAQUEL , RUIZ‐GARCÍA MARTHA E. , ZÚÑIGA‐VÁZQUEZ GUILLERMO , MARTÍNEZ‐RAMÍREZ FILIBERTO , VARGAS MARIO H. 
Published: February 2012

ABSTRACTBackground and objective:  Several studies have determined reference values for airway resistance measured by the interrupter technique (Rint) in paediatric populations, but only one has been done on Latin American children, and no studies have been performed on Mexican children. Moreover, these previous studies mostly included children aged 3 years and older; therefore, information regarding Rint reference values for newborns and infants is scarce.Methods:  Rint measurements were performed on preschool children attending eight kindergartens (Group 1) and also on sedated newborns, infants and preschool children admitted to a tertiary‐level paediatric hospital due to non‐cardiopulmonary disorders (Group 2).Results:  In both groups, Rint values were inversely associated with age, weight and height, but the strongest association was with height. The linear regression equation for Group 1 (n = 209, height 86–129 cm) was Rint = 2.153 − 0.012 × height (cm) (standard deviation of residuals 0.181 kPa/L/s). The linear regression equation for Group 2 (n = 55, height 52–113 cm) was Rint = 4.575 − 0.035 × height (cm) (standard deviation of residuals 0.567 kPa/L/s). Girls tended to have slightly higher Rint values than boys, a difference that diminished with increasing height.Conclusions:  In this study, Rint reference values applicable to Mexican children were determined, and these values are probably also applicable to other paediatric populations with similar Spanish‐Amerindian ancestries. There was an inverse relationship between Rint and height, with relatively large between‐subject variability.
Method for identifying eligible individuals for a prevalence survey in the absence of a disease register or population register
Authors: Richardson A. K. , Clarke G. , Sabel C. E. , Pearson J. F. , Mason D. F. , Taylor B. V. 
Published: February 2012

AbstractBackgroundIdentifying eligible individuals for a prevalence survey is difficult in the absence of a disease register or a national population register.AimTo develop a method to identify and invite eligible individuals to participate in a national prevalence survey while maintaining confidentiality and complying with privacy legislation.MethodsA unique identifier (based on date of birth, sex and initials) was developed so that database holders could identify eligible individuals, notify us and invite them on our behalf to participate in a national multiple sclerosis prevalence survey while maintaining confidentiality and complying with privacy legislation.ResultsSeveral organisations (including central government, health and non‐governmental organisations) used the method described to assign unique identifiers to individuals listed on their databases and to forward invitations and consent forms to them. The use of a unique identifier allowed us to recognise and record all the sources of identification for each individual. This prevented double counting or approaching the same individual more than once and facilitated the use of capture–recapture methods to improve the prevalence estimate. Capture–recapture analysis estimated that the method identified over 96% of eligible individuals in this prevalence survey.ConclusionsThis method was developed and used successfully in a national prevalence survey of multiple sclerosis in New Zealand. The method may be useful for prevalence surveys of other diseases in New Zealand and for prevalence surveys in other countries with similar privacy legislation and lack of disease registers and population registers.
Prognostic value of apoptotic markers in squamous cell carcinoma of the urinary bladder
Authors: Youssef Ramy , Kapur Payal , Shariat Shahrokh F. , Arendt Tyler , Kabbani Wareef , Mosbah Ahmed , Abol‐Enein Hassan , Ghoneim Mohamed , Lotan Yair 
Published: February 2012

Study Type – Prognosis (case series)Level of Evidence 4What's known on the subject? and What does the study add?Apoptotic pathways are important in carcinogenesis. Many studies, involving small numbers of patients, have found an association between one or two apoptotic markers and some of the pathological features of squamous cell carcinoma (SCC).This study included a large number of patients who had undergone radical cystectomy (RC) for SCC with long‐term follow‐up, allowing us to study biomarker alterations and their prognostic role. This is the first study on the prognostic role of a panel of apoptotic‐related markers in SCC of the urinary bladder, introducing the novel concept of a prognostic marker score based on the number of altered markers. We found that apoptotic markers can improve prediction of oncological outcomes after RC for SCC and might potentially help in patient selection for adjunct therapies.OBJECTIVE
To evaluate the association of cleaved caspase‐3 (CC‐3), Bax, COX‐2, and p53 expression with pathological features and clinical outcomes in patients with squamous cell carcinoma (SCC) of the urinary bladder.
METHODS
Immunohistochemistry for CC‐3, Bax, COX‐2, and p53 was performed on tissue microarray sections of radical cystectomy specimens with pure SCC from 1997 to 2003. The relationship between the expression of these markers and pathological features was assessed.
A prognostic marker score (PS) was defined as favourable if ≤2 biomarkers were altered and unfavourable if >2 biomarkers were altered and the association of the PS with oncological outcomes was examined.
RESULTS
The study included 151 patients, of whom 98 were men and 53 were women, with a mean age of 52 years. SCC was associated with schistosomiasis (bilharziasis) in 122 (81%) patients.
Pathological stage was T2 in 50%, T3 in 38%, T1 in 6% and T4 in 6% of patients. Tumours were low grade in 53%, lymph node metastasis was found in 30.5% and lymphovascular invasion was found in 16% of patients.
Median follow‐up was 63.2 months.
Advanced stage was associated with COX‐2, p53 and CC‐3 alterations and high grade was associated with COX‐2 alterations (P < 0.05). The total number of altered markers and unfavourable PS were associated with both disease recurrence and bladder cancer‐specific mortality in Kaplan–Meier analyses (P < 0.05). Unfavourable PS was an independent predictor of disease recurrence (hazard ratio [HR] 2.694, 95% confidence interval [CI] 1.386–5.235, P= 0. 003) and bladder cancer‐specific mortality (HR 2.868, 95% CI 1.209–6.802, P= 0. 017) in multivariable Cox regression analysis.
CONCLUSION
Markers of apoptosis pathways may play an important role in the prognosis of SCC of the bladder. An increased number of altered markers and an unfavourable PS may identify patients who might benefit from multimodal therapies.
Flexible ureterorenoscopy versus extracorporeal shock wave lithotripsy for treatment of lower pole stones of 10–20 mm
Authors: El‐Nahas Ahmed R. , Ibrahim Hamdy M. , Youssef Ramy F. , Sheir Khaled Z. 
Published: February 2012

Study Type – Therapy (case series)Level of Evidence 4What's known on the subject? and What does the study add?Shock wave lithotripsy and flexible ureterorenoscopy are acceptable treatment options for lower pole stones smaller than 10 mm, while percutaneous nephrolithotomy is the favoured treatment for stones larger than 20 mm.For treatment of lower pole stones of 10–20 mm, flexible ureterorenoscopy has a significantly higher stone‐free rate and lower retreatment rate than shock wave lithotripsy.OBJECTIVE
To compare the outcomes of flexible ureterorenoscopy (F‐URS) and extracorporeal shock wave lithotripsy (ESWL) for treatment of lower pole stones of 10–20 mm.
PATIENTS AND METHODS
The database of patients with a single lower pole stone of 10–20 mm was examined to obtain two matched groups who were treated with F‐URS or ESWL. Matching criteria were stone length, side and patient gender.
Stone‐free rates were evaluated 3 months after the last treatment session by non‐contrast computed tomography. Both groups were compared for retreatment rate, complications and stone‐free rate.
RESULTS
The matched groups included 37 patients who underwent F‐URS and 62 patients who underwent ESWL. Retreatment rate was significantly higher for ESWL (60% vs 8%, P < 0.001).
Complications were more after F‐URS (13.5% vs 4.8%), but the difference was not significant (P= 0.146). All complications were grade II or IIIa on modified Clavien classification.
The stone‐free rate was significantly better after F‐URS (86.5% vs 67.7%, P= 0.038). One failure of F‐URS (2.7%) and five failures (8%) of ESWL were treated with percutaneous nephrolithotomy.
Significant residual fragments in three patients (8%) after F‐URS were treated with ESWL, while significant residual fragments after ESWL in five patients (8%) were treated with F‐URS. Residual fragments (<4 mm) were followed every 3 months in one patient (2.7%) after F‐URS and in 10 patients (16%) after ESWL.
CONCLUSIONS
For treatment of lower pole stones of 10–20 mm, F‐URS provided significantly higher stone‐free rate and lower retreatment rate compared with ESWL.
The incidence of complications after F‐URS was not significantly more than after ESWL.