bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disulfide bond cleavage in TEMPO‐free radical initiated peptide sequencing mass spectrometry
Authors: Lee Minhee , Lee Younjin , Kang Minhyuk , Park Hyeyeon , Seong Yeonmi , June Sung Bong , Moon Bongjin , Bin Oh Han 
Published: August 2011

AbstractThe gas‐phase free radical initiated peptide sequencing (FRIPS) fragmentation behavior of o‐TEMPO‐Bz‐conjugated peptides with an intra‐ and intermolecular disulfide bond was investigated using MSn tandem mass spectrometry experiments. Investigated peptides included four peptides with an intramolecular cyclic disulfide bond, Bactenecin (RLCRIVVIRVCR), TGF‐α (CHSGYVGVRC), MCH (DFDMLRCMLGRVFRPCWQY) and Adrenomedullin (16–31) (CRFGTCTVQKLAHQIY), and two peptides with an intermolecular disulfide bond. Collisional activation of the benzyl radical conjugated peptide cation, which was generated through the release of a TEMPO radical from o‐TEMPO‐Bz‐conjugated peptides upon initial collisional activation, produced a large number of peptide backbone fragments in which the SS or CS bond was readily cleaved. The observed peptide backbone fragments included a‐, c‐, x‐ or z‐types, which indicates that the radical‐driven peptide fragmentation mechanism plays an important role in TEMPO‐FRIPS mass spectrometry. FRIPS application of the linearly linked disulfide peptides further showed that the SS or CS bond was selectively and preferentially cleaved, followed by peptide backbone dissociations. In the FRIPS mass spectra, the loss of •SH or •SSH was also abundantly found. On the basis of these findings, FRIPS fragmentation pathways for peptides with a disulfide bond are proposed. For the cleavage of the SS bond, the abstraction of a hydrogen atom at Cβ by the benzyl radical is proposed to be the initial radical abstraction/transfer reaction. On the other hand, H‐abstraction at Cα is suggested to lead to CS bond cleavage, which yields [ion ± S] fragments or the loss of •SH or •SSH. Copyright © 2011 John Wiley & Sons, Ltd.
New cloud and microphysics parameterisation for use in high‐resolution dynamical downscaling: application for summer extreme temperature over Belgium
Authors: Hamdi R. , Van de Vyver H. , Termonia P. 
Published: August 2011

AbstractWe explore the use of high‐resolution dynamical downscaling as a means to simulate extreme values of summer maximum surface air temperature over Belgium (TMAX). We use the limited area version of the ARPEGE‐IFS model, ALADIN. Our approach involves a sequence of daily integrations driven by perfect boundary conditions at the lateral boundaries provided by the ERA40 reanalysis. In this study, three different recent past (1961–1990) simulations are evaluated against different station datasets: (1) 40 km spatial resolution (ALD40), (2) 10 km spatial resolution (ALD10), and (3) 4 km spatial resolution (ALR04) using a new parameterisation of deep convection, and microphysics allowing the use of ALADIN at resolutions ranging from a few tens of kilometers down to less than 4 km. The validation of ALD40 reveals a positive summer bias (2.2 °C), even though the considerable spatial resolution enhancement by a factor of 4, ALD10 reduces slightly the warm biases (1.7 °C). This warm bias on TMAX is strongly correlated with cloud cover representation. Result shows an overestimate of clear‐sky occurrences by ALD10 and a developing solar radiation overestimate through the diurnal cycle, with 116 W m−2 maximum overestimate at noon. ALR04 reduces considerably the warm biases (−0.2 °C) which suggests of its ability to simulate weakly forced convective cloud in the summer over Belgium. In addition, the Generalized Pareto Distribution (GPD) of the extreme high temperatures produced by the different simulations has been compared to observations of the same period. ALD40 and ALD10 gave a GPD distribution that did not replicate the observed distribution well and, thus, overestimated the extremes. This study shows that the consistent treatment of deep convection and cloud–radiation interaction when increasing the horizontal resolution is very important when studying extremely high temperatures events. Copyright © 2011 Royal Meteorological Society
Semi‐supervised multivariate regression trees: putting the ‘circulation’ back into a ‘circulation‐to‐environment’ synoptic classifier
Authors: Cannon Alex J. 
Published: August 2011

AbstractMultivariate regression trees (MRTs) have been used in synoptic climatology to construct “circulation‐to‐environment” synoptic classifications. Because the goal of an MRT is to maximize discrimination of the environmental predictand variables, performance in terms of the synoptic‐scale circulation predictors is typically sacrificed. This paper introduces a semi‐supervised approach in which a weighted combination of synoptic‐scale predictors and environmental variables serve as predictands in a MRT. Results for southern British Columbia, Canada, indicate that (1) a semi‐supervised MRT can outperform a fully supervised MRT in terms of discrimination of the surface environment; (2) weighting allows the synoptic classifier to behave as a fully unsupervised model, a fully supervised model, or intermediate between the two ends of the spectrum; and (3) the optimum trade‐off between circulation and environment must be chosen by the user depending on specific needs. © 2011 Crown in the right of Canada. Published by John Wiley & Sons Ltd.
Hyperbaric oxygen therapy in a mouse model of implant‐associated osteomyelitis
Authors: Shandley Sabrina , Matthews Krista Prato , Cox Jennifer , Romano Desiree , Abplanalp Allison , Kalns John 
Published: August 2011

AbstractImplant associated osteomyelitis (OM) is difficult to treat with antibiotics, and outcomes remain poor. Some reports suggest that hyperbaric oxygen treatment is a safe and effective means of treating OM. We tested this hypothesis in a murine model. Clinical isolates of methicillin‐resistant Staphylococcus aureus (MRSA), Pseudomonas aeruginosa, and Klebsiella pneumoniae were used. The mice were infected with each of the three pathogens, treated with 100% oxygen at high pressure, hyperbaric oxygen (HBO), and monitored for the ability of HBO to prevent and/or clear the OM infection. Assessments included bacterial burden of the tibias and lesion scores, as well as receptor activator of NF‐κB ligand (RANKL) and myeloperoxidase (MPO) concentrations. HBO resulted in more severe lesion scores and higher RANKL and MPO concentrations for MRSA. A significant positive correlation was found between RANKL concentration and lesion score. No significant difference was found with HBO in P. aeruginosa infections and K. pneumoniae seems to either not infect bone well or get cleared before establishing an infection. The model is useful for studying OM infections caused by MRSA and P. aeruginosa, but HBO does not appear to be an efficacious treatment of an implant‐associated OM infection. © 2011 Orthopaedic Research Society Published by Wiley Periodicals, Inc. J Orthop Res 30:203–208, 2012
Pedogenic carbonate recrystallization assessed by isotopic labeling: a comparison of 13C and 14C tracers
Authors: Gocke Martina , Pustovoytov Konstantin , Kuzyakov Yakov 
Published: August 2011

AbstractThe C isotopic composition (δ13C) of pedogenic carbonates reflects the photosynthetic pathway of the predominant local vegetation because pedogenic (secondary) CaCO3 is formed in isotopic equilibrium with soil CO2 released by root and rhizomicrobial respiration. Numerous studies show the importance of pedogenic carbonates as a tool for reconstructing paleoecological conditions in arid and semiarid regions. The methodological resolution of these studies strongly depends on the time scale of pedogenic carbonate formation, which remains unknown. The initial formation rate can be assessed by 14C labeling of plants grown on loess and subsequent incorporation of 14C from rhizosphere CO2 into newly formed carbonate by recrystallization of loess CaCO3. We tested the feasibility of 14C and 13C tracers for estimating CaCO3 recrystallization rates by simultaneous 14C and 13C labeling and comparison with literature data. 14C labeling was more efficient and precise in assessing recrystallization rates than 13C labeling. This is connected with higher sensitivity of 14C liquid scintillation counting when compared with δ13C measurement by IRMS. Further, assessment of very low amounts of incorporated tracer is more precise with low background signal (natural abundance), which is true for 14C, but is rather high for 13C. Together, we obtained better reproducibility, higher methodological precision, and better plausibility of recrystallization rates calculated based on 14C labeling. Periods for complete CaCO3 recrystallization, extrapolated from rates based on 14C labeling, ranged from 130 (125–140) to 240 (225–255) y, while it was ≈ 600 (365–1600) y based on the 13C approach. In terms of magnitude, data from late‐Holocene soil profiles of known age provide better fit with modeled recrystallization periods based on the 14C approach.
Response of five citrus rootstocks to iron deficiency
Authors: Pestana Maribela , Correia Pedro José , David Manuela , Abadía Anunciación , Abadía Javier , de Varennes Amarilis 
Published: August 2011

AbstractCitrus established in calcareous soils can be affected by iron (Fe)‐deficiency chlorosis which limits yield and the farmers' income. The degree of deficiency depends on the rootstock, but the resistance to Fe chlorosis still requires further investigation. To study physiological parameters of citrus rootstocks that could be used to evaluate resistance to Fe deficiency, plants of Troyer citrange (Citrus sinensis L. Osb. × Poncitrus trifoliata L. Raf.), Carrizo citrange, Volkamer lemon (Citrus volkameriana Ten. & Pasq.), alemow (Citrus macrophylla Wester), and sour orange (Citrus aurantium L.) were grown in nutrient solutions with 0, 5, 10, 15, or 20 μM Fe. For each rootstock, plant height, root and shoot dry weights, and concentration of Fe in the shoots and roots were measured at the end of the experiment. Chlorophyll (CHL) concentration was estimated throughout the experimental period using a portable CHL meter (SPAD‐502) calibrated for each rootstock. At the end of the experiment, CHL fluorescence parameters were measured in each rootstock with a portable fluorimeter. Maximal and variable fluorescence values indicated that the photochemistry of Troyer was more affected by a low concentration of Fe in the nutrient solution than that of other rootstocks. To compare rootstocks, the absolute CHL concentration was converted into relative yield by employing a scaling divisor based on the maximum value of total CHL in plants without Fe‐deficiency symptoms. Exponential models were developed to determine the minimum Fe concentration in nutrient solution required to maintain leaf CHL at 50% of the maximum CHL concentration (IC50). Models were also developed to assess the period of time the rootstocks were able to grow under Fe‐stress conditions before they reached IC50. Volkamer lemon and sour orange needed the lowest Fe concentration (between 4 and 5 μM Fe) to maintain IC50, and Troyer citrange had the highest Fe requirement (14 μM Fe). Citrus macrophylla and Carrizo citrange required 7 and 9 μM of Fe, respectively. Similarly, Volkamer lemon and sour orange rootstocks withstood more days under total Fe depletion or with a low concentration of Fe (5 μM Fe in nutrient solution) until they reached IC50, compared to the other rootstocks. The approach used led to a classification of the rootstocks into three categories, regarding their internal tolerance to Fe chlorosis: resistance (sour orange and Volkamer lemon), intermediate resistance (C. macrophylla and Carrizo citrange), and reduced resistance (Troyer citrange).
Effects of beech and ash on small‐scale variation of soil acidity and nutrient stocks in a mixed deciduous forest
Authors: Holzwarth Frédéric M. , Daenner Max , Flessa Heiner 
Published: August 2011

AbstractTrees interact in a complex manner with soils: they recycle and redistribute nutrients via many ecological pathways. Nutrient distribution via leaf litter is assumed to be of major importance. Beech is commonly known to have lower nutrient concentrations in its litter than other hardwood tree species occurring in Central Europe. We examined the influences of distribution of beech (Fagus sylvatica L.), ash (Fraxinus excelsior L.), lime (Tilia cordata Mill. and T. platyphyllos Scop.), maple (Acer spp. L.), and clay content on small‐scale variability of pH and exchangeable Ca and Mg stocks in the mineral soil and of organic‐C stocks in the forest floor in a near‐natural, mature mixed deciduous forest in Central Germany. The soil is a Luvisol developed in loess over limestone. We found a positive effect of the proportion of beech on the organic‐C stocks in the forest floor and a negative effect on soil pH and exchangeable Ca and Mg in the upper mineral soil (0 to 10 cm). The proportion of ash had a similar effect in the opposite direction, the other species did not show any such effect. The ecological impact of beech and ash on soil properties at a sample point was explained best by their respective proportion within a radius of 9 to 11 m. The proportion of the species based on tree volume within this radius was the best proxy to explain species effects. The clay content had a significant positive influence on soil pH and exchangeable Ca and Mg with similar effect sizes. Our results indicate that beech, in comparison to other co‐occurring deciduous tree species, mainly ash, increased acidification at our site. This effect occurred on a small spatial scale and was probably driven by species‐related differences in nutrient cycling via leaf litter. The distribution of beech and ash resulted not only in aboveground diversity of stand structures but also induced a distinct belowground diversity of the soil habitat.
Underweight patients show an increased rate of postoperative death after surgery for hepatocellular carcinoma
Authors: Ishizuka Mitsuru , Kubota Keiichi , Kita Junji , Shimoda Mitsugi , Kato Masato , Sawada Tokihiko 
Published: August 2011

AbstractObjectiveTo evaluate the influence of body mass index (BMI) on postoperative death in patients undergoing surgery for HCC.MethodsThree hundred forty‐two patients were enrolled, and divided into three groups: Group A, BMI <22.5; Group B, BMI ≥22.5 to <25; Group C, BMI ≥25. Univariate and multivariate analyses of postoperative death were performed to compare BMI with clinical factors. Kaplan–Meier analysis and log rank test were used to compare such outcome in Groups A, B, and C.ResultsKaplan–Meier analysis and log rank test revealed that Group A had a higher rate of postoperative death than Group B or C (P = 0.010). Univariate and multivariate analyses selected being underweight (Group B, C/Group A) (odds ratio, 1.829; 95% C.I., 1.091–3.068; P = 0.022) as one of the factors predictive of postoperative death, together with aspartate aminotransferase level (P = 0.042) and HCC growth pattern (P = 0.032).ConclusionsBMI is a simple but important predictor of postoperative death in patients undergoing surgery for HCC, and is able to classify such patients into three independent groups. J. Surg. Oncol. 2011; 104:809–813. © 2011 Wiley Periodicals, Inc.
The toxicity and long‐term efficacy of nedaplatin and paclitaxel treatment as neoadjuvant chemotherapy for locally advanced cervical cancer
Authors: Yin Mingzhu , Zhang Haiyu , Li Huiyan , Li Xia , Liu Yunduo , Chen Xiuwei , Lou Ge , Li Kang 
Published: August 2011

AbstractBackgroundThe use of neoadjuvant chemotherapy (NACT) for the treatment of locally advanced cervical cancer (LACC) remains controversial. In current clinical practice, platinum‐based chemotherapy is the major option for patients with LACC. However, serious adverse events have been reported after platinum‐based chemotherapy treatment for LACC patients. In this study, the authors evaluated whether nedaplatin and paclitaxel (NP), as a new NACT regimen, offers less toxicity and better long‐term efficacy for LACC (stages IB2‐IIB) treatment. Comparisons between NP and paclitaxel and cisplatin (PC) in terms of toxicity and long‐term efficacy are also presented.MethodsThe authors retrospectively reviewed 252 consecutive patients with LACC, of whom 104 received NP; the others received PC. Toxicity was assessed according to the International WHO (1979) criteria for chemotherapy side effects, and the chi‐squared test was used to identify whether there was a statistically significant difference in toxicity between the NP regimen and the PC regimen. A univariate and a Cox regression model were used to assess whether the patients who were administered NP were statistically significantly different from those who were administered PC with respect to the disease‐free survival rate (DFS) and the overall survival rate (OS).ResultsThe overall response rate for NP and PC were 80.77% and 68.24%, respectively (P = 0.0267). The incidences of toxic reactions for NP and PC were 32.69% and 85.14%, respectively (P < 0.0001). The DFS for patients who were given the NP and the PC regimens were 81.41% and 67.28%, respectively (P = 0.014). The OS was 81.54% for patients who received the PC program and 93.89% for those who received the NP program (P = 0.0084). The NP program participants experienced a significant increase in the survival rate when compared to the group that received the PC program (DFS hazard ratio = 0.539, P = 0.0144 and OS hazard ratio = 0.354, P = 0.0077).ConclusionsNP NACT followed by radical hysterectomy offers a higher response rate, lower incidence of toxic reactions and better long‐term DFS and OS for patients with LACC compared with the chemotherapy regimen of PC followed by radical hysterectomy. J. Surg. Oncol. 2012; 105:206–211. © 2011 Wiley Periodicals, Inc.
Overall survival peri‐hilar cholangiocarcinoma: R1 resection with curative intent compared to primary endoscopic therapy
Authors: Schiffman Suzanne C. , Reuter Nathaniel P. , McMasters Kelly M. , Scoggins Charles R. , Martin Robert C.G. 
Published: August 2011

AbstractBackground and ObjectivesPatients with peri‐hilar cholangiocarcinoma who undergo R1 resection with curative intent will have an improved survival compared to patients who were not resected.MethodsReview of a prospective hepatobiliary database identified 130 patients. Survival was compared using the log‐rank test.ResultsSeventy‐nine patients (61%) were resected while 51 (49%) patients were not. Forty‐two patients (54%) had an R0 resection. There was no difference in mean age (69 vs. 67; P = 0.8), BMI (27.8 vs. 27.9; P = 1.0), gender (73% vs. 43% male; P = 0.1), presence of jaundice (77% vs. 64%; P = 0.5), vascular involvement on pre operative imaging (77% vs. 64%; P = 0.5), stent (73.1% vs. 64.3%; P = 0.72), and lobar atrophy (27% vs. 7%, P = 0.2) in the resected versus non‐resected patients. All patients underwent chemotherapy and/or radiation therapy. After a median follow up of 35.6 months the median OSl for all peri‐hilar patients was 16.2 months (95% CI = 11.2–23.4). The median OS for resected patients was 18.9 months (95% CI = 12.5–24.7) versus 5.0 months (95% CI = 0–6.9) for patients not resected (P < 0.001). The only pre‐operative predictor of OS was resection (P = 0.041). Vascular invasion, lobar atrophy, and stent placement were not statistically significant predictors.ConclusionOverall survival is improved in patients undergoing R1 resection and multi‐modality therapy compared to patients not resected. J. Surg. Oncol. 2012; 105:91–96. © 2011 Wiley Periodicals, Inc.
Expressive levels of MUC1 and MUC5AC and their clinicopathologic significances in the benign and malignant lesions of gallbladder
Authors: Xiong Li , Yang Zhulin , Yang Leping , Liu Jieqiong , Miao Xiongying 
Published: August 2011

AbstractObjectiveThis article is intended to make a study on the expressive levels of mucin core proteins (MUC1 and MUC5AC) and detect their clinicopathologic significances in the benign and malignant lesions of gallbladder.MethodsEnVision immunohistochemical method for determining the expressions of MUC1 and MUC5AC was used in routinely paraffin‐embedded sections of surgically resected specimens from gallbladder adenocarcinoma (n = 108), peritumoral tissues (n = 46), adenoma (n = 15), and chronic cholecystitis (n = 35).ResultsThe positive rate of MUC1 expression was significantly higher in gallbladder adenocarcinoma than that in peritumoral tissues (χ2 = 16.49, P < 0.01), adenoma (χ2 = 7.40, P < 0.01), and chronic cholecystitis (χ2 = 28.57, P < 0.01), while the positive rate of MUC5AC expression was significantly lower in gallbladder adenocarcinoma than that in peritumoral tissues (χ2 = 12.83, P < 0.01), adenoma (χ2 = 4.22, P < 0.05), and chronic cholecystitis (χ2 = 20.25, P < 0.01). The positive cases of MUC1 and the negative ones of MUC5AC in the benign lesions showed moderate‐ or severe‐dysplasia of gallbladder epithelium. The positive rates of MUC1 were significantly lower in gallbladder adenocarcinomas with maximal diameter of mass <2 cm, no metastasis of lymph node, and no invasiveness of regional tissues (P < 0.05 or P < 0.01) than those in gallbladder adenocarcinomas with maximal diameter of mass >2 cm, metastasis of lymph node, and invasiveness of regional tissues (P < 0.05 or P < 0.01). However, the positive rates of MUC5AC were significantly higher in the highly differentiated adenocarcinoma with maximal diameter of mass <2 cm than those in the low‐differentiated adenocarcinoma with maximal diameter of mass ≥2 cm. Univariate Kaplan–Meier analysis showed that increased expression of MUC1 (P = 0.064) or decreased expression of MUC5AC (P = 0.017) was associated with decreased overall survival. Multivariate Cox regression analysis showed that decreased expression of MUC5AC (P = 0.008) was an independent prognostic predictor to gallbladder adenocarcinoma.ConclusionsThe expression of MUC1 and MUC5AC might be closely related to the carcinogenesis, clinical biological behaviors, and prognosis of gallbladder adenocarcinoma. J. Surg. Oncol. 2012; 105:97–103. © 2011 Wiley Periodicals, Inc.
Survival analysis of patients with femoral metastases
Authors: Mavrogenis Andreas F. , Pala Elisa , Romagnoli Carlo , Romantini Matteo , Calabro Teresa , Ruggieri Pietro 
Published: August 2011

AbstractBackgroundPrevious studies reported on surgical indications for patients with femoral metastases. However, few studies analyzed the spectrum of femoral metastatic presentation. We performed this study to evaluate the survival of patients with femoral metastases, and clarify the treatment of femoral impending and actual pathological fractures.Materials and MethodsWe retrospectively studied 110 patients with femoral metastases from various cancers treated with nailing or resection and megaprosthetic reconstruction from 1995 to 2010. The mean follow‐up was 18 months. Survival was analyzed with respect to different metastatic presentations regarding gender, type of cancer, number, and location of femoral metastases, type of surgery, and pathological fracture.ResultsUnivariate predictors of survival were the pathological fracture and type of surgery; multivariate predictor was only the pathological fracture. Survival was significantly higher in patients with resection compared to nailing, impending compared to actual fracture, solitary metastasis and impending fracture, actual fracture treated with resection, proximal femoral actual fracture and distal femoral impending fracture treated with resection.ConclusionsPatients with femoral metastases have better survival when present with impending compared to actual pathological fracture. Although with a higher rate of complications, patients with pathological fractures of the proximal and distal femur may benefit from resection. J. Surg. Oncol. 2012; 105:135–141. © 2011 Wiley Periodicals, Inc.