bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low-cost estimates of mortality rate from single tag recoveries: addressing short-term trap-happy and trap-shy bias
Authors: McGarvey Richard , Matthews Janet M. 
Published: March 2012

Conventional single tag-recovery data are widely available for stock assessments, notably of invertebrate fisheries, worldwide. Though not commonly used for this purpose, the times-at-large in single tag-recovery data provide (relatively) direct information about average mortality rate as a sample of survival times. Mortality rate is estimated using simple formulas given as functions of the mean time-at-large of tagged and recaptured animals. Here we extend an earlier time-at-large mortality estimator to address a potentially common source of bias: trap-happy or trap-shy behavior shortly following tag release. A maximum likelihood solution is derived, yielding an unbiased estimate of instantaneous mortality rate where the interval of usable times-at-large for observed recaptures may be truncated on both sides to any biologist-chosen experimental (recapture) time frame. In tests of the new doubly-truncated mortality estimator using simulated tag-recovery times-at-large, omitting the first 8 weeks of recaptures from the mortality estimate largely eliminated the bias introduced by simulated short-term trap-happy and trap-shy behavior. Bias in the mortality estimate declined by an order of magnitude more than the observed increase in standard error.
Characterizing the structural diversity of a bacterial community associated with filter materials in recirculating aquaculture systems of Scortum barcoo
Authors: Zhu Peng , Ye Yangfang , Pei Fangfang , Lu Kaihong 
Published: March 2012

The bacterial community structure associated with filter materials in the recirculating aquaculture system of Scortum barcoo was investigated using the 16S rRNA gene clone library method. Preliminary results showed that the clone library constructed from the initial operation condition was characterized by 31 taxa of bacteria belonging to eight phyla including Proteobacteria, Acidobacteria, Firmicutes, Fusobacteria, Sphingobacteria, Bacteroidetes, Verrucomicrobiae, and Actinobacteria. There were 14 taxa of bacteria belonging to four phyla including Proteobacteria, Acidobacteria, Planctomycetacia, and Nitrospirae from the stable operation condition where the water quality was well maintained. Nitrospirae was only found under the stable operation condition in this study. Our results further indicated that Nitrospira was dominated by members of the Nitrospira sp. lineages, with a minor fraction related to Nitrospira moscoviensis and an unknown Nitrospira cluster. These great differences of both diversity and composition between two operation conditions suggested that the composition of the microbial community varied with the degree of water quality in the recirculating aquaculture system of S. barcoo.
Change in antimicrobial susceptibility of Escherichia coli urinary tract isolates at a single institution over a period of 10 years
Authors: Walkty A. , Lagacé-Wiens P.R.S. , Karlowsky J.A. , Hoban D.J. , Manickam K. , Adam H. , Pieroni P. , Alfa M. 
Published: March 2012

Urinary tract infections are common. Few published studies have demonstrated the change in Escherichia coli urinary isolate antimicrobial susceptibility over time within a given area and (or) population. The purpose of this study was to evaluate the change in susceptibility of E. coli clinical isolates obtained from urine specimens at a single institution over a period of 10 years. The microbiology laboratory information system at St. Boniface Hospital (Winnipeg, Manitoba, Canada) was searched retrospectively from 1 January 2000 to 31 December 2009, for all E. coli isolates from either a midstream or catheter urine source that had susceptibility testing performed. Only one isolate per patient was included during the entire study period. Antimicrobial susceptibility testing was carried out with either a Microscan instrument (pre-April 2004) or a Vitek instrument (May 2004 onwards). In total, 7353 E. coli urinary isolates were included for evaluation. Ciprofloxacin susceptibility declined significantly, from 99% in 2000 to 85% in 2009 (p < 0.0001). A small but statistically significant decline in susceptibility was also observed for ampicillin, cefazolin, trimethoprim–sulfamethoxazole, gentamicin, and nitrofurantoin. These data suggest that certain antimicrobials recommended for the treatment of urinary tract infections (ciprofloxacin, trimethoprim–sulfamethoxazole) may no longer be optimal.
GENERALIZED β-CONFORMAL CHANGE AND SPECIAL FINSLER SPACES
Authors: YOUSSEF NABIL L. , ABED S. H. , ELGENDI S. G. 
Published: March 2012

This work is a continuation of the paper [Generalized beta-conformal change of Finsler metrics, Int. J. Geom. Meth. Mod. Phys. 7(4) (2010) 565–582]. In the present paper, we investigate the change of Finsler metrics [Formula: see text] which we refer to as a generalized β-conformal change. Under this change, we study some special Finsler spaces, namely, quasi-C-reducible, semi-C-reducible, C-reducible, C2-like, S3-like and S4-like Finsler spaces. We obtain some characterizations of the energy β-change, the Randers change and the Kropina change. We also obtain the transformation of the T-tensor under this change and study some interesting special cases. We then impose a certain condition on the generalized β-conformal change, which we call the b-condition, and investigate the geometric consequences of such a condition. Finally, we give the conditions under which a generalized β-conformal change is projective and generalize some known results in the literature.
Using probabilistic shale smear modelling to relate SGR predictions of column height to fault-zone heterogeneity
Authors: Yielding Graham 
Published: March 2012

Fault-seal analysis in hydrocarbon exploration often involves prediction of the sealing capacity of fault rock at reservoir–reservoir juxtapositions on subsurface faults. A proxy property, such as Shale Gouge Ratio (SGR), is mapped on to the fault surface, and then SGR is either (a) calibrated by observations of known sealing faults, to define its sealing capacity (empirical approach), or (b) assumed to be equal to the composition of the fault rock, for which a database of capillary threshold pressures is available from cores (deterministic approach). The deterministic approach implicitly assumes that capillary pressures measured on centimetre-scale samples are representative of seismically mappable faults, for example that faults of intermediate SGR are equivalent to phyllosilicate framework fault rocks.
This contribution builds on earlier outcrop and modelling work to suggest an alternative explanation for the observed progressive increase in sealing capacity on faults of increasing SGR. Stochastic models of disrupted shale smears display the same pattern of increasing sealing capacity as SGR increases. These models have a bimodal ‘fault rock’ composed only of sealing shale smears and non-sealing matrix and, yet, at intermediate SGR the predicted column heights are similar to those normally ascribed to intermediate composition fault rocks. The resulting ‘fault-seal envelope’ in the models is a statistical estimate of the maximum trappable column height, dependent on the random occurrence of a gap in the smeared fault surface.
A survey on automated dynamic malware-analysis techniques and tools
Authors: Egele Manuel , Scholte Theodoor , Kirda Engin , Kruegel Christopher 
Published: March 2012

Anti-virus vendors are confronted with a multitude of potentially malicious samples today. Receiving thousands of new samples every day is not uncommon. The signatures that detect confirmed malicious threats are mainly still created manually, so it is important to discriminate between samples that pose a new unknown threat and those that are mere variants of known malware.
This survey article provides an overview of techniques based on dynamic analysis that are used to analyze potentially malicious samples. It also covers analysis programs that leverage these It also covers analysis programs that employ these techniques to assist human analysts in assessing, in a timely and appropriate manner, whether a given sample deserves closer manual inspection due to its unknown malicious behavior.
Characterisation of the covalent structure of proteins from biological material by MALDI mass spectrometry ‣ possibilities and limitations
Authors: Kussmann Martin , Roepstorff Peter 
Published: March 2012

Matrix‐assisted laser desorption/ionisation mass spectrometry (MALDI‐MS) has become a primary tool for the detailed characterisation of the covalent structure of proteins isolated from biological material, mainly because of its following potentials: high sensitivity and specificity, speed of analysis, appropriateness for mixture analysis, high tolerance towards contaminants, and compatibility with separation techniques, e.g., gel electrophoresis. These characteristics enable the structural analysis of proteins even if they are only available in limited amounts and/or in mixtures, and even if the protein preparations contain large amounts of salts, buffers, detergents and denaturants. Additionally, structural data can be generated within a relatively short time.Whereas X‐ray crystallography and multidimensional NMR techniques can provide “absolute” structural data, i.e., a three‐dimensional “picture” of the protein of interest, MALDI‐MS‐especially in combination with selective protein chemistry – yields information on particular aspects of the entire protein structure, e.g., primary structure, active site(s), binding sites, and posttranslational modifications, all of which are often of crucial interest for the understanding of the protein function. Taking into account that protein crystallography and protein NMR studies require large quantities of highly purified sample, MALDI‐MS can be even more regarded as a powerful complement in protein structure analysis.This review aims at describing the state‐of‐the‐art of MALDI‐MS for characterisation of proteins from biological material by evaluating its potential and limitations.
Spectroscopic scale protection factor (SSPF) of solar ultraviolet radiation molecular screens. II. Substituent effect on salicylideneaniline
Authors: Morales Raúl G. E. , Hidrobo Alexis , Jara Gregorio P. 
Published: March 2012

Salicylideneanilines present a broad absorption band and a high molar absorption coefficient in the UV‐A and UV‐B regions. In addition, they are photostable compounds to the solar radiation exposition. Therefore, we have recently established their potential use as a solar ultraviolet radiation molecular screens.In the present work we have determined the dependence of the Spectroscopic Scale Protection Factor (SSPF) values with the substituent effect on the aniline ring of the salicylidene, when the substituent is an electron‐acceptor group (–CN, –COCH3, –NO2) and we have compared this effect with and without an electron‐donor group (–OCH3) at para position in the salicylidene ring.In order to determine and compare these SSPF values versus the usual Sun Protection Factor (SPF) values, a relative scale of biological nature, we have determined the electronic absorption spectra of these substituted salicylideneaniline compounds, and we have compared these spectroscopic data with homosalate, as an SPF standard compound. Our results are conclusive respect to determine the salicylideneanilines as a new family of molecular species highly efficient in the molecular screen role.
Aggregation and properties of α‒synuclein and related proteins
Authors: El-Agnaf Omar M. A. , Irvine G. Brent 
Published: March 2012

α‐Synuclein has been identified as a component of intracellular fibrillar protein deposits in several neurodegenerative diseases, and two mutant forms have been associated with early onset Parkinson′s disease. A fragment of α‐synuclein has also been identified as the non‐Aβ component of Alzheimer′s disease amyloid (NAC). Ageing solutions of α‐synuclein and NAC leads to formation of β‐sheet, detectable by circular dichroism spectroscopy, and aggregation to form amyloid‐like fibrils, detectable by electron microscopy. Differences in the rates of aggregation of the fibrils formed by α‐synuclein and the two mutant proteins are presented. The toxicity of α‐synuclein and related peptides towards neurons is also discussing in relation to the aetiology of neurodegenerative diseases.Experiments on fragments of NAC have enabled the region of NAC responsible for its aggregation and toxicity to be identified.
Infrared spectra of some fructans
Authors: Grube M. , Bekers M. , Upite D. , Kaminska E. 
Published: March 2012

The FT–IR spectra of fructan – inulin (RAFTILINE), widely applied in the food industry and crystalline fructose as the main component of fructans, were studied. Special interest was to study the spectra of the levan precipitate and fructan syrup – produced by Zymomonas mobilis during the fermentation on sucrose–based medium.It was shown that levan precipitate and fructose syrup does not contain lipids and nucleic acids. Levan precipitate consists of ∼93% of fructose and admixture of glucose, mannan and enzyme – levansucrase. Fructan polymer inulin consists principally of linear chains of fructosyl units linked by a β(2–1) bonds ended by a glycosyl unit. The links between the molecules are of a very special type: the β(2–1) form (2) [8]. The bacterial fructans of the levan type are high molecular weight polymers, i.e., they are composed ofβ–(2,6)–ructosyl–fructose linked molecules and side chains [17]. The FT–IR spectra of levan, apart from inulin’s, in the carbohydrate region 900–1200 cm–1, shows overlapping broad band with maximum at ∼1030 cm–1 and stronger absorption at ∼940 cm–1. The differences in both spectra could be caused by different structure and glucose, sucrose and mannan influence.
Quantification of urine 17‐ketosteroid sulfates and their age correlations
Authors: Jia Qi , Hong Mei-Feng , Pan Zhao-Xing , Ritter Cheryl , Vance Susan , Cortes-Guzman Miriam , Cherniske Stephen 
Published: March 2012

Dehydroepiandrosterone (DHEA) is a steroid secreted primarily by the adrenal gland and plays an important role as the primary precursor of many important sex steroids. The negative correlation between age and the secretion of DHEA (I) and in its sulfate form (II, DHEA‐S) has been documented in human studies. Serum DHEA (I) and/or DHEA‐S (II) levels have been associated with central nervous system function, immunity, cardiovascular functions, insulin sensitivity, and body composition.A high‐performance liquid chromatography/ion trap mass spectroscopic method with sonic spray ionization (SSI) for the quantification of individual and total urinary 17‐ketosteroid sulfates was developed. This quantification method had broad linearity range, low detection limit and high throughput. The amount of 17‐KS‐S, normalized by creatinine, in urine secreted over 24 hours versus that in early morning urines was found inversely correlated to age for both genders.
Biosensors based on nucleic acid interaction
Authors: Minunni M. 
Published: March 2012

DNA sensing is an emerging technology based on hybridisation reaction between an immobilised DNA probe and a molecular target, consisting of a probe complementary sequence in solution. Many application have been developed in the field of environmental, food and clinical analysis.Surface plasmon resonance and piezoelectric sensing are reported as transduction principles for DNA‐based devices. These techniques are able to monitor in real‐time and without the use of any label the hybridisation reaction between nucleic acids. Particular attention is given to Genetically Modified Organism detection.
Simultaneous in‐situ NIRS of liver and bowel during septic shock
Authors: Gagnon R. E. , Hahum E. , Skarsgard E. , Macnab A. J. 
Published: March 2012

We wished to use near infrared spectroscopy (NIRS) to evaluate changes in blood perfusion in the liver and small bowel. However, conventional clinical NIRS probes use adhesive light shielding appliqués that fail in direct contact with the wetness and softness of the liver and small bowel surfaces. We describe our development and testing of customized NIRS probe holders.Methods: Studies were conducted in 11 juvenile (9–17 kg) anesthetized Yorkshire piglets, with intact liver and bowel exposed during experimental septic shock induced by infusion of Escherichia coli. Internally, the emitter and detector of one NIRO‐300 channel were sheathed, directed towards each other, and affixed to the opposite arms of a long‐jawed ratchet clamp applied directly to the liver. The emitter and detector of the NIRO‐300′s second channel were applied, facing each other, on opposite inner surfaces of a semicircular, semi‐rigid, reinforced rubber tube through which a loop of the small bowel was drawn. Externally, optodes from a NIRO‐500 were applied to the skin over the liver. NIRS data were collected at 1second intervals for 180 minutes. Results: A wide range of optical neutral density filters was required to attenuate the emissions because of the diversity of tissue density between subjects. There were no complications with the liver clamp, and the initial tendency for the bowel to slip from the NIRS holder was solved by securing it with surgical ribbon. Conclusion: Since the NIRO‐300 control algorithm did not halt monitoring; the NIRO‐300 data correlated with the NIRO‐500 data (r2=0.292 to 0.659) and both were correlated with the mean arterial blood pressure (range: r2=0.309 to 0.918, p< 0.05 for r2 > 0.105), our modifications were deemed successful.
Pharmacokinetics and Antitumor Efficacy of XMT-1001, a Novel, Polymeric Topoisomerase I Inhibitor, in Mice Bearing HT-29 Human Colon Carcinoma Xenografts
Authors: Walsh Mark D. , Hanna Suzan K. , Sen Jeremy , Rawal Sumit , Cabral Carolina B. , Yurkovetskiy Alex V. , Fram Robert J. , Lowinger Timothy B. , Zamboni William C. 
Published: March 2012

Abstract
Purpose: To evaluate the pharmacokinetics and tissue disposition of macromolecular camptothecin (CPT) drug conjugate, XMT-1001, and irinotecan (CPT-11) in mice bearing HT-29 xenograft tumors.
Experimental Design: The antitumor efficacy of XMT-1001 was evaluated in the mouse HT-29 human colon carcinoma xenograft model. XMT-1001 was administered intravenously to female athymic nude (nu/nu) mice bearing established HT-29 xenograft tumors (n = 10) at 15, 30, and 60 mg CPT equivalents/kg on weekly or biweekly schedules. The tumor growth inhibition and tumor growth delay endpoints were used for efficacy evaluation. In the pharmacokinetic study, XMT-1001 was administered intravenously at a pharmacologically relevant dose of 60 mg CPT equivalents/kg × 1 via tail vein or an equimolar dose of CPT-11 at 100 mg/kg i.p. × 1. Mice (n = 3 per time point) were euthanized from 0.083 to 336 hours after XMT-1001 administration and from 0.083 to 24 hours after CPT-11. Plasma, tumor, and tissues were collected from all animals. A liquid chromatography–tandem mass spectrometry assay was used to measure XMT-1001, conjugate release products, CPT-20-O-(N-succinimido-glycinate; CPT-SI) and CPT-20-O-(N-succinamidoyl-glycinate; CPT-SA), and CPT.
Results: After XMT-1001 administration, the majority of the plasma exposure is accounted for by conjugated CPT. XMT-1001 exhibited a prolonged exposure of conjugated drug, active conjugate primary release products, CPT-SI and CPT-SA, and active CPT, which was associated with greater antitumor response compared with CPT-11.
Conclusions: XMT-1001 provides an extended systemic and tumor exposure of conjugated drug and shows improved antitumor effect compared with CPT-11. Clin Cancer Res; 18(9); 2591–602. ©2012 AACR.
The HDAC Inhibitor LBH589 Enhances the Antimyeloma Effects of the IGF-1RTK Inhibitor Picropodophyllin
Authors: Lemaire Miguel , Fristedt Charlotte , Agarwal Prasoon , Menu Eline , Van Valckenborgh Els , De Bruyne Elke , Österborg Anders , Atadja Peter , Larsson Olle , Axelson Magnus , Van Camp Ben , Jernberg-Wiklund Helena , Vanderkerken Karin 
Published: March 2012

AbstractPurpose: We have previously shown the use of the insulin-like growth factor type 1 receptor tyrosine kinase (IGF-1RTK) inhibitor picropodophyllin (PPP) as an attractive strategy to combat multiple myeloma (MM) in vitro and in vivo. After a combinatorial drug screening, the histone deacetylase inhibitor LBH589 was shown to act in synergy with PPP reducing survival of MM cells. In this study, we tried to elucidate the molecular mechanisms underlying this combinatorial effect.Experimental Design: The in vitro anti-MM effects of PPP and LBH589 alone and in combination were evaluated by studying apoptosis, cell cycle distribution, and downstream transcriptome using both human MM cell lines and cells from the murine 5T3MM model. In vivo the effect on survival of 5T33MM-inoculated mice was evaluated.Results: In the human MM cell line RPMI8226, treatment with PPP and LBH589 in combination resulted in a five-fold increase of apoptosis, and an additive effect on the cleavage of the active forms of caspase-8 was observed as compared with the single drug treatments. Cell cycle analysis revealed an accumulation of cells in the G2–M phase and subsequent downregulation of cell cycle regulating proteins. These data were also confirmed in the 5T33MM cells in vitro. Also, the transcriptome was analyzed by Affymetrix arrays showing gene expression alterations mainly in categories of genes regulating apoptosis and cell adhesion. Combined treatment in vivo resulted in a significantly prolonged survival of 5T33MM-inoculated mice.Conclusions: The results indicate an improved MM treatment opportunity in using a combination of PPP and LBH589. Clin Cancer Res; 18(8); 2230–9. ©2012 AACR.