bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Importance of Knowing When to Stop
Authors: Hofner B. , Schmid M. , Mayr A. 
Published: February 2012

SummaryObjectives: Component-wise boosting algorithms have evolved into a popular estimation scheme in biomedical regression settings. The iteration number of these algorithms is the most important tuning parameter to optimize their performance. To date, no fully automated strategy for determining the optimal stopping iteration of boosting algorithms has been proposed.Methods: We propose a fully data-driven sequential stopping rule for boosting algorithms. It combines resampling methods with a modified version of an earlier stopping approach that depends on AIC-based information criteria. The new “subsampling after AIC” stopping rule is applied to component-wise gradient boosting algorithms.Results: The newly developed sequential stopping rule outperformed earlier approaches if applied to both simulated and real data. Specifically, it improved purely AIC-based methods when used for the microarray-based prediction of the recurrence of meta-stases for stage II colon cancer patients.Conclusions: The proposed sequential stopping rule for boosting algorithms can help to identify the optimal stopping iteration already during the fitting process of the algorithm, at least for the most common loss functions.
Characterization of a PIAS4 Homologue from Zebrafish: Insights into Its Conserved Negative Regulatory Mechanism in the TRIF, MAVS, and IFN Signaling Pathways during Vertebrate Evolution
Authors: Xiong Ran , Nie Li , Xiang Li-xin , Shao Jian-zhong 
Published: February 2012

Abstract
Members of the protein inhibitor of activated STAT (PIAS) family are key regulators of various human and mammalian signaling pathways, but data on their occurrence and functions in ancient vertebrates are limited. This study characterizes for the first time to our knowledge a PIAS4 homologue (PIAS4a) from zebrafish. Structurally, this zebrafish PIAS4a (zfPIAS4a) shares a number of conserved functional domains with mammalian PIAS4 proteins, including the scaffold attachment factor A/B/acinus/PIAS box, PINIT, and RING-finger–like zinc-binding domains and a highly acidic domain in the C-terminal region. Subcellular localization analysis shows that zfPIAS4a is a nuclear-localized protein and that the C terminus of the molecule harbors strict nuclear localization signals. Functionally, zfPIAS4a expression can be dramatically induced by the stimulation of polyinosinic-polycytidylic acid and zebrafish IFNϕ1. It acts as a critical negative regulator of the TIR domain-containing adapter inducing IFN-β, mitochondrial antiviral signaling (MAVS), and IFN signaling pathways, and it is the first PIAS protein that plays a role in the MAVS-mediated pathway to be identified. The structure and functionality of PIAS4 seem highly conserved from zebrafish to mammals, making zebrafish an attractive model for screens designed to uncover genes involved in IFN- and inflammatory cytokine-induced signaling pathways. This study provides preliminary evidence that the PIAS regulatory mechanism already existed in fish during vertebrate evolution. It presents valuable clues for improving the understanding of not only the negative regulation of cytokine signaling in fish but also the evolutionary history of the PIAS family from fish to mammals as a whole.
Germline Deletion of Igh 3′ Regulatory Region Elements hs 5, 6, 7 (hs5–7) Affects B Cell-Specific Regulation, Rearrangement, and Insulation of the Igh Locus
Authors: Volpi Sabrina A. , Verma-Gaur Jiyoti , Hassan Rabih , Ju Zhongliang , Roa Sergio , Chatterjee Sanjukta , Werling Uwe , Hou Harry , Will Britta , Steidl Ulrich , Scharff Matthew , Edelman Winfried , Feeney Ann J. , Birshtein Barbara K. 
Published: February 2012

Abstract
Regulatory elements located within an ∼28-kb region 3′ of the Igh gene cluster (3′ regulatory region) are required for class switch recombination and for high levels of IgH expression in plasma cells. We previously defined novel DNase I hypersensitive sites (hs) 5, 6, 7 immediately downstream of this region. The hs 5–7 region (hs5–7) contains a high density of binding sites for CCCTC-binding factor (CTCF), a zinc finger protein associated with mammalian insulator activity, and is an anchor for interactions with CTCF sites flanking the DH region. To test the function of hs5–7, we generated mice with an 8-kb deletion encompassing all three hs elements. B cells from hs5–7 knockout (KO) (hs5–7KO) mice showed a modest increase in expression of the nearest downstream gene. In addition, Igh alleles in hs5–7KO mice were in a less contracted configuration compared with wild-type Igh alleles and showed a 2-fold increase in the usage of proximal VH7183 gene families. Hs5–7KO mice were essentially indistinguishable from wild-type mice in B cell development, allelic regulation, class switch recombination, and chromosomal looping. We conclude that hs5–7, a high-density CTCF-binding region at the 3′ end of the Igh locus, impacts usage of VH regions as far as 500 kb away.
Inflammasome-Derived IL-1β Regulates the Production of GM-CSF by CD4+ T Cells and γδ T Cells
Authors: Lukens John R. , Barr Maggie J. , Chaplin David D. , Chi Hongbo , Kanneganti Thirumala-Devi 
Published: February 2012

Abstract
Recent findings have demonstrated an indispensable role for GM-CSF in the pathogenesis of experimental autoimmune encephalomyelitis. However, the signaling pathways and cell populations that regulate GM-CSF production in vivo remain to be elucidated. Our work demonstrates that IL-1R is required for GM-CSF production after both TCR- and cytokine-induced stimulation of immune cells in vitro. Conventional αβ and γδ T cells were both identified to be potent producers of GM-CSF. Moreover, secretion of GM-CSF was dependent on IL-1R under both IL-12– and IL-23–induced stimulatory conditions. Deficiency in IL-1R conferred significant protection from experimental autoimmune encephalomyelitis, and this correlated with reduced production of GM-CSF and attenuated infiltration of inflammatory cells into the CNS. We also find that GM-CSF production in vivo is not restricted to a defined CD4+ T cell lineage but is rather heterogeneously expressed in the effector CD4+ T cell population. In addition, inflammasome-derived IL-1β upstream of IL-1R is a critical regulator of GM-CSF production by T cells during priming, and the adapter protein, MyD88, promotes GM-CSF production in both αβ and γδ T cells. These findings highlight the importance of inflammasome-derived IL-1β and the IL-1R/MyD88 signaling axis in the regulation of GM-CSF production.
Determination of Total Choline by Liquid Chromatography– Electrospray Ionization–Tandem Mass Spectrometry in Infant Formulas
Authors: Fu Shishan , Tao Baohua , Lai Shiyun , Zhang Jingshun , Yiping Ren 
Published: February 2012

Abstract
Choline is a water-soluble nutrient important for infants' brain and neural development. In infant formulas, choline is one of the important fortified nutrients. A single-laboratory validation study conducted an LC-electrospray ionization-MS/MS to determine total choline in infant formulas. Sample preparation was adopted from AOAC Official MethodSM 999.14, and instrumental running conditions were optimized. The LOQ was 0.2 μg/100 g, which is significant for measuring total choline in infant formulas. Average recoveries for milk-, rice-, soybean-, and hydrolyzed protein-based samples ranged from 86.45 ± 6.04% to 108.98 ± 3.68%, with RSD less than 7%. The repeatability RSD (RSDr) range was 0.24–3.59% in within-day evaluation and 1.16–3.24% in day-to-day evaluation. Matrix effect was also investigated, and can be effectively eliminated by using an internal standard. Therefore, this method has high credibility, and could be used as a routine method of quality control, or for clinical studies and other research areas.
Determination of Natural Pesticides in Fresh Fruits Using Liquid Chromatography/Mass Spectrometry
Authors: Ruiz Irene , Morales Ascensión , Barba Alberto , Oliva José 
Published: February 2012

Abstract
An analytical procedure was developed for the determination of some natural pesticides (piperonyl butoxide, nicotine, rotenone, spinosad, and abamectin B1a) in fruit matrixes. The quick, easy, cheap, effective, rugged, and safe (QuEChERS) method was used for extraction. Analysis of the extract was performed by LC-electrospray ionization (ESI)-MS/MS. The ions prominent in the ESI spectra were [M+Na]+ for abamectin B1a, [M+NH4]+ for piperonyl butoxide, and [M+H]+ for the rest of the compounds. A Zorbax SB-C18 column was used with a programmed gradient mobile phase consisting of (A) water containing 0.1% formic acid and 5 mM ammonium formate, and (B) acetonitrile containing 2 mM sodium acetate. The method was linear within the investigated concentration range, displaying a calibration curve correlation factor of 0.99. The CVs obtained were below 20%, and recoveries were in the 70–110% range.
Determination of Total Iodine in Infant Formula and Nutritional Products by Inductively Coupled Plasma/Mass Spectrometry: Single-Laboratory Validation
Authors: Pacquette Lawrence H , Levenson Alan M , Thompson Joseph J 
Published: February 2012

Abstract
A single-laboratory validation by inductively coupled plasma-mass spectrometry was developed for the determination total iodine (m/z 127) in infant formula and adult nutritional products. All samples were digested in nitric acid using a closed vessel microwave oven system; Te (m/z 130) was used as an internal standard. To prevent loss of iodine, ammonium hydroxide solution was added to the samples immediately after digestion. The method quantitation limit for total iodine was 0.3 ng/mL, but a practical LOQ was used at 1.0 ng/mL, a concentration at which there was a negligible bias due to nonlinearity. The total iodine concentrations (112–1900 ng/g) in 14 out of 15 nutritional products were within specification limits. Within-day and day-to-day (6 independent days) precision values were &lt;10% RSD. The observed precision for the overall mean (18 independent days) of a control sample was approximately 4% RSD. In two National Institute of Standards and Technology standard reference materials, total iodine results were within certified limits. Sample spike recoveries for all 15 nutritional products were 92–105%. The data show that a conventional microwave oven digestion procedure can be used to prepare samples for iodine determination. Therefore, this technique is very compatible with other methods being proposed as modern official methods for the analysis of minerals in nutritional products.
New Role of Antibody in Bacterial Isolation
Authors: Xiao Xizhi , Chen Yu , Deng Mingjun , Gao Hongwei , Wu Zhenxing , Zhu Laihua , Yuan Fei , Xu Biao , Liang Chengzhu , Zhang Yanming 
Published: February 2012

Abstract
To eliminate the interference caused by Pseudomonas aeruginosa in the isolation of Salmonella, a rabbit polyclonal antibody against P. aeruginosa was prepared by inoculating four New Zealand rabbits with the pathogen. The antiserum was purified using saturated ammonium sulfate and added into Rappaport-Vassiliadis medium with soya (RVS) broth and Muller-Kauffmann tetrathionate novobiocin broth (MKTTn broth) to evaluate whether it could inhibit the growth of P. aeruginosa. Observations by scanning electron microscopy demonstrated that P. aeruginosa was attacked and destroyed by the antibody when incubated for 10 min at 37°C. The activity of the antibody was also effective against 11 other strains of P. aeruginosa. Twenty-six strains of Salmonella were mixed with P. aeruginosa in RVS and MKTTn broth at 37°C for 12 h, respectively, and the cultures were plated on Salmonella chromogenic medium (SCM; Oxoid, Basingstoke, UK). Only Salmonella grew on SCM; five colonies were randomly selected for identification by VITEK 2 (bioMérieux, Lyon, France). Additionally, when mixed with two strains of Enterobacter cloacae (ATCC 700323 and YG001), the prepared antibody did not affect the growth of E. cloacae. The results demonstrated that the microbicidal activity of the antibody did not affect the tested Salmonella sp. or E. cloacae strains. Therefore, the antibody generated could be used to increase the accuracy of Salmonella isolation.
Evaluation of Microwave-Assisted Extraction for the Analysis of Organophosphorus and Pyrethroid Pesticides in Green Onions
Authors: Otake Takamitsu , Kuroda Youko , Aoyagi Yoshie , Yarita Takashi 
Published: February 2012

Abstract
The aim of this study was to evaluate the efficiency of microwave-assisted extraction (MAE) for the analysis of organophosphorus (OP) and pyrethroid (PYR) pesticides in green onions by GC/MS. We optimized MAE extraction solvent, temperature, and time by using a certified reference material. As a result, the concentrations of two OP and two PYR target pesticides obtained by MAE with acetonitrile at 110°C for 10 min were in good agreement with certified concentrations and comparable to the results by homogenization used as reference extraction technique. When the recovery test, performed by spiking the target pesticides into blank samples (5.0 g), was carried out with our optimized MAE conditions, mean recoveries of 16 OP and 10 PYR pesticides were 72–108% for a 1.0 μg spiking level and 70–119% for a 0.2 μg level. These results were acceptable according to the validation guideline for testing method of agricultural chemicals in food by Ministry of Health, Labour, and Welfare in Japan. The results suggested that MAE can be used for the analysis of OP and PYR pesticides in green onions.
Detection of Salmonella in Meat: Comparative and Interlaboratory Validation of a Noncomplex and Cost-Effective Pre-PCR Protocol
Authors: Löfström Charlotta , Hansen Flemming , Mansdal Susanne , Hoorfar Jeffrey 
Published: February 2012

Abstract
Cost-effective and rapid monitoring of Salmonella in the meat production chain can contribute to food safety. The objective of this study was to validate an easy-to-use pre-PCR sample preparation method based on a simple boiling protocol for screening of Salmonella in meat and carcass swab samples using a real-time PCR method. The protocol included incubation in buffered peptone water, centrifugation of an aliquot, and a boiling procedure. The validation study included comparative and interlaboratory trials recommended by the Nordic Organization for Validation of Alternative Microbiological Methods (NordVal). The comparative trial was performed against a reference method (NMKL 187, 2007) and a PCR method previously approved by NordVal with a semiautomated magnetic bead-based DNA extraction step using 122 artificially contaminated samples. The LOD was found to be 3.0, 3.2, and 3.4 CFU/sample for the boiling, magnetic bead-based, and NMKL 187 methods, respectively. When comparing the boiling method with the magnetic beads, the relative accuracy (AC), relative sensitivity (SE), and relative specificity (SP) were 98, 102, and 98%, respectively (Cohen's kappa index 0.95). When comparing results obtained by the boiling to the culture-based method, the AC, SE, and SP were found to be 98, 102, and 98%, respectively (kappa index 0.93). In the interlaboratory trial including valid results from 11 laboratories, apart from two false-positive samples by the boiling method combined with PCR, no deviating results were obtained (SP, SE, and AC were 100, 95, and 97%, respectively). This test is under implementation by the Danish meat industry, and can be useful for screening of large number of samples in the meat production, especially for fast release of minced meat with a short shelf life.
Differentiating the Gum Resins of Two Closely Related Indian Gardenia Species, G. gummifera and G. lucida, and Establishing the Source of Dikamali Gum Resin Using High-Performance Thin-Layer Chromatography and Ultra-Performance Liquid Chromatography-UV/MS
Authors: Lakavath Suryanarayana , Avula Bharathi , Wang Yan-Hong , Rumalla Chidananda Swamy , Gandhe Sreekanth , Venkatrao Adavi Rao Belvotagi , Satishchandra Prabhakar Achanta , Bobbala Ravi Kumar , Khan Ikhlas A , Narasimha Appa Rao Achanta Venkata 
Published: February 2012

Abstract
Dikamali is a gum resin obtained from the leaf buds of Gardenia lucida or G. gummifera. There is controversy regarding the botanical source of this gum resin with some stating it to be from G. lucida while others claim it to be from G. gummifera. Analytical methods including UPLC and HPTLC were developed for the qualitative analysis of Gardenia species and various commercial samples. The separation using a UPLC method was achieved within 12.0 min by using C18 column material, a water/acetonitrile mobile phase, both containing formic acid, a gradient system, and a temperature of 40°C. Extensive studies of dikamali collected from various parts of India in comparison with the gum resins collected from G. lucida and G. gummifera clearly indicated that the botanical source of commercially available dikamali is G. lucida, not G. gummifera. The marker compounds isolated from a market sample of dikamali were present only in the gum resin of G. lucida and the compounds isolated from G. gummifera were not present in any of the dikamali samples, confirming the botanical source of dikamali. This work is of utmost importance, given the ambiguity regarding the botanical source of the gum resin dikamali. LC/MS coupled with electrospray ionization is described for the identification and confirmation of nine compounds from various samples of the gum resin. An HPTLC method was also developed for the fast chemical fingerprint analysis of Gardenia samples.
Influence of Thiol Self‐Assembled Monolayer Processing on Bottom‐Contact Thin‐Film Transistors Based on n‐Type Organic Semiconductors
Authors: Youn Jangdae , Dholakia Geetha R. , Huang Hui , Hennek Jonnathan W. , Facchetti Antonio , Marks Tobin J. 
Published: February 2012

AbstractThe performance of bottom‐contact thin‐film transistor (TFT) structures lags behind that of top‐contact structures owing to the far greater contact resistance. The major sources of the contact resistance in bottom‐contact TFTs are believed to reflect a combination of non‐optimal semiconductor growth morphology on the metallic contact surface and the limited available charge injection area versus top‐contact geometries. As a part of an effort to understand the sources of high charge injection barriers in n‐channel TFTs, the influence of thiol metal contact treatment on the molecular‐level structures of such interfaces is investigated using hexamethyldisilazane (HMDS)‐treated SiO2 gate dielectrics. The focus is on the self‐assembled monolayer (SAM) contact surface treatment methods for bottom‐contact TFTs based on two archetypical n‐type semiconductors, α,ω‐diperfluorohexylquarterthiophene (DFH‐4T) and N,N′bis(n‐octyl)‐dicyanoperylene‐3,4:9,10‐bis(dicarboximide) (PDI‐8CN2). TFT performance can be greatly enhanced, to the level of the top contact device performance in terms of mobility, on/off ratio, and contact resistance. To analyze the molecular‐level film structural changes arising from the contact surface treatment, surface morphologies are characterized by atomic force microscopy (AFM) and scanning tunneling microscopy (STM). The high‐resolution STM images show that the growth orientation of the semiconductor molecules at the gold/SAM/semiconductor interface preserves the molecular long axis orientation along the substrate normal. As a result, the film microstructure is well‐organized for charge transport in the interfacial region.
Travel demand estimation risk for high‐speed railway transport considering travel price competition
Authors: Uchida Kenetsu , Sugiki Nao 
Published: February 2012

SUMMARYThe Hokkaido Shinkansen (HS) bullet train line is under consideration to open in 2020. In this study, travel demand is estimated for the HS. Because some explanatory variables that are used for such estimation can have estimation errors, travel demand estimation risk is also calculated. In addition, because the HS can compete with airlines for modal share, the impacts of travel price competition (TPC) on the travel demand and the demand estimation risk are also estimated. In this study, the travel demand estimation risk is measured as the variance or the SD of the stochastic travel demand. The analysis reveals the following: the modal share of HS is 16% less when TPC is considered than when it is not considered; TPC causes the travel demand estimation risk to decrease; the probabilities of the HS operating at a deficit with and without consideration of TPC are calculated as 31.2% and 1.25%, respectively, and the increase in the mean consumer surplus accruing from the HS is calculated as JPY 47bn/year ($US588m/year) without TPC and as JPY 66bn/year ($US825m/year) with TPC. Copyright © 2012 John Wiley & Sons, Ltd.
Alternate capacity reliability measures for transportation networks
Authors: Chen Anthony , Kasikitwiwat Panatda , Yang Chao 
Published: February 2012

SUMMARYCapacity reliability is defined as the probability that the network capacity can accommodate a certain volume of traffic demand at a required service level. It is a supply‐side reliability measure for assessing the adequacy of a degradable transportation network. The network capacity model used to calculate the capacity reliability measure is based on the concept of reserve capacity, which requires preserving a pre‐determined origin–destination (O–D) demand pattern. In this paper, we relax this assumption by allowing a non‐uniform growth in the spatial distribution of the O–D demand pattern. By using this non‐uniform O–D growth approach, two network capacity models related to the concepts of ultimate capacity and practical capacity are developed to estimate alternate capacity reliability measures. Numerical results are provided to analyze the features of three capacity reliability measures for transportation networks. Copyright © 2012 John Wiley & Sons, Ltd.
Comparative study on altered hepatic metabolism of CYP3A substrates in rats with glycerol‐induced acute renal failure
Authors: Kusaba Jun‐ichi , Kajikawa Noriko , Kawasaki Hiromu , Kurosaki Yuji , Aiba Tetsuya 
Published: February 2012

ABSTRACTTo examine the mechanism accounting for the diverse alteration of hepatic metabolism of CYP3A substrates observed with renal function being severely impaired, the hepatic drug metabolizing activity was evaluated using liver microsomes prepared from rats with glycerol‐induced acute renal failure (ARF). Midazolam, nifedipine and rifabutin were employed as representative CYP3A substrates. When the Michaelis‐Menten parameters, Km and Vmax, were examined in the incubation study, the Km values of midazolam and nifedipine in ARF rats were shown to decrease by 50.9% and 29.9% compared with the normal value, respectively. The Vmax values of midazolam and nifedipine in ARF rats also decreased by 49.3% and 28.0%, respectively, showing that their decreased Km values accompanied the decreased Vmax values. The parameters of nifedipine seemed to alter to a lesser extent than those of midazolam. As for rifabutin metabolism, the decrease in the Km value was observed in ARF rats, but it did not accompany the decrease in the Vmax value. Then, the hepatic expressions of the CYP3A subfamily were examined with western blotting using anti‐CYP3A1 and anti‐CYP3A2 antibodies. It was revealed that the hepatic expression of CYP3A2 decreased, while that of CYP3A1 was unaffected. Additionally, a band signal deduced to originate from CYP3A9 was clearly detected in ARF, but not in normal rats. Considering each substrate having different specificities for CYP3A subfamily member proteins, individual alterations of hepatic CYP3A subfamily expression seem to underlie the diverse alterations of hepatic metabolism of CYP3A substrates in ARF rats. Copyright © 2012 John Wiley & Sons, Ltd.