bluuebunny/crossref_metadata_2025_split huggingface dataset:
Subcellular location prediction of apoptosis proteins
Authors: Zhou Guo‐Ping , Doctor Kutbuddin 
Published: December 2002

AbstractApoptosis proteins have a central role in the development and homeostasis of an organism. These proteins are very important for understanding the mechanism of programmed cell death. Many efforts in pharmaceutical research have been aimed at understanding their structure and function. Unfortunately, thus far, very few apoptosis protein structures have been determined. In contrast, many apoptosis protein sequences are known, and many more are expected to come in the near future. Because of the extremely unbalanced state, it would be worthwhile to develop a fast sequence‐based method to identify their subcellular location so as to gain some insight about their biological function. In view of this, a study was initiated in an attempt to identify the subcellular location of apoptosis proteins according to their sequences by means of the covariant discriminant function, which was established based on the Mahalanobis distance and Chou's invariance theorem (Chou, Proteins 1995;21:319–344). The results were quite promising, indicating that the subcellular location of apoptosis proteins are predictable to a considerably accurate extent if a good training data set can be established. It is expected that, with a continuous improvement of the training data set by incorporating more and more new data, the current method might eventually become a useful tool in this area because the function of an apoptosis protein is closely related to its subcellular location. Proteins 2003;50:44–48. © 2002 Wiley‐Liss, Inc.
Role of the protein side‐chain fluctuations on the strength of pair‐wise electrostatic interactions: Comparing experimental with computed pKas
Authors: Alexov Emil 
Published: December 2002

AbstractThe effect of the protein side‐chain fluctuations on the strength of electrostatic interactions was studied. The effect was modeled on 7 different crystal structures on the same enzyme as well as on 20 molecular dynamics snapshot structures. It was shown that the side‐chain flexibility affects predominantly the magnitude of the strong pair‐wise interactions, that is, the pair‐wise interaction among ion pairs, and practically does not affect the interactions with the rest of the protein. This was used to suggest a correction function that should be applied to the original pair‐wise electrostatic interaction to mimic the effects of the fluctuations. The procedure is applied on three ion pairs identified in lysozyme. It was shown that sampling different side‐chain rotamers and modifying the strength of the pair‐wise interaction energies makes calculated pKas less sensitive to the fluctuations of the structure and improves the prediction accuracy. Proteins 2003;50:94–103. © 2002 Wiley‐Liss, Inc.
Analysis of the binding energies of testosterone, 5α‐dihydrotestosterone, androstenedione and dehydroepiandrosterone sulfate with an antitestosterone antibody
Authors: Nordman Nana , Valjakka Jarkko , Peräkylä Mikael 
Published: December 2002

AbstractMolecular dynamics simulations and molecular mechanics–Poisson–Boltzmann surface area (MM‐PBSA) free energy calculations were used to study the binding of testosterone (TES), 5α‐dihydrotestosterone (5ADHT), androstenedione (AND), and dehydroepiandrosterone sulfate (DHEAS) to the monoclonal antitestosterone antibody 3‐C4F5. The relative binding free energy of TES and AND was also calculated with free energy perturbation (FEP) simulations. The antibody 3‐C4F5 has a relatively high affinity (3 × 108 M−1) and on overall good binding profile for testosterone but its cross‐reactivity with DHEAS has been the main reason for the failure to use this antibody in clinical immunoassays. The relative binding free energies obtained with the MM‐PBSA method were 1.5 kcal/mol for 5ADHT, 3.8 kcal/mol for AND, and 4.3 kcal/mol for DHEAS, as compared to TES. When a water molecule of the ligand binding site, observed in the antibody–TES crystal structure, was explicitly included in MM‐PBSA calculations, the relative binding energies were 3.4, 4.9, and 5.4 kcal/mol for 5ADHT, AND, and DHEAS, respectively. The calculated numbers are in correct order but larger than the corresponding experimental energies of 1.3, 1.5, and 2.6 kcal/mol, respectively. The fact that the MM‐PBSA method reproduced the relative binding free energies of DHEAS, a steroid having a negatively charged sulfate group, and the neutrally charged TES, 5ADHT, and AND in satisfactory agreement with experiment shows the robustness of the method in predicting relative binding affinities. The 800‐ps FEP simulations predicted that the antibody 3‐C4F5 binds TES 1.3 kcal/mol tighter than AND. Computational mutagenesis of selected amino acid residues of the ligand binding site revealed that the lower affinities of AND and DHEAS as compared to TES are due to a combined effect of several residues, each contributing a small fraction to the tighter binding of TES. An exception to this is Tyr99H, whose mutation to Ala lowered the binding of DHEAS 0.7 kcal/mol more than the binding of TES. This is probably due to the hydrogen bonding interaction formed between the OH group of Tyr99H and the sulfate group of DHEAS. Computational mutagensis data also showed that the affinity of the steroids to the antitestosterone antibody 3‐C4F5 would be enhanced if Trp47H were repositioned so that it would make more extensive contacts with the bound ligands. In addition, the binding of steroids to antitestosterone, antiprogesterone, and antiestradiol antibodies is discussed. Proteins 2003;50:135–143. © 2002 Wiley‐Liss, Inc.
Testing similarity measures with continuous and discrete protein models
Authors: Wallin Stefan , Farwer Jochen , Bastolla Ugo 
Published: December 2002

AbstractThere are many ways to define the distance between two protein structures, thus assessing their similarity. Here, we investigate and compare the properties of five different distance measures, including the standard root‐mean‐square deviation (cRMSD). The performance of these measures is studied from different perspectives with two different protein models, one continuous and the other discrete. Using the continuous model, we examine the correlation between energy and native distance, and the ability of the different measures to discriminate between the two possible topologies of a three‐helix bundle. Using the discrete model, we perform fits to real protein structures by minimizing different distance measures. The properties of the fitted structures are found to depend strongly on the distance measure used and the scale considered. We find that the cRMSD measure very effectively describes long‐range features but is less effective with short‐range features, and it correlates weakly with energy. A stronger correlation with energy and a better description of short‐range properties is obtained when we use measures based on intramolecular distances. Proteins 2003;50:144–157. © 2002 Wiley‐Liss, Inc.
Modeling repair events under intermittent failures and failures subject to unsuccessful repair
Authors: Hansen C. K. , Ascher H. E. 
Published: December 2002

AbstractIntermittent failures are sometimes observed for a repairable system, such as an automobile. Such failures often lead to a series of unsuccessful repair attempts before the source of the failure has been identified and removed. Unsuccessful repair is also observed in cases where the failures are not intermittent. In order to model data involving repeated repair attempts related to the same failure, repair times cannot usually be assumed negligible and the model must be designed or modified to account for these. In this paper, we propose a modified version of the branching Poisson process model introduced by Lewis (1964). We discuss statistical inference procedures for this model and demonstrate these procedures using the service history of a new automobile. Copyright © 2002 John Wiley & Sons, Ltd.
The reliability analysis of balking and reneging in a repairable system with warm standbys
Authors: Ke Jau‐Chuan , Wang Kuo‐Hsiung 
Published: December 2002

AbstractWe study the reliability analysis of a repairable system with $m$ operating units, $w$ warm standby units and $R$ repairmen in which the balking and reneging of units are considered. It is assumed that failed units balk (refuse to join) with a constant probability ($1-b$) and renege (leave the queue after joining) according to a negative exponential distribution with parameter $r$. The failure times of the operating unit and of a standby unit are assumed to be exponentially distributed with parameters λ and α, respectively. The repair time distribution is also exponential. The repairable system is $K$ out of $m+w$, in which $K=1,2,\dots,m$. The reliability characteristics, such as the system reliability and the mean time to system failure (MTTF), in a repairable system are derived. Several cases are analysed graphically to study the effect of various parameters on the reliability and MTTF of the system. Copyright © 2002 John Wiley & Sons, Ltd.
Ant algorithm for single and multiobjective reliability optimization problems
Authors: Shelokar Prakash S. , Jayaraman V. K. , Kulkarni B. D. 
Published: December 2002

AbstractThe paper illustrates the application of the ant colony optimization algorithm to solve both continuous function and combinatorial optimization problems in reliability engineering. The ant algorithm is combined with the strength Pareto fitness assignment procedure to handle multiobjective problems. Further, a clustering procedure has been applied to prune the Pareto set and to maintain diversity. Benchmark case examples show the superiority of the ant algorithm to such problems. Copyright © 2002 John Wiley & Sons, Ltd.
Relationship between STS approach, scientific literacy, and achievement in biology
Authors: Mbajiorgu N. M. , Ali A. 
Published: December 2002

AbstractThis study set out to investigate the relationship between STS approach, scientific literacy (SL), and achievement in biology. A quasi‐experimental design of the nonequivalent group was employed. Four secondary schools, eight teachers, and 246 students from Nigeria were involved in the study. Two classes were randomly selected from each school and assigned to either the experimental or control group. Two instruments were used to collect data: an Achievement Test on Reproduction and Family Planning and a SL Scale. Results showed that there is no relationship between SL and achievement in biology. The split‐wise posttest regression showed a weak positive relationship between SL and achievement in biology for the experimental group and a no relationship for the control group. However, STS approach mediated between SL and achievement to effect a slightly stronger significant positive relationship. The slope of SL was greater when we controlled for instruction showing that the relationship between SL and achievement is not spurious when instruction is taken into account. We therefore conclude that STS approach might be affecting other variables in the science classroom that in turn affect achievement in the sciences. © 2002 Wiley Periodicals, Inc. Sci Ed 87:31–39, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/sce.10012
“Change is hard”: What science teachers are telling us about reform and teacher learning of innovative practices
Authors: Davis Kathleen S. 
Published: December 2002

AbstractOver the last decade, significant efforts have been made to bring change to science classrooms. Educational researchers (Anderson, R. D., & Helms, J. V. (2001). Journal of Research in Science Teaching, 38(1), 3–16.) have pointed to the need to examine reform efforts systemically to understand the pathways and impediments to successful reform. This study provides a critical analysis of the implementation of an innovative science curriculum at a middle school site. In particular, the author explores the issues that surround teacher learning of new practices including the structures, policies, and practices that were in place within the reform context that supported or impeded teacher learning. Parallels are drawn between student and teacher learning and the importance of autonomy and decision‐making structures for both populations of learners. Findings presented include (1) how staff development with constructivist underpinnings facilitated teacher learning; (2) how regular and frequent opportunities for interactions with colleagues and outside support personnel contributed to teacher learning; (3) how the decline of such interactive forums and the continuation of old decision‐making structures restricted the development of teacher knowledge, expertise, and a common vision of the science program; and (4) how the process of field‐testing at this site limited the incorporation of teachers' prior knowledge and impacted teacher acquisition of new knowledge and skills. © 2002 Wiley Periodicals, Inc. Sci Ed 87:3–30, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/sce.10037
Examining classroom interactions related to difference in students' science achievement
Authors: Zady Madelon F. , Portes Pedro R. , Dan Ochs V. 
Published: December 2002

AbstractThe current study examines the cognitive supports that underlie achievement in science by using a cultural historical framework (L. S. Vygotsky (1934/1986), Thought and Language, MIT Press, Cambridge, MA.) and the activity setting (AS) construct (R. G. Tharp & R. Gallimore (1988), Rousing minds to life: Teaching, learning and schooling in social context, Cambridge University Press, Cambridge, MA.) with its five features: personnel, motivations, scripts, task demands, and beliefs. Observations were made of the classrooms of seventh‐grade science students, 32 of whom had participated in a prior achievement‐related parent–child interaction or home study (P. R. Portes, M. F. Zady, & R. M. Dunham (1998), Journal of Genetic Psychology, 159, 163–178). The results of a quantitative analysis of classroom interaction showed two features of the AS: personnel and scripts. The qualitative field analysis generated four emergent phenomena related to the features of the AS that appeared to influence student opportunity for conceptual development. The emergent phenomenon were science activities, the building of learning, meaning in lessons, and the conflict over control. Lastly, the results of the two‐part classroom study were compared to those of the home science AS of high and low achievers. Mismatches in the AS features in the science classroom may constrain the opportunity to learn. Educational implications are discussed. © 2002 Wiley Periodicals, Inc. Sci Ed 87:40–63, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/sce.1053
Shallow cylindrical tuned liquid damper for vibration control of high‐rise structures
Authors: Li S. J. , Li G. Q. , Tang J. , Li Q. S. 
Published: December 2002

AbstractA new simplified model for the application of a shallow cylindrical tuned liquid damper (TLD) in structural vibration control is presented in this paper. The dynamic properties of a shallow liquid in cylindrical containers subjected to forced horizontal oscillation are analysed directly from the continuity and momentum equations of fluids. Following some practical assumptions, the nonlinear partial differential equations describing the wave movement of a shallow liquid in cylindrical containers is established and a numerical procedure for the solution of these equations is proposed using the finite element method. The formula for determining the control force provided by the shallow cylindrical TLD is presented and the effect of several parameters on the control efficiency of a shallow cylindrical TLD controlled structure under wind action is investigated. Copyright © 2002 John Wiley & Sons, Ltd.
Analysis of a Medication Safety Intervention in the Pediatric Emergency Department
Authors: Samuels-Kalow Margaret E. , Tassone Randall , Manning William , Cash Rebecca , Davila-Parrilla Laura , Hayes Bryan D. , Porter Stephen , Camargo Carlos A. 
Published: January 2024

ImportanceStrategies to reduce medication dosing errors are crucial for improving outcomes. The Medication Education for Dosing Safety (MEDS) intervention, consisting of a simplified handout, dosing syringe, dose demonstration and teach-back, was shown to be effective in the emergency department (ED), but optimal intervention strategies to move it into clinical practice remain to be described.ObjectiveTo describe implementation of MEDS in routine clinical practice and associated outcomes.Design, Setting, and ParticipantsThis mixed-methods interrupted time series study of MEDS was conducted April 2021 to December 2022 in an academic pediatric ED using a hybrid type 1 design. Parents and guardians of children aged 90 days to 11.9 years who were discharged with acetaminophen, ibuprofen, or both were eligible for inclusion in the quantitative portion. Clinicians from a diversity of role groups (attending physician, resident, and nurse) were eligible for the qualitative portion.ExposuresThe study was conducted in 5 stages (baseline, intervention 1, washout, intervention 2, and sustainability phases). The 2 intervention phases taught clinical staff the MEDS intervention using different implementation strategies. During the intervention 1 phase, in-depth interviews were conducted until thematic saturation was reached; results were analyzed using thematic analysis. Interviews informed intervention 2 phase interventions.Main Outcomes and MeasuresThe primary outcome was any error (defined as dosing or frequency error) at a 48- to 72-hour follow-up phone call.ResultsThere were 256 participants (median [IQR] child age, 1.7 [3.0-7.0] years; median [IQR] parent and guardian age, 36.0 [31.0-41.0] years; 200 females among parents and guardians [78.1%]) who consented and completed follow-up. At baseline, 44 of 68 participants (64.7%) made an error compared with 34 of 65 participants (52.3%) during intervention 1, 31 of 63 participants (49.X%) during intervention 2, and 34 of 60 participants (57.X%) during sustainability. After adjustment for language and health literacy, the adjusted odds ratio for error during the combined intervention phases was 0.52 (95% CI, 0.28-0.97) compared with baseline.Conclusions and RelevanceThis study found that both MEDS intervention phases were associated with decreased risk of error and that some improvement was sustained without active intervention. These findings suggest that attempts to develop simplified, brief interventions may be associated with improved medication safety for children after discharge from the ED.
Effects of different levels of gibberellic acid and potassium nitrate solutions on the emergence and seedling vigor of amaranth and Cleome gynandra
Authors: Tapfumaneyi Linda , Dube Praxedis , Mavengahama Sydney , Ngezimana Wonder 
Published: January 2024

AbstractThe effects of gibberellic acid and potassium nitrate on seed emergence and seedling growth of amaranth and Cleome gynandra were investigated in the greenhouse at Marondera University of Agricultural Sciences and Technology. The study was laid out in a factorial layout within a completely randomized design replicated three times. Potassium nitrate (dry seeds, 0.1%, 0.2%, 0.3%, 0.4%, 0.5%, 0.6%, 0.7%, 0.8%, 0.9%, and 1%) and gibberellic acid (dry seeds, 100, 200, 300, 400, 500, 600, 700, 800, 900, and 1000 parts per million) were used, respectively. A total of 100 seeds of both crops were planted in each plastic pocket. Seed emergence percentage and vigor index of amaranth and C. gynandra were evaluated. The effects were more pronounced in seeds treated with gibberellic acid than in potassium nitrate. Seed emergence and vigor index of amaranth and C. gynandra seeds treated with gibberellic acid showed a significant difference at p < 0.01, while potassium nitrate showed no significant difference at p > 0.05. The maximum seed emergence percentage of amaranth and C. gynandra was 67.1% and 64.8%, which was obtained in 2022 and 2021, while the lowest was 35.5% and 37.5%, which was obtained in 2021. The highest vigor index I of amaranth and C. gynandrawas 590.3 and 586.2, which was observed in 2022 and 2021, while the lowest vigor index I was 45.2 and 170, which was obtained in 2021 and 2022. The results obtained indicated that the application of gibberellic acid on seeds of amaranth and C. gynandra can alleviate seed dormancy.
Dual Nickel/Photoredox‐Catalyzed Asymmetric Carbamoylation of Benzylic C(sp3)−H Bonds
Authors: Cuesta‐Galisteo Sergio , Schörgenhumer Johannes , Hervieu Cedric , Nevado Cristina 
Published: January 2024

AbstractRadical‐mediated Hydrogen Atom Abstraction of Csp3−H bonds has become a powerful tool for the asymmetric functionalization of organic feedstocks. Here, we present an asymmetric synthesis of α‐aryl amides via carbamoylation of alkylarenes with isocyanates as electrophiles. The synergistic combination of a photoredox and a chiral nickel‐catalyst, enables the use of readily available and neutral reagents under mild reaction conditions and provides straightforward access to pharmacologically relevant motifs in enantiomerically pure form.
Automated identification of invasive rabbitfishes in underwater images from the Mediterranean Sea
Authors: Fleuré Valentine , Magneville Camille , Mouillot David , Villéger Sébastien 
Published: January 2024

Abstract

Coastal ecosystems of the Mediterranean Sea are among the richest in non‐indigenous species, mostly due to the establishment of species coming from the Red Sea through the Suez Canal. Two herbivorous rabbitfishes, Siganus rivulatus and Siganus luridus, are already invasive in the south‐eastern part of the Mediterranean Sea where they cause ecological damage by overgrazing algae.
The early detection and the counting of these non‐indigenous species in the rest of the Mediterranean Sea is thus a major challenge for scientists and ecosystem managers. However, analysing images from divers or remote cameras is a demanding task.
Here, a dataset of 31,285 images of Siganus spp. and of six common native fishes to the Mediterranean Sea was built from 40 underwater videos recorded at three reef habitats. A deep learning algorithm was then trained to identify Siganus spp. on images containing the eight Mediterranean species. Finally, the algorithm and a post‐processing filtering were tested with an independent dataset of 2024 images.
The model had a recall of 0.92 for the Siganus genus (i.e., two Siganus species combined). After a confidence‐based post‐processing, the recall increased to 0.98 with only 4 out of 272 images of Siganus spp. being misclassified. Accuracy reached a score of 0.61 meaning that experts would have to discard false positives. Images of five native species not present in the training dataset yielded similar false positive rates than species present in the training dataset. Overall, the automatic processing of images by the model and then the checking of putative Siganus images by experts required up to five times less effort than a full processing by experts.
The algorithm can help to efficiently detect these two invasive fishes in underwater images to evaluate progress towards conservation objectives and accelerate citizen‐based monitoring of coastal ecosystems.