bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two Kinds of Observation: Why van Fraassen Was Right to Make a Distinction, but Made the Wrong One
Authors: Vollmer Sara 
Published: February 2004

van Fraassen's constructivist empiricist account of theories makes an epistemic distinction between entities that can and cannot be observed with the naked eye. A belief about the correctness of a theoretical description of an entity that is observable with the naked eye can be warranted by a theory. In contrast, no theory can warrant a belief about the correctness of a description of an unobservable entity.I argue that we ought to instead adopt a view that takes account of the fact that some entities that cannot be observed with the naked eye can nevertheless be observed on the basis of the same physical principle as those entities that can be. This suggests that there is a distinction different from van Fraassen's that might do the work van Fraassen intends his to do, but a distinction that is principled. Understanding why this is so suggests that his distinction is grounded merely in human chauvinism.
Science, Values, and the Value of Science
Authors: Koertge Noretta 
Published: February 2004

Protagonists in the so-called Science Wars differ most markedly in their views about the role of values in science and what makes science valuable. Scientists and philosophers of science have traditionally considered the principal aims of science to be explanation and application. Only cognitive values should influence what is taken to be explanatory. Social and political values affect the priority assigned to various scientific problems and the ways in which scientific results are applied. Ethical considerations may be brought to bear on the treatment of human and animal subjects, and the manner in which scientific results are communicated.Recent critiques of science allege that the content of scientific explanations reflects the dominant ideology and interests of scientists and their patrons. Instead of calling for more value neutrality, some now urge that science take as a principal aim the emancipation of oppressed subcultures. Not only should progressive political values be allowed to set the problems attempted, they also should be used to constrain the types of answers which are pursued. Since scientific knowledge is constructed by us, we should take responsibility for its content.This paper argues that the project of Emancipationist science is impractical and self-defeating. There is good reason to believe that there would be unresolvable political disputes concerning which kinds of scientific theories are truly emancipiatory. Furthermore, just as placebos cease to work when recognized as such, so would a science known to be constrained by political considerations lose its special epistemic authority.
Models Of and Models For: Theory and Practice in Contemporary Biology
Authors: Keller Evelyn Fox 
Published: February 2004

Two decades of critique have sensitized historians and philosophers of science to the inadequacies of conventional dichotomies between theory and practice, thereby prompting the search for new ways of writing about science that are less beholden than the old ways to the epistemological mores of theoretical physics, and more faithful to the actual practices not only of physics but of all the natural sciences. The need for alternative descriptions seems particularly urgent if one is to understand the place of theory (and, in parallel, the role of modeling) in contemporary molecular biology, a science where, until now, no division between theory and experiment has obtained, and where distinctions between representing and intervening, and more generally, between basic and applied science, are daily becoming more blurred.Indeed, the very division between theory and experiment threatens to slight the extensive and sophisticated theoretical analyses (and even modeling) on which experimental work in contemporary molecular biology so often depends. My aim in this paper is to find a way of talking about theoretical practices in biology that is directly rooted in the mix of conceptual and material work that biologists do. As an example of such theoretical practices, I choose for the focus of my analysis the development of a model for gene regulation out of the experimental work of Eric Davidson and his colleagues at Cal Tech.
Logic, Probability, and Coherence
Authors: Vickers John M. 
Published: February 2004

How does deductive logic constrain probability? This question is difficult for subjectivistic approaches, according to which probability is just strength of (prudent) partial belief, for this presumes logical omniscience. This paper proposes that the way in which probability lies always between possibility and necessity can be made precise by exploiting a minor theorem of de Finetti: In any finite set of propositions the expected number of truths is the sum of the probabilities over the set. This is generalized to apply to denumerable languages. It entails that the sum of probabilities can neither exceed nor be exceeded by the cardinalities of all consistent and closed (within the set) subsets. In general any numerical function on sentences is said to be logically coherent if it satisfies this condition. Logical coherence allows the relativization of necessity: A function p on a language is coherent with respect to the concept T of necessity iff there is no set of sentences on which the sum of p exceeds or is exceeded by the cardinality of every T-consistent and T-closed (within the set) subset of the set. Coherence is easily applied as well to sets on which the sum of p does not converge.Probability should also be relativized by necessity: A T-probability assigns one to every T-necessary sentence and is additive over disjunctions of pairwise T-incompatible sentences. Logical T-coherence is then equivalent to T-probability: All and only T-coherent functions are T-probabilities.
Quantum Logic Is Alive ∧ (It Is True v It Is False)
Authors: Dickson Michael 
Published: February 2004

Is the quantum-logic interpretation dead? Its near total absence from current discussions about the interpretation of quantum theory suggests so. While mathematical work on quantum logic continues largely unabated, interest in the quantum-logic interpretation seems to be almost nil, at least in Anglo-American philosophy of physics.This paper has the immodest purpose of changing that fact. I shall argue that while the quantum-logic interpretation faces challenges, it remains a live option. The usual objections either miss the mark, or admit a reasonable answer, or fail to decide the issue conclusively.
SaRAD: a Simple and Robust Abbreviation Dictionary
Authors: Adar Eytan 
Published: February 2004

Abstract
Motivation: Due to recent interest in the use of textual material to augment traditional experiments it has become necessary to automatically cluster, classify and filter natural language information.
Results: The Simple and Robust Abbreviation Dictionary (SaRAD) provides an easy to implement, high performance tool for the construction of a biomedical symbol dictionary. The algorithms, applied to the MEDLINE document set, result in a high quality dictionary and toolset to disambiguate abbreviation symbols automatically.
Availability: The SaRAD tool, supplementary information and pseudo-code are available at http://www.hpl.hp.com/shl/projects/abbrev.html
A multi-algorithm, multi-timescale method for cell simulation
Authors: Takahashi Kouichi , Kaizu Kazunari , Hu Bin , Tomita Masaru 
Published: February 2004

Abstract
Motivation: Many important problems in cell biology require the dense nonlinear interactions between functional modules to be considered. The importance of computer simulation in understanding cellular processes is now widely accepted, and a variety of simulation algorithms useful for studying certain subsystems have been designed. Many of these are already widely used, and a large number of models constructed on these existing formalisms are available. A significant computational challenge is how we can integrate such sub-cellular models running on different types of algorithms to construct higher order models.
Results: A modular, object-oriented simulation meta-algorithm based on a discrete-event scheduler and Hermite polynomial interpolation has been developed and implemented. It is shown that this new method can efficiently handle many components driven by different algorithms and different timescales. The utility of this simulation framework is demonstrated further with a ‘composite’ heat-shock response model that combines the Gillespie–Gibson stochastic algorithm and deterministic differential equations. Dramatic improvements in performance were obtained without significant accuracy drawbacks. A multi-timescale demonstration of coupled harmonic oscillators is also shown.
Availability: An implementation of the method is available as part of E-Cell Simulation Environment Version 3 downloadable from http://www.e-cell.org/software. Benchmark models are included in the package, and also available upon request.
Supplementary information: Complete lists of reactions and parameters of the heat-shock model, and more results are available at http://www.e-cell.org/bioinfo/takahashi03-1-supp.pdf
Translational polymorphism as a potential source of plant proteins variety in Arabidopsis thaliana
Authors: Kochetov Alex V. , Sarai Akinori 
Published: February 2004

Abstract
Motivation: According to scanning model, 40S ribosomal subunits can either initiate translation at start AUG codon in suboptimal context or miss it and initiate translation at downstream AUG(s), thereby producing several proteins. Functional significance of such a protein translational polymorphism is still unknown.
Results: We compared predicted subcellular localizations of annotated Arabidopsis thaliana proteins and their potential N-terminally truncated forms started from the nearest downstream in-frame AUG codons. It was found that localizations of full and N-truncated proteins differ in many cases: 12.2% of N-truncated proteins acquired sorting signals de novo and 5.7% changed their predicted subcellular locations (mitochodria, chloroplast or secretory pathway). It is likely that the in-frame downstream AUGs may be frequently utilized to synthesize proteins possessing new functional properties and such a translational polymorphism may serve as an important source of cellular and organelle proteomes.
Availability: Detailed description of arabidopsis mRNAs potentially producing novel functional protein forms is available by request.
Predicting subcellular localization of proteins using machine-learned classifiers
Authors: Lu Z. , Szafron D. , Greiner R. , Lu P. , Wishart D.S. , Poulin B. , Anvik J. , Macdonell C. , Eisner R. 
Published: February 2004

Abstract
Motivation: Identifying the destination or localization of proteins is key to understanding their function and facilitating their purification. A number of existing computational prediction methods are based on sequence analysis. However, these methods are limited in scope, accuracy and most particularly breadth of coverage. Rather than using sequence information alone, we have explored the use of database text annotations from homologs and machine learning to substantially improve the prediction of subcellular location.
Results: We have constructed five machine-learning classifiers for predicting subcellular localization of proteins from animals, plants, fungi, Gram-negative bacteria and Gram-positive bacteria, which are 81% accurate for fungi and 92–94% accurate for the other four categories. These are the most accurate subcellular predictors across the widest set of organisms ever published. Our predictors are part of the Proteome Analyst web-service.
Availability: http://www.cs.ualberta.ca/~bioinfo/PA/Sub, http://www.cs.ualberta.ca/~bioinfo/PA
Supplementary information: http://www.cs.ualberta.ca/~bioinfo/PA/Subcellular
Enrichment of transcriptional regulatory sites in non-coding genomic region
Authors: Xue Wen , Wang Jin , Shen Zhirong , Zhu Huaiqiu 
Published: February 2004

Abstract
Motivation: Over-represented k-mers in non-coding genomic regions often lead to identification of potential transcriptional regulatory sites (TRS). This phenomenon has been employed by many algorithms to predict TRS in silico. Yet, the improvement of these algorithms should be based on deeper understanding of the enrichment feature. To obtain a general distributional profile of TRS in different regions of genomes as well as in different genomes, we here performed a systematic analysis on the over-representation of TRS in intergenic regions and gene upstream regions of yeasts and viral genomes, and the distributional pattern of TRS in intergenic and intron regions of the Drosophila genome. We also explored the way to evaluate the accuracy of TRS consensus sequences by measuring their enrichment.
Results: To measure enrichment, a statistical background model was introduced by comparing TRS frequency in certain regions of genome to either the frequency in the whole genome or the frequency in exon region. This model was applied to different classes of non-coding genomic regions in four genomes. Most of the TRS were observed to be over-represented in the intergenic regions of the Saccharomyces cerevisiae, Schizosaccharomyces pombe and Epstein-Barr virus (EBV) genomes. The enrichment of S.cerevisiae TRS in the 600 bp upstream region of genes was also significant. In Drosophila genome, TRS did not show enrichment in intergenic and intron regions when TRS frequency in the whole genome was taken as background, as we did in other genomes. However, when we took TRS frequency in exon region as background, over 70% TRS are over-represented in those two classes of non-coding regions. This fact indicates the existence of transcriptional regulatory signals in introns. The analysis of some S.cerevisiae TRS, which have inconsistent consensus sequences with different levels of enrichment in intergenic region, suggests the possibility of evaluating the accuracy of experimentally determined TRS by measuring their enrichment in non-coding genomic regions.
Availability: Free programs are available at http://dii.nju.edu.cn/~xuewen/enrichment/
A simple fold with variations: the pacifastin inhibitor family
Authors: Gáspári Zoltán , Ortutay Csaba , Perczel András 
Published: February 2004

Abstract
Summary: Members of the pacifastin family are small, ∼35-residue serine protease inhibitors isolated from arthropod species. Several locust inhibitors exhibit intriguing taxon specificity while others do not. The structural basis of this phenomenon may lie in the different dynamical properties of the proteins originating from different stabilizing interactions. In this study, we identify new members of the family to confirm the universal role of these interactions in the family. Structural investigations show that both the disulfide pattern and the stabilizing interactions are unique among small all-beta proteins.
Availability: Detailed description of the results can be found at http://www.chem.elte.hu/departments/protnmr/pif
Support vector machine classification on the web
Authors: Pavlidis Paul , Wapinski Ilan , Noble William Stafford 
Published: February 2004

Abstract
Summary: The support vector machine (SVM) learning algorithm has been widely applied in bioinformatics. We have developed a simple web interface to our implementation of the SVM algorithm, called Gist. This interface allows novice or occasional users to apply a sophisticated machine learning algorithm easily to their data. More advanced users can download the software and source code for local installation. The availability of these tools will permit more widespread application of this powerful learning algorithm in bioinformatics.
Availability: Web interface at svm.sdsc.edu. Binaries and source code at microarray.cpmc.columbia.edu/gist.
Safety of Modified Radical Neck Dissection for Differentiated Thyroid Carcinoma
Authors: Kupferman Michael E. , Patterson D. Michael , Mandel Susan J. , LiVolsi Virginia , Weber Randal S. 
Published: February 2004

AbstractObjectives/Hypothesis The management of cervical metastases from differentiated thyroid carcinoma (DTC) remains controversial. Most surgeons perform a neck dissection (ND) for clinically apparent disease. The extent of nodal dissection varies from regional to comprehensive. Morbidity from ND in the setting of DTC remains high, particularly when performed in the setting of a thyroidectomy (TT). To determine complications from ND for DTC, we retrospectively reviewed our surgical experience of modified radical neck dissection for nodal metastases.Study Design Retrospective chart review.Methods Between 1997 and 2002, 39 consecutive patients (31 females and 8 males) underwent 44 comprehensive NDs of levels II–V for DTC. Central compartment dissection (CCD) (levels VI and VII) was also performed during 23 of these procedures. Twenty (45.5%) patients had prior treatment elsewhere. Preoperative pathology revealed papillary carcinoma in 22 patients (56.4%), tall cell variant in 11 (28.2%), and follicular variant in 6 (15.4%).Results Ten patients (20%) underwent ND alone, whereas 6 (14%) underwent simultaneous ND and TT. Fifteen patients underwent simultaneous ND, TT, and CCD (30%). Temporary hypocalcemia occurred after 21% of NDs that were performed in the setting of either TT or CCD or both. There were no cases of permanent hypoparathyroidism. Transient regional lymph node (RLN) paresis occurred in two patients and was associated with a concomitant central compartment nodal dissection; there were no permanent RLN palsies. Transient spinal accessory nerve paresis developed after 27% of NDs performed. Two patients developed chyle leaks.Conclusions When ND is necessary for the treatment of thyroid malignancies, the procedure can be performed safely with acceptable morbidity.
Endoscopic Neck Surgery: Resection of the Submandibular Gland in a Cadaver Model
Authors: Terris David J. , Haus Brian M. , Gourin Christine G. 
Published: February 2004

AbstractObjectives/Hypothesis The objective was to evaluate the feasibility of performing a totally endoscopic resection of the submandibular gland in a cadaver model.Study Design Prospective, nonrandomized experimental investigation in a cadaver model.Methods A modified endoscopic surgical approach (representing a hybrid of balloon dissection and low‐pressure carbon dioxide insufflation) previously developed in a porcine model was implemented in fresh cadavers. Once a reliable protocol was achieved, eight procedures were performed in six cadavers. Data collected prospectively included the operative time, inadvertent neurovascular injury, and size of the glands.Results All eight endoscopic submandibular gland resections were successfully performed in six consecutive cadavers (no conversions to open resection were necessary). The duration of the procedures ranged from 50 to 150 minutes, with a median duration of 65.5 minutes and a steady trend toward a shorter duration. Histological examination confirmed the presence of normal glandular architecture without evidence of excessive trauma or thermal injury. The optimal spacing of the instrument ports was 4 cm from the camera port. There were no cases of neurovascular injury. In two cadavers, a minimal amount of subcutaneous emphysema could be appreciated, which was limited to the skin overlying the dissection.Conclusion Totally endoscopic resection of the submandibular gland is possible by combining balloon dissection with low‐pressure carbon dioxide insufflation. The excellent visualization afforded by the endoscope provided a safe operative approach. Ultimately, a number of endoscopic neck procedures may be possible, and clinical trials are under way.
Factors Predictive of Local Disease Control after Intra‐arterial Concomitant Chemoradiation (RADPLAT)
Authors: Robbins K. Thomas , Doweck Ilana , Samant Sandeep , Vieira Francisco , Kumar Parvesh 
Published: February 2004

AbstractObjectives To determine the relative risk of prognostic factors for local disease control following RADPLAT.Study Design Prospective study, academic medical center.Methods Analyses of nine categories of risk factors among 240 patients with Stage II‐IV carcinoma consecutively treated with RADPLAT (cisplatin 150 mg/m2 IA and sodium thiosulfate 9 g/m2 IV, weekly ×4; radiotherapy 2 Gy/fraction/d, 5× weekly, 68–74 Gy over 6 to 7 weeks). Median follow‐up: 58 months (range, 12–96 mo).Results The percentage of patients who had local disease control was 87.5%. Univariant analysis showed T classification (P = .01), laterality of neck disease (P = .026), number of neck levels involved (P = .008), total dose of radiation greater versus less than 60 Gy (P = .027), and presence of pathologically positive lymph nodes following chemoradiation (P = .01) to be significant. Logistic regression analysis showed total dose of radiation (P = .03) and the presence of pathologically positive lymph nodes following chemoradiation (P = .05) to be significant. For Kaplan‐Meier estimates of local disease control at 5 years, T classification (P = .038), number of levels with nodal disease (P = .006), and total dose of radiation therapy (P = .0001) were significant. The log‐rank test identified as significant the total dose of radiation therapy (P < .0001), the presence of pathologically positive lymph nodes following chemoradiation (P = .005), and the number of neck levels with positive nodes (P = .006). The Cox regression model showed significance for the total dose of radiation (P = .001), the presence of pathologically positive lymph nodes following chemoradiation (P = .007), and the T classification (P = .029).Conclusion Risk factors significantly associated with local disease control after RADPLAT appears to differ from more traditional therapy and is suggestive of a paradigm shift.
Clinical Results with the Med‐El Compressed and Split Arrays in the United States
Authors: Bauer Paul W. , Roland Peter S. 
Published: February 2004

AbstractObjective To determine the indications for which the Med‐El compressed and split arrays have been used in the United States, to assess the success achieved in insertion, to determine hearing outcomes, and assess complications associated with using these arrays.Study Design Retrospective review of data gathered during the US clinical trial.Methods Data were extracted concerning indications for use, depth of insertion, number of electrodes in use, 3 and 6 month performance outcomes, and complications. The results obtained in postmeningitic patients using the compressed array were compared with results of patients using the split array.Results Six adults and 22 children have been implanted with the compressed array. The principal indications have been postmeningitis or congenital cochlear malformations. The average improvement seen in the Meaningful Auditory Integration Scale scores was 17.6 for the compressed array group and 13.9 for the split array group. The same number of electrodes was inserted on average for both groups, with comparable numbers of electrodes in use.Conclusions The Med‐El compressed array is an alternative to a standard or split array in managing patients with postmeningitic deafness or congenital cochlear malformations. Benefits to these patients are most clearly seen in subjective measures.