bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated de-identification of free-text medical records
Authors: Neamatullah Ishna , Douglass Margaret M , Lehman Li-wei H , Reisner Andrew , Villarroel Mauricio , Long William J , Szolovits Peter , Moody George B , Mark Roger G , Clifford Gari D 
Published: July 2008

Abstract

Background
Text-based patient medical records are a vital resource in medical research. In order to preserve patient confidentiality, however, the U.S. Health Insurance Portability and Accountability Act (HIPAA) requires that protected health information (PHI) be removed from medical records before they can be disseminated. Manual de-identification of large medical record databases is prohibitively expensive, time-consuming and prone to error, necessitating automatic methods for large-scale, automated de-identification.

Methods
We describe an automated Perl-based de-identification software package that is generally usable on most free-text medical records, e.g., nursing notes, discharge summaries, X-ray reports, etc. The software uses lexical look-up tables, regular expressions, and simple heuristics to locate both HIPAA PHI, and an extended PHI set that includes doctors' names and years of dates. To develop the de-identification approach, we assembled a gold standard corpus of re-identified nursing notes with real PHI replaced by realistic surrogate information. This corpus consists of 2,434 nursing notes containing 334,000 words and a total of 1,779 instances of PHI taken from 163 randomly selected patient records. This gold standard corpus was used to refine the algorithm and measure its sensitivity. To test the algorithm on data not used in its development, we constructed a second test corpus of 1,836 nursing notes containing 296,400 words. The algorithm's false negative rate was evaluated using this test corpus.

Results
Performance evaluation of the de-identification software on the development corpus yielded an overall recall of 0.967, precision value of 0.749, and fallout value of approximately 0.002. On the test corpus, a total of 90 instances of false negatives were found, or 27 per 100,000 word count, with an estimated recall of 0.943. Only one full date and one age over 89 were missed. No patient names were missed in either corpus.

Conclusion
We have developed a pattern-matching de-identification system based on dictionary look-ups, regular expressions, and heuristics. Evaluation based on two different sets of nursing notes collected from a U.S. hospital suggests that, in terms of recall, the software out-performs a single human de-identifier (0.81) and performs at least as well as a consensus of two human de-identifiers (0.94). The system is currently tuned to de-identify PHI in nursing notes and discharge summaries but is sufficiently generalized and can be customized to handle text files of any format. Although the accuracy of the algorithm is high, it is probably insufficient to be used to publicly disseminate medical data. The open-source de-identification software and the gold standard re-identified corpus of medical records have therefore been made available to researchers via the PhysioNet website to encourage improvements in the algorithm.
Increased plasma apoM levels in the patients suffered from hepatocellular carcinoma and other chronic liver diseases
Authors: Jiang Jingting , Zhang Xiaoying , Wu Changping , Qin Xihu , Luo Guanghua , Deng Haifeng , Lu Minyang , Xu Bin , Li Min , Ji Mei , Xu Ning 
Published: July 2008

Abstract

Objective
To determine plasma apolipoprotein M (apoM) levels and other lipid profiles in hepatocellular carcinoma (HCC) patients compared to other chronic liver diseases and normal subjects.

Materials and methods
36 HCC, 68 chronic hepatitis, 29 liver cirrhosis patients and 64 normal controls were subjected in the present study. Serum lipids, lipoproteins, apolipoprotein AI (apoAI) and apoB were determined by the conventional methods. Plasma apoM levels were semi-quantitatively determined by both dot-blotting and western blotting analysis.

Results
Serum levels of triglycerides (TG), HDL-cholesterol, apoAI and lipoprotein (a) (Lp(a)) were significantly lower in the HCC patients than in the normal subjects, whereas there were no obvious differences on serum total cholesterol, LDL-cholesterol and apoB between HCC patients and normal subjects. However, plasma apoM levels in HCC patients were significantly increased than those in the normal subjects, but lower than those in the chronic hepatitis and cirrhosis patients.

Conclusion
It is concluded that serum TG, apoAI, HDL-C and Lp(a) were significantly decreased in HCC patients than in controls, whereas plasma apoM levels were significantly increased in the HCC patients. Decreased serum TG, apoAI, HDL-C and Lp(a) may reflect the liver damage in HCC patients, whereas the clinical significance of increased plasma apoM levels in relation to HCC is not clear.
Characterization of eight novel proteins with male germ cell-specific expression in mouse
Authors: Baek Namhoe , Woo Jong-Min , Han Cecil , Choi Eunyoung , Park Inju , Kim Do Han , Eddy Edward M , Cho Chunghee 
Published: July 2008

Abstract

Background
Spermatogenesis and fertilization are highly unique processes. Discovery and characterization of germ cell-specific genes are important for the understanding of these reproductive processes. We investigated eight proteins encoded by novel spermatogenic cell-specific genes previously identified from the mouse round spermatid UniGene library.

Methods
Polyclonal antibodies were generated against the novel proteins and western blot analysis was performed with various protein samples. Germ cell specificity was investigated using testes from germ cell-less mutant mice. Developmental expression pattern was examined in testicular germ cells, testicular sperm and mature sperm. Subcellular localization was assessed by cell surface biotin labeling and trypsinization. Protein localization and properties in sperm were investigated by separation of head and tail fractions, and extractabilities by a non-ionic detergent and urea.

Results
The authenticity of the eight novel proteins and their specificity to spermatogenic cells were confirmed. In examining the developmental expression patterns, we found the presence of four proteins only in testicular germ cells, a single protein in testicular germ cells and testicular sperm, and three proteins in the testicular stages and mature sperm from the epididymis. Further analysis of the three proteins present in sperm disclosed that one is located at the surface of the acrosomal region and the other two are associated with cytoskeletal structures in the sperm flagellum. We name the genes for these sperm proteins Shsp1 (Sperm head surface protein 1), Sfap1 (Sperm flagellum associated protein 1) and Sfap2 (Sperm flagellum associated protein 2).

Conclusion
We analyzed eight novel germ cell-specific proteins, providing new and inclusive information about their developmental and cellular characteristics. Our findings will facilitate future investigation into the biological roles of these novel proteins in spermatogenesis and sperm functions.
Two specific drugs, BMS-345541 and purvalanol A induce apoptosis of HTLV-1 infected cells through inhibition of the NF-kappaB and cell cycle pathways
Authors: Agbottah Emmanuel , Yeh Wen-I , Berro Reem , Klase Zachary , Pedati Caitlin , Kehn-Hall Kyleen , Wu Weilin , Kashanchi Fatah 
Published: July 2008

Abstract
Human T-cell leukemia virus type-1 (HTLV-1) induces adult T-cell leukemia/lymphoma (ATL/L), a fatal lymphoproliferative disorder, and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), a chronic progressive disease of the central nervous system after a long period of latent infection. Although the mechanism of transformation and leukemogenesis is not fully elucidated, there is evidence to suggest that the viral oncoprotein Tax plays a crucial role in these processes through the regulation of several pathways including NF-κB and the cell cycle pathways. The observation that NF-κB, which is strongly induced by Tax, is indispensable for the maintenance of the malignant phenotype of HTLV-1 by regulating the expression of various genes involved in cell cycle regulation and inhibition of apoptosis provides a possible molecular target for these infected cells. To develop potential new therapeutic strategies for HTLV-1 infected cells, in this present study, we initially screened a battery of NF-κB and CDK inhibitors (total of 35 compounds) to examine their effects on the growth and survival of infected T-cell lines. Two drugs namely BMS-345541 and Purvalanol A exhibited higher levels of growth inhibition and apoptosis in infected cell as compared to uninfected cells. BMS-345541 inhibited IKKβ kinase activity from HTLV-1 infected cells with an IC50 (the 50% of inhibitory concentration) value of 50 nM compared to 500 nM from control cells as measured by in vitro kinase assays. The effects of Purvalanol A were associated with suppression of CDK2/cyclin E complex activity as previously shown by us. Combination of both BMS-345541 and Purvalanol A showed a reduced level of HTLV-1 p19 Gag production in cell culture. The apparent apoptosis in these infected cells were associated with increased caspase-3 activity and PARP cleavage. The potent and selective apoptotic effects of these drugs suggest that both BMS-345541 and Purvalanol A, which target both NF-κB and CDK complex and the G1/S border, might be promising new agents in the treatment of these infected patients.
Machine learning based analyses on metabolic networks supports high-throughput knockout screens
Authors: Plaimas Kitiporn , Mallm Jan-Phillip , Oswald Marcus , Svara Fabian , Sourjik Victor , Eils Roland , König Rainer 
Published: July 2008

Abstract

Background
Computational identification of new drug targets is a major goal of pharmaceutical bioinformatics.

Results
This paper presents a machine learning strategy to study and validate essential enzymes of a metabolic network. Each single enzyme was characterized by its local network topology, gene homologies and co-expression, and flux balance analyses. A machine learning system was trained to distinguish between essential and non-essential reactions. It was validated by a comprehensive experimental dataset, which consists of the phenotypic outcomes from single knockout mutants of Escherichia coli (KEIO collection). We yielded very reliable results with high accuracy (93%) and precision (90%). We show that topologic, genomic and transcriptomic features describing the network are sufficient for defining the essentiality of a reaction. These features do not substantially depend on specific media conditions and enabled us to apply our approach also for less specific media conditions, like the lysogeny broth rich medium.

Conclusion
Our analysis is feasible to validate experimental knockout data of high throughput screens, can be used to improve flux balance analyses and supports experimental knockout screens to define drug targets.
Social rejection in social anxiety disorder: The role of performance deficits, evoked negative emotions and dissimilarity
Authors: Voncken Marisol J. , Alden Lynn E. , Bögels Susan M. , Roelofs Jeffrey 
Published: July 2008

ObjectivesPatients with social anxiety disorder (SAD) not only fear social rejection, but accumulating evidence also shows that they are indeed less liked than their non‐anxious counterparts. Three factors are hypothesized to play a role in this social anxiety–social rejection relationship: (1) social performance; (2) elicited negative emotions, and (3) perceived similarity.MethodPatients with SAD (N = 63) and control participants (N = 27) were observed during a 5 minutes ‘getting acquainted’ conversation with a male and female confederate who rated their social performance. Video‐observers rated their own negative emotions and perceived similarity with the patients, while other video‐observers rated their wish to engage in future contact with them (a measure of social rejection).ResultsAnalysed by way of structural equation modelling (SEM), the results supported the social anxiety–social rejection relationship. More specifically, poor social performance was associated with perceived dissimilarity ratings and mediated by evoked negative emotions, both of which were in turn associated with social rejection.ConclusionThese results suggest that a sequence of events links social anxiety to social rejection. Treatment should aim to improve social performance and perceived similarity to reverse SAD's vicious, negative interpersonal cycle.
Defected/decorated benzenoid/graphitic nanostructures
Authors: Klein D. J. 
Published: July 2008

Abstract
Various decorations, functionalizations, or defects of conjugated benzenoid or graphitic networks are considered, with special attention to the case that the structures are possibly extended in one or two dimensions. This includes various polymers, their end structures, and defects of side groups or vacancies along the chain, strip, or nanotube. This approach further includes various boundary (or edge) structures on semi-infinite graphite, as well as various "quasi-local" defects in what is otherwise two-dimensionally infinite graphite, such defects encompassing vacancy defects, selected substitutional defects, and perhaps even dislocations and disclinations. There are many possible such nanostructures, but property characterization is ultimately desired. Attention is paid to consequent occurrences of defect-localized unpaired (or weakly paired) electrons, as formulated within a resonating valence bond (RVB) framework, especially as regards simple classically appealing theorems or rules. But a further molecular orbital (MO) view is developed. Note is made of associated modifications in the local density of states near the Fermi energy. Consonance of predictions from RVB and MO viewpoints is taken as an indicator of reliable prediction.
Pyridinium-N-phenolate betaine dyes as empirical indicators of solvent polarity: Some new findings
Authors: Reichardt Christian 
Published: July 2008

AbstractSolutions of the zwitterionic betaine dye 2,6-diphenyl-4-(2,4,6-triphenylpyridinium-1-yl)phenolate (hereinafter calledstandard betaine dye) and its derivatives are solvatochromic, thermochromic, piezochromic, and halochromic. That is, the position of its longest-wavelength intramolecular charge-transfer (CT) absorption band depends on solvent polarity, solution temperature, external pressure, and the type and concentration of salts (ionophores) added to the betaine dye solution. The outstanding large negative solvatochromism of this standard betaine dye has been used to establish UV/vis spectroscopically a comprehensive set of empirical parameters of solvent polarity, calledET(30) resp.ETNvalues, now known for many molecular and ionic solvents as well as for a great variety of solvent mixtures. This report describes relevant physicochemical properties of this standard betaine dye as well as the definition and some more recent practical applications of these solvent polarity parameters, derived from the standard betaine dye and its derivatives. In particular, the perichromism of the standard betaine dye can be used to study the polarity of microheterogeneous solutions (e.g., micelles and other organized media), surfaces (e.g., silica, alumina, cellulose), glasses (e.g., sol-gel systems), and solids (e.g., polymers), and for the construction of chemical sensors. As extension to solvatochromism, the more general term perichromism describes UV/vis band shifts of chromophore-containing solutes which are caused not only by changes in the surrounding solvent sphere, but also by their embedding in other surroundings such as micelles, vesicles, glasses, polymers, solids, interfaces, and surfaces. Some representative examples for such extended applications of the perichromic standard betaine dye are given.
Comparative analysis of electron-phonon relaxation in a semiconducting carbon nanotube and a PbSe quantum dot
Authors: Habenicht Bradley F. , Kilina Svetlana V. , Prezhdo Oleg V. 
Published: July 2008

AbstractThe key features of the phonon-induced relaxation of electronic excitations in the (7,0) zig-zag carbon nanotube (CNT) and the Pb16Se16quantum dot (QD) are contrasted using a time-domain ab initio density functional theory (DFT) simulation. Upon excitation from the valence to the conduction band (CB), the electrons and holes nonradiatively decay to the band-edge in both materials. The paper compares the electronic structure, optical spectra, important phonon modes, and decay channels in the CNT and QD. The relaxation is faster in the CNT than in the QD. In the PbSe QD, the electronic energy decays by coupling to low-frequency acoustic modes. The decay is nonexponential, in agreement with non-Lorentzian line-shapes observed in optical experiments. In contrast to the QD, the excitation decay in the CNT occurs primarily via high-frequency optical modes. Even though the holes have a higher density of states (DOS), they relax more slowly than the electrons, due to better coupling to low-frequency vibrations. Further, the expected phonon bottleneck is not observed in the QD, as rationalized by a high density of optically dark states. The same argument applies to the CNT. The computed results agree well with experimentally measured ultrafast relaxation time-scales and provide a unique atomistic picture of the electron-phonon relaxation processes.
Calixarene receptors of environmentally hazardous and biorelevant molecules and ions
Authors: Kalchenko Vitaly I. 
Published: July 2008

Abstract
In the paper, a report on the rational design of the calixarene receptors bearing ligating, H-donor, H-acceptor fragments at the wide and/or narrow rim of the macrocycle is presented. The calixarenes form supramolecular complexes with various cations, anions, organic molecules, and biomolecules in solution, in the crystalline state and even in the gas phase. The calixarenes or their complexes can be used as materials for radionuclide extraction, construction of chemosensors, and drug design.
Advances in physical chemistry and pharmaceutical applications of cyclodextrins
Authors: Funasaki Noriaki , Ishikawa Seiji , Neya Saburo 
Published: July 2008

Abstract
Cyclodextrins (CDs) attract much attention for industrial applications and academic research. A few experimental methods for determination of the binding constant between CD and a guest molecule were reviewed critically. A hydrophile–hydrophobe matching model for host–guest docking was proposed for estimation of the binding constant and the solution structure of the complex. Rather detailed solution structures of CD complexes were determined by proton NMR spectroscopy, aided by calculations of molecular mechanics and surface areas, and were used to analyze the binding constants. The binding constants of CDs with multi-site guests were analyzed on the basis of their solution structures. The working mechanisms and physicochemical predictions in a few pharmaceutical applications of CDs were proposed on the basis of detailed solution structures and accurate binding constants.
Photonics and molecular design of dye-doped polymers for modern light-sensitive materials
Authors: Ishchenko Alexander A. 
Published: July 2008

Abstract
The advantages of dye-doped polymer matrices over polymers and dyes, separately, are analyzed. The effects of the polymer nature and chemical constitution of organic dyes on the spectral and luminescent properties of these matrices are discussed. The processes of dye aggregation in polymers are characterized, and their influence on the photophysical properties and photochemical stability of dye-doped nonphotoconducting and photoconducting polymers is discussed. The different approaches for the struggle with dye aggregation in polymers are offered. The main paths of energy degradation of electronic excitation in such materials are analyzed. The prospects for the applications of dye-doped polymer materials as passive Q-switches of solid-state lasers, active laser media (ALM), luminescent solar concentrator (LSCs), photovoltaic cells, and electroluminescent (EL) emitters are demonstrated.
Quantitative physicochemical analysis of equilibria on chemically modified silica surfaces
Authors: Kholin Yuriy , Zaitsev Vladimir 
Published: July 2008

AbstractQuantitative physicochemical analysis (QPCA) enables the determination of the stoichiometric compositions and physicochemical parameters of species in equilibrium systems proceeding from the composition-property dependencies. The paper discusses modifications to the routine QPCA procedures required to characterize properties of reagents fixed on surfaces of silica-organic hybrid materials. The cooperative effects and the energetic heterogeneity of fixed reagents are especially important in this context. It follows that the main peculiarities of silica surfaces chemically modified by aliphatic amines are (a) the pronounced energetic heterogeneity of reagents caused by the non-random surface topography, (b) the decrease of the bacisity of amines induced by their interactions with residual surface silanols, and (c) the expressed sensibility of reactions in the near-surface layer to the state of its hydration. The interaction of grafted organic bases with metal ions results in the preferred formation ofbismetal-ligand coordination compounds. Stability constants of complexes are decreased as a consequence of fixation and depend on not only donor but also acceptor ability of a solvent. Also, the denticity of polydentate ligands may decrease as a result of grafting. The changes of protolytic and complexing properties in the case of grafting of weak acids and phosphorus-containing complexons are due to their interactions with other surface groups and the influence of hydration effects in the near-surface layer.
Epistemic and Ethical Duties in Clinical Decision-making
Authors: O'Donohue William , Henderson Deborah 
Published: July 2008

AbstractIn the course of psychotherapy, psychologists need to make important clinical decisions regarding treatment goal selection, measurement procedures, and treatment methods. These decisions can be made without regard to the epistemic and ethical responsibilities that accompany professional status. Epistemic duties are obligations to obtain and have knowledge, while ethical duties are obligations to apply this knowledge accurately. We argue that these epistemic and ethical responsibilities are invoked and can be adequately addressed in the informed consent process. When the informed consent process is violated or done poorly, our epistemic and ethical responsibilities are not met and the client may be harmed. We argue that what the public assumes it is buying from us (and what we purport to sell) are specialised knowledge and skills; when psychologists are not meeting their epistemic duties, what our clients are receiving instead is intuition and performance art. We discuss errors that occur in the course of psychotherapy, as well as how we as professionals must seek to reduce or eliminate them.