bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probabilistic cross‐link analysis and experiment planning for high‐throughput elucidation of protein structure
Authors: Ye Xiaoduan , O'Neil Patrick K. , Foster Adrienne N. , Gajda Michal J. , Kosinski Jan , Kurowski Michal A. , Bujnicki Janusz M. , Friedman Alan M. , Bailey‐Kellogg Chris 
Published: November 2004

AbstractEmerging high‐throughput techniques for the characterization of protein and protein‐complex structures yield noisy data with sparse information content, placing a significant burden on computation to properly interpret the experimental data. One such technique uses cross‐linking (chemical or by cysteine oxidation) to confirm or select among proposed structural models (e.g., from fold recognition, ab initio prediction, or docking) by testing the consistency between cross‐linking data and model geometry. This paper develops a probabilistic framework for analyzing the information content in cross‐linking experiments, accounting for anticipated experimental error. This framework supports a mechanism for planning experiments to optimize the information gained. We evaluate potential experiment plans using explicit trade‐offs among key properties of practical importance: discriminability, coverage, balance, ambiguity, and cost. We devise a greedy algorithm that considers those properties and, from a large number of combinatorial possibilities, rapidly selects sets of experiments expected to discriminate pairs of models efficiently. In an application to residue‐specific chemical cross‐linking, we demonstrate the ability of our approach to plan experiments effectively involving combinations of cross‐linkers and introduced mutations. We also describe an experiment plan for the bacteriophage λ Tfa chaperone protein in which we plan dicysteine mutants for discriminating threading models by disulfide formation. Preliminary results from a subset of the planned experiments are consistent and demonstrate the practicality of planning. Our methods provide the experimenter with a valuable tool (available from the authors) for understanding and optimizing cross‐linking experiments.
On the use of DXMS to produce more crystallizable proteins: Structures of the T. maritima proteins TM0160 and TM1171
Authors: Spraggon Glen , Pantazatos Dennis , Klock Heath E. , Wilson Ian A. , Woods Virgil L. , Lesley Scott A. 
Published: November 2004

AbstractThe structure of two Thermotoga maritima proteins, a conserved hypothetical protein (TM0160) and a transcriptional regulator (TM1171), have now been determined at 1.9 Å and 2.3 Å resolution, respectively, as part of a large‐scale structural genomics project. Our first efforts to crystallize full‐length versions of these targets were unsuccessful. However, analysis of the recombinant purified proteins using the technique of enhanced amide hydrogen/deuterium exchange mass spectroscopy (DXMS) revealed substantial regions of rapid amide deuterium hydrogen exchange, consistent with flexible regions of the structures. Based on these exchange data, truncations were designed to selectively remove the disordered C‐terminal regions, and the resulting daughter proteins showed greatly enhanced crystallizability. Comparative DXMS analysis of full‐length protein versus truncated forms demonstrated complete and exact preservation of the exchange rate profiles in the retained sequence, indicative of conservation of the native folded structure. This study presents the first structures produced with the aid of the DXMS method for salvaging intractable crystallization targets. The structure of TM0160 represents a new fold and highlights the use of this approach where any prior structural knowledge is absent. The structure of TM1171 represents an example where the lack of a substrate/cofactor may impair crystallization. The details of both structures are presented and discussed.
Financial Development and Intersectoral Allocation: A New Approach
Authors: FISMAN RAYMOND , LOVE INESSA 
Published: November 2004

ABSTRACTThis paper uses a new methodology based on industry comovement to examine the role of financial market development in intersectoral allocation. Based on the assumption that there exist common global shocks to growth opportunities, we hypothesize that country pairs should have correlated patterns of sectoral growth if they are able to respond to these shocks. Consistent with financial markets promoting responsiveness to shocks, countries have more highly correlated growth rates across sectors when both countries have well‐developed financial markets. This effect is stronger between country pairs at similar levels of economic development, which are more likely to experience similar growth shocks.
Do Initial Public Offering Firms Purchase Analyst Coverage with Underpricing?
Authors: CLIFF MICHAEL T. , DENIS DAVID J. 
Published: November 2004

ABSTRACTWe report that initial public offering (IPO) underpricing is positively related to analyst coverage by the lead underwriter and to the presence of an all‐star analyst on the research staff of the lead underwriter. These findings are robust to controls for other determinants of underpricing and to controls for the endogeneity of underpricing and analyst coverage. In addition, we find that the probability of switching underwriters between IPO and seasoned equity offering is negatively related to the unexpected amount of post‐IPO analyst coverage. These findings are consistent with the hypothesis that underpricing is, in part, compensation for expected post‐IPO analyst coverage from highly ranked analysts.
Apical Organelle Discharge by
Cryptosporidium parvum
Is Temperature, Cytoskeleton, and Intracellular Calcium Dependent and Required for Host Cell Invasion
Authors: Chen Xian-Ming , O'Hara Steven P. , Huang Bing Q. , Nelson Jeremy B. , Lin Jim Jung-Ching , Zhu Guan , Ward Honorine D. , LaRusso Nicholas F. 
Published: November 2004

ABSTRACT

The apical organelles in apicomplexan parasites are characteristic secretory vesicles containing complex mixtures of molecules. While apical organelle discharge has been demonstrated to be involved in the cellular invasion of some apicomplexan parasites, including
Toxoplasma gondii
and
Plasmodium
spp., the mechanisms of apical organelle discharge by
Cryptosporidium parvum
sporozoites and its role in host cell invasion are unclear. Here we show that the discharge of
C. parvum
apical organelles occurs in a temperature-dependent fashion. The inhibition of parasite actin and tubulin polymerization by cytochalasin D and colchicines, respectively, inhibited parasite apical organelle discharge. Chelation of the parasite's intracellular calcium also inhibited apical organelle discharge, and this process was partially reversed by raising the intracellular calcium concentration by use of the ionophore A23187. The inhibition of parasite cytoskeleton polymerization by cytochalasin D and colchicine and the depletion of intracellular calcium also decreased the gliding motility of
C. parvum
sporozoites. Importantly, the inhibition of apical organelle discharge by
C. parvum
sporozoites blocked parasite invasion of, but not attachment to, host cells (i.e., cultured human cholangiocytes). Moreover, the translocation of a parasite protein, CP2, to the host cell membrane at the region of the host cell-parasite interface was detected; an antibody to CP2 decreased the
C. parvum
invasion of cholangiocytes. These data demonstrate that the discharge of
C. parvum
sporozoite apical organelle contents occurs and that it is temperature, intracellular calcium, and cytoskeleton dependent and required for host cell invasion, confirming that apical organelles play a central role in
C. parvum
entry into host cells.
SYNCHRONIZATION OF CHAOS
Authors: ANISHCHENKO V. S. , VADIVASOVA T. E. , POSTNOV D. E. , SAFONOVA M. A. 
Published: November 2004

This paper is devoted to the problem of synchronization of dynamical systems in chaotic oscillations regimes. The authors attempt to use the ideas of synchronization and its mechanisms on a certain class of chaotic oscillations. These are chaotic oscillations for which one can pick out basic frequencies in their power spectra. The physical and computer experiments were carried out for the system of two coupled auto-oscillators. The experimental installation permitted one to realize both unidirectional coupling (external synchronization) and symmetrical coupling (mutual synchronization). An auto-oscillator with an inertial nonlinearity was chosen as a partial subsystem. It possesses a chaotic attractor of spiral type in its phase space. It is known that such chaotic oscillations have a distinguished peak in the power spectrum at the frequency f0 (basic frequency). In the experiments, one could make the basic frequencies of partial oscillators equal or different. The bifurcation diagrams on the plane of control parameters "detuning" and "coupling" were constructed and analyzed. The results of investigations permit one to conclude that classical ideas of synchronization can be applied to chaotic systems of the mentioned type. Two mechanisms of chaos synchronization were established: 1) basic frequency locking and 2) basic frequency suppression. The bifurcational background of these mechanisms was created using numerical analysis on a computer. This allowed one to analyze the evolution of different oscillation characteristics under the influence of synchronization.
TWO TREE DRAWING CONVENTIONS
Authors: EADES PETER , LIN TAO , LIN XUEMIN 
Published: November 2004

Rooted trees abound in computing and it is often necessary to draw them for visualization and documentation purposes. In the classical convention for tree drawing, the tree is drawn in a “level” fashion, with nodes (represented by boxes) at depth k lying on a horizontal line at a distance of k units below the root. The parent — child relationships are represented by lines between the boxes. Several algorithms have been developed for constructing a compact layout of a tree in the classical convention. In this paper we investigate algorithms for drawing trees according to two new conventions. In the inclusion convention, nodes are represented by boxes, and the parent — child relationship is represented by inclusion of one box in another. The tip-over convention again represents nodes as boxes, and, like the classical convention, represents the parent — child relationship by lines between the boxes; however, we allow siblings to be arranged vertically rather than horizontally. For many of the cases which arise in visualization of trees (for example, binary trees with textual information at the leaves) we present polynomial time algorithms. However, the general problem of finding minimum size layouts for either of the new conventions is shown to be NP-hard.
Chronic Lymphocytic Leukemia
Authors: Byrd John C. , Stilgenbauer Stephan , Flinn Ian W. 
Published: November 2004

AbstractChronic lymphocytic leukemia (CLL) is one of the most commonly diagnosed leukemias managed by practicing hematologists. For many years patients with CLL have been viewed as similar, with a long natural history and only marginally effective therapies that rarely yielded complete responses. Recently, several important observations related to the biologic significance of VH mutational status and associated ZAP-70 overexpression, disrupted p53 function, and chromosomal aberrations have led to the ability to identify patients at high risk for early disease progression and inferior survival. Concurrent with these investigations, several treatments including the nucleoside analogues, monoclonal antibodies rituximab and alemtuzumab have been introduced. Combination of these therapies in clinical trials has led to high complete and overall response rates when applied as initial therapy for symptomatic CLL. Thus, the complexity of initial risk stratification of CLL and treatment has increased significantly. Furthermore, when these initial therapies do not work, approach of the CLL patient with fludarabine-refractory disease can be quite challenging. This session will describe the natural history of a CLL patient with emphasis on important decision junctures at different time points in the disease.In Section I, Dr. Stephan Stilgenbauer focuses on the discussion that occurs with CLL patients at their initial evaluation. This includes a review of the diagnostic criteria for CLL and prognostic factors utilized to predict the natural history of the disease. The later discussion of risk stratification focuses on molecular and genomic aberrations that predict rapid progression, poor response to therapy, and inferior survival. Ongoing and future efforts examining early intervention strategies in high risk CLL are reviewed.In Section II, Drs. Ian Flinn and Jesus G. Berdeja focus on the discussion of CLL patients when symptomatic disease has developed. This includes an updated review of monotherapy trials with nucleoside analogs and recent trials that have combined these with monoclonal antibodies and/or alternative chemotherapy agents. Appropriate application of more aggressive therapies such as autologous and allogeneic immunotherapy and less aggressive treatments for appropriate CLL patient candidates are discussed.In Section III, Dr. John Byrd focuses on the discussion that occurs with CLL patients whose disease is refractory to fludarabine. The application of genetic risk stratification in choosing therapy for this subset of patients is reviewed. Available data with conventional combination based therapies and monoclonal antibodies are discussed. Finally, alternative promising investigational therapies including new antibodies, kinase inhibitors (CDK, PDK1/AKT, PKC) and alternative targeted therapies (DNA methyltransferase inhibitors, histone deacetylase inhibitors, etc.) are reviewed with an emphasis on the most promising agents for this patient population.
Immunotherapeutic Approaches for Hematologic Malignancies
Authors: Caligiuri Michael A. , Velardi Andrea , Scheinberg David A. , Borrello Ivan M. 
Published: November 2004

AbstractThe immune system has two complementary arms: one is older and seemingly more primitive, called the innate immune system, found in both plants and animals. The second (already many millions of years old!) is the adaptive or antigen-specific immune system, limited to vertebrate animals. The human innate immune system has many cellular elements that include granulocytes, monocytes, macrophages, natural killer (NK) cells, mast cells, eosinophils, and basophils. Receptors for these cells are non-clonal, fixed in the genome, requiring no rearrangement, and recognize conserved molecular patterns that are specific to pathogens. The adaptive immune system (B cells and T cells) have receptors with great variation, able to recognize an almost an unlimited number of highly specific pathogens through rearrangement of receptor gene segments, and can also provide immunological memory so critical for vaccination. As the immune system has evolved to recognize non-self, malignant transformation of self can likely escape immune surveillance with relative ease. Contributors to this chapter are utilizing distinct components of either the innate or adaptive immune system that recognize non-self, in combination with what we know about differences between malignant and normal self, in an effort to develop novel and effective immunologic approaches against hematologic malignancies.In Section I, Dr. Andrea Velardi reviews the benefits of NK cell alloreactivity in mismatched hematopoietic transplantation, provides updates on current clinical trials, and discusses further therapeutic perspectives emerging from murine bone marrow transplant models.In Section II, Dr. David Scheinberg reviews novel leukemic antigens being targeted by humanized monoclonal antibodies as well as mechanisms by which antibody-mediated cytotoxicity occurs in vivo.In Section III, Dr. Ivan Borrello reviews vaccine and adoptive T cell immunotherapy in the treatment of hematologic malignancies. Specifically, he discusses the various vaccine approaches used as well as strategies aimed at augmenting the tumor specificity of T cell therapies.
Prediction of peak oxygen uptake in patients fulfilling the 1994 CDC criteria for chronic fatigue syndrome
Authors: Nijs Jo , De Meirleir Kenny 
Published: November 2004

Purpose: To establish an inexpensive, simple method of predicting peak oxygen uptake (VO2peak) in patients fulfilling the 1994 Centers for Disease Control and Prevention (CDC) criteria for chronic fatigue syndrome (CFS). Design: A retrospective observational study. Setting: An outpatient tertiary care chronic fatigue clinic. Subjects: Two hundred and forty consecutive patients fulfilling the 1994 CDC criteria for CFS. Interventions: Heart rate, metabolic and ventilatory parameters were measured continuously during a maximal exercise stress test on a bicycle ergometer. Using the equation peak oxygen uptake / 13.1 / peak workload / 284 (used by Mullis et al., Br J Sports Med1999; 33: 352 / 56), VO2peak was predicted from the peak workload of a maximal exercise capacity test. Pearson correlation coefficient and linear regression analysis were used to establish the most accurate way to predict VO2peak. Results: Percentage error encountered when comparing actual measured Vo2peak with predicted value was 17.3% (9-10.0). A strong correlation between Vo2peak and peak workload was observed (r / 0.89, p< 0.001). A regression analysis established the relation as Vo2peak= 10.47 × peak workload +284.1, where Vo2peak is given in ml/min and peak workload in W (error in prediction = 11.09±9.5%). Conclusions: Monitoring of the peak workload during a maximal, graded bicycle ergometric test suffices to predict the Vo2peak. When predicting Vo2peak the used operational definition for the diagnosis of CFS could be taken into account. Compared with the equation used by Mullis et al., peak workload is multiplied by 10.47 in order to predict peak oxygen uptake in CDC-defined CFS patients.
A randomized trial to evaluate an education programme for patients and carers after stroke
Authors: Smith Jane , Forster Anne , Young John 
Published: November 2004

Objectives: To evaluate the effectiveness of an education programme for patients and carers recovering from stroke. Design: Randomized controlled trial. Subjects and setting: One hundred and seventy patients admitted to a stroke rehabilitation unit and 97 carers of these patients. Interventions: The intervention group received a specifically designed stroke information manual and were invited to attend education meetings every two weeks with members of their multidisciplinary team. The control group received usual practice. Measures: Primary outcome was knowledge of stroke and stroke services. Secondary outcomes were handicap (London Handicap Scale), physical function (Barthel Index), social function (Frenchay Activities Index), mood (Hospital Anxiety and Depression Scale) and satisfaction (Pound Scale). Carer mood was measured by the General Health Questionnaire-28. Results: There was no statistical evidence for a treatment effect on knowledge but there were trends that favoured the intervention. The education programme was associated with a significantly greater reduction in patient anxiety score at both three months (p=0.034) and six months (p=0.021) and consequently fewer ‘cases’ (Hospital Anxiety and Depression Scale anxiety subscale score ≥ 11). There were no other significant statistical differences between the patient or carer groups for other outcomes, although there were trends in favour of the education programme. Conclusion: An education programme delivered within a stroke unit did not result in improved knowledge about stroke and stroke services but there was a significant reduction in patient anxiety at six months post stroke onset.
Prismatic correction in patients affected by age-related macular degeneration
Authors: Parodi Maurizio Battaglia , Toto Lisa , Mastropasqua Leonardo , Depollo Marta , Ravalico Giuseppe 
Published: November 2004

Objective: To evaluate by means of a controlled clinical trial the effectiveness and the tolerance of prismatic correction in improving visual function in patients affected by advanced bilateral age-related macular degeneration. Setting: Department of Ophthalmology, Eye Clinic, University of Trieste. Subjects and interventions: Each patient underwent an ophthalmologic examination, complete with distance visual acuity measurement using the Standard Early Treatment Diabetic Retinopathy Study chart. Patients were then randomly assigned to the treatment or control group. The treatment group received spectacles lenses with a prismatic correction of low power (5–7 prismatic dioptres) in the better eye. Main measures: Visual acuity was measured at baseline and 1, 90, 180 and 360 days after prescription in both groups. Results: The treatment group consisted of 14 patients, while the control group was of 14 patients. The prismatic correction was well tolerated in 85.7% of cases. Visual acuity in the treatment group improved mostly at three-month follow-up, with a slight further improvement at the sixand 12-month follow-ups, showing a statistically significant difference in comparison with the control group. No visual acuity improvement was registered in the control group. Conclusion: Monolateral prismatic correction may be considered a viable means to improve visual function in patients affected by bilateral age-related macular degeneration at an advanced stage.
Book Reviews
Authors: Mooney James 
Published: November 2004

Book reviewed in this article:Die Anmut des Frauenleibes. Von Friedrich S. Krauss. Leipzig: Adolph SchumannEin Geniestreich. Volkstück in fünf Aufzügen oder neun Bildern. Von Milovan Gj. Gliŝiĉ. Deutsch von Friedrich S. Krauss. Mit echten serbischen Sang‐ und zigeunerischen Spielweisen von Vladimir R. Gjorgjević.Künstlerblut! Ein Schauspiel in vier Aufzügen. Von Friedrich S. Krauss und Leo Norberg.
Book Reviews
Authors: Starr Frederick 
Published: November 2004

Book reviewed in this article:AFRICA: The Akamba of British East Africa; An Ethnological Monograph. Gerhard Lindblom.AFRICA: Die Kpelle: ein Negerstamm in Liberia dargestellt auf der Grundlage von Eingeborenen‐Berichten. Mit zwei Nachträgen: Texte in der Golasprache und Kpelle‐Beiträge von H. Rohde
BOOK REVIEW
Authors: Steward Julian H. 
Published: November 2004

Book reviewed in this article:Mangaian Society. Te Rangi Hiroa (P. H. Buck).The Legends of Maui and Tahaki. J. F. Stimson.Outline of Hawaiian Physical Therapeutics. E. S. Craighill Handy, Mary Kawena Pukui, and Katherine Livermore.Notes on the Ethnology of Pukapuka. Gordon MacGregor.
Book Reviews
Authors: Gillen John 
Published: November 2004

Book reviewed in this article:GENERAL AND THEORETICAL: Ways of Mankind: Thirteen Dramas of Peoples of the World and How They Live. Lister Sinclair, Len Peterson, Eugene Hallman, George Salverson. Walter GoldschmidtGENERAL AND THEORETICAL: The Ways of Mankind, Series IGENERAL AND THEORETICAL: The Ways of Mankind, Series II
Book Reviews
Authors: Miner Horace 
Published: November 2004

Book reviewed in this article:ETHNOLOGY AND ETHNOGRAPHY: The Azande, and Related Peoples of the Anglo‐Egyptian Sudan and Belgian Congo. P. T. W. Baxter and Audrey Butt.ETHNOLOGY AND ETHNOGRAPHY: Peoples of the Horn of Africa: Somali, Afar and Saho. I. M. Lewis.
Book Reviews
Authors: Shimkin D. B. 
Published: November 2004

Book reviewed in this article:REVIEW ARTICLE: Les Lapons des Montagues Suédoises. Ernst Manker.REVIEW ARTICLE: Changing Lapps: A Study in Culture Relations in Northernmost Norway. Gutorm Gjessing.REVIEW ARTICLE: Social Relations in a Nomadic Lappish Community. Ian Whitaker. Preface by Sibjorn Nesheim.