bluuebunny/crossref_metadata_2025 huggingface dataset:
An approach to evaluate the topological significance of motifs and other patterns in regulatory networks
Authors: Goemann Björn , Wingender Edgar , Potapov Anatolij P
Published: May 2009

Background

The identification of network motifs as statistically over-represented topological patterns has become one of the most promising topics in the analysis of complex networks. The main focus is commonly made on how they operate by means of their internal organization. Yet, their contribution to a network's global architecture is poorly understood. However, this requires switching from the abstract view of a topological pattern to the level of its instances. Here, we show how a recently proposed metric, the pairwise disconnectivity index, can be adapted to survey if and which kind of topological patterns and their instances are most important for sustaining the connectivity within a network.

Results

The pairwise disconnectivity index of a pattern instance quantifies the dependency of the pairwise connections between vertices in a network on the presence of this pattern instance. Thereby, it particularly considers how the coherence between the unique constituents of a pattern instance relates to the rest of a network. We have applied the method exemplarily to the analysis of 3-vertex topological pattern instances in the transcription networks of a bacteria (E. coli), a unicellular eukaryote (S. cerevisiae) and higher eukaryotes (human, mouse, rat). We found that in these networks only very few pattern instances break lots of the pairwise connections between vertices upon the removal of an instance. Among them network motifs do not prevail. Rather, those patterns that are shared by the three networks exhibit a conspicuously enhanced pairwise disconnectivity index. Additionally, these are often located in close vicinity to each other or are even overlapping, since only a small number of genes are repeatedly present in most of them. Moreover, evidence has gathered that the importance of these pattern instances is due to synergistic rather than merely additive effects between their constituents.

Conclusion

A new method has been proposed that enables to evaluate the topological significance of various connected patterns in a regulatory network. Applying this method onto transcriptional networks of three largely distinct organisms we could prove that it is highly suitable to identify most important pattern instances, but that neither motifs nor any pattern in general appear to play a particularly important role per se. From the results obtained so far, we conclude that the pairwise disconnectivity index will most likely prove useful as well in identifying other (higher-order) pattern instances in transcriptional and other networks.
Bioprospecting metagenomes: glycosyl hydrolases for converting biomass
Authors: Li Luen-Luen , McCorkle Sean R , Monchy Sebastien , Taghavi Safiyh , van der Lelie Daniel
Published: May 2009

Throughout immeasurable time, microorganisms evolved and accumulated remarkable physiological and functional heterogeneity, and now constitute the major reserve for genetic diversity on earth. Using metagenomics, namely genetic material recovered directly from environmental samples, this biogenetic diversification can be accessed without the need to cultivate cells. Accordingly, microbial communities and their metagenomes, isolated from biotopes with high turnover rates of recalcitrant biomass, such as lignocellulosic plant cell walls, have become a major resource for bioprospecting; furthermore, this material is a major asset in the search for new biocatalytics (enzymes) for various industrial processes, including the production of biofuels from plant feedstocks. However, despite the contributions from metagenomics technologies consequent upon the discovery of novel enzymes, this relatively new enterprise requires major improvements. In this review, we compare function-based metagenome screening and sequence-based metagenome data mining, discussing the advantages and limitations of both methods. We also describe the unusual enzymes discovered via metagenomics approaches, and discuss the future prospects for metagenome technologies.
The apoptotic machinery as a biological complex system: analysis of its omics and evolution, identification of candidate genes for fourteen major types of cancer, and experimental validation in CML and neuroblastoma
Authors: Di Pietro Cinzia , Ragusa Marco , Barbagallo Davide , Duro Laura R , Guglielmino Maria R , Majorana Alessandra , Angelica Rosario , Scalia Marina , Statello Luisa , Salito Loredana , Tomasello Luisa , Pernagallo Salvo , Valenti Salvo , D'Agostino Vito , Triberio Patrizio , Tandurella Igor , Palumbo Giuseppe A , La Cava Piera , Cafiso Viviana , Bertuccio Taschia , Santagati Maria , Li Destri Giovanni , Lanzafame Salvatore , Di Raimondo Francesco , Stefani Stefania , Mishra Bud , Purrello Michele
Published: May 2009

Background

Apoptosis is a critical biological phenomenon, executed under the guidance of the Apoptotic Machinery (AM), which allows the physiologic elimination of terminally differentiated, senescent or diseased cells. Because of its relevance to BioMedicine, we have sought to obtain a detailed characterization of AM Omics inHomo sapiens, namely its Genomics and Evolution, Transcriptomics, Proteomics, Interactomics, Oncogenomics, and Pharmacogenomics.

Methods

This project exploited the methodology commonly used in Computational Biology (i.e., mining of manyomicsdatabases of the web) as well as the High Throughput biomolecular analytical techniques.

Results

InHomo sapiensAM is comprised of 342 protein-encoding genes (possessing either anti- or pro-apoptotic activity, or a regulatory function) and 110 MIR-encoding genes targeting them: some have a critical role within the system (coreAM nodes), others perform tissue-, pathway-, or disease-specific functions (peripheralAM nodes). By overlapping the cancer type-specific AM mutation map in the fourteen most frequent cancers in western societies (breast, colon, kidney, leukaemia, liver, lung, neuroblastoma, ovary, pancreas, prostate, skin, stomach, thyroid, and uterus) to their transcriptome, proteome and interactome in the same tumour type, we have identified the most prominent AM molecular alterations within each class. The comparison of the fourteen mutated AM networks (both protein- as MIR-based) has allowed us to pinpoint the hubs with a general and critical role in tumour development and, conversely, in cell physiology: in particular, we found that some of these had already been used as targets for pharmacological anticancer therapy. For a better understanding of the relationship between AM molecular alterations and pharmacological induction of apoptosis in cancer, we examined the expression of AM genes in K562 and SH-SY5Y after anticancer treatment.

Conclusion

We believe that our data on the Apoptotic Machinery will lead to the identification of new cancer genes and to the discovery of new biomarkers, which could then be used to profile cancers for diagnostic purposes and to pinpoint new targets for pharmacological therapy. This approach could pave the way for future studies and applications in molecular and clinical Medicine with important perspectives both for Oncology as for Regenerative Medicine.
Comparison between Flotrac-Vigileo and Bioreactance, a totally noninvasive method for cardiac output monitoring
Authors: Marqué Sophie , Cariou Alain , Chiche Jean-Daniel , Squara Pierre
Published: May 2009

Introduction

This study was designed to compare the clinical acceptability of two cardiac output (CO) monitoring systems: a pulse wave contour-based system (FloTrac-Vigileo) and a bioreactance-based system (NICOM), using continuous thermodilution (PAC-CCO) as a reference method.

Methods

Consecutive patients, requiring PAC-CCO monitoring following cardiac surgery, were also monitored by the two other devices. CO values obtained simultaneously by the three systems were recorded continuously on a minute-by-minute basis.

Results

Continuous recording was performed on 29 patients, providing 12,099 simultaneous measurements for each device (417 ± 107 per patient). In stable conditions, correlations of NICOM and Vigileo with PAC-CCO were 0.77 and 0.69, respectively. The bias was -0.01 ± 0.84 for NICOM and -0.01 ± 0.81 for Vigileo (NS). NICOM relative error was less than 30% in 94% of the patients and less than 20% in 79% vs. 91% and 79% for the Vigileo, respectively (NS). The variability of measurements around the trend line (precision) was not different between the three methods: 8 ± 3%, 8 ± 4% and 8 ± 3% for PAC-CCO, NICOM and Vigileo, respectively. CO changes were 7.2 minutes faster with Vigileo and 6.9 minutes faster with NICOM (P < 0.05 both systems vs. PAC-CCO, NS). Amplitude of changes was not significantly different than thermodilution. Finally, the sensitivity and specificity for predicting significant CO changes were 0.91 and 0.95 respectively for the NICOM and 0.86 and 0.92 respectively for the Vigileo.

Conclusions

This study showed that the NICOM and Vigileo devices have similar monitoring capabilities in post-operative cardiac surgery patients.
Cross-gradients joint 3D inversion with applications to gravity and magnetic data
Authors: Fregoso Emilia , Gallardo Luis A.
Published: May 2009

We extend the cross-gradient methodology for joint inversion to three-dimensional environments and introduce a solution procedure based on a statistical formulation and equality constraints for structural similarity resemblance. We apply the proposed solution to the joint 3D inversion of gravity and magnetic data and gauge the advantages of this new formulation on test and field-data experiments. Combining singular-value decomposition (SVD) and other conventional regularizing constraints, we determine 3D distributions of the density and magnetization with enhanced structural similarity. The algorithm reduces some misleading features of the models, which are introduced commonly by conventional separate inversions of gravity and magnetic data, and facilitates an integrated interpretation of the models.
Improvements in Survival After Follicular Lymphoma by Race/Ethnicity and Socioeconomic Status: A Population-Based Study
Authors: Keegan Theresa H.M. , McClure Laura A. , Foran James M. , Clarke Christina A.
Published: May 2009

Purpose

A recent report suggested improvements in survival after follicular lymphoma (FL), but not for all racial/ethnic groups. To better understand the reasons for these FL survival differences, we examined the joint influences of diagnostic period, race/ethnicity, and neighborhood socioeconomic status (SES) on survival in a large population-based case series.

Methods

All patients (n = 15,937) diagnosed with FL between 1988 and 2005 in California were observed for vital status through November 2007. Overall and FL-specific survival were analyzed with Kaplan-Meier and Cox proportional hazards regression. Neighborhood SES was assigned from United States Census data using residence at diagnosis.

Results

Overall and FL-specific survival improved 22% and 37%, respectively, from 1988 to 1997 to 1998 to 2005, and were observed in all racial/ethnic groups. Asian/Pacific Islanders had better survival than non-Hispanic white, Hispanic, and black patients who had similar outcomes. Lower neighborhood SES was associated with worse survival in patients across all stages of disease (P for trend < .01). Patients with the lowest SES quintile had a 49% increased risk of death from all causes (hazard ratio [HR] = 1.49, 95% CI, 1.30 to 1.72) and 31% increased risk of death from FL (HR = 1.31; 95% CI, 1.06 to 1.60) than patients with the highest SES.

Conclusion

Evolving therapies have likely led to improvements in survival after FL. Although improvements have occurred within all racial/ethnic groups, lower neighborhood SES was significantly associated with substantially poorer survival.
Sorafenib for Treatment of Renal Cell Carcinoma: Final Efficacy and Safety Results of the Phase III Treatment Approaches in Renal Cancer Global Evaluation Trial
Authors: Escudier Bernard , Eisen Tim , Stadler Walter M. , Szczylik Cezary , Oudard Stéphane , Staehler Michael , Negrier Sylvie , Chevreau Christine , Desai Apurva A. , Rolland Frédéric , Demkow Tomasz , Hutson Thomas E. , Gore Martin , Anderson Sibyl , Hofilena Gloria , Shan Minghua , Pena Carol , Lathia Chetan , Bukowski Ronald M.
Published: May 2009

Purpose

Mature survival data and evaluation of vascular endothelial growth factor (VEGF) as a prognostic biomarker from the Treatment Approaches in Renal Cancer Global Evaluation Trial (TARGET) study in patients with renal cell carcinoma (RCC) are reported.

Patients and Methods

Nine hundred three previously treated patients were randomly assigned to receive sorafenib versus placebo. On demonstration of progression-free survival (PFS) benefit with sorafenib, patients assigned to placebo were offered sorafenib. Overall survival (OS) was determined at two planned interim analyses and one final analysis, with a secondary OS analysis conducted by censoring placebo patients who crossed over to sorafenib. The relationships between baseline VEGF level and prognosis and efficacy were evaluated.

Results

The final OS of patients receiving sorafenib was comparable with that of patients receiving placebo (17.8 v 15.2 months, respectively; hazard ratio [HR] = 0.88; P = .146); however, when post–cross-over placebo survival data were censored, the difference became significant (17.8 v 14.3 months, respectively; HR = 0.78; P = .029). Adverse events at 16 months after cross over were similar to those previously reported. Baseline VEGF levels correlated with Eastern Cooperative Oncology Group performance status (P < .0001), Memorial Sloan-Kettering Cancer Center score (P < .0001), and PFS and OS in univariate (PFS, P = .0013; OS, P = .0009) and multivariate (PFS, P = .0231; OS, P = .0416) analyses of placebo patients and with short OS by multivariate analysis of patients receiving sorafenib (P = .0145). Both high-VEGF (P < .01) and low-VEGF (P < .01) groups benefited from sorafenib.

Conclusion

Although an OS benefit was not seen on a primary intent-to-treat analysis, results of a secondary OS analysis censoring placebo patients demonstrated a survival advantage for those receiving sorafenib, suggesting an important cross-over effect. VEGF levels are prognostic for PFS and OS in RCC. The results of TARGET establish the efficacy and safety of sorafenib in advanced RCC.
Humanized Anti-CD20 Antibody, Veltuzumab, in Refractory/Recurrent Non-Hodgkin's Lymphoma: Phase I/II Results
Authors: Morschhauser Franck , Leonard John P. , Fayad Luis , Coiffier Bertrand , Petillon Marie-Odile , Coleman Morton , Schuster Stephen J. , Dyer Martin J.S. , Horne Heather , Teoh Nick , Wegener William A. , Goldenberg David M.
Published: May 2009

Purpose

This is a multicenter phase I/II dose-finding study in relapsed/refractory B-cell non-Hodgkin's lymphoma (NHL) evaluating veltuzumab, a humanized anti-CD20 antibody with structure-function differences from chimeric rituximab.

Patients and Methods

Eighty-two patients (median age, 64 years; 79% stage III/IV, one to nine prior treatments) received four once-weekly doses of 80 to 750 mg/m2 of veltuzumab and were assessed for safety, efficacy, pharmacodynamics, pharmacokinetics, and immunogenicity.

Results

Veltuzumab was well tolerated, with no grade 3 to 4 drug-related adverse events despite short infusion times (typically 2 hours initially, 1 hour subsequently at doses < 375 mg/m2). In follicular lymphoma, 24 (44%) of 55 patients had objective responses (OR), with 15 (27%) complete responses (CRs) or CRs unconfirmed (CRus) by International Working Group criteria, and with some responses occurring despite two to five prior rituximab-containing regimens, less favorable prognosis (elevated lactate dehydrogenase, tumors > 5 cm, and Follicular Lymphoma International Prognostic Index ≥ 2), and at all dose levels. The CRs/CRus were durable (median duration, 19.7 months), with five patients still ongoing (15.9 to 37.6 months duration). In marginal zone lymphoma, five (83%) of six patients had ORs, with two CRs/CRus (33%), and in diffuse large B-cell lymphoma, three (43%) of seven patients achieved partial responses. At all dose levels studied, B cells were depleted after the first infusion, veltuzumab serum half-lives were similar after the fourth infusion, and mean antibody serum levels exceeded values considered important for anti-CD20 therapy (ie, 25 μg/mL).

Conclusion

Veltuzumab appeared safe and active at all tested doses, encouraging further study, including dose levels less than those typically used with rituximab.
Imatinib Plasma Levels Are Correlated With Clinical Benefit in Patients With Unresectable/Metastatic Gastrointestinal Stromal Tumors
Authors: Demetri George D. , Wang Yanfeng , Wehrle Elisabeth , Racine Amy , Nikolova Zariana , Blanke Charles D. , Joensuu Heikki , von Mehren Margaret
Published: May 2009

Purpose

To study the pharmacokinetics (PK) of imatinib (IM) in patients with advanced GI stromal tumors (GISTs) treated in a randomized phase II study and to explore the potential relationship between IM plasma levels and long-term clinical outcomes.

Patients and Methods

Patients were randomly assigned to receive IM at 400 mg versus 600 mg daily. IM plasma levels were analyzed in a subset of patients (n = 73) for whom PK data on day 1 and at steady-state (SS, day 29) were available. IM PK was evaluated using a population PK approach. The relationship between IM plasma exposure and clinical outcome was explored by grouping patients into quartiles according to IM trough concentration (Cmin). The clinical outcome parameters evaluated include overall objective benefit rate (OOBR; complete response plus partial response plus stable disease) time to progression (TTP), and KIT genotyping.

Results

IM PK exposure showed a high inter-patient variability, and clinical outcomes were correlated with IM trough levels at SS. The median TTP was 11.3 months for patients in the lowest Cmin quartile (Q1, < 1,110 ng/mL) compared with more than 30 months for Q2 to Q4 (P = .0029). OOBR was also inferior in Q1 patients. In patients with GIST with KIT exon 11 mutations (n = 39), the OOBR was 67% for Q1 patients versus 100% for all others (P = .001).

Conclusion

In patients with advanced GIST, IM trough levels at SS were associated with clinical benefit. Patients with IM Cmin below 1,100 ng/mL showed a shorter TTP and lower rate of clinical benefit (OOBR). Further studies are justified to test whether monitoring IM plasma levels might optimize clinical outcomes for patients with GIST.
Safety and Efficacy of Patupilone in Patients With Advanced Ovarian, Primary Fallopian, or Primary Peritoneal Cancer: A Phase I, Open-Label, Dose-Escalation Study
Authors: ten Bokkel Huinink Wim W. , Sufliarsky Jozef , Smit Willem M. , Spanik Stanislav , Wagnerova Maria , Hirte Hal W. , Kaye Stan , Johri Anandhi R. , Oza Amit M.
Published: May 2009

Purpose

To evaluate the safety, maximum tolerated dose (MTD), and pharmacokinetics of patupilone administered once every 3 weeks with proactive standardized diarrhea management in patients with resistant or refractory ovarian, fallopian, or peritoneal cancer.

Patients and Methods

Patients received patupilone (6.5 to 11.0 mg/m2) every 3 weeks via 20-minute infusion. Adverse events, dose-limiting toxicities (DLT), MTD, and tumor response were determined. The tumor response was measured by Response Evaluation Criteria in Solid Tumors (RECIST) and cancer antigen 125 levels.

Results

Forty-five patients were enrolled. Adverse events were mild to moderate in intensity, and grade 3 diarrhea (13%) was the most commonly reported serious adverse event. Grade 3 peripheral neuropathy was noted in two patients (4%). Diarrhea, peripheral neuropathy, and fatigue were the most common DLTs; however, these were uncommon in the first cycle and the MTD was therefore not reached in this study. Overall response (OR; complete and partial responses; median cycles, 8) per RECIST in patients with measurable disease (n = 36) was 19.5%. Median duration of disease stabilization (complete and partial responses and stable disease) was 15.8 months. These results appear improved from a previous study in a similar patient population using a weekly schedule (2.5 mg/m2/week; N = 53; OR, 5.7%).

Conclusion

Patupilone once every 3 weeks was well-tolerated at doses up to 11.0 mg/m2. Patupilone demonstrated promising antitumor activity in patients with drug-resistant/refractory disease. An ongoing phase III study in this patient population is testing the 10.0 mg/m2 dose.
Multicenter Phase II Trial of Sunitinib in the Treatment of Nongastrointestinal Stromal Tumor Sarcomas
Authors: George Suzanne , Merriam Priscilla , Maki Robert G. , Van den Abbeele Annick D. , Yap Jeffrey T. , Akhurst Timothy , Harmon David C. , Bhuchar Gauri , O'Mara Margaret M. , D'Adamo David R. , Morgan Jeffrey , Schwartz Gary K. , Wagner Andrew J. , Butrynski James E. , Demetri George D. , Keohan Mary L.
Published: May 2009

Purpose

To evaluate the potential benefit of continuous daily dosing sunitinib in patients with advanced nongastrointestinal stromal tumor (GIST) sarcomas.

Patients and Methods

A total of 53 patients with advanced non-GIST soft tissue sarcomas received sunitinib 37.5 mg daily. Primary end point was Response Evaluation Criteria in Solid Tumors defined response. Secondary end points were stable disease at 16 and 24 weeks. [18F]-fluorodeoxyglucose positron emission tomography was performed on a subset of 24 patients at baseline and after 10 to 14 days of therapy.

Results

Forty-eight patients were eligible for response. One patient (desmoplastic round cell tumor [DSRCT]) achieved a confirmed partial response (PR) and remained on study for 56 weeks. Ten patients (20%) achieved stable disease for at least 16 weeks. Metabolic PR was seen in 10 (47%) of 21 of patients. Metabolic stable disease was seen in 11 (52%) of 21. There were no unexpected toxicities observed.

Conclusion

Sunitinib demonstrated notable evidence of metabolic response in several patients with non-GIST sarcoma. The relevance of disease control observed in subtypes with an indolent natural history is unknown, however, the durable disease control observed in DSRCT, solitary fibrous tumor, and giant cell tumor of bone suggests that future evaluation of sunitinib in these subtypes may be warranted.
Pazopanib, a Multikinase Angiogenesis Inhibitor, in Patients With Relapsed or Refractory Advanced Soft Tissue Sarcoma: A Phase II Study From the European Organisation for Research and Treatment of Cancer–Soft Tissue and Bone Sarcoma Group (EORTC Study 62043)
Authors: Sleijfer Stefan , Ray-Coquard Isabelle , Papai Zsuzsa , Le Cesne Axel , Scurr Michelle , Schöffski Patrick , Collin Françoise , Pandite Lini , Marreaud Sandrine , De Brauwer Annick , van Glabbeke Martine , Verweij Jaap , Blay Jean-Yves
Published: May 2009

Purpose

Given the importance of angiogenesis in soft tissue sarcoma (STS), pazopanib, an oral angiogenesis inhibitor that targets vascular endothelial growth factor receptor and platelet-derived growth factor receptor, was explored in patients with advanced STS.

Patients and Methods

Patients with intermediate- or high-grade advanced STS who were ineligible for chemotherapy or who had received no more than two prior cytotoxic agents for advanced disease, who had documented progression, who had adequate performance status, and who had good organ function were eligible. Pazopanib 800 mg was given daily. The primary end point was progression-free rate at 12 weeks (PFR12 weeks). Secondary end points were response, safety, and overall survival. Four different strata were studied: adipocytic STS, leiomyosarcomas, synovial sarcomas, and other STS types. A Simon two-stage design was applied (P1 = 40%; P0 = 20%; α = β = .1) for each stratum.

Results

One hundred forty-two patients were enrolled. The adipocytic STS stratum was closed after the first stage, given insufficient activity (PFR12 weeks, five [26%] of19). PFR12 weeks was 18 (44%) of 41 patients in the leiomyosarcoma cohort, 18 (49%) of 37 in the synovial sarcomas, and 16 (39%) of 41 in the other STS types. Compared with historical controls who were treated with second-line chemotherapy, progression-free and overall survivals were prolonged in the three cohorts in which the primary end point was reached. The most frequent drug-related toxicities were hypertension, fatigue, hypopigmentation, and nausea. Other toxicities included liver enzyme elevations, myelosuppression, and proteinuria, all of which were mostly grades 1 to 2. The most frequent grades 3 to 4 toxicities were hyperbilirubinemia (6.3%), hypertension (7.7%), and fatigue (7.7%).

Conclusion

Pazopanib is well tolerated in patients with relapsed, advanced STS and demonstrates interesting activity that warrants additional study in patients with leiomyosarcomas, synovial sarcomas, and other STS types.
Reading Democratically: Pedagogies of Difference and Practices of Listening in The House of Mirth and Passing
Authors: Bromell Nick
Published: May 2009

Bromell's essay argues that Edith Wharton's The House of Mirth and Nella Larsen's Passing both represent and enact a core problem in theories of deliberative democracy: how to assess the value of differences among citizens (of race, gender, or age) when democracy is understood primarily in terms of its communicative practices. On the one hand, a deliberative democracy would appear to need some minimal “common standards” of what constitutes reasoned communication. On the other, it also seeks to allow as much genuine difference to enter into democratic deliberations as possible. What exactly does it mean for democratic citizens to communicate successfully? How should they understand the act of communication with an “Other” who is different, and how should they understand what it means to “know” this Other?

These questions animate both novels. The House of Mirth is concerned with gender difference primarily and Passing mainly with racial difference, but both are careful also to situate these differences within an explicitly acknowledged range of other differences, including those of class and sexuality. These novels depict the failed and successful communicative strategies adopted by their characters as they encounter others who are “different” and struggle to “know” and communicate with them. Both novels go beyond merely representing the problem of knowing and communicating difference to deploy sophisticated narrative methods that and pull their readers into this problem, requiring us to employ and test various strategies ourselves. They thereby offer a democratic pedagogy that encourages readers to understand that knowing an “Other” means acknowledging also that we can never completely know and fix the meaning of difference.
Ghosts of Essentialism: Racial Memory as Epistemological Claim
Authors: Su John J.
Published: May 2009

Su calls for a reexamination of essentialism in light of a resurging interest in identity and identity politics. Since the mid-1990s, poststructuralist dismissals of identity as “pernicious and metaphysically inaccurate” have increasingly been challenged by feminist philosophers and cultural critics, race theorists, and, most recently, “postpositivist realists.” Yet academic scholarship continues to read essentialism in ontological terms, as Walter Benn Michaels does. Ontological readings focus attention on the ways in which essentialism involves positing a presocial being who is defined by an essence that predetermines an individual's identity in racial terms. Su proposes to shift the way essentialism is analyzed, to consider it in epistemological rather than ontological terms. This would involve focusing on the extent to which racial memory in these texts enables, prohibits, or otherwise transforms cultural knowledge. Through a close analysis of works by Frank Chin and N. Scott Momaday, Su argues that essentialism does not necessarily imply the existence of static identities or common experiences that define a people; rather, it implies the possibility for certain personal experiences to yield reliable knowledge about broader social patterns of exploitation.
For a New Atlantic Alliance
Authors: Minuto-Rizzo Alessandro
Published: May 2009

The start of the Obama administration offers an opportunity to rebuild the US–NATO transatlantic link on the foundation of shared values during the Cold War and the immediate post–9/11 response. Use of military power is not sufficient, and torture should never again be condoned. Europe and the United States should take the lead in drafting new rules for the global economic order. A renewed NATO is also needed, as is a better relationship with Russia. NATO's eastward expansion to include Georgia and Ukraine makes sense in the long term but should not be pressed now.
Spanish Post-3/11 Antiterror Policy: Zapatero's Tyranny of Circumstance and the Dashing of Good Intentions
Authors: Celso Anthony N.
Published: May 2009

Elected on a platform of withdrawal from Iraq after the 3/11 train bombings, Spanish socialists sought early on to embark on an antiterrorist policy of negotiation and dialogue with disgruntled Arab and Basque communities. The socialists' early efforts at achieving a historic accord with the Basque separatist organization ETA and its willingness to accommodate and integrate North African diaspora communities have floundered. Faced with repeated terrorist attacks and plots, the socialists have reversed course and have moved decisively toward a more draconian law enforcement model in their prosecution of Basque and Islamist militants.
European Colonialism and Territorial Disputes in Africa: The Gulf of Guinea and the Indian Ocean
Authors: Yoon Mi Yung
Published: May 2009

This essay examines how European colonialism continues to underlie most territorial disputes in Africa. How these disputes have been resolved or are likely to be resolved is described, based on the following four long drawn-out disputes: the Nigeria–Cameroon dispute over the Bakassi Peninsula; the Gabon–Equatorial Guinea dispute over the islands of Mbanié, Cocotiers, and Conga in the Corisco Bay; the Mauritius–United Kingdom dispute over the Chagos Archipelago; and the Comoros–France dispute over Mayotte.
Racism, Society, and Law in Israel on the Appomattox
Authors: Schmidt James D.
Published: May 2009

James Schmidt evaluates the analysis of law and society in Israel on the Appomattox. Schmidt notes that Ely makes a signal contribution to our understanding about how the daily practice of law regarding free people of color in the antebellum South diverged significantly from the restrictive assertions of statute. Southern legal sources from outside Virginia support Ely's view. From a broader viewpoint, Schmidt suggests, these everyday legal enactments shored up social categories asserted through the raced language of the law, authorizing the in-between status of “free people of color” and constricting access to citizenship for free people of color.
Freedom, Ideology, and White Supremacy: A Comment on Melvin Patrick Ely's Israel on the Appomattox
Authors: Capers Corey
Published: May 2009

This commentary focuses on the discrepancies between the use of the concepts freedom and ideology in Ely's Israel on the Appomattox. Though the slippage between the two terms is pervasive in the historiography and not limited to Ely's book, Corey Capers argues that we need a more scrupulous accounting of their historical and historiographic use. Through contrasting the deployment of both concepts in discussions of American Revolutionary discourse and practice by Ely and Bernard Bailyn (among others), Capers demonstrates how freedom and ideology function differently for free African Americans and free whites in Ely's book. For example, in Ely's discussion, revolutionary ideology motivates Richard Randolph's action to liberate his slaves, while racist ideology supporting white supremacy is presented as distinct from actual behavior. Similarly, for American revolutionaries freedom meant some form of political sovereignty (republican or popular), whereas for formerly enslaved African Americans freedom is limited to freedom from enslavement. Finally, Capers takes issue with Ely's interpretation of the impact of the capriciousness of white supremacy, arguing that such capriciousness is itself endemic to power and terror.
Comments on Israel on the Appomattox: A Southern Experiment in Black Freedom from the 1790s Through the Civil War, by Melvin Patrick Ely
Authors: Dailey Jane
Published: May 2009

Jane Dailey's commentary raises methodological issues at play in Ely's book but also of concern to the wider world of historical writing. Ely focuses on human behavior in antebellum Virginia rather than on human thought or ideology. This kind of division between behavior and thought visible in Israel on the Appomattox is reproduced at the methodological level in the historical discipline as a whole. Some historians claim the triumph of social history, others economic or intellectual or cultural history. This sort of oppositional choice—behavior matters more than ideas—needs to be thought of not dogmatically but strategically. It is one thing to divide thought and action heuristically, in order to discover something unknown about one or the other—we can separate x from y in order to see x more clearly. However, privileging day-to-day behavior over law and ideology does not take us any closer to a model of history that accounts for the complexity of society and for the possibility of that society to generate all types of potential and conflicting histories, many of which are never realized. Dividing cognitive and ideological structures from everyday behavior constrains our ability to explain why behavior matters. Histories are punctuated equilibriums. The behavioral model can go a long way toward explaining equilibriums, but it has a hard time explaining punctuations.
Reforming Repression: Labor, Anarchy, and Reform in the Shaping of the Chicago Police Department, 1879-1888
Authors: Mitrani Sam
Published: May 2009

In the article “Reforming Repression: Labor, Anarchy, and Reform in the Shaping of the Chicago Police Department, 1879-1888,” Sam Mitrani examines the dramatic strengthening of the Chicago Police Department in the 1880s. Beginning in 1879, Mayor Carter Harrison pulled the department back from its least popular activities, such as enforcing temperance regulations and breaking strikes, to increase the legitimacy of the force. This was part of Harrison's policy of class collaboration aimed at calming the tension in the city after the strike and riot of 1877. His administration also hired hundreds of new officers and funded an extensive police telegraph system. Meanwhile, the city's workers were organizing in new unions, anarchist organizations were growing, and the city's business leaders were preparing for new clashes by organizing themselves in a citizens' association and an organization known as the Commercial Club. When a new strike wave began in 1885 and his class collaborationist policies ceased to ensure civic peace, Harrison deployed the newly strengthened force against strikers and their anarchist allies, with telling effect. After the Haymarket bombing and the repression of the anarchists in 1886, the police department further consolidated and reinforced itself with increased support from the city's business leaders and their organizations. The article concludes that the Chicago Police Department was largely built in this era in reaction to the labor movement. The department's main task was to contain that movement and protect “order” as defined by businessmen.
Artificial Neural Networks in Multivariate Calibration
Authors: Næs Tormod , Kvaal Knut , Isaksson Tomas , Miller Charles
Published: May 2009

This paper is about the use of artificial neural networks for multivariate calibration. We discuss network architecture and estimation as well as the relationship between neural networks and related linear and non-linear techniques. A feed-forward network is tested on two applications of near infrared spectroscopy, both of which have been treated previously and which have indicated non-linear features. In both cases, the network gives more precise prediction results than the linear calibration method of PCR.
Predicting Elements in White Pine and Red Oak Foliage with Visible-Near Infrared Reflectance Spectroscopy
Authors: Hallett R.A. , Hornbeck J.W. , Martin M.E.
Published: May 2009

Near infrared (NIR) reflectance spectroscopy was evaluated for its effectiveness at predicting Al, Ca, Fe, K, Mg and Mn concentrations in white pine ( Pinus strobus L.) and red oak ( Quercus rubra L.) foliage. A NIR spectrophotometer was used to scan 470 dried, ground foliage samples. These samples were used to develop calibration equations using a modified partial least squares (MPLS) regression technique. For the calibration equations, concentrations of Al, Ca, Fe, K, Mg and Mn as determined by acid digestion and laboratory analysis were regressed against second-difference absorbance values measured from 400 to 2498 nm. The regression models developed by NIR reflectance spectroscopy were unable to predict Fe. Predictions were satisfactory for Al, Ca, K, Mn and Mg. It still is uncertain which mineral/organic associations are being detected by NIR reflectance spectroscopy. Future applications may include prediction of element concentrations in the forest canopy via remote sensing.
Detection of Cheese Batches Exposed to Clostridium Tyrobutyricum Spoilage by near Infrared Spectroscopy
Authors: Sørensen Lambert K. , Jepsen Rita
Published: May 2009

Thirty-two batches of semi-hard cheese were produced in a pilot plant in an experimental design with pH, moisture and microbiological contamination as controlled variables. Near infrared reflectance spectra were taken every week during the ripening period of 11 weeks. Sensory properties were evaluated and the cheeses were analysed by chemical and gas chromatographic methods. The data were treated by soft independent modelling of class analogy. Generally it was possible by near infrared spectroscopy to identify cheese batches with developing defects caused by Clostridium tyrobutyricum. These were often identified before defects could be registered by sensory evaluations or by gas chromatographic analyses of free volatile acids.
Use of Visible-Near Infrared Diffuse Reflectance Spectroscopy to Discriminate between Kiwifruit with Properties Altered by Preharvest Treatments
Authors: Mowat Alistair D. , Poole Philip R.
Published: May 2009

Visible-near infrared (NIR) spectra of kiwifruit berries were processed by discriminant analysis techniques to differentiate berries treated during on-vine development. Treatments applied were leaf removal or shading berries with aluminium foil through crop development, or dipping the berries in ethephon two weeks prior to harvest. In order to accentuate the treatment effects, the canes used for individual treatments were cinctured to cut the phloem layer near the central cordon. Diffuse reflectance visible-NIR spectra were measured for all berries at harvest and after storing at 0°C for 16 weeks, and in sound ripened berries, for which the mass, skin colour, soluble solids and dry matter content were also determined. Principal components (PCs) were calculated for the 550–990 nm region of the visible-NIR absorption spectra for 500 berries randomly selected from all treatments. Canonical variate analyses of the PC were used to distinguish the berries from the original treatment groups. At harvest and after storage, discriminant algorithms, based on training spectra, were applied to validation spectra sets and correctly classified 99% and 87% of the berries, respectively, by their on-vine treatment. In the sound ripened berries, discrimination based on the visible-NIR data was superior to that achieved using combinations of mass, skin colour, dry matter and soluble solids.
Analysis of the Scattering Properties of Granular Materials
Authors: Ventura Céline , Papini Marie
Published: May 2009

The present study concerns diffuse reflectance spectroscopy of polymer powders and of their binary mixtures with inorganic materials. The total near-normal hemispherical spectral reflectance R of granular materials was measured in the near infrared wavelength range with a dispersive spectrophotometer. The measurement of the reflectance illustrated the influence of different parameters by taking into account (a) the morphology: powders or pellets and (b) the optical property of the material: semi-transparent, opaque or reflecting powders. The statistical treatment of the reflectance data by principal component analysis (PCA) allowed these data to be displayed in a reduced dimensionality space. As a result, the clustering of samples related to their chemical or their physical nature was carried out, giving a simpler description of the data in a new representation. The cross-correlation analysis of the reflectance values allowed similarities between absorption bands to be highlighted.
Developing a Robust Sampling and Measuring Unit for At-Line NIR Analysis of Esters
Authors: Wiedemann S.C.C. , Hansen W.G. , Wortel V.A.L. , Gielen J.W.J.
Published: May 2009

The use of Near Infrared (NIR) Spectroscopy as a tool for routine chemical process control has often revealed the differences between laboratory and process analysers. In-line applications are usually preferable because they can be integrated easily with the control system for direct monitoring. However, for some special applications, inherent technical problems brought by in-line measurement have still not been solved in practice. At-line analyses on the plant site can then be the first step towards continuous process control. In addition to a reliable spectrometer, these types of application demand accessories rugged enough to be used in a plant environment. The analysis procedure must also be operator-friendly. However, up to now, most of the commercial NIR sampling accessories have been developed for laboratory equipment and still require analytical skills to operate them. A sampling unit for transmittance NIR measurement of esters has been constructed using commercially available parts, making it a cost-effective device. Inspired from the “flow cell” used for in-line applications, the normal cleaning procedure between two analyses uses the sample to be measured itself. It does not require additional solvents, thereby reducing significantly chemical handling and waste disposal. Cross-contamination has been extensively tested, using esters of various viscosity. As indicated by all results, the sampling and measuring unit presented in this paper simplifies both analysis and maintenance procedures and is thus especially well-suited to a factory environment. Last but not least, with its fixed path length and its accurate temperature control, it has proven to be a valuable tool for research studies.
Near Infrared Spectroscopy of Dry Extracts from High Moisture Food Products on Solid Support—A Review
Authors: Thyholt Kari , Isaksson Tomas
Published: May 2009

This review article discusses studies published on diffuse near infrared spectroscopy of dry extracts from high moisture foods on solid support. The method can be used for rapid quantification and classification of low concentration nutrient components in aqueous samples. The volume most frequently used for measurement has been 0.5 ± 0.1 mL. The present paper aims to give a full review of journal papers and a selection of other reports, covering the method and applications on mixed model solutions, fruit juices and other beverages and on meat juices.
Discriminant Analysis of Selected Food Ingredients by near Infrared Diffuse Reflectance Spectroscopy
Authors: Reeves James B. , Zapf Charles M.
Published: May 2009

The objective of this research was to determine if near infrared spectroscopy could be used to discriminate among various food ingredients, and the influence of the type of instrumentation used on the discrimination. One hundred and six samples consisting of 15 milk-egg, 24 buttermilk, 14 cheese and 12 dehydrated onion powders, 20 wheat flours, 10 cheese and 11 ranch seasonings were scanned from 1100 to 2498 nm using diffuse reflectance on a NIRSystems model 6500 scanning spectrophotometer equipped with a rotating sample cup and a Digilab FTS-60 Fourier transform spectrometer (4 and 16 cm−1 resolution) equipped with a custom-made sample transport device. All samples were in a powdered state and were used as is. Discriminant analysis was performed using “Mahalanobis Distance by Principal Component Analysis with Residuals” using the “Averaged Predicted Distance” indicator to determine the number of factors to use for each grouping, obtained from a one-out cross validation analysis. Discrimination models were developed using either all available samples, or 2/3 of the samples in each group with the other third used as a validation set. Results using all available samples demonstrated that calibrations capable of discriminating among the various groups of food ingredients could be developed (100% correct classification) using either spectrometer. Initial results using an independent test set were, however, less satisfactory with many samples often misclassified. While derivatisation did not appear to be of much benefit when all samples were used, it was found to be beneficial in reducing the misclassification rate when samples were divided into calibration and test sets. Also for the Fourier transform spectrometer, results were considerably better at 4 cm−1 resolution than at 16 cm−1 when samples were divided into calibration and validation sets. It was also determined that increasing the distance criteria for group inclusion from 3 to 10 or more resulted in greatly increased discrimination robustness with no increased risk of misclassification. In conclusion, results demonstrated that near infrared spectra of food ingredients obtained from either a scanning spectrophotometer or a Fourier transform spectrometer can be used for product discrimination.
Two-Dimensional near Infrared Correlation Spectroscopy: Principle and its Applications
Authors: Ozaki Yukihiro , Wang Yan
Published: May 2009

The basic principle and applications of generalised two-dimensional (2D) near infrared (NIR) correlation spectroscopy are reviewed in this paper. A brief history and the basic principle of 2D correlation spectroscopy are described first, and then its importance for NIR spectroscopy is discussed. An outline of the mathematical treatment of generalised 2D correlation spectroscopy is given. Several examples of generalised 2D NIR and 2D NIR-mid IR (MIR) heterospectral correlation analysis are introduced.
NIR Radiative Transfer Investigations to Characterise Pharmaceutical Powders and Their Mixtures
Authors: Burger T. , Fricke J. , Kuhn J.
Published: May 2009

A measurement and data evaluation technique to determine quantitatively and separately the scattering and absorption coefficients of disperse media has been applied to pharmaceutical powders and their mixtures. This technique uses a 3-flux approximation of the equation of radiative transfer to evaluate analytically directional-hemispherical reflectance and transmittance data with the boundary conditions adjusted to the experimental set-up in order to derive the scattering and absorption coefficient. The performance of this technique is demonstrated by applying it to a variety of pharmaceutical powders and comparing it to Kubelka–Munk's 2-flux approximation. By applying this technique, more information about the investigated powders (e.g. particle size, degree of agglomeration or chemical composition) compared to diffuse reflectance measurements on optically thick samples can be obtained. From the latter only the ratio of the scattering to the absorption coefficient is determined. Using lactose and ascorbic acid, the effects of varying particle size and particles size distribution on the scattering and absorption coefficients are shown. Additionally this technique has been applied to powder mixtures with different contents of acetylsalicylacid and microcrystalline cellulose to demonstrate the usefullness of this technique for quantitative analysis.