First-in-human implantation of a mid-field powered neurostimulator at the sacral nerve: Results from an acute study.

INTRODUCTION: Commercially approved implantable systems for sacral neuromodulation require the implantation of a multipolar lead subcutaneously connected to an implantable pulse generator (IPG). Eliminating the need for an IPG would eliminate the need for tunneling of the lead, reduce procedure time, infection risk, and the need for IPG replacement. The objective was to demonstrate the feasibility of implanting the AHLeveeS System in the S3 Foramen to stimulate the S3 sacral nerve. MATERIALS AND METHODS: A first-in-human, prospective, single center, nonrandomized, acute feasibility clinical investigation at the Maastricht University Medical Center+. Patients with refractory overactive bladder underwent acute implantation of the AHLeveeS neurostimulator before the InterStim procedure. Outcome measurements included motor responses, procedural time and a scoring of the difficulty of the implant and explant procedure. Retrospectively, qualitative responses to the stimulation protocol were assessed by video motion analyses. Only descriptive statistics were used. RESULTS: During the stimulation a motor response to stimulation was seen in four of the five subjects. In all implantations the AHLeveeS was correctly placed. The median time for complete procedure was 24 minutes. The implant and explant procedures were successfully performed and no device or procedure related adverse events occurred. CONCLUSIONS: The results from this acute first-in-human study demonstrate the feasibility of implantation and acute stimulation of the sacral nerve with this mid-field powered system. Future clinical studies will focus on safety and efficacy of a chronically implanted device.

Wirelessly powered, fully internal optogenetics for brain, spinal and peripheral circuits in mice.

To enable sophisticated optogenetic manipulation of neural circuits throughout the nervous system with limited disruption of animal behavior, light-delivery systems beyond fiber optic tethering and large, head-mounted wireless receivers are desirable. We report the development of an easy-to-construct, implantable wireless optogenetic device. Our smallest version (20 mg, 10 mm(3)) is two orders of magnitude smaller than previously reported wireless optogenetic systems, allowing the entire device to be implanted subcutaneously. With a radio-frequency (RF) power source and controller, this implant produces sufficient light power for optogenetic stimulation with minimal tissue heating (<1 °C). We show how three adaptations of the implant allow for untethered optogenetic control throughout the nervous system (brain, spinal cord and peripheral nerve endings) of behaving mice. This technology opens the door for optogenetic experiments in which animals are able to behave naturally with optogenetic manipulation of both central and peripheral targets.

Screening for depression in cancer patients receiving radiotherapy: Feasibility and identification of effective tools in the NRG Oncology RTOG 0841 trial.

BACKGROUND: Brief tools are needed to screen oncology outpatients for depressive symptoms. METHODS: Patients starting radiotherapy for the first diagnosis of any tumor completed distress screening tools, including the 9-item Patient Health Questionnaire (PHQ-9), the 2-item Patient Health Questionnaire (PHQ-2), the National Comprehensive Cancer Network Distress Thermometer (NCCN-DT), and the Hopkins Symptom Checklist (HSCL) (25-item version). Patients exceeding validated cutoff scores and a systematic sample of patients whose screening was negative completed the Structured Clinical Interview for DSM-IV (SCID) mood disorder modules via telephone. RESULTS: Four hundred sixty-three patients from 35 community-based radiation oncology sites and 2 academic radiation oncology sites were recruited. Sixty-six percent of the 455 eligible patients (n = 299) were women, and the eligible patients had breast (45%), gastrointestinal (11%), lung (10%), gynecologic (6%), or other cancers (27%). Seventy-five (16.5%) exceeded screening cutoffs for depressive symptoms. Forty-two of these patients completed the SCID. Another 37 patients whose screening was negative completed the SCID. Among the 79 patients completing the SCID, 8 (10.1%) met the criteria for major depression, 2 (2.5%) met the criteria for dysthymia, and 6 (7.6%) met the criteria for an adjustment disorder. The PHQ-2 demonstrated good psychometric properties for screening for mood disorders with a cutoff score of ≥3 (receiver operating characteristic area under the curve [AUC], 0.83) and was comparable to the PHQ-9 ( > 9; AUC = 0.85). The NCCN-DT did not detect depression (AUC = 0.59). CONCLUSIONS: The PHQ-2 demonstrated good psychometric properties for screening for mood disorders, which were equivalent to the PHQ-9 and superior to the NCCN-DT. These findings support using the PHQ-2 to identify patients in need of further assessment for depression, which has a low prevalence but is a clinically significant comorbidity. These findings could inform the implementation of distress screening accreditation standards. Cancer 2017;123:485-493. © 2016 American Cancer Society.

Wireless power transfer to deep-tissue microimplants.

The ability to implant electronic systems in the human body has led to many medical advances. Progress in semiconductor technology paved the way for devices at the scale of a millimeter or less ("microimplants"), but the miniaturization of the power source remains challenging. Although wireless powering has been demonstrated, energy transfer beyond superficial depths in tissue has so far been limited by large coils (at least a centimeter in diameter) unsuitable for a microimplant. Here, we show that this limitation can be overcome by a method, termed midfield powering, to create a high-energy density region deep in tissue inside of which the power-harvesting structure can be made extremely small. Unlike conventional near-field (inductively coupled) coils, for which coupling is limited by exponential field decay, a patterned metal plate is used to induce spatially confined and adaptive energy transport through propagating modes in tissue. We use this method to power a microimplant (2 mm, 70 mg) capable of closed-chest wireless control of the heart that is orders of magnitude smaller than conventional pacemakers. With exposure levels below human safety thresholds, milliwatt levels of power can be transferred to a deep-tissue (>5 cm) microimplant for both complex electronic function and physiological stimulation. The approach developed here should enable new generations of implantable systems that can be integrated into the body at minimal cost and risk.

Origins of Stereoselectivity of Chiral Vicinal Diamine-Catalyzed Aldol Reactions.

The sources of asymmetric induction in aldol reactions catalyzed by cinchona alkaloid-derived amines, and chiral vicinal diamines in general, have been determined by density functional theory calculations. Four vicinal diamine-catalyzed aldol reactions were examined. The cyclic transition states of these reactions involve nine-membered hydrogen-bonded rings in distinct conformations. Using nomenclature from eight-membered cycloalkanes, the heavy atoms of the low-energy transition states are in crown (chair-chair) and chair-boat conformations. The factors that control which of these are favored have been identified.

Xerostomia health-related quality of life: NRG oncology RTOG 0537.

PURPOSE: The purpose of this secondary analysis was to determine change in overall health-related quality of life (HRQOL) based on patient data obtained from NRG Oncology RTOG 0537 as measured by the RTOG-modified University of Washington Head and Neck Symptom Score (RM-UWHNSS). METHODS: A multi-site prospective randomized clinical trial design stratified 137 patients with post-radiation therapy xerostomia according to prior pilocarpine (PC) treatment and time after radiation therapy and/or chemotherapy and randomized patients into two groups. Patients were assigned to acupuncture or PC. Twenty-four sessions of acupuncture-like transcutaneous electrical nerve stimulation (ALTENS) were administered over 12 weeks, or oral PC (5 mg) three times daily over the same 12 weeks. The RM-UWHNSS was administered at baseline and at 4, 6, 9, and 15 months after the date of randomization. RESULTS: There were no between-arm differences in change scores on the RM-UWHNSS in the individual items, total score, or factor scores. For statistical modeling, race and time were significant for all outcomes (total and factor scores), while treatment arm was not significant. The ALTENS arm showed greater yet nonsignificant improvement in outcomes compared to the PC arm. CONCLUSION: Although no significant treatment differences were seen in this trial, patients receiving ALTENS consistently had lower scores, indicating better function, as compared to those receiving PC. Radiation-induced xerostomia improved over time for all patients.

Phase 2 results from Radiation Therapy Oncology Group Study 0537: a phase 2/3 study comparing acupuncture-like transcutaneous electrical nerve stimulation versus pilocarpine in treating early radiation-induced xerostomia.

BACKGROUND: In this phase 2 component of a multi-institutional, phase 2/3, randomized trial, the authors assessed the feasibility and preliminary efficacy of acupuncture-like transcutaneous electrical nerve stimulation (ALTENS) in reducing radiation-induced xerostomia. METHODS: Patients with cancer of the head and neck who were 3 to 24 months from completing radiotherapy with or without chemotherapy (RT ± C) and who were experiencing xerostomia symptoms with basal whole saliva production ≥0.1 mL per minute and were without recurrence were eligible. Patients received twice weekly ALTENS sessions (24 sessions over 12 weeks) using a proprietary electrical stimulation unit. The primary study objective was to assess the feasibility of ALTENS treatment. Patients were considered compliant if 19 of 24 ALTENS sessions were delivered, and the targeted compliance rate was 85%. Secondary objectives measured treatment-related toxicities and the effect of ALTENS on overall radiation-induced xerostomia burden using the University of Michigan Xerostomia-Related Quality of Life Scale (XeQOLS). RESULTS: Of 48 accrued patients, 47 were evaluable. The median age was 60 years, 84% of patients were men, 70% completed RT ± C for >12 months, and 21% had previously received pilocarpine. Thirty-four patients completed all 24 ALTENS sessions, 9 patients completed 20 to 23 sessions, and 1 patient completed 19 sessions, representing a 94% total compliance rate. Six-month XeQOLS scores were available for 35 patients and indicated that 30 patients (86%) achieved a positive treatment response with a mean ± standard deviation reduction of 35.9% ± 36.1%. Five patients developed grade 1 or 2 gastrointestinal toxicity, and 1 had a grade 1 pain event. CONCLUSIONS: The current results indicated that ALTENS treatment for radiation-induced xerostomia can be delivered uniformly in a cooperative, multicenter setting and produces possible beneficial treatment response. Given these results, the phase 3 component of this study was initiated.

Reproducibility of elemental profile across two vintages in Pinot noir wines from fourteen different vineyard sites.

The reproducibility of elemental profile in wines produced across vintages of 2015 and 2016 has been studied using grapes from a single scion clone of Vitis vinifera L. cv. Pinot noir. Grapevines were grown on fourteen different vineyard sites, from Oregon to southern California in the U.S.A., which span distances from approximately hundreds of meters to 1450 km, while elevations range from near sea level to nearly 500 m. The number of elements quantified in the wines made from the 2016 vintage was thirty, by using inductively coupled plasma mass spectrometry (ICP-MS). These data were compared with the twenty-seven elements quantified and previously reported in wines made from 2015 vintage, including twenty-four elements reported in both vintages. The composition of each element was analyzed by analysis of variance with main effect of vineyard. Wines were classified according to vineyard origin and environmental growing site with a combination of factors correlated with the wine elemental profile. The low variability (< 25%) of certain elements in wines from at least eight sites across both vintages, including Group 1 (Cs, K, Na and Rb), Group 2 (Ba, Ca, Mg and Sr), Group 3B (Eu), Group 13 (Al, B and Ga), Group 15 (As and P) and Co, Fe, Mn, Ni and V, demonstrated the reproducibility over the seasons analyzed (2015 and 2016). The comparison of elemental profile of wines across growing seasons demonstrates the opportunity to reproduce one key aspect of wine chemistry across vintages.

Vineyard site impact on the elemental composition of Pinot noir wines.

Elemental composition was used to characterize and differentiate 14 wines made from the identical clone of Vitis vinifera cv. Pinot noir (clone 667). The vineyards span distances which range from several hundred meters to 1540 km and their elevations vary from near sea level to nearly 500 m. Twenty-seven elements were observed above the limit of quantitation by using inductively coupled plasma mass spectrometry (ICP-MS) in the wines from at least half of the 14 sites. Concentrations of several elements, including Mo, Er, Na, Li, Cs and Pb, varied by 10-fold across the 14 wines. Multiple factor analysis (MFA) of elemental composition with juice chemistry and site characterization show associations consistent with expectations, such as high Ca with high clay content. These results demonstrate that even when grapevine clone and winemaking protocol are controlled, composition differences in wines produced from sites are mediated by diverse soil and microclimate conditions.

Exploratory Factor Analysis of NRG Oncology's University of Washington Quality of Life Questionnaire-RTOG Modification.

CONTEXT: The 15-item University of Washington Quality of Life questionnaire-Radiation Therapy Oncology Group (RTOG) modification (UW-QOL-RTOG modification) has been used in several trials of head and neck cancer conducted by NRG Oncology such as RTOG 9709, RTOG 9901, RTOG 0244, and RTOG 0537. OBJECTIVES: This study is an exploratory factor analysis (EFA) to establish validity and reliability of the instrument subscales. METHODS: EFA on the UW-QOL-RTOG modification was conducted using baseline data from NRG Oncology's RTOG 0537, a trial of acupuncture-like transcutaneous electrical nerve stimulation in treating radiation-induced xerostomia. Cronbach α coefficient was calculated to measure reliability; correlation with the University of Michigan Xerostomia Related Quality of Life Scale was used to evaluate concurrent validity; and correlations between consecutive time points were used to assess test-retest reliability. RESULTS: The 15-item EFA of the modified tool resulted in 11 items split into four factors: mucus, eating, pain, and activities. Cronbach α ranged from 0.71 to 0.93 for the factors and total score, consisting of all 11 items. There were strong correlations (ρ ≥ 0.60) between consecutive time points and between total score and the Xerostomia Related Quality of Life Scale total score (ρ > 0.65). CONCLUSION: The UW-QOL-RTOG modification is a valid tool that can be used to assess symptom burden of head and neck cancer patients receiving radiation therapy or those who have recently completed radiation. The modified tool has acceptable reliability, concurrent validity, and test-retest reliability in this patient population, as well as the advantage of having being shortened from 15 to 11 items.

Whole-abdomen radiotherapy for non-Hodgkin's lymphoma using twice-daily fractionation.

PURPOSE: To report the tolerability and efficacy of twice-daily whole-abdomen irradiation (WAI) for non-Hodgkin's lymphoma (NHL). METHODS AND MATERIALS: Of 123 patients treated for NHL with WAI, 37% received previous chemotherapy, 28% received WAI as part of comprehensive lymphatic irradiation (CLI), and 32% received WAI for palliation. The median dose to the whole abdomen was 25.0 Gy, followed by a median tumor boost of 9.8 Gy in 58 patients. Fractionation was 1.0 Gy once daily (54%) or 0.8 Gy twice daily (46%). Blood counts were measured weekly. RESULTS: At a median follow-up of 4.3 years, local control was 72% and overall survival was 55% at 5 years. Median time of WAI was 42 days for once-daily treatment and 32 days for twice-daily treatment. Patients receiving twice-daily WAI did not have a significantly higher rate of acute side effects (e.g., nausea, diarrhea, platelet or red blood cell toxicity). Overall, acute thrombocytopenia was the most frequent side effect of treatment; 24 of 96 patients (25%) with available hematologic data had Grade 3+ toxicity. There was no acute Grade 3 gastrointestinal toxicity and no late small bowel obstruction. Multiple regression indicated that patients with four or less involved sites and disease size < or =6 cm had improved local control and overall survival. CONCLUSIONS: Twice-daily WAI using 0.8 Gy/fraction does not appear to have any greater toxicity compared with once-daily treatment using 1 Gy/fraction. Small doses per fraction (0.8-1 Gy/fx) are effective, tolerated well in the acute setting, and associated with a low rate of late toxicity.

Overview of BioCreAtIvE: critical assessment of information extraction for biology.

BACKGROUND: The goal of the first BioCreAtIvE challenge (Critical Assessment of Information Extraction in Biology) was to provide a set of common evaluation tasks to assess the state of the art for text mining applied to biological problems. The results were presented in a workshop held in Granada, Spain March 28-31, 2004. The articles collected in this BMC Bioinformatics supplement entitled "A critical assessment of text mining methods in molecular biology" describe the BioCreAtIvE tasks, systems, results and their independent evaluation. RESULTS: BioCreAtIvE focused on two tasks. The first dealt with extraction of gene or protein names from text, and their mapping into standardized gene identifiers for three model organism databases (fly, mouse, yeast). The second task addressed issues of functional annotation, requiring systems to identify specific text passages that supported Gene Ontology annotations for specific proteins, given full text articles. CONCLUSION: The first BioCreAtIvE assessment achieved a high level of international participation (27 groups from 10 countries). The assessment provided state-of-the-art performance results for a basic task (gene name finding and normalization), where the best systems achieved a balanced 80% precision / recall or better, which potentially makes them suitable for real applications in biology. The results for the advanced task (functional annotation from free text) were significantly lower, demonstrating the current limitations of text-mining approaches where knowledge extrapolation and interpretation are required. In addition, an important contribution of BioCreAtIvE has been the creation and release of training and test data sets for both tasks. There are 22 articles in this special issue, including six that provide analyses of results or data quality for the data sets, including a novel inter-annotator consistency assessment for the test set used in task 2.

Overview of BioCreAtIvE task 1B: normalized gene lists.

BACKGROUND: Our goal in BioCreAtIve has been to assess the state of the art in text mining, with emphasis on applications that reflect real biological applications, e.g., the curation process for model organism databases. This paper summarizes the BioCreAtIvE task 1B, the "Normalized Gene List" task, which was inspired by the gene list supplied for each curated paper in a model organism database. The task was to produce the correct list of unique gene identifiers for the genes and gene products mentioned in sets of abstracts from three model organisms (Yeast, Fly, and Mouse). RESULTS: Eight groups fielded systems for three data sets (Yeast, Fly, and Mouse). For Yeast, the top scoring system (out of 15) achieved 0.92 F-measure (harmonic mean of precision and recall); for Mouse and Fly, the task was more difficult, due to larger numbers of genes, more ambiguity in the gene naming conventions (particularly for Fly), and complex gene names (for Mouse). For Fly, the top F-measure was 0.82 out of 11 systems and for Mouse, it was 0.79 out of 16 systems. CONCLUSION: This assessment demonstrates that multiple groups were able to perform a real biological task across a range of organisms. The performance was dependent on the organism, and specifically on the naming conventions associated with each organism. These results hold out promise that the technology can provide partial automation of the curation process in the near future.

BioCreAtIvE task 1A: gene mention finding evaluation.

BACKGROUND: The biological research literature is a major repository of knowledge. As the amount of literature increases, it will get harder to find the information of interest on a particular topic. There has been an increasing amount of work on text mining this literature, but comparing this work is hard because of a lack of standards for making comparisons. To address this, we worked with colleagues at the Protein Design Group, CNB-CSIC, Madrid to develop BioCreAtIvE (Critical Assessment for Information Extraction in Biology), an open common evaluation of systems on a number of biological text mining tasks. We report here on task 1A, which deals with finding mentions of genes and related entities in text. "Finding mentions" is a basic task, which can be used as a building block for other text mining tasks. The task makes use of data and evaluation software provided by the (US) National Center for Biotechnology Information (NCBI). RESULTS: 15 teams took part in task 1A. A number of teams achieved scores over 80% F-measure (balanced precision and recall). The teams that tried to use their task 1A systems to help on other BioCreAtIvE tasks reported mixed results. CONCLUSION: The 80% plus F-measure results are good, but still somewhat lag the best scores achieved in some other domains such as newswire, due in part to the complexity and length of gene names, compared to person or organization names in newswire.

Data preparation and interannotator agreement: BioCreAtIvE task 1B.

BACKGROUND: We prepared and evaluated training and test materials for an assessment of text mining methods in molecular biology. The goal of the assessment was to evaluate the ability of automated systems to generate a list of unique gene identifiers from PubMed abstracts for the three model organisms Fly, Mouse, and Yeast. This paper describes the preparation and evaluation of answer keys for training and testing. These consisted of lists of normalized gene names found in the abstracts, generated by adapting the gene list for the full journal articles found in the model organism databases. For the training dataset, the gene list was pruned automatically to remove gene names not found in the abstract; for the testing dataset, it was further refined by manual annotation by annotators provided with guidelines. A critical step in interpreting the results of an assessment is to evaluate the quality of the data preparation. We did this by careful assessment of interannotator agreement and the use of answer pooling of participant results to improve the quality of the final testing dataset. RESULTS: Interannotator analysis on a small dataset showed that our gene lists for Fly and Yeast were good (87% and 91% three-way agreement) but the Mouse gene list had many conflicts (mostly omissions), which resulted in errors (69% interannotator agreement). By comparing and pooling answers from the participant systems, we were able to add an additional check on the test data; this allowed us to find additional errors, especially in Mouse. This led to 1% change in the Yeast and Fly "gold standard" answer keys, but to an 8% change in the mouse answer key. CONCLUSION: We found that clear annotation guidelines are important, along with careful interannotator experiments, to validate the generated gene lists. Also, abstracts alone are a poor resource for identifying genes in paper, containing only a fraction of genes mentioned in the full text (25% for Fly, 36% for Mouse). We found that there are intrinsic differences between the model organism databases related to the number of synonymous terms and also to curation criteria. Finally, we found that answer pooling was much faster and allowed us to identify more conflicting genes than interannotator analysis.

Accessible gold clusters using calix[4]arene N-heterocyclic carbene and phosphine ligands.

We investigate the synthesis of accessible calix[4]arene-bound gold clusters consisting of open "coordinatively unsaturated" active sites, using a comparative approach that relies on calix[4]arene ligands with various upper- and lower-rim substituents. In contrast with a reported Au(I)-tert-butyl-calixarene phosphine complex, which exhibits a single cone conformer in solution, the H upper-rim analog exhibits multiple conformers in solution. This contrasts with observations of the tert-butyl upper-rim analog, which exhibits a single cone conformer in solution under similar conditions. In the solid state, as determined by single-crystal X-ray diffraction, both H and tert-butyl upper-rim analogs exhibit exclusively cone conformer. A detailed structural analysis of these two solid-state structures highlights a CH-π interaction involving a methoxy lower-rim substituent and phenyl substituent on P as the key feature that enforces a tight configuration of Au(I) atoms on the same side of the calix[4]arene lower-rim plane. We hypothesize that such a configuration promotes chelation of the ligand to a gold surface and facilitates the synthesis of small Au11-sized clusters after reduction of both complexes. The new cluster, like the one reported with the tert-butyl analog, has an extraordinary 25% of surface atoms that are open and accessible to a 2-NT (2-naphthalenethiol) probe in solution. We also investigated the effect of calix[4]arene lower-rim substituents that coordinate to the metal, by using N-heterocyclic carbene (NHC) functional groups rather than phosphines. Four small (<1.6 nm diameter) calix[4]arene NHC-bound gold clusters were synthesized, including three using novel calix[4]arene NHC ligands. The smallest calix[4]arene NHC-bound Au cluster consisted of a 1.2 nm gold core, and its number density of accessible and open surface sites was measured. This required development of a new titration method for open sites on gold clusters, using a SAMSA fluorescein dye molecule, which excites and emits at lower energy relative to the previously used 2-NT probe. The number density of open sites on the new calix[4]arene NHC-bound gold cluster measured by the SAMSA fluorescein probe strongly supports the generality of a mechanical model of accessibility, which does not depend on the functional group involved in binding to the gold surface and rather depends on the relative radii of curvature of bound ligands and the gold cluster core.

MITRE system for clinical assertion status classification.

OBJECTIVE: To describe a system for determining the assertion status of medical problems mentioned in clinical reports, which was entered in the 2010 i2b2/VA community evaluation 'Challenges in natural language processing for clinical data' for the task of classifying assertions associated with problem concepts extracted from patient records. MATERIALS AND METHODS: A combination of machine learning (conditional random field and maximum entropy) and rule-based (pattern matching) techniques was used to detect negation, speculation, and hypothetical and conditional information, as well as information associated with persons other than the patient. RESULTS: The best submission obtained an overall micro-averaged F-score of 0.9343. CONCLUSIONS: Using semantic attributes of concepts and information about document structure as features for statistical classification of assertions is a good way to leverage rule-based and statistical techniques. In this task, the choice of features may be more important than the choice of classifier algorithm.

Site-specific S-glutathiolation of mitochondrial NADH ubiquinone reductase.

The generation of reactive oxygen species in mitochondria acts as a redox signal in triggering cellular events such as apoptosis, proliferation, and senescence. Overproduction of superoxide (O2*-) and O2*--derived oxidants changes the redox status of the mitochondrial GSH pool. An electron transport protein, mitochondrial complex I, is the major host of reactive/regulatory protein thiols. An important response of protein thiols to oxidative stress is to reversibly form protein mixed disulfide via S-glutathiolation. Exposure of complex I to oxidized GSH, GSSG, resulted in specific S-glutathiolation at the 51 kDa and 75 kDa subunits (Beer et al. (2004) J. Biol. Chem. 279, 47939-47951). Here, to investigate the molecular mechanism of S-glutathiolation of complex I, we prepared isolated bovine complex I under nonreducing conditions and employed the techniques of mass spectrometry and EPR spin trapping for analysis. LC/MS/MS analysis of tryptic digests of the 51 kDa and 75 kDa polypeptides from glutathiolated complex I (GS-NQR) revealed that two specific cysteines (C206 and C187) of the 51 kDa subunit and one specific cysteine (C367) of the 75 kDa subunit were involved in redox modifications with GS binding. The electron transfer activity (ETA) of GS-NQR in catalyzing NADH oxidation by Q1 was significantly enhanced. However, O2*- generation activity (SGA) mediated by GS-NQR suffered a mild loss as measured by EPR spin trapping, suggesting the protective role of S-glutathiolation in the intact complex I. Exposure of NADH dehydrogenase (NDH), the flavin subcomplex of complex I, to GSSG resulted in specific S-glutathiolation on the 51 kDa subunit. Both ETA and SGA of S-glutathiolated NDH (GS-NDH) decreased in parallel as the dosage of GSSG increased. LC/MS/MS analysis of a tryptic digest of the 51 kDa subunit from GS-NDH revealed that C206, C187, and C425 were glutathiolated. C425 of the 51 kDa subunit is a ligand residue of the 4Fe-4S N3 center, suggesting that destruction of 4Fe-4S is the major mechanism involved in the inhibition of NDH. The result also implies that S-glutathiolation of the 75 kDa subunit may play a role in protecting the 4Fe-4S cluster of the 51 kDa subunit from redox modification when complex I is exposed to redox change in the GSH pool.

Direct and indirect roles of cytochrome b in the mediation of superoxide generation and NO catabolism by mitochondrial succinate-cytochrome c reductase.

Mitochondrial superoxide (O2*-) production is an important mediator of oxidative cellular injury. Succinate-cytochrome c reductase (SCR) of the electron transport chain has been implicated as an essential part of the mediation of O2*- generation and an alternative target of nitric oxide (NO) in the regulation of mitochondrial respiration. The Q cycle mechanism plays a central role in controlling both events. In the present work, O2*- generation by SCR was measured with the EPR spin-trapping technique using DEPMPO (5-diethoxylphosphoryl-5-methyl-1-pyrroline N-oxide) as the spin trap. In the presence of succinate, O2*- generation from SCR was detected as the spin adduct DEPMPO/*OOH. Inhibitors of the Q(o*-) site only marginally reduced (20-30%) this O2*- production, suggesting a secondary role of Q(o*-) in the mediation of O2*- generation. Addition of cyanide significantly decreased (approximately 70%) O2*- production, indicating the involvement of the heme component. UV-visible spectral analysis revealed that oxidation of ferrocytochrome b was accompanied by cytochrome c(1) reduction, and the reaction was mediated by the formation of an O2*- intermediate, indicating a direct role for cytochrome b in O2*- generation. In the presence of NO, DEPMPO/*OOH production was progressively diminished, implying that NO interacted with SCR or trapped the O2*-. The consumption of NO by SCR was investigated by electrochemical detection using an NO electrode. In the presence of succinate, SCR-mediated NO consumption was observed and inhibited by the addition of superoxide dismutase, suggesting the involvement of O2*-. Under the conditions of argon saturation, the NO consumption rate was not enhanced by succinate, suggesting a direct role for O2*- in the mediation of NO consumption. In the presence of succinate, oxidation of the ferrocytochrome b moiety of SCR was accelerated by the addition of NO, and was inhibited by argon saturation, indicating an indirect role for cytochrome b in the mediation of NO consumption.

Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup.

MOTIVATION: The biological literature is a major repository of knowledge. Many biological databases draw much of their content from a careful curation of this literature. However, as the volume of literature increases, the burden of curation increases. Text mining may provide useful tools to assist in the curation process. To date, the lack of standards has made it impossible to determine whether text mining techniques are sufficiently mature to be useful. RESULTS: We report on a Challenge Evaluation task that we created for the Knowledge Discovery and Data Mining (KDD) Challenge Cup. We provided a training corpus of 862 articles consisting of journal articles curated in FlyBase, along with the associated lists of genes and gene products, as well as the relevant data fields from FlyBase. For the test, we provided a corpus of 213 new ('blind') articles; the 18 participating groups provided systems that flagged articles for curation, based on whether the article contained experimental evidence for gene expression products. We report on the evaluation results and describe the techniques used by the top performing groups.