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PubMed1977

Neonatal scalp abscess following intrapartum fetal monitoring: prospective comparison of two spiral electrodes.

During a six-month period, 929 newborn infants had continuous, direct fetal heart rate monitoring during labor. Of these, 481 were monitored with the Berkeley Bio-Electronics spiral electrode and 448 were monitored with the Corometrics spiral electrode. The over-all incidence of scalp abscess complicating fetal monitoring was 4.5 per cent. In the group monitored with the Berkeley electrode, 25 newborn infants (5.2 per cent) developed a scalp abscess; in the group with the Corometrics electrode, 17 newborn infants (3.8 per cent) developed scalp abscess. The incidence of scalp abscess was not significantly different in the two groups.

Abscess↗
PubMed1978

Analysis of the pigment content of an antenna pigment-protein complex from three strains of Rhodopseudomonas sphaeroides.

The pigment content of a B800-850 light-harvesting pigment-protein complex isolated from three different stains of Rhodopseudomonas sphaeroides has been determined. In each case the ratio of carotenoid to bacteriochlorophyll present is very nearly 1 : 3 an no specificity with regard to carotenoid type was observed. The fourth derivative of the infra-red absorption bands of the complex was determined and it is concluded that the minimal functional unit of B800-850 complex consists of 1 carotenoid molecule and three bacteriochlorophyll molecules. The data presented here, together with the previous study of Austin, (Austin, L.A. (1976) Ph.D. Thesis, University of California at Berkeley, Lawrence Berkeley Laboratory Report No. LBL 5512) suggest that the 800 nm absorption band represents one of these bacteriochlorophyll molecules while the remaining two bacteriochlorophylls are responsible for the 850 nm band. The absorption spectra and circular dichroism spectra of the complexes suggests that their structure has not been greatly altered during the purification.

Bacterial Chromatophores↗
PubMed1990

Detection of induced mitotic chromosome loss in Saccharomyces cerevisiae--an interlaboratory assessment of 12 chemicals.

Induced mitotic chromosome loss was assayed using diploid yeast strain S. cerevisiae D61.M. The test relies upon the uncovering and expression of multiple recessive markers reflecting the presumptive loss of the chromosome VII homologue carrying the corresponding wild-type alleles. An interlaboratory study was performed in which 12 chemicals were tested under code in 2 laboratories. The results generated by the Berkeley and the Darmstadt laboratories were in close agreement. The solvents benzonitrile and methyl ethyl ketone induced significantly elevated chromosome loss levels. However, a treatment regime that included overnight storage at 0 degree C was required to optimize chromosome loss induction. Hence, these agents are postulated to induce chromosome loss via perturbation of microtubular assembly. Fumaronitrile yielded inconsistent results: induction of chromosome loss and respiratory deficiency was observed in both laboratories, but the response was much more pronounced in the Darmstadt trial than that observed in Berkeley. The mammalian carcinogens, benzene, acrylonitrile, trichloroethylene, 1,1,1-trichloroethane and 1,1,1,2-tetrachloroethane failed to induce chromosome loss but elicited high levels of respiratory deficiency, reflecting anti-mitochondrial activity. Trifluralin, cyclophosphamide monohydrate, diazepam and diethylstilbestrol dipropionate failed to induce any detectable genetic effects. These data suggest that the D61.M system is a reproducible method for detecting induced chromosome loss in yeast.

Alleles↗
PubMed1994

Estimation of risk based on multiple events in radiation carcinogenesis of rat skin.

In the multistage theory of carcinogenesis, cells progress to cancer through a series of discrete, irreversible, heritable genetic alterations or mutations. However data on radiation-induced cancer incidence in rat skin suggests that some part of an intermediate repairable alteration may occur. Data are presented on cancer induction in rat skin exposed to the following radiations: 1. an electron beam (LET=0.34 keV/um, 2. a neon ion beam (LET=25 keV/um and 3. an argon ion beam (LET=125 keV/um. The latter 2 beams were generated by the Bevalac at the Lawrence Berkeley Laboratory, Berkeley, CA. About 6.0 cm2 of skin was irradiated per rat. The rats were observed every 6 weeks for at least 78 weeks and tumors were scored at first occurrence. Several histological types of cancer, including squamous and basal cell carcinomas, were induced. The cancer yield versus radiation dose was fitted by the quadratic equation (Y(D)=CLD+BD2), and the parameters C and B were estimated for each type of radiation. Analysis of the DNA from the electron-induced carcinomas indicated that K-ras and/or c-myc oncogenes were activated in all tumors tested, although only a small proportion of neon-induced tumors showed similar activation. In situ hybridization indicated that the cancers contain subpopulations of cells with differing amounts of c-myc and H-ras amplification. The results are consistent with the idea that ionizing radiation produces carcinogenically relevant lesions via 2 repairable events at low LET and via a non-repairable, linked event pathway at high LET; either pathway may advance the cell by 1 stage in the multistage model. The model, if validated, permits the direct calculation of cancer risk in rat skin in a way that can be subjected to experimental testing.

Animals↗
PubMed1994

Experience in charged particle irradiation of tumors of the skull base: 1977-1992.

PURPOSE: To review the experience at University of California Lawrence Berkeley Laboratory in using charged particles to irradiate primary neoplasms of the skull base and those extending to the skull base from the nasopharynx and paranasal sinuses. METHODS AND MATERIALS: During the period from 1977 to 1992, 223 patients were irradiated with charged particles at the Lawrence Berkeley Laboratory for tumors either arising in or extending to the skull base, of whom 48 (22%) had recurrent lesions, either post previous surgery or radiotherapy. One hundred twenty-six patients had lesions arising in the cranial base, mostly chordoma (53), chondrosarcoma (27), paraclival meningioma (27) with 19 patients having other histologies such as osteosarcoma or neurofibrosarcoma. There were also 31 patients with primary or recurrent squamous carcinoma of the nasopharynx extending to the skull base, 44 patients with major or minor salivary gland tumors, mostly adenocarcinoma, and 22 patients with squamous carcinoma of the paranasal sinuses, all with cranial base extension. RESULTS: Local control and survival appeared improved in tumors arising in the skull base, following the ability with charged particles to deliver high doses (mean of 65 Gy-equivalent) with relative sparing of the adjacent normal tissues. The Kaplan-Meier 5-year local control was 85% for meningioma, 78% for chondrosarcoma, 63% for chordoma and 58% for other sarcoma. Follow-up ranged from 4-191 months with a median of 51 months. CONCLUSION: Charged particle radiotherapy is highly effective in controlling cranial base lesions which have have been partially resected. Better tumor localization with CT and MRI, improved 3-D treatment planning and beam delivery techniques have continued to reduce the level of serious complications and increase local control and survival.

Female↗
PubMed2005

Q & A. [interview].

George Oster is Professor of Biophysics, University of California, Berkeley. He received his B.S. at the U.S. Merchant Marine Academy and his Ph.D. at Columbia University. He began his career in biophysics as a postdoc at the Weizmann Institute under Aharon Katchalsky, where his research involved membrane biophysics and irreversible thermodynamics. His concern for environmental issues led him into population biology, which shaded into evolutionary biology and thence to developmental biology, cell biology and, most recently, protein motors and bacterial motility and pattern formation. His tools are mathematics, physics and computer simulation. He is currently a faculty member in the Departments of Molecular and Cellular Biology and the College of Natural Resources at Berkeley.

Bacteria↗
PubMed2005

Q & A. [interview].

Elaine and Gary Ostrander spent their youth in New Jersey and New York before heading to Nebraska for their teen years and eventually Washington State for High School and college, as their father moved around in library administration. Elaine was an undergraduate at the University of Washington, a graduate student at the Oregon Health Sciences University and a postdoc with James Wang at Harvard, studying DNA supercoiling. She next went to Berkeley, where she began the canine genome project, initiating the meiotic linkage map and working on human chromosome 21 at the Lawrence Berkeley National Labs. In 1993 she moved to the Fred Hutchinson Cancer Research Center where she is now a Member of the Divisions of Clinical Research and Human Biology. She is also an Affiliate Professor of Genome Sciences and Biology at the University of Washington, and heads the Program in Genetics at the Hutchinson Center. Gary completed his undergraduate degree in Biology at Seattle University, a M.S. degree at Illinois State University and a Ph.D at the University of Washington in Ocean and Fisheries Science. He went on to be a postdoc in the Department of Pathology at the University of Washington Medical School while being mentored by Senitroh Hakomori of the Fred Hutchinson Cancer Research Center and Eric Holmes of the Pacific Northwest Research Foundation. His work focused on using novel aspects of the biology of fishes to address fundamental questions about cancer. He subsequently held both faculty and administrative positions at Oklahoma State University. Since 1996, he has been at the Johns Hopkins University, where he currently holds academic appointments in the Departments of Biology and Comparative Medicine and is the Associate Provost for Research.

Biomedical Research↗
PubMed2025

The Elements of Life, Photosynthesis and Genomics.

I am a Professor of Biochemistry, Biophysics and Structural Biology and Plant and Microbial Biology at the University of California in Berkeley. I was born and raised in India, emigrated to the United States to attend university, earning a B.S. in Molecular Biology and a Ph.D. in Biochemistry at the University of Wisconsin in Madison. Following post-doctoral studies with Lawrence Bogorad at Harvard University where I became interested in genetic control of trace element quotas, I joined the department of Chemistry and Biochemistry at UCLA. One of the first to appreciate essential trace metals as potential regulators of gene expression, I articulated the details of the nutritional Cu regulon in Chlamydomonas. In parallel, I used genetic approaches to discover the genes governing missing steps in tetrapyrrole metabolism, including the attachment of heme to apocytochromes in the thylakoid lumen and the factors catalyzing the formation of ring V in chlorophyll. After biochemistry and classical genetics, I embraced genomics, taking a leadership role on the Joint Genome Institute's efforts on the Chlamydomonas genome and more recently, contributing to high quality assemblies of several genomes in the green algal radiation, and large transcriptomic and proteomic datasets - focusing on the diel metabolic cycle in synchronized cultures and acclimation to key environmental and nutritional stressors - that are well-used and appreciated by the community. A new venture in Berkeley is the promotion of Auxenochlorella protothecoides as the true "green yeast" and as a platform for engineering algae to produce useful bioproducts.

Photosynthesis↗
PubMed2005

The importance in fishery management of leaving the big ones.

Research by Berkeley et al. and by Bobko and Berkeley has recently demonstrated that older individuals of some fish species produce larvae that have substantially better survival potential than do larvae from younger fishes. These new findings augment established knowledge that larger individuals usually have exponentially greater fecundity. This is important because commercial fisheries and especially recreational fishing often target the larger fish. The protection of larger or older individuals is necessary for the sustainability of species currently exploited by humans.

Journal Article↗
PubMed2003

Spreading disease: integro-differential equations old and new.

We investigate an integro-differential equation for a disease spread by the dispersal of infectious individuals and compare this to Mollison's [Adv. Appl. Probab. 4 (1972) 233; D. Mollison, The rate of spatial propagation of simple epidemics, in: Proc. 6th Berkeley Symp. on Math. Statist. and Prob., vol. 3, University of California Press, Berkeley, 1972, p. 579; J. R. Statist. Soc. B 39 (3) (1977) 283] model of a disease spread by non-local contacts. For symmetric kernels with moment generating functions, spreading infectives leads to faster traveling waves for low rates of transmission, but to slower traveling waves for high rates of transmission. We approximate the shape of the traveling waves for the two models using both piecewise linearization and a regular-perturbation scheme.

Communicable Diseases↗
PubMed2002

Profile--Richard A. Mathies. Interview by Suzanne Berry.

Richard A. Mathies (Fig. 1) is a professor of chemistry at the University of California (UC) at Berkeley. His early work at UC was on the use of resonance Raman and time-resolved optical spectroscopy to elucidate the structure and reaction dynamics of energy and information-transducing photoactive proteins called rhodopsins. His work on the Human Genome Project led to the development of high-throughput platform technologies including capillary array electrophoresis and energy transfer fluorescent dye labels for DNA sequencing and analysis. He has also pioneered the development of microfabricated capillary electrophoresis devices, capillary array electrophoresis microplates and microfabriated integrated sample preparation and detection methods. He is the co-founder of the Center for Analytical Biotechnology at UC Berkeley. Mathies was interviewed at the BIOMEMS and Biomedical Nanotechnology conference in Columbus, Ohio, 21-25 September 2001, where he gave a talk about capillary array electrophoresis-based microprocessors. Such devices could be used as point-of-care clinical and genetic analyzers, in integrated microfluidic sequencing chips and in DNA-based computing.

Awards and Prizes↗
PubMed2001

Lensless imaging: a workshop on "new approaches to the phase problem for non-periodic objects.".

Over the past two decades, theoretical tools and algorithms have been developed which, under not very restrictive conditions, allow the reconstruction of images from diffraction patterns of non-periodic objects. These methods promise lensless imaging for any radiation, free of aberrations, with wavelength-limited resolution. Recent experimental successes prompted an interdisciplinary international workshop on this topic at the Lawrence Berkeley National Laboratory, Berkeley, CA, USA, on May 17-19 2001, supported by the DOE, LBL and the Advanced Light Source. Our aim was to review the field, and to stimulate communication between the Signal Recovery, Coherent Optics, X-ray, Electron Microscopy and Applied Mathematics communities. The results are summarized in this paper and on the web. A second workshop is planned for 2003.

Journal Article↗
PubMedDate not supplied

Survival following alpha particle pituitary irradiation for diabetic retinopathy.

The purpose of this study was to evaluate the mortality experience of persons with longstanding diabetes who had received pituitary irradiation for diabetic retinopathy compared to a matched group of persons with diabetes who had not had pituitary ablation. The irradiated cohort consisted of 167 patients treated at the Donner Pavilion (Lawrence Berkeley Laboratory, University of California, Berkeley), and the comparison cohort was the population evaluated in the Wisconsin Epidemiologic Study of Diabetic Retinopathy (WESDR). Survival analyses were performed comparing the two cohorts using three different sets of matching criteria, each more restrictive than the previous analyses. The three different strategies were (1) matched only on severity of diabetic retinopathy; (2) matched on severity of retinopathy and age; and (3) matched on severity of retinopathy, age, gender, and hypertension status. Tests of comparison were the log-rank test, the Wilcoxon test, and the likelihood ratio test. For the model matching only on severity of retinopathy, mean survival was 8.3 years for the WESDR group and 9.4 years for the ablated group (p > 0.05 for all three statistical tests). For the model matched on retinopathy and age, mean survival was 8.9 years for the WESDR group and 9.2 years for the ablated group (p=0.05 log-rank test, 0.32 Wilcoxon test, and 0.06 likelihood ratio test). For the model matching on retinopathy, age, gender, and hypertension status, mean survival was 8.9 years for the WESDR group and 11.6 years for the ablated group (p=0.72 log-rank test, 0.08 Wilcoxon test, and 0.82 likelihood ratio test). These data are compatible with the notion that pituitary ablation, and therefore induced pituitary growth hormone deficiency, may not decrease survival in those with severe diabetic retinopathy.

Adult↗
PubMed2003

Structure-based functional inference in structural genomics.

The dramatically increasing number of new protein sequences arising from genomics and proteomics requires the need for methods to rapidly and reliably infer the molecular and cellular functions of these proteins. One such approach, structural genomics, aims to delineate the total repertoire of protein folds in nature, thereby providing three-dimensional folding patterns for all proteins and to infer molecular functions of the proteins based on the combined information of structures and sequences. The goal of obtaining protein structures on a genomic scale has motivated the development of high throughput technologies and protocols for macromolecular structure determination that have begun to produce structures at a greater rate than previously possible. These new structures have revealed many unexpected functional inferences and evolutionary relationships that were hidden at the sequence level. Here, we present samples of structures determined at Berkeley Structural Genomics Center and collaborators' laboratories to illustrate how structural information provides and complements sequence information to deduce the functional inferences of proteins with unknown molecular functions. Two of the major premises of structural genomics are to discover a complete repertoire of protein folds in nature and to find molecular functions of the proteins whose functions are not predicted from sequence comparison alone. To achieve these objectives on a genomic scale, new methods, protocols, and technologies need to be developed by multi-institutional collaborations worldwide. As part of this effort, the Protein Structure Initiative has been launched in the United States (PSI; www.nigms.nih.gov/funding/psi.html). Although infrastructure building and technology development are still the main focus of structural genomics programs, a considerable number of protein structures have already been produced, some of them coming directly out of semiautomated structure determination pipelines. The Berkeley Structural Genomics Center (BSGC) has focused on the proteins of Mycoplasma or their homologues from other organisms as its structural genomics targets because of the minimal genome size of the Mycoplasmas as well as their relevance to human and animal pathogenicity (http://www.strgen.org). Here we present several protein examples encompassing a spectrum of functional inferences obtainable from their three-dimensional structures in five situations, where the inferences are new and testable, and are not predictable from protein sequence information alone.

Adenosine Triphosphate↗
PubMed2003

Advances in biotreatment of acid mine drainage and biorecovery of metals: 1. Metal precipitation for recovery and recycle.

Acid mine drainage (AMD), an acidic metal-bearing wastewater, poses a severe pollution problem attributed to post mining activities. The metals usually encountered in AMD and considered of concern for risk assessment are arsenic, cadmium, iron, lead, manganese, zinc, copper and sulfate. The pollution generated by abandoned mining activities in the area of Butte, Montana has resulted in the designation of the Silver Bow Creek-Butte Area as the largest Superfund (National Priorities List) site in the U.S. This paper reports the results of bench-scale studies conducted to develop a resource recovery based remediation process for the clean up of the Berkeley Pit. The process utilizes selective, sequential precipitation (SSP) of metals as hydroxides and sulfides, such as copper, zinc, aluminum, iron and manganese, from the Berkeley Pit AMD for their removal from the water in a form suitable for additional processing into marketable precipitates and pigments. The metal biorecovery and recycle process is based on complete separation of the biological sulfate reduction step and the metal precipitation step. Hydrogen sulfide produced in the SRB bioreactor systems is used in the precipitation step to form insoluble metal sulfides. The average metal recoveries using the SSP process were as follows: aluminum (as hydroxide) 99.8%, cadmium (as sulfide) 99.7%, cobalt (as sulfide) 99.1% copper (as sulfide) 99.8%, ferrous iron (sulfide) 97.1%, manganese (as sulfide) 87.4%, nickel (as sulfide) 47.8%, and zinc (as sulfide) 100%. The average precipitate purity for metals, copper sulfide, ferric hydroxide, zinc sulfide, aluminum hydroxide and manganese sulfide were: 92.4, 81.5, 97.8, 95.6, 92.1 and 75.0%, respectively. The final produced water contained only calcium and magnesium and both sulfate and sulfide concentrations were below usable water limits. Water quality of this agriculturally usable water met the EPA's gold standard criterion.

Acids↗
PubMed2000

Developmental paths of psychological health from early adolescence to later adulthood.

Developmental paths of psychological health were examined for 236 participants of the Berkeley Growth Study, the Berkeley Guidance Study, and the Oakland Growth Study. A clinician-reported aggregate index, the Psychological Health Index (PHI), based on California Q-Sort ratings, was created for subsets of participants at 14, 18, 30, 40, 50, and 62 years of age. Latent curve analysis was then used to explicate the life span development of psychological health. Psychological health development could be successfully modeled via 2 piecewise latent growth curves. Psychological health appears to be stable in adolescence and to steadily increase from 30 to 62 years of age. A moderately strong positive correlation between the 2 developmental curves indicates that those with greater psychological health in adolescence show more improvement in adult psychological health tend to also. Results illustrate the value of the PHI and the power of latent curve analysis to explicate longitudinal stability and change.

Adolescent↗
PubMed1995

Proton radiobiology, radiosurgery and radiotherapy.

This review briefly traces the historical developments of proton radiobiology, radiosurgery and radiotherapy for the benefit of young researchers and clinicians entering into this field. In preparing to use protons in radiosurgery and radiotherapy, radiobiological effects of protons were studied extensively by various groups, including the University of California at Berkeley, the University of Uppsala, Massachusetts General Hospital, and the Harvard Cyclotron Laboratory. Considerable work on proton radiobiology was also done because protons are a major component of the radiation environment in space. The biological effects of proton beams were found to be quantitatively and qualitatively similar to conventional radiations used in radiotherapy. The relative biological effectiveness (RBE) of protons suitable for large-field radiotherapy, compared with 60Co gamma-rays, is generally in the range 1.0-1.25, and remains the same with depth of penetration, except for the descending portion of the depth-dose curve. Also, unlike other heavier charged particles and neutrons, the RBE of high-energy protons, which are suitable for large-field radiotherapy, compared with 60Co gamma-rays, is generally found to be independent of the fraction size in in vivo experiments. The oxygen enhancement ratio for high-energy protons is not significantly different from that of X-rays. An RBE = 1.1, compared with 60Co gamma-rays, is generally used in the clinical application of protons; however, the radiobiological data on mouse, rat, rabbit and primate suggest that the gastrointestinal tissues may be relatively more sensitive to protons. About 13,000 patients have been treated with protons at about 15 facilities around the world. Nearly half of these patients were neurosurgical patients treated with stereotactic radiosurgery. The pioneering efforts at the Harvard Cyclotron in collaboration with the Massachusetts General Hospital and the Massachusetts Eye and Ear Infirmary were responsible for the development of proton treatment for choroidal melanoma and for the tumours of the skull base and spine. There has been extensive confirmation of these results by other groups, especially the groups at Lawrence Berkeley Laboratory and Paul Scherrer Institute. The first medically dedicated proton facility is in operation at Loma Linda University in California. The construction in the USA of another proton treatment facility at Massachusetts General Hospital has been decided upon, and there are plans for many more worldwide.

Animals↗
PubMedDate not supplied

Comparison of coal mine dust size distributions and calibration standards for crystalline silica analysis.

Since 1982 standard calibration materials recommended for respirable crystalline silica analysis by the Mine Safety and Health Administration (MSHA) P7 Infrared Method and the National Institute for Occupational Safety and Health (NIOSH) X-ray Diffraction (XRD) Analytical Method 7500 have undergone minor changes in size distribution. However, a critical assumption has been made that the crystalline silica in ambient mine atmosphere respirable dust samples has also remained essentially unchanged in particle size distribution. Therefore, this work compared recent particle size distributions of underground coal mine dust and the silica component of these dusts with estimated aerodynamic particle size distributions of calibration standard materials MIN-U-SIL 5, Berkeley 5, and SRM 1878 used by two crystalline silica analysis techniques. Dust impactor sampling data for various locations in 13 underground coal mines were analyzed for the respirable mass median aerodynamic diameters. The data suggest that the MSHA P7 method will underestimate the silica content of the sample by at most 7.4% in the median size range 0.9 to 3.6 microm, and that it is unlikely one would obtain any significant error in the MSHA P7 method analysis when the method uses Berkeley 5, MIN-U-SIL 5, or SRM 1878 as a calibration standard material. The results suggest that the NIOSH Analytical Method 7500 would be more appropriate for a dust sample that is representative of the total (no cyclone classifier) rather than the respirable airborne dust, particularly because the mass fraction in the size range below 4 microm is usually a small percentage of the total airborne dust mass. However, NIOSH Analytical Method 7500 is likely to underestimate the silica content of an airborne respirable dust sample by only 5 to 10%. The results of this study also suggest that any changes that may have occurred in the median respirable size of airborne coal mine dust are not significant enough to cause any appreciable error in the current methods used for respirable crystalline silica analysis.

Coal↗