A review of the International Seabed Authority database DeepData from a biological perspective: challenges and opportunities in the UN Ocean Decade

There is an urgent need for high-quality biodiversity data in the context of rapid environmental change. Nowhere is this need more urgent than in the deep ocean, with the possibility of seabed mining moving from exploration to exploitation, but where vast knowledge gaps persist. Regions of the seabed beyond national jurisdiction, managed by the International Seabed Authority (ISA), are undergoing intensive mining exploration, including the Clarion-Clipperton Zone (CCZ) in the Central Pacific. In 2019, the ISA launched its database 'DeepData', publishing environmental (including biological) data. Here, we explore how DeepData could support biological research and environmental policy development in the CCZ (and wider ocean regions) and whether data are findable, accessible, interoperable and reusable (FAIR). Given the direct connection of DeepData with the regulator of a rapidly developing potential industry, this review is particularly timely. We found evidence of extensive duplication of datasets; an absence of unique record identifiers and significant taxonomic data-quality issues, compromising FAIRness of the data. The publication of DeepData records on the OBIS ISA node in 2021 has led to large-scale improvements in data quality and accessibility. However, limitations in the usage of identifiers and issues with taxonomic information were also evident in datasets published on the node, stemming from mismapping of data from the ISA environmental data template to the data standard Darwin Core prior to data harvesting by OBIS. While notable data-quality issues remain, these changes signal a rapid evolution for the database and significant movement towards integrating with global systems, through the usage of data standards and publication on the global data aggregator OBIS. This is exactly what has been needed for biological datasets held by the ISA. We provide recommendations for the future development of the database to support this evolution towards FAIR. Database URL https://data.isa.org.jm/isa/map.

Pediatric Hodgkin lymphoma: are we over-scanning our patients?

Despite the favorable outcome of most pediatric patients with Hodgkin lymphoma (HL), there is rising concern about risks of carcinogenesis from both diagnostic and therapeutic radiation exposure for patients treated on study protocols. Although previous studies have investigated radiation exposure during treatment, radiation from post-treatment surveillance imaging may also increase the likelihood of secondary malignancies. All diagnostic imaging examinations involving ionizing radiation exposure performed for surveillance following completion of therapy were recorded for 99 consecutive pediatric patients diagnosed with HL from 2000 to 2010. Cumulative radiation dosage from these examinations and the frequency of relapse detection by these examinations were recorded. In the first 2 years following completion of therapy, patients in remission received a median of 11 examinations (range 0-26). Only 13 of 99 patients relapsed, 11 within 5 months of treatment completion. No relapse was detected by 1- or 2-view chest radiographs (n = 38 and 296, respectively), abdomen/pelvis computed tomography (CT) scans (n = 211), or positron emission tomography (PET) scans alone (n = 11). However, 10/391 (2.6%) of chest CT scans, 4/364 (1.1%) of neck CT scans, and 3/47 (6.4%) of PET/CT scans detected relapsed disease. Thus, only 17 scans (1.3%) detected relapse in a total of 1358 scans. Mean radiation dosages were 31.97 mSv for Stage 1, 37.76 mSv for Stage 2, 48.08 mSv for Stage 3, and 51.35 mSv for Stage 4 HL. Approximately 1% of surveillance imaging examinations identified relapsed disease. Given the very low rate of relapse detection by surveillance imaging stipulated by current protocols for pediatric HL patients, the financial burden of the tests themselves, the high cure rate, and risks of second malignancy from ionizing radiation exposure, modification of the surveillance strategy is recommended.

Endogenous knock-down of survival genes improves chemotherapeutic response in a T-ALL cell line

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Background: New targets for more effective, less toxic therapeutic approaches to childhood acute lymphoblastic leukemia (ALL) can be developed by discovering pathways unique to the blast. Using microarray technology, we identified potential target genes that are up-regulated at relapse compared to diagnosis (Blood 2006;108:711–7). Two genes, survivin and securin, were selected for analysis because they are involved in cell cycle regulation, apoptosis and cellular transformation. We hypothesized that decreasing endogenous expression of these genes would increase apoptosis and sensitize cells to chemotherapy. Methods: Short hairpin RNA constructs (shRNA) targeting both transcripts and a control shRNA were engineered. LSN2181295 (sodium salt of LY2181308), an antisense molecule targeting survivin developed by Eli Lilly and its mismatch control (LSN2293329) were also tested. The T- ALL cell line Molt4 was transiently transfected with shRNA constructs or antisense oligos. Western blot and qRT-PCR were performed to determine the time course of target knock-down while apoptosis was assessed by annexin-V labeling. Following transfection, cells were also treated with varying doses of etoposide and doxorubicin for 24 hrs prior to FACS analysis. Results: The survivin and securin shRNAs blocked endogenous gene expression by 80–90%, with maximal effect achieved at 48 hrs. Transfection of Molt4 cells with survivin and securin shRNAs induced ∼13% and 35% apoptosis, respectively, as compared to a control shRNA. When used in combination with chemotherapeutic agents, the shRNA constructs potentiated the effect of both doxorubicin and etoposide at low dosages (≤100 nM and ≤0.4 uM respectively, p values <0.01). The antisense survivin drug had a similar effect as the survivin shRNA and also potentiated the effect of vincristine. Conclusion: Targeting levels of survivin and securin in conjunction with standard chemotherapy maximizes leukemia cell kill and effectively lowers the amount of chemotherapy needed to achieve cell death. Such an approach may improve overall survival for patients at relapse and could also lead to the delivery of effective chemotherapy at less toxic doses.

No significant financial relationships to disclose.

Identification, definition and quantification of goods and services provided by marine biodiversity: implications for the ecosystem approach

This paper identifies and defines ecosystem goods and services provided by marine biodiversity. Case studies have been used to provide an insight into the practical issues associated with the assessment of marine ecosystem goods and services at specific locations. The aim of this research was to validate the definitions of goods and services, and to identify knowledge gaps and likely difficulties of quantifying the goods and services. A validated theoretical framework for the assessment of goods and services is detailed, and examples of the goods and services at a variety of case study areas are documented. These results will enable future assessments of marine ecosystem goods and services. It is concluded that the utilisation of this goods and services approach has the capacity to play a fundamental role in the Ecosystem Approach, by enabling the pressures and demands of society, the economy and the environment to be integrated into environmental management.

Post-haemorrhagic anaemia in sea bass, Dicentrarchus labrax (L.), caused by blood feeding of Ceratothoa oestroides (Isopoda: Cymothoidae)

The effects of the fish parasitic isopod, Ceratothoa oestroides (Risso), on haematological parameters of its cage-cultured sea bass host, Dicentrarchus labrax (L.), were studied. Analyses of blood parameters (cell counts, haemoglobin content and haematocrit) were carried out on parasitized and unparasitized sea bass from a fish farm in Turkey. Parasitized fish had significantly lowered erythrocyte counts, haematocrit and haemoglobin values and significantly increased leucocyte counts. Blood feeding by C. oestroides thus produces a post-haemorrhagic anaemia and the fish appear to mount an immune response to the presence of parasites.

Cymothoid isopod parasites in aquaculture: a review and case study of a Turkish sea bass (Dicentrarchus labrax) and sea bream (Sparus auratus) farm

This paper reviews the occurrence of cymothoid isopod parasitism in aquaculture, reports the first case of infection by a cymothoid isopod (Ceratothoa oestroides) in Turkish aquaculture, and analyses its effects on sea bass Dicentrarchus labrax. Analyses revealed that C. oestroides negatively affects the weights and lengths of sea bass hosts. These effects have been previously underestimated because host age has not been accounted for. The analysis of condition factors as a means of assessing parasite effects is therefore likely to be misleading. Infection of fish of all ages by all cymothoid stages indicates that sea bass are not intermediate hosts but that C. oestroides has effected a complete host shift.

Endocrine regulation of exercise substrate utilization in women compared to men

During low to moderate intensity exercise, women utilize proportionally more lipid and less carbohydrate compared to men. Estrogen and progesterone may have direct effects on these differences by increasing lipolysis and/or constraining glucose production and utilization. Furthermore, sex steroids may have indirect effects through interactions with other hormones, especially catecholamines.

Regulation of macronutrient balance in healthy young and older men

OBJECTIVE

To determine the influence of age on the ability to adjust macronutrient oxidation to changes in diet composition. Our hypothesis was that the ability to adjust macronutrient oxidation to changes in diet composition would be impaired with age.

DESIGN

Cross-sectional, randomized to three different isocaloric diets containing a constant percentage protein but varying in percentage fat and percentage carbohydrate: mixed diet (M; 15/30/55); high-fat diet (HF; 15/60/25), and high-carbohydrate (HC; 15/15/70).

SUBJECTS

Six young (YM; age=25+/-1 y) and five middle-aged and older men (OM; age=63+/-3 y).

MEASUREMENTS

Each subject underwent 24 h whole-room calorimetry on day 4 of each diet to determine 24 h macronutrient oxidation rates. Macronutrient balance was calculated from the individual macronutrient oxidation rates and the corresponding macronutrient intake.

RESULTS

Body mass, percentage fat, and fat-free mass were similar in the two groups. Twenty-four-hour energy expenditure (EE) and energy balance did not differ across diets or between groups; 24 h EE was approximately 7% lower (NS) in the OM. Macronutrient oxidation rates were not significantly different in YM vs OM during M. Protein oxidation was similar across diets, but higher (P<0.05) in OM. Fat oxidation contributed 28.8+/-7.0% vs 37.8+/-4.7% to 24 h EE on M (NS) in the OM vs YM, respectively. This increased to 58.4+/-6.7 vs 51.9+/-5.3% of 24 h EE (NS) in the OM vs YM, respectively, during HF and decreased to 25.4+/-9.7 vs 20.2+/-14.3% (NS) during HC (diet effect, both P<0.05). Carbohydrate oxidation contributed 54.3+/-10.5% vs 56.6+/-2.4% of 24 h EE (NS) on M in the OM vs YM, respectively. This decreased to 19.5+/-10.6 vs 29.9+/-12.6% (NS) during HF and increased to 53.6+/-12.3 vs 64.7+/-14.3% (NS) in the OM vs YM, respectively during HC (diet effect, P<0.05).

CONCLUSION

Taken together, these results suggest that the ability to adjust macronutrient oxidation to changes in diet composition is maintained in OM and, thus, is unlikely to contribute to the increased susceptibility to weight gain and obesity development that accompanies aging.

Injuries to restrained occupants in far-side crashes

Occupants exposed to far-side crashes are those seated on the side of the vehicle opposite the struck side. This study uses the NASS/CDS 1988-98 to determine distributions of AIS 3+ injuries among occupants exposed to far-side crashes and the sources of the injuries. The William Lehman Injury Research Center (WLIRC) data from 1994-98 is used to assess injury mechanisms among seriously injured crash exposed far-side occupants. The NASS/CDS indicated that injury patterns for far-side restrained drivers were different from far-side restrained front passengers. For the driver, the head accounted for 40% of the AIS 3+ injuries in far-side collisions and the chest/abdomen accounted for 45.5%. For the right front passengers, head injuries contributed 27.2%, while chest and abdominal injuries accounted for 64.5%. The opposite-side interior was the most frequent contact associated with driver AIS 3+ injuries (30.5%). The seat belt was second, accounting for 22.6%. Among thirteen WLIRC cases of far-side belted occupants with MAIS 3+ injuries, five of the most serious injuries were attributed to the seat belt. The liver or the spleen was the most seriously injured body organ in all five cases. The seat was the most frequent source of passenger AIS 3+ injuries for the NASS/CDS weighted cases. However, non-contacts, contacts with other occupants, and the seat belt contacts were more frequent sources when considering the raw number of injuries. Overall, contacts with the opposite side of the car interior and with safety belts were the most frequent causes of AIS 3+ injuries in far-side crashes. The presence of an occupant on the near-side changed the injury pattern of the far-side occupant, mitigating injuries from contacts with the opposite side interior of the vehicle.

Dummy measurement of chest injuries induced by two-point shoulder belts

The University of Miami's William Lehman Injury Research Center at the Jackson Memorial Medical Center conducts interdisciplinary investigations to study seriously injured restrained occupants in frontal automobile collisions. Engineering analysis of these crashes is conducted in conjunction with the National Crash Analysis Center at the George Washington University. The multidisciplinary research team includes expertise in crash investigation, crash reconstruction, computer graphics, biomechanics of injuries, crash data analysis, trauma care, and all of the medical specialties associated with the Ryder Trauma Center at Jackson Memorial Hospital. More than 350 injured occupants and their crashes have been studied in depth. The purpose of this paper is to report on an observed pattern of liver lacerations suffered by drivers wearing shoulder belts, without the lap belt fastened and to assess the ability of existing crash test dummies to measure the potential for these injuries. During the initial years of the study, 48 cases of drivers protected by shoulder belts but without the lap belt fastened met the criteria for the study. Fifty percent of these drivers suffered liver lacerations. Further study showed that 22 of the crashes involved damage to the right front of the vehicle. Among the drivers in vehicles with right front damage, 92% sustained injuries to the liver. This observation indicated that 2-point belts were most likely to produce liver injuries in low severity frontal collisions when the crash direction is 1 to 2 o'clock. An analysis of the National Accident Sampling System for the years 1988-95 indicated that liver injuries constitute about 0.5% of the injuries suffered by drivers who are in tow-away crashes. NASS data showed that the risk of chest injury is more likely among drivers with automatic shoulder belts than drivers with 3-point manual belts. The crash test dummies showed no difference in chest injury measures. Finite element computer modeling demonstrated that the high deflection of the right lower rib on the Hybrid III dummy predicts the liver injuries in the 1 o'clock crashes. These higher deflections were less apparent at the location of the center chest deflection measurement device on the Hybrid III.

Apoptosis-specific protein (ASP) identified in apoptotic Xenopus thymus tumor cells

A novel apoptosis-specific protein (ASP) has recently been identified in the cytoplasm of apoptotic mammalian cells. This paper investigates whether ASP is found in Xenopus thymus tumor-derived lymphoid cell lines undergoing apoptosis and also in apoptotic, nontransformed splenocytes. Cultured Xenopus tumor lymphoid cells induced to undergo apoptosis by serum deprivation or treatment with the calcium ionophore, ionomycin, displayed altered morphology typical of apoptotic cells, as judged by flow cytometric light-scatter characteristics and by fluorescence microscopy of acridine-orange-stained cells. Flow cytometry of permeabilized cells and fluorescence microscopy of acetone-fixed cytospins revealed that apoptotic Xenopus tumor cells, especially those displaying loss or condensation of DNA, displayed increased expression of epitopes recognized by a rabbit polyclonal antibody against ASP. Flow cytometry confirmed that ASP is also expressed in splenocytes induced to apoptose by culture in ionomycin or following concanavalin A stimulation. No increased expression of ASP was seen when lymphoid tumor cells or splenocytes were induced into necrosis by overdose with the antifungal agent amphotericin B. Western blotting with antibody against ASP identified the emergence of several protein bands in cell lysates from apoptotic, but not necrotic, Xenopus tumor cells. The new and simple methodology for identifying apoptotic cells described here is likely to be of value to those studying immune system development and associated programmed cell death in Xenopus.

Using clinical laboratory specialists for in-service education: an important aspect of cross training

Cross training of clinical laboratory professionals is on the rise because of hospital mergers and downsizing. Confusion and uncertainty during mergers, plus the added stress of cross training or learning a new "bench" can be overwhelming. Utilizing clinical laboratory specialists to provide continuing education as support for cross training laboratorians can be beneficial to both the laboratory employee and to management. This manuscript describes a model for continuing education support for laboratory personnel returning to the hematology "bench" after many years away from the high complexity level tests in this area of the clinical laboratory. The article addresses the cross-functioning role of laboratory specialists as educators as well as high-level bench technologists. This model for in-service education may serve several purposes, such as documentation for continuing education and personnel competency testing, while giving other laboratorians support for learning new tasks and enhancing their resume.

Diacylglycerol and phosphatidate generated by phospholipases C and D, respectively, have distinct fatty acid compositions and functions. Phospholipase D-derived diacylglycerol does not activate protein kinase C in porcine aortic endothelial cells

Stimulation of cells with certain agonists often activates both phospholipases C and D. These generate diacylglycerol and phosphatidate, respectively, although the two lipids are also apparently interconvertable through the actions of phosphatidate phosphohydrolase and diacylglycerol kinase. Diacylglycerol activates protein kinase C while one role for phosphatidate is the activation of actin stress fiber formation. Therefore, if the two lipids are interconvertable, it is theoretically possible that an uncontrolled signaling loop could arise. To address this issue structural analysis of diacylglycerol, phosphatidate, and phosphatidylbutanol (formed in the presence of butan-1-ol) from both Swiss 3T3 and porcine aortic endothelial cells was performed. This demonstrated that phospholipase C activation generates primarily polyunsaturated species while phospholipase D activation generates saturated/monounsaturated species. In the endothelial cells, where phospholipase D was activated by lysophosphatidic acid independently of phospholipase C, there was no activation of protein kinase C. Thus we propose that only polyunsaturated diacylglycerols and saturated/monounsaturated phosphatidates function as intracellular messengers and that their interconversion products are inactive.

Acquired immune deficiency syndrome. Knowledge, experiences, and attitudes of hospital-based registered nurses

BACKGROUND AND OBJECTIVES

Because of the rapidly increasing number of people affected by acquired immune deficiency syndrome, an increasing number of health care providers are involved. The knowledge, experiences, and attitudes of hospital-based registered nurses can affect the quality and quantity of care provided people with acquired immune deficiency syndrome.

GOALS

To determine the knowledge, experiences, and attitudes about acquired immune deficiency syndrome of registered nurses employed in hospitals in Oklahoma and delineate changes in that knowledge and attitudes over time. This should provide a measure of the preparedness of hospital-based registered nurses in Oklahoma to facilitate initial and continued care of people with acquired immune deficiency syndrome.

STUDY DESIGN

This study surveyed hospital-based registered nurses in Oklahoma in 1986 and again in 1994. In 1986, 75 (51%) of the hospitals and 446 (68% response rate) of the registered nurses participated in the study. In 1994, 85 (53%) of the hospitals and 564 (74% response rate) of the registered nurses participated in the study. The study sample demographics closely matched the state and national populations of hospital-based registered nurses.

RESULTS

The average scores on general and clinical knowledge tests increased significantly from 1986 to 1994. In general, infection control registered nurses had statistically significantly greater knowledge than did registered nurses assigned to other areas of work. However, deficiencies were evident in specific areas of knowledge. The attitudes of registered nurses toward people with acquired immune deficiency syndrome have become more positive since 1986. Some confusion and unjustifiable fear may exist among some registered nurses regarding certain aspects of acquired immune deficiency syndrome.

CONCLUSIONS

The hospital-based registered nurses in Oklahoma have increased their preparedness to facilitate initial and continued care of people with acquired immune deficiency syndrome. Because of the representative sample of this study, that conclusion probably is applicable to the nation.

Mitochondrial DNA mutations in human degenerative diseases and aging

A wide variety of mitochondrial DNA (mtDNA) mutations have recently been identified in degenerative diseases of the brain, heart, skeletal muscle, kidney and endocrine system. Generally, individuals inheriting these mitochondrial diseases are relatively normal in early life, develop symptoms during childhood, mid-life, or old age depending on the severity of the maternally-inherited mtDNA mutation; and then undergo a progressive decline. These novel features of mtDNA disease are proposed to be the product of the high dependence of the target organs on mitochondrial bioenergetics, and the cumulative oxidative phosphorylation (OXPHOS) defect caused by the inherited mtDNA mutation together with the age-related accumulation mtDNA mutations in post-mitotic tissues.

Marked changes in mitochondrial DNA deletion levels in Alzheimer brains

Levels of the common 4977 nucleotide pair (np) mitochondrial DNA (mtDNA) deletion (mtDNA4977) were quantitated in the cortex, putamen, and cerebellum of patients with Alzheimer disease (AD) and compared to age-matched controls. Although cerebellum deletion levels were comparably low in AD patients and controls of all ages, cortical deletion levels were clearly different. The levels of mtDNA deletions in control brains started low, but rose markedly after age 75, while those of AD patients started high and declined to low levels by age 80. Choosing age 75 to arbitrarily delineate between younger and older subjects, younger patients had 15 times more mtDNA deletions than younger controls, while older patients had one-fifth the deletion level of older controls. Younger AD patients also had fourfold more deletions than older AD patients. These results support the hypothesis that OXPHOS defects resulting from somatic mtDNA mutations may play a role in AD pathophysiology.

Mitochondrial DNA deletions in human brain: regional variability and increase with advanced age

We have examined the role of somatic mitochondrial DNA (mtDNA) mutations in human ageing by quantitating the accumulation of the common 4977 nucleotide pair (np) deletion (mtDNA4977) in the cortex, putamen and cerebellum. A significant increase in the mtDNA4977 deletion was seen in elderly individuals. In the cortex, the deleted to total mtDNA ratio ranged from 0.00023 to 0.012 in 67-77 year old brains and up to 0.034 in subjects over 80. In the putamen, the deletion level ranged from 0.0016 to 0.010 in 67 to 77 years old up to 0.12 in individuals over the age of 80. The cerebellum remained relatively devoid of mtDNA deletions. Similar changes were observed with a different 7436 np deletion. These changes suggest that somatic mtDNA deletions might contribute to the neurological impairment often associated with ageing.

Normal caffeine consumption: influence on thermogenesis and daily energy expenditure in lean and postobese human volunteers

Single-dose oral administration of 100 mg caffeine increased the resting metabolic rate of both lean and postobese human volunteers by 3-4% (p less than 0.02) over 150 min and improved the defective diet-induced thermogenesis observed in the postobese subjects. Measurements of energy expenditure (EE) in a room respirometer indicate that repeated caffeine administration (100 mg) at 2-h intervals over a 12-h day period increased the EE of both subject groups by 8-11% (p less than 0.01) during that period but had no influence on the subsequent 12-h night EE. The net effect was a significant increase (p less than 0.02) in daily EE of 150 kcal in the lean volunteers and 79 kcal in the postobese subjects. Caffeine at commonly consumed doses can have a significant influence on energy balance and may promote thermogenesis in the treatment of obesity.

Orientational anisotropy in the human visual system: an evoked potential and psychophysical study

Orientational anisotropy in the human visual system was investigated using electrophysiological and psychophysical techniques. Grating patterns of various orientations were presented and contrast detection thresholds were measured using a two alternative forced choice procedure. Using the same observers, visual evoked cortical potentials (VECPs) were elicited by identical gratings set at various contrasts ranging from subthreshold to high levels. Plots of contrast sensitivity versus grating orientation were derived using the amplitude of a negative wave of the VECP for low contrast data and the amplitude of a positive wave for moderate to high contrast data. These plots were compared with plots obtained during the psychophysical experiment. The results indicate that the low contrast VECP functions exhibit an orientational anisotropy that is qualitatively and quantitatively similar to that observed in the psychophysical data. The high contrast VECP functions, however, exhibit an orientational effect that is qualitatively similar but greater in magnitude than that found in the low contrast VECP or psychophysical experiments. These findings suggest that the amplitudes of VECPs elicited by low contrast stimuli are highly correlated with psychophysical detection performance, and that an additional physiological mechanism is reflected in the VECPs elicited by moderate to high contrast stimuli.