Introduced populations as genetic reservoirs for imperiled species: a case study of the Arkansas River Shiner (Notropis girardi)

The Arkansas River Shiner is a threatened species that has been extirpated throughout much of its native range (Arkansas River drainage) and remaining populations are imperiled. Prior to 1978, this species was accidently introduced to the Pecos River (Rio Grande drainage) via bait bucket, and has since persisted for over 30 years. Genetic data show that the Pecos River population maintains comparable levels of diversity at mitochondrial DNA and microsatellite loci relative to native range populations. Hence, we examined several factors that could be responsible for high introduced genetic diversity including (a) multiple introductions from genetically distinct sources (b) introduction of individuals from a genetically diverse source followed by rapid population expansion, (c) presence of life-history traits that foster propagule diversity and wide spatio-temporal demographic and genetic mixing; and (d) introduction to a suitable habitat in the non-native range. Our findings indicate Arkansas River Shiner was likely introduced from the Canadian River and subsequently experienced rapid population expansion that mitigated loss of diversity during the founding event. Threats to native Arkansas River Shiner have increased due to ongoing drought and water resource development, thus a finding of high diversity in the Pecos River suggests conservation significance of this non-native population. Further, it identifies the Pecos River as both a refuge for native endemic fishes and of genetic diversity of introduced, yet threatened, species.     

The case for survivin as a regulator of microtubule dynamics and cell-death decisions

Survivin has aroused keen interest in disparate areas of basic and translational research. This stems from the complexity of a 'survivin network', which appears to intersect multiple pathways of cell division, resistance to apoptosis, surveillance checkpoints and adaptation to unfavorable environments. Such intricacy has also engendered different models for survivin function and its implications. As antagonists of survivin are being evaluated in the clinic, a critical reassessment of the pathway, especially with respect to cell division and cell survival, is now a priority. Building a unifying model to reconcile the differing views on survivin will aid in the design and interpretation of molecularly based clinical trials targeting this network in humans.     

Principal component analysis as an alternative treatment for morphometric characters: phylogeny of caseids as a case study

In a recent study, the phylogeny of Caseidae (a herbivorous family of Palaeozoic synapsids belonging to the paraphyletic grade known as pelycosaurs) was analysed with a dataset employing more than three hundred continuous morphological characters in an effort to follow the principles of total evidence. Continuous characters are a source of great debate, with disagreements surrounding their suitability for and treatment in phylogenetic analysis. A number of shortcomings were identified in the handling of continuous characters in this study of caseids, including the use of gap weighting to discretize the characters and potential issues with redundancy and character non‐independence. Therefore, an alternative treatment for these characters is suggested here. First, rather than using gap weighting, the continuous characters were analysed in the program TNT, in which the raw values can be treated as continuous rather than discrete. Second, prior to the phylogenetic analysis, the continuous characters were subjected to a log‐ratio principal component analysis, and then the principal components were included in the character matrix rather than the raw ratios. Analysing the original data in TNT produced little difference in the results, but using the principal components as continuous characters resulted in alternative positions for Caseopsis agilis, Ennatosaurus tecton and Caseoides sanangeloensis. The differences are judged to be due to the reduced redundancy of the characters, the smaller number of principal components not overwhelming the discrete characters and the use of a scaling method which allows principal components with a higher variance to have a greater influence on the analysis. The positions of highly fragmentary fossils depended heavily on the method used to treat the missing characters in the principal component analysis, and so the method proposed here is not recommended for analysing very incomplete taxa.     

Medical malpractice: a case study in medical and legal decision making

The conference was organized in part to dispel some of the misinformation that interferes with cooperative efforts of attorneys and physicians to redress the malpractice situation. During discussion of the hypothetical case, participants identified how medical decision-making responsibilities were allocated among health care providers caring for the patient. Panel members suggested ways in which medical decision making might be affected by non-medical factors such as third-party reimbursement (e.g., selection of inpatient or outpatient setting, the opportunity to discuss issues related to informed consent prior to the day of a procedure) and potential malpractice litigation (e.g., documentation in charts, use of diagnostic procedures). The characterization of decision-making roles and responsibilities differed somewhat for purposes of malpractice litigation; that is, which caregivers might be named as defendants. Panel members reconstructed the development of the medical incident into a legal case. Plaintiff's attorney commented that it is often a hospital employee who advises the family to consult an attorney and described some of the constraints on information gathering (e.g., the rule of "discovery" requiring that suit be filed before defendants can be forced to give statements about what happened, insurance contract provisions prohibiting physicians from talking without legal counsel present to persons who indicate that they plan to file suit). He also briefly explained the rationale for the contingency fee arrangement in these cases. Describing the role of the medical expert witness and the need to review the medical record, he outlined the process of deciding whether to pursue a malpractice case. In making this decision, plaintiff's attorney evaluates the facts to identify issues in the case, to determine if there are deviations from the standard of care, and to try to predict jury reaction. If a suit is filed, defense attorneys employed by the hospital, insurance company, or individual defendants will decide, based on facts including coverage limits, possible publicity, and likelihood of successful prosecution, whether the case should be settled and for what amount. Interests represented by the defense attorneys differ and may affect settlement strategies. Physician feelings of concern for the patient/family or desire for vindication will, to varying degrees, be factors in the decision to try or settle a case. Panel members explored several important policy issues. Among these were the effect of malpractice cases on doctor-patient communications and ethical issues concerning expert witnesses.(ABSTRACT TRUNCATED AT 400 WORDS)     

Interfaces to PeptideAtlas: a case study of standard data access systems

Access to public data sets is important to the scientific community as a resource to develop new experiments or validate new data. Projects such as the PeptideAtlas, Ensembl and The Cancer Genome Atlas (TCGA) offer both access to public data and a repository to share their own data. Access to these data sets is often provided through a web page form and a web service API. Access technologies based on web protocols (e.g. http) have been in use for over a decade and are widely adopted across the industry for a variety of functions (e.g. search, commercial transactions, and social media). Each architecture adapts these technologies to provide users with tools to access and share data. Both commonly used web service technologies (e.g. REST and SOAP), and custom-built solutions over HTTP are utilized in providing access to research data. Providing multiple access points ensures that the community can access the data in the simplest and most effective manner for their particular needs. This article examines three common access mechanisms for web accessible data: BioMart, caBIG, and Google Data Sources. These are illustrated by implementing each over the PeptideAtlas repository and reviewed for their suitability based on specific usages common to research. BioMart, Google Data Sources, and caBIG are each suitable for certain uses. The tradeoffs made in the development of the technology are dependent on the uses each was designed for (e.g. security versus speed). This means that an understanding of specific requirements and tradeoffs is necessary before selecting the access technology.     

Proximate determinants of fertility in the Kathmandu Valley, Nepal: an anthropological case study

The analytical model of Bongaarts and Potter is employed to compare the proximate determinants of fertility among 3 populations in Nepal's Kathmandu valley. 3 sub-groups are studied: high caste (Brahmin and Chetri) urban residents, high caste urban fringe residents, and low caste untouchables (Sarki). Both survey and anthropological methods are employed. According to the analytical model, the transition in fertility follows 4 phases. The changes in fertility levels from Phase 1 to Phase 4 generally indicate that the transition from natural to controlled fertility is characterized by declines in the proportions of women married and the duration of postpartum infecundability, and a substantial increase in the prevalence and effectiveness of contraceptive practices. The results of this study show that Nepal as a whole is entrenched in Phase 1 of the fertility transition. However, data from the 3 populations reported here clearly indicate that each has begun to experience a demographic transition to different degrees. The Sarkis in this study fall between Phases 2 and 3, as indicated by the total fertility rate (TFR). The rural high castes most closely approximate a population in Phase 3, while urban high castes included in this study are approaching Phase 4. Each of the 3 populations is characterized by a decline in the proportion of women married when compared to all of Nepal. It is also apparent that the relative use-effectiveness of contraceptive methods currently employed is high. Gains in the reduction of fertility, then, will have to be made from increasing and retaining the number of acceptors and in reducing the desired family size of those at reproductive risk.     

CHARGE Association in newborns: a registry-based study

The CHARGE Association is a nonrandom occurrence of congenital malformations that has been described in clinical series. Reported patients have been selected on the basis of certain prior criteria. In this article, we try to identify a congenital malformation pattern corresponding to the CHARGE Association, using statistical methods and analyzing 5,260 infants with multiple malformations collected from four large registries of congenital malformations. Care was taken to identify a number of confounding characteristics that can influence the ascertainment and registration of specific congenital malformations. We have identified a cluster of malformations that generally agreed with the current clinical definition of the CHARGE Association and have added some further malformations (e.g., facial clefts). We demonstrate that others (e.g. , esophageal atresia) are probably not part of the pattern. Heart defects (H in the acronym) seems to be less helpful in identifying infants with the association. We suggest a method to select infants who probably represent the CHARGE Association for analyses of possible risk factors.     

Ethically problematic treatment decisions: a physician survey

BACKGROUND: Experiencing ethical problems requires both ethically problematic situations and ethical sensitivity. Ethically problematic treatment decisions are distressing and might reflect health care quality problems. Whether all physicians actually experience ethical problems, what these problems are and how they vary according to physician age, gender and work sector are largely unknown. METHODS: A mail survey of all non-retired physicians licensed in Finland (n = 17,172, response rate 75.6%). RESULTS: The proportion of physicians reporting having made ethically problematic treatment decisions decreased in linear fashion from 60% at ages below 30 years to 21% at ages over 63 years. The only problem that did not decrease in frequency with age was having withdrawn necessary treatments. Women and primary care physicians reported problematic decisions most often, although gender differences were small. Primary care physicians most often reported having performed too many investigations or having pressured patients, whereas hospital physicians emphasized having withdrawn necessary treatments. Performing unnecessary treatments or investigations was explained by pressure from patients or relatives, and performing too few treatments or investigations was explained by inadequate resources. CONCLUSIONS: In general, young physicians felt pressured to do too much, whereas older physicians felt they could not do enough due to inadequate resources. Older physicians might be less exposed to ethically problematic situations, be more able to handle them or have lower ethical sensitivity. Young physicians could benefit from support in resisting pressure to perform unnecessary treatments, whereas older physicians might benefit from training in recognizing ethical issues.     

Hungarian paediatricians' attitudes regarding the treatment and non-treatment of defective newborns: a comparative study

Conclusion: The four compared surveys clearly show that paediatricians from different backgrounds encounter these moral dilemmas in their everyday practice. Hungarian paediatricians facing morally significant decisions of discontinuation of treatment in defective newborns were permissive toward passive euthanasia like their Australian and Canadian colleagues, but were almost unanimously against active euthanasia like their Polish colleagues. The results of our study revealed a strong paternalistic attitude among Hungarian doctors, unwillingness to include other professionals in a discussion of moral problems and neglect of the nurses' views in these matters. Many physicians in the Hungarian study group were not aware of the legal ramifications in such cases. These findings were similar to the results of the Polish study. It is plausible that the paternalistic attitude and ignorance of the relevant law is common in all 'former' socialist countries. The Australian, Canadian and Hungarian doctors displayed more understanding and tolerance towards passive euthanasia. Many physicians in all study groups seemed to be not familiar with the legal regulations of their own country. The paediatricians of the four studies showed the greatest difference in their attitudes towards active euthanasia, with the Australian community being more permissive, the Canadian, Polish and Hungarian community rejecting it.     

Multiscale modelling of Potts shunt as a potential palliative treatment for suprasystemic idiopathic pulmonary artery hypertension: a paediatric case study

Biomechanics and Modeling in Mechanobiology - Potts shunt (PS) was suggested as palliation for patients with suprasystemic pulmonary arterial hypertension (PAH) and right ventricular (RV) failure....     

Intra-household relations and treatment decision-making for childhood illness: a Kenyan case study

This study, conducted on the Kenyan coast, assesses the effect of intra-household relations on maternal treatment-seeking. Rural and urban Mijikenda mothers' responses to childhood fevers in the last 2 weeks (n=317), and to childhood convulsions in the previous year (n=43), were documented through survey work. The intra-household relations and decision-making dynamics surrounding maternal responses were explored through in-depth individual and group interviews, primarily with women (n=223). Responses to convulsions were more likely than responses to fevers to include a healer consultation (p<0.0001), and less likely to include the purchase of over-the-counter medications (p<0.0001). Mothers received financial or advisory assistance from others in 71% (n=236) of actions taken outside the household in response to fevers. In-depth interviews suggested that general agreement on appropriate therapy results in relatively few intra-household conflicts over the treatment of fevers. Disputes over perceived cause and appropriate therapy of convulsions, however, highlighted the importance of age, gender and relationship to household head in intra-household relations and treatment decision-making. Although mothers' treatment-seeking preferences are often circumscribed by these relations, a number of strategies can be drawn upon to circumvent 'inappropriate' decisions, sometimes with implications for future household responses to similar syndromes. The findings highlight the complexity of intra-household relations and treatment decision-making dynamics. Tentative implications for interventions aimed at improving the home management of malaria, and for further research, are presented.     

Process analytical technology implementation for protein refolding: GCSF as a case study

Process analytical technology is gaining interest in the biopharmaceutical industry as a means to enable consistency in processing and thereby in product quality via process control. Protein refolding is known to be significantly impacted by critical process parameters and feed material attributes including composition and pH of the solubilisation and refolding buffers. Hence, to achieve robust process control and product quality, these attributes and parameters need to be monitored. This paper presents an approach towards statistical process control and monitoring of protein refolding, from buffer preparation to refold quenching, during manufacturing of therapeutic proteins from Escherichia coli based systems. The proposed approach utilises measurements of online redox potential, temperature, and pH for development of a statistical model. The model has then been integrated with LabView to permit real-time monitoring of the refolding process. The proposed system has been demonstrated to successfully identify process deviations and thereby enable process control for manufacturing product of consistent quality.     

Social referents for dairy farmers: who dairy farmers consult when making management decisions

Social referents provide information that aid in farmer decision making. Some social referents, such as veterinarians, have been well studied in the context of dairy farms, but others have not and the role of social referents may change across management practices. This study aimed to understand (1) who farmers consult when making management decisions across different animal care practices and (2) what characteristics of these social referents influence farmer decision making. Secondary thematic analysis was used on two qualitative datasets with dairy farmers from the lower Fraser Valley region of British Columbia, Canada. The two datasets included non-naturalistic data (i.e. interviews, participatory discussion groups) investigating two dairy farm management practices (calf care and transition period management). Analysis revealed four themes: (1) who farmers consult when making management decisions across practices and the role of these social referents, (2) personal and professional characteristics, and the diversity of opinions of social referents, (3) actions of social referents, and (4) the strength of the relationship between the social referent and farmer. Similarities were found across practices regarding the personal and professional characteristics of social referents, even though the role of these referents varied across contexts. Farmers valued diverse opinions and actions that social referents could provide, such as the provision of resources, recommendations, and interpretation of farm data. We recommend future research focused on strengthening the relationship between farmers and social referents.     

Cellular responses to naphthoquinones: juglone as a case study

The effects of juglone (JG) on the endogenous growth, growth in the presence of either indoleacetic acid (IAA) or fusicoccin (FC) and on proton extrusion were studied in maize coleoptile segments. In addition, membrane potential changes were also determined at chosen JG concentrations. It was found that JG, when added to the incubation medium, inhibited endogenous growth as well as growth in the presence of either IAA or FC. Simultaneous measurements of growth and external pH indicated that inhibition of either IAA-induced growth or proton extrusion by JG was a linear function of JG concentration. Addition of JG to the control medium caused depolarization of the membrane potential (E_m), value of which was dependent on JG concentration and time after its administration. Hyperpolarization of E_m induced by IAA was suppressed in the presence of JG. It was also found that for coleoptile segments initially preincubated with JG, although subsequently removed, addition of IAA was not effective in the stimulation of growth and medium acidification. Taken together, these results suggest that the mechanism by which JG inhibits the IAA-induced growth of maize coleoptile segments involves inhibition of PM H⁺-ATPase activity.     

Testing the island rule: primates as a case study

The island rule states that after island colonization, larger animals tend to evolve reduced body sizes and smaller animals increased sizes. Recently, there has been disagreement about how often, if ever, this rule applies in nature, and much of this disagreement stems from differences in the statistical tests employed. This study shows, how different tests of the island rule assume different null hypotheses, and that these rely on quite different biological assumptions. Analysis and simulation are then used to quantify the biases in the tests. Many widely used tests are shown to yield false support for the island rule when island and mainland evolution are indistinguishable, and so a Monte Carlo permutation test is introduced that avoids this problem. It is further shown that tests based on independent contrasts lack power to detect the island rule under certain conditions. Finally, a complete reanalysis is presented of recent data from primates. When head-body length is used as the measure of body size, reports of the island rule are shown to stem from methodological artefacts. But when skull length or body mass are used, all tests agree that the island rule does hold in primates.     

Uncomfortable prescribing decisions: a critical incident study.

OBJECTIVE--To explore the discomfort experienced by general practitioners in relation to decisions about whether or not to prescribe. DESIGN--Focused interviews of general practitioners about prescribing decisions that made them uncomfortable. Analysis based on the critical incident technique. SETTING--One family practitioner committee area in the north of England. RESPONDENTS--69 principals and five trainee general practitioners. MAIN OUTCOME MEASURES--Drugs and clinical problems associated with prescribing discomfort. Reasons given by doctors for making the prescribing decisions they did and reasons for feeling uncomfortable. RESULTS--Antibiotics, tranquillisers, hypnotics, and symptomatic remedies were most often associated with discomfort, but any prescribable item could be associated with discomfort. Respiratory diseases, musculoskeletal problems, and anxiety were most often associated with discomfort, but again any condition could be associated. The main reasons given for the decisions made were patient expectation, clinical appropriateness, factors related to the doctor-patient relationship, and precedents. The main reasons given for feeling uncomfortable were concern about drug toxicity, failure to live up to the general practitioner''s own expectations, concern about the appropriateness of treatment, and ignorance or uncertainty. CONCLUSIONS--Many considerations, including medical, social, and logistic ones, influence the decision to prescribe in general practice. The final action taken depends on a complex interaction of these disparate influences.