Public goods games on adaptive coevolutionary networks

Productive societies feature high levels of cooperation and strong connections between individuals. Public Goods Games (PGGs) are frequently used to study the development of social connections and cooperative behavior in model societies. In such games, contributions to the public good are made only by cooperators, while all players, including defectors, reap public goods benefits, which are shares of the contributions amplified by a synergy factor. Classic results of game theory show that mutual defection, as opposed to cooperation, is the Nash Equilibrium of PGGs in well-mixed populations, where each player interacts with all others. In this paper, we explore the coevolutionary dynamics of a low information public goods game on a complex network in which players adapt to their environment in order to increase individual payoffs relative to past payoffs parameterized by greediness. Players adapt by changing their strategies, either to cooperate or to defect, and by altering their social connections. We find that even if players do not know other players' strategies and connectivity, cooperation can arise and persist despite large short-term fluctuations.

Semantically enabling pharmacogenomic data for the realization of personalized medicine

Understanding how each individual's genetics and physiology influences pharmaceutical response is crucial to the realization of personalized medicine and the discovery and validation of pharmacogenomic biomarkers is key to its success. However, integration of genotype and phenotype knowledge in medical information systems remains a critical challenge. The inability to easily and accurately integrate the results of biomolecular studies with patients' medical records and clinical reports prevents us from realizing the full potential of pharmacogenomic knowledge for both drug development and clinical practice. Herein, we describe approaches using Semantic Web technologies, in which pharmacogenomic knowledge relevant to drug development and medical decision support is represented in such a way that it can be efficiently accessed both by software and human experts. We suggest that this approach increases the utility of data, and that such computational technologies will become an essential part of personalized medicine, alongside diagnostics and pharmaceutical products.

The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside

BACKGROUND

Translational medicine requires the integration of knowledge using heterogeneous data from health care to the life sciences. Here, we describe a collaborative effort to produce a prototype Translational Medicine Knowledge Base (TMKB) capable of answering questions relating to clinical practice and pharmaceutical drug discovery.

RESULTS

We developed the Translational Medicine Ontology (TMO) as a unifying ontology to integrate chemical, genomic and proteomic data with disease, treatment, and electronic health records. We demonstrate the use of Semantic Web technologies in the integration of patient and biomedical data, and reveal how such a knowledge base can aid physicians in providing tailored patient care and facilitate the recruitment of patients into active clinical trials. Thus, patients, physicians and researchers may explore the knowledge base to better understand therapeutic options, efficacy, and mechanisms of action.

CONCLUSIONS

This work takes an important step in using Semantic Web technologies to facilitate integration of relevant, distributed, external sources and progress towards a computational platform to support personalized medicine.

AVAILABILITY

TMO can be downloaded from http://code.google.com/p/translationalmedicineontology and TMKB can be accessed at http://tm.semanticscience.org/sparql.

Linked open drug data for pharmaceutical research and development

There is an abundance of information about drugs available on the Web. Data sources range from medicinal chemistry results, over the impact of drugs on gene expression, to the outcomes of drugs in clinical trials. These data are typically not connected together, which reduces the ease with which insights can be gained. Linking Open Drug Data (LODD) is a task force within the World Wide Web Consortium's (W3C) Health Care and Life Sciences Interest Group (HCLS IG). LODD has surveyed publicly available data about drugs, created Linked Data representations of the data sets, and identified interesting scientific and business questions that can be answered once the data sets are connected. The task force provides recommendations for the best practices of exposing data in a Linked Data representation. In this paper, we present past and ongoing work of LODD and discuss the growing importance of Linked Data as a foundation for pharmaceutical R&D data sharing.

The BioPAX community standard for pathway data sharing

BioPAX (Biological Pathway Exchange) is a standard language to represent biological pathways at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data (http://www.biopax.org). Pathway data captures our understanding of biological processes, but its rapid growth necessitates development of databases and computational tools to aid interpretation. However, the current fragmentation of pathway information across many databases with incompatible formats presents barriers to its effective use. BioPAX solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. BioPAX was created through a community process. Through BioPAX, millions of interactions organized into thousands of pathways across many organisms, from a growing number of sources, are available. Thus, large amounts of pathway data are available in a computable form to support visualization, analysis and biological discovery.

[Spondylitis: borderline findings in magnetic resonance tomography]

MR studies of 41 patients with confirmed spondylitis were evaluated with regard to imaging findings resembling metastases or fracture. 30 patients had MR results considered typical for spondylitis (contiguous changes in two vertebrae and disc, soft tissue tumour). 11 patients had MR studies differing from this pattern. Absence of soft tissue involvement and discontinuous marrow changes may be misdiagnosed as bone marrow metastases.

Clinical study with recombinant interferon gamma versus interferon alpha-2c in patients with condylomata acuminata

A multi-centre, randomized, open-label trial was conducted to evaluate the safety and efficacy of recombinant interferon (rIFN) alpha-2c versus rIFN gamma in patients with recurrent or persistent condylomata acuminata (CA). Thirty-three such patients were treated either with 6 micrograms rIFN alpha-2c or with 0.1 mg rIFN gamma (both equivalent to 2 x 10E6 IU), single dose, subcutaneously 3 times a week for 6 weeks. In case of no complete clearance at week 10, a second course of treatment with the other type of rIFN was given. There was no significant difference in the complete clearance proportions at week 10 between the two treatment groups (3/16 vs 6/17). No relapses occurred in these patients during the 16 weeks' follow-up. Further clearances during the follow-up resulted in a total complete clearance proportion of 14/33 at the end of study. The treatment was well tolerated. Repeated interferon therapy has its place in treating persistent or recurrent condylomas.

[AIDS--mucous membrane manifestations]

In the course of the infection with the human immunodeficiency virus (HIV), we frequently observe disorders of the mucous membranes and, occasionally, they present the first manifestation of HIV-induced immunodeficiency. Like in other organs, opportunistic infections and malignant tumors prevail as a result of the impaired immune system. Opportunistic infections are characterized by frequency (candidiasis), aggressive expansion, persistence, frequent recurrences, and resistance to therapy (gingivitis, parodontitis, herpes simplex, warts). Oral hairy leucoplakia is considered a specific lesion of HIV infection. Malignant tumors, such as Kaposi's sarcoma, non-Hodgkin's lymphoma, and squamous cell carcinoma, may cause marked morbidity in AIDS patients; occasionally, the clinical picture of Kaposi's sarcoma and non-Hodgkin's lymphoma is rather uncharacteristic. Other manifestations on the mucous membranes may arise in association with systemic reactions, such as drug eruptions, thrombocytopenic purpura, or acute HIV infection. The etiology of still other lesions of the mucous membranes (e.g. chronic recurrent ulcers, xerostomia, disorders of pigmentation) is incompletely understood. The awareness of these disorders of the mucous membranes in HIV infection is of diagnostic, therapeutic and epidemiological importance.

Amyloid elastosis: analysis of the role of amyloid P component

We report the second case of amyloid elastosis. Our patient had an underlying primary systemic amyloidosis with lambda light chain paraproteinemia. Salient clinical features included a sclerodermatous facial appearance, cordlike thickening of superficial blood vessels, neck skin resembling that in pseudoxanthoma elasticum, livedo reticularis-like changes on the trunk, Raynaud's phenomenon, arterial and venous thromboses, and the nephrotic syndrome. Amyloid deposits were present in the dermis, around appendages, in blood vessel walls, and in a striking distribution surrounding individual elastic fibers, that appeared shortened and fragmented. Immunofluorescence, electron microscopic, and immunoultrastructural studies with antibodies to lambda light chain, localized the amyloid deposits to the region of the elastic fiber microfibrils, with which amyloid P component (AP) is invariably associated in normal tissues. Because AP binds amyloid fibrils, codistribution of amyloid deposits and AP in amyloid elastosis strongly supports the theory that elastic fiber-associated AP may act as a nidus for amyloid deposition.

[Cystic Kaposi's sarcoma]

A patient with the rare, cystic variant of classic Kaposi sarcoma is presented. The immunohistochemical and enzyme-histochemical phenotype of the cells lining the cysts is the same as that of lymphoendothelial cells. The response to electron beam radiation therapy is good.

[Perioral dermatitis]

A unifying concept of the pathogenesis of perioral dermatitis is presented: perioral dermatitis is a cutaneous intolerance reaction linked to constitutionally dry skin and often accompanied by a history of mild atopic dermatitis. It is precipitated by the habitual use of one or - more often - a variety of moisturizing creams. The type and content of the creams used appear to play a much less important role than the mode of application (regular and abundant). The proposed pathomechanism is: persistent hydration of the horny layer, impairment of barrier function, an proliferation of the skin flora. Topical corticosteroids can aggravate but do not cause perioral dermatitis. This concept of pathogenesis leads to a simple and effective concept of therapy: reduction of the frequency with which moisturizing creams are applied from "regularly" to "as required" (only when dry and smarting skin makes this necessary) generally leads to lasting disappearance of symptoms within approximately 1 month.

Hemangiosarcoma in chronic leg ulcer

We recently evaluated a patient with an angiosarcoma arising in a long-standing ulceration of his leg, which appeared representative of a characteristic, though fairly uncommon, subgroup of angiosarcomas. The clinical and immunohistochemical features of the tumor enabled us to define its origin from vascular endothelial cells.

Macular amelanotic melanoma in situ

This report aims at directing the attention to the rare entity of amelanotic melanoma in situ, as exemplified in a patient who had an amelanotic lentigo maligna 10 years ago and a recurrent lesion of identical clinical and histological (except for pagetoid tumor cells in the epidermis) appearance 4 years ago. Amelanotic melanomas in situ appear as inconspicuous reddish macules, which can hardly be diagnosed or even suspected on clinical grounds.

[Mycetoma caused by Petriellidium boydii: treatment with ketoconazole]

A case of mycetoma of the lower leg (Madura foot) with bone involvement caused by Petriellidium boydii is presented. After an initially favourable therapeutic response to ketoconazole (2 X 200 mg/die) the process recurred despite proven sensitivity of the fungus in vitro. It could not be controlled with conservative treatment and ultimately necessitated amputation of the lower leg. A striking, hitherto unreported feature of mycetoma was the episodic occurrence of circulating immune complexes with febrile monoarthritis of the adjacent ankle.

[Xeroderma pigmentosum: prevention of tumors with etretinate]

A 46-year-old woman with xeroderma pigmentosum has had more than one hundred skin tumours in her life, in recent years largely keratoacanthomas. Two and a half years ago, a low-dose prophylactic treatment with etretinate (25 mg/day) was initiated. Since then, no further skin tumours have arisen except for several very small, rapidly resolving keratoacanthomas.

Results of LSA2-L2 therapy in 26 children with non-Hodgkin's lymphoma

Twenty-six children with non-Hodgkin's lymphoma (NHL), 17 boys and nine girls, were treated with the LSA2-L2 protocol. Seven children had stage I or II, 16 Stage III and three Stage IV according to Murphy's staging system. Eight children had their primaries in peripheral lymph nodes, eight in the abdomen, six in the mediastinum and four in other sites. All tumors were classified histologically according to four different classifications. Overall disease-free actuarial survival is 53.6%. Complete responders show a disease-free survival of 77.8%. Fourteen children survived for 9-56 months. Included are all seven children with Stage I or II who survive irrespective of histologic type of the tumor. Of the remaining 12 children in Stage III or IV three children died in remission and nine of progressive disease. Eight of these nine patients did not attain complete remission. Whereas four of five children with the convoluted type of NHL survive, four of five patients with the Burkitt's type (small noncleaved follicle center cell lymphomas) died of progressive disease. According to Rappaport's classification, four of six children with diffuse undifferentiated lymphoma (DUL) are dead due to tumour progression. Considering the classification of lymphoblastic lymphomas introduced by Nathwani et al., 23 five of seven children suffering from lymphoblastic lymphomas but only two of eight children with nonlymphoblastic lymphomas belong to the survivors. Therefore histologic findings do hold prognostic significance in our series of children with NHL.

[Concept for the total care of families of children with leukemia and tumors based on conversations with the parents]

In order to create a foundation for prophylactic and therapeutic measures the problems of children with leucaemia and other malignancies and of their families were assessed in detail with parents of these children in single or group discussions. The necessity for integrated therapy including families of children with leucaemia or tumours became apparent. Care should include extensive talks with all family members and also with teachers of patients and of healthy siblings, the use of aids such a painting or puppet theatre for recognition of problems and needs, particularly in small children, home visits to explore problems of health siblings, involvement of social workers, aftercare for the whole family after the death of a child, and, finally the help for overcoming problems of the treating team. Care to such an extent has been found to be necessary and requires an increase in posts in oncological units. Lack of time for the patients as human beings is unacceptable even from an economical point of view. A psychotherapeutically versed medical doctor or a clinical psychologist and a social worker should be permanent members of any oncological team.

[Progress in the treatment of juvenile leukemias]

Between January 1979 and December 1980 64 children with acute lymphoblastic leukemia were treated in 9 pediatric clinics in austria according to the BFM study 76/790-protocol. For remission induction all patients received an 8 week multidrug regimen (West-Berlin ALL-protocol). High risk patients were defined according to a risk score at diagnosis and additionally treated with a 6 week reinforced reinduction protocol during the first half year after diagnosis. Maintenance therapy was stopped after about 22 months. The life table-analysis after 30 months showed a 75.5% disease free survival for the total group of patients. Compared with a control group of 228 patients treated between 1974 and 1980 in 9 different clinics in Austria according to 3 consecutive national treatment regimens (modifications of Memphis protocol VII and VIII), therapeutic results were markedly improved. After a follow-up of 36 to 90 months the overall oumulative remission rate was 37.7%. The results could be improved especially in the group of high risk patients for replase by 35% in contrast to the historical studies. A prognostic difference between low- and high risk-patients was not seen in the BFM study (84.3% vs. 69.9%). Without doubt, the marked improvement of prognosis is due to the intensification of therapy.

[Treatment of orbital rhabdomyosarcoma (author's transl)]

From March 1973 to December 1981 embryonal rhabdomyosarcoma of the orbit was diagnosed in 5 children. In two children exenteration was done after a previous local radiotherapy. In one child the exenteration of the orbit was done after a primary chemo- and radiotherapy because of local progression of the tumor. In two children the exenteration was avoidable by this therapy. In four of these five children this was followed by vincristine, actinomycin D and cyclophosphamide for 16 to 24 months. After the diagnosis these four children survived until now from 3 1/2 to more than 8 years. They are free of treatment and free of disease. Seven months after diagnosis one child died with an acute respiratory distress syndrome (at post mortem: hyaline membranes). In patients with rhabdomyosarcoma of the orbit it is justified to avoid the mutilating exenteration by primary chemotherapy followed by irradiation of the reduced manner. If exenteration becomes subsequently necessary the chance for survival is not diminished in our opinion.

[Diagnostic and therapeutic problems of nasopharyngeal carcinoma in childhood (author's transl)]

Between 1974 and 1978 three children with a nasopharyngeal carcinoma (stages: T3N3MO, T4N2MO, T4N1MO) were treated with primary radiotherapy (tumor dose: 45-67 Gy). Local control was achieved in two children, one of these (T4 primarily) had a local relapse five months after diagnosis. Only one of the three children had radiotherapy to the neck region. This child developed lung and mediastinal metastases with hypertrophic osteoarthropathy twelve months after diagnosis. In the other two children lung metastases were observed two and seven weeks after the diagnosis respectively. In these two radiotherapy of metastases and chemotherapy were considered more important than radiotherapy of the neck region. All three children showed disappearance or considerable reduction of lung metastases due to radio- and chemotherapy. Yet, all three died of progressive disease within a few months. Early diagnosis of nasopharyngeal carcinoma in children will only be possible when pediatricians are more aware of this disease, also in our regions. Radiotherapy should be done only with megavoltage equipment using extensive radiation fields for the primary tumor area and elective radiation of the neck region. The use of additional primary chemotherapy is suggested for stages T3/T4. This mode of management may help to prevent distant metastases.

[Treatment of Wilms' tumor (author's transl)]

Uniform treatment based on the therapeutic approach of the 1st and 2nd US National Wilms' Tumor Study was decided on in March 1976 by paediatricians, surgeons, urologists and radiotherapists in Austria. Wilms' tumour was diagnosed in 34 children between 1 january 1976 an 29 february 1980 (stage I: n = 11, stage II: n = 8, stage III: n = 8, stage IV: n = 7). Parents of two children refused treatments; both children have since died of metastases. Of the remaining 32 children 29 (90.6%) are alive, 10 for more than 4, 15 for more than 3 and 19 for more than 2 years after diagnosis. 21 children are without need of treatment. Three children have died, one due to postoperative complications, one due to haemorrhagic chickenpox, but free of tumour, and one after insufficient treatment. Two of the five children with a recurrence between 2 1/4 to 15 months after diagnosis had been treated inadequately in the initial phase. The tumour free survival rate in 74.2%. Two children with early occurring or recurrent lung metastases have survived for 53 1/2 and 54 months up to now.

[Systemic lupus erythematosus in twins (author's transl)]

A report is given of systemic lupus erythematosus (SLE) in monozygotic twins. One sister developed coombs-positive haemolytic anaemia at the age of 11 years and suffered from five haemolytic crises over a period of 8 months. SLE could not be proven at that time, but following a 3-year symptom-free period, characteristic clinical and immunological evidence of SLE became manifest. The second sister developed classical SLE at the age of 15 years. Clinical, immunological, etiological and therapeutical aspects of SLE are being discussed.

[Polycythaemia as sole symptom of renal adenoma (author's transl)]

In two children, a 9 year-old boy and a 10 1/2 year-old girl, who presented with polycythaemia as the only symptom, the expected renal tumour was only found after exclusion of all other causes of polycythaemia. The delay in diagnosis was caused by technically inadequate intravenous urograms, which were erroneously passed as normal. In one child low kv X-ray exposition of the kidneys led to the diagnosis of a renal tumour. In the other child high-dose urography and tomography gave the indication for selective angiography. Normalization of the red blood count postoperatively verifies the connection between preoperative erythrocytosis and the renal tumour. Histologically both cases proved to be renal adenomas, which are extremely rare in childhood.

[Congenital hepatic fibrosis and polycystic disease of the kidneys in two siblings (author's transl)]

Report of 2 siblings, aged 12 1/2 and 9 years, with congenital hepatic fibrosis and polycystic disease of the kidneys. Hepatosplenomegaly had been noted in both children at birth. The younger child had suffered from oliguria aged 2 1/2 years. At diagnosis both children had low platelet counts, one also had leucopenia. The cystic disease of the kidneys was verified by angiography. Coeliacography and splenopartography were diagnostically irrelevant. The diagnosis only became apparent from liver biopsy which was performed during splenectomy. After splenectomy there was an increase of platelets, white blood cells and the clotting factors II, V and X. The three years follow-up showed a constancy of renal impairment and of the minor oesophageal varices observed in the one patient who did not have a spontaneous spleno-renal anastomosis. So far no bleeding has been observed. Porto caval anastomosis was omitted in both children. Pros and cons are being discussed.

[Cytostatic therapy in a patient with histologically verified, but not irradiatied, brain stem glioma (author's transl)]

A boy, aged 8 1/2 years, was operated becuase of a brainstem tumor (polymorph mixed glioma) more than 4 years ago. Because of its dimension and location in the medulla oblongata the tumor was resected only partially. Radiotherapy was refused at that time. A combined cytostatic therapy proved to be successful. The marked neurological symptoms diminished considerably during treatment. The patient (with minor neurological symptoms) has been living a normal and active life for the last 4 years.

[Cerebellar vincristine toxicity (author's transl)]

The diagnosis of Wilms tumor stage IV was established in a girl of 5 1/2 years of age in July 1972. Nephrektomy was followed by radiotherapy of the tumorbed and the lung metastasis. Thereafter the child was treated with Vincristine (VCR) and Actinomycine D (AMD) for two years. The child has been off treatment for the last 14 months and is free of disease. An intention tremor of the right hand was noted 4 weeks after the 32nd application of VCR and 2 weeks after a viral infection of unknown etiology. The writing proved to be hypermetric. There was no loss of proprioception and thus the symptoms were localized into the right cerebellum. Having excluded other causes (hemorrhage, metastasis) as far as possible and considering unilateral cerebellar encephalitis as very unlikely the cerebellar symptoms were thought to be VCR toxicity.

[Slow-virus "encephalitis" following measles in a child with cytostatically-treated leukaemia (author's transl)]

A child with acute infantile lymphoblastic leukaemia in remission after cytostatic therapy contracted apparently uncomplicated measles. 8 weeks later, an acute neurological syndrome developed, which led to death within 2 weeks. At autopsy, a peculiar type of inclusion body "encephalitis" almost without signs of inflammatory infiltration was found. Electron microscopic examination showed changes of paramyxovirus infection, which were attributable to slow measles virus disease of the CNS. There was evidence of disturbed nucleocapside synthesis, which is considered to be one of the basic defects in the development of slow-virus processes and their altered viral maturation. Possible pathogenetic factors are discussed in the light of our case.

SSPE-like inclusion body disorder in treated childhood leukemia

Clinico-pathological report on a boy with cytostatically treated leukemia, dying with cerebral symptoms after passing clinical measles 10 weeks before death. At autopsy, numerous nuclear inclusion bodies in glial and nerve cells were found. By electron microscopy, nuclear inclusions appeared as loosely arranged smooth tubules, corresponding to paramyxovirus nucleocapsids. Frequently, cytoplasmic changes appeared too, consisting of incomplete tubular structures and an abundant dense "fuzzy" material. No regular tubuli of the coated granular type were present, as in common measles virus infection, nor any mature viral structures or differentiation of the surface membrane. The lack of maturation in cytoplasm together with a predominance of nuclear changes suggested a slow type of measles virus infection, while the particular cytoplasmic changes suggested a defect in synthesis of granular nucleocapsids, possibly a basic factor for the slow type of the viral infection. Possible pathogenetic factors are discussed.