A rigorous approach to facilitate and guarantee the correctness of the genetic testing management in human genome information systems

Abstract Background Recent medical and biological technology advances have stimulated the development of new testing systems that have been providing huge, varied amounts of molecular and clinical data. Growing data volumes pose significant challenges for information processing systems in research centers. Additionally, the routines of genomics laboratory are typically characterized by high parallelism in testing and constant procedure changes. Results This paper describes a formal approach to address this challenge through the implementation of a genetic testing management system applied to human genome laboratory. We introduced the Human Genome Research Center Information System (CEGH) in Brazil, a system that is able to support constant changes in human genome testing and can provide patients updated results based on the most recent and validated genetic knowledge. Our approach uses a common repository for process planning to ensure reusability, specification, instantiation, monitoring, and execution of processes, which are defined using a relational database and rigorous control flow specifications based on process algebra (ACP). The main difference between our approach and related works is that we were able to join two important aspects: 1) process scalability achieved through relational database implementation, and 2) correctness of processes using process algebra. Furthermore, the software allows end users to define genetic testing without requiring any knowledge about business process notation or process algebra. Conclusions This paper presents the CEGH information system that is a Laboratory Information Management System (LIMS) based on a formal framework to support genetic testing management for Mendelian disorder studies. We have proved the feasibility and showed usability benefits of a rigorous approach that is able to specify, validate, and perform genetic testing using easy end user interfaces.

A new population of the Cone-billed Tanager Conothraupis mesoleuca, with information on the biology, behaviour and type locality of the species

The `Critically Endangered` Cone-billed Tanager Conothraupis mesoleuca was described in 71 93 9, based on a single specimen collected in the state of Mato Grosso, western Brazil. Not seen again in the wild until 2003, this poorly-known species was rediscovered in Emas National Park, in the Brazilian state of Goias. We describe here the discovery of a new population of Cone-billed Tanager in Chapada dos Parecis, along the upper Juruena River basin, in the state of Mato Grosso. The birds were always detected in (or near) flooded habitats along rivers. At least 40 individuals were found, but the population may be larger since areas of potential habitat are available in the upper Juruena basin and these have not yet been surveyed. We also provide here the first information on the biology and behaviour of the species based on observations in Juruena and Emas, as well as a first description of the female. Historical documents and our records support our suggestion that ""Juruena"", i.e. the type locality of the Cone-billed Tanager, refers to the Juruena telegraph station (12 degrees 50`S, 58 degrees 55`W). Considering that the range of the species is being settled, research on different aspects of its biology are urgent.

LIMB REPLANTATION AFTER AVULSION INJURIES: TECHNIQUES AND TACTICS FOR SUCCESS

Objectives: Retrospective evaluation of cases of limb replantation after avulsion injuries. Evaluation of the techniques and tactics used, that contributed to success and good functional results. Methods: Forty-three patients' records were assessed. All the cases had been submitted to limb replantation after avulsion injuries. Results: The majority of the cases were young men. The most common injury was to the thumbs. The surgical techniques and tactics used were: nerve grafting, vein grafting, transposition of the digital vessels, limb shortening, and heterotopic replantation. The most commonly used technique was vein graft. The limb survival rate was high (93%), as was patient satisfaction. Conclusion: Replantation after avulsion injury depends on the correct diagnosis of the limb viability and the use of appropriate surgical techniques and tactics for each case. The experience of the team of surgeons and a good hospital structure are essential for good results. There are few articles in medical literature about the indications, techniques and results of limb replantation after avulsion injuries. We believe that this retrospective evaluation can bring new information and contributions to the correct management of this highly complex situation. Level of evidence IV, Case Series.

Flexibility and modeling in business processes: a multi-dimensional relationship

Over the last few years, Business Process Management (BPM) has achieved increasing popularity and dissemination. An analysis of the underlying assumptions of BPM shows that it pursues two apparently contradicting goals: on the one hand it aims at formalising work practices into business process models; on the other hand, it intends to confer flexibility to the organization - i.e. to maintain its ability to respond to new and unforeseen situations. This paper analyses the relationship between formalisation and flexibility in business process modelling by means of an empirical case study of a BPM project in an aircraft maintenance company. A qualitative approach is adopted based on the Actor-Network Theory. The paper offers two major contributions: (a) it illustrates the sociotechnical complexity involved in BPM initiatives; (b) it points towards a multidimensional understanding of the relation between formalization and flexibility in BPM projects.

NEW RECORDS OF ANOPHELES HOMUNCULUS IN CENTRAL AND SERRA DO MAR BIODIVERSITY CORRIDORS OF THE ATLANTIC FOREST, BRAZIL

Two new records of Anopheles homunculus in the eastern part of the Atlantic Forest are reported. This species was found for the first time in Barra do Ouro district, Maquine municipality, Rio Grande do Sul state, located in the southern limit of the Atlantic Forest. The 2nd new record was in the Serra Bonita Reserve, Camacan municipality, southeast Bahia state. These records extend the geographical distribution of An. homunculus, suggesting that the species may be widely distributed in coastal areas of the Atlantic Forest. It is hypothesized that the disjunct distribution of the species may be caused by inadequate sampling, and also difficulties in species identification based only on female external characteristics. Species identification was based on morphological characters of the male, larva, and pupa, and corroborated by DNA sequence analyses, employing data from both 2nd internal transcribed spacer of nuclear ribosomal DNA and of mitochondrial cytochrome c oxidase subunit I.

Egg surface structure of the freshwater toadfish Thalassophryne amazonica (Teleostei: Batrachoididae) with information on its distribution and natural habitat

The egg surface structure of Thalassophryne amazonica, a freshwater toadfish from the Amazon basin is described. Eggs of this species show a remarkable, highly unusual system of parallel ridges and intermittent grooves that originate at the equator of the egg and lead to the micropylar pit, at which they end in a spiralling pattern. A similar egg surface structure has so far been described only from a group of Asian anabantoid percomorphs, obviously not closely related to Thalassophryne. This egg surface pattern may enhance fertilization success by guiding sperm to the micropyle. We review museum records for T amazonica, present an updated map of its occurrence in the Amazon basin, and provide information on its habitat.

Lithiasis in 1,313 Kidney Transplants: Incidence, Diagnosis, and Management

Background. Renal transplantation remains the optimal treatment of patients with end-stage renal disease. Urinary lithiasis represents an unusual urologic complication in renal transplantation, with an incidence of <1%. Today, recipients of kidneys from deceased donors are more likely to receive grafts with undiagnosed lithiasis, which does not occur in patients from living donors, owing to screening with computerized tomography. Objective. The aim of this study was to evaluate the incidence, diagnosis, and therapeutic management of renal lithiasis in transplanted kidneys at a single institution. Methods. We reviewed the medical records for 1,313 patients who underwent kidney transplantation from February 1968 to February 2011. Results. Among the grafts, 17 patients (1.29%) had nephrolithiasis: 9 women and 8 men. Ages ranged from 32 to 63 years (mean = 45.6 years). Fifteen patients received kidneys from cadaveric and only 2 from living related donors. Two stones, both located inside the ureter, were identified during transplant surgery (11.7%). Three instances of lithiasis were incidentally diagnosed by ultrasound during graft evaluation, within 7 days after surgery (17.6%); all 3 were in the calyces. The 12 remaining patients had the stones diagnosed later (70.58%): 6 in the calyces, 3 in the renal pelvis, and 3 inside the ureter. Conclusions. Urinary lithiasis is a rare complication in renal transplantation. In most patients the condition occurs without pain. The diagnosis and treatment options for graft urolithiasis are similar to those patients with nephrofithiasis in the general population. Extracorporeal shock wave lithotripsy (ESWL) was the most common treatment method.

TRAUMATIC SPONDYLOLISTHESIS OF THE AXIS: EPIDEMIOLOGY, MANAGEMENT AND OUTCOME

Objective: To evaluate cases of traumatic spondylolisthesis of the axis and describe them in relation to epidemiology, classification, neurological deficit, healing time and treatment method. Method: A retrospective analysis of the medical records of patients treated between 2002 and 2010 at IOT-FMUSP. Inclusion criteria: pars interarticularis fracture of C2. Results: 68% were male patients, with a mean age of 39.1 years. We used the classification by Effendi, modified by Levine-Edwards. Type I fractures were observed in five patients (31.2%) and type II in eight patients (50%). Only three patients (18%) had type IIa fracture. There were no cases of type III. Mechanism: Eight car accidents and four falls. Other mechanisms: being run over, and diving accidents. Treatment with halo traction was used in eleven patients, using minerva cast and halo-cast. Healing time: 3.6 months. Follow-up time: 9.6 months. Discussion: In general, hangman fracture has a good prognosis, which is confirmed by our results. There was no need for surgery in any of the cases. The incidence of neurological deficit is low. No patient had unstable fracture (type III). Conclusion: This paper suggests that traumatic spondylolisthesis of the axis continues to be an injury that is successfully treated by conservative treatment in most cases. Level of Evidence IV, Case series.

Two new genera, ten new species and new records of Amazonian Stygnidae Simon, 1879 (Opiliones: Laniatores)

As a result of recent expeditions to two mountains in the Amazon basin, Tapirapeco and Pico da Neblina, two new genera of Stygnidae, Imeri g. nov. (type species Imeri lomanhungae sp. nov.) and Jime g. nov. (type species Jime chifrudo sp. nov.), and ten new species are described: Auranus hehu sp. nov., Auranus tepui sp. nov., Imeri lomanhungae sp. nov.; Jime chifrudo sp. nov.; Stygnoplus ianomami sp. nov.; Stygnus magalhaesi sp. nov.; Stygnoplus neblina sp. nov.; Stygnoplus tapirapeco sp. nov.; Stygnus nogueirai sp. nov., Stygnus kuryi sp. nov.. Additionally, new distributional records in Amazonas (Brazil) are presented for Stygnidius guerinii Soerensen, 1932, Minax tetraspinosus Pinto-da-Rocha, 1997 and Protimesius longipalpis (Roewer, 1943). Keys for genera of Heterostygninae and Stygninae are provided.

Using Machine Learning Classifiers to Assist Healthcare-Related Decisions: Classification of Electronic Patient Records

Surveillance Levels (SLs) are categories for medical patients (used in Brazil) that represent different types of medical recommendations. SLs are defined according to risk factors and the medical and developmental history of patients. Each SL is associated with specific educational and clinical measures. The objective of the present paper was to verify computer-aided, automatic assignment of SLs. The present paper proposes a computer-aided approach for automatic recommendation of SLs. The approach is based on the classification of information from patient electronic records. For this purpose, a software architecture composed of three layers was developed. The architecture is formed by a classification layer that includes a linguistic module and machine learning classification modules. The classification layer allows for the use of different classification methods, including the use of preprocessed, normalized language data drawn from the linguistic module. We report the verification and validation of the software architecture in a Brazilian pediatric healthcare institution. The results indicate that selection of attributes can have a great effect on the performance of the system. Nonetheless, our automatic recommendation of surveillance level can still benefit from improvements in processing procedures when the linguistic module is applied prior to classification. Results from our efforts can be applied to different types of medical systems. The results of systems supported by the framework presented in this paper may be used by healthcare and governmental institutions to improve healthcare services in terms of establishing preventive measures and alerting authorities about the possibility of an epidemic.

Description of the female and new records of Triatoma baratai Carcavallo & Jurberg, 2000 (Hemiptera: Heteroptera: Reduviidae: Triatominae) from Mato Grosso do Sul, Brazil, with a key to the species of the Triatoma matogrossensis subcomplex

Triatoma baratai Carcavallo & Jurberg, 2000, a species similar to Triatoma williami Galvao, Souza & Lima, 1967 and belonging to the T. matogrossensis subcomplex, was described based on a male specimen collected in a sylvatic environment, near a cave, in Bonito county, Bodoquena mountain range, state of Mato Grosso do Sul, Brazil. In the present work we describe the female of T. baratai, captured in a chicken house, in Nioaque county, state of Mato Grosso do Sul, Brazil. Furthermore, we recorded the occurrence of T. baratai in domiciles and peridomestic environment in another four municipalities (Bodoquena, Bela Vista, Corumba, and Miranda), extending its geographical distribution. Finally, we present a key to the species of the Triatoma matogrossensis subcomplex.

Knowledge management and strategic orientation: leveraging innovativeness and performance

Purpose - The aim of this study is to investigate whether knowledge management (KM) contributes to the development of strategic orientation and to enhance innovativeness, and whether these three factors contribute to improve business performance. Design/methodology/approach - A sample of 241 Brazilian companies was surveyed, using Web-based questionnaires with 54 questions, using ten-point scales to measure the degree of agreement on each item of each construct. Structural equation modeling techniques were applied for model assessment and analysis of the relationships among constructs. Exploratory factor analysis, confirmatory factor analysis, and path analysis using the technique of structural equation modeling were applied to the data. Findings - Effective KM contributes positively to strategic orientation. Although there is no significant direct effect of KM on innovativeness, the relationship is significant when mediated by strategic orientation. Similarly effective KM has no direct effect on business performance, but this relationship becomes statistically significant when mediated by strategic orientation and innovativeness. Research limitations/implications - The findings indicate that KM permeates all relationships among the constructs, corroborating the argument that knowledge is an essential organizational resource that leverages all value-creating activities. The results indicate that both KM and innovativeness produce significant impacts on performance when they are aligned with a strategic orientation that enables the organization to anticipate and respond to changing market conditions. Originality/value - There is a substantial body of research on several types of relationships involving KM, strategic orientation, innovativeness and performance. This study offers an original contribution by analyzing all of those constructs simultaneously using established scales so that comparative studies are possible.

Descriptions of Thereza murutinga sp. nov. and Pristocnemis caipira sp. nov., and new records of Caelopyginae (Opiliones: Laniatores: Gonyleptidae)

Two new species of Caelopyginae are described: Pristocnemis caipira sp. nov. from Parque Nacional da Serra da Canastra, Minas Gerais, Brazil, and Thereza murutinga sp. nov., from Parati, Rio de Janeiro, Brazil. Pristocnemis caipira sp. nov. is diagnosed by shallow grooves on the dorsal scutum, a lower number of tarsal segments, presence of a spine on the anal operculum, large, pointed tubercles on the lateral margins of the dorsal scutum, and an absence of white patches on the dorsal scutum. Thereza murutinga sp. nov. is diagnosed by the combination of the following characters: incomplete median longitudinal groove on area III and absent on area II, prosoma much smaller than opisthosoma, and a large white patch covering the prosoma and whole areas of the opisthosomal scutum. A cladistic analysis including the two new species was performed to investigate their relationship within the subfamily. We obtained 927 trees of 185 steps (CI=0.4, RI=0.74), which corroborated the generic assignments of the new species, but infrageneric relationships remained unsolved. In addition, male genitalia of Ampheres luteus (Giltay) and genera Pristocnemis and Thereza are redescribed, new distribution records for Caelopyginae species are presented, and biogeographical implications are discussed.

The Global Paleomonsoon as seen through speleothem records from Asia and the Americas

The regional monsoons of the world have long been viewed as seasonal atmospheric circulation reversal-analogous to a thermally-driven land-sea breeze on a continental scale. This conventional view of monsoons is now being integrated at a global scale and accordingly, a new paradigm has emerged which considers regional monsoons to be manifestations of global-scale seasonal changes in response to overturning of atmospheric circulation in the tropics and subtropics, and henceforth, interactive components of a singular Global Monsoon (GM) system. The paleoclimate community, however, tends to view 'paleomonsoon' (PM), largely in terms of regional circulation phenomena. In the past decade, many high-quality speleothem oxygen isotope (delta O-18) records have been established from the Asian Monsoon and the South American Monsoon regions that primarily reflect changes in the integrated intensities of monsoons on orbital-to-decadal timescales. With the emergence of these high-resolution and absolute-dated records from both sides of the Equator, it is now possible to test a concept of the 'Global-Paleo-Monsoon' (GPM) on a wide-range of timescales. Here we present a comprehensive synthesis of globally-distributed speleothem delta O-18 records and highlight three aspects of the GPM that are comparable to the modern GM: (1) the GPM intensity swings on different timescales; (2) their global extent; and (3) an anti-phased inter-hemispheric relationship between the Asian and South American monsoon systems on a wide range of timescales.

Records of sedimentary dynamics in the continental shelf and upper slope between Aveiro-Espinho (N Portugal)

The sedimentary unconsolidated cover of the Aveiro-Espinho continental shelf and upper slope (NW Portugal) records a complex interplay of processes including wave energy and currents, fluvial input, sediment transport alongshore and cross-shelf, geological and oceanographic processes and sediment sources and sinks. In order to study this record, a set of surface sediment samples was studied. Sediment grain size and composition, as well as the mineralogical composition (by XRD) of the fine (<63 mu m) and clay (<2 mu m) fractions and benthic microfaunal (foraminifera) data were analysed. Cluster analysis applied to the sedimentological data (grain size, sediment composition and mineralogy) allowed the establishment of three main zones corresponding to the: inner-, mid- and outer-shelf/upper slope. On the inner-shelf, the sedimentary coverture is composed of siliciclastic fine to very fine sand, essentially comprising modern (immature) terrigenous particles. The sediment grain size, as well as mineralogical and microfaunal composition, denote the high energetic conditions of this sector in which the alongshore transport of sand is predominantly southward and occurs mostly during the spring-summer oceanographic regime, when the main river providing sediments to this area, the River Douro, undergoes periods of drought. This effect may emphasize the erosive character of this coastal sector at present, since the Ria de Aveiro provides the shelf with few sediments. On the mid-shelf, an alongshore siliciclastic band of coarse sand and gravel can be found between the 40 m and 60 m isobaths. This gravelly deposit includes relic sediments deposited during lower sea-level stands. This structure stays on the surface due to the high bottom energy, which promotes the remobilization of the fine-grained sediments, and/or events of sediments bypassing. Benthic foraminifera density and "Benthic Foraminifera High Productivity" (BFHP) proxy values are in general low, which is consistent with the overall small supply of organic matter to the oceanic bottom in the inner- and mid-shelf. However, the Ria de Aveiro outflow, which delivers organic matter to the shelf, leaves its imprint mainly on the mid-shelf, identifiable by the increase in foraminifera density and BFHP values in front of the lagoon mouth. The higher values of BFHP along the 100 m isobath trace the present position of an oceanic thermal front whose situation may have changed in the last 3/5 ka BP. This zone marks a clear difference in the density, diversity and composition of benthic foraminifera assemblages. Here, in addition, sediment composition changes significantly, giving rise to carbonate-rich fine to medium sand in the deeper sector. The low bottom energy and the small sedimentation rate of the outer-shelf contributed to the preservation of a discontinuous carbonate-rich gravel band, between the 100 m and 140 m isobaths, also related to paleo-littorals, following the transgression that has occurred since the Last Glacial Maximum. The winter oceanographic regime favours the transport of fine grained sediments to the outer-shelf and upper slope. The inner- and mid-shelf, however, have low amounts of this kind of sediment and the Cretacic carbonated complexes Pontal da Galega and Pontal da Cartola, rocky outcrops located at the mid- and outer-shelf, act as morphological barriers to the cross-shelf transport of sediments. Thus a reduced sedimentation rate occurs in these deeper sectors, as indicated by the lower abundance of detrital minerals, which is compensated for the high sedimentary content of biogenic carbonates. The relatively high BFHP and Shannon Index values indicate water column stratification, high supply of organic matter and environmental stability, which provide favourable conditions for a diversified benthic fauna to flourish. These conditions also encourage authigenic chemical changes, favourable to glauconite formation, as well as illite and kaolinite degradation. Benthic foraminifera and clay mineral assemblages also reveal the effect of the internal waves pushing upward, and downslope losses of the sediments on the outer-shelf and upper slope.