Glass box machine learning for retrospective cohort studies using many patient records. The complex example of bleeding peptic ulcer.

Glass Box Machine Learning is, in this study, a type of partially supervised data mining and prediction technique, like a neural network in which each weight or pattern of mutually relevant weights is now replaced by a meaningful "probabilistic knowledge element." We apply it to retrospective cohort studies using large numbers of structured medical records to help select candidate patients for future cohort studies and similar clinical trials. Here it is applied to aid analysis of approaches to aid Deep Learning, but the method lends itself well to direct computation of odds with "explainability" in study design that can complement "Black Box" Deep Learning. Cohort studies and clinical trials traditionally involved at least one 2 × 2 contingency table, but in the age of emerging personalized medicine and the use of machine learning to discover and incorporate further relevant factors, these tables can extend into many extra dimensions as a 2 × 2 x 2 × 2 x ….data structure by considering different conditional demographic and clinical factors of a patient or group, as well as variations in treatment. We consider this in terms of multiple 2 × 2 x 2 data substructures where each one is summarized by an appropriate measure of risk and success called DOR*. This is the diagnostic odds ratio DOR for a specified disease conditional on a favorable outcome divided by the corresponding DOR conditional on an unfavorable outcome. Bleeding peptic ulcer was chosen as a complex disease with many influencing factors, one that is still subject to controversy and that highlights the challenges of using Real World Data.

Effects of atmospheric low-level jets on the mixing process of a large tropical reservoir.

Changes in the physical and biogeochemical properties of water columns are frequently associated with cold fronts and mesoscale convective systems due to increased cloud cover. The effects of low-level jet (LLJ) events on thermal stratification and water quality, however, remain undescribed, particularly for tropical reservoirs. Here, water temperature time series are combined with meteorological data, LIDAR observations, ERA5 reanalysis data, and hydrodynamical modeling to investigate the impact of an event of LLJ over the Furnas hydropower reservoir in Brazil. The LLJ event was characterized by dry, intense, and persistent winds (~10 m s-1) blowing for more than 12 hours over the main fetch of the reservoir. In the downwind side of the lake, the surface mixed layer depth increased by 50% during the LLJ event. The changes to the water column were produced by a combination of wind-induced upwelling, shear-driven mixing, and nocturnal convective overturning, different from the heat balance expected during passing cold fronts and mesoscale convective systems. The results suggest that both momentum and heat fluxes during LLJ events need to be accounted for in lake modelings to reproduce the vertical mixing process.

Towards faster response against emerging epidemics and prediction of variants of concern.

The author, the journal, Computers in Biology and Medicine (CBM), and Elsevier Press more generally, played a helpful very early role in responding to COVID-19. Within a few days of the appearance of the "Wuhan Seafood isolate" genome on GenBank, a bioinformatics study was posted by the present author in ResearchGate in January 2020, "Preliminary Bioinformatics Studies on the Design of Synthetic Vaccines and Preventative Peptidomimetic Antagonists against the Wuhan Seafood Market Coronavirus. Possible Importance of the KRSFIEDLLFNKV Motif" DOI: 10.13140/RG.2.2.18275.09761. On February 2nd, 2020, a more thorough analysis was submitted to CBM, e-published on February 26, and formally published in April 2020, at about the same time as the virus named as 2019n-CoV was identified as essentially SARS and renames SARS-COV-2. This was followed by four further papers describing in more detail some previously unreported aspects of the early investigation. The speed of research and writing of the papers was made possible by knowledge-gathering tools. Based on this and earlier experiences with fast responses to emerging epidemics such as HIV and Mad Cow Disease, it is possible to envisage the nature of a speedier response to emerging epidemics and new variants of concern in established epidemics.

Techniques assisting peptide vaccine and peptidomimetic design. Sidechain exposure in the SARS-CoV-2 spike glycoprotein.

The aim of the present study is to discuss the design of peptide vaccines and peptidomimetics against SARS-COV-2, to develop and apply a method of protein structure analysis that is particularly appropriate to applying and discussing such design, and also to use that method to summarize some important features of the SARS-COV-2 spike protein sequence. A tool for assessing sidechain exposure in the SARS-CoV-2 spike glycoprotein is described. It extends to assessing accessibility of sidechains by considering several different three-dimensional structure determinations of SARS-CoV-2 and SARS-CoV-1 spike protein. The method is designed to be insensitive to a distance limit for counting neighboring atoms and the results are in good agreement with the physical chemical properties and exposure trends of the 20 naturally occurring sidechains. The spike protein sequence is analyzed with comment regarding exposable character. It includes studies of complexes with antibody elements and ACE2. These indicate changes in exposure at sites remote to those at which the antibody binds. They are of interest concerning design of synthetic peptide vaccines, and for peptidomimetics as a basis of drug discovery. The method was also developed in order to provide linear (one-dimensional) information that can be used along with other bioinformatics data of this kind in data mining and machine learning, potentially as genomic data regarding protein polymorphisms to be combined with more traditional clinical data.

Quantitative study of wild animals received at the Wild Animals Triage Centers (CETAS) in Bahia and identification of trafficking routes

ABSTRACT: In Brazil, the illegal capture of wild animals is a crime that contributes to the extinction of species, besides causing environmental imbalance and suffering to the animals. Here, we undertook a quantitative survey of animals sent to the Centro de Triagem de Animais Silvestres (CETAS - Wild Animals Triage Centers) from units of Porto Seguro, Salvador, and Vitória da Conquista during 2009-2019. The 19,317, 34,460, and 43,874 specimens were registered in the units of Porto Seguro, Vitória da Conquista, and Salvador, respectively. The distribution of the totals by class included 80,948 (82.90%) birds, 12,007 (12.30%) reptiles, 4,661 (4.77%) mammals, and 35 arachnids (0.03%). The operations that generated registration at the CETAS were most frequently apprehensions (67,974; 69.67%), followed by voluntary surrender (13,367; 13.69%), rescues (12,803; 13.11%), and transfers (2,735; 2.67%). The animals came from 236 municipalities in the state of Bahia, with emphasis on the municipalities of Salvador, Vitória da Conquista, Feira de Santana, Lençóis, Jequié, and Paulo Afonso. The evaluation of the quantitative seizures by municipalities indicates that the BR-116 is one of the most representative routes for the illegal traffic of wild animals in the state of Bahia and the country.

RESUMO: No Brasil a captura ilegal de animais silvestres é crime e contribui para a extinção das espécies, além de causar desequilíbrios ambientais e sofrimentos aos animais. Este trabalho apresenta quantitativos de animais recebidos e/ou armazenados nos Centros de Triagem de Animais Silvestres (CETAS) do estado da Bahia, no período de 2009-2019. Os totais de 19.317, 34.460 e 43.874 espécimes foram registrados nas unidades de Porto Seguro, Vitória da Conquista e Salvador, respectivamente. A distribuição dos totais por classe incluiu 80.948 (82,90%) aves, 12.007 (12,30%) répteis, 4.661 (4,77%) mamíferos e 35 aracnídeos. Quanto à natureza da operação que gerou o registro nos CETAS, as mais frequentes foram apreensão (67.974; 69,67%), entrega voluntária (13.367; 13,69%), resgate (12.803; 13,11%) e transferência (2.735; 2,67%). Os animais foram apreendidos em 236 municípios do estado da Bahia, com destaque para Salvador, Vitória da Conquista, Feira de Santana, Lençóis, Jequié e Paulo Afonso. A avaliação dos quantitativos das apreensões por municípios indica que a BR-116 é uma das rotas de escoamento mais representativa do tráfico ilegal de animais silvestres, no estado da Bahia e no país.

Quantitative study of wild animals received at the Wild Animals Triage Centers (CETAS) in Bahia and identification of trafficking routes / Estudo quantitativo de animais silvestres recebidos nos Centros de Triagens de Animais Silvestres (CETAS) da Bahia e identificação de rotas de tráfico

In Brazil, the illegal capture of wild animals is a crime that contributes to the extinction of species, besides causing environmental imbalance and suffering to the animals. Here, we undertook a quantitative survey of animals sent to the "Centro de Triagem de Animais Silvestres" (CETAS - Wild Animals Triage Centers) from units of Porto Seguro, Salvador, and Vitória da Conquista during 2009-2019. The 19,317, 34,460, and 43,874 specimens were registered in the units of Porto Seguro, Vitória da Conquista, and Salvador, respectively. The distribution of the totals by class included 80,948 (82.90%) birds, 12,007 (12.30%) reptiles, 4,661 (4.77%) mammals, and 35 arachnids (0.03%). The operations that generated registration at the CETAS were most frequently apprehensions (67,974; 69.67%), followed by voluntary surrender (13,367; 13.69%), rescues (12,803; 13.11%), and transfers (2,735; 2.67%). The animals came from 236 municipalities in the state of Bahia, with emphasis on the municipalities of Salvador, Vitória da Conquista, Feira de Santana, Lençóis, Jequié, and Paulo Afonso. The evaluation of the quantitative seizures by municipalities indicates that the BR-116 is one of the most representative routes for the illegal traffic of wild animals in the state of Bahia and the country.(AU)

No Brasil a captura ilegal de animais silvestres é crime e contribui para a extinção das espécies, além de causar desequilíbrios ambientais e sofrimentos aos animais. Este trabalho apresenta quantitativos de animais recebidos e/ou armazenados nos Centros de Triagem de Animais Silvestres (CETAS) do estado da Bahia, no período de 2009-2019. Os totais de 19.317, 34.460 e 43.874 espécimes foram registrados nas unidades de Porto Seguro, Vitória da Conquista e Salvador, respectivamente. A distribuição dos totais por classe incluiu 80.948 (82,90%) aves, 12.007 (12,30%) répteis, 4.661 (4,77%) mamíferos e 35 aracnídeos. Quanto à natureza da operação que gerou o registro nos CETAS, as mais frequentes foram apreensão (67.974; 69,67%), entrega voluntária (13.367; 13,69%), resgate (12.803; 13,11%) e transferência (2.735; 2,67%). Os animais foram apreendidos em 236 municípios do estado da Bahia, com destaque para Salvador, Vitória da Conquista, Feira de Santana, Lençóis, Jequié e Paulo Afonso. A avaliação dos quantitativos das apreensões por municípios indica que a BR-116 é uma das rotas de escoamento mais representativa do tráfico ilegal de animais silvestres, no estado da Bahia e no país.(AU)

Lesions of the sheep reproductive system found in a slaughterhouse in the state of Bahia, Brazil / Lesões do sistema reprodutor em ovelhas de abatedouros frigoríficos no estado da Bahia

The present study aimed to evaluate and diagnose pathologies of the reproductive system of slaughtered sheep in slaughterhouses in the state of Bahia since there are few data on the subject as well as it is important to note the diagnosis of these diseases to apply appropriate control and prophylaxis measures. The research was carried out in slaughterhouses in the state of Bahia according to the "Serviço de Inspeção Federal" and "Serviço de Inspeção Estadual" for sheep slaughter. From July 2018 to February 2019, visits and monitoring of 1,072 slaughtered sheep were carried out. The animals came from 22 municipalities in the state of Bahia, aged from six to 18 months. During slaughter, the sheep reproductive systems were sectioned for evisceration and lesion collection. Additionally, epidemiological surveys related to origin, age, and race were obtained. For bacteriological examination, collections were performed with sterile scalpel slides and swabs in Stuart medium sterile tubes and refrigerated in a thermal box. For histopathological analysis, fragments were fixed in 10% formaldehyde and routinely processed for histology, stained with Hematoxylin and Eosin (HE). A study of the sheep's main pathological changes in slaughterhouses in the state of Bahia was carried out, in which 1.072 genital systems were evaluated, and 211 alterations were identified. The most affected reproductive organs were the ovaries (65.3%), followed by the uterus (29.4%) and uterine tubes (5.3%). In the ovaries, the most frequent lesion was a follicular cyst (34.1%); in the fallopian tubes, the cysts represented 3.3% of the lesions, and in the womb, endometritis was observed in 9% of the animals. Other pathologies identified in the ovaries were: luteinized cyst (2.3%); cystic granulosa cell tumor (0.5%); benign lesion (0.5%); agenesis unilateral (0.5%), in addition to other changes of little clinical significance, such as corpus luteum cysts (11.8%) and paraovarian cysts (15.6%). In the fallopian tubes, hydrosalpinx was observed (1%), as well as adenoma (0.5%), agenesis (0.5%), and cysts (3.3%). Uterine lesions included hydrometra (2.3%); Cystic Endometrial Hyperplasia (CEH), abscess, and pyometra (1.4% each); adenomyosis, womb sera petechiae, and total segmental aplasia (1% each); two pregnant uterus, in early pregnancy, presented pyometra (0.9%), however, no change was observed in the fetuses; and uterine polyp (0.5%). Ectopic pregnancy with fetal maceration (0.5%) was observed; vaginitis occurred in 0.5% of the animals, and endometrial melanosis in 8.5%. The high incidence of follicular cysts and endometritis are characterized as diseases that reduce the reproductive efficiency in herds, causing infertility and economic losses in production.(AU)

O objetivo do presente trabalho foi avaliar e diagnosticar alterações do sistema reprodutor de ovelhas abatidas em abatedouros frigoríficos no estado da Bahia. A pesquisa foi realizada em abatedouros frigoríficos do estado da Bahia com Serviços de Inspeção Federal e Estadual no abate de ovinos. No período de julho de 2018 a fevereiro de 2019 foram realizadas visitas e acompanhamento do abate de 1.072 ovelhas. Os animais eram provenientes de 22 municípios do estado da Bahia, com idade entre 6 a 18 meses. Durante o abate, na evisceração foram seccionados os sistemas reprodutores das ovelhas para avaliação e coleta das lesões. Adicionalmente foram obtidos inquéritos epidemiológicos relacionados à procedência, idade e raça. Para o exame bacteriológico, as coletas foram realizadas com lâminas de bisturi estéreis e swabs em tubos estéreis com meio Stuart e refrigeradas em caixa térmica. Para análise histopatológica, os fragmentos foram fixados em formol a 10% e processados de forma rotineira para histologia e corados pela hematoxilina e eosina (HE). Entre 1.072 sistemas genitais avaliados, identificou-se 211 alterações. Os órgãos do sistema reprodutor mais acometidos foram os ovários (65,3%), útero (29,4%) e tubas uterinas (5,3%). Nos ovários, a lesão mais frequente foi o cisto folicular (34,1%); no útero a endometrite (9%) e nas tubas uterinas, os cistos representaram (3,3%). Outras lesões identificadas nos ovários foram: cisto luteinizado (2,3%); tumor de células da granulosa (0,5%); adenoma (0,5%); agenesia unilateral (0,5%), além de outras alterações de pouco significado clínico, como cistos paraovarianos (15,6%) e corpo lúteo cístico (11,8%). Nas tubas uterinas observou-se, além dos cistos tubo-ovarianos (3,3%), hidrossalpinge (1%), adenoma (0,5%) e agenesia (0,5%). As lesões uterinas foram endometrite (9%), hidrometra (2,3%); hiperplasia endometrial cística, abscesso e piometra (1,4% cada); adenomiose, petéquias na serosa do útero e aplasia segmentar (1% cada); dois úteros gravídicos, em início de gestação, apresentaram piometra (0,9%), porém os fetos não apresentaram alterações; e pólipo uterino (0,5%). Observou-se uma gestação ectópica com maceração fetal (0,5%); a vaginite ocorreu em 0,5%, e melanose endometrial em 8,5%. Destaca-se a elevada incidência de cistos foliculares e endometrite que são doenças que reduzem a eficiência reprodutiva dos rebanhos, provocando infertilidade e perdas econômicas na produção.(AU)

The use of knowledge management tools in viroinformatics. Example study of a highly conserved sequence motif in Nsp3 of SARS-CoV-2 as a therapeutic target.

Knowledge management tools that assist in systematic review and exploration of scientific knowledge generally are of obvious potential importance in evidence based medicine in general, but also to the design of therapeutics based on the protein subsequences and fold motifs of virus proteins as considered here. Rapid access to bundles (clusters) of related elements of knowledge gathered from diverse sources on the Internet and from growing knowledge repositories seem particularly helpful when exploring less obvious therapeutic targets in viruses (for which knowledge new to the researcher is important), and when using the following concept. Subsequences of amino acid residue sequences of proteins that are conserved across strains and species are (a) more likely to be important targets and (b) less likely to exhibit escape mutations that would make them resistant to vaccines and therapeutic agents. However, the terms "conserved" and even "highly conserved" used by authors are matters of degree, depending on how distant from SARS-CoV-2 they wished to go in comparing other sequences. The binding site to the human ACE2 protein as virus receptor and human antibody CR3022 binding site on the spike glycoprotein are rather variable by the criteria used in the present and preceding studies. To look for more strongly conserved targets, open reading frames of SARS-CoV-2 were examined for extremely highly conserved regions, meaning recognizable across many viruses and organisms. Most prominent is a motif found in SARS-CoV-2 non-structural protein 3 (Nsp3). It relates to a fold called type called the macro domain and has remarkably wide distribution across organisms including humans with significant homologies involving three especially conserved subsequences (a) VVVNAANVYLKHGGGVAGALNK, (b) LHVVGPNVNKG, and (c) PLLSAGIFG. Careful study of the variations of these and of the more variable sequences between and around them might provide a finer "scalpel" to ensure inhibition of a vital function of the virus without impairing the functions of related host macro domains.

Bioinformatics studies on a function of the SARS-CoV-2 spike glycoprotein as the binding of host sialic acid glycans.

SARS-CoV and SARS-CoV-2 do not appear to have functions of a hemagglutinin and neuraminidase. This is a mystery, because sugar binding activities appear essential to many other viruses including influenza and even most other coronaviruses in order to bind to and escape from the glycans (sugars, oligosaccharides or polysaccharides) characteristic of cell surfaces and saliva and mucin. The S1 N terminal Domains (S1-NTD) of the spike protein, largely responsible for the bulk of the characteristic knobs at the end of the spikes of SARS-CoV and SARS-CoV-2, are here predicted to be "hiding" sites for recognizing and binding glycans containing sialic acid. This may be important for infection and the ability of the virus to locate ACE2 as its known main host cell surface receptor, and if so it becomes a pharmaceutical target. It might even open up the possibility of an alternative receptor to ACE2. The prediction method developed, which uses amino acid residue sequence alone to predict domains or proteins that bind to sialic acids, is naïve, and will be advanced in future work. Nonetheless, it was surprising that such a very simple approach was so useful, and it can easily be reproduced in a very few lines of computer program to help make quick comparisons between SARS-CoV-2 sequences and to consider the effects of viral mutations.

COVID-19 Coronavirus spike protein analysis for synthetic vaccines, a peptidomimetic antagonist, and therapeutic drugs, and analysis of a proposed achilles' heel conserved region to minimize probability of escape mutations and drug resistance.

This paper continues a recent study of the spike protein sequence of the COVID-19 virus (SARS-CoV-2). It is also in part an introductory review to relevant computational techniques for tackling viral threats, using COVID-19 as an example. Q-UEL tools for facilitating access to knowledge and bioinformatics tools were again used for efficiency, but the focus in this paper is even more on the virus. Subsequence KRSFIEDLLFNKV of the S2' spike glycoprotein proteolytic cleavage site continues to appear important. Here it is shown to be recognizable in the common cold coronaviruses, avian coronaviruses and possibly as traces in the nidoviruses of reptiles and fish. Its function or functions thus seem important to the coronaviruses. It might represent SARS-CoV-2 Achilles' heel, less likely to acquire resistance by mutation, as has happened in some early SARS vaccine studies discussed in the previous paper. Preliminary conformational analysis of the receptor (ACE2) binding site of the spike protein is carried out suggesting that while it is somewhat conserved, it appears to be more variable than KRSFIEDLLFNKV. However compounds like emodin that inhibit SARS entry, apparently by binding ACE2, might also have functions at several different human protein binding sites. The enzyme 11ß-hydroxysteroid dehydrogenase type 1 is again argued to be a convenient model pharmacophore perhaps representing an ensemble of targets, and it is noted that it occurs both in lung and alimentary tract. Perhaps it benefits the virus to block an inflammatory response by inhibiting the dehydrogenase, but a fairly complex web involves several possible targets.

Physical Inactivity is Liable to the Increased Cardiovascular Risk and Impaired Cognitive Profile.

BACKGROUND: Sedentary life-style is a significant public health issue. It increases the incidence of type-2 diabetes mellitus (DM2) and systemic arterial hypertension (SAH), which in turn may impair physical and mental health. In fact, disrupted glucose metabolism is characteristic of Alzheimer's dementia, and it is often dubbed as type-3 diabetes. OBJECTIVE: The purpose of this study was to assess the level of activity, body composition, cardiovascular risk and cognitive profile of patients with DM2 and/or SAH. The study was cross-sectional design. METHOD: The sample consisted of 120 individuals which 35% men and 65% women, with an average of 64±9 years old and 60±11 years old, respectively. Various parameters were evaluated such as anthropometric variables, pedometer recordings and brief cognitive screening battery (BCSB), which assesses the immediate memory, verbal fluency, learning, late memory and recognition. Chi-square and Fisher's exact test were applied to observe possible differences between men and women. In addition to Kruskall-Wallis, in the comparison between patients with SAH; DM2 and SAH + DM2. RESULTS: A high rate of physical inactivity was found among those enrolled in this project. Females were characterized by increased body fat, whereas men displayed visceral fat excess. BCSB demonstrated reduced verbal fluency, late memory and recognition, with women presenting significantly worse results. CONCLUSION: Low level of daily physical activity is apparently correlated with obesity, elevated cardiovascular risk, and cognitive dysfunction.

Computers and viral diseases. Preliminary bioinformatics studies on the design of a synthetic vaccine and a preventative peptidomimetic antagonist against the SARS-CoV-2 (2019-nCoV, COVID-19) coronavirus.

This paper concerns study of the genome of the Wuhan Seafood Market isolate believed to represent the causative agent of the disease COVID-19. This is to find a short section or sections of viral protein sequence suitable for preliminary design proposal for a peptide synthetic vaccine and a peptidomimetic therapeutic, and to explore some design possibilities. The project was originally directed towards a use case for the Q-UEL language and its implementation in a knowledge management and automated inference system for medicine called the BioIngine, but focus here remains mostly on the virus itself. However, using Q-UEL systems to access relevant and emerging literature, and to interact with standard publically available bioinformatics tools on the Internet, did help quickly identify sequences of amino acids that are well conserved across many coronaviruses including 2019-nCoV. KRSFIEDLLFNKV was found to be particularly well conserved in this study and corresponds to the region around one of the known cleavage sites of the SARS virus that are believed to be required for virus activation for cell entry. This sequence motif and surrounding variations formed the basis for proposing a specific synthetic vaccine epitope and peptidomimetic agent. The work can, nonetheless, be described in traditional bioinformatics terms, and readily reproduced by others, albeit with the caveat that new data and research into 2019-nCoV is emerging and evolving at an explosive pace. Preliminary studies using molecular modeling and docking, and in that context the potential value of certain known herbal extracts, are also described.

Seroprevalence and risk factors associated with equineleptospirosis in the metropolitan region of Salvador and Recôncavo Baiano region, Bahia state (NE Brazil).

Equine leptospirosis, although usually asymptomatic, has been associated with recurrent uveitis, abortion, and other systemic signs, constituting a major economic loss in the equine agribusiness sector. The occurrence of anti-Leptospira spp. agglutinins were investigated in 1200 serum samples of horses from 27 municipalities of the Recôncavo Baiano region, Bahia state (NE Brazil), besides the risk factors related to animals and their cattle farms. The microscopic agglutination test (MAT) was performed using 13 serogroups of Leptospira spp. as antigens. From 1200 analyzed equines, 97 (8%) were considered as positive, which obtained titer equal to or higher than 200. In 22 (78.6%) from the 28 properties, at least one animal was detected as seropositive. The most prevalent serogroup in animals, raised in stables, was the Australis (serovar Bratislava) 67%; in mounted police animals was the Sejroe (serovar Wolffi and Hardjobovis) 50%; and equestrian animals was the Australis (serovar Bratislava) 25% and Icterohaemorrhagiae (serovar Copenhageni) 25%. Equine leptospirosis is present in most cattle farms of the region studied. The risk factors of major importance regarded the semi-extensive livestock farming, the land topography of the cattle farm, the contact with animals in neighboring properties, and cohabitation with goats.

Fine sediment and particulate organic matter: A review and case study on ridge-to-reef transport, transformations, fates, and impacts on marine ecosystems.

Studies documenting the effects of land-derived suspended particulate matter (SPM, i.e., particulate organic matter and mineral sediment) on marine ecosystems are typically disconnected from terrestrial studies that determine their origin, transport and fate. This study reviews sources, transport, transformations, fate and effects of SPM along the 'ridge-to-reef' continuum. We show that some of the SPM can be transported over long distances and transformed into large and easily resuspendible organic-rich sediment flocs. These flocs may lead to prolonged reductions in water clarity, impacting upon coral reef, seagrass and fish communities. Using the Great Barrier Reef (NE Australia) as a case study, we identify the latest research tools to determine thresholds of SPM exposure, allowing for an improved appreciation of marine risk. These tools are used to determine ecologically-relevant end-of-basin load targets and reliable marine water quality guidelines, thereby enabling enhanced prioritisation and management of SPM export from ridge-to-reef.

Simulated fate of catchment-derived sediment on the Great Barrier Reef shelf.

Numerical experiments using a 3D model of fine sediment transport in the Great Barrier Reef region indicate deposition of the bulk mass of catchment sediments from river plumes within a few tens of kilometres from river mouths. A very fine fraction of easily resuspended catchment sediment has a capacity to propagate over much greater distances reaching out into the mid-shelf and outer-shelf regions. The model suggests such particles, instrumental to the development of low density flocs in the marine environment, can play a critical role in altering optical properties of water masses over the shelf during wet years. The mid-term (4 year) impact of Great Barrier Reef catchments on the probability of suspended sediment concentration exceeding the ecologically significant trigger value of 2 mg/L is confined to inshore regions adjacent to river mouth locations.

Nem todo abscesso em pequenos ruminantes é causado por Corynebacterium pseudotuberculosis / Not all abscesses in small ruminants are caused by Corynebacterium pseudotuberculosis

O presente estudo objetivou determinar a prevalência e distribuição de lesões abscedativas, identificação do agente etiológico e avaliação das lesões histológicas em caprinos e ovinos abatidos em um matadouro-frigorífico com Serviço de Inspeção Federal do estado da Bahia. Foram coletadas 153 amostras de vísceras e linfonodos com abscessos de 1.148 animais abatidos. A maior prevalência na espécie ovina foi em macho, com faixa etária de 12 meses, sendo os principais órgãos acometidos fígado (21,2%) e linfonodo pré-escapular (20,3%). Na espécie caprina, a prevalência maior foi em macho, com faixa etária de 30 meses, sendo os linfonodos retro faríngeo (25%) e pré-escapular os mais acometidos (25%). Isolou-se os seguintes micro-organismos das amostras: Corynebacterium pseudotuberculosis em 33,33%, Escherichia coli (19,61%), Proteus mirabilis (9,80%), Pseudomonas aeruginosa (7,19%), Trueperella pyogenes (5,22%), Streptococcusspp. (5,22%) e Staphylococcus aureus (4,57%). As lesões macroscópicas e histológicas dos abscessos coletados não apresentaram diferenças entre micro-organismos isolados.(AU)

The study aimed to determine the prevalence and distribution of abscessed lesions, etiologic agent identification and assessment of histological lesions in sheep and goats slaughtered in a slaughter plant refrigerator with Federal Inspection Service in the State of Bahia. The amount of 153 samples of viscera and lymph nodes with abscesses of 1.148 slaughtered animals were collected. The highest prevalence in sheep was in males, aged 12 months, as in liver (21.2%) and prescapular lymph nodes (20.3%) the main affected organs. The prevalence in goats in male, aged 30 months and in retropharyngeal (25%) and prescapular lymph nodes (25%). The following microorganisms were isolated from the samples: Corynebacterium pseudotuberculosis 33.33%, Escherichia coli 19.61%, Proteus mirabilis 9.80%, Pseudomonas aeruginosa 7.19%, Trueperella pyogenes 5.22%, Streptococcus spp. 5.22% and Staphylococcus aureus 4.57%. The macroscopic and histological lesions of abscesses collected presented no difference between isolated microorganisms.(AU)

In vitro antimicrobial and antimycobacterial activity and HPLC-DAD screening of phenolics from Chenopodium ambrosioides L

Abstract The main objective of this study was to demonstrate the antimicrobial potential of the crude extract and fractions of Chenopodium ambrosioides L., popularly known as Santa-Maria herb, against microorganisms of clinical interest by the microdilution technique, and also to show the chromatographic profile of the phenolic compounds in the species. The Phytochemical screening revealed the presence of cardiotonic, anthraquinone, alkaloids, tannins and flavonoids. The analysis by HPLC-DAD revealed the presence of rutin in the crude extract (12.5 ± 0.20 mg/g), ethyl acetate (16.5 ± 0.37 mg/g) and n-butanol (8.85 ± 0.11 mg/g), whereas quercetin and chrysin were quantified in chloroform fraction (1.95 ± 0.04 and 1.04 ± 0.01 mg/g), respectively. The most promising results were obtained with the ethyl acetate fraction, which inhibited a greater number of microorganisms and presented the lowest values of MIC against Staphylococcus aureus and Enterococcus faecalis (MIC = 0.42 mg/mL), Pseudomonas aeruginosa (MIC = 34.37 mg/mL), Paenibacillus apiarus (MIC = 4.29 mg/mL) and Paenibacillus thiaminolyticus (MIC = 4.29 mg/mL). Considering mycobacterial inhibition, the best results were obtained by chloroform fraction against M. tuberculosis, M. smegmatis, and M. avium (MIC ranging from 156.25 to 625 µg/mL). This study proves, in part, that the popular use of C. ambrosioides L. can be an effective and sustainable alternative for the prevention and treatment of diseases caused by various infectious agents.

Studies in the extensively automatic construction of large odds-based inference networks from structured data. Examples from medical, bioinformatics, and health insurance claims data.

Theoretical and methodological principles are presented for the construction of very large inference nets for odds calculations, composed of hundreds or many thousands or more of elements, in this paper generated by structured data mining. It is argued that the usual small inference nets can sometimes represent rather simple, arbitrary estimates. Examples of applications in clinical and public health data analysis, medical claims data and detection of irregular entries, and bioinformatics data, are presented. Construction of large nets benefits from application of a theory of expected information for sparse data and the Dirac notation and algebra. The extent to which these are important here is briefly discussed. Purposes of the study include (a) exploration of the properties of large inference nets and a perturbation and tacit conditionality models, (b) using these to propose simpler models including one that a physician could use routinely, analogous to a "risk score", (c) examination of the merit of describing optimal performance in a single measure that combines accuracy, specificity, and sensitivity in place of a ROC curve, and (d) relationship to methods for detecting anomalous and potentially fraudulent data.

In vitro antimicrobial and antimycobacterial activity and HPLC-DAD screening of phenolics from Chenopodium ambrosioides L.

The main objective of this study was to demonstrate the antimicrobial potential of the crude extract and fractions of Chenopodium ambrosioides L., popularly known as Santa-Maria herb, against microorganisms of clinical interest by the microdilution technique, and also to show the chromatographic profile of the phenolic compounds in the species. The Phytochemical screening revealed the presence of cardiotonic, anthraquinone, alkaloids, tannins and flavonoids. The analysis by HPLC-DAD revealed the presence of rutin in the crude extract (12.5±0.20mg/g), ethyl acetate (16.5±0.37mg/g) and n-butanol (8.85±0.11mg/g), whereas quercetin and chrysin were quantified in chloroform fraction (1.95±0.04 and 1.04±0.01mg/g), respectively. The most promising results were obtained with the ethyl acetate fraction, which inhibited a greater number of microorganisms and presented the lowest values of MIC against Staphylococcus aureus and Enterococcus faecalis (MIC=0.42mg/mL), Pseudomonas aeruginosa (MIC=34.37mg/mL), Paenibacillus apiarus (MIC=4.29mg/mL) and Paenibacillus thiaminolyticus (MIC=4.29mg/mL). Considering mycobacterial inhibition, the best results were obtained by chloroform fraction against M. tuberculosis, M. smegmatis, and M. avium (MIC ranging from 156.25 to 625µg/mL). This study proves, in part, that the popular use of C. ambrosioides L. can be an effective and sustainable alternative for the prevention and treatment of diseases caused by various infectious agents.

Predicting of biomass in Brazilian tropical dry forest: a statistical evaluation of generic equations.

Dry tropical forests are a key component in the global carbon cycle and their biomass estimates depend almost exclusively of fitted equations for multi-species or individual species data. Therefore, a systematic evaluation of statistical models through validation of estimates of aboveground biomass stocks is justifiable. In this study was analyzed the capacity of generic and specific equations obtained from different locations in Mexico and Brazil, to estimate aboveground biomass at multi-species levels and for four different species. Generic equations developed in Mexico and Brazil performed better in estimating tree biomass for multi-species data. For Poincianella bracteosa and Mimosa ophthalmocentra, only the Sampaio and Silva (2005) generic equation was the most recommended. These equations indicate lower tendency and lower bias, and biomass estimates for these equations are similar. For the species Mimosa tenuiflora, Aspidosperma pyrifolium and for the genus Croton the specific regional equations are more recommended, although the generic equation of Sampaio and Silva (2005) is not discarded for biomass estimates. Models considering gender, families, successional groups, climatic variables and wood specific gravity should be adjusted, tested and the resulting equations should be validated at both local and regional levels as well as on the scales of tropics with dry forest dominance.