Water infiltration under different land use in miombo woodlands outside Morogoro, Tanzania

Infiltration capacity is a measure of how much water that can enter the soil and hence become available to plant roots and micro organisms. A high infiltration capacity also means that less water is available for runoff and subsequent erosion. Infiltration capacity, bulk density and soil organic carbon content were measured in six land use types in miombo woodlands; natural forest, degraded forest, intensive agriculture, abandoned agriculture, degraded regenerating forest and Albizia plantation. The measurements were carried out in miombo woodlands about 50 km west of Morogoro, Tanzania. In the intensive agriculture and the abandoned agriculture the higher infiltration capacity was created by the mechanical disturbance and in the abandoned agricultural case also by the subsequent dense grass vegetation. The mechanical disturbance is, together with the presence of the tree roots, probably the cause of the high infiltration capacity in the Albizia plantation. Since the infiltration capacity increased after the establishment of an Albizia plantation, as well as the ability of the soil to receive high intensity rain increased when a degraded forest was left to regenerate and an Albizia plantation was established, this suggests that improved vegetation on a previously degraded land is positive. The mechanical disturbance created a low bulk density in the intensive agriculture and the abandoned agriculture; the dense grass may also have caused the bulk density in the abandoned agriculture to be the lowest of all land uses. Since a large number of measurements have been performed in this study it is also possible to estimate the variation within the land uses. The analysis showed that the variation within the intensive agriculture was significantly higher than in the natural forest, which may be a result of the mechanical disturbance in the intensive agriculture and a small variation in the natural forest.Infiltrationskapaciteten är ett mått på hur mycket vatten som kan tas upp av en jord och därmed bli tillgänglig för växtrötter och mikroorganismer. En god infiltrationskapacitet innebär därför att det finns mindre vatten kvar som kan orsaka ytavrinning och erosion. Infiltrationskapacitet, bulkdensitet och andel organiskt kol i marken mättes i sex markanvändningstyper: mindre störd skog, degenererad skog, intensivt jordbruk, övergivet jordbruk, degenererad återuppväxande skog samt Albizia-plantering. Mätningarna utfördes i miombo som är en tropisk torrskog, ca 50 km väster om Morogoro, Tanzania. Mekanisk bearbetning av jorden i det intensiva jordbruket och det övergivna jordbruket samt tätt, högväxande gräs i det övergivna jordbruket har skapat en hög infiltrationskapacitet i dessa markanvändningstyper. Den mekaniska bearbetningen av jorden är tillsammans med närvaron av trädrötter även troligtvis orsaken till den höga infiltrationskapaciteten i Albizia-planteringen. Då infiltrationskapaciteten var större i Albizia-planteringen än i den återuppväxande skogen, liksom jordens förmåga att ta emot regn av hög intensitet ökade efter att den degraderade skogen fick återuppväxa och då Albizia planterades, är det sannolikt att en ökad vegetation på tidigare degenererad mark är positiv. En låg bulkdensitet kan ha skapats i det intensiva jordbruket och det övergivna jordbruket på grund av den mekaniska bearbetningen av jorden. Det täta, högväxande gräset har även gjort att bulkdensiteten för det övergivna jordbruket är den lägsta. Då ett stort antal mätningar har genomförts har infiltrationskapacitetens variation inom markanvändningstyperna kunnat bedömas. Beräkningarna visade att variationen inom det intensiva jordbruket var större än variationen inom den mindre störda skogen, vilket kan bero på den mekaniska bearbetningen av jorden på det intensiva jordbruket och att variationen i den mindre störda skogen var mindre än förväntat

Токсикологическая безопасность спиртосодержащих лекарственных средств для профилактической антисептики

ЛЕКАРСТВА СОЗДАНИЕЛЕКАРСТВА КОНСТРУИРОВАНИЕЛЕКАРСТВА МОДЕЛИРОВАНИЕПРОТИВОИНФЕКЦИОННЫЕ СРЕДСТВА ЛОКАЛЬНЫЕ /АНАЛ /ТОКСИЧАНТИСЕПТИКИ /АНАЛ /ТОКСИЧАНТИСЕПТИЧЕСКИЕ СРЕДСТВА /АНАЛ /ТОКСИЧПРОТИВОИНФЕКЦИОННЫЕ СРЕДСТВА МЕСТНЫЕ /АНАЛ /ТОКСИЧЛЕКАРСТВ ТОКСИЧНОСТЬЭТАНОЛ /ТОКСИЧСПИРТ ЭТИЛОВЫЙ /ТОКСИЧЛЕКАРСТВ ФИЗИОЛОГИЧЕСКОЕ ДЕЙСТВИЕИОДХЛОРГЕКСИДИНЭКСПЕРИМЕНТЫ НА ЖИВОТНЫХКРЫСЫЦелью работы было изучение показателей токсикологической безопасности разработанных спиртосодержащих лекарственных средств "Витасепт" для профилактической антисептики. Выполнено 4 серии опытов на половозрелых белых крысах мужского пола массой 250±25 г, содержащихся в стандартных условиях. Однократное внутрижелудочное введение крысам нативных антисептических средств, содержащих спирт этиловый 72% марки "Люкс" с бриллиантовым зеленым 0,001%, с йодом кристаллическим 0,25%, с хлоргексидина биглюконатом 0,1%, а также "Этанол, раствор для наружного применения, 70%" в дозе 5300 мг/кг массы тела крыс, не вызывает гибель подопытных животных. После однократной 4-часовой аппликации в дозе 20 мг/см{2} закрытым способом и десятикратных повторных аппликаций на выстриженный участок кожи, а также хвосты крыс через 1,16 ч и в последующие 12 суток наблюдения после аппликации не вызывают гибель подопытных животных, клинические симптомы интоксикации и раздражение кожи. Все исследуемые средства имели специфический спиртовой запах, были прозрачными, подлинными, с плотностью 0,877 до 0,885 г/см{3}. Полученные результаты позволяют заключить, что исследованные инновационные лекарственные антисептические средства, содержащие экологически чистый спирт этиловый марки "Люкс" 72% с бриллиантовым зеленым 0,001%, с йодом кристаллическим 0,25%, с хлоргексидина биглюконатом 0,5% и 0,1%, а также оригинальные лекарственные антисептические средства, содержащие экологически чистый спирт этиловый марки "Люкс" 72% с бриллиантовым зеленым 0,01%, с йодом кристаллическим 0,5%, являются малоопасными, практически безвредными и не обладают кожно-раздражающим действием. Разработанные нами в настоящее время спиртосодержащие антисептики, а также производимые ОАО "Бобруйский завод биотехнологий" средства под маркой "Витасепт-СКЗ", "Витасепт-СКИ" и "Витасепт-СКО" соответствуют нормативным требованиям по токсикологическим показателям безопасности, предъявляемым к кожным антисептикам, средствам для гигиенической и хирургической обработки рук, кожи операционного и инъекционного полей.The aim of this work was to study the toxicological safety indicators of the developed alcohol-containing medicinal agents "Vitasept" for prophylactic antisepsis. 4 series of experiments were performed on adult white male rats weighing 250±25 g kept in standard conditions. A single intragastric administration to rats of native antiseptics containing 72% ethanol of the brand de luxe with diamond green 0.001%, with crystalline iodine 0.25%, with chlorhexidine bigluconate 0.1%, as well as "Ethanol, solution for external use, 70%" at a dose of 5300 mg/kg of rat body weight does not cause the death of experimental animals. After a single 4-hour application at a dose of 20 mg/cm{2} in a closed manner and ten times repeated applications on a sheared skin area, as well as rat tails after 1,16 hours and in the next 12 days of observation after application, they do not cause the death of experimental animals, clinical symptoms of intoxication and skin irritation. All studied agents had a specific alcoholic smell, were transparent, genuine, with a density of 0.877 up to 0.885 g/cm{3}. The results obtained allow us to conclude that the studied innovative medicinal antiseptic agents containing environmentally friendly 72% ethanol of the brand de luxe with brilliant green 0.001%, with crystalline iodine 0.25%, with chlorhexidine bigluconate 0.5% and 0.1%, as well as original medicinal antiseptic agents containing environmentally friendly 72% ethanol of the brand de luxe with brilliant green 0.01%, with crystalline iodine 0.5%, are slightly hazardous, practically harmless and do not produce a skin-irritating effect. Currently developed alcohol-containing antiseptics, as well as products manufactured by "Bobruisk plant of biotechnologies" under the brand names "Vitasept-SKZ", "Vitasept-SKI" and "Vitasept-SKO", comply with the regulatory requirements for toxicological safety indicators of skin antiseptics, agents for hygienic and surgical treatment of hands, skin of the operative and injection fields

Points to consider for prioritizing clinical genetic testing services: a European consensus process oriented at accountability for reasonableness.

Given the cost constraints of the European health-care systems, criteria are needed to decide which genetic services to fund from the public budgets, if not all can be covered. To ensure that high-priority services are available equitably within and across the European countries, a shared set of prioritization criteria would be desirable. A decision process following the accountability for reasonableness framework was undertaken, including a multidisciplinary EuroGentest/PPPC-ESHG workshop to develop shared prioritization criteria. Resources are currently too limited to fund all the beneficial genetic testing services available in the next decade. Ethically and economically reflected prioritization criteria are needed. Prioritization should be based on considerations of medical benefit, health need and costs. Medical benefit includes evidence of benefit in terms of clinical benefit, benefit of information for important life decisions, benefit for other people apart from the person tested and the patient-specific likelihood of being affected by the condition tested for. It may be subject to a finite time window. Health need includes the severity of the condition tested for and its progression at the time of testing. Further discussion and better evidence is needed before clearly defined recommendations can be made or a prioritization algorithm proposed. To our knowledge, this is the first time a clinical society has initiated a decision process about health-care prioritization on a European level, following the principles of accountability for reasonableness. We provide points to consider to stimulate this debate across the EU and to serve as a reference for improving patient management

No evidence that protein truncating variants in BRIP1 are associated with breast cancer risk: implications for gene panel testing.

BACKGROUND: BRCA1 interacting protein C-terminal helicase 1 (BRIP1) is one of the Fanconi Anaemia Complementation (FANC) group family of DNA repair proteins. Biallelic mutations in BRIP1 are responsible for FANC group J, and previous studies have also suggested that rare protein truncating variants in BRIP1 are associated with an increased risk of breast cancer. These studies have led to inclusion of BRIP1 on targeted sequencing panels for breast cancer risk prediction. METHODS: We evaluated a truncating variant, p.Arg798Ter (rs137852986), and 10 missense variants of BRIP1, in 48 144 cases and 43 607 controls of European origin, drawn from 41 studies participating in the Breast Cancer Association Consortium (BCAC). Additionally, we sequenced the coding regions of BRIP1 in 13 213 cases and 5242 controls from the UK, 1313 cases and 1123 controls from three population-based studies as part of the Breast Cancer Family Registry, and 1853 familial cases and 2001 controls from Australia. RESULTS: The rare truncating allele of rs137852986 was observed in 23 cases and 18 controls in Europeans in BCAC (OR 1.09, 95% CI 0.58 to 2.03, p=0.79). Truncating variants were found in the sequencing studies in 34 cases (0.21%) and 19 controls (0.23%) (combined OR 0.90, 95% CI 0.48 to 1.70, p=0.75). CONCLUSIONS: These results suggest that truncating variants in BRIP1, and in particular p.Arg798Ter, are not associated with a substantial increase in breast cancer risk. Such observations have important implications for the reporting of results from breast cancer screening panels.The COGS project is funded through a European Commission's Seventh Framework Programme grant (agreement number 223175 - HEALTH-F2-2009-223175). BCAC is funded by Cancer Research UK [C1287/A10118, C1287/A12014] and by the European Community´s Seventh Framework Programme under grant agreement number 223175 (grant number HEALTH-F2-2009-223175) (COGS). Funding for the iCOGS infrastructure came from: the European Community's Seventh Framework Programme under grant agreement n° 223175 (HEALTH-F2-2009-223175) (COGS), Cancer Research UK (C1287/A10118, C1287/A 10710, C12292/A11174, C1281/A12014, C5047/A8384, C5047/A15007, C5047/A10692, C8197/A16565), the National Institutes of Health (CA128978) and Post-Cancer GWAS initiative (1U19 CA148537, 1U19 16 CA148065 and 1U19 CA148112 - the GAME-ON initiative), the Department of Defense (W81XWH-10-1- 0341), the Canadian Institutes of Health Research (CIHR) for the CIHR Team in Familial Risks of Breast Cancer, Komen Foundation for the Cure, the Breast Cancer Research Foundation, and the Ovarian Cancer Research Fund. This study made use of data generated by the Wellcome Trust Case Control consortium. Funding for the project was provided by the Wellcome Trust under award 076113. The results published here are in part based upon data generated by The Cancer Genome Atlas Project established by the National Cancer Institute and National Human Genome Research Institute.This is the author accepted manuscript. The final version is available from BMJ Group at http://dx.doi.org/10.1136/jmedgenet-2015-103529

Fine-Scale Mapping of the 4q24 Locus Identifies Two Independent Loci Associated with Breast Cancer Risk

Background: A recent association study identified a common variant (rs9790517) at 4q24 to be associated with breast cancer risk. Independent association signals and potential functional variants in this locus have not been explored. Methods: We conducted a fine-mapping analysis in 55,540 breast cancer cases and 51,168 controls from the Breast Cancer Association Consortium. Results: Conditional analyses identified two independent association signals among women of European ancestry, represented by rs9790517 [conditional P = 2.51 × 10−4; OR, 1.04; 95% confidence interval (CI), 1.02–1.07] and rs77928427 (P = 1.86 × 10−4; OR, 1.04; 95% CI, 1.02–1.07). Functional annotation using data from the Encyclopedia of DNA Elements (ENCODE) project revealed two putative functional variants, rs62331150 and rs73838678 in linkage disequilibrium (LD) with rs9790517 (r2 ≥ 0.90) residing in the active promoter or enhancer, respectively, of the nearest gene, TET2. Both variants are located in DNase I hypersensitivity and transcription factor–binding sites. Using data from both The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), we showed that rs62331150 was associated with level of expression of TET2 in breast normal and tumor tissue. Conclusion: Our study identified two independent association signals at 4q24 in relation to breast cancer risk and suggested that observed association in this locus may be mediated through the regulation of TET2. Impact: Fine-mapping study with large sample size warranted for identification of independent loci for breast cancer risk

Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus

A locus at 19p13 is associated with breast cancer (BC) and ovarian cancer (OC) risk. Here we analyse 438 SNPs in this region in 46,451 BC and 15,438 OC cases, 15,252 BRCA1 mutation carriers and 73,444 controls and identify 13 candidate causal SNPs associated with serous OC (P=9.2 × 10-20), ER-negative BC (P=1.1 × 10-13), BRCA1-associated BC (P=7.7 × 10-16) and triple negative BC (P-diff=2 × 10-5). Genotype-gene expression associations are identified for candidate target genes ANKLE1 (P=2 × 10-3) and ABHD8 (P<2 × 10-3). Chromosome conformation capture identifies interactions between four candidate SNPs and ABHD8, and luciferase assays indicate six risk alleles increased transactivation of the ADHD8 promoter. Targeted deletion of a region containing risk SNP rs56069439 in a putative enhancer induces ANKLE1 downregulation; and mRNA stability assays indicate functional effects for an ANKLE1 3′-UTR SNP. Altogether, these data suggest that multiple SNPs at 19p13 regulate ABHD8 and perhaps ANKLE1 expression, and indicate common mechanisms underlying breast and ovarian cancer risk

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Common germline polymorphisms associated with breast cancer-specific survival

Abstract Introduction Previous studies have identified common germline variants nominally associated with breast cancer survival. These associations have not been widely replicated in further studies. The purpose of this study was to evaluate the association of previously reported SNPs with breast cancer-specific survival using data from a pooled analysis of eight breast cancer survival genome-wide association studies (GWAS) from the Breast Cancer Association Consortium. Methods A literature review was conducted of all previously published associations between common germline variants and three survival outcomes: breast cancer-specific survival, overall survival and disease-free survival. All associations that reached the nominal significance level of P value <0.05 were included. Single nucleotide polymorphisms that had been previously reported as nominally associated with at least one survival outcome were evaluated in the pooled analysis of over 37,000 breast cancer cases for association with breast cancer-specific survival. Previous associations were evaluated using a one-sided test based on the reported direction of effect. Results Fifty-six variants from 45 previous publications were evaluated in the meta-analysis. Fifty-four of these were evaluated in the full set of 37,954 breast cancer cases with 2,900 events and the two additional variants were evaluated in a reduced sample size of 30,000 samples in order to ensure independence from the previously published studies. Five variants reached nominal significance (P <0.05) in the pooled GWAS data compared to 2.8 expected under the null hypothesis. Seven additional variants were associated (P <0.05) with ER-positive disease. Conclusions Although no variants reached genome-wide significance (P <5 x 10−8), these results suggest that there is some evidence of association between candidate common germline variants and breast cancer prognosis. Larger studies from multinational collaborations are necessary to increase the power to detect associations, between common variants and prognosis, at more stringent significance levels