Jaccard/Tanimoto similarity test and estimation methods

Binary data are used in a broad area of biological sciences. Using binary presence-absence data, we can evaluate species co-occurrences that help elucidate relationships among organisms and environments. To summarize similarity between occurrences of species, we routinely use the Jaccard/Tanimoto coefficient, which is the ratio of their intersection to their union. It is natural, then, to identify statistically significant Jaccard/Tanimoto coefficients, which suggest non-random co-occurrences of species. However, statistical hypothesis testing using this similarity coefficient has been seldom used or studied. We introduce a hypothesis test for similarity for biological presence-absence data, using the Jaccard/Tanimoto coefficient. Several key improvements are presented including unbiased estimation of expectation and centered Jaccard/Tanimoto coefficients, that account for occurrence probabilities. We derived the exact and asymptotic solutions and developed the bootstrap and measurement concentration algorithms to compute statistical significance of binary similarity. Comprehensive simulation studies demonstrate that our proposed methods produce accurate p-values and false discovery rates. The proposed estimation methods are orders of magnitude faster than the exact solution. The proposed methods are implemented in an open source R package called jaccard (https://cran.r-project.org/package=jaccard). We introduce a suite of statistical methods for the Jaccard/Tanimoto similarity coefficient, that enable straightforward incorporation of probabilistic measures in analysis for species co-occurrences. Due to their generality, the proposed methods and implementations are applicable to a wide range of binary data arising from genomics, biochemistry, and other areas of science

LEARNING A PARENTAL ROLE DURING THE PROCESS OF REHABILITATION AND FAMILY INTEGRATION, WITHIN PRISON SETTINGS

Family relationships can give people a valuable sense of identity, belonging, security and responsibility. Families are important to us all, but for prisoners, they can make a huge difference to rehabilitation. They can provide emotional support and a home to go to on release. They can also provide financial assistance and help to find work. All of these things can help to reduce the risk of re-offending: Research suggests that having family ties can reduce the likelihood of re-offending by 39 percent. However, not all family relationships are positive and helpful.Not all imprisoned parents have the opportunity to learn a parenting role before they are sentenced—they may have a negative experience of being parented, themselves. Therefore, prison might offer their first opportunity to learn a parental role and to learn about parental responsibilities. These new skills may enable them to break the cycle of crime, desist from future offending, and may impact on the prevention of intergenerational crime. To ensure that the process of learning parenting skills delivers its full potential, all members of a family should be involved, with adults and children learning together

The therapeutic properties of Lemon balm (Melissa officinalis L.): Reviewing novel findings and medical indications

Melissa officinalis, a perennial plant in the family Lamiacae, known as lemon balm, is a popular herb with multiple therapeutic properties. Significant content of active compounds (including rosmarinic acid) is reported to be responsible for the broad health effects of lemon balm. Melissa officinalis has antioxidant, anti-inflammatory, antimicrobial and antidepressant activities. It can be used in the treatment of sleep disorders, neurodegenerative diseases and obesity as well as in ophthalmology, gynaecology, oncology, gastroenterology and cardiology. This review includes literature on the chemical composition of Melissa officinalis and the possibilities of its use in medicine as well as functional food. Furthermore, the side effects and the contraindications to the usage of this herb were summarized

Genomic parasites or symbionts? Modeling the effects of environmental pressure on transposition activity in asexual populations

AbstractTransposable elements are DNA segments capable of persisting in host genomes by self-replication in spite of deleterious mutagenic effects. The theoretical dynamics of these elements within genomes has been studied extensively, and population genetic models predict that they can invade and maintain as a result of both intra-genomic and inter-individual selection in sexual species. In asexuals, the success of selfish DNA is more difficult to explain. However, most theoretical work assumes constant environment. Here, we analyze the impact of environmental change on the dynamics of transposition activity when horizontal DNA exchange is absent, based on a stochastic computational model of transposable element proliferation. We argue that repeated changes in the phenotypic optimum in a multidimensional fitness landscape may induce explosive bursts of transposition activity associated with faster adaptation. However, long-term maintenance of transposition activity is unlikely. This could contribute to the significant variation in the transposable element copy number among closely related species

masstodon: A Tool for Assigning Peaks and Modeling Electron Transfer Reactions in Top-Down Mass Spectrometry

Top-down mass spectrometry methods are becoming continuously more popular in the effort to describe the proteome. They rely on the fragmentation of intact protein ions inside the mass spectrometer. Among the existing fragmentation methods, electron transfer dissociation is known for its precision and wide coverage of different cleavage sites. However, several side reactions can occur under electron transfer dissociation (ETD) conditions, including nondissociative electron transfer and proton transfer reaction. Evaluating their extent can provide more insight into reaction kinetics as well as instrument operation. Furthermore, preferential formation of certain reaction products can reveal important structural information. To the best of our knowledge, there are currently no tools capable of tracing and analyzing the products of these reactions in a systematic way. In this Article, we present in detail masstodon: a computer program for assigning peaks and interpreting mass spectra. Besides being a general purpose tool, masstodon also offers the possibility to trace the products of reactions occurring under ETD conditions and provides insights into the parameters driving them. It is available free of charge under the GNU AGPL V3 public license

The Wasserstein Distance as a Dissimilarity Measure for Mass Spectra with Application to Spectral Deconvolution

We propose a new approach for the comparison of mass spectra using a metric known in the computer science under the name of Earth Mover\u27s Distance and in mathematics as the Wasserstein distance. We argue that this approach allows for natural and robust solutions to various problems in the analysis of mass spectra. In particular, we show an application to the problem of deconvolution, in which we infer proportions of several overlapping isotopic envelopes of similar compounds. Combined with the previously proposed generator of isotopic envelopes, IsoSpec, our approach works for a wide range of masses and charges in the presence of several types of measurement inaccuracies. To reduce the computational complexity of the solution, we derive an effective implementation of the Interior Point Method as the optimization procedure. The software for mass spectral comparison and deconvolution based on Wasserstein distance is available at https://github.com/mciach/wassersteinms

PEMFC MEA and System Design Considerations

Proton exchange membrane fuel cells (PEMFCs) are being developed and sold commercially for multiple near term markets. Ballard Power Systems is focused on the near term markets of backup power, distributed generation, materials handling, and buses. Significant advances have been made in cost and durability of fuel cell products. Improved tolerance to a wide range of system operation and environmental noises will enable increased viability across a broad range of applications. In order to apply the most effective membrane electrode assembly (MEA) design for each market, the system requirements and associated MEA failures must be well understood. The failure modes associated with the electrodes and membrane degradation are discussed with respect to associated system operation and mitigating approaches. A few key system considerations that influence MEA design include expected fuel quality, balance-of-plant materials, time under idle or open circuit operation, and start-up and shut-down conditions

Wpływ podłoża i nawożenia na cechy morfologiczne i walory odmian niecierpka nowogwinejskiego z grupy Sonic i z grupy Super Sonic. Część II. Kwitnienie roślin

Oceniano wpływ pięciu podłoży, różniących się składem i zasobnością w składniki pokarmowe, na obfitość kwitnienia i trwałość walorów dekoracyjnych odmian niecierpka nowogwinejskiego (NGI) z grupy Sonic i z grupy Super Sonic. Wszystkie odmiany NGI miały najwięcej kwiatów w pełni lata, w lipcu. Na równomierność kwitnienia i ogólną liczbę kwiatów na roślinie miały wpływ cechy odmianowe oraz okresowy niedobór składników pokarmowych w niektórych podłożach. Niecierpki najwcześniej zaczęły kwitnąć i kwitły najobficiej w gotowym podłożu TG, najsłabiej w podłożu TM B 400. Najlepsze wyniki uzyskano, stosując Osmocote Plus 5 - 6, nawóz o działaniu spowolnionym, i - dodatkowo - od ósmego tygodnia uprawy Peters Professional.The effects of five media, differing in composition and nutrient resources, on the abundance of flowering and permanence of decorative value of NGI belonging to Sonic and Super Sonic groups were determined. All NGI cultivars had most flowers hi the high summer, i.e. in July. Even flowering and total number of flowers per plant were affected by the cultivar traits and a periodical nutrient deficiency in some media. The earliest and the most abundant flowering was observed in plants from TG medium and the poorest from TM B 400. Good results were obtained using Osmocote Plus 5-6 - a slow-release fertilizer and additionally Peters Professional after seven weeks of cultivation

Wplyw podloza i nawozenia bratkow ogrodowych [viola x wittrockiana Gams] na ich dynamike wzrostu, kwitnienie oraz trwalosc walorow dekoracyjnych

Eight cultivars of garden pansy were included in the studies: three Delta and Delta Premium cultivars from Dutch firm Syngenta Seeds (S & G) and two Dynamite cultivars from the Japanese firm Sakata. Plants were cultivated in pots in spring-summer cycle using two kinds of medium (peat and coconut fibre) and three fertilizers: a traditional one - Azofoska, and two slow-release fertilizers: Osmocote Plus 5-6 and Polyon. The following morphological traits were evaluated: height and diameter of plants, the number and size of leaves, the number and diameter of flowers, the length of peduncles. It was found that irrespective of the cultivar pansies grew and developed faster on coconut fibre than on the peat. The effect of medium was more obvious at a juvenile stage than at later stages. Slow-release fertilizers Osmocote Plus 5-6 and Polyon significantly increased the number of flowers and the number of leaves per one plant and favourably affected the permanence of decorative value.Do badań użyto osiem odmian bratka ogrodowego: po trzy odmiany z grupy Delta i Delta Premium holenderskiej firmy Syngenta Seeds (S&G) oraz dwie odmiany z grupy Dynamite japońskiej firmy Sakata. Bratki uprawiano w cyklu wiosenno-letnim w doniczkach, stosując dwa rodzaje podłoża (torf i włókno kokosowe) oraz trzy nawozy: Azofoskę - nawóz tradycyjny, Osmocote Plus 5-6 i Polyon - nawozy o działaniu spowolnionym. Oceniano następujące cechy morfologiczne: wysokość i średnicę roślin, liczbę i wielkość liści, liczbę i średnicę kwiatów, długość szypułek kwiatowych. Stwierdzono, że niezależnie od odmiany bratki szybciej rosły i rozwijały się we włóknie kokosowym niż w torfie. Wpływ podłoża był bardziej widoczny w fazie juwenilnej niż w okresie późniejszym. Nawozy o działaniu spowolnionym Osmocote Plus 5-6 i Polyon istotnie zwiększyły liczbę kwiatów oraz liczbę liści na jednej roślinie oraz wpłynęły korzystnie na trwałość walorów dekoracyjnych

Porownanie dzialania czterech retardantow, stosowanych do moczenia cebul, na tulipany uprawiane w doniczkach

W uprawie doniczkowej tulipanów badano wpływ retardantów: chloromekwatu, stosowanego w postaci preparatu Cycocel 460 SL - w stężeniu 230, 460 i 920 mg·dm⁻³; daminozydu - w postaci B-Nine 85 SP - w stężeniu 4250, 8500 i 7000 mg·dm⁻³; flurprimidolu - w postaci Topflor 015 SL - w stężeniu 7,5, 15 i 30 mg·dm⁻³; paklobutrazolu - jako Bonzi SC - w stężeniu 4, 8 i 16 mg·dm⁻³. Tulipany czterech odmian: ’Candela’, ’Madame Lafeber’, ’Blue Parrot’ i ’Gordon Cooper’, pędzono metodą tradycyjną w terminie późnym. Retardanty stosowano poprzez moczenie w ich roztworze cebul bezpośrednio przed sadzeniem do doniczek. Odmiany tulipanów reagowały niejednakowo na retardanty oraz stężenia, w jakich je stosowano. Topflor 015 SL, w stężeniu 0,1% i 0,2% (15 i 30 mg·dm⁻³) wpłynął silnie skarlająco na wszystkie odmiany i tulipany nim potraktowane. W fazie generatywnej były niższe, wyrównane oraz miały większą wartość dekoracyjną niż rośliny kontrolne. Cycocel 460 SL i B-Nine 85 SP wpłynęły raczej stymulująco na wzrost roślin. Retardanty nie wpłynęły na termin kwitnienia, spowodowały przyrost plonu cebul tulipanów.In pot cultivation of tulips the effects of the following retardants were examined: chlormequat in the form of Cycocel 460 SL - at the concentration of 230, 460 and 920 mg·dm⁻³; daminozyde, in the form of B-Nine 85 SP - at the co ncentration of 4250, 8500 and 17000 mg·dm⁻³; flurprimidol in the form of Topflor 015 SL - at the concentration of 7.5, 15 and 30 mg·dm⁻³; paclobutrazol in the form of Bonzi SC - at the concentration 4, 8 and 16 mg·dm⁻³. Four tulip cultivars: ’Candela’, ’Madame Lafeber’, ’Blue Parrof and ’Gordon Cooper’ were forced traditionally in the later period. Bulbs were soaked in retardant solutions before being planted into pots. Tulip cultivars responded in a different way to retardants and their concentrations. Only Topflor at the concentration of 0.1% and 0.2% (15 and 80 mg·dm⁻³) stunted all cultivars and the tulips treated with it were shorter or the same height and had a greater decorative value than the control plants. Cycocel 460 SL and B-Nine 85 SSP had a rather stimulating effect on the plant growth. The examined retardants had no effect on the date of flowering but increased the bulb yield