Evidence for a pervasive 'idling-mode' activity template in flying and pedestrian insects

This is the final version. Available on open access from the Royal Society via the DOI in this recordUnderstanding the complex movement patterns of animals in natural environments is a key objective of 'movement ecology'. Complexity results from behavioural responses to external stimuli but can also arise spontaneously in their absence. Drawing on theoretical arguments about decision-making circuitry, we predict that the spontaneous patterns will be scale-free and universal, being independent of taxon and mode of locomotion. To test this hypothesis, we examined the activity patterns of the European honeybee, and multiple species of noctuid moth, tethered to flight mills and exposed to minimal external cues. We also reanalysed pre-existing data for Drosophila flies walking in featureless environments. Across these species, we found evidence of common scale-invariant properties in their movement patterns; pause and movement durations were typically power law distributed over a range of scales and characterized by exponents close to 3/2. Our analyses are suggestive of the presence of a pervasive scale-invariant template for locomotion which, when acted on by environmental cues, produces the movements with characteristic scales observed in nature. Our results indicate that scale-finite complexity as embodied, for instance, in correlated random walk models, may be the result of environmental cues overriding innate behaviour, and that scale-free movements may be intrinsic and not limited to 'blind' foragers as previously thought.Rothamsted research receives grant aided support from the Biotechnology and Biological Sciences Research Council. S.W. was funded jointly by a grant from BBSRC, Defra, NERC, the Scottish Government and the Wellcome Trust, under the Insect Pollinators Initiative (grant nos. BB/I00097/1). A.J.P. was funded by a BBSRC Doctoral Training Partnership in Food Security awarded to K.W. and J.W.C. H.B.C.J. was funded by a BBSRC Quota studentship awarded to J.W.C. and J.K.

Time to Pregnancy for Women Using a Fertility Awareness Based Mobile Application to Plan a Pregnancy

Background: Time to pregnancy (TTP) is a biomarker of fecundability and has been associated with behavioral and environmental characteristics; however, these associations have not been examined in a large population-based sample of application (app) users. Materials and Methods: This observational study followed 5,376 women with an age range of 18 to 45 years who used an app to identify their fertile window. We included women who started trying to conceive between September 30, 2017 and August 31, 2018. TTP was calculated as the number of menstrual cycles from when the user switched to "Plan" mode up to and including the cycle in which they logged a positive pregnancy test. We examined associations with several characteristics, including age, gravidity, body mass index, cycle length and cycle length variation, frequency of sexual intercourse, and temperature measuring frequency. Discrete time fecundability models were used to estimate fecundability odds ratios. Results: For the complete cohort the 6-cycle and 12-cycle cumulative pregnancy probabilities were found to be 61% (95% confidence interval [CI]: 59-62) and 74% (95% CI: 73-76), respectively. The median TTP was four cycles. The highest fecundability was associated with an age of less than 35 years, with cycle length variation <5 days and logging sexual intercourse on at least 20% of days added (the proportion of days in which intercourse was logged) (11.5% [n = 613] of entire sample). This group achieved a 6- and 12-cycle cumulative pregnancy probability of 88% (95% CI: 85-91) and 95% (95% CI: 94-97), respectively, and a TTP of 2 cycles. Conclusions: Natural Cycles was an effective method of identifying the fertile window and a noninvasive educational option for women planning a pregnancy. Women under age 35 with regular cycles showed a high pregnancy rate

Munchausen by internet: current research and future directions.

The Internet has revolutionized the health world, enabling self-diagnosis and online support to take place irrespective of time or location. Alongside the positive aspects for an individual's health from making use of the Internet, debate has intensified on how the increasing use of Web technology might have a negative impact on patients, caregivers, and practitioners. One such negative health-related behavior is Munchausen by Internet

Testing statistical significance scores of sequence comparison methods with structure similarity

BACKGROUND: In the past years the Smith-Waterman sequence comparison algorithm has gained popularity due to improved implementations and rapidly increasing computing power. However, the quality and sensitivity of a database search is not only determined by the algorithm but also by the statistical significance testing for an alignment. The e-value is the most commonly used statistical validation method for sequence database searching. The CluSTr database and the Protein World database have been created using an alternative statistical significance test: a Z-score based on Monte-Carlo statistics. Several papers have described the superiority of the Z-score as compared to the e-value, using simulated data. We were interested if this could be validated when applied to existing, evolutionary related protein sequences. RESULTS: All experiments are performed on the ASTRAL SCOP database. The Smith-Waterman sequence comparison algorithm with both e-value and Z-score statistics is evaluated, using ROC, CVE and AP measures. The BLAST and FASTA algorithms are used as reference. We find that two out of three Smith-Waterman implementations with e-value are better at predicting structural similarities between proteins than the Smith-Waterman implementation with Z-score. SSEARCH especially has very high scores. CONCLUSION: The compute intensive Z-score does not have a clear advantage over the e-value. The Smith-Waterman implementations give generally better results than their heuristic counterparts. We recommend using the SSEARCH algorithm combined with e-values for pairwise sequence comparisons

RegExpBlasting (REB), a Regular Expression Blasting algorithm based on multiply aligned sequences

Background: One of the most frequent uses of bioinformatics tools concerns functional characterization of a newly produced nucleotide sequence (a query sequence) by applying Blast or FASTA against a set of sequences (the subject sequences). However, in some specific contexts, it is useful to compare the query sequence against a cluster such as a MultiAlignment (MA). We present here the RegExpBlasting (REB) algorithm, which compares an unclassified sequence with a dataset of patterns defined by application of Regular Expression rules to a given-as-input MA datasets. The REB algorithm workflow consists in i. the definition of a dataset of multialignments ii. the association of each MA to a pattern, defined by application of regular expression rules; iii. automatic characterization of a submitted biosequence according to the function of the sequences described by the pattern best matching the query sequence. Results: An application of this algorithm is used in the "characterize your sequence" tool available in the PPNEMA resource. PPNEMA is a resource of Ribosomal Cistron sequences from various species, grouped according to nematode genera. It allows the retrieval of plant nematode multialigned sequences or the classification of new nematode rDNA sequences by applying REB. The same algorithm also supports automatic updating of the PPNEMA database. The present paper gives examples of the use of REB within PPNEMA. Conclusion: The use of REB in PPNEMA updating, the PPNEMA "characterize your sequence" option clearly demonstrates the power of the method. Using REB can also rapidly solve any other bioinformatics problem, where the addition of a new sequence to a pre-existing cluster is required. The statistical tests carried out here show the powerful flexibility of the method

The South Asian genome

Genetics of disease Microarrays Variant genotypes Population genetics Sequence alignment AllelesThe genetic sequence variation of people from the Indian subcontinent who comprise one-quarter of the world's population, is not well described. We carried out whole genome sequencing of 168 South Asians, along with whole-exome sequencing of 147 South Asians to provide deeper characterisation of coding regions. We identify 12,962,155 autosomal sequence variants, including 2,946,861 new SNPs and 312,738 novel indels. This catalogue of SNPs and indels amongst South Asians provides the first comprehensive map of genetic variation in this major human population, and reveals evidence for selective pressures on genes involved in skin biology, metabolism, infection and immunity. Our results will accelerate the search for the genetic variants underlying susceptibility to disorders such as type-2 diabetes and cardiovascular disease which are highly prevalent amongst South Asians.Whole genome sequencing to discover genetic variants underlying type-2 diabetes, coronary heart disease and related phenotypes amongst Indian Asians. Imperial College Healthcare NHS Trust cBRC 2011-13 (JS Kooner [PI], JC Chambers)

Meeting the global protein supply requirements of a growing and ageing population

\ua9 The Author(s) 2024.Human dietary patterns are a major cause of environmental transformation, with agriculture occupying ~ 50% of global land space, while food production itself is responsible for ~ 30% of all greenhouse gas emissions and 70% of freshwater use. Furthermore, the global population is also growing, such that by 2050, it is estimated to exceed ~ 9 billion. While most of this expansion in population is expected to occur in developing countries, in high-income countries there are also predicted changes in demographics, with major increases in the number of older people. There is a growing consensus that older people have a greater requirement for protein. With a larger and older population, global needs for protein are set to increase. This paper summarises the conclusions from a Rank Prize funded colloquium evaluating novel strategies to meet this increasing global protein need