cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/2345
title: Data from computer simulation of neutral drift among limbal epithelial stem cells of mosaic mice

description: It was previously shown that limbal epithelial stem cells (LESCs) around the periphery of the cornea maintain radial sectors of the corneal epithelium but that radial stripe numbers declined with age in mosaic mice. Originally, these results were interpreted as progressive, age-related loss or irreversible inactivation of some clones of LESCs. We used computer simulations to show that these results could also be explained by stochastic replacement of LESCs by neighbouring LESCs, leading to neutral drift of LESC populations. This was shown to reduce the number of coherent clones of LESCs and hence would coarsen the mosaic pattern in the corneal epithelium without reducing the absolute number of LESCs. Simulations also showed that corrected stripe numbers declined more slowly when LESCs were grouped, non-randomly and that mosaicism was rarely lost unless simulated LESC numbers were unrealistically low. The data comprise the source code for the simulation program and data from 154 sets of simulations (20 simulations per set) grouped into parts 1-9. Data from simulations comprise PNG images and raw data (CSV files) of individual simulations plus Excel workbooks with summaries of numerical data. There are also word and pdf versions of a 'Read-me' file, which provides some explanatory notes about the data, and a file, which explains some abbreviations and the file structure.
DOI: 10.7488/ds/3253
title: Assessing the feasibility and effectiveness of introducing pulse oximetry in IMCI services to manage acute respiratory infections at first level health facilities in Bangladesh

description: Observation: This dataset contains data on observation of the use of pulse oximetry by IMCI service providers (government) by study nurses/paramedics to assess pulse oximeter use outcome and timing. This data was collected in two rounds. The same IMCI service providers took part in both rounds of data collection. Reassessment: This dataset contains data on the reassessment of the SpO2 status by study nurses/paramedics to assess the validity of SpO2 assessment in routine practice. It also includes the assessment of the children according to IMCI guidelines. This data was collected in two rounds. Exit interview: This dataset contains data on interviews of the caretakers of the sick children visiting IMCI corners to understand the community acceptance. This data was collected in two rounds. Phone follow-up: This dataset contains data on phone follow-up of the study participants visiting IMCI corners to assess their status on hospitalization, the occurrence of danger signs, and mortality. The follow-up was conducted on the 2nd and 14th days of visiting IMCI corners. This data was collected in two rounds. Register data extraction: This dataset contains data extracted from the IMCI registers for children aged 2-59 months during the six months of data collection period of both rounds. Knowledge assessment: This dataset contains data on knowledge assessment scores of the IMCI service providers participating in the study on hypoxaemia and the use of pulse oximetry. This knowledge assessment was conducted during the pretest and post-test of the IMCI training and also during the first and second rounds of data collection. IMCI corner monitoring assessment: This dataset contains data on IMCI service availability and readiness of IMCI corners of the demonstration facilities including availability of functioning pulse oximeters. This data was collected twice from the same facility: 1) at baseline (before the start of field implementation), and 2) at round 2. Challenges of using pulse oximetry: This dataset contains data on challenges faced by IMCI service providers participating in this study on using pulse oximetry using a Likert scale. This data was collected at the end of round 2 of data collection. We don't have a data codebook. However, for a better understanding of the variables, we have attached the questionnaire that corresponds to this dataset.
DOI: 10.7488/ds/3190
title: The use of missense variations in functional annotation of the human ARID family of DNA binding proteins

description: Missense variants are alterations to protein coding sequences that alter the identity of an amino acid at a specific site. They can be deleterious if the site is required for function but are likely to be tolerated at other sites. Consequently, missense variation within a healthy population mirrors the effects of negative selection on protein structure and function. Advances in high-throughput sequencing have dramatically increased the sample size of human variation data, allowing for population-wide interpretations of selective pressures. In this study, we developed a convenient framework for mapping missense variants onto solved or modelled protein structures and applied it to characterize the ARID family of gene regulators. ARID family members are implicated in multiple cancer types, developmental disorders, and immunological diseases but current understanding of their mechanistic roles is incomplete. Combined with phylogenetic and structural analyses, our approach allowed us to identify important sites for protein-protein interactions, histone code recognition, and DNA binding by the ARID proteins. We propose that missense variants can serve as a valuable tool for complementing experimental findings and formulating mechanistic hypotheses.
DOI: 10.7488/ds/2215
title: Spatiotemporal data on pedunculate oak leafing and peak frass dates for the UK

description: Data to accompany paper on “Tritrophic mismatch in space and time”. Observations are on the phenology of oak first leaf date and the peak caterpillar frass date across the UK for the period 1998 to 2016. The oak phenology data were collected by the Nature’s Calendar citizen science scheme (https://naturescalendar.woodlandtrust.org.uk/). We request that anyone who wishes to use these data informs naturescalendar@woodlandtrust.org.uk. The caterpillar frass data were collected by various groups. We request that anyone wishing to use these data contacts Malcolm Burgess (M.D.Burgess@exeter.ac.uk).
description: oakandfrass.txt is a tab delimited file of phenological observations for pedunculate oak first leafing and peak (caterpillar) frass. README file contains explanation of data columns and contents.
DOI: 10.7488/ds/2921
title: Sequences of the most common strains used in Pilizota lab

description: Data description files are given with the data. All strains are Escherichia coli. These are background strains used in a variety of experiments, the results of which the group has published elsewhere. As strains get grown and regrown in the labs they can acquire mutations. Therefore, these sequences are provided for reference, and for transparency.
DOI: 10.7488/ds/2579
title: Data from: Adaptive phenotypic plasticity in malaria parasites is not constrained by previous responses to environmental change.

description: Infection dynamics data for P. chabaudi parasites in treatment groups that include parasites in mice treated with 30mg/kg phenylhydrazine (“PHZ”), parasites in untreated mice (“Control”), or parasites currently in untreated mice after being transferred either from “Control” donor mice (“ExControl”) or “PHZ” treated donor mice (“ExPHZ”).
DOI: 10.7488/ds/2460
title: Adaptive plasticity in the gametocyte conversion rate of malaria parasites

description: Malaria parasites in the host replicate asexually and, during each replication cycle, some asexuals transform into sexual stages that enable between-host transmission. It is not understood why the rate of conversion to sexual stages varies during infections despite its importance for the severity and spread of the disease. We combined a mathematical model and experiments to show that parasites adjust conversion rates depending on changes in their in-host population size. When population sizes plummet, between-host transmission is prioritised. However, smaller losses in number elicit reproductive restraint, which facilitates in-host survival and future transmission. We show that increased and decreased conversion in response to a range of in-host environments are actually part of one continuum: a sophisticated reproductive strategy similar to that of multicellular organisms.
DOI: 10.7488/ds/2485
title: Time-of-day of blood feeding: effects on mosquito life history and malaria transmission

description: Biological rhythms allow organisms to compartmentalise and coordinate aspects of their life with the predictable daily rhythms of their environment. There is increasing recognition that understanding the biological rhythms of mosquitoes that transmit parasites is important for global health. For example, perturbations in blood foraging rhythms as a consequence of vector control measures may undermine disease control. To address this, we explore the impacts of altered timing of blood feeding on mosquito life history traits and malaria transmission. We carried out three experiments in which Anopheles stephensi mosquitoes were fed in the morning or evening on blood that had different qualities, including: chemical or Plasmodium chabaudi infection induced anaemia, Plasmodium berghei infection but no anaemia, or originating from hosts at different times of day. We then compared mosquito fitness proxies relating to survival and reproduction, and malaria transmission proxies where relevant, using mixed-effects models and survival analysis. Mosquito lifespan is not influenced by the time of day they received a blood meal but several reproductive metrics are affected, in some experiments. Overall, receiving a blood meal in the morning makes mosquitoes more likely to lay eggs. Furthermore, in the experiment with the largest sample size, morning fed mosquitoes laid sooner and have a larger clutch size. In keeping with previous work, P. berghei infection reduces mosquito lifespan and the likelihood of laying eggs, but time of day of blood feeding does not impact upon these metrics nor on parasite transmission. The time of day of blood feeding does not appear to have major consequences for mosquito fitness or transmission of asynchronous malaria species. If our results from a lab colony of mosquitoes living in benign conditions hold for wild mosquitoes, it suggests that mosquitoes have sufficient flexibility in their physiology to cope with changes in biting time induced by evading insecticide treated bed nets. Future work should consider the impact of multiple feeding cycles and the abiotic stresses imposed by the need to forage for blood when hosts are not protected by bed nets.
DOI: 10.7488/ds/3002
title: Daily rhythms of both host and parasite affect antimalarial drug efficacy

description: Circadian rhythms contribute to treatment efficacy in several non-communicable diseases. However, chronotherapy (administering drugs at a particular time-of-day) against infectious diseases has been overlooked. Yet, the daily rhythms of both hosts and disease-causing agents can impact the efficacy of drug treatment. We use the rodent malaria parasite Plasmodium chabaudi, to test if the daily rhythms of hosts, parasites, and their interactions, affect sensitivity to the key antimalarial, artemisinin. Asexual malaria parasites develop rhythmically in the host’s blood, in a manner timed to coordinate with host daily rhythms. Our experiments coupled or decoupled the timing of parasite and host rhythms, and we administered artemisinin at different times of day to coincide with when parasites were either at an early (ring) or later (trophozoite) developmental stage. We quantified the impacts of parasite developmental stage, and alignment of parasite and host rhythms, on drug sensitivity. We find that rings were less sensitive to artemisinin than trophozoites, and this difference was exacerbated when parasite and host rhythms were misaligned, with little direct contribution of host time-of-day on its own. Furthermore, the blood concentration of haem at the point of treatment correlated positively with artemisinin efficacy but only when parasite and host rhythms were aligned. Parasite rhythms influence drug sensitivity in vivo. The hitherto unknown modulation by alignment between parasite and host daily rhythms suggests that disrupting the timing of parasite development could be a novel chronotherapeutic approach.
DOI: 10.7488/ds/2475
title: Data from: Evolutionary sex allocation theory explains sex ratios in natural Plasmodium falciparum infections.

description: Male and female gametocyte counts forming the basis of the sex ratio analysis of P. falciparum parasites in natural infections.
DOI: 10.7488/ds/2622
title: Host circadian clocks do not set the schedule for the within-host replication of malaria parasites

description: Circadian clocks coordinate organisms' activities with daily cycles in their environment. Parasites are subject to daily rhythms in the within-host environment, resulting from clock-control of host activities, including immune responses. Parasites also exhibit rhythms in their activities: the timing of within-host replication by malaria parasites is coordinated to host feeding rhythms. Precisely which host feeding-related rhythm(s) parasites align with and how this is achieved are unknown. Understanding rhythmic replication in malaria parasites matters because it underpins disease symptoms and fuels transmission investment. We test if rhythmicity in parasite replication is coordinated with the host's feeding-related rhythms and/or rhythms driven by the host's canonical circadian clock. We find that parasite rhythms coordinate with the time of day that hosts feed in both wild-type and clock-mutant hosts, whereas parasite rhythms become dampened in clock-mutant hosts that eat continuously. Our results hold whether infections are initiated with synchronous or with desynchronized parasites. We conclude that malaria parasite replication is coordinated to rhythmic host processes that are independent of the core-clock proteins PERIOD 1 and 2; most likely, a periodic nutrient made available when the host digests food. Thus, novel interventions could disrupt parasite rhythms to reduce their fitness, without interference by host clock-controlled homeostasis.
DOI: 10.7488/ds/2984
title: The ecology of asynchronous asexual replication: Plasmodium berghei’s intraerythrocytic development cycle is resistant to host rhythms

description: Daily periodicity in the diverse activities of parasites occurs across a broad taxonomic range. The rhythms exhibited by parasites are thought to be adaptations that allow parasites to cope with, or exploit, the consequences of host activities that follow daily rhythms. Malaria (Plasmodium) parasites are well-known for their synchronised cycles of replication within host red blood cells. Whilst most species of Plasmodium appear sensitive to the timing of the daily rhythms of hosts, and even vectors, some species present no detectable rhythms in blood-stage replication. Why the intraerythrocytic development cycle (IDC) of, for example P. chabaudi, is governed by host rhythms, yet seems completely independent of host rhythms in P. berghei, another rodent malaria species is mysterious. This study reports a series of five experiments probing the relationships between the asynchronous IDC schedule of P. berghei and the rhythms of hosts and vectors by manipulating host time-of-day, photoperiod and feeding rhythms. The results reveal that: (i) a lack coordination between host and parasite rhythms does not impose appreciable fitness costs on P. berghei; (ii) P. berghei’s IDC schedule is impervious to host rhythms, including altered photoperiod and host-feeding-related rhythms; (iii) there is weak evidence for daily rhythms in the density and activities of transmission stages; but (iv), these rhythms have little consequence for successful transmission to mosquitoes. Overall, host rhythms do not affect the performance of P. berghei and its asynchronous IDC is resistant to the scheduling forces that underpin synchronous replication in closely related parasites. This suggests that natural variation in the IDC schedule across species represents different parasite strategies that maximize fitness. Thus, subtle differences in the ecological interactions between parasites and their hosts/vectors may select for the evolution of very different IDC schedules.
DOI: 10.7488/ds/2121
title: Data in support of 'Drug-tunable multidimensional Synthetic Gene Control using Inducible Degron-tagged dCas9 Effectors'

description: This dataset contains a file with images of the full Western blots used in the manuscript "Drug-tunable multidimensional Synthetic Gene Control using Inducible Degron-tagged dCas9 Effectors", plus a file with DNA sequences of constructs used in the study. The nuclease-deactivated variant of CRISPR/Cas9 proteins (dCas9) fused to heterologous transactivation domains can act as a potent guide RNA sequence-directed inducer or repressor of gene expression in mammalian cells. In such a system the long-term presence of a stable dCas9 effector can be a draw-back precluding the ability to switch rapidly between repressed and activated target gene expression states, imposing a static environment on the synthetic regulatory circuits in the cell. To address this issue we have generated a toolkit of conditionally degradable or stabilisable orthologous dCas9/Cpf1 effector proteins, thus opening options for multidimensional control of functional activities through combinations of orthogonal, drug-tunable artificial transcription factors.
DOI: 10.7488/ds/288
title: Mn2FeReO6 Angew Chem 2015

description: Measurements data for McNally et al, Angew Chem 2015 (In Submission). File contents are evident from directory and file names. All files can be opened using Notepad or other commonly available programs.
DOI: 10.7488/ds/1689
title: Crystallographic and magnetic data for the complexes in the paper entitled "Pressure induced enhancement of the magnetic ordering temperature in rhenium(IV) monomers" published in Nature Communications, 2016, 7, 13870. doi:10.1038/ncomms13870

description: Materials that demonstrate long range magnetic order are synonomous with information storage and the electronics industry, with the phenomenon commonly associated with metals, metal alloys or metal oxides and sulfides. A lesser know family of magnetically ordered complexes are the monometallic compounds of highly anisotropic d-block transition metals; the ‘transformation’ from isolated zero-dimensional molecule to ordered, spin-canted, three-dimensional lattice being the result of through-space interactions arising from the combination of large magnetic anisotropy and spin-delocalization from metal to ligand which induces important intermolecular contacts. Herein we report the effect of pressure on two such mononuclear ReIV compounds that exhibit long-range magnetic order under ambient conditions via a spin canting mechanism, with Tc controlled by the strength of the intermolecular interactions. As these are determined by intermolecular distance, “squeezing” the molecules closer together generates remarkable enhancements in ordering temperatures, with a linear dependence of Tc with pressure.
DOI: 10.7488/ds/2902
title: The Implementation and Impact of Isotope Depletion for Improved Protein Mass Spectrometry.

description: One of the fundamental challenges of high-resolution mass spectrometry (MS) analysis of protein occurs as the molecular weight increases. Which is due to the increased chemical complexity of the protein analyte. Larger molecular weight proteins display a wider isotopologue distribution caused by an increased incorporation of heavier isotopes. This phenomenon increases the inherent complexity of a protein mass spectrum and makes achieving comprehensive analysis, like top-down fragmentation difficult. Ultimately due to the increased isotopologue overlap and reduced ion signal hindering assignment. One potential method to improve protein analysis via mass spectrometry is to apply an isotope depletion strategy. This involves recombinant expression of protein in defined growth media containing carbon and nitrogen sources depleted in heavy isotopes (notably 13C and 15N). Thus, the resulting recombinant proteins are produced with limited, heavier isotope incorporation. An efficient and cost-effective method for isotope depletion was developed in E. coli and applied to several proteins of increasing molecular weight. After optimisation, expression in isotopically depleted media, produced recombinant protein containing 12C 99.95% and 14N 99.99%. The benefit of applying isotope depletion was assessed using top down fragmentation, mainly electron-based, techniques on both 12T FT-ICR and orbitrap Eclipse instruments. Isotopic depletion produces simplified isotopologue distributions and increases the net contribution of the monoisotopic peak intensity to that distribution. In top-down fragmentation spectra this results in reduced overlap in fragment ion distribution and greater mass accuracy due to the presence of the abundant monoisotopic peak. Furthermore, isotopically depleted protein is observed with greater total ion signal and dramatically increased S/N. Ultimately, with these accumulative benefits, top-down fragmentation of isotopically depleted protein allows assignment of 2-3 times greater number of fragment ions. Translating into a greater sequence coverage. Particularly when the isotope depletion technique is coupled to other processes designed to increase top-down sequence coverage, like proton transfer charge reduction. The increased number of assigned ions in isotopically depleted protein fragmentation spectra also permits a dramatic reduction in the number of averaged transients without a corresponding reduction in the sequence coverage. Permitting acquisition of greater top-down fragmentation coverage in LC-MS/MS workflows. As the changes the isotope depletion technique causes to the isotopologue distribution are consistent, it has the potential to improve a range of protein MS analysis. This was demonstrated using isotopically depleted protein with native electrospray process, maintaining the higher order structure of protein in the gas phase. With the isotopically depleted protein it was possible to extend the feasible working mass limit of native analysis of 12T FT-ICR.
DOI: 10.7488/ds/1486
title: ESI-(-)-FT-ICR MS of 85 Scotch Whisky Samples
title: Chemical Diversity and Complexity of Scotch Whisky as Revealed by High-Resolution Mass Spectrometry

description: Data were acquired as part of research into advanced spectroscopic methods for the analysis of Scotch Whisky. 85 Scotch Whisky samples, representing the broad range of Scotch Whisky produced and sold, were analysed by ESI-(-)-FT-ICR MS. The data provided include the raw and processed data in a proprietary and open access format. The results are described in an article in the Journal of The American Society for Mass Spectrometry: "Chemical Diversity and Complexity of Scotch Whisky as Revealed by High-Resolution Mass Spectrometry". The files include 4MW FIDs, processed Fourier transformed data (Bruker .d format) and .mzML formatted processed data. The spectra were acquired on a 12T SolariX FT-ICR MS instrument. The spectra are negative mode ESI. The proprietary format, including raw, data have been separated from the mzML files. Both have been compressed into .zip formats. A detail of sample names is included in the files. The samples were acquired in sequential order, so file name goes "[Order]-[SampleName]". Samples were acquired on two days, and the data have been separated into folders reflecting this.