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Raw Data for: Mode III tear resistance of Bombyx mori silk cocoons
No full textRaw Data for the published article: Mode III tear resistance of Bombyx mori silk cocoons. PAPER ABSTRACT: This paper concerns the tear properties and behavior of Bombyx mori (B. Mori) silk cocoons. The tear resistance of cocoon layers is found to increase progressively from the innermost layer to the outermost layer. Importantly, the increase in tear strength correlates with increased porosity, which itself affects fiber mobility. We propose a microstructural mechanism for tear failure, which begins with fiber stretching and sliding, leading to fiber piling, and eventuating in fiber fracture. The direction of fracture is then deemed to be a function of the orientation of piled fibers, which is influenced by the presence of junctions where fibers cross at different angles and which may then act as nucleating sites for fiber piling. The interfaces between cocoon wall layers in B. mori cocoon walls account for 38% of the total wall tear strength. When comparing the tear energies and densities of B. mori cocoon walls against other materials, we find that the B. mori cocoon walls exhibit a balanced trade-off between tear resistance and lightweightness
Video animation for TRAFIR Ulster Travelling Fire Test 1 scaled-up model vs. Test.
No full textThis video was created to support the work within the TRAFIR project and subsequent projects and publications. It contains a comparison of the modelled (using computational fluid dynamics) versus experimental test results of one of the three tests conducted at Ulster University (which can be found here - https://doi.org/10.1016/j.firesaf.2022.103575). It was originally created in 2023 and hosted on another data sharing platform, but has been moved to DataShare for a more permanent home
Achang Village
No full text“The Village Achang” or “Achang Village” is a long story (48 minutes), recorded in 4 parts, each in a separate wav file with its own annotation (TextGrid). The brief summary of the four parts is as follows – Part 1: Achang Village is beautiful and clean and its people are hard working. With some of the lazy people like Ongay. But drought that started late in August caused a lot of confusion. Part 2: People have to change the ways of cultivation and move to the fertile inland, because the land they used to cultivate has lost its fertility due to overuse, and this was spearheaded by a man called Pakwan. Part 3: The third activity is parallel to moving inland, and that is growing maize and vegetables on the Nile coupled with fishing. Part 4: Then the focus of the story shifts to a family in a different village. The husband Okic had married his wife Abac against the will of her family because he was poor, i.e., he had few cows. She was brutally beaten by her own relatives who wanted a better dowry. But she stuck with her choice to marry him. Now they are considering a marriage proposal in relation to their own daughter, Nyaburo; the suitor is Gano, the son of Pakwan, from the village Achang, who were protagonists in Part 3 of the story. Because Gano’s family has been working hard, they are in a good position to pay the dowry, so Okic has no concern that the difficulty which he faced when marrying will be repeated. In this way, the story leads the listener to conclude that if you work hard, these difficulties can be avoided. The recording and annotation of this narrative took place with the financial support of the Leverhulme Trust, through two grants: a) “A descriptive analysis of the Shilluk language” (RPG-2015-055) and "Suprasegmentals in three West Nilotic languages" (RPG-20202-040) to Bert Remijsen (PI). Further details can be found in the metadata file, and the excel sheet.This item consists of an audio recording of a Shilluk narrative, recorded in four parts (four wav files, all in 48kHz, 16 bit mono uncompressed wav). For each of these, there is a file with time-aligned annotations (four Praat TextGrid files). The TextGrid annotations includes tiers for the Shilluk orthography, translation, phonemic transcription, morpheme glosses, and comments. In addition, there is a metadata file, the speaker permissions document and speaker questionnaire. The associated information is also summarized in a spreadsheet
SUPERSEDED - Trained neural networks and model data for `Online learning in idealized ocean gyres`
No full text## This item has been replaced by the one which can be found at https://doi.org/10.7488/ds/8068 ## Calculations performed using bt_ocean. bt_ocean is a differentiable finite difference solver for the barotropic vorticity equation on a beta-plane, for classic wind-forced barotropic ocean gyre simulations.
The latest version of bt_ocean is available at https://github.com/jrmaddison/bt_ocean.
For documentation and examples please visit https://jrmaddison.github.io/bt_ocean
Source Data
No full text## This item has been replaced by the one which can be found at https://doi.org/10.7488/ds/7857 ## These are the source data underlying the figures presented in the manuscript accepted in Nature Communications.
These are the source data underlying the figures presented in a manuscript entitled "The NE/AAT/CBG axis regulates adipose tissue glucocorticoid exposure", which has been provisionally accepted for publication in Nature Communications. Once published, the metadata for this dataset will be updated with the DOI of the published paper.
Corticosteroid binding globulin (CBG; SERPINA6) binds >85% of circulating glucocorticoids but its influence on their metabolic actions is unproven. Targeted proteolytic cleavage of CBG by neutrophil elastase (NE; ELANE) significantly reduces CBG binding affinity, potentially increasing ‘free’ glucocorticoid levels at sites of inflammation. NE is inhibited by alpha-1-antitrypsin (AAT; SERPINA1). Using complementary approaches in mice and humans to manipulate NE or AAT, we show high-fat diet (HFD) increases the NE:AAT ratio specifically in murine visceral adipose tissue, an effect only observed in males. Notably, HFD-fed male mice lacking NE have reduced glucocorticoid levels and action specifically in visceral adipose tissue, with improved glucose tolerance and insulin sensitivity, independent of systemic changes in free glucocorticoids. The protective effect of NE deficiency is lost when the adrenals are removed. Moreover, human asymptomatic heterozygous carriers of deleterious mutations in SERPINA1 resulting in lower AAT levels have increased adipose tissue glucocorticoid levels and action. However, in contrast to mice, humans present with systemic increases in free circulating glucocorticoid levels, an effect independent of HPA axis activation. These findings show that NE and AAT regulate local tissue glucocorticoid bioavailability in vivo, providing crucial evidence of a mechanism linking inflammation and metabolism
REALITIES in Health Disparities: Researching Evidence-based Alternatives in Living, Imaginative, Traumatised, Integrated, Embodied Systems
No full textREALITIES (Researching Evidence-based Alternatives to Living, Imaginative, Traumatised, Integrated and Embodied Systems) is a multi-disciplinary project made up of a collective of community researchers, local councils, third-sector organizations, artists, environmentalists, government bodies, and academics from various fields. The project focuses on addressing the fragmentation and trauma within systems.
The second phase, which ran for 9 months, focused on facilitating cross-collaborations in three Scottish localities (Clackmannanshire, Easter Ross, and North Lanarkshire) to establish asset hubs within them connecting employability, health, transport, and the environment; and to integrate marginalised groups. The REALITIES team sought to co-design and test a scalable REALITIES model, aiming to bring systemic change by fostering collaboration at hyper-local levels, addressing health disparities, and integrating diverse methodologies to improve community wellbeing across Scotland
Data supporting Davies & Beadman (2025) "Self-organization, error-correction and homeorhesis in renal development"
Get PDFThe dataset consists of one slide deck in pdf format; within the slide deck there are two sections, each supporting one sentence in the paper referred to in the title of this data set.
Development is often described as following a ‘genetic programme’, yet perturbations to normal development, whether applied by an experimenter, the environment, or a mutation affecting development of a nearby part of the body, show developmental biology to be remarkably adaptable. This paper examines the evidence for adaptability in kidney development, focusing specifically on error-correction, self-organization, and homeorhesis (the dynamic equivalent to homeostasis: return of a perturbed system to a standard developmental trajectory rather than a return to a fixed state that is seen in homeostasis). We present evidence for self-organization of renal tissue from randomly-aggregated progenitor cells, and also for the limitations of this self-organization and how they can be transcended by experimentally-applied symmetry-breaking cues. We provide evidence for error-correcting systems, and some evidence in the literature, generally in papers devoted to other problems, for genuine homeorhesis in aspects of kidney development. This review is not intended to be a ‘last word’ on any of these topics, and certainly not on the last-mentioned, for which data are very scant. It is instead intended to stimulate research in these areas, particularly homeorhesis, partly to increase understanding of natural development and partly as an aid to renal tissue engineering.The dataset consists of one slide deck in pdf format; within the slide deck there are two sections, each supporting one sentence in the paper referred to in the title of this data set.
Development is often described as following a ‘genetic programme’, yet perturbations to normal development, whether applied by an experimenter, the environment, or a mutation affecting development of a nearby part of the body, show developmental biology to be remarkably adaptable. This paper examines the evidence for adaptability in kidney development, focusing specifically on error-correction, self-organization, and homeorhesis (the dynamic equivalent to homeostasis: return of a perturbed system to a standard developmental trajectory rather than a return to a fixed state that is seen in homeostasis). We present evidence for self-organization of renal tissue from randomly-aggregated progenitor cells, and also for the limitations of this self-organization and how they can be transcended by experimentally-applied symmetry-breaking cues. We provide evidence for error-correcting systems, and some evidence in the literature, generally in papers devoted to other problems, for genuine homeorhesis in aspects of kidney development. This review is not intended to be a ‘last word’ on any of these topics, and certainly not on the last-mentioned, for which data are very scant. It is instead intended to stimulate research in these areas, particularly homeorhesis, partly to increase understanding of natural development and partly as an aid to renal tissue engineering
Time-series of HXT-GFP expression in budding yeast
No full textCells can match expression of a series of genes to a signal, so that each gene expresses in a particular range of the signal. An example is glucose transport in budding yeast where cells express different hexose-transporter (\g{HXT}) genes in different ranges of concentrations of extracellular glucose. Here we determine mechanistically how this matching to glucose occurs using time-lapse microscopy, microfluidics, dynamic glucose inputs, and mathematical modelling. We show that the glucose-sensing network works to generate a push-pull system of two pairs of repressors: as glucose rises, cells `pull' repression by two regulators, Mth1 and Std1, decreasing their activity while `pushing' repression by two others, Mig1 and Mig2; in falling glucose, cells reverse the push-pull. The combined activity of these repressors is an intracellular readout of extracellular glucose. Cells express those transporters with an affinity matching the current glucose concentration because the HXT promoters couple to the repressors in three principal ways, each specific to either low, medium, or high-affinity transporters. Through this regulation, budding yeast likely excels at importing glucose rapidly. Matching gene expression to a pattern of input is fundamental, and we believe that push-pull repression is likely widespread.Please see README.tx
Minimizing Profligacy of Searches with Reset
No full textThis submission contains associated materials (as two .zip files) relevant to the paper "Minimizing Profligacy of Searches with Reset." The materials include Julia programs for computing phase diagrams and Mathematica notebooks detailing calculations for Landau-like expansion.
(i) Julia Programs:
The Julia programs compute the the optimal value of resetting rate which minizmizes the profligacy of the search process and also computes the phase diagrams as obtained in the paper. These programs calculate the resetting rate that minimizes profligacy by scanning over a range of values for R, λ, and m in discrete steps. The programs compute transitions in the systems as parameters vary and classify them as continuous or discontinuous. The Julia programs utilize the Euler inversion algorithm, as described in "A Unified Framework for Numerically Inverting Laplace Transforms" by J. Abate and W. Whitt (INFORMS Journal on Computing, 2006) to numerically compute the inverse Laplace transform for the probability of success. gnuplot files and data used for generating figures in the paper are also provided.
(ii) Mathematica Notebooks:
The Mathematica notebook contains the detailed calculation for the Landau-like expansion performed in the supplemental materials for the paper.See readme.txt file
Suffering Due To Conflict, by Asunta Atag
Get PDFThis is a recorded narrative in the Thuri language, just under 3 minutes in duration, in which the speaker tells the story of her life. The translation is as follows. "What I say here, is about the suffering that we went through during the conflict. And me, I became blind when I was young, I was still breastfeeding, I am sure; I was two years when I became blind. What happened to us is armed conflict. [editors: She is referencing the civil war between Sudan and the South that started in 1983.] When fleeing from the armed conflict, it is my mother who led me. And whenever she became tired, she then tied me on her back. At one point, my mother and I were surrounded by burning grass in which we were hiding. My father had already been killed in the conflict [editors: so he could not protect them]. We were surrounded by burning grass with my mother. It is because she is a Thuri woman, she knew the name of a Thuri god [editors: There are gods within the traditional Thuri belief system, and people can invoke their names in time of danger for help. Afterwards they are expected to approach a guardian of this god within the community to offer a sacrifice in compensation], and she was able to save our lives by invoking the name of this Thuri god; and by so doing, we safely escaped the fire. If not for this, I am sure, we would have burnt to death in the grass. Again, another suffering we went through, my father was killed when we were still young. So my mother fed us singlehandedly using termites from burnt anthills in the bush during the conflict. Again, cloth, what is called cloth, we didn’t have, not even for tying a child on the back. I was tied on the back using a rope made from the bark of a tree known as upod in Thuri language [editors: thon upod ‘the rope of the upod tree’]. During that time that is what was used for tying a child on the back. When you sleep at night, mosquitos are problematic to people. You need to light a fire and keep rubbing your child’s body with your hand constantly to protect them from mosquito bites. This is the small story I had, about our suffering. [editors: The narrator was ready to stop speaking, but she was encouraged to continue by the listeners.] There are some fruits from trees known in the Thuri language as jier anyieyi, which my mother used to collect from the bushes there, which I do not know until now. They are soaked in water for five days before they can be pounded and cooked as food. These are the things that Thuri children suffered from. And these sufferings that Thuri children underwent, are being experienced until now. Nothing has changed in the Thuri land. This is what I want to report to you all, you Thuri children who are there [editors: She is referring to Thuri people who have migrated abroad.]. [editors: The term children can be extended to refer to the members of a community or the inhabitants of a place. In this sense ‘children of the Thuri land’ means Thuri people in general, not just children.] And I am still suffering until now. I do not have the ability [editors: because she is blind] to go the bush to go and dig roots such as muodi and dhaamo [editors: these are not domesticated / cultivated plants; they are collected through foraging rather than from agriculture.] as my mother did, so that I can feed myself. What remains (that I am able to do) to feed myself now is to sell water at the market. And I have also given birth. I give birth and I feed them with earnings from selling water. This is my suffering, which I want to tell you, Thuri children. Some people will die of hunger, others, those that God will help will be saved. Thank you. My name is Asunta Atag." The recording and translation of this narrative took place with the financial support of the Leverhulme Trust, through the grant "Suprasegmentals in three West Nilotic languages" (RPG-20202-040) to Bert Remijsen (PI). Further details can be found in the metadata file, and the excel sheet.The item includes the following three components: a) the sound recording of the narrative in Thuri (wav format, 48kHz sampling frequency, bit depth of 16 bit); b) a summary and a translation of its contents (pdf format); and c) a metadata file that provides details re. the speaker and the recording (excel format). Later on, we hope to add a file with annotations that are time-aligned with the recording. The recording was made on the understanding that the recording can be made public, and can be disseminated. Moreover, the speaker asked to be acknowledged by name for their contribution