cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7654958
title: Dataset for Unrolled-DOT: An Interpretable Deep Network for Diffuse Optical Tomography

description: Official dataset repository for Unrolled-DOT: An Interpretable Deep Network for Diffuse Optical Tomography. The repository contains both the experimental dataset (allTrainingDat_30-Sep-2021.mat) as well as data that is a dependency for running our code (5_29_21_src-det_10x10_scene_4cm.zip).
description: This research was developed with funding from the Defense Advanced Research Projects Agency (DARPA) (Grant No. N66001-19-C-4020). The views, opinions and/or findings expressed are those of the authors and should not be interpreted as representing the official views or policies of the Department of Defense or the U.S. Government. In addition, this project was also funded in part by the NSF Expeditions in Computing (Grant No. 1730574). Author Yongyi Zhao was supported by a training fellowship from the NLM Training Program (Grant No. T15LM007093); author Fay Wang was supported by a National Science Foundation Graduate Research Fellowship (Grant No. DGE-2036197). In addition, this project was also funded in part by the NSF CAREER award (Grant No. 1652633).
DOI: 10.5281/zenodo.7654959
title: Dataset for Unrolled-DOT: An Interpretable Deep Network for Diffuse Optical Tomography

description: Official dataset repository for Unrolled-DOT: An Interpretable Deep Network for Diffuse Optical Tomography. The repository contains both the experimental dataset (allTrainingDat_30-Sep-2021.mat) as well as data that is a dependency for running our code (5_29_21_src-det_10x10_scene_4cm.zip).
description: This research was developed with funding from the Defense Advanced Research Projects Agency (DARPA) (Grant No. N66001-19-C-4020). The views, opinions and/or findings expressed are those of the authors and should not be interpreted as representing the official views or policies of the Department of Defense or the U.S. Government. In addition, this project was also funded in part by the NSF Expeditions in Computing (Grant No. 1730574). Author Yongyi Zhao was supported by a training fellowship from the NLM Training Program (Grant No. T15LM007093); author Fay Wang was supported by a National Science Foundation Graduate Research Fellowship (Grant No. DGE-2036197). In addition, this project was also funded in part by the NSF CAREER award (Grant No. 1652633).
DOI: 10.6084/m9.figshare.21975644.v1
title: Supplementary Material for: Comparing single-incision midurethral sling with bulking agents for female stress urinary incontinence: rationale for a non-randomised controled trial

description: Objectives: Midurethral slings are considered the gold standard for the surgical treatment of stress-urinary incontinence (SUI), with an efficacy up to 80%. Another therapeutic option is the use of bulking agents, which create an artificial mass into the urethral submucosa, with an efficacy varying from 64% to 74%. Although bulking agents have a lower risk of complications than midurethral sling surgery, they are mainly used in case a midurethral sling is not an option or if midurethral sling surgery failed to cure stress urinary incontinence. In this study we offer all patients with SUI in secondary care a choice between a single incision midurethral sling procedure and treatment with a bulking agent. We want to examine patient preference and patient satisfaction for both procedures. We expect that offering both interventions in combination with standardized counselling will result in high patient satisfaction. Design: In this non-randomized controlled trial 266 patients will be objectively counselled for both interventions, after which all patients will choose between single-incision midurethral slings (SIMS) and Polyacrylamide hydrogel (PAHG), followed by the standard care procedure for women with SUI. Participants/Materials, Setting, Methods: From 1 January 2021 onwards, all consecutive adult patients (between 18 and 80 years of age) attending the outpatient gynaecology department with objectively confirmed, moderate to severe SUI will be eligible for enrolment in this non-randomized study. The primary outcome is patient satisfaction at 1 year, measured by the Patient Global Impression of Improvement; secondary outcomes are patient satisfaction at 3 months, objective and subjective cure at 3 months and 1 year, adverse events, postoperative pain and cost-effectiveness. Differences in outcome measures will be assessed through logistic and linear regression analyses, both unadjusted and adjusted with covariate adjustment using the propensity score. Results: No results are available yet. Limitations: The major disadvantage of this study design is the potential confounding bias. We intend to eliminate this bias by applying propensity scoring. Conclusion: By designing a non-randomized patient preference trial, we not only expect to demonstrate high patient satisfaction with both interventions, but also provide insight in the possible role of PAHG-injections in the treatment of female SUI as a first-choice non-conservative treatment. Trial Registration: This study is retrospectively registered at the Dutch Trial Registry on 22-03-2021 under the number NL9353.
DOI: 10.17638/datacat.liverpool.ac.uk/2181
title: STMBJ data for two indole end group compounds

description: Scanning tunnelling microscopy break junction (STMBJ or STM-BJ) data for two indole end group organic and organometallic molecular wire compounds.
DOI: 10.5255/ukda-sn-856316
title: Water and Fire Household Surveys, 2019

description: These data are responses to surveys administer via structured interviews with households in three Cape Flats townships in 2019. The surveys focused on household experiences of and responses to episodes of flooding (Sweet Home Farm); water scarcity (Delft South); and runaway fires (Overcome Heights). Responses were recorded from approximately 200 adults representing their households in each site. Due to the Covid-19 restrictions in place at the time, survey data was collected via telephone/digital device interviews. All interviews were undertaken in the language of the respondent’s choice – generally isiXhosa, Afrikaans or English. Responses have been translated into English to produce this final data set. The survey was organised in two parts: Section One recorded mainly demographic and macro-level quantitative data. Section Two focused on respondent disaster and resilience experiences and included both quantitative and open-ended, qualitative responses.
DOI: 10.6084/m9.figshare.22242055.v1
title: Supplementary Material for: Efficacy of Intravenous Immunoglobulins Against Chronic Lymphocytic Inflammation with Pontine Perivascular Enhancement Responsive to Steroids (CLIPPERS): A Case Report

description: Chronic lymphocytic inflammation with pontine perivascular enhancement responsive to steroids (CLIPPERS) is an inflammatory disease of the central nervous system that predominantly affects the brainstem. Apart from corticosteroids, there are few reported treatment options for CLIPPERS, and there is no standard therapy. A 77-year-old man presented with diplopia that had persisted for 5 months. Dysarthria and numbness of the distal right upper extremity and right lips were also observed. Brain magnetic resonance imaging (MRI) revealed a hyperintense area around the brainstem. Symptoms were relieved immediately following intravenous methylprednisolone (IVMP) administration. However, after gradual tapering of oral prednisolone to 5 mg/day, the symptoms relapsed, and brain imaging revealed that the condition had worsened. Intravenous immunoglobulins (IVIg) were administered for recurrence, with no clinical improvement. After each IVMP treatment, the patient recovered promptly. Based on the patient’s symptoms and characteristic MRI findings, exclusion of other diseases, and the significant efficacy of corticosteroids, he was diagnosed with CLIPPERS. There was no recurrence at a maintenance prednisolone dose of 8 mg/day. IVIg had a poor effect on the acute phase of CLIPPERS symptoms. Compared with other immunosuppressants, IVIg is less effective in suppressing the relapse of CLIPPERS.
DOI: 10.6084/m9.figshare.22116200.v1
title: Supplementary Material for: A recurrent Pleomorphic Xanthoastrocytoma in the cerebellum in a young adult: A case report and review of the literature.

description: Pleomorphic xanthoastrocytoma (PXA) is a rare glioma. It accounts for less than 1% of all astrocytomas. About 98% of PXAs originate supratentorially with the temporal lobe being the most common location. Cases of infratentorial PXAs are rarely reported in the medical literature. The tumor presents with a wide variation of symptoms based on the neuroanatomy involved with the location and size of the tumor, with seizures being the most reported symptom. The diagnosis depends on histological and clinical features along with radiologic features. We searched the keywords “Pleomorphic xanthastrocytoma, PXA, cerebellum, infratentorium, astrocytoma, gliomas” in the pubmed database; from 1979 to the current date, 28 cases were found in the medical literature featuring PXA in the infratentorium. We present the 29th case in the literature and the first in Syria. Our patient had a lesion in the right cerebellum and presented with a history of intermittent headache for 5 months followed by progressive gait disturbances and blurry vision and was misdiagnosed at the time of presentation with a high-grade glioma which is a common confusion because of the histological and clinical similarities. The patient underwent a suboccipital craniotomy and adjuvant therapy with a combination of radiotherapy and chemotherapy with Temozolomide (TMZ) was initiated at first. Then the patient presented with a relapse of symptoms and went through another surgery where frozen sections suggested the diagnosis of pleomorphic xanthoastrocytoma (PXA), further histopathological and immunohistochemical studies confirmed the diagnosis. Alongside highlighting the diagnostic challenge of this rare tumor, we did a brief review of the literature.
DOI: 10.5281/zenodo.7501231
title: Underlying data of Impact of shipping temperature on cell viability and T cell responses to bacterial antigens

description: <strong>Abstract</strong> <strong>Background: </strong>Interferon-γ (IFN-γ) secretion by T cells is a key correlate of immune protection against many pathogens including tuberculosis and the neglected tropical disease melioidosis. Clinical studies in tropical regions of immune responses to pathogens and vaccine monitoring studies require the collection of samples in resource-limited rural areas and subsequent shipment to central laboratories for downstream assays and long-term storage. Here, we studied the impact of two different shipping temperatures on the viability, composition and function of peripheral blood mononuclear cells (PBMC) using multi-colour flow cytometry and IFN-g enzyme-linked immunospot assay (IFN-g ELISpot), in order to provide guidance on sample shipment conditions for future clinical studies. <strong>Methods</strong>: Paired peripheral blood mononuclear cell (PBMC) samples from recovered melioidosis patients were stored in liquid nitrogen (-196°C) and then shipped from Bangkok, Thailand to Oxford, UK at either -80°C (dry ice) or -196°C (dry shipper). After thawing, cell viability and composition were assessed by flow cytometry and antigen specific responses to <em>Burkholderia pseudomallei</em> (BP) were measured using IFN-g ELISpot. <strong>Results</strong>: We observed modest lowering of viability in the majority of samples and a reduction in IFN-g responses to BP which correlated to a decrease of monocytes and NK cells in samples shipped at -80°C compared to -196°C. Despite being lower in magnitude antigen-specific responses remained detectable in the majority of samples. <strong>Conclusions:</strong>Here we demonstrate that shipment of cryopreserved PBMC at -196°C has a benefit on cell viability, recovery and T cell responses to bacterial antigens, although useful information can still be obtained from samples shipped at -80°C, thus providing important guidance for sample management in future clinical trials.
DOI: 10.5281/zenodo.7501230
title: Underlying data of Impact of shipping temperature on cell viability and T cell responses to bacterial antigens

description: <strong>Abstract</strong> <strong>Background: </strong>Interferon-γ (IFN-γ) secretion by T cells is a key correlate of immune protection against many pathogens including tuberculosis and the neglected tropical disease melioidosis. Clinical studies in tropical regions of immune responses to pathogens and vaccine monitoring studies require the collection of samples in resource-limited rural areas and subsequent shipment to central laboratories for downstream assays and long-term storage. Here, we studied the impact of two different shipping temperatures on the viability, composition and function of peripheral blood mononuclear cells (PBMC) using multi-colour flow cytometry and IFN-g enzyme-linked immunospot assay (IFN-g ELISpot), in order to provide guidance on sample shipment conditions for future clinical studies. <strong>Methods</strong>: Paired peripheral blood mononuclear cell (PBMC) samples from recovered melioidosis patients were stored in liquid nitrogen (-196°C) and then shipped from Bangkok, Thailand to Oxford, UK at either -80°C (dry ice) or -196°C (dry shipper). After thawing, cell viability and composition were assessed by flow cytometry and antigen specific responses to <em>Burkholderia pseudomallei</em> (BP) were measured using IFN-g ELISpot. <strong>Results</strong>: We observed modest lowering of viability in the majority of samples and a reduction in IFN-g responses to BP which correlated to a decrease of monocytes and NK cells in samples shipped at -80°C compared to -196°C. Despite being lower in magnitude antigen-specific responses remained detectable in the majority of samples. <strong>Conclusions:</strong>Here we demonstrate that shipment of cryopreserved PBMC at -196°C has a benefit on cell viability, recovery and T cell responses to bacterial antigens, although useful information can still be obtained from samples shipped at -80°C, thus providing important guidance for sample management in future clinical trials.
DOI: 10.5281/zenodo.7737476
title: Underlying data of Impact of shipping temperature on cell viability and T cell responses to bacterial antigens

description: <strong>Abstract</strong> <strong>Background: </strong>Interferon-γ (IFN-γ) secretion by T cells is a key correlate of immune protection against many pathogens including tuberculosis and the neglected tropical disease melioidosis. Clinical studies in tropical regions of immune responses to pathogens and vaccine monitoring studies require the collection of samples in resource-limited rural areas and subsequent shipment to central laboratories for downstream assays and long-term storage. Here, we studied the impact of two different shipping temperatures on the viability, composition and function of peripheral blood mononuclear cells (PBMC) using multi-colour flow cytometry and IFN-g enzyme-linked immunospot assay (IFN-g ELISpot), in order to provide guidance on sample shipment conditions for future clinical studies. <strong>Methods</strong>: Paired peripheral blood mononuclear cell (PBMC) samples from recovered melioidosis patients were stored in liquid nitrogen (-196°C) and then shipped from Bangkok, Thailand to Oxford, UK at either -80°C (dry ice) or -196°C (dry shipper). After thawing, cell viability and composition were assessed by flow cytometry and antigen specific responses to <em>Burkholderia pseudomallei</em> (BP) were measured using IFN-g ELISpot. <strong>Results</strong>: We observed modest lowering of viability in the majority of samples and a reduction in IFN-g responses to BP which correlated to a decrease of monocytes and NK cells in samples shipped at -80°C compared to -196°C. Despite being lower in magnitude antigen-specific responses remained detectable in the majority of samples. <strong>Conclusions:</strong>Here we demonstrate that shipment of cryopreserved PBMC at -196°C has a benefit on cell viability, recovery and T cell responses to bacterial antigens, although useful information can still be obtained from samples shipped at -80°C, thus providing important guidance for sample management in future clinical trials.
DOI: 10.5281/zenodo.7737659
title: Underlying data of Impact of shipping temperature on cell viability and T cell responses to bacterial antigens

description: <strong>Abstract</strong> <strong>Background: </strong>Interferon-γ (IFN-γ) secretion by T cells is a key correlate of immune protection against many pathogens including tuberculosis and the neglected tropical disease melioidosis. Clinical studies in tropical regions of immune responses to pathogens and vaccine monitoring studies require the collection of samples in resource-limited rural areas and subsequent shipment to central laboratories for downstream assays and long-term storage. Here, we studied the impact of two different shipping temperatures on the viability, composition and function of peripheral blood mononuclear cells (PBMC) using multi-colour flow cytometry and IFN-g enzyme-linked immunospot assay (IFN-g ELISpot), in order to provide guidance on sample shipment conditions for future clinical studies. <strong>Methods</strong>: Paired peripheral blood mononuclear cell (PBMC) samples from recovered melioidosis patients were stored in liquid nitrogen (-196°C) and then shipped from Bangkok, Thailand to Oxford, UK at either -80°C (dry ice) or -196°C (dry shipper). After thawing, cell viability and composition were assessed by flow cytometry and antigen specific responses to <em>Burkholderia pseudomallei</em> (BP) were measured using IFN-g ELISpot. <strong>Results</strong>: We observed modest lowering of viability in the majority of samples and a reduction in IFN-g responses to BP which correlated to a decrease of monocytes and NK cells in samples shipped at -80°C compared to -196°C. Despite being lower in magnitude antigen-specific responses remained detectable in the majority of samples. <strong>Conclusions:</strong>Here we demonstrate that shipment of cryopreserved PBMC at -196°C has a benefit on cell viability, recovery and T cell responses to bacterial antigens, although useful information can still be obtained from samples shipped at -80°C, thus providing important guidance for sample management in future clinical trials.
DOI: 10.5281/zenodo.7737754
title: Underlying data of Impact of shipping temperature on cell viability and T cell responses to bacterial antigens

description: <strong>Abstract</strong> <strong>Background: </strong>Interferon-γ (IFN-γ) secretion by T cells is a key correlate of immune protection against many pathogens including tuberculosis and the neglected tropical disease melioidosis. Clinical studies in tropical regions of immune responses to pathogens and vaccine monitoring studies require the collection of samples in resource-limited rural areas and subsequent shipment to central laboratories for downstream assays and long-term storage. Here, we studied the impact of two different shipping temperatures on the viability, composition and function of peripheral blood mononuclear cells (PBMC) using multi-colour flow cytometry and IFN-g enzyme-linked immunospot assay (IFN-g ELISpot), in order to provide guidance on sample shipment conditions for future clinical studies. <strong>Methods</strong>: Paired peripheral blood mononuclear cell (PBMC) samples from recovered melioidosis patients were stored in liquid nitrogen (-196°C) and then shipped from Bangkok, Thailand to Oxford, UK at either -80°C (dry ice) or -196°C (dry shipper). After thawing, cell viability and composition were assessed by flow cytometry and antigen specific responses to <em>Burkholderia pseudomallei</em> (BP) were measured using IFN-g ELISpot. <strong>Results</strong>: We observed modest lowering of viability in the majority of samples and a reduction in IFN-g responses to BP which correlated to a decrease of monocytes and NK cells in samples shipped at -80°C compared to -196°C. Despite being lower in magnitude antigen-specific responses remained detectable in the majority of samples. <strong>Conclusions:</strong>Here we demonstrate that shipment of cryopreserved PBMC at -196°C has a benefit on cell viability, recovery and T cell responses to bacterial antigens, although useful information can still be obtained from samples shipped at -80°C, thus providing important guidance for sample management in future clinical trials.
DOI: 10.5281/zenodo.7737333
title: FABLE Dataset

description: Dataset used to train FABLE model.
DOI: 10.5281/zenodo.7737332
title: FABLE Dataset

description: Dataset used to train FABLE model.
DOI: 10.5281/zenodo.7736089
title: A neural substrate for negative affect dictates female parental behavior

description: Parental behaviors secure the well-being of newborns and concomitantly limit negative affective states in adults, which emerge when coping with neonatal distress becomes challenging. Whether negative-affect-related neuronal circuits orchestrate parental actions is unknown. Here, we identify parental signatures in lateral habenula neurons receiving bed nucleus of stria terminalis innervation (<sup>BNST</sup>LHb). We find that LHb neurons of virgin female mice increase their activity following pup distress vocalization and are necessary for pup-call-driven aversive behaviors. LHb activity rises during pup retrieval, a behavior worsened by LHb inactivation. Intersectional cell identification and transcriptional profiling associate <sup>BNST</sup>LHb cells to parenting and outline a gene expression in female virgins similar to that in mothers but different from that in non-parental virgin male mice. Finally, tracking and manipulating <sup>BNST</sup>LHb cell activity demonstrates their specificity for encoding negative affect and pup retrieval. Thus, a negative affect neural circuit processes newborn distress signals and may limit them by guiding female parenting.
DOI: 10.5281/zenodo.7736090
title: A neural substrate for negative affect dictates female parental behavior

description: Parental behaviors secure the well-being of newborns and concomitantly limit negative affective states in adults, which emerge when coping with neonatal distress becomes challenging. Whether negative-affect-related neuronal circuits orchestrate parental actions is unknown. Here, we identify parental signatures in lateral habenula neurons receiving bed nucleus of stria terminalis innervation (<sup>BNST</sup>LHb). We find that LHb neurons of virgin female mice increase their activity following pup distress vocalization and are necessary for pup-call-driven aversive behaviors. LHb activity rises during pup retrieval, a behavior worsened by LHb inactivation. Intersectional cell identification and transcriptional profiling associate <sup>BNST</sup>LHb cells to parenting and outline a gene expression in female virgins similar to that in mothers but different from that in non-parental virgin male mice. Finally, tracking and manipulating <sup>BNST</sup>LHb cell activity demonstrates their specificity for encoding negative affect and pup retrieval. Thus, a negative affect neural circuit processes newborn distress signals and may limit them by guiding female parenting.