cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc2h2mt1
title: CCDC 2296443: Experimental Crystal Structure Determination

description: Related Article: Pagidi Sudhakar, Abhishek Kumar Gupta, David B. Cordes, Eli Zysman-Colman|2024|Chemical Science|15|545|doi:10.1039/D3SC05188A
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.10080972
title: Raw data for environment and behaviour in Zhang et al The demise of the giant ape Gigantopithecus blacki

description: The largest ever primate, and one of the largest of the southeast Asian megafauna, Gigantopithecus blacki1, persisted in China from ~2.0 million years until the late middle Pleistocene when it became extinct2,3,4. Its demise is enigmatic considering that it was one of the few Asian great apes to go extinct in the last 2.6 million years, while others, including orangutan, survived until the present day5. The cause of G. blacki's disappearance remains unresolved but could shed light on primate resilience and the fate of megafauna in this region6. Here, we applied three multidisciplinary analyses; chronology, past environments, and behaviour, to 22 caves in southern China. We employed 157 radiometric ages from six dating techniques to establish a timeline for G. blacki demise. We show that from 2.3 million years ago the environment was a mosaic of forests and grasses, providing ideal conditions for thriving G. blacki populations. However, just before and during the extinction window between 295-215,000 yrs ago (ka) there was enhanced environmental variability from increased seasonality, which caused changes in plant communities and an increase in open forest environments. While its taxonomic relative Pongo weidenreichi managed to adapt its dietary preferences and behaviour to this variability, G. blacki displayed signs of chronic stress and dwindling populations. Ultimately its struggle to adapt led to the demise of the greatest hominid to ever inhabit the Earth.
DOI: 10.5281/zenodo.10080973
title: Raw data for environment and behaviour in Zhang et al The demise of the giant ape Gigantopithecus blacki

description: The largest ever primate, and one of the largest of the southeast Asian megafauna, Gigantopithecus blacki1, persisted in China from ~2.0 million years until the late middle Pleistocene when it became extinct2,3,4. Its demise is enigmatic considering that it was one of the few Asian great apes to go extinct in the last 2.6 million years, while others, including orangutan, survived until the present day5. The cause of G. blacki's disappearance remains unresolved but could shed light on primate resilience and the fate of megafauna in this region6. Here, we applied three multidisciplinary analyses; chronology, past environments, and behaviour, to 22 caves in southern China. We employed 157 radiometric ages from six dating techniques to establish a timeline for G. blacki demise. We show that from 2.3 million years ago the environment was a mosaic of forests and grasses, providing ideal conditions for thriving G. blacki populations. However, just before and during the extinction window between 295-215,000 yrs ago (ka) there was enhanced environmental variability from increased seasonality, which caused changes in plant communities and an increase in open forest environments. While its taxonomic relative Pongo weidenreichi managed to adapt its dietary preferences and behaviour to this variability, G. blacki displayed signs of chronic stress and dwindling populations. Ultimately its struggle to adapt led to the demise of the greatest hominid to ever inhabit the Earth.
DOI: 10.5281/zenodo.10080907
title: Raw data for the dating techniques employed in Zhang et al The demise of the giant ape Gigantopithecus blacki

description: The largest ever primate, and one of the largest of the southeast Asian megafauna, Gigantopithecus blacki1, persisted in China from ~2.0 million years until the late middle Pleistocene when it became extinct2,3,4. Its demise is enigmatic considering that it was one of the few Asian great apes to go extinct in the last 2.6 million years, while others, including orangutan, survived until the present day5. The cause of G. blacki's disappearance remains unresolved but could shed light on primate resilience and the fate of megafauna in this region6. Here, we applied three multidisciplinary analyses; chronology, past environments, and behaviour, to 22 caves in southern China. We employed 157 radiometric ages from six dating techniques to establish a timeline for G. blacki demise. We show that from 2.3 million years ago the environment was a mosaic of forests and grasses, providing ideal conditions for thriving G. blacki populations. However, just before and during the extinction window between 295-215,000 yrs ago (ka) there was enhanced environmental variability from increased seasonality, which caused changes in plant communities and an increase in open forest environments. While its taxonomic relative Pongo weidenreichi managed to adapt its dietary preferences and behaviour to this variability, G. blacki displayed signs of chronic stress and dwindling populations. Ultimately its struggle to adapt led to the demise of the greatest hominid to ever inhabit the Earth.
DOI: 10.5281/zenodo.10080908
title: Raw data for the dating techniques employed in Zhang et al The demise of the giant ape Gigantopithecus blacki

description: The largest ever primate, and one of the largest of the southeast Asian megafauna, Gigantopithecus blacki1, persisted in China from ~2.0 million years until the late middle Pleistocene when it became extinct2,3,4. Its demise is enigmatic considering that it was one of the few Asian great apes to go extinct in the last 2.6 million years, while others, including orangutan, survived until the present day5. The cause of G. blacki's disappearance remains unresolved but could shed light on primate resilience and the fate of megafauna in this region6. Here, we applied three multidisciplinary analyses; chronology, past environments, and behaviour, to 22 caves in southern China. We employed 157 radiometric ages from six dating techniques to establish a timeline for G. blacki demise. We show that from 2.3 million years ago the environment was a mosaic of forests and grasses, providing ideal conditions for thriving G. blacki populations. However, just before and during the extinction window between 295-215,000 yrs ago (ka) there was enhanced environmental variability from increased seasonality, which caused changes in plant communities and an increase in open forest environments. While its taxonomic relative Pongo weidenreichi managed to adapt its dietary preferences and behaviour to this variability, G. blacki displayed signs of chronic stress and dwindling populations. Ultimately its struggle to adapt led to the demise of the greatest hominid to ever inhabit the Earth.
DOI: 10.5281/zenodo.10077254
title: Code for Zhang et al The demise of the giant ape Gigantopithecus blacki

description: The largest ever primate, and one of the largest of the southeast Asian megafauna, Gigantopithecus blacki1, persevered in China from ~2.0 million years until the late middle Pleistocene when it went extinct2,3,4. Its demise is enigmatic considering that it was one of the few Asian great apes to go extinct in the last 2.6 million years when other great apes, including orang-utan, survived up to the present5. The cause of G. blacki's abrupt disappearance remains unresolved but could shed light on primate resilience and the fate of other megafauna in this region6. Here, we applied three combined multidisciplinary analyses concerning the; 1) chronology, 2) past environments, and 3) behaviour of G. blacki, to 22 caves in two regions of southern China. 157 radiometric ages from six dating techniques were modelled to establish a timeline for G. blacki demise. We show that from 2.3 Ma the environment was a mosaic of forests and grasses, which supported the flourishing G. blacki, and many other primate populations. However, just prior to and during the extinction window between 295-215,000 yrs ago (ka) there was enhanced environmental variability due to an increase in seasonality, which caused a change in forest plant communities and an increase in open forest environments. The data reveal that although its taxonomic relative Pongo weidenreichi was able to adapt its dietary preferences and behaviour to this variability, G. blacki displayed signs of chronic stress and struggled to adapt, causing dwindling populations and ultimately this led to the demise of the greatest hominid to walk the Earth.
DOI: 10.5281/zenodo.10077255
title: Code for Zhang et al The demise of the giant ape Gigantopithecus blacki

description: The largest ever primate, and one of the largest of the southeast Asian megafauna, Gigantopithecus blacki1, persevered in China from ~2.0 million years until the late middle Pleistocene when it went extinct2,3,4. Its demise is enigmatic considering that it was one of the few Asian great apes to go extinct in the last 2.6 million years when other great apes, including orang-utan, survived up to the present5. The cause of G. blacki's abrupt disappearance remains unresolved but could shed light on primate resilience and the fate of other megafauna in this region6. Here, we applied three combined multidisciplinary analyses concerning the; 1) chronology, 2) past environments, and 3) behaviour of G. blacki, to 22 caves in two regions of southern China. 157 radiometric ages from six dating techniques were modelled to establish a timeline for G. blacki demise. We show that from 2.3 Ma the environment was a mosaic of forests and grasses, which supported the flourishing G. blacki, and many other primate populations. However, just prior to and during the extinction window between 295-215,000 yrs ago (ka) there was enhanced environmental variability due to an increase in seasonality, which caused a change in forest plant communities and an increase in open forest environments. The data reveal that although its taxonomic relative Pongo weidenreichi was able to adapt its dietary preferences and behaviour to this variability, G. blacki displayed signs of chronic stress and struggled to adapt, causing dwindling populations and ultimately this led to the demise of the greatest hominid to walk the Earth.
DOI: 10.6084/m9.figshare.24487248.v1
title: Understanding the age-related alterations in the testis-specific proteome

description: Fertility rates in developing countries have declined over the past decades, and the trend of delayed fatherhood is rising as societies develop. The reasons behind the decline in male fertility with advancing age remain mysterious, making it a compelling and crucial area for further research. However, the limited number of studies dedicated to unraveling this enigma poses a challenge. Thus, our objective is to illuminate some of the upregulated and downregulated mechanisms in the male testis during the aging process. Herein, we present a critical overview of the studies addressing the alterations of testicular proteome through the aging process, starting from sexually matured young males to end-of-life-expectancy aged males. The comparative studies of the proteomic testicular profile of men with and without spermatogenic impairment are also discussed and key proteins and pathways involved are highlighted. The difficulty of making age-comparative studies, especially of advanced-age study subjects, makes this topic of study quite challenging. Another topic worth mentioning is the heterogeneous nature and vast cellular composition of testicular tissue, which makes proteome data interpretation tricky. The cell type sorting and comorbidities testing in the testicular tissue of the studied subjects would help mitigate these problems.
DOI: 10.6084/m9.figshare.24459567
title: A computational method for the prediction and functional analysis of potential <i>Mycobacterium tuberculosis</i> adhesin-related proteins

description: Mycobacterial adherence plays a major role in the establishment of infection within the host. Adhesin-related proteins attach to host receptors and cell-surface components. The current study aimed to utilize in-silico strategies to determine the adhesin potential of conserved hypothetical (CH) proteins. Computational analysis was performed on the whole <i>Mycobacterium tuberculosis</i> H37Rv proteome using a software program for the prediction of adhesin and adhesin-like proteins using neural networks (SPAAN) to determine the adhesin potential of CH proteins. A robust pipeline of computational analysis tools: Phyre2 and pFam for homology prediction; Mycosub, PsortB, and Loctree3 for subcellular localization; SignalP-5.0 and SecretomeP-2.0 for secretory prediction, were utilized to identify adhesin candidates. SPAAN revealed 776 potential adhesins within the whole MTB H37Rv proteome. Comprehensive analysis of the literature was cross-tabulated with SPAAN to verify the adhesin prediction potential of known adhesin (<i>n</i> = 34). However, approximately a third of known adhesins were below the probability of adhesin (P<sub>ad</sub>) threshold (P<sub>ad</sub> ≥0.51). Subsequently, 167 CH proteins of interest were categorized using essential in-silico tools. The use of SPAAN with supporting in-silico tools should be fundamental when identifying novel adhesins. This study provides a pipeline to identify CH proteins as functional adhesin molecules.
DOI: 10.6084/m9.figshare.24459567.v1
title: A computational method for the prediction and functional analysis of potential <i>Mycobacterium tuberculosis</i> adhesin-related proteins

description: Mycobacterial adherence plays a major role in the establishment of infection within the host. Adhesin-related proteins attach to host receptors and cell-surface components. The current study aimed to utilize in-silico strategies to determine the adhesin potential of conserved hypothetical (CH) proteins. Computational analysis was performed on the whole <i>Mycobacterium tuberculosis</i> H37Rv proteome using a software program for the prediction of adhesin and adhesin-like proteins using neural networks (SPAAN) to determine the adhesin potential of CH proteins. A robust pipeline of computational analysis tools: Phyre2 and pFam for homology prediction; Mycosub, PsortB, and Loctree3 for subcellular localization; SignalP-5.0 and SecretomeP-2.0 for secretory prediction, were utilized to identify adhesin candidates. SPAAN revealed 776 potential adhesins within the whole MTB H37Rv proteome. Comprehensive analysis of the literature was cross-tabulated with SPAAN to verify the adhesin prediction potential of known adhesin (<i>n</i> = 34). However, approximately a third of known adhesins were below the probability of adhesin (P<sub>ad</sub>) threshold (P<sub>ad</sub> ≥0.51). Subsequently, 167 CH proteins of interest were categorized using essential in-silico tools. The use of SPAAN with supporting in-silico tools should be fundamental when identifying novel adhesins. This study provides a pipeline to identify CH proteins as functional adhesin molecules.
DOI: 10.6084/m9.figshare.24487248
title: Understanding the age-related alterations in the testis-specific proteome

description: Fertility rates in developing countries have declined over the past decades, and the trend of delayed fatherhood is rising as societies develop. The reasons behind the decline in male fertility with advancing age remain mysterious, making it a compelling and crucial area for further research. However, the limited number of studies dedicated to unraveling this enigma poses a challenge. Thus, our objective is to illuminate some of the upregulated and downregulated mechanisms in the male testis during the aging process. Herein, we present a critical overview of the studies addressing the alterations of testicular proteome through the aging process, starting from sexually matured young males to end-of-life-expectancy aged males. The comparative studies of the proteomic testicular profile of men with and without spermatogenic impairment are also discussed and key proteins and pathways involved are highlighted. The difficulty of making age-comparative studies, especially of advanced-age study subjects, makes this topic of study quite challenging. Another topic worth mentioning is the heterogeneous nature and vast cellular composition of testicular tissue, which makes proteome data interpretation tricky. The cell type sorting and comorbidities testing in the testicular tissue of the studied subjects would help mitigate these problems.
DOI: 10.6084/m9.figshare.24941364
title: Chatbot input and responses

description: This Excel sheet contains responses to spatial tasks given to 4 chatbots, which are GPT-4, Bard, Claude-2, and Copilot.
DOI: 10.6084/m9.figshare.24941364.v1
title: Chatbot input and responses

description: This Excel sheet contains responses to spatial tasks given to 4 chatbots, which are GPT-4, Bard, Claude-2, and Copilot.
DOI: 10.6084/m9.figshare.24941441.v1
title: MATLAB code from Scattering kernel of an array of floating ice floes: application to water wave transport in the marginal ice zone

description: MATLAB codes used to produce the results in the paper.
DOI: 10.6084/m9.figshare.24941441
title: MATLAB code from Scattering kernel of an array of floating ice floes: application to water wave transport in the marginal ice zone

description: MATLAB codes used to produce the results in the paper.
DOI: 10.5281/zenodo.10457354
title: Date

description: Provides basic data for articles
DOI: 10.5281/zenodo.10457353
title: Date

description: Provides basic data for articles
DOI: 10.6084/m9.figshare.24941453
title: Graphical-Summary-and-Animations-Explorations-of-the-Holonomy-of-a-Sphere.mov;Source-code-files-Explorations-of-the-Holomony-of-a-Sphere.zip from Explorations of the holonomy of a rolling sphere

description: Graphical summary of the paper and animations of the ;Matlab files used to compute the holonomy of the sphere
DOI: 10.6084/m9.figshare.24941453.v1
title: Graphical-Summary-and-Animations-Explorations-of-the-Holonomy-of-a-Sphere.mov;Source-code-files-Explorations-of-the-Holomony-of-a-Sphere.zip from Explorations of the holonomy of a rolling sphere

description: Graphical summary of the paper and animations of the ;Matlab files used to compute the holonomy of the sphere
DOI: 10.34740/kaggle/dsv/7332914
title: 🏦 Credit Approval Dataset
DOI: 10.5519/qd.xodc0g36
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (50 records)
DOI: 10.5519/qd.bci1adtb
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (50 records)
DOI: 10.6084/m9.figshare.24941485
title: Supplementary Code from Combining single-molecule and expansion microscopy in fission yeast to visualize protein structures at the nanostructural level

description: In this work, we have developed an expansion microscopy (ExM) protocol that combines ExM with photoactivated localization microscopy (ExPALM) for yeast cell imaging, and report a robust protocol for single-molecule and expansion microscopy of fission yeast, short SExY. Our optimized SExY protocol retains about 50% of the fluorescent protein signal, doubling the amount obtained compared to the original protein retention ExM (proExM) protocol. It allows for a fivefold, highly isotropic expansion of fission yeast cells, which we carefully controlled while optimizing protein yield. We demonstrate the SExY method on several exemplary molecular targets and explicitly introduce low-abundant protein targets, e.g. nuclear proteins such as cbp1 and mis16 and the centromere-specific histone protein cnp1. The SExY protocol optimizations increasing protein yield could be beneficial for many studies, i.e. when targeting low abundance proteins or studies that rely on genetic labelling for various reasons, e.g. for proteins that cannot be easily targeted by extrinsic staining or in case artefacts introduced by unspecific staining interfere with data quality.
DOI: 10.6084/m9.figshare.24941485.v1
title: Supplementary Code from Combining single-molecule and expansion microscopy in fission yeast to visualize protein structures at the nanostructural level

description: In this work, we have developed an expansion microscopy (ExM) protocol that combines ExM with photoactivated localization microscopy (ExPALM) for yeast cell imaging, and report a robust protocol for single-molecule and expansion microscopy of fission yeast, short SExY. Our optimized SExY protocol retains about 50% of the fluorescent protein signal, doubling the amount obtained compared to the original protein retention ExM (proExM) protocol. It allows for a fivefold, highly isotropic expansion of fission yeast cells, which we carefully controlled while optimizing protein yield. We demonstrate the SExY method on several exemplary molecular targets and explicitly introduce low-abundant protein targets, e.g. nuclear proteins such as cbp1 and mis16 and the centromere-specific histone protein cnp1. The SExY protocol optimizations increasing protein yield could be beneficial for many studies, i.e. when targeting low abundance proteins or studies that rely on genetic labelling for various reasons, e.g. for proteins that cannot be easily targeted by extrinsic staining or in case artefacts introduced by unspecific staining interfere with data quality.
DOI: 10.5519/qd.6ix5kxyh
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (50 records)
DOI: 10.34740/kaggle/dsv/7335407
title: Billboard
DOI: 10.34740/kaggle/dsv/7335410
title: Billboard
DOI: 10.34740/kaggle/dsv/7335413
title: Billboard
DOI: 10.34740/kaggle/dsv/7335415
title: Billboard
DOI: 10.34740/kaggle/dsv/7335417
title: Billboard
DOI: 10.34740/kaggle/dsv/7335420
title: Billboard
DOI: 10.34740/kaggle/dsv/7335421
title: Billboard
DOI: 10.34740/kaggle/dsv/7335422
title: Billboard
DOI: 10.34740/kaggle/dsv/7335424
title: Billboard
DOI: 10.34740/kaggle/dsv/7335426
title: Billboard
DOI: 10.34740/kaggle/dsv/7335447
title: Billboard
DOI: 10.6084/m9.figshare.24551383.v1
title: Supplementary Material for: A Phase 1b Study of Lenvatinib Plus Pembrolizumab in Patients With Unresectable Hepatocellular Carcinoma: Extended Analysis of Study 116

description: Background: Treatment with lenvatinib (dosing for patients who weigh ≥60 kg was 12 mg/day; for patients who weigh &lt;60 kg, the dose was 8 mg/day) plus pembrolizumab 200 mg once every 3 weeks demonstrated antitumor activity and a manageable safety profile in patients with first-line unresectable hepatocellular carcinoma (uHCC) in the open-label phase 1b Study 116/KEYNOTE-524 (primary analysis data cutoff date: October 31, 2019; median follow-up: 10.6 months). 
Objective: This analysis (updated data cutoff date: March 31, 2021) reports efficacy results from 17 months of additional follow-up time. 
Methods: 100 Patients with uHCC were included in the primary analysis (median follow-up: 27.6 months). Endpoints included overall survival (OS) and investigator-assessed progression-free survival (PFS), objective response rate (ORR), and duration of response (DOR) per modified RECIST. Landmark analyses of OS by best response at 3 and 9 months were performed. Pembrolizumab antidrug antibodies (ADAs) and concentrations were also measured (cutoff date: August 7, 2020). 
Results: ORR was 43.0% (95% CI 33.1% to 53.3%) and median DOR was 17.1 months (95% CI 6.9 to 19.3 months). Median PFS and OS were 9.3 months (95% CI 7.4 to 9.8 months) and 20.4 months (95% CI 14.4 to 25.9 months), respectively. No treatment-emergent ADAs were detected. 
Conclusion: Results show a sustained treatment effect with lenvatinib plus pembrolizumab in patients with uHCC in the first-line setting.