cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc2d0y9p
title: CCDC 2205442: Experimental Crystal Structure Determination

description: Related Article: Yuji Mikata, Minori Kaneda, Shizuka Yonemura, Miyu Akedo, Hideo Konno, Takashi Matsuo|2022|Dalton Trans.|51|17170|doi:10.1039/D2DT02948K
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: 10.6084/m9.figshare.21598695
title: Understanding Software Agents

description: This paper discussed software agents by examples, their broad characteristics in relation to environment, structure and applications. The article is built up in the following way: firstly, the notion of software agents is characterized in order to explain, why software agent systems can be useful. This is followed by general remarks about application domains and categories. Finally, some examples of applications – both past and present ones – are described. The article ends with a discussion on future applications. <br>
DOI: 10.6084/m9.figshare.21598614.v1
title: Figure 1 Data

description: <strong>Figure 1.</strong> <strong>The melanin-based immune response is implicated in killing </strong><em><strong>C. neoformans</strong></em><strong> during infection.</strong> (A) During infection of G. mellonella, melanized nodules are formed within the hemolymph, which encapsulate C. neoformans. Melanin pigment produced by the fungus, is located typically within the cell wall, while the melanin produced by the insect during encapsulation within nodules is found around and within the fungal polysaccharide capsule. (B) GFP fluorescence is lost in heat killed C. neoformans cells expressing GFP under an actin promoter. Data represents counts of 1,640-1,750 single cells from two separate biological replicates. (C) Using a GFP-expressing strain of C. neoformans, we can visualize cell viability within the nodule, with living fungi fluorescing green and dead cells having no signal. (D) Melanin-encapsulated fungi are statistically less likely to have a GFP-positive signal at 24 h after infection at 30˚C, and at 72 h post infection at room temperature and 30˚C (Chi-squared test, p&lt;0.00001, p=0.00004, and p=0.0001, respectively) indicating that melanin-encapsulation is associated with fungal death. Numbers within bars represent the number of fungi enumerated in that condition. (E) In GFP-positive cells, the brighter fluorescence signal correlates with little to no melanization, with no cells that have strong GFP signals and large amounts of melanin encapsulation (n = 40). Each point represents data from one GFP-positive fungus within a nodules from three biological replicates. (F) Propidium Iodide viability staining does not appear to penetrate the inner space of the nodule where the fungus is located, but the staining does show that the hemocytes surrounding the fungus are not viable. (G) Colony forming units (CFUs) correlate directly to melanin inhibition using PTU (inset) in vitro, which indicates that melanin has a role in controlling growth of C. neoformans. Line represents the mean and error bars indicate 95% Confidence Interval of four independent biological replicates with 10-12 total technical replicates. (H) CFUs also inversely correlated to the Mean Gray Value of these wells, meaning that the darker wells with more melanization had higher CFUs recovered compared to the melanin-inhibited wells (Simple Linear Regression, p&lt;0.00001, F= 40.59). Each data point indicates measurements from individual wells from across three biological replicates, dotted lines represent the 95% confidence interval of the linear regression. (A-C,F) Data shown is representative of three biological replicates. All experiments performed in biological triplicate, with (G) representing 5 biological replicates. Scale bars represent 10 µm.
DOI: 10.6084/m9.figshare.21598761
title: Figure 2 Data

description: <strong>Figure 2. Using in vitro timelapse microscopy to visualize the melanin-based immune response</strong>. (A) Using a developed timelapse microscopy protocol, we were able to record the dynamics of hemolymph melanization in response to C. neoformans from 0 (B) up to 24 hours (C). We can then use particle measurement software to visualize and quantify the melanization reactions over time (D), representative of three biological replicates. This method can be used to gain insight into how different virulence factors, such as laccase, influence the melanization response, where we see that the laccase knockout mutant causes less of a melanization response without much change in time until onset of melanization (E), represented by three biological replicates, and normalized to the wildtype control melanization area at 360 minutes. (F) Overall, the lac1∆ triggers ~40% as much of a melanization immune response compared to the WT (one sample t-test, p = 0.0028, t = 18.78, df =2). (G) Isolated fungal melanins are associated with activation of the insect melanin based immune response, whereas the heat killed acapsular cryptococcal cells are not, as represented by 3-6 biological replicates. (H) Additionally, we can compare the activation of the melanin-based immune response from different fungal species such as C. neoformans and C. albicans, which strongly activates the melanization immune response, represented by 3-6 biological replicates. (B-D, G) are representative images and graphs from three biological replicates. Error bars indicate Standard Deviation. (D, E, G, H) Solid lines indicate mean melanization, and light colored points indicate individual replicate data points. Scale bars represent 50 µm.
DOI: 10.6084/m9.figshare.21598782
title: Figure 3 Data

description: <strong>Figure 3. Using tissue clearing to visualize the melanin-based immune response against C. neoformans</strong> <strong>in situ.</strong> Using tissue clearing techniques (A), we allowed for better visualization of melanized nodules within the intact G. mellonella, as seen in a before (top) and after (bottom) view of the same infected larvae (B). Under microscopy, the uninfected larvae had little to no melanized nodules (red arrows indicate dark, irregular, or opaque areas in the tissue) (C), whereas the C. neoformans larvae had very clear and distinct nodules (D). These nodules were viewed under high magnification, where the nodule structure and encapsulated fungus were apparent (E-F). These structures were very similar in appearance to the nodules extracted from hemolymph (G). (H) The size of the melanized nodules were quantified using particle measuring software. Infected particles represent n = 771, uninfected particles represent n =104, (Mann-Whitney test, p = 0.016). Error bars signify median with 95% Confidence Interval. (I) The melanized nodules of C. neoformans appeared to have no tissue tropism, but were found in distinct clumps or areas throughout the larvae (red arrows). (B-G, I) are representative images from three biological replicates. Scale bars in (E-G, I) represent 10 µm, (C,D) represent 500 µm, and (B) represent 500 mm.
DOI: 10.6084/m9.figshare.21598782.v1
title: Figure 3 Data

description: <strong>Figure 3. Using tissue clearing to visualize the melanin-based immune response against C. neoformans</strong> <strong>in situ.</strong> Using tissue clearing techniques (A), we allowed for better visualization of melanized nodules within the intact G. mellonella, as seen in a before (top) and after (bottom) view of the same infected larvae (B). Under microscopy, the uninfected larvae had little to no melanized nodules (red arrows indicate dark, irregular, or opaque areas in the tissue) (C), whereas the C. neoformans larvae had very clear and distinct nodules (D). These nodules were viewed under high magnification, where the nodule structure and encapsulated fungus were apparent (E-F). These structures were very similar in appearance to the nodules extracted from hemolymph (G). (H) The size of the melanized nodules were quantified using particle measuring software. Infected particles represent n = 771, uninfected particles represent n =104, (Mann-Whitney test, p = 0.016). Error bars signify median with 95% Confidence Interval. (I) The melanized nodules of C. neoformans appeared to have no tissue tropism, but were found in distinct clumps or areas throughout the larvae (red arrows). (B-G, I) are representative images from three biological replicates. Scale bars in (E-G, I) represent 10 µm, (C,D) represent 500 µm, and (B) represent 500 mm.
DOI: 10.6084/m9.figshare.21598785
title: Figure 4

description: <strong>Figure 4</strong>. <strong>Visualizing the melanization response to infection with Candida albicans.</strong> (A) Similar to the hemolymph from larvae infected with C. neoformans, we are able to see melanized nodules within the hemolymph. The melanized spot within these nodules appears more diffuse/less defined, and in some, the presence of less-melanized hyphae is distinct (red arrows). (B) We can also use tissue clearing to visualize the melanized nodules during C. albicans infection. (C-D) The melanized C. albicans seem to cluster in specific areas, in long strips within the larvae (yellow arrows). (E-F) Under higher magnification, we can see hyphal structures of C. albicans, which corresponds to what is previously known about C. albicans morphology in G. mellonella. Interestingly, the hyphae appear less melanized (red arrows) compared to the spherical yeast (white arrows) (F). All panels show representative images from 3 biological replicates. Scale bars in (A,D-F) represent 10 µm, in (C) represent 500 µm, and in (B) represent 500 mm.
DOI: 10.6084/m9.figshare.21598785.v1
title: Figure 4

description: <strong>Figure 4</strong>. <strong>Visualizing the melanization response to infection with Candida albicans.</strong> (A) Similar to the hemolymph from larvae infected with C. neoformans, we are able to see melanized nodules within the hemolymph. The melanized spot within these nodules appears more diffuse/less defined, and in some, the presence of less-melanized hyphae is distinct (red arrows). (B) We can also use tissue clearing to visualize the melanized nodules during C. albicans infection. (C-D) The melanized C. albicans seem to cluster in specific areas, in long strips within the larvae (yellow arrows). (E-F) Under higher magnification, we can see hyphal structures of C. albicans, which corresponds to what is previously known about C. albicans morphology in G. mellonella. Interestingly, the hyphae appear less melanized (red arrows) compared to the spherical yeast (white arrows) (F). All panels show representative images from 3 biological replicates. Scale bars in (A,D-F) represent 10 µm, in (C) represent 500 µm, and in (B) represent 500 mm.
DOI: 10.7295/w9cil54862
title: CIL:54862, Mouse lung tumor, Lung tumor tissue
DOI: 10.7295/w9cil54863
title: CIL:54863, Mouse lung tumor, Lung tumor tissue
DOI: 10.6084/m9.figshare.21598791
title: Figure 5 Data

description: <strong>Figure 5. Using timelapse microscopy to gain insight into C. albicans yeast and hyphae interactions with the melanization immune response. </strong>(A) Kinetics of the melanization reaction within hemolymph incubated with C. albicans yeast, with a distinct tri-phastic response in which the yeast begin non-encapsulated with melanin (1), followed by an initial peak of the melanization reaction (2), an extended plateau (3), and a greater second peak of the melanization reaction (4). (B) Using microscopy, we saw that the yeast start off non-melanized (B1), and most reached their peak melanin-encapsulation by 120 minutes (B2). After which, the yeast began to filament, and hyphae grew between 120 min and 750 minutes with minimal melanin encapsulation occurring. At 750 minutes (B3), blastoconidium (yeast) began to form on the hyphae, which then corresponded to a rapid increase in melanization (B4). Scale bars in (B) indicate 100 µm. (C) The time until this melanin bloom was approximately 14 hours (n = 15, mean = 874 minutes, 95% Confidence Interval 762 to 985 minutes). (D) Through these movies, we also saw that some melanin-encapsulated yeast were able to survive the immune response and grew from underneath the layer of pigment. The melanin-encapsulated C. albicans in panel (D) began to grow through the melanin by 250 minutes. Scale bars in (D) indicate 10 µm. (E) Overall, approximately 23% of melanin-encapsulated yeast were able to grow following melanin-encapsulation. Pairs of melanin-encapsulated yeast had the highest percentage of growth following melanin encpasulation, with a 33% frequency. (F) In the yeast that grew following melanin-encapsulation, the time until germ tube formation was delayed 230 minutes on average (n = 26), while in non-encapsulated yeast, the average time was 90 minutes (n = 111) (Two-tailed unpaired t-test, p&lt; 0.00001, t = 8.878, df =135) and error bars indicate mean with 95% Confidence Interval. (A,B,D) show representative data from three biological replicates. Each data point in (C) represents an independent biological replicate. (E,F) show data from 4 biological replicates.
DOI: 10.6084/m9.figshare.21598791.v1
title: Figure 5 Data

description: <strong>Figure 5. Using timelapse microscopy to gain insight into C. albicans yeast and hyphae interactions with the melanization immune response. </strong>(A) Kinetics of the melanization reaction within hemolymph incubated with C. albicans yeast, with a distinct tri-phastic response in which the yeast begin non-encapsulated with melanin (1), followed by an initial peak of the melanization reaction (2), an extended plateau (3), and a greater second peak of the melanization reaction (4). (B) Using microscopy, we saw that the yeast start off non-melanized (B1), and most reached their peak melanin-encapsulation by 120 minutes (B2). After which, the yeast began to filament, and hyphae grew between 120 min and 750 minutes with minimal melanin encapsulation occurring. At 750 minutes (B3), blastoconidium (yeast) began to form on the hyphae, which then corresponded to a rapid increase in melanization (B4). Scale bars in (B) indicate 100 µm. (C) The time until this melanin bloom was approximately 14 hours (n = 15, mean = 874 minutes, 95% Confidence Interval 762 to 985 minutes). (D) Through these movies, we also saw that some melanin-encapsulated yeast were able to survive the immune response and grew from underneath the layer of pigment. The melanin-encapsulated C. albicans in panel (D) began to grow through the melanin by 250 minutes. Scale bars in (D) indicate 10 µm. (E) Overall, approximately 23% of melanin-encapsulated yeast were able to grow following melanin-encapsulation. Pairs of melanin-encapsulated yeast had the highest percentage of growth following melanin encpasulation, with a 33% frequency. (F) In the yeast that grew following melanin-encapsulation, the time until germ tube formation was delayed 230 minutes on average (n = 26), while in non-encapsulated yeast, the average time was 90 minutes (n = 111) (Two-tailed unpaired t-test, p&lt; 0.00001, t = 8.878, df =135) and error bars indicate mean with 95% Confidence Interval. (A,B,D) show representative data from three biological replicates. Each data point in (C) represents an independent biological replicate. (E,F) show data from 4 biological replicates.
DOI: 10.6084/m9.figshare.21598803
title: Figure 6 Data

description: <strong>Figure 6. </strong><em><strong>Candida auris</strong></em><strong> produces pseudohypae in response to hemolymph. </strong>Following incubation of <em>C. auris </em>with hemolymph, the yeast get encapsulated with melanin by 120 min (A,B). Pseudohyphae form clearly by 480 min, while not eliciting a melanization response (C, inset), however, after approximately 720 minutes, there is a sharp increase in melanization within the hemolymph (D). A representative graph of the melanization in response to <em>C. auris </em>over time is shown in (E). The cell morphologies were confirmed as pseudohyphae through light microscopy at 100X magnification (F,G, red arrows), while the presence of enlarged giant cells was occasionally noted (H, white arrows) and dense clusters of yeast (H, yellow arrows). (I) Melanized aggregates of <em>C. auris</em> can be seen in <em>G. mellonella</em> larvae following tissue clearing. Melanized clusters of fungi can be seen in the head capsule (J), associated with trachea (K, t label) and freely within the tissue (L). In these melanized areas, we can see aggregates of yeast (M, yellow arrows) and pseudohyphae (N-O, red arrows). All panels are representative images and data from three independent replicates. Scale bars in Panel (I) represent 500 mm, (J-L) represent 500 µm, (A-D) represent 100 µm, while (F-H, M-O) represent 10 µm.
DOI: 10.6084/m9.figshare.21598818
title: Figure S1 Data

description: <strong>Supplementary Figure 1.</strong> <strong>Fungal melanization does not affect GFP signal in the H99-GFP strain</strong>. (A-B) GFP signal is lost upon heat treatment for 1 hour, and cells become exclusively propidium iodine positive Insets in (A) indicate representative images of cells in untreated condition, with the white arrows pointing to a PI-only positive cell, and a blue arrow pointing to a PI and GFP double positive cell. Non-melanized H99-GFP (C) and melanized H99-GFP (D) have comparable levels of GFP-fluorescence. Insets in (D) indicate representative selections of melanized cells that have GFP signal (white arrows) and melanized cells that lack GFP signal (red arrow). Scale bars represent 50 µm
DOI: 10.6084/m9.figshare.21598818.v1
title: Figure S1 Data

description: <strong>Supplementary Figure 1.</strong> <strong>Fungal melanization does not affect GFP signal in the H99-GFP strain</strong>. (A-B) GFP signal is lost upon heat treatment for 1 hour, and cells become exclusively propidium iodine positive Insets in (A) indicate representative images of cells in untreated condition, with the white arrows pointing to a PI-only positive cell, and a blue arrow pointing to a PI and GFP double positive cell. Non-melanized H99-GFP (C) and melanized H99-GFP (D) have comparable levels of GFP-fluorescence. Insets in (D) indicate representative selections of melanized cells that have GFP signal (white arrows) and melanized cells that lack GFP signal (red arrow). Scale bars represent 50 µm
DOI: 10.5517/ccdc.csd.cc2c266w
title: CCDC 2176857: Experimental Crystal Structure Determination

description: Related Article: Masrat Bashir, Imtiyaz Yousuf, Mushtaq Ahmad, Farukh Arjmand, Sartaj Tabassum|2023|Polyhedron|229|116189|doi:10.1016/j.poly.2022.116189
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: 10.5517/ccdc.csd.cc2c9d69
title: CCDC 2183770: Experimental Crystal Structure Determination

description: Related Article: Ya-Zhuo Dong, Chong-An Chen, Juan Chen, Jian-Wen Cheng, Jin-Hua Li, Guo-Yu Yang|2022|CrystEngComm|24|8027|doi:10.1039/D2CE01336C
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: 10.5517/ccdc.csd.cc2d39mg
title: CCDC 2207715: Experimental Crystal Structure Determination

description: Related Article: Koichiro Omasa, Masato Ito, Yuji Kubo|2022|New J.Chem.|46|21845|doi:10.1039/D2NJ04781K
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: 10.5517/ccdc.csd.cc28y4q3
title: CCDC 2113385: Experimental Crystal Structure Determination

description: Related Article: Maheswar Reddy Gowri, Gurunath Ramanathan|2022|J.Mol.Struct.|1274|134481|doi:10.1016/j.molstruc.2022.134481
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: 10.5517/ccdc.csd.cc28y4t6
title: CCDC 2113388: Experimental Crystal Structure Determination

description: Related Article: Maheswar Reddy Gowri, Gurunath Ramanathan|2022|J.Mol.Struct.|1274|134481|doi:10.1016/j.molstruc.2022.134481
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: 10.5517/ccdc.csd.cc1mj2rz
title: CCDC 1505011: Experimental Crystal Structure Determination

description: Related Article: Shital Harihar, Nishigandha Mone, Surekha K. Satpute, Dattatray Chadar, Debamitra Chakravarty, Thomas Weyhermüller, Ray J. Butcher, Sunita Salunke-Gawali|2022|Dalton Trans.|51|17338|doi:10.1039/D2DT02748H
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: 10.5517/ccdc.csd.cc281yny
title: CCDC 2087250: Experimental Crystal Structure Determination

description: Related Article: Shital Harihar, Nishigandha Mone, Surekha K. Satpute, Dattatray Chadar, Debamitra Chakravarty, Thomas Weyhermüller, Ray J. Butcher, Sunita Salunke-Gawali|2022|Dalton Trans.|51|17338|doi:10.1039/D2DT02748H
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: 10.5517/ccdc.csd.cc2d58f9
title: CCDC 2209600: Experimental Crystal Structure Determination

description: Related Article: Hai-Yue Lu, Liang-Jin Xu, Jin-Yun Wang, Zhong-Ning Chen|2022|J.Mater.Chem.C|10|16666|doi:10.1039/D2TC04250A
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.