cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7781472
title: An in vitro and ex vivo model of biomimetic regenerative devices to treat bone metastases and soft tissue tumors: BIOBOS PROJECT (Moh GR-2016-02364704)

description: Biobos is a project funded by Italian MoH GR-2016-02364704 Other Italian Institutes involved: Istituto Ortopedico Rizzoli, Bologna CNR, Faenza


The hypothesis of BIOBOS is that the development of nanostructured biomimetic materials medicated with a chemotherapeutic drug and with one used for tissue regeneration will be an innovative strategy to be integrated with the current multidisciplinary treatment options on patients with bone metastases from breast cancer and on patients with soft tissue sarcomas. Three types of medicated materials have been developed: i) porous scaffolds and ii) self-regulating biomimetic pastes (bone cements) with anti-osteoporotic functions to be applied in the future in patients with bone metastases; both materials were functionalized with the standard chemotherapy doxorubicin, and an anti-RANKL antibody, which by blocking osteoclast differentiation, helps tissue regeneration in lytic-type metastases; iii) polymeric nanofibrous tissue-nonwoven mesh functionalized with the chemotherapeutic epirubicin and the anti-inflammatory diclofenac, used to evaluate its regenerative potential. After the synthesis and characterization of the materials, the functionalization of the drugs at optimal concentrations for local release was optimized for the bone cements and for the meshes, so as to have the release of the chemotherapeutic and subsequently of the regenerative drug. Meanwhile, on non-medicated materials, the monoculture and coculture conditions of tumor cells (of breast cancer for bone metastasis applications; an epithelial sarcoma cell line for application on sarcomas) and stromal cells (osteoclasts and osteoblasts for applications on bone metastases, a cell line of healthy murine fibroblasts for application on sarcomas. For both pathologies, after approval by the Local Ethics Committee, biological samples were collected to test the ex vivo efficacy of the materials medicated on explants or primary cultures.
DOI: 10.5517/ccdc.csd.cc2bh6bd
title: CCDC 2159563: Experimental Crystal Structure Determination

description: Related Article: Yuzhong Shi, Jinqiu Fu, Yingying Wang, Yihang Hou, Rongxi Guo, Mengyang Cai, Yajie Zhang, Hanjie Ying, Pengpeng Yang, Keke Zhang|2024|J.Mol.Liq.|395|123871|doi:10.1016/j.molliq.2023.123871
description: Related Article: Yingying Wang, Pengpeng Yang, Zihan Li, Jinqiu Fu, Yuzhong Shi, Yajie Zhang, Keke Zhang, Wei Zhuang, Hanjie Ying|2022|CrystEngComm|24|5642|doi:10.1039/D2CE00388K
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.25012550
title: Supplementary Material for: Brain functional correlates of recall of life events in medication-naïve adolescents with borderline personality disorder

description: Introduction: Recall of autobiographical events has been found to be impaired in borderline personality disorder (BPD), but few studies have examined if this impairment has brain functional correlates. This study evaluated brain functional alterations during autobiographical recall, using medication-naive adolescent patients to avoid potential confounding effects of treatment. Methods: 32 adolescent female patients with BPD who were never-medicated and without psychiatric comorbidity and 33 matched healthy females underwent fMRI while they viewed individualized cue words that evoked autobiographical memories. Control conditions included viewing non-memory-evoking cues and a low-level baseline (cross fixation). Results: During autobiographical recall, in comparison to the low-level baseline, the BPD patients showed increased brain activity in regions including the posterior hippocampus, the lingual and calcarine cortex and the precuneus compared to the healthy controls. The BPD patients also showed a failure to de-activate the right dorsolateral prefrontal cortex during autobiographical recall. No patient-control differences were found when memory-evoking words were compared to non-memory-evoking words. Discussion/Conclusions: This study finds evidence of hippocampal/lingual/calcarine/precuneus hyperactivation to stimuli that evoke autobiographical memories in patients with BPD. As the changes were seen in never-treated patients without other comorbidities, they could be considered intrinsic to the disorder. Our study also adds to existing evidence for failure of de-activation in BPD, this time outside the default mode network.
DOI: 10.5281/zenodo.7785708
title: Spatial Transcriptomics in HCC

description: The morbidity of Hepatocellular carcinoma (HCC) is highest in individuals with chronic liver diseases (CLD). However, the effects of cell composition on the progression of CLDs to HCC remain elusive. To gain a better understanding of the spatial distribution of cells and their interactions, we created spatial transcriptome data from two HCC and their normal adjacent FFPE tissues using the 10x visium platform. We processed the data using cellRanger and mapped it to the Human Hg38 reference genome with GRCh38.p3 annotation. All data generated by cellRanger is provided here
DOI: 10.5281/zenodo.10551644
title: Data for the Discrete Image correlation tutorial of spam

description: Data and folder structure for the Discrete Image Correlation tutorial of spam available here: spam DDIC tutorial. 

The objective of the tutorial is to measure particle kinematics (i.e., particle tracking) with the scripts available in spam. The data used is from a study on granular materials using x-ray tomography, available here: Article. The experiment is called LENGP04, and correspond to a cylinder full of lentils initially oriented at 45° and deformed under triaxial compression. Repeated x-ray tomography scans are taken each 1% of axial shortening. The data of the tutorial correspond to the grey-scale volumes of the first six scans, (from LENGP04_00.tif to LENGP05_00.tif), as well as the segmentation of the initial scan (LENGP04_00-lab.tif).

The complete dataset with the grey-scale volumes for all the specimens of the experimental campaign, along with the processed results, is available here: Zenodo link.
DOI: 10.5281/zenodo.10551645
title: Data for the Discrete Image correlation tutorial of spam

description: Data and folder structure for the Discrete Image Correlation tutorial of spam available here: spam DDIC tutorial. 

The objective of the tutorial is to measure particle kinematics (i.e., particle tracking) with the scripts available in spam. The data used is from a study on granular materials using x-ray tomography, available here: Article. The experiment is called LENGP04, and correspond to a cylinder full of lentils initially oriented at 45° and deformed under triaxial compression. Repeated x-ray tomography scans are taken each 1% of axial shortening. The data of the tutorial correspond to the grey-scale volumes of the first six scans, (from LENGP04_00.tif to LENGP05_00.tif), as well as the segmentation of the initial scan (LENGP04_00-lab.tif).

The complete dataset with the grey-scale volumes for all the specimens of the experimental campaign, along with the processed results, is available here: Zenodo link.
DOI: 10.5281/zenodo.10303293
title: Feeding mango peel silage improved feed intake, energy supply and growth performances of dairy male calves

description: The major challenges for disposal of waste from fruit processing factories are high transportation costs, limited landfill availability and environmental pollution. Therefore, developing efficient waste management techniques to reduce transportation costs and environment pollution is important. Mango peels (MP) are abundant during the mango season and high in fermentable carbohydrate, which can easily breakdown and pollute the environment if a proper waste management method is not implemented. Thus, in this study, fresh MP were ensiled after sun-dried for one day and then fed to dairy male calves as the roughage source to evaluate its effect on feed intake, digestibility, energy balance, body weight gain, feed efficiency and blood metabolites. Eight growing crossbred dairy male calves (Holstein Friesians × Zebu) were allocated into two groups [Control (n = 4) and mango peel silage (MPS, n = 4)]. This experiment lasted for 12 weeks and daily feed offered and refusal were recorded to determine the daily feed intake. Digestion trial was performed at the last five days of experiment. Body weight and measurement were recorded every two weeks interval to determine the weight gain and body physical improvement. Blood was collected at the end of experiment to analyze the serum biochemical parameters. Ensiling improved the energy and protein contents and decreased fibre content of MP, thereby improving the forage quality.  Feeding MPS to calves increased (P < 0.05) feed intake, energy supply and energy balance, changes in body measurements, weight gain, feed efficiency, and glucose concentration, as well as lowered (P < 0.05) the urea nitrogen concentration. Ensiling fresh MP after sun-drying for one day improved silage quality, and feeding MPS to dairy male calves as a roughage source improved feed intake, energy supply and growth performances. Therefore, ensiling fresh MP could improve the feed supply for ruminant production and be an effective waste management strategy for fruit processing businesses.
DOI: 10.5281/zenodo.10303292
title: A diet containing mango peel silage impacts upon feed intake, energy supply and growth performances of dairy male calves

description: The major challenges for disposal of waste from fruit processing factories are high transportation costs, limited landfill availability and environmental pollution. Therefore, developing efficient waste management techniques to reduce transportation costs and environment pollution is important. Mango peels (MP) are abundant during the mango season and high in fermentable carbohydrate, which can easily breakdown and pollute the environment if a proper waste management method is not implemented. Thus, in this study, fresh MP were ensiled after sun-dried for one day and then fed to dairy male calves as the roughage source to evaluate its effect on feed intake, digestibility, energy balance, body weight gain, feed efficiency and blood metabolites. Eight growing crossbred dairy male calves (Holstein Friesians × Zebu) were allocated into two groups [Control (n = 4) and mango peel silage (MPS, n = 4)]. This experiment lasted for 12 weeks and daily feed offered and refusal were recorded to determine the daily feed intake. Digestion trial was performed at the last five days of experiment. Body weight and measurement were recorded every two weeks interval to determine the weight gain and body physical improvement. Blood was collected at the end of experiment to analyze the serum biochemical parameters. Ensiling improved the energy and protein contents and decreased fibre content of MP, thereby improving the forage quality.  Feeding MPS to calves increased (P < 0.05) feed intake, energy supply and energy balance, changes in body measurements, weight gain, feed efficiency, and glucose concentration, as well as lowered (P < 0.05) the urea nitrogen concentration. Ensiling fresh MP after sun-drying for one day improved silage quality, and feeding MPS to dairy male calves as a roughage source improved feed intake, energy supply and growth performances. Therefore, ensiling fresh MP could improve the feed supply for ruminant production and be an effective waste management strategy for fruit processing businesses.
DOI: 10.5281/zenodo.10546626
title: A diet containing mango peel silage impacts upon feed intake, energy supply and growth performances of dairy male calves

description: The major challenges for disposal of waste from fruit processing factories are high transportation costs, limited landfill availability and environmental pollution. Therefore, developing efficient waste management techniques to reduce transportation costs and environment pollution is important. Mango peels (MP) are abundant during the mango season and high in fermentable carbohydrate, which can easily breakdown and pollute the environment if a proper waste management method is not implemented. Thus, in this study, fresh MP were ensiled after sun-dried for one day and then fed to dairy male calves as the roughage source to evaluate its effect on feed intake, digestibility, energy balance, body weight gain, feed efficiency and blood metabolites. Eight growing crossbred dairy male calves (Holstein Friesians × Zebu) were allocated into two groups [Control (n = 4) and mango peel silage (MPS, n = 4)]. This experiment lasted for 12 weeks and daily feed offered and refusal were recorded to determine the daily feed intake. Digestion trial was performed at the last five days of experiment. Body weight and measurement were recorded every two weeks interval to determine the weight gain and body physical improvement. Blood was collected at the end of experiment to analyze the serum biochemical parameters. Ensiling improved the energy and protein contents and decreased fibre content of MP, thereby improving the forage quality.  Feeding MPS to calves increased (P < 0.05) feed intake, energy supply and energy balance, changes in body measurements, weight gain, feed efficiency, and glucose concentration, as well as lowered (P < 0.05) the urea nitrogen concentration. Ensiling fresh MP after sun-drying for one day improved silage quality, and feeding MPS to dairy male calves as a roughage source improved feed intake, energy supply and growth performances. Therefore, ensiling fresh MP could improve the feed supply for ruminant production and be an effective waste management strategy for fruit processing businesses.
DOI: 10.25381/cput.25041392
title: FIGURE 5 in Worming its way in-Polydora websteri (Annelida: Spionidae) increases the number of non-indigenous shell-boring polydorin pests of cultured molluscs in South Africa

description: FIGURE 5. Polydora websteri specimens from South Africa showing variation in methyl-green staining patterns. (A) dorsal anterior of SAMC-A089086, (B) palps with magenta arrow indicating a line of blue staining pigment adjacent to the black continuous pigmentation lines indicated with a yellow arrow, (C) unstained palp with yellow arrow head indicating faded portion of the black continuous pigmentation line, (D) dorsal anterior of SAMC-A089085 with magenta arrow indicating stained cells on prostomium forming two bars and magenta arrow-head indicating staining on peristomium concentrated along ridge of prostomium, (E) dorsal mid-body of SAMC-A089085, (F) ventral anterior of SAMC-A089088 with magenta arrow indicating stained cells forming a wide band across the anterior part of chaetiger and green arrow indicating hooded hooks on chaetiger 7, (G) ventral mid-body of SAMC-A089088 with magenta arrow-head indicating stained cells forming a thin band across the anterior part of chaetiger, (H) dorsal posterior of SAMC-A089085, (J) ventral anterior of SAMC-A089086 with green arrow indicating spines on chaetiger 5, (K) ventral mid-body of SAMC-A089084, (L) lateral anterior of SAMC-A089086 with green arrow indicating branchiae beginning at chaetiger 7, (M) lateral anterior of SAMC-A089085 with green arrow indicating spines in curved row on chaetiger 5, (N) dorsal posterior of SAMC-A089087 with magenta arrow indicating stained cells forming a bar; scale bars: 0.5 mm.
DOI: 10.25381/cput.25041392.v1
title: FIGURE 5 in Worming its way in-Polydora websteri (Annelida: Spionidae) increases the number of non-indigenous shell-boring polydorin pests of cultured molluscs in South Africa

description: FIGURE 5. Polydora websteri specimens from South Africa showing variation in methyl-green staining patterns. (A) dorsal anterior of SAMC-A089086, (B) palps with magenta arrow indicating a line of blue staining pigment adjacent to the black continuous pigmentation lines indicated with a yellow arrow, (C) unstained palp with yellow arrow head indicating faded portion of the black continuous pigmentation line, (D) dorsal anterior of SAMC-A089085 with magenta arrow indicating stained cells on prostomium forming two bars and magenta arrow-head indicating staining on peristomium concentrated along ridge of prostomium, (E) dorsal mid-body of SAMC-A089085, (F) ventral anterior of SAMC-A089088 with magenta arrow indicating stained cells forming a wide band across the anterior part of chaetiger and green arrow indicating hooded hooks on chaetiger 7, (G) ventral mid-body of SAMC-A089088 with magenta arrow-head indicating stained cells forming a thin band across the anterior part of chaetiger, (H) dorsal posterior of SAMC-A089085, (J) ventral anterior of SAMC-A089086 with green arrow indicating spines on chaetiger 5, (K) ventral mid-body of SAMC-A089084, (L) lateral anterior of SAMC-A089086 with green arrow indicating branchiae beginning at chaetiger 7, (M) lateral anterior of SAMC-A089085 with green arrow indicating spines in curved row on chaetiger 5, (N) dorsal posterior of SAMC-A089087 with magenta arrow indicating stained cells forming a bar; scale bars: 0.5 mm.
DOI: 10.25381/cput.25041377
title: FIGURE 3 in Worming its way in-Polydora websteri (Annelida: Spionidae) increases the number of non-indigenous shell-boring polydorin pests of cultured molluscs in South Africa

description: FIGURE 3. (a) Phylogenetic tree of Polydora websteri inferred from Cyt b sequences with Boccardia proboscidea and Polydora onagawaensis serving as the outgroup taxa. Maximum likelihood bootstrap support ≥ 97 % is given above every branch and the Bayesian support ≥ 97 % given below the branch. (b) Phylogenetic tree of Polydora websteri inferred from 18S rRNA sequences. (c) Cyt b haplotype network of P. websteri from South Africa, Namibia, Australia and China. Each region is represented by a different colour as in (a), circle sizes are proportional to number of sequences in each haplotype (Hap), lines perpendicular to the connecting lines indicate mutation differences and black dots indicate missing haplotypes. (d) 18S rRNA haplotype network of P. websteri from South Africa, Namibia, Australia, China and Japan. Each region is represented by a different colour as in (b). Sequences generated in this study are shown in bold, asterisk (*) indicates specimens previously identified as Polydora cf. websteri.
DOI: 10.25381/cput.25041377.v1
title: FIGURE 3 in Worming its way in-Polydora websteri (Annelida: Spionidae) increases the number of non-indigenous shell-boring polydorin pests of cultured molluscs in South Africa

description: FIGURE 3. (a) Phylogenetic tree of Polydora websteri inferred from Cyt b sequences with Boccardia proboscidea and Polydora onagawaensis serving as the outgroup taxa. Maximum likelihood bootstrap support ≥ 97 % is given above every branch and the Bayesian support ≥ 97 % given below the branch. (b) Phylogenetic tree of Polydora websteri inferred from 18S rRNA sequences. (c) Cyt b haplotype network of P. websteri from South Africa, Namibia, Australia and China. Each region is represented by a different colour as in (a), circle sizes are proportional to number of sequences in each haplotype (Hap), lines perpendicular to the connecting lines indicate mutation differences and black dots indicate missing haplotypes. (d) 18S rRNA haplotype network of P. websteri from South Africa, Namibia, Australia, China and Japan. Each region is represented by a different colour as in (b). Sequences generated in this study are shown in bold, asterisk (*) indicates specimens previously identified as Polydora cf. websteri.
DOI: 10.25381/cput.25041236
title: FIGURE 6 in Worming its way in-Polydora websteri (Annelida: Spionidae) increases the number of non-indigenous shell-boring polydorin pests of cultured molluscs in South Africa

description: FIGURE 6. Chaetal structures of Polydora websteri (SAMC-A089181) from South Africa. (A) falcate spines on chaetiger 5 with white arrow indicating the flange on the concave side and green arrow indicating pennoned companion chaetae, (B) hooded hooks on neuropodium of posterior chaetigers with white arrow indicating the hood and green arrow the constriction at the shaft, (C) spine indicated by white arrow with superior winged chaetae on chaetiger 5, (D) inferior winged chaetae on chaetiger 5; scale bars: 0.05 mm.
DOI: 10.25381/cput.25041236.v1
title: FIGURE 6 in Worming its way in-Polydora websteri (Annelida: Spionidae) increases the number of non-indigenous shell-boring polydorin pests of cultured molluscs in South Africa

description: FIGURE 6. Chaetal structures of Polydora websteri (SAMC-A089181) from South Africa. (A) falcate spines on chaetiger 5 with white arrow indicating the flange on the concave side and green arrow indicating pennoned companion chaetae, (B) hooded hooks on neuropodium of posterior chaetigers with white arrow indicating the hood and green arrow the constriction at the shaft, (C) spine indicated by white arrow with superior winged chaetae on chaetiger 5, (D) inferior winged chaetae on chaetiger 5; scale bars: 0.05 mm.
DOI: 10.5519/qd.m2wh547l
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (3250 records)
DOI: 10.25381/cput.25041353
title: FIGURE 4 in Worming its way in-Polydora websteri (Annelida: Spionidae) increases the number of non-indigenous shell-boring polydorin pests of cultured molluscs in South Africa

description: FIGURE 4. Polydora websteri specimens from South Africa stained with methyl-green. (A) dorsal anterior of SAMC-A089084, (B) ventral anterior of SAMC-A089088, (C) lateral anterior of SAMC-A089084, (D) dorsal mid-body of SAMC-A089084, (E) ventral mid-body of SAMC-A089088, (F) lateral mid-body of SAMC-A089084, (G) dorsal posterior of SAMC-A089084, (H) ventral posterior of SAMC-A089084; scale bars: 0.5 mm.
DOI: 10.25381/cput.25041353.v1
title: FIGURE 4 in Worming its way in-Polydora websteri (Annelida: Spionidae) increases the number of non-indigenous shell-boring polydorin pests of cultured molluscs in South Africa

description: FIGURE 4. Polydora websteri specimens from South Africa stained with methyl-green. (A) dorsal anterior of SAMC-A089084, (B) ventral anterior of SAMC-A089088, (C) lateral anterior of SAMC-A089084, (D) dorsal mid-body of SAMC-A089084, (E) ventral mid-body of SAMC-A089088, (F) lateral mid-body of SAMC-A089084, (G) dorsal posterior of SAMC-A089084, (H) ventral posterior of SAMC-A089084; scale bars: 0.5 mm.
DOI: 10.25381/cput.25041329
title: FIGURE 7 in Worming its way in-Polydora websteri (Annelida: Spionidae) increases the number of non-indigenous shell-boring polydorin pests of cultured molluscs in South Africa

description: FIGURE 7. Lectotype specimen of Polydora websteri (LACM-AHF POLY 1628) from oyster shells and deposited in the Los Angeles County Museum of Natural History (Radashevsky, 1999), stained with methyl-green. (A) dorsal anterior, scale bar: 1 mm, (B) dorsal anterior, scale bar: 0.25 mm, (C) ventral anterior, scale bar: 1 mm, (D) dorsal mid-body, scale bar: 1 mm, (E) latero-posterior; scale bar: 0.25mm (F) posterior; scale bar: 1 mm. Photographed by Adam Wall (Los Angeles County Museum of Natural History, August 2019).