cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13078613.v1
title: The impact of HIPEC <i>vs.</i> EPIC for the treatment of mucinous appendiceal carcinoma: a study from the US HIPEC collaborative

description: Mucinous appendiceal carcinoma is a rare malignancy that commonly spreads to the peritoneum leading to peritoneal metastases. Complete cytoreduction with perioperative intraperitoneal chemotherapy (PIC) is the mainstay of treatment, administered as either hyperthermic intra peritoneal chemotherapy (HIPEC) or early post-operative intraperitoneal chemotherapy (EPIC). Our goal was to assess the perioperative and long term survival outcomes associated with these two PIC methods. Patients with mucinous appendiceal carcinoma were identified in the US HIPEC Collaborative database from 12 academic institutions. Patient demographics, clinical characteristics, and survival outcomes were compared among patients who underwent HIPEC <i>vs.</i> EPIC with inverse probability weighting (IPW) used for adjustment. Among 921 patients with mucinous appendiceal carcinoma, 9% underwent EPIC while 91% underwent HIPEC. There was no difference in Grade III–V complications between the two groups (18.5% for HIPEC <i>vs.</i> 15.0% for EPIC, <i>p</i>=.43) though patients who underwent HIPEC had higher rates of readmissions (21.2% <i>vs.</i> 8.8%, <i>p</i> Among patients with mucinous appendiceal carcinoma, both EPIC and HIPEC appear to be associated with similar perioperative and long-term outcomes.
DOI: 10.6084/m9.figshare.13273119
title: High-intensity focused ultrasound (HIFU) therapy for benign thyroid nodules: a 3-year retrospective multicenter follow-up study

description: Outcomes of high-intensity focused ultrasound (HIFU), as a non-surgical treatment option for benign symptomatic thyroid nodules, has mainly been based on single-center studies and short-term follow-up. Therefore, we assessed the safety, and long-term efficacy of HIFU in benign thyroid nodules among four centers with expertise in thyroid mini-invasive procedures. Retrospective three year follow-up study in four European centers, treating solid benign thyroid nodules causing pressure symptoms and/or cosmetic concerns. Nodule volume reduction was assessed at 1, 3, 6, 12, 24, and 36 months post-treatment. Technical efficacy, defined as a volume reduction rate (VVR) &gt;50% was evaluated at 6, 12, 24 and 36 months. Predictive factors of efficacy were assessed using logistic models. Complications and side effects were classified according to the Interventional Radiology Guidelines and changes in local symptoms were scored on a visual-analog scale. Sixty-five patients (mean age 51.1 ± 14.0 years; 86.2% women) with a single thyroid nodule and a mean baseline nodule volume of 9.8 ± 10.3 mL were treated with a mean energy of 7.1 ± 3.1 kJ (range: 2.0 to 15.5 kJ). Median nodule volume reduction was 31.5% (IQR: −38.6% to −23.1%) at 12 months and 31.9% (IQR: −36.4% to −16.1%) at 36 months. Technical efficacy was obtained in 17.2% of cases at 6 months, 17.8% at 12 months, 3.4% at 24 months, and 7.4% at 36 months. The number of treated pixels and the mean energy delivered were positively correlated to VRR at 1, 6 and 12 months. The risk of treatment failure decreased by 4.3% for each additional unit of energy delivered. The procedure duration was inversely correlated with treatment failure (OR 1.043, 95% CI: 1.011–1.083; <i>p = 0.014</i>). Improvement of cervical pressure symptoms or cosmetic complaints were observed in less than 15% of the cases at 12, 24 and 36 months. Horner’s syndrome occurred in one case (1.5%) and minor complications, not requiring treatment, in three (4.6%) patients. No change in thyroid function was registered. HIFU carried a low risk of complications. A single treatment resulted in a 30–35% thyroid nodule volume decrease within one year, reduction that remained stable for 2 years. Outcomes varied significantly between centers with different HIFU expertise. Focus on improved HIFU technology, adequate training, and appropriate selection of patients is needed to achieve efficacy comparable to other thermal ablation procedures.
DOI: 10.6084/m9.figshare.11993733
title: Analysis of the effects of mEHT on the treatment-related toxicity and quality of life of HIV-positive cervical cancer patients

description: HIV infection is associated with increased treatment-related toxicity and worse outcomes in locally advanced cervical cancer patients (LACC), especially in resource-constrained settings. Local control (LC) in a phase III randomized, controlled trial investigating modulated electro-hyperthermia (mEHT) on LACC patients in South Africa (ethics registration: M120477/M190295), was significantly higher in participants randomized to receive chemoradiotherapy (CRT) with mEHT compared to CRT alone (stratum: HIV status, accounting for age and stage). This analysis investigates whether mEHT adds to the toxicity profile of CRT in HIV-positive LACC participants. Inclusion criteria: signed informed consent; International Federation of Gynecology and Obstetrics stages IIB to IIIB squamous cell carcinoma of the cervix; HIV-positive patients: CD4 count &gt;200 cell/µL/on antiretroviral treatment for &gt;6 months; eligible for CRT with radical intent. Recruitment: January 2014 to November 2017 (ClinicalTrials.gov: NCT03332069). Acute toxicity (evaluated using CTCAE v4 criteria) and quality of life (according to EORTC forms) in 206 participants randomized for treatment were evaluated alongside the LC results to determine safety and efficacy in HIV-positive participants. Compliance to mEHT treatment was high (97% completed ≥8 treatments) with no significant differences in CRT-related toxicity between treatment groups or between HIV-positive and -negative participants. Adverse events attributed to mEHT were minor, even in obese patients, and did not affect CRT compliance. Participants treated with mEHT reported improved fatigue, pain, emotional and cognitive functioning. mEHT did not cause unexpected CRT-related toxicities and is a safe treatment modality for HIV-positive patients, with minor limitations regarding body weight, even in a low-resource setting.
DOI: 10.6084/m9.figshare.13273119.v1
title: High-intensity focused ultrasound (HIFU) therapy for benign thyroid nodules: a 3-year retrospective multicenter follow-up study

description: Outcomes of high-intensity focused ultrasound (HIFU), as a non-surgical treatment option for benign symptomatic thyroid nodules, has mainly been based on single-center studies and short-term follow-up. Therefore, we assessed the safety, and long-term efficacy of HIFU in benign thyroid nodules among four centers with expertise in thyroid mini-invasive procedures. Retrospective three year follow-up study in four European centers, treating solid benign thyroid nodules causing pressure symptoms and/or cosmetic concerns. Nodule volume reduction was assessed at 1, 3, 6, 12, 24, and 36 months post-treatment. Technical efficacy, defined as a volume reduction rate (VVR) &gt;50% was evaluated at 6, 12, 24 and 36 months. Predictive factors of efficacy were assessed using logistic models. Complications and side effects were classified according to the Interventional Radiology Guidelines and changes in local symptoms were scored on a visual-analog scale. Sixty-five patients (mean age 51.1 ± 14.0 years; 86.2% women) with a single thyroid nodule and a mean baseline nodule volume of 9.8 ± 10.3 mL were treated with a mean energy of 7.1 ± 3.1 kJ (range: 2.0 to 15.5 kJ). Median nodule volume reduction was 31.5% (IQR: −38.6% to −23.1%) at 12 months and 31.9% (IQR: −36.4% to −16.1%) at 36 months. Technical efficacy was obtained in 17.2% of cases at 6 months, 17.8% at 12 months, 3.4% at 24 months, and 7.4% at 36 months. The number of treated pixels and the mean energy delivered were positively correlated to VRR at 1, 6 and 12 months. The risk of treatment failure decreased by 4.3% for each additional unit of energy delivered. The procedure duration was inversely correlated with treatment failure (OR 1.043, 95% CI: 1.011–1.083; <i>p = 0.014</i>). Improvement of cervical pressure symptoms or cosmetic complaints were observed in less than 15% of the cases at 12, 24 and 36 months. Horner’s syndrome occurred in one case (1.5%) and minor complications, not requiring treatment, in three (4.6%) patients. No change in thyroid function was registered. HIFU carried a low risk of complications. A single treatment resulted in a 30–35% thyroid nodule volume decrease within one year, reduction that remained stable for 2 years. Outcomes varied significantly between centers with different HIFU expertise. Focus on improved HIFU technology, adequate training, and appropriate selection of patients is needed to achieve efficacy comparable to other thermal ablation procedures.
DOI: 10.6084/m9.figshare.11993733.v1
title: Analysis of the effects of mEHT on the treatment-related toxicity and quality of life of HIV-positive cervical cancer patients

description: HIV infection is associated with increased treatment-related toxicity and worse outcomes in locally advanced cervical cancer patients (LACC), especially in resource-constrained settings. Local control (LC) in a phase III randomized, controlled trial investigating modulated electro-hyperthermia (mEHT) on LACC patients in South Africa (ethics registration: M120477/M190295), was significantly higher in participants randomized to receive chemoradiotherapy (CRT) with mEHT compared to CRT alone (stratum: HIV status, accounting for age and stage). This analysis investigates whether mEHT adds to the toxicity profile of CRT in HIV-positive LACC participants. Inclusion criteria: signed informed consent; International Federation of Gynecology and Obstetrics stages IIB to IIIB squamous cell carcinoma of the cervix; HIV-positive patients: CD4 count &gt;200 cell/µL/on antiretroviral treatment for &gt;6 months; eligible for CRT with radical intent. Recruitment: January 2014 to November 2017 (ClinicalTrials.gov: NCT03332069). Acute toxicity (evaluated using CTCAE v4 criteria) and quality of life (according to EORTC forms) in 206 participants randomized for treatment were evaluated alongside the LC results to determine safety and efficacy in HIV-positive participants. Compliance to mEHT treatment was high (97% completed ≥8 treatments) with no significant differences in CRT-related toxicity between treatment groups or between HIV-positive and -negative participants. Adverse events attributed to mEHT were minor, even in obese patients, and did not affect CRT compliance. Participants treated with mEHT reported improved fatigue, pain, emotional and cognitive functioning. mEHT did not cause unexpected CRT-related toxicities and is a safe treatment modality for HIV-positive patients, with minor limitations regarding body weight, even in a low-resource setting.
DOI: 10.6084/m9.figshare.14446900.v1
title: Reducing mental illness stigma: What types of images are most effective?

description: Public stigma against mental illness is a barrier to treatment and recovery. Research into the design of anti-stigma messages has focused heavily on text; there is limited information on what types of images are most persuasive in eliciting anti-stigma outcomes. This is important to study because the type of image used to depict an illness can influence how the illness is perceived, which in turn can affect how people with the illness are treated. Through an online experiment with 162 American adults, this study investigated whether mental illness narratives about depression illustrated with photographs are more effective than those illustrated with cartoons at reducing stigma. It was found that the illustrated narratives, whether with photo or cartoon, produced more anti-stigma effects than the text-only narrative (control). Further, the photographic narrative was more effective than the cartoon narrative in eliciting closeness to the story protagonist and willingness to donate to mental health services. The study’s findings indicate that images should be used in anti-stigma messages on depression; further, regarding image type, photographs should be considered over cartoons as they are more effective in eliciting certain anti-stigma outcomes.Implications for PracticeThis study suggests that images have strong anti-stigma effects and that photographs are sometimes more persuasive than cartoons. These findings can inform best-practice guidelines for designing anti-stigma messages, created and disseminated by organisations such as the United States’ National Alliance on Mental Illness and Mental Health America. Images in these messages should be selected carefully as they can influence how people with mental illness are perceived and treated. This study suggests that images have strong anti-stigma effects and that photographs are sometimes more persuasive than cartoons. These findings can inform best-practice guidelines for designing anti-stigma messages, created and disseminated by organisations such as the United States’ National Alliance on Mental Illness and Mental Health America. Images in these messages should be selected carefully as they can influence how people with mental illness are perceived and treated.
DOI: 10.5281/zenodo.5535856
title: Ara ambiguus decontaminated FSCR

description: .
DOI: 10.5281/zenodo.5535855
title: Ara ambiguus decontaminated FSCR

description: .
DOI: 10.6084/m9.figshare.4616155
title: DNA barcodes for dragonflies and damselflies (Odonata) of Mindanao, Philippines

description: Reliable species identification provides a sounder basis for use of species in the order Odonata as biological indicators and for their conservation, an urgent concern as many species are threatened with imminent extinction. We generated 134 COI barcodes from 36 morphologically identified species of Odonata collected from Mindanao Island, representing 10 families and 19 genera. Intraspecific sequence divergences ranged from 0 to 6.7% with four species showing more than 2%, while interspecific sequence divergences ranged from 0.5 to 23.3% with seven species showing less than 2%. Consequently, no distinct gap was observed between intraspecific and interspecific DNA barcode divergences. The numerous islands of the Philippine archipelago may have facilitated rapid speciation in the Odonata and resulted in low interspecific sequence divergences among closely related groups of species. This study contributes DNA barcodes for 36 morphologically identified species of Odonata reported from Mindanao including 31 species with no previous DNA barcode records.
DOI: 10.6084/m9.figshare.4214433.v2
title: Massive parallel sequencing of human whole mitochondrial genomes with Ion Torrent technology: an optimized workflow for Anthropological and Population Genetics studies

description: Investigation of human mitochondrial DNA variation patterns and phylogeny has been extensively used in Anthropological and Population Genetics studies and sequencing the whole mitochondrial genome is progressively becoming the gold standard. Among the currently available massive parallel sequencing technologies, Ion Torrent™ semiconductor sequencing represents a promising approach for such studies. Nevertheless, an experimental protocol conceived to enable the achievement of both as high as possible yield and of the most homogeneous sequence coverage through the whole mitochondrial genome is still not available. The present work was thus aimed at improving the overall performance of whole mitochondrial genomes Ion Torrent™ sequencing, with special focus on the capability to obtain robust coverage and highly reliable variants calling. For this purpose, a series of cost-effective modifications in standard laboratory workflows was fine-tuned to optimize them for medium- and large-scale population studies. A total of 54 human samples were thus subjected to sequencing of the whole mitochondrial genome with the Ion Personal Genome Machine™ System in four distinct experiments and using Ion 314 chips. Seven of the selected samples were also characterized by means of conventional Sanger sequencing for the sake of comparison. Obtained results demonstrated that the implemented optimizations had definitely improved sequencing outputs in terms of both variants calling efficiency and coverage uniformity, enabling to setup an effective and accurate protocol for whole mitochondrial genome sequencing and a considerable reduction in experimental time consumption and sequencing costs.
DOI: 10.6084/m9.figshare.3750294
title: Structure and variation of the Fringillidae (Aves: Passeriformes) mitochondrial DNA control region and their phylogenetic relationship

description: The control region is the major noncoding segment of animal mitochondrial DNA. To infer the structure and variation of Fringillidae mitochondrial DNA control region, the entire control region sequences of 25 species were analyzed. The length of the control region sequences was very conserved (1230 ± 18) and can be separated into three domains. The frequency of both substitutions and gaps was highest in the third domain and lowest in the central region. The control region has the same flanking gene order from tRNA<sup>Glu</sup> to tRNA<sup>Phe</sup>. Genetic distances between species ranged from 1.80% (between <i>Carduelis pinus</i> and <i>Carduelis spinus</i>) to 25.34% (between <i>Carduelis sinica</i> and <i>Coccothraustes vespertinus</i>). The average genetic distances among the species within the genera varied from 5.11% (<i>Leucosticte</i>) to 14.31% (<i>Carpodacus</i>). The average genetic distances showed insignificantly negative correlation with ts/tv. Domain III is the most variable of the three domains among all the genera. The control region of Fringillidae contains a putative TAS element and the highly conserved CSB-1, and F, E, D, C boxes. However, neither CSB-2 nor CSB-3 could be unambiguously identified in the Fringillidae. The maximum likelihood method was used to construct a phylogenetic tree. Control region analysis demonstrated that some currently recognized genera may be polyphyletic, including <i>Carpodacus, Carduelis</i> and <i>Serinus</i>.
DOI: 10.6084/m9.figshare.4616155.v3
title: DNA barcodes for dragonflies and damselflies (Odonata) of Mindanao, Philippines

description: Reliable species identification provides a sounder basis for use of species in the order Odonata as biological indicators and for their conservation, an urgent concern as many species are threatened with imminent extinction. We generated 134 COI barcodes from 36 morphologically identified species of Odonata collected from Mindanao Island, representing 10 families and 19 genera. Intraspecific sequence divergences ranged from 0 to 6.7% with four species showing more than 2%, while interspecific sequence divergences ranged from 0.5 to 23.3% with seven species showing less than 2%. Consequently, no distinct gap was observed between intraspecific and interspecific DNA barcode divergences. The numerous islands of the Philippine archipelago may have facilitated rapid speciation in the Odonata and resulted in low interspecific sequence divergences among closely related groups of species. This study contributes DNA barcodes for 36 morphologically identified species of Odonata reported from Mindanao including 31 species with no previous DNA barcode records.
DOI: 10.6084/m9.figshare.6026732
title: Mitochondrial DNA genetic diversity in six Italian donkey breeds (<i>Equus asinus</i>)

description: Donkeys have played an important role in agricultural land practices and in human historical periods of recent past and, still today, are used as a working power in several world areas. The objective of this study was to identify genetic variability in six Italian donkey breeds using mtDNA D-loop. Fifteen haplotypes, grouped in three haplogroups, were identified. The genetic indices were informative and showed a high population genetic variability. The results of AMOVA analyses based on geographic structuring of Italian populations highlighted that the majority of the observed variance is due to differences among samples within breeds. Comparison among Italian haplotypes and mtDNA D-loop sequences belonging to European domestic and Ethiopian donkeys and wild asses, clearly define two clades referred to Nubian lineage. The results can be useful to complement safeguard planes for donkey breeds that are considered to extinction endangered.
DOI: 10.6084/m9.figshare.4557673
title: Genetic identification of prey species from teeth in faeces from the Endangered leopard cat <i>Prionailurus bengalensis</i> using mitochondrial <i>cytochrome b</i> gene sequence

description: To understand the dietary ecology of the leopard cat (<i>Prionailurus bengalensis</i>), DNA analysis was performed to identify prey species using DNA isolated from teeth harvested from the faeces of this feline species. From 70 DNA samples, a total of 52 mitochondrial DNA (mtDNA) <i>cytochrome b</i> (<i>cytb</i>) gene sequences of mammals were identified. The results of a sequence identity test indicated that those sequences were derived from four rodent species (<i>Apodemus agrarius</i>, <i>Apodemus peninsulae</i>, <i>Eothenomys regulus</i> and <i>Tamias sibiricus</i>) and two shrew species (<i>Crocidura lasiura</i> and <i>Crocidura shantungensis</i>). The sequences contained nine unique <i>cytb</i> sequences from site 1 and 13 from site 2. These results indicate that the leopard cat hunts rodents and shrews, and at least nine animals at site 1 and 13 animals at site 2 were eaten. These findings suggest that the animal molecular signatures that remain undigested in the faeces may provide useful ecological information about food items and may contribute to a better understanding of the leopard cat’s feeding ecology.
DOI: 10.6084/m9.figshare.4557673.v1
title: Genetic identification of prey species from teeth in faeces from the Endangered leopard cat <i>Prionailurus bengalensis</i> using mitochondrial <i>cytochrome b</i> gene sequence

description: To understand the dietary ecology of the leopard cat (<i>Prionailurus bengalensis</i>), DNA analysis was performed to identify prey species using DNA isolated from teeth harvested from the faeces of this feline species. From 70 DNA samples, a total of 52 mitochondrial DNA (mtDNA) <i>cytochrome b</i> (<i>cytb</i>) gene sequences of mammals were identified. The results of a sequence identity test indicated that those sequences were derived from four rodent species (<i>Apodemus agrarius</i>, <i>Apodemus peninsulae</i>, <i>Eothenomys regulus</i> and <i>Tamias sibiricus</i>) and two shrew species (<i>Crocidura lasiura</i> and <i>Crocidura shantungensis</i>). The sequences contained nine unique <i>cytb</i> sequences from site 1 and 13 from site 2. These results indicate that the leopard cat hunts rodents and shrews, and at least nine animals at site 1 and 13 animals at site 2 were eaten. These findings suggest that the animal molecular signatures that remain undigested in the faeces may provide useful ecological information about food items and may contribute to a better understanding of the leopard cat’s feeding ecology.