cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6653417.v1
title: Domain transfer convolutional attribute embedding

description: In this paper, we study the problem of transfer learning with the attribute data. In the transfer learning problem, we want to leverage the data of the auxiliary and the target domains to build an effective model for the classification problem in the target domain. Meanwhile, the attributes are naturally stable cross different domains. This strongly motives us to learn effective domain transfer attribute representations. To this end, we proposed to embed the attributes of the data to a common space using the powerful convolutional neural network (CNN) model. The convolutional representations of the data points are mapped to the corresponding attributes so that they can be effective embedding of the attributes. We also represent the data of different domains by a domain-independent CNN, ant a domain-specific CNN and combine their outputs with the attribute embedding to build the classification model. An joint learning framework is constructed to minimise the classification errors, the attribute mapping error, the mismatching of the domain-independent representations cross different domains, and to encourage the neighbourhood smoothness of representations in the target domain. The minimisation problem is solved by an iterative algorithm based on gradient descent. Experiments over benchmark data-sets of person re-identification, bankruptcy prediction and spam email detection show the effectiveness of the proposed method.
DOI: 10.6084/m9.figshare.6653393.v1
title: Plant Diversity of the Tropical Research and Education Center, University of Florida, Homestead

description: This dataset (`TRECflora.csv`) and accompanying metadata file (`TRECflora-metadata.doc`) are presented in the 2018 Proceedings of the Florida State Horticultural Society.<br><i>Abstract</i>. The Tropical Research and Education Center (TREC) is the southernmost campus of the University of Florida and is in Miami-Dade County, FL. TREC is dedicated to research, teaching, and extension in natural resources, agriculture, and ornamental, vegetable, fruit, and biofuel crops. As part of this mission, a large diversity of cultivated plants was established at TREC, while also preserving native pine rockland and rockdale hammock. The mission of TREC was recently expanded to include agroecology, which investigates the production, diversity, and resilience of agricultural systems relative to surrounding areas. Identifying TREC plant species is a first step in establishing this context for agricultural systems. Although many partial lists of vascular plant species have been made for TREC, there has been no comprehensive list. We report a comprehensive inventory of plant species diversity completed over the last decade (`TRECflora.csv`). Each plant species was identified with botanical keys and confirmed with online specimens or a previous report from a trusted source. The inventory currently has 658 species including 216 native; 226 established, non-native; 178 non-established, cultivated; and 38 unknowns. We gathered detailed information for each species identified, including plant use, general habitat, weediness, specific location, and identification sources other than the authors. This data will support agroecological research into the effects of plant diversity and surrounding areas on crop physiology and production.
DOI: 10.6084/m9.figshare.6653393.v2
title: Plant Diversity of the Tropical Research and Education Center, University of Florida, Homestead

description: This dataset (`TRECflora.csv`) and accompanying metadata file (`TRECflora-metadata.doc`) are presented in the 2018 Proceedings of the Florida State Horticultural Society.<br><i>Abstract</i>. The Tropical Research and Education Center (TREC) is the southernmost campus of the University of Florida and is in Miami-Dade County, FL. TREC is dedicated to research, teaching, and extension in natural resources, agriculture, and ornamental, vegetable, fruit, and biofuel crops. As part of this mission, a large diversity of cultivated plants was established at TREC, while also preserving native pine rockland and rockdale hammock. The mission of TREC was recently expanded to include agroecology, which investigates the production, diversity, and resilience of agricultural systems relative to surrounding areas. Identifying TREC plant species is a first step in establishing this context for agricultural systems. Although many partial lists of vascular plant species have been made for TREC, there has been no comprehensive list. We report a comprehensive inventory of plant species diversity completed over the last decade (`TRECflora.csv`). Each plant species was identified with botanical keys and confirmed with online specimens or a previous report from a trusted source. The inventory currently has 657 species including 216 native; 226 established, non-native; 178 non-established, cultivated; and 37 unknowns. We gathered detailed information for each species identified, including plant use, general habitat, weediness, specific location, and identification sources other than the authors. This data will support agroecological research into the effects of plant diversity and surrounding areas on crop physiology and production.
DOI: 10.6084/m9.figshare.6653384
title: α-helices in (α+β)+(α/β) proteins

description: Dataset containing physical-chemical and strucutural descriptors for α-helices and its flanking regions.<br><br>Only α-helices from <b>(α+β)+(α/β) proteins</b> are eligible for this dataset.<br>Data is organized into sections. Each section begins with the following header: l<b>ength, pdb_name, chain_id, flag, position, [parameter]</b>.<br><b>length </b>is the number of amino acid residues comprising the α-helix.<br><b>flag </b>indicates the amino acid residue underlying region, namely: flanking region before the α-helix().<br><b>[parameter]</b>: paramater's value for the given amino acid residue. All parameters are extracted from the STING Database.
DOI: 10.6084/m9.figshare.6653297
title: PA42.3.0.protein_new.txt

description: Daphnia pulex genome-wide protein sequences
DOI: 10.6084/m9.figshare.6653192.v1
title: Drosophila genes used to build phylogeny

description: List of Genbank accession numbers for genes used for building phylogenic trees for Drosophila study
DOI: 10.6084/m9.figshare.6652802
title: Supplementary Material for: Survival of Immunoglobulins from Human Milk to Preterm Infant Gastric Samples at 1, 2, and 3 h Postprandial

description: <b><i>Background:</i></b> Human milk immunoglobulins (Ig) are an important support for the naïve infant immune system; yet the extent to which these proteins survive within the infant digestive tract, particularly for preterm infants, is poorly studied. <b><i>Objectives:</i></b> Our objective was to evaluate the survival of human milk Igs in the preterm stomach across postprandial time. <b><i>Methods:</i></b> Human milk and infant gastric samples were collected from 11 preterm (23–32 weeks gestational age) mother-infant pairs within 7–98 days postnatal age. Preterm gastric samples were collected 1, 2, and 3 h after the beginning of the feeding. Samples were analyzed for concentration of total IgA (secretory IgA [SIgA]/IgA), total secretory component (SC/SIgA/SIgM), total IgM (SIgM/IgM), and IgG via enzyme-linked immunosorbent assay. Ig-chain fragment peptides were determined using peptidomic analysis. One-way analysis of variance with repeated measures followed by Tukey’s multiple comparison tests was applied. <b><i>Results:</i></b> Concentrations of total IgA were lower in the gastric contents at 3 h postprandial compared with human milk and gastric contents at 1 and 2 h. Human milk SC/SIgA/SIgM, IgG, and total IgM concentrations remained stable in the preterm stomach across postprandial time. Peptide counts from the Ig alpha-chain and the Ig gamma-chain increased in gastric contents from 1 to 2 h postprandial. Peptide counts from the human milk Ig-chain, Ig-chain, and SC were stable across postprandial time. These peptides from Ig-chains were not present in human milk but were released in the stomach due to their partial degradation. <b><i>Conclusions:</i></b> Human milk total SC (SIgA/SC/SIgM), total IgM, and IgG survived mostly intact through the preterm infant stomach, while total IgA was ­partially digested.
DOI: 10.6084/m9.figshare.6652802.v1
title: Supplementary Material for: Survival of Immunoglobulins from Human Milk to Preterm Infant Gastric Samples at 1, 2, and 3 h Postprandial

description: <b><i>Background:</i></b> Human milk immunoglobulins (Ig) are an important support for the naïve infant immune system; yet the extent to which these proteins survive within the infant digestive tract, particularly for preterm infants, is poorly studied. <b><i>Objectives:</i></b> Our objective was to evaluate the survival of human milk Igs in the preterm stomach across postprandial time. <b><i>Methods:</i></b> Human milk and infant gastric samples were collected from 11 preterm (23–32 weeks gestational age) mother-infant pairs within 7–98 days postnatal age. Preterm gastric samples were collected 1, 2, and 3 h after the beginning of the feeding. Samples were analyzed for concentration of total IgA (secretory IgA [SIgA]/IgA), total secretory component (SC/SIgA/SIgM), total IgM (SIgM/IgM), and IgG via enzyme-linked immunosorbent assay. Ig-chain fragment peptides were determined using peptidomic analysis. One-way analysis of variance with repeated measures followed by Tukey’s multiple comparison tests was applied. <b><i>Results:</i></b> Concentrations of total IgA were lower in the gastric contents at 3 h postprandial compared with human milk and gastric contents at 1 and 2 h. Human milk SC/SIgA/SIgM, IgG, and total IgM concentrations remained stable in the preterm stomach across postprandial time. Peptide counts from the Ig alpha-chain and the Ig gamma-chain increased in gastric contents from 1 to 2 h postprandial. Peptide counts from the human milk Ig-chain, Ig-chain, and SC were stable across postprandial time. These peptides from Ig-chains were not present in human milk but were released in the stomach due to their partial degradation. <b><i>Conclusions:</i></b> Human milk total SC (SIgA/SC/SIgM), total IgM, and IgG survived mostly intact through the preterm infant stomach, while total IgA was ­partially digested.
DOI: 10.6084/m9.figshare.6652790
title: Supplementary Material for: Do <b><i>Plantago lanceolata</i></b> Skin Prick Test-Positive Patients Display IgE to Genuine Plantain Pollen Allergens? Investigation of Pollen Allergic Patients from the North-East of France

description: <b><i>Background:</i></b> English plantain (<i>Plantago lanceolata</i>) is an important weed pollen allergen source triggering allergic symptoms during summer. To elucidate genuine versus cross-reactive sensitization, we investigated IgE reactivity patterns and inhibition capacities of plantain-sensitized patients. <b><i>Methods:</i></b> Sera of 35 rhinoconjunctivitis patients from the north-east of France with positive skin prick tests (SPT) to <i>Plantago lanceolata</i> pollen were tested with clinically relevant allergen sources using ELISA, ImmunoCAP, and immunoblot inhibition. <b><i>Results:</i></b> The patients were multisensitized with additional reactivity to grass (94.3%), ash (74.3%), birch (71.4%), and mugwort (55.2%) pollen in SPT. Sensitization prevalence to allergen molecules was 34.3% (Pla l 1), 94.3% (Phl p 1/5), 60.0% (Ole e 1), 65.7% (Bet v 1), 37.1% (profilin), and 40.0% (CCD). In immunoblot, IgE reactivity to plantain pollen was inhibited with relevant pollen extracts and purified rPla l 1. Two sera did not reveal any IgE cross-reactivity, while reactivity to plantain was efficiently inhibited by grass pollen in the sera of 10 patients. The sera from 17 different patients could be inhibited by grass, birch, or ash pollen to varying degrees. Thus, only 37.1% of our patients demonstrated true plantain pollen sensitization, while 62.9% were solely positive due to IgE cross-reactive molecules from other clinically relevant pollen. <b><i>Conclusions:</i></b> Plantain pollen-sensitized patients are multi-reactors demonstrating varying and complex IgE-reactivity profiles. In vivo and in vitro tests using extracts are typically blurred due to the presence of homologous allergens or CCD in grass, birch, or ash pollen. So far, Pla l 1 represents the only indicative marker allergen for the diagnosis of genuine plantain pollen sensitization.
DOI: 10.6084/m9.figshare.6652790.v1
title: Supplementary Material for: Do <b><i>Plantago lanceolata</i></b> Skin Prick Test-Positive Patients Display IgE to Genuine Plantain Pollen Allergens? Investigation of Pollen Allergic Patients from the North-East of France

description: <b><i>Background:</i></b> English plantain (<i>Plantago lanceolata</i>) is an important weed pollen allergen source triggering allergic symptoms during summer. To elucidate genuine versus cross-reactive sensitization, we investigated IgE reactivity patterns and inhibition capacities of plantain-sensitized patients. <b><i>Methods:</i></b> Sera of 35 rhinoconjunctivitis patients from the north-east of France with positive skin prick tests (SPT) to <i>Plantago lanceolata</i> pollen were tested with clinically relevant allergen sources using ELISA, ImmunoCAP, and immunoblot inhibition. <b><i>Results:</i></b> The patients were multisensitized with additional reactivity to grass (94.3%), ash (74.3%), birch (71.4%), and mugwort (55.2%) pollen in SPT. Sensitization prevalence to allergen molecules was 34.3% (Pla l 1), 94.3% (Phl p 1/5), 60.0% (Ole e 1), 65.7% (Bet v 1), 37.1% (profilin), and 40.0% (CCD). In immunoblot, IgE reactivity to plantain pollen was inhibited with relevant pollen extracts and purified rPla l 1. Two sera did not reveal any IgE cross-reactivity, while reactivity to plantain was efficiently inhibited by grass pollen in the sera of 10 patients. The sera from 17 different patients could be inhibited by grass, birch, or ash pollen to varying degrees. Thus, only 37.1% of our patients demonstrated true plantain pollen sensitization, while 62.9% were solely positive due to IgE cross-reactive molecules from other clinically relevant pollen. <b><i>Conclusions:</i></b> Plantain pollen-sensitized patients are multi-reactors demonstrating varying and complex IgE-reactivity profiles. In vivo and in vitro tests using extracts are typically blurred due to the presence of homologous allergens or CCD in grass, birch, or ash pollen. So far, Pla l 1 represents the only indicative marker allergen for the diagnosis of genuine plantain pollen sensitization.
DOI: 10.6084/m9.figshare.6652739.v1
title: Understand the full impact of your institution’s researchUntitled Item

description: In this webinar Ben McLeish, Director of Engagement and Advocacy at Altmetric and Dimensions, demonstrates how institutions can effectively monitor the activity surrounding their research, benchmark against peer organizations, report on outreach and assist the evaluation and review process.
DOI: 10.6084/m9.figshare.6652415
title: Sequence information of pIPKTA48 and pIPKTA49

description: The transient expression vector pIPKTA9 (1) was double-digested with XhoI, and XbaI. The gateway cassette including the YFP tag from the binary vector pGWB42 (2) was doubledigested with XbaI-EcoICRI (Ecl136II) and ligated into pIPKTA9 between the XhoI-XbaI sites. This resulted in the Gateway-compatible transient expression vector pIPKTA48 and pIPKTA49 to allow N- and C-terminal YFP fusions, respectively. <b>References</b><br>1.) Zimmermann G, Baumlein H, Mock HP, Himmelbach A, Schweizer P: The multigene family encoding germin-like proteins of barley. Regulation and function in basal host resistance. Plant Physiology 2006, 142:181-192.<br>2.) Nakagawa T, Kurose T, Hino T, Tanaka K, Kawamukai M, Niwa Y, Toyooka K, Matsuoka K, Jinbo T, Kimura T: Development of series of gateway binary vectors, pGWBs, for realizing efficient construction of fusion genes for plant transformation. J Biosci Bioeng 2007, 104:34-41 <br><br>
DOI: 10.6084/m9.figshare.6652406
title: TrackingData.csv

description: Movement data (velocity, mm per s) recorded by video tracking software of 629 mature <i>Daphnia magna</i> when exposed to 37 deg C. Individuals came from either 17 (n = 315) or 22 (n = 314) deg C acclimation temperatures.<br>
DOI: 10.6084/m9.figshare.6652406.v1
title: TrackingData.csv

description: Movement data (velocity, mm per s) recorded by video tracking software of 629 mature <i>Daphnia magna</i> when exposed to 37 deg C. Individuals came from either 17 (n = 315) or 22 (n = 314) deg C acclimation temperatures.<br>
DOI: 10.6084/m9.figshare.6652391
title: Supplementary Material for: Distinctive Olfactory Pattern in Parkinson’s Disease and Non-Neurodegenerative Causes of Hyposmia

description: <b><i>Background:</i></b> Olfactory dysfunction is common in Parkinson’s disease (PD). The characteristics of the hyposmia in PD have not been well defined. <b><i>Objective:</i></b> To characterize the pattern of the olfactory deficit in PD and in other non-neurodegenerative aetiologies of hyposmia. <b><i>Methods:</i></b> We evaluated 36 PD patients, 20 patients with hyposmia secondary to acute respiratory infection (ARI), and 19 patients with hyposmia secondary to traumatic brain injury (TBI). For comparison purposes, we included a group of 15 controls age and sex matched with PD patients. PD patients were classified based on disease duration and severity in de novo PD, and PD with and without chronic levodopa-related complications. The Barcelona Smell Identification Test was applied to all participants. <b><i>Results:</i></b> For the first cranial nerve odours, PD patients scored lower than controls on smell detection (85.28 vs. 97.67%, <i>p</i> = 0.006), definition (79.58 vs. 93.33%, <i>p</i> = 0.007), recognition (63.33 vs. 81%, <i>p</i> = 0.020), and forced choice (58.06 vs. 82%, <i>p</i> &lt; 0.001). Compared with ARI, forced choice was significantly better in PD patients (<i>p</i> &lt; 0.001), but no differences were found regarding other olfactory characteristics. TBI patients showed significantly lower scores than the other study groups in all the olfaction items. For the fifth cranial nerve odours, recognition (<i>p</i> = 0.003) and identification (<i>p</i> = 0.019) were lower in the TBI group than in the others. No differences were found among PD subgroups regarding any olfactory characteristic. <b><i>Conclusions:</i></b> A differential pattern of hyposmia was observed in PD patients compared to other non-neurodegenerative aetiologies. Further studies with larger samples should replicate our results.
DOI: 10.6084/m9.figshare.6652391.v1
title: Supplementary Material for: Distinctive Olfactory Pattern in Parkinson’s Disease and Non-Neurodegenerative Causes of Hyposmia

description: <b><i>Background:</i></b> Olfactory dysfunction is common in Parkinson’s disease (PD). The characteristics of the hyposmia in PD have not been well defined. <b><i>Objective:</i></b> To characterize the pattern of the olfactory deficit in PD and in other non-neurodegenerative aetiologies of hyposmia. <b><i>Methods:</i></b> We evaluated 36 PD patients, 20 patients with hyposmia secondary to acute respiratory infection (ARI), and 19 patients with hyposmia secondary to traumatic brain injury (TBI). For comparison purposes, we included a group of 15 controls age and sex matched with PD patients. PD patients were classified based on disease duration and severity in de novo PD, and PD with and without chronic levodopa-related complications. The Barcelona Smell Identification Test was applied to all participants. <b><i>Results:</i></b> For the first cranial nerve odours, PD patients scored lower than controls on smell detection (85.28 vs. 97.67%, <i>p</i> = 0.006), definition (79.58 vs. 93.33%, <i>p</i> = 0.007), recognition (63.33 vs. 81%, <i>p</i> = 0.020), and forced choice (58.06 vs. 82%, <i>p</i> &lt; 0.001). Compared with ARI, forced choice was significantly better in PD patients (<i>p</i> &lt; 0.001), but no differences were found regarding other olfactory characteristics. TBI patients showed significantly lower scores than the other study groups in all the olfaction items. For the fifth cranial nerve odours, recognition (<i>p</i> = 0.003) and identification (<i>p</i> = 0.019) were lower in the TBI group than in the others. No differences were found among PD subgroups regarding any olfactory characteristic. <b><i>Conclusions:</i></b> A differential pattern of hyposmia was observed in PD patients compared to other non-neurodegenerative aetiologies. Further studies with larger samples should replicate our results.
DOI: 10.6084/m9.figshare.6652370
title: Supplementary Material for: Pityriasis Rosea during Pregnancy: Major and Minor Alarming Signs

description: <b><i>Background:</i></b> Pityriasis rosea (PR) is a self-limiting exanthematous disease associated with human herpesvirus (HHV)-6 and/or HHV-7 reactivation. In pregnant women, PR may be associated with pregnancy complications. <b><i>Objective:</i></b> To determine relevant risk factors in the development of negative pregnancy outcome in PR. <b><i>Methods:</i></b> Between 2005 and 2017 at the Department of Dermatology, University of Genoa, we recruited 76 women who developed PR during pregnancy. In 60 patients without known risk factors for intrauterine fetal death (30 with pregnancy complications and 30 without) we analyzed the pregnancy week of PR onset, presence of enanthem and of constitutional symptoms, PR body surface area involvement, age, and in 50 patients (20 with pregnancy complications and 30 without), the viral load of HHV-6 and HHV-7 (copies/mL). <b><i>Results:</i></b> In logistic regression analysis, early onset of PR (<i>p</i> = 0.0017) and enanthem (<i>p</i> = 0.0392) proved to be significantly associated with pregnancy complications. HHV-6 viral load (copies/mL) (<i>p</i> &lt; 0.0001), constitutional symptoms (<i>p</i> &lt; 0.001), and PR body surface area involvement (<i>p</i> &lt; 0.004) were also significantly associated with pregnancy complications. <b><i>Conclusion:</i></b> The onset of PR before week 15 and enanthem may be considered major risk factors that should alarm the dermatologist. Constitutional symptoms and involvement of &gt; 50% of the body area may be considered minor risk factors.
DOI: 10.15131/shef.data.6652367
title: Changes in silk feedstock during cocoon construction

description: Datasets for figures in paper: 'Changes in Silk Feedstock Rheology during Cocoon Construction: The Role of Calcium and Potassium Ions'<br>
DOI: 10.6084/m9.figshare.6652352
title: MinimumGPSPointsData.mat

description: It's a little GPS points data set including longitude and latitude in a small area. The first column is longitude and the second column is latitude.
DOI: 10.6084/m9.figshare.6652352.v1
title: MinimumGPSPointsData.mat

description: It's a little GPS points data set including longitude and latitude in a small area. The first column is longitude and the second column is latitude.