cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20038222.v1
title: Construction and characterization of a bacterial artiﬁcial chromosome library of the maize inbred line Qi319

description: Abstract Zea mays L. has been the most cultivated crop and the crop with the largest yield in China since 2012. We constructed a bacterial artificial chromosome (BAC) library for the maize inbred line Qi319, which may be used as a key source for disease-resistant maize breeding in China. The BAC contains 270,720 clones, with an average insert size of 90 kb. The coverage of the library is about 10.43 genome equivalents when considering a haploid genome size of 2300 Mb, providing a 99.99% likelihood of isolating any maize gene or sequence in the library. An average of 12 clones were obtained by polymerase chain reaction screening by using primer pairs linked to the genes for resistance to maize southern rust and rough dwarf. The results indicate that the library can satisfy the requirements for recovering specific sequences. The library is available to researchers to whom it may be of interest.
DOI: 10.6084/m9.figshare.12173997.v2
title: Online contextual learning with perishable resources allocation

description: We formulate a novel class of online matching problems with learning. In these problems, randomly arriving customers must be matched to perishable resources so as to maximize a total expected reward. The matching accounts for variations in rewards among different customer–resource pairings. It also accounts for the perishability of the resources. Our work is motivated by a healthcare application, but it can be easily extended to other service applications. Our work belongs to the online resource allocation streams in service systems. We propose the first online algorithm for contextual learning and resource allocation with perishable resources. Our algorithm explores and exploits in distinct interweaving phases. We prove that our algorithm achieves an expected regret per period that increases sub-linearly with the number of planning cycles.
DOI: 10.6084/m9.figshare.14795338
title: Additional file 3 of Rapid identification of mutations caused by fast neutron bombardment in Medicago truncatula

description: Additional file 3: Table S2. The potential deletions in yl1 mutant. The details of potential deletions in yl1 mutant populations were listed, which include the location, sequence, length, genotype in different samples and the mutant type of deletions.
DOI: 10.6084/m9.figshare.14795338.v1
title: Additional file 3 of Rapid identification of mutations caused by fast neutron bombardment in Medicago truncatula

description: Additional file 3: Table S2. The potential deletions in yl1 mutant. The details of potential deletions in yl1 mutant populations were listed, which include the location, sequence, length, genotype in different samples and the mutant type of deletions.
DOI: 10.6084/m9.figshare.14795153.v1
title: Additional file 5 of Genome-wide DNA methylation analysis in Chinese Chenghua and Yorkshire pigs

description: Additional file 5: Table S5. Summary of Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis in CHP vs. YP.
DOI: 10.6084/m9.figshare.14795341.v1
title: Additional file 4 of Rapid identification of mutations caused by fast neutron bombardment in Medicago truncatula

description: Additional file 4: Table S3. The list of primers. The details of primers for genotyping of SymCRK and MtEGY1 were listed.
DOI: 10.6084/m9.figshare.14795341
title: Additional file 4 of Rapid identification of mutations caused by fast neutron bombardment in Medicago truncatula

description: Additional file 4: Table S3. The list of primers. The details of primers for genotyping of SymCRK and MtEGY1 were listed.
DOI: 10.6084/m9.figshare.16892610.v1
title: Building optimization testing framework (BOPTEST) for simulation-based benchmarking of control strategies in buildings

description: Development of new building HVAC control algorithms has grown due to needs for energy efficiency and operational flexibility. However, case studies demonstrating new algorithms are largely individualized, making algorithm performance difficult to compare directly. In addition, the effort and expertise required to implement case studies in real or simulated buildings limits rapid prototyping potential. Therefore, this paper presents the Building Optimization Testing Framework (BOPTEST) and associated software for simulation-based benchmarking of building HVAC control algorithms. A containerized run-time environment (RTE) enables rapid, repeatable deployment of common building emulators representing different system types. Emulators use Modelica to represent realistic physical dynamics, embed baseline control, and enable overwriting supervisory and local-loop control signals. Finally, a common set of key performance indicators are calculated within the RTE and reported to the user. This paper details the design and implementation of software and demonstrates its usage to benchmark a Model Predictive Control strategy.
DOI: 10.6084/m9.figshare.25195823
title: Supplementary Material for: Anal Canal Melanoma: Challenging the Odds

description: <b><i>Introduction:</i></b> Anal canal melanoma is a rare form of both anal cancer and skin melanoma, representing 1% of all anal cancers. Diagnosis is often made at an advanced disease stage. Because of late diagnosis and aggressive clinical course, anal canal melanoma has a very poor prognosis. <b><i>Case Presentation:</i></b> We present the case of a 61-year-old female with anal canal melanoma and lung, liver, pelvic and central nervous system (CNS) metastasis, BRAF V600E mutated. Combined BRAF/MEK inhibition and CNS radiation therapy were able to achieve excellent local and distant disease control. <b><i>Conclusion:</i></b> Anal canal melanoma is a rare and aggressive form of melanoma. Multidisciplinary management in experienced centers is mandatory for good clinical outcomes.
DOI: 10.6084/m9.figshare.14795269.v1
title: Additional file 2 of Machine learning-based prediction of survival prognosis in cervical cancer

description: Additional file 2
DOI: 10.6084/m9.figshare.25195832
title: Supplementary Material for: Breast Cancer and Chronic Lymphocytic Leukemia and Renal Cell Carcinoma: A Case Report of a Rare Cancer Combination

description: <b><i>Introduction:</i></b> The incidence of second malignancies in breast cancer survivors has increased because of early detection and improved cancer treatment modalities. The synchronous occurrence of chronic lymphocytic lymphoma (CLL) and renal cell carcinoma (RCC) in the same patient is higher than in the general population. Several factors, including the history of chemotherapy with alkylating agents, genetic alteration, and long-term survival of breast cancer patients may explain this condition, but further research is needed. <b><i>Case Presentation:</i></b> In the present report, we discussed the case of a 48-year-old female who had clear cell RCC; 5 months after the diagnosis of CLL and 15 years after invasive ductal carcinoma. <b><i>Conclusion:</i></b> Considering the continued elevated risk of second cancers in patients with breast cancer and CLL in a clinical setting, clinicians should be made aware of ongoing medical surveillance.
DOI: 10.6084/m9.figshare.25195832.v1
title: Supplementary Material for: Breast Cancer and Chronic Lymphocytic Leukemia and Renal Cell Carcinoma: A Case Report of a Rare Cancer Combination

description: <b><i>Introduction:</i></b> The incidence of second malignancies in breast cancer survivors has increased because of early detection and improved cancer treatment modalities. The synchronous occurrence of chronic lymphocytic lymphoma (CLL) and renal cell carcinoma (RCC) in the same patient is higher than in the general population. Several factors, including the history of chemotherapy with alkylating agents, genetic alteration, and long-term survival of breast cancer patients may explain this condition, but further research is needed. <b><i>Case Presentation:</i></b> In the present report, we discussed the case of a 48-year-old female who had clear cell RCC; 5 months after the diagnosis of CLL and 15 years after invasive ductal carcinoma. <b><i>Conclusion:</i></b> Considering the continued elevated risk of second cancers in patients with breast cancer and CLL in a clinical setting, clinicians should be made aware of ongoing medical surveillance.
DOI: 10.6084/m9.figshare.12173997.v1
title: Online Contextual Learning with Perishable Resources Allocation

description: We formulate a novel class of online matching problems with learning. In these problems, randomly arriving customers must be matched to perishable resources so as to maximize a total expected reward. The matching accounts for variations in rewards among different customer-resource pairings. It also accounts for the perishability of the resources. Our work is motivated by a healthcare application, but it can be easily extended to other service applications. Our work belongs to the online resource allocation streams in service system. We propose the first online algorithm for contextual learning and resource allocation with perishable resources. Our algorithm explores and exploits in distinct interweaving phases. We prove that our algorithm achieves an expected regret per period that increases sub-linearly with the number of planning cycles.
DOI: 10.6084/m9.figshare.22655345
title: Additional file 2 of FACI is a novel clathrin adaptor protein 2-binding protein that facilitates low-density lipoprotein endocytosis

description: Additional file 2: Table S2. BioID-mass spectrometric data. Lists of potential FACI-interacting proteins in AML12 identified with the BioID approach.
DOI: 10.5281/zenodo.10636274
title: Data and code for "Exploring Two-dimensional Coherent Spectroscopy with Exact Diagonalization: Spinons and Confinement in 1D Quantum Magnets"

description: Two-dimensional coherent spectroscopy (2DCS) with terahertz radiation offers a promising new avenue for the exploration of many-body phenomena in quantum magnets. This includes the potential diagnosis of fractionalized excitations, for which linear response often struggles due to the indistinguishability of a continuum of fractional excitations from that caused by disorders or impurities. However, the interpretation of the complex results produced by 2DCS remains a challenge, and a general prediction of the spectral characteristics of different types of excitations has not yet been established. In this paper, we develop a numerical approach based on exact diagonalization (ED) to push our understanding of 2DCS towards different scenarios. We first validate our approach by comparing numerical ED and exact analytical results for the spectroscopic signatures of spinons in one-dimensional transverse field Ising model and develop how to deal with the inherently small system sizes in ED calculations. Augmenting the model by a longitudinal field, we demonstrate significant changes to the 2DCS spectrum upon the field-induced spinon pair confinement, which can be rationalized in our ED calculations and from a "two-kink" model (in the absence of integrability). One advantage of our ED approach is its possible extension to finite temperatures, which we explore using thermally pure quantum states and demonstrate to change the intensity and spectroscopical patterns of 2DCS when going beyond the integrable model. Our numerically exact results provide a benchmark for future experiments and theoretical studies relying on approximation methods, and pave the way for the exploration of fractionalized excitations in quantum magnets.
DOI: 10.6084/m9.figshare.22655396
title: Additional file 1 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

description: Additional file 1: Supplementary Tables. Collection of small supplementary tables (S1-2,4-5,7-8,11-12) plus all table captions; large supplementary tables are saved as separate csv files in the following.
DOI: 10.6084/m9.figshare.21087066
title: Diagnostic utility of rapid sequencing in critically ill infants: a systematic review and meta-analysis

description: Genetic disorders are a major cause of death in critically ill infants. Several studies have assessed the diagnostic yield of rapid genomic sequencing in critically ill infants. This meta-analysis aimed to summarize the diagnostic utility of rapid genomic sequencing in critically ill infants. PubMed, Scopus, Web of Science, and Cochrane Library, were searched before 1 July 2022. Studies reported diagnostic rate of rapid genomic sequencing in critically ill infants were selected. Two authors screened and extracted data regarding the method of genetic test, total number of patients, and number of diagnosed patients. Twenty-three studies, comprising 1567 critically ill infants were included in the meta-analysis. In the overall analysis, the pooled diagnostic utility of rapid genomic sequencing was 0.42 (95% CI: 0.37–0.49, I<sup>2</sup> = 79%, <i>P</i> &lt; 0.1). Moreover, the pooled diagnostic rates of rapid whole-exome and rapid whole-genome sequencing were 0.50 (95% CI: 0.41–0.61; I<sup>2</sup> = 74%; P &lt; 0.01) and 0.37 (95% CI: 0.30–0.46; I<sup>2</sup> = 77%; P &lt; 0.01), respectively. Sensitive analysis showed that the results were stable in the overall analysis. Additionally, publication bias was not observed in the overall analysis. This meta-analysis proved that rapid genomic sequencing has a good diagnostic utility for critically ill infants.
DOI: 10.6084/m9.figshare.21087066.v1
title: Diagnostic utility of rapid sequencing in critically ill infants: a systematic review and meta-analysis

description: Genetic disorders are a major cause of death in critically ill infants. Several studies have assessed the diagnostic yield of rapid genomic sequencing in critically ill infants. This meta-analysis aimed to summarize the diagnostic utility of rapid genomic sequencing in critically ill infants. PubMed, Scopus, Web of Science, and Cochrane Library, were searched before 1 July 2022. Studies reported diagnostic rate of rapid genomic sequencing in critically ill infants were selected. Two authors screened and extracted data regarding the method of genetic test, total number of patients, and number of diagnosed patients. Twenty-three studies, comprising 1567 critically ill infants were included in the meta-analysis. In the overall analysis, the pooled diagnostic utility of rapid genomic sequencing was 0.42 (95% CI: 0.37–0.49, I<sup>2</sup> = 79%, <i>P</i> &lt; 0.1). Moreover, the pooled diagnostic rates of rapid whole-exome and rapid whole-genome sequencing were 0.50 (95% CI: 0.41–0.61; I<sup>2</sup> = 74%; P &lt; 0.01) and 0.37 (95% CI: 0.30–0.46; I<sup>2</sup> = 77%; P &lt; 0.01), respectively. Sensitive analysis showed that the results were stable in the overall analysis. Additionally, publication bias was not observed in the overall analysis. This meta-analysis proved that rapid genomic sequencing has a good diagnostic utility for critically ill infants.
DOI: 10.6084/m9.figshare.20038578
title: Role of sweet potato GST genes in abiotic stress tolerance revealed by genomic and transcriptomic analyses

description: Abstract Glutathione S-transferases (GSTs) are proteins synthesized in plants and responsible for their tolerance to environmental stresses. However, little information is available on the GST gene family of sweet potato, a globally important crop. The genetic evolution of GSTs in sweet potato remains unclear. The present study investigated the GST gene family in sweet potato by transcriptomic and comparative genomic analyses. A total of 51 GSTs were identified. Gene expression analysis showed differential expression patterns of the GSTs between two investigated varieties. Some GST expression levels were either up- or downregulated under oxidative, salinity and drought stresses. The results of the investigation provided new insights on the GST gene family in sweet potato, which may further the understanding of the roles of these genes in regulating abiotic stresses.
DOI: 10.6084/m9.figshare.14266768
title: Additional file 4 of Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics

description: Additional file 3: Supplementary dataset. The functional annotation, differential expression profile, and potential producer (represented by MAG) of label-free quantified proteins.
DOI: 10.6084/m9.figshare.20038578.v1
title: Role of sweet potato GST genes in abiotic stress tolerance revealed by genomic and transcriptomic analyses

description: Abstract Glutathione S-transferases (GSTs) are proteins synthesized in plants and responsible for their tolerance to environmental stresses. However, little information is available on the GST gene family of sweet potato, a globally important crop. The genetic evolution of GSTs in sweet potato remains unclear. The present study investigated the GST gene family in sweet potato by transcriptomic and comparative genomic analyses. A total of 51 GSTs were identified. Gene expression analysis showed differential expression patterns of the GSTs between two investigated varieties. Some GST expression levels were either up- or downregulated under oxidative, salinity and drought stresses. The results of the investigation provided new insights on the GST gene family in sweet potato, which may further the understanding of the roles of these genes in regulating abiotic stresses.
DOI: 10.25345/c56d5pn63
title: MassIVE MSV000094048 - Comparison of Three Mitochondria Enrichment Methods for Glycoprotein/Glycopeptide Analysis
title: Mitochondria proteome research has increased dramatically over the years owing to their implication in several diseases including cancer. With the aid of advanced technology such as mass spectrometry, over 1500 mitochondria proteins have been identified. Protein folding and function are significantly impacted by glycosylation; however, little is known about the glycosylation of mitochondria proteins. There are various techniques for isolating mitochondria, and the most suitable method is chosen based on the specific research objective. Hence, to identify a suitable protocol for comprehensive analysis of mitochondria glycoproteome, we compared three mitochondria enrichment methods. Our data showed that the differential centrifugation method yielded either a similar or a higher total number of mitochondria proteins/peptides compared to the two commercial kits, MITOISO2 (Sigma Aldrich) and Pierce (Thermo Scientific).
DOI: 10.6084/m9.figshare.22655405.v1
title: Additional file 4 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

description: Additional file 4: Table S3. eQTLs for major cell types.
DOI: 10.21258/1334833
title: Swiss national forest inventory - Result table No. 155790
DOI: 10.21258/1334823
title: Swiss national forest inventory - Result table No. 155801
DOI: 10.21258/1334824
title: Swiss national forest inventory - Result table No. 155798
DOI: 10.21258/1334825
title: Swiss national forest inventory - Result table No. 155796
DOI: 10.21258/1334826
title: Swiss national forest inventory - Result table No. 155797
DOI: 10.21258/1334827
title: Swiss national forest inventory - Result table No. 155794
DOI: 10.21258/1334828
title: Swiss national forest inventory - Result table No. 155793
DOI: 10.21258/1334820
title: Swiss national forest inventory - Result table No. 155803
DOI: 10.21258/1334822
title: Swiss national forest inventory - Result table No. 155799
DOI: 10.21258/1334816
title: Swiss national forest inventory - Result table No. 155808
DOI: 10.21258/1334817
title: Swiss national forest inventory - Result table No. 155805
DOI: 10.21258/1334818
title: Swiss national forest inventory - Result table No. 155804
DOI: 10.21258/1334819
title: Swiss national forest inventory - Result table No. 155802
DOI: 10.21258/1334821
title: Swiss national forest inventory - Result table No. 155800
DOI: 10.21258/1334810
title: Swiss national forest inventory - Result table No. 155811
DOI: 10.21258/1334811
title: Swiss national forest inventory - Result table No. 155815
DOI: 10.21258/1334812
title: Swiss national forest inventory - Result table No. 155809
DOI: 10.21258/1334813
title: Swiss national forest inventory - Result table No. 155810
DOI: 10.21258/1334814
title: Swiss national forest inventory - Result table No. 155806
DOI: 10.21258/1334815
title: Swiss national forest inventory - Result table No. 155807
DOI: 10.21258/1334809
title: Swiss national forest inventory - Result table No. 155816
DOI: 10.21258/1334805
title: Swiss national forest inventory - Result table No. 155819
DOI: 10.21258/1334806
title: Swiss national forest inventory - Result table No. 155818
DOI: 10.21258/1334807
title: Swiss national forest inventory - Result table No. 155817
DOI: 10.21258/1334808
title: Swiss national forest inventory - Result table No. 155826
DOI: 10.15156/bio/sh2099909.08fu
title: SH2099909.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3255619.08fu
title: SH3255619.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.