cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7700576.v1
title: An ensemble method for multi-type Gram-negative bacterial secreted protein prediction by integrating different PSSM-based features

description: In Gram-negative bacteria, a wide range of proteins are secreted by highly specialized secretion systems. These secreted proteins play essential roles in the response of bacteria to their environment and also in several physiological processes such as adhesion, pathogenicity, adaptation and survival. Therefore, identifying secreted proteins in Gram-negative bacteria may assist in understanding the secretion mechanism and development of new antimicrobial strategies. Considering that a single-feature model is less likely to comprehensively cover this information, three kinds of feature models were used in this paper to represent protein samples by composition analysis, correlation analysis and smoothing encoding method on position-specific scoring matrix profiles. A support vector machine-based ensemble method with these hybrid features was developed to predict multi-type Gram-negative bacterial secreted proteins. Finally, our method achieves overall accuracies of 97.09% and 96.51% using an independent dataset test and jackknife test on a public test dataset, which are 3.49% and 2.32% higher, respectively, than results obtained by other methods. These results show the effectiveness and stability of the proposed ensemble method. It is anticipated that our method will provide useful information for further research on bacterial secreted proteins and secreted systems.
DOI: 10.6084/m9.figshare.7700582.v1
title: Supplementary Table from The earliest equatorial record of frogs from the Late Triassic of Arizona

description: Table of CT scanning parameters for specimens included in this work.
DOI: 10.7284/117221
title: Meteorological Station data collected during research cruise AT26-28 using a Vaisala WXT520 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/117222
title: Meteorological Station data collected during research cruise AT26-28 using a Vaisala WXT520 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/117224
title: Radiometer data collected during research cruise AT26-28 using a Eppley PIR instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7700534
title: Diversity and functions of microbes in surface sediments of western Chaohu Lake

description: Diversity and functions of microbes in surface sediments of western Chaohu Lake
DOI: 10.7284/117225
title: Radiometer data collected during research cruise AT26-28 using a Eppley PSP instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7700534.v1
title: Diversity and functions of microbes in surface sediments of Chaohu Lake

description: Diversity and functions of microbes in surface sediments of Chaohu Lake
DOI: 10.7284/117226
title: Water Temperature data collected during research cruise AT26-28 using a Sea-Bird SBE-48 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7700528.v1
title: A novel location-routing problem in electric vehicle transportation with stochastic demands

description: This is the experimental data of the manuscript entitled "A novel location-routing problem in electric vehicle transportation with stochastic demands". All data are saved in the file with txt format.
DOI: 10.7284/117223
title: TSG (Thermosalinograph) data collected during research cruise AT26-28 using a Sea-Bird SBE-45 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7700495
title: Turkey’s Position Among World Countries In Light of Innovation Indicators (GII) and Issues That Turkey Should Primarily Settle

description: Günümüz dünyasında, ülkelerin gelişmişlik seviyelerini iyileştirebilmeleri için, esas olarak rekabet gücü yüksek malların üretimi ve pazarlanmasına bağlıdır. Sürekli küreselleşen dünyanın rekabetçi yapısında varlığını sürdürebilmesi ve başarılı olabilmesi için daha yüksek kalitede ürünler üretebilmesi, üretimde daha yenilikçi yaklaşımlar elde etmeyi gerektirir. Hükümetlerden şirketlere, üründen hizmete, üretimden satış ve pazarlamaya ve teknolojiden klasik sistemlere, yeniliklerin açıkça gözlenmesi ve algılanması gerekir. Bu çalışmada, 2017 Dünya İnovasyon Göstergelerine atıfta bulunarak, hem Türkiye'nin hem de diğer ülkelerin konumlarını öğrenmek amaçlanmıştır. Bu sayede tüm ülkelerin ve şehirlerin göz önüne alındığı 61 inovasyon göstergesinin (ana gruplar için göstergeler dahil) dikkate alınmasıyla, 119 ülkenin verisinin analizi, birden fazla değişkenli istatistiksel yöntemlerden biri olan hiyerarşik kümeleme yoluyla gerçekleştirilmiştir. Anlaşıldığı üzere, bu analiz sürecine dahil olan ülkelerin hepsi 9 farklı grupta toplanmış ve Türkiye'nin Arjantin, Brezilya, Kolombiya, Peru, Rusya, Suudi Arabistan, Ukrayna, Şili, Çin ile birlikte 3. grupta yer aldığı görülmüştür. , Malezya, Meksika, Güney Afrika, Tayland, Birleşik Arap Emirlikleri ve Vietnam. İnovasyon endeksinin sınıflandırılmasında lider ülkelerin bulunduğu 5. grupta ülkeler var; Avustralya, Avusturya, Belçika, Kanada, Danimarka, Finlandiya, Fransa, Almanya, İrlanda, İsrail, İtalya, Japonya, Kore, Hollanda, Yeni Zelanda, Norveç, Singapur, İspanya, İsveç, İsviçre, İngiltere ve Amerika. Bu bağlamda, yetersiz performans gösterdiğimiz yirmi (20) temel konu, 5. gruptaki ülkelerin ve Türkiye’nin endeks ortalamaları arasındaki farklar göz önünde bulundurularak belirlenmiştir.
DOI: 10.6084/m9.figshare.7700495.v1
title: Turkey’s Position Among World Countries In Light of Innovation Indicators (GII) and Issues That Turkey Should Primarily Settle

description: Günümüz dünyasında, ülkelerin gelişmişlik seviyelerini iyileştirebilmeleri için, esas olarak rekabet gücü yüksek malların üretimi ve pazarlanmasına bağlıdır. Sürekli küreselleşen dünyanın rekabetçi yapısında varlığını sürdürebilmesi ve başarılı olabilmesi için daha yüksek kalitede ürünler üretebilmesi, üretimde daha yenilikçi yaklaşımlar elde etmeyi gerektirir. Hükümetlerden şirketlere, üründen hizmete, üretimden satış ve pazarlamaya ve teknolojiden klasik sistemlere, yeniliklerin açıkça gözlenmesi ve algılanması gerekir. Bu çalışmada, 2017 Dünya İnovasyon Göstergelerine atıfta bulunarak, hem Türkiye'nin hem de diğer ülkelerin konumlarını öğrenmek amaçlanmıştır. Bu sayede tüm ülkelerin ve şehirlerin göz önüne alındığı 61 inovasyon göstergesinin (ana gruplar için göstergeler dahil) dikkate alınmasıyla, 119 ülkenin verisinin analizi, birden fazla değişkenli istatistiksel yöntemlerden biri olan hiyerarşik kümeleme yoluyla gerçekleştirilmiştir. Anlaşıldığı üzere, bu analiz sürecine dahil olan ülkelerin hepsi 9 farklı grupta toplanmış ve Türkiye'nin Arjantin, Brezilya, Kolombiya, Peru, Rusya, Suudi Arabistan, Ukrayna, Şili, Çin ile birlikte 3. grupta yer aldığı görülmüştür. , Malezya, Meksika, Güney Afrika, Tayland, Birleşik Arap Emirlikleri ve Vietnam. İnovasyon endeksinin sınıflandırılmasında lider ülkelerin bulunduğu 5. grupta ülkeler var; Avustralya, Avusturya, Belçika, Kanada, Danimarka, Finlandiya, Fransa, Almanya, İrlanda, İsrail, İtalya, Japonya, Kore, Hollanda, Yeni Zelanda, Norveç, Singapur, İspanya, İsveç, İsviçre, İngiltere ve Amerika. Bu bağlamda, yetersiz performans gösterdiğimiz yirmi (20) temel konu, 5. gruptaki ülkelerin ve Türkiye’nin endeks ortalamaları arasındaki farklar göz önünde bulundurularak belirlenmiştir.
DOI: 10.7284/117229
title: Multiplexed data collected during research cruise AT26-29 using a WHOI Calliope instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7700504.v1
title: SUKUK AS ONE THE ISLAMIC FINANCIAL INSTRUMENTES: INVESTIGATION OF THE MURABAHAH CONTRACTS IN THE HYBRID SUKUK IN TERMS OF COMPLIANCE WİTH THE ISLAMIC PROVISION

description: Sukuk is an interest-free Capital market tool developed for use in Islamic finance. Sukuk is an Islamic compliant certificate, which is developed as an alternative to traditional bonds and which is based on asset-based securities with different characteristics from bond-based securities and revenue-share certificates, which are traditional financial market instrumentsby structure. It is seen that sukuk certificates resemble bonds in order to provide the financing required by the investor. However, while bonds are indebted to the structure while investors offer interest income, sukuk is not a debt instrument, but should be based on an asset and its investor, not a fixed interest income, but right to benefit from the income from the underlying asset. Sukuk, on the other hand, is also different from the company shares that give the company the right to partnership and management. Although the sukuk may grant the right of ownership to the holders of the underlying rights subject to sukuk, this right of ownership has a limited rights structure that does not contain any management exc. rights on the underlying assets.In thisstudy, firstly, types of sukuk and its importance are mentioned and the differences between the traditional financial market instruments are revealed. Then, it is mentioned about the issue sukuk and types of issues in the World and Turkey.Purpose of the study; one of the types of sukuk, and both in the World and in our country is issued with large numbers of hybrid sukuk which is including in murabahah sukuk are examined the direction of conformity to Islam. In this study, it was found that there was no consistent legal basis for the use of murabahah in the hybrid sukuk and the fact that it was/was not suitable for Islam in the secondary markets.According to this, an important financial source hybrid sukuk based asset pool in the secondary markets will beexperienced in the process of trading problems should not be placed in murabahah contracts. Murabahah sukuk should be issued separately and these murabahah certificates should not be traded in the secondary markets.As a result; The insertion of murabahahcontracts into hybrid sukuk is not appropriate as it will create a ban on trading in the secondary markets. The fact that all parties, especially Islamic Banking activities are more sensitive about this issue is very important for the future of Islamic financial market.
DOI: 10.7284/117231
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AT26-29 using a Hawaii UHDAS instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/117232
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AT26-29 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7700462
title: ARTPapua

description: Database for HIVART Papua study, published in PLOS ONE.<br>
DOI: 10.7284/117230
title: Expendable Probe data collected during research cruise AT26-29 using a Sippican MK12 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7700462.v3
title: ARTPapua

description: Database for HIVART Papua study, published in PLOS ONE.<br>
DOI: 10.7284/117228
title: Fluorometer data collected during research cruise AT26-29 using a WET Labs WETStar instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7700417
title: A comparison of the type I error rates of three assessment methods for indirect effects

description: Mediation analysis is a popular statistical analysis verifying the relation between an independent variable and a dependent variable through a mediator. There are three traditional tests to assess indirect effects: the Baron and Kenny test (BK), the Sobel test (ST) and the bootstrap method (BT). Previous studies have showed that the BT is more powerful and more conceptually appropriate. However, no study has systematically compared these tests regarding the type I error rate. A Monte-Carlo simulation is carried out with 19 scenarios varying paths (but no indirect effect), 9 scenarios varying the direct effect, and 6 sample sizes (1056 different scenarios). Results show that the BT had an overall good performance even for small sample size and whatever the effect sizes. The ST and the BK test were conservative, especially with small sample size and low effect sizes. In conclusion, these tests should be avoided, and the BT is recommended.
DOI: 10.7284/117227
title: GNSS (Global Navigation Satellite System) data collected during research cruise AT26-29 using a C&C C-Nav 2050G instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7700417.v1
title: A comparison of the type I error rates of three assessment methods for indirect effects

description: Mediation analysis is a popular statistical analysis verifying the relation between an independent variable and a dependent variable through a mediator. There are three traditional tests to assess indirect effects: the Baron and Kenny test (BK), the Sobel test (ST) and the bootstrap method (BT). Previous studies have showed that the BT is more powerful and more conceptually appropriate. However, no study has systematically compared these tests regarding the type I error rate. A Monte-Carlo simulation is carried out with 19 scenarios varying paths (but no indirect effect), 9 scenarios varying the direct effect, and 6 sample sizes (1056 different scenarios). Results show that the BT had an overall good performance even for small sample size and whatever the effect sizes. The ST and the BK test were conservative, especially with small sample size and low effect sizes. In conclusion, these tests should be avoided, and the BT is recommended.
DOI: 10.6084/m9.figshare.7700369
title: Timing and tectonic significance of Paleozoic magmatism in the Sakar unit of the Sakar-Strandzha Zone, SE Bulgaria

description: Palaeozoic granitoids and meta-granitoids dominate the metamorphic basement of the Sakar unit of the Sakar-Strandzha Zone (SASTZ) in southeast Bulgaria. In this article, we present new whole-rock geochemical data and U–Pb zircon geochronology for the Sakar unit granitoids. The igneous minerals and textures are preserved, except the meta-granitoids that experienced a weak amphibolite-facies overprint. Geochemistry reveals compositions of peraluminous high-K calc-alkaline I- to S-type granitoids of volcanic arc origin. A major group of LILE-LREE-enriched granitoids and meta-granitoids and a single HFSE-HREE-enriched meta-granitoid are distinguished. U–Pb geochronology has yielded crystallization ages between 305 and 295 Ma for the major group granitoids and a ca. 462 Ma crystallization age of HFSE-HREE-enriched meta-granitoid. Late Palaeozoic granitoids of the Sakar unit show similar compositions and a similar tectonic setting when compared to other granitoids of the SASTZ, confirming a uniform region-wide tectono-magmatic event. As the Late Carboniferous-Permian magmatic arc components extend across the SASTZ, they trace the time-correspondent active continental margin along the Eurasian plate during subduction of the Palaeotethys oceanic lithosphere. The late Palaeozoic Eurasian active continental margin magmatic arc evolution of the SASTZ can be extended into the Serbo-Macedonian-Rhodope zones to the west, where time equivalent meta-granitoids support the same geodynamic context.
DOI: 10.6084/m9.figshare.7700405
title: Proteomic characterization of the arsenic response locus in S. cerevisiae

description: Arsenic exposure is a global health problem. Millions of people encounter arsenic through contaminated drinking water, consumption, and inhalation. The arsenic response locus in budding yeast is responsible for the detoxification of arsenic and its removal from the cell. This locus constitutes a conserved pathway ranging from prokaryotes to higher eukaryotes. The goal of this study was to identify how transcription from the arsenic response locus is regulated in an arsenic dependent manner. An affinity enrichment strategy called CRISPR-Chromatin Affinity Purification with Mass Spectrometry (CRISPR-ChAP-MS) was used, which provides for the proteomic characterization of a targeted locus. CRISPR-ChAP-MS was applied to the promoter regions of the activated arsenic response locus and uncovered 40 nuclear-annotated proteins showing enrichment. Functional assays identified the histone acetyltransferase SAGA and the chromatin remodelling complex SWI/SNF to be required for activation of the locus. Furthermore, SAGA and SWI/SNF were both found to specifically organize the chromatin structure at the arsenic response locus for activation of gene transcription. This study provides the first proteomic characterization of an arsenic response locus and key insight into the mechanisms of transcriptional activation that are necessary for detoxification of arsenic from the cell.
DOI: 10.7284/117234
title: Meteorological Station data collected during research cruise AT26-29 using a Vaisala WXT520 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7700369.v1
title: Timing and tectonic significance of Paleozoic magmatism in the Sakar unit of the Sakar-Strandzha Zone, SE Bulgaria

description: Palaeozoic granitoids and meta-granitoids dominate the metamorphic basement of the Sakar unit of the Sakar-Strandzha Zone (SASTZ) in southeast Bulgaria. In this article, we present new whole-rock geochemical data and U–Pb zircon geochronology for the Sakar unit granitoids. The igneous minerals and textures are preserved, except the meta-granitoids that experienced a weak amphibolite-facies overprint. Geochemistry reveals compositions of peraluminous high-K calc-alkaline I- to S-type granitoids of volcanic arc origin. A major group of LILE-LREE-enriched granitoids and meta-granitoids and a single HFSE-HREE-enriched meta-granitoid are distinguished. U–Pb geochronology has yielded crystallization ages between 305 and 295 Ma for the major group granitoids and a ca. 462 Ma crystallization age of HFSE-HREE-enriched meta-granitoid. Late Palaeozoic granitoids of the Sakar unit show similar compositions and a similar tectonic setting when compared to other granitoids of the SASTZ, confirming a uniform region-wide tectono-magmatic event. As the Late Carboniferous-Permian magmatic arc components extend across the SASTZ, they trace the time-correspondent active continental margin along the Eurasian plate during subduction of the Palaeotethys oceanic lithosphere. The late Palaeozoic Eurasian active continental margin magmatic arc evolution of the SASTZ can be extended into the Serbo-Macedonian-Rhodope zones to the west, where time equivalent meta-granitoids support the same geodynamic context.
DOI: 10.6084/m9.figshare.7700405.v2
title: Proteomic characterization of the arsenic response locus in S. cerevisiae

description: Arsenic exposure is a global health problem. Millions of people encounter arsenic through contaminated drinking water, consumption, and inhalation. The arsenic response locus in budding yeast is responsible for the detoxification of arsenic and its removal from the cell. This locus constitutes a conserved pathway ranging from prokaryotes to higher eukaryotes. The goal of this study was to identify how transcription from the arsenic response locus is regulated in an arsenic dependent manner. An affinity enrichment strategy called CRISPR-Chromatin Affinity Purification with Mass Spectrometry (CRISPR-ChAP-MS) was used, which provides for the proteomic characterization of a targeted locus. CRISPR-ChAP-MS was applied to the promoter regions of the activated arsenic response locus and uncovered 40 nuclear-annotated proteins showing enrichment. Functional assays identified the histone acetyltransferase SAGA and the chromatin remodelling complex SWI/SNF to be required for activation of the locus. Furthermore, SAGA and SWI/SNF were both found to specifically organize the chromatin structure at the arsenic response locus for activation of gene transcription. This study provides the first proteomic characterization of an arsenic response locus and key insight into the mechanisms of transcriptional activation that are necessary for detoxification of arsenic from the cell.
DOI: 10.7284/117235
title: Meteorological Station data collected during research cruise AT26-29 using a Vaisala WXT520 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7700405.v1
title: Proteomic Characterization of the Arsenic Response Locus in S. cerevisiae

description: Arsenic exposure is a global health problem. Millions of people encounter arsenic through contaminated drinking water, consumption, and inhalation. The arsenic response locus in budding yeast is responsible for the detoxification of arsenic and its removal from the cell. This locus constitutes a conserved pathway ranging from prokaryotes to higher eukaryotes. The goal of this study was to identify how transcription from the arsenic response locus is regulated in an arsenic dependent manner. An affinity enrichment strategy called CRISPR-Chromatin Affinity Purification with Mass Spectrometry (CRISPR-ChAP-MS) was used, which provides for the proteomic characterization of a targeted locus. CRISPR-ChAP-MS was applied to the promoter regions of the activated arsenic response locus and uncovered 40 nuclear-annotated proteins showing enrichment. Functional assays identified the histone acetyltransferase SAGA and the chromatin remodelling complex SWI/SNF to be required for activation of the locus. Furthermore, SAGA and SWI/SNF were both found to specifically organize the chromatin structure at the arsenic response locus for activation of gene transcription. This study provides the first proteomic characterization of an arsenic response locus and key insight into the mechanisms of transcriptional activation that are necessary for detoxification of arsenic from the cell.
DOI: 10.5281/zenodo.4004794
title: Data for research on nurse rostering in Denmark

description: A report describing data for nurse rostering in Denmark, along with 12 instances.
description: This version includes the original data (Formulation_WeightedSum.zip) along with the data needed to formulate the problem using targets and acceptance thresholds (Reformulation_TargetsAcceptanceThresholds.zip).
DOI: 10.7284/117233
title: Multibeam Echosounder data collected during research cruise AT26-29 using a Kongsberg EM122 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/117236
title: Radiometer data collected during research cruise AT26-29 using a Eppley PIR instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7700138
title: LP-UFC 722 CT Scans

description: CT scans of the specimen LP-UFC 722 covering the entire specimen, the neural series, the head and neck and only the head. The scans are in .mcs format to be run on Mimics or similar software.