cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
The complete mitochondrial genome of Membranipora villosa Hincks, 1880 (Bryozoa: Gymnolaemata: Cheilostomatida): phylogenetic relationship of two kelp-encrusting bryozoans within the suborder Membraniporina
Creators: name: Noh, Geon Woo
name: Lee, Sang-Hwa
name: Chae, Hyun Sook
name: Yang, Ho Jin
name: Yoo, Hyun Il
name: Seo, Ji Eun
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: The two commonest kelp-encrusting bryozoans, Membranipora villosa and M. membranacea, are difficult to distinguish morphologically. Molecular studies of M. villosa should thus be helpful for the identification of both species because the mitogenome of M. membranacea was already sequenced. The complete mitogenome of M. villosa collected from Sinjido was determined in this study through Illumina NovaSeq sequencing. Maximum-likelihood (ML) analysis was based on concatenated 13 protein-coding genes dataset from nine bryozoan species. The mitogenome length was 15,407 bp, and its gene arrangement was similar to those of the mitogenome of other membraniporids, having 13 PCGs, two ribosomal RNAs, and 22 tRNAs. It had an overall A + T content of 63.7% (29.7% A, 16.7% C, 19.6% G, and 34.0% T). M. villosa and M. membranacea showed sequence differences of 20% for the total length of mitogenome and 16.1.% for 13 PCGs. Molecular data definitely consider them to be separate species. Phylogenetic analyses based on the amino acids of 13 PCGs indicated that M. villosa has the closest relationship with another kelp-encrusting bryozoan, M. membranacea of membraniporids. The phylogenetic position of genera and families within the suborder Membraniporina coincides with the Bayesian phylogenetic analysis of the mixed concatenated alignment consisting of three partitions.
The complete chloroplast genome sequence of Ampelopsis delavayana Planchon. ex Franch 1886 (Vitaceae)
Creators: name: Hu, Qun
name: Luo, Yongjian
name: Li, Qing
name: Deng, Zhijun
name: Liu, Jun
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Plant Biology

description: Ampelopsis delavayana Planchon. ex Franch 1886 is a plant with significant pharmacological effects and ornamental importance. This research unveiled the complete chloroplast (cp) genome sequence of A. delavayana. The study highlights that the cp genome of A. delavayana possesses a distinct tetrameric structure spanning 162,497 base pairs, comprising a small single-copy (SSC) region of 18,902 base pairs, a large single-copy (LSC) region of 90,441 base pairs, and two inverted-repeat regions (IRs), each 26,577 base pairs in length. The GC content of the SSC, LSC, and IR regions of the genome was 31.80%, 35.16%, and 42.82%, respectively, culminating in an overall GC content of 37.27%. The genome comprised 130 genes, which included eight rRNAs, 36 tRNAs, and 86 protein-coding genes. Through phylogenetic analysis utilizing the maximum-likelihood method, it was established that A. delavayana was closely related to Ampelopsis glandulosa var. brevipedunculata, positioning it as a sister species. This report not only provides a scientific reference for understanding the phylogeny of the family Vitaceae but also enriches our genetic information of Ampelopsis.
Rhinolophus fumigatus Ruppell 1842
Creators: name: Cakenberghe, Victor Van
name: Tungaluna, Guy-Crispin Gembu
name: Akawa, Prescott Musaba
name: Seamark, Ernest
name: Verheyen, Erik
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Chiroptera
Rhinolophidae
Rhinolophus
Rhinolophus fumigatus

description: Rhinolophus fumigatus Rüppell, 1842
Fig. 15 E–F
* Rhinolophus fumigatus Rüppell, 1842: 132.
In their synonymy list for R. fumigatus, Hayman et al. (1966: 38) include Rhinolophus abae J.A. Allen, 1917, and they refer to Koopman, who considered abae to be very close to fumigatus at the species level and indicated that abae might only be a subspecies of fumigatus. The records for these two taxa were grouped together in the text, but they still provided two separate maps: 36 for R. abae and 40 for R. fumigatus. These maps indicate that the two taxa occur in the northeastern RDC. Further fumigatus records were reported from Rwanda and the southern provinces of Tanganyika, Lualaba and Haut- Katanga. Hayman et al. (1966) also reported a series from 74 km on the Banana-Boma Road (RMCA 20649, 20651 to 20653), but these were re-identified as Rhinolophus lobatus (= R. landeri; Wim Wendelen, pers. comm.). However, two other R. fumigatus specimens have surfaced from the Kongo Central Province (Thysville: RBINS 22428 and 22429). Cotterill & Happold (2013a: 330) indicate that R. fumigatus inhabits savanna areas (miombo and mopane woodlands in south-central Africa). Their distribution map shows a patchy covering of sub-Saharan Africa consisting of a number of red areas in West Africa, northeast Africa (including NE DRC, Rwanda, Uganda, Kenya and Ethiopia), and southwestern Africa (Angola and Namibia) as well as a number of individual records in southeastern Africa (Zambia, Zimbabwe, Mozambique). From the data in ACR (2016) we know that the distribution in southern Africa is more extensive than Cotterill & Happold’s map suggests, and this probably might also be the case in West Africa. As such, our distribution map is more extensive, indicating that R. fumigatus occurs over the major part of sub-Saharan Africa, with the exception of the coastal areas in West Africa, the Central African forest region and extreme southern Africa.
description: Published as part of Cakenberghe, Victor Van, Tungaluna, Guy-Crispin Gembu, Akawa, Prescott Musaba, Seamark, Ernest & Verheyen, Erik, 2017, The bats of the Congo and of Rwanda and Burundi revisited (Mammalia: Chiroptera), pp. 1-327 in European Journal of Taxonomy 382 (382) on page 38, DOI: 10.5852/ejt.2017.382, http://zenodo.org/record/3860077
Complete mitochondrial genome of Devario shanensis (Cypriniformes: Danionidae: Danioninae): genome characterization and phylogenetic consideration
Creators: name: Xu, Chun Hui
name: Song, Lin
name: Wang, Quan
name: Chen, Xiao Jiang
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified

description: In this study, a comprehensive analysis is presented on the complete mitochondrial genome and phylogenetic relationships of Devario shanensis, an endemic species to the Irrawaddy drainage in southwestern China. The complete mitogenome sequence of D. shanensis was sequenced to be 16,860 bp long and encompassed 13 protein-coding genes, 22 tRNA genes, two rRNA genes and a non-coding control region. The overall AT content (61.1%) was much higher than GC content (38.9%). Phylogenetic analyses employing maximum-likelihood and Bayesian inference methods on the complete mitogenomes, including D. shanensis and 13 other species, unveiled a close genomic relationship between D. shanensis and Devario interruptus. This work will contribute to the genetic resource enrichment and phylogenetic researches on genus Devario.
Complete mitochondrial genome of the worm snail Thylacodes adamsii (Littorinimorpha: Vermetidae) from South Korea
Creators: name: Lee, Yumin
name: Kim, Ki Beom
name: Choi, Eun Hwa
name: Hwang, Ui Wook
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Infectious Diseases
subject: FOS: Health sciences

description: The worm snail Thylacodes adamsii (Mörch, 1859) (Littorinimorpha: Vermetidae) is a sessile gastropod that mainly inhabits rocky shores along the warm temperate to tropical ocean. Herein, the complete mitochondrial genome (mitogenome) of T. adamsii from South Korea was characterized. The genome is 14,913 bp in length and contains 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. The genome organization and base composition of T. adamsii are similar to those of other vermetids. A phylogenetic tree was reconstructed using maximum likelihood based on the nucleotide sequences of the 13 PCGs; this tree supported the monophyly of Vermetidae. The complete mitogenome of T. adamsii can assist with molecular species identification and vermetid phylogenetic research in the future.
title: Crisis as (Asylum) Governance: The Evolving Normalisation of Non-access to Protection in the EU
Creators: name: Moreno-Lax, Violeta
Publisher: name: European Papers (www.europeanpapers.eu)
Year: 2024
Subjects: subject: crisification
subject: asylum governance
subject: New Pact on Migration and Asylum
subject: access to international protection
subject: exceptionalisation
subject: rule of law

description: European Papers - A Journal on Law and Integration, 2024 9(1), 179-208
description: I. Introduction: structuralising crisis. – II. “Crisification”: the incremental normalisation of exceptions. – III. The 2015 ”Refugee Crisis”: the suspension of governance (as a form of governance) – III.1. Relocation (and Dublin prorogation) – III.2. The Hotspot Fiasco – IV. The New Pact Reforms: generalising derogations – IV.1. Screening process: hotspots extended – IV.2. Border Procedure: hotspots normalised – V. Conclusion: reversing the rule, decreasing legality.
description: This Article problematises the role of crisis in the governance of asylum in Europe. It unveils its nature, predominance, and implications as a structural component of EU law and policy in this domain. The main point I intend to convey is that crisis, in and by itself, constitutes a system of governance producing very problematic effects. The association between (unwanted) migration and refugee flows with crisis in the European context has allowed for the exceptionalisation of rights and legal safeguards, with the pre-emption of unauthorised arrivals becoming the main concern. The danger, instability, and abnormality connected with crisis pervades law and policy, justifying mechanisms that contravene minimal rule of law standards, including due process guarantees and effective judicial protection. The incremental normalisation of exceptions has led to a position where the suspension of (rule of law-based) governance has become a form of governance. The prorogation of “normal” (rule of law-compliant) arrangements has given way to “exceptional” means of managing asylum, starting with the 2015 “refugee crisis” and the relocation-plus-hotspots scheme, which have now been streamlined as part of the New Pact on Migration and Asylum reforms. The resulting generalisation of derogations, the proliferation of legal fictions and rights negations that the envisaged amendments involve, is progressively normalising a situation of non-access to international protection in the EU, with deleterious consequences not only for asylum seekers, but for the integrity of the EU legal order and fundamental rights at large.
Cardioderma cor
Creators: name: Cakenberghe, Victor Van
name: Tungaluna, Guy-Crispin Gembu
name: Akawa, Prescott Musaba
name: Seamark, Ernest
name: Verheyen, Erik
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Chiroptera
Megadermatidae
Cardioderma
Cardioderma cor

description: Cardioderma cor (Peters, 1872)
Fig. 13 E–F
Megaderma cor Peters, 1872: 194.
The distribution area for Cardioderma cor reported by Happold (2013n: 404) covers part of northeastern Africa, from eastern Sudan at the border with Eritrea, over Eritrea and central Ethiopia and central Kenya to northern Tanzania, with an extention into western Somalia and some individual localities in eastern Ethiopia and easternmost Somalia. The westernmost occurrence of C. cor is northeastern Uganda and just across the border into South Sudan.
The DRC specimen reported here was collected by the Congolese authors at Rubi-Tele in Tshopo Province, which is a westward extension of about 800 km from the hereto closest known locality.
description: Published as part of Cakenberghe, Victor Van, Tungaluna, Guy-Crispin Gembu, Akawa, Prescott Musaba, Seamark, Ernest & Verheyen, Erik, 2017, The bats of the Congo and of Rwanda and Burundi revisited (Mammalia: Chiroptera), pp. 1-327 in European Journal of Taxonomy 382 (382) on page 34, DOI: 10.5852/ejt.2017.382, http://zenodo.org/record/3860077
Rhinolophus hildebrandtii Peters 1878
Creators: name: Cakenberghe, Victor Van
name: Tungaluna, Guy-Crispin Gembu
name: Akawa, Prescott Musaba
name: Seamark, Ernest
name: Verheyen, Erik
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Chiroptera
Rhinolophidae
Rhinolophus
Rhinolophus hildebrandtii

description: Rhinolophus hildebrandtii Peters, 1878
Fig. 16 A–B
Rhinolophus Hildebrandtii Peters, 1878: 195.
* Rhinolophus hildebrandti Peters, 1878.
Hayman et al. (1966: 39) distinguished two forms in R. hildebrandtii; one they identified to subspecific level (see below) and one to specific level. However, they only included one distribution map (map 41) for these two forms. The distribution within CRB was restricted to the eastern part of the DRC and Rwanda, with specimens in the Congolese provinces of Nord-Kivu, Ituri and Haut-Uélé in the north on the one hand and in Tanganyika, Haut-Lomami and Haut-Katanga Provinces in the south on the other hand. Some of the specimens from Rwanda (Magachi, INPBC V1903; Lugarama, INPBC 3041) were re-identified as R. fumigatus, which might account for the remark made by Monfort (1992: 146) on the species being plotted on map 41 in Hayman et al. (1966), but being absent in their listing. Additional specimens of R. hildebrandtii are reported from Burundi and the southern Congolese provinces, but also from Gangala-na-Bodio (Haut-Uélé Province, RMCA 26664 and 26665) and Ibembo (Bas-Uélé Province, RMCA 89.004-M-0002). Based on their geographic location, the specimens from the Uélé Provinces might possibly need to be re-assigned to R. eloquens, but even for that species, the Ibembo specimen was found too far to the west.
description: Published as part of Cakenberghe, Victor Van, Tungaluna, Guy-Crispin Gembu, Akawa, Prescott Musaba, Seamark, Ernest & Verheyen, Erik, 2017, The bats of the Congo and of Rwanda and Burundi revisited (Mammalia: Chiroptera), pp. 1-327 in European Journal of Taxonomy 382 (382) on page 39, DOI: 10.5852/ejt.2017.382, http://zenodo.org/record/3860077
Prompt Optimizer of Text-to-Image Diffusion Models for Abstract Concept Understanding
Creators: name: Fan, Zezhong
name: Li, Xiaohan
name: Fang, Chenhao
name: Biswas, Topojoy
name: Nag, Kaushiki
name: Xu, Jianpeng
name: Achan, Kannan
Publisher: name: arXiv
Year: 2024
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Artificial Intelligence (cs.AI)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: The rapid evolution of text-to-image diffusion models has opened the door of generative AI, enabling the translation of textual descriptions into visually compelling images with remarkable quality. However, a persistent challenge within this domain is the optimization of prompts to effectively convey abstract concepts into concrete objects. For example, text encoders can hardly express "peace", while can easily illustrate olive branches and white doves. This paper introduces a novel approach named Prompt Optimizer for Abstract Concepts (POAC) specifically designed to enhance the performance of text-to-image diffusion models in interpreting and generating images from abstract concepts. We propose a Prompt Language Model (PLM), which is initialized from a pre-trained language model, and then fine-tuned with a curated dataset of abstract concept prompts. The dataset is created with GPT-4 to extend the abstract concept to a scene and concrete objects. Our framework employs a Reinforcement Learning (RL)-based optimization strategy, focusing on the alignment between the generated images by a stable diffusion model and optimized prompts. Through extensive experiments, we demonstrate that our proposed POAC significantly improves the accuracy and aesthetic quality of generated images, particularly in the description of abstract concepts and alignment with optimized prompts. We also present a comprehensive analysis of our model's performance across diffusion models under different settings, showcasing its versatility and effectiveness in enhancing abstract concept representation.
description: WWW 2024 Companion
The complete chloroplast genome of Arachis lutescens Krapov. & Rigoni (Fabaceae)
Creators: name: Cui, Hexin
name: Xu, He
name: Zhang, Yu
name: Xu, Chunrui
name: Wang, Han
name: Li, Qinghua
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Plant Biology

description: Arachis lutescens Krapov. & Rigoni 1958 is an important species due to their potentially extensive applications for cultivated peanut breeding. The whole chloroplast genome of A. lutescens was successfully assembled and annotated for the first time. The complete chloroplast genome of A. lutescens is a typically circular structure of 156,398 bp with a GC content of 36.3%. It comprises a large single-copy (LSC) region of 85,950 bp, a small single-copy (SSC) region of 18,800 bp, and two inverted repeat regions (IRs) of 25,824 bp, each. The plastome of A. lutescens contains a total of 125 genes, including 81 protein-coding genes, 36 tRNAs, and eight rRNAs. The phylogenetic analysis strongly supports the close relationship between A. lutescens and cultivated peanut clades. This study contributes to our understanding of the molecular characteristics and evolutionary relationships of this plant species.
Exploring 2D and 3D Human Generation and Editing
Creators: name: Zhang, Jichao
Publisher: name: Università degli studi di Trento
Year: 2024
Subjects: subject: Generative Model, Generative Adversarial Networks, Generative Neural Radiance Field, Face Generation and Editing, Generative Digital Human.
subject: Generative Model
subject: Generative Adversarial Networks
subject: Generative Neural Radiance Field
subject: Face Generation and Editing
subject: Generative Digital Human

description: In modern society, cameras on intelligent devices can generate a huge amount of natural images, including images of the human body and face. Therefore, there is a huge social demand for more efficient editing of images to meet human production and life needs, including entertainment, such as image beauty. In recent years, Generative Models with Deep Learning techniques have attracted lots of attention in the Artificial Intelligence field, and some powerful methods, such as Variational Autoencoder and Generative Adversarial Networks, can generate very high-resolution and realistic images, especially for facial images, human body image. In this thesis, we follow the powerful generative model to achieve image generation and editing tasks, and we focus on human image generation and editing tasks, including local eye and face generation and editing, global human body generation, and editing. We introduce different methods to improve previous baselines based on different human regions. 1) Eye region of human image: Gaze correction and redirection aim to manipulate the eye gaze to a desired direction. Previous common gaze correction methods require annotating training data with precise gaze and head pose information. To address this issue, we proposed the new datasets as training data and formulated the gaze correction task as a generative inpainting problem, addressed using two new modules. 2) Face region of human image: Based on a powerful generative model for face region, many papers have learned to control the latent space to manipulate face attributes. However, they need more precise controls on 3d factors such as camera pose because they tend to ignore the underlying 3D scene rendering process. Thus, we take the pre-trained 3D-Aware generative model as the backbone and learn to manipulate the latent space using the attribute labels as conditional information to achieve the 3D-Aware face generation and editing task. 3) Human Body region of human image: 3D-Aware generative models have been shown to produce realistic images representing rigid/semi-rigid objects, such as facial regions. However, they usually struggle to generate high-quality images representing non-rigid objects, such as the human body, which greatly interests many computer graphics applications. Thus, we introduce semantic segmentation into the model. We split the entire generation pipeline into two stages and use intermediate segmentation masks to bridge these two stages. Furthermore, our model can control pose, semantic, and appearance codes by using multiple latent codes to achieve human image editing.
The complete mitochondrial genome of Trematomus hansoni Boulenger, 1902 (Perciformes, Nototheniidae)
Creators: name: Jo, Euna
name: Lee, Seungyeon
name: Kim, Jihun
name: Hettiarachchi, Sachithra Amarin
name: Kim, Sanghee
name: Kim, Il-Chan
name: Kang, Seunghyun
name: Kim, Jin-Hyoung
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Infectious Diseases
subject: FOS: Health sciences

description: The striped notothen Trematomus hansoni is an Antarctic fish species belonging to the family Nototheniidae (cod icefishes) that is distributed throughout the Southern Ocean. In this study, the complete mitochondrial genome of T. hansoni was sequenced using an Illumina MiSeq platform. The circular mitochondrial genome is 19,218 bp long and contains 13 protein-coding genes, 23 tRNA genes, two rRNA genes, and one control region. Notably, there are two trnG-UCC genes and the second gene, located between trnE-UUC and trnI-GAU, has no D-arm structure. The base composition is 56.18% of A + T and 43.82% of G + C. The phylogenetic analysis supports that T. hansoni is grouped into a single clade with T. bernacchii. This study will be a valuable resource for further research on the phylogeny and evolution of the genus Trematomus.
The complete chloroplast genome of the first registered Paeonia Itoh hybrid cv. Hexie in China
Creators: name: Duan, Shuaishuai
name: Dai, Rui
name: Hao, Mingyang
name: Shrestha, Deny K.
name: Dijkwel, Paul P.
name: Gao, Kai
name: Wu, Jiang
name: Fan, Bingyou
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Marine Biology
subject: Plant Biology

description: The first registered Paeonia Itoh hybrid cv. Hexie in China is a naturally occurring intersectional hybrid of Sect. Paeonia and Sect. Moutan. In this study, we sequenced, assembled, and analyzed the complete chloroplast genome of Paeonia Itoh hybrid cv. Hexie. The result showed that the chloroplast genome of Hexie, with a typical circular tetrad structure, is 152,958 bp in length, comprising a large single copy (LSC) region of 84,613 bp, a small single copy (SSC) region of 17,051 bp, and two reverse complementary sequences (IRs) of 25,647 bp. The chloroplast genome encoded 116 genes, including 80 protein-coding genes, 32 tRNA genes, and 4 rRNA genes. Phylogenetic analysis inferred from the shared protein-coding genes showed that the Paeonia Itoh hybrid cv. Hexie had the closest phylogenetic relationship with P. suffruticosa, followed by P. ostii, indicating that P. suffruticosa was its maternal parent. This study provides a molecular resource for phylogenetic and maternal parent studies of Paeonia Itoh hybrid, contributing to a basis for Paeonia Itoh hybrid breeding strategies in the future.
Characterization of the complete chloroplast genome of the rare medicinal plant: Mandragora caulescens (Solanaceae)
Creators: name: Ma, Heqin
name: Zhang, Erdong
name: An, Yajing
name: Wei, Yuqing
name: Zhang, Lei
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Plant Biology

description: In this study, we assembled high-quality chloroplast genomes of Mandragora caulescens through a reference-guided approach using high-throughput Illumina sequencing reads. The resulting chloroplast genome assembly displayed a typical quadripartite structural organization, comprising a large single-copy (LSC) region of 85,233 bp, two inverted repeat (IR) regions of 25,685 bp each, and a small single-copy (SSC) region of 18,207 bp. The chloroplast genome harbored 141 complete genes, and its overall GC content was 38.0%. In maximum-likelihood (ML) and Bayesian inference (BI) trees, the 19 Solanaceae species formed a monophyletic group, dividing into two main clades. M. caulescens and Nicandra physalodes formed a monophyletic group, suggesting a close relationship between the two species. The M. caulescens cp genome presented in this study lays a good foundation for further genetic and genomic studies of the Solanaceae.
The complete mitochondrial genome of a Biwa goby, Gymnogobius isaza (Tanaka, 1916)
Creators: name: Nagao, Nao
name: Hiraoka, Saki
name: Mori, Tsuyoshi
name: Shimizu, Norio
name: Kurabayashi, Atsushi
name: Kambayashi, Chiaki
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified

description: We determined the complete mitochondrial DNA sequence of a Biwa goby, Gymnogobius isaza (Tanaka, 1916) using next-generation sequencing methods. The composition of its mitogenome is the same as that observed in most other vertebrates, comprising of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two control regions. Our molecular phylogenetic analysis confirmed the close phylogenetic relationship between G. isaza and G. petschiliensis. This mitogenome information will be useful for distribution surveys using environmental DNA and the development of conservation strategies for this species.
Rhinolophus hilli Aellen 1973
Creators: name: Cakenberghe, Victor Van
name: Tungaluna, Guy-Crispin Gembu
name: Akawa, Prescott Musaba
name: Seamark, Ernest
name: Verheyen, Erik
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Chiroptera
Rhinolophidae
Rhinolophus
Rhinolophus hilli

description: Rhinolophus hilli Aellen, 1973
Fig. 16 C–D
Rhinolophus hilli Aellen, 1973: 101.
Although the type specimen of Rhinolophus hilli was already collected in 1964, it was only described after the publication of Hayman et al. (1966). The species is only known from two specimens: the type specimen from Uwinka, at the top of a hill at 2300 m, and another specimen from Ruta Bansugera (=Routabansougera) at the bottom of the same hill at 1750 m and 8 km to the northwest (Baeten et al. 1984: 194; Fahr 2013b: 335).
description: Published as part of Cakenberghe, Victor Van, Tungaluna, Guy-Crispin Gembu, Akawa, Prescott Musaba, Seamark, Ernest & Verheyen, Erik, 2017, The bats of the Congo and of Rwanda and Burundi revisited (Mammalia: Chiroptera), pp. 1-327 in European Journal of Taxonomy 382 (382) on page 39, DOI: 10.5852/ejt.2017.382, http://zenodo.org/record/3860077
The complete mitochondrial genome of a ground beetle Synuchus nitidus (Carabidae: Harpalinae: Sphodrini) from South Korea
Creators: name: Kim, Dooyoung
name: Kim, Gyeongmin
name: Shin, Cho Rong
name: Park, Bia
name: Choi, Eun Hwa
name: Hwang, Ui Wook
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified

description: The ground beetle Synuchus nitidus (Motschulsky, 1861) (Carabidae: Harpalinae: Sphodrini) is one of the most common species in the forests of South Korea, which has the potential to be utilized as an environmental indicator. Here, we characterized the complete mitochondrial genome (mitogenome) of S. nitidus, which is the first in the harpaline tribe Sphodrini. Its genome is 16,392 bp in length and composed of 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and an A + T rich region. In addition, we reconstructed a maximum likelihood tree to elucidate the phylogenetic position of Sphodrini among the seven harpaline tribes using nucleotide sequences of the 13 PCGs. The ML tree supported a monophyletic clade of the subfamily Harpalinae and showed a close relationship between Sphodrini and Lebinii with a low bootstrap value. The complete mitogenome of S. nitidus could be helpful for molecular species identification and exploring phylogenetic relationships among carabids.
The complete mitochondrial genome of a jujube geometrid, Sucra jujuba (Lepidoptera: Geometridae) and its phylogenetic analysis
Creators: name: Wei, Xue-Lian
name: Zhai, Ying-Yan
name: Wang, Kai
name: Li, Yang
name: Hong, Bo
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Sucra jujuba Chu, 1979 (Lepidoptera: Geometridae) is a major insect pest in jujube plantation. In this study, we have sequenced the complete mitochondrial genome of S. jujuba. The circular genome was 15,557 bp in length and contained 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and one AT-rich region (GenBank accession no. MZ507574). The nucleotide composition was significantly biased (A, T, C, and G were 41.85%, 39.65%, 10.97%, and 7.53%, respectively) with A + T contents of 81.50%. The Bayesian phylogenetic analysis of the concatenated nucleotide sequences of 13 PCGs from 30 species in the subfamily Ennominae and two outgroup species was performed. The results indicated that S. jujuba was closely related to Amraica recursaria in the subfamily Ennominae.
Complete mitogenome and phylogenetic analysis of Hyalinocerus flavoscutatus Cai and Shen 1998 (Hemiptera: Eurymelinae: Idiocerini)
Creators: name: Zhu, Shijia
name: Guo, Mengrong
name: Liu, Hui
name: Wang, Jiajia
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Computational Biology

description: This study presents the initial sequencing and characterization of the complete mitochondrial genome (mitogenome) of Hyalinocerus flavoscutatus, making the first comprehensive exploration of the mitogenome in the Hyalinocerus. Utilizing next-generation sequencing techniques, we identified a circular DNA molecule spanning 15,307 bp. The mitogenome comprises 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a primary non-coding region. Maximum likelihood phylogenetic evaluation, based on 13 protein-coding genes and two ribosomal RNA genes, robustly supports H. flavoscutatus as the basal group within Idiocerini. This research unveils valuable insights into the mitogenome of H. flavoscutatus and enhances our understanding of phylogenetic placement within the broader context of related tribes.
A eukaryotic platform for the enhancement of Cas nucleases
Creators: name: Ruta, Giulia Vittoria
Publisher: name: Università degli studi di Trento
Year: 2024

description: A large repertoire of CRISPR-Cas systems from bacteria, archaea and phages is available for a large variety of genome editing applications. Nevertheless, a limited number of orthologs have the same editing efficiency as SpCas9 in mammalian cells. Moreover, Cas with reduced molecular size that have been characterized and could give an advantage in delivery, are poorly active in human cells. Directed evolution was proved as a valid approach to identify Cas proteins with altered functions, however unbiased screenings to enhance Cas nucleases have been described only in bacterial cells. Here we develop a fully eukaryotic platform to evolve inefficient Cas proteins toward highly active nucleases. A first step of directed evolution is performed in yeast to isolate enhanced variants by auxotrophic selection; a further screening of the mutants directly in mammalian cells is achieved through a fluorescence activation system. We have first applied the platform to the smallest Type II Cas9 ortholog, CjCas9 (984aa): this double screening for improved activity led to the identification of the enhanced multiple mutant UltraCjCas9. Our variant showed increased efficiency in comparison with CjCas9 WT and the rational designed mutant enCjCas9, while maintaining similar precision editing profile. Several modifications of the screening platform were applied to evolve another small Cas, the hypercompact CasΦ2 from phages: yeast and mammalian cells steps were optimized resulting in a platform suitable for the enhancement of almost inactive Cas nucleases. Our directed evolution approach to enhance Cas nucleases activity in eukaryotic cells enables the improvement of these enzymes directly within the chromatin environment, expanding the toolbox of available genome editors. Moreover, mutations identified applying this screening can give an insight into protein residues or interactions with key roles for efficiency in human cells.
Complete mitochondrial genome of the European common barnacle Perforatus perforatus Bruguière, 1789 (balanomorpha: balanidae)
Creators: name: Jeong, Jun Seong
name: Kim, Hyun Kyong
name: Park, Jeong Sun
name: Hwang, Hee-Seung
name: Kim, Iksoo
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: This study is the first to sequence the complete mitochondrial genome (mitogenome) of Perforatus perforatus Bruguière, 1789 (Balanomorpha: Balanidae). The 15,536-bp long P. perforatus mitogenome contained a typical set of animal mitochondrial genes, along with one control region. The P. perforatus mitogenome had an inverted gene block (trnP-ND4L-ND4-trnH-ND5-trnF) between trnS(gct) and trnT. This inverted gene block had been detected six species in three subfamilies of the Balanidae family (Balaninae, Acastinae and Megabalaninae), but our results show that it is also present in Concavinae, in which P. perforatus is included. The phylogenetic tree based on the concatenated sequences of the 13 protein-coding genes and two rRNA genes showed that P. perforatus is closely associated with Acasta sulcate and Balanus trigonus within Balanidae.
Rhinolophus kahuzi Fahr & Kerbis Peterhans 2013
Creators: name: Cakenberghe, Victor Van
name: Tungaluna, Guy-Crispin Gembu
name: Akawa, Prescott Musaba
name: Seamark, Ernest
name: Verheyen, Erik
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Chiroptera
Rhinolophidae
Rhinolophus
Rhinolophus kahuzi

description: Rhinolophus kahuzi Fahr & Kerbis Peterhans, 2013
Fig. 16 E–F
Rhinolophus kahuzi Fahr & Kerbis Peterhans, 2013: 192, 194.
This recently described species is only known from the type specimen (Kerbis Peterhans et al. 2013: 194).
description: Published as part of Cakenberghe, Victor Van, Tungaluna, Guy-Crispin Gembu, Akawa, Prescott Musaba, Seamark, Ernest & Verheyen, Erik, 2017, The bats of the Congo and of Rwanda and Burundi revisited (Mammalia: Chiroptera), pp. 1-327 in European Journal of Taxonomy 382 (382) on page 39, DOI: 10.5852/ejt.2017.382, http://zenodo.org/record/3860077
title: Towards Understanding and Arguing with Classifiers: Recent Progress
Creators: name: Shao, Xiaoting
name: Rienstra, Tjitze
name: Thimm, Matthias
name: Kersting, Kristian
Publisher: name: Springer
Year: 2024

description: Machine learning and argumentation can potentially greatly benefit from each other. Combining deep classifiers with knowledge expressed in the form of rules and constraints allows one to leverage different forms of abstractions within argumentation mining. Argumentation for machine learning can yield argumentation-based learning methods where the machine and the user argue about the learned model with the common goal of providing results of maximum utility to the user. Unfortunately, both directions are currently rather challenging. For instance, combining deep neural models with logic typically only yields deterministic results, while combining probabilistic models with logic often results in intractable inference. Therefore, we review a novel deep but tractable model for conditional probability distributions that can harness the expressive power of universal function approximators such as neural networks while still maintaining a wide range of tractable inference routines. While this new model has shown appealing performance in classification tasks, humans cannot easily understand the reasons for its decision. Therefore, we also review our recent efforts on how to "argue" with deep models. On synthetic and real data we illustrate how "arguing" with a deep model about its explanations can actually help to revise the model, if it is right for the wrong reasons.
When is the automorphism group of an affine variety nested?
Creators: name: Perepechko, Alexander
name: Regeta, Andriy
Publisher: name: arXiv
Year: 2019
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14R05, 14R20, 14R25

description: For an affine algebraic variety $X$, we study the subgroup $\mathrm{Aut}_{\text{alg}}(X)$ of the group of regular automorphisms $\mathrm{Aut}(X)$ of $X$ generated by all the connected algebraic subgroups. We prove that $\mathrm{Aut}_{\text{alg}}(X)$ is nested, i.e., is a direct limit of algebraic subgroups of $\mathrm{Aut}(X)$, if and only if all the $\mathbb{G}_a$-actions on $X$ commute. Moreover, we describe the structure of such a group $\mathrm{Aut}_{\text{alg}}(X)$.
description: 10 pages; minor corrections
Initial Reports of the Deep Sea Drilling Project - Volume 23
Creators: name: Whitmarsh, R.B.
name: Weser, O.E.
name: Ross, D.A.
name: The Leg 23 Science Party
Publisher: name: U.S. Government Printing Office
Year: 1974
Subjects: Deep Sea Drilling Project
Glomar Challenger
DSDP
Leg 23
Site 219
Site 220
Site 221
Site 222
Site 223
Site 224
Site 225
Site 226
Site 227
Site 228
Site 229
Site 230
Arabian Sea
Red Sea

description: This volume covers Leg 23 of the cruises of the Drilling Vessel Glomar Challenger. The twenty-third cruise of the drilling vessel Glomar Challenger, under contract to the JOIDES Deep Sea Drilling Project, lasted from 8 March to 1 May 1972. The cruise began at Colombo, Sri Lanka (formerly Ceylon) and ended at Djibouti in the French Territory of the Afars and Issas. A total of 12 drill sites was occupied, six each in the Arabian Sea and the Red Sea. At all sites there was an obvious interest in reconstructing the stratigraphic record both from a sedimentological and paleontological viewpoint. An objective of all the sites was also to sample and date one or more reflectors and to relate these to the regional stratigraphy.
Vehicle Allocation Modeling: Optimizing the Logistics Behind a Free-Flow Carsharing in Milan, Italy
Creators: name: Jo, Hanbyul
name: Laras, Azaria
name: Song, Junru
name: Deng, Zhuohao
name: Messa, Federico
name: Ceccarelli, Giulia
name: Gorrini, Andrea
name: Choubassi, Rawad
name: Figuera, Thiago Soares
name: Remondini, Miriam
Publisher: name: Zenodo
Year: 2024
Subjects: Mobility
Carsharing
Transit Accessibility
Demand Modelling
GWR

description: This study examines the demand patterns of Zity, a free-floating electric car-sharing company operating in Milan and identifies temporal and spatial dynamics that influence mobility demand to optimize its reallocation strategy. The findings emphasize the importance of considering specific timeframes for operational activities and highlight the role of residential and working populations as driving factors behind demand. Additionally, the study reveals Zity’s value as a complement to existing transportation options. By understanding these dynamics, stakeholders can optimize resource allocation, enhance accessibility, and promote sustainable shared mobility services in urban areas like Milan.
Multistep schemes for solving backward stochastic differential equations on GPU
Creators: name: Kapllani, Lorenc
name: Teng, Long
Publisher: name: arXiv
Year: 2019
Subjects: subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: FOS: Computer and information sciences
subject: 68U99, 65C30

description: The goal of this work is to parallelize the multistep scheme for the numerical approximation of the backward stochastic differential equations (BSDEs) in order to achieve both, a high accuracy and a reduction of the computation time as well. In the multistep scheme the computations at each grid point are independent and this fact motivates us to select massively parallel GPU computing using CUDA. In our investigations we identify performance bottlenecks and apply appropriate optimization techniques for reducing the computation time, using a uniform domain. Finally, some examples with financial applications are provided to demonstrate the achieved acceleration on GPUs.
description: 24 pages, 4 figures, 10 tables
Rhinolophus landeri Martin 1838
Creators: name: Cakenberghe, Victor Van
name: Tungaluna, Guy-Crispin Gembu
name: Akawa, Prescott Musaba
name: Seamark, Ernest
name: Verheyen, Erik
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Chiroptera
Rhinolophidae
Rhinolophus
Rhinolophus landeri

description: Rhinolophus landeri Martin, 1838
Fig. 17 A–B
Rhinolophus landeri Martin, 1838: 101.
* Rhinolophus landeri lobatus Peters, 1852: 41.
The form lobatus is currently still accepted to be a valid subspecies of R. landeri, occurring from Sudan and Ethiopia, southwards to the former Transvaal (RSA) (Happold 2013g: 340). The nominate subspecies (R. l. landeri) occurs from Gambia to Cameroon and further south to the mouth of the Congo River. This means that the specimens from Banana (RMCA 20746 and 20747) and from 74 km on the Banana-Boma Road (RMCA 20643 to 20653) might be assigned to R. landeri landeri and all other specimens to R. l. lobatus. The distribution map presented by Happold (2013g: 340) suggests there might be a connection between the eastern and western populations in the DRC, but that is not yet supported by evidence. Based on climatic data, the SDM map suggests that there probably might not be a direct connection between the eastern and western populations, but that the latter could be connected to the specimens from Angola, which implies that the specimens from the Kongo Central Province may possibly be assigned to R. l. angolensis Seabra, 1898. To resolve the subspecific status of these specimens, further material from western Gabon, Congo, Angola and DRC is required.
description: Published as part of Cakenberghe, Victor Van, Tungaluna, Guy-Crispin Gembu, Akawa, Prescott Musaba, Seamark, Ernest & Verheyen, Erik, 2017, The bats of the Congo and of Rwanda and Burundi revisited (Mammalia: Chiroptera), pp. 1-327 in European Journal of Taxonomy 382 (382) on page 39, DOI: 10.5852/ejt.2017.382, http://zenodo.org/record/3860077
Rhinolophus ruwenzorii J. Eric Hill 1942
Creators: name: Cakenberghe, Victor Van
name: Tungaluna, Guy-Crispin Gembu
name: Akawa, Prescott Musaba
name: Seamark, Ernest
name: Verheyen, Erik
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Chiroptera
Rhinolophidae
Rhinolophus
Rhinolophus ruwenzorii

description: Rhinolophus ruwenzorii Hill, 1942
Fig. 17 C–D
* Rhinolophus ruwenzorii J. Eric Hill, 1942: 1.
Rhinolophus ruwenzorii has a very restricted distribution of approximately 360 km 2 in the DRC provinces of Nord-Kivu and Ituri (Fahr 2013c: 342). Some authors (e.g., Smith & Hood 1980) consider ruwenzorii to be a subspecies of the west African R. maclaudi, which would result in an extremely disjunct distribution for this species (Baeten et al. 1984). However, Fahr et al. (2002) showed that both forms differ substantially and should be considered as separate species.
description: Published as part of Cakenberghe, Victor Van, Tungaluna, Guy-Crispin Gembu, Akawa, Prescott Musaba, Seamark, Ernest & Verheyen, Erik, 2017, The bats of the Congo and of Rwanda and Burundi revisited (Mammalia: Chiroptera), pp. 1-327 in European Journal of Taxonomy 382 (382) on page 41, DOI: 10.5852/ejt.2017.382, http://zenodo.org/record/3860077
Affine cones over cubic surfaces are flexible in codimension one
Creators: name: Perepechko, Alexander
Publisher: name: arXiv
Year: 2020
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14R20, 14L30

description: Let Y be a smooth del Pezzo surface of degree 3 polarized by a very ample divisor that is not proportional to the anticanonical one. Then the affine cone over Y is flexible in codimension one. Equivalently, such a cone has an open subset with an infinitely transitive action of the special automorphism group on it.
description: 11 pages; added an example of a flexible cone