bluuebunny/crossref_metadata_2025 huggingface dataset:
Low-impact rearing of a commercially valuable shellfish: sea-based container culture of European lobster Homarus gammarus in the United Kingdom
Authors: Clarke LJ , Griffin RA , Domoney E , Smith HCM , Tilsley LJ , Ellis C , Theobald E , Slater M , Scolding J , Cuthbertson S , Jones RE , Johanning L , Daniels CL
Published: May 2023

There is increasing interest in the aquaculture of high-value shellfish species such as European lobster Homarus gammarus. Recent years have seen the development of extractive rearing equipment requiring no additional feed input, including novel sea-based container culture (SBCC) systems designed specifically for lobster mariculture. Here, we report the results of a study which assessed the impact of SBCC systems on the local ecology surrounding a pilot-scale lobster farm (Lobster Grower) integrated into an existing mussel farm in St Austell Bay, Cornwall, UK, across 2 monitoring surveys. We assessed the impact of SBCC systems on the macrobenthic, epifaunal, and mobile species ecology across the study area through benthic grab sampling, drop-down camera, and baited-remote underwater video (BRUV) monitoring. We detected no changes to local sediment composition around SBCC systems, nor changes in macrobenthic diversity or community structure. Increased detritus and biodeposition originating from SBCC systems may be attracting increased epifaunal scavengers, while the presence of the containers and associated infrastructure may act as fish-aggregating devices and provide additional foraging opportunities for mobile fish. These extractive systems may provide low-impact and low-carbon opportunities for coastal mariculture in the face of increased global demand for shellfish.
Interpretable predictions with Convolutional Neural Networks for complex data
Authors:   , Lancia Giacomo
Published: May 2023

Deep Learning (DL) and Artificial Intelligence (AI) are nowadays one of the most used tools to analyze massive and complex data sets.
Despite being very flexible and powerful, Artificial Neural Networks (ANN) are often denoted as "black-box" methods; the causal association between predictions and data is not straightforward and easy to explain.
This thesis is focused on three applications with complex data of 1-D Convolutional Neural Networks (1-D CNN), a specific type of ANN.
Through Explainable Artificial Intelligence (XAI) algorithms, 1-D CNN-based predictions can be made interpretable.
Firstly, we considered the possibility of improving the diagnosis of malignant tumors through the classification of Raman spectra of genomic DNA. Much of the focus is dedicated to discerning different sub-cell lines of the same tumor.
Next, 1-D CNN has been implemented to predict El Niño Southen Oscillation (ENSO) from Zebiack-Cane (ZC) simulated data. We tried to understand what 1-D CNN can learn about these events' physical dynamics when trying to distort the parameters ruling the ocean-atmosphere coupling.
Last, a joint work with the ICU-Department at UMCU for improving the treatment of ICU patients is presented: 1-D CNN was utilized to predict nosocomial ICU-Acquired Infections (ICU-AI) dynamically. Specifically, 1-D CNN has been trained to score the risk of an ICU-AI onset only by analyzing the massive amount of information available from the ICU monitors. The actual ICU-AI prediction has been provided through Survival Analysis techniques after embedding the 1-D CNN analysis into a wider set of traditional explainable variables.
RENCANA AKSI BADAN PENGELOLA KAWASAN GEOPARK KABUPATEN NATUNA DALAM PENGEMBANGAN PARIWISATA MENUJU UNESCO GLOBAL GEOPARK (UGGp)
Authors: Mustajadli Mustajadli , Junriana Junriana
Published: May 2023

The Natuna Islands will be proposed as a UNESCO geopark site through a Letter Of Intent (LOL) that Indonesia will submit to the UN organization at the end of 2019, which is submitted by the Head of the Agency for the Study and Policy Development (BPPK) of the Ministry of Foreign Affairs. The purpose of this study is to see and find out the Action Plan from BPKGN as the authorized agency which is planned in geopark management to improve the status of the Natuna National geopark to become a UNESCO Global Geopark. The research uses qualitative research methods which aim to put more emphasis on the process and meaning by describing something. This research is descriptive, namely to describe the reality of the events studied by using a sampling technique, namely Purposive Sampling. His research is based on the reference of Presidential Regulation which describes 2 planning dimensions, namely implementing guidelines and amenities. From the results of the analysis, it can be concluded from the findings that it can be explained that from the dimensions of the Implementing Guidelines, it is found that there are still many findings from the Planned Action Plan. This is due to the weakness in the budget sector which still relies on CSR funds. Furthermore, in its implementation, the majority still involve district government structural officials so that in managing geoparks there is no focus, in determining the delineation boundary it is not yet specific in each existing geosite, land status is still unclear, because it is still community property, and there is no Masterplan so that it still relies on action plans. regions and the lack of education about geoparks, so there is a need for socialization about the existence of geoparks. Furthermore, in the Amenity dimension, there are still many incomplete ones, only the sandstone geosite is complete, and the majority of cooperation partners still rely on local communities.
MEMOTRET PENERAPAN AKUNTANSI AKAD MUDHARABAH BERDASARKAN PSAK SYARIAH NOMOR 105 PADA KOPERASI SIMPAN PINJAM SYARIAH
Authors: Diah Nurdiwaty  , Hestin Sri Widiawati
Published: May 2023

Aktivitas keuangan syariah di Indonesia semakin berkembang pesat, hal ini dibuktikan dengan banyaknya lembaga keuangan yang berbasis syariah. Dalam prakteknya masih banyak masyarakat yang belum memahami kesesuaian aturan yang digunakan dengan praktek yang diterapkan.  Salah satu produk pembiayaan produktif yang terdapat pada lembaga keuangan syariah adalah mudharabah. PSAK yang digunakan adalah PSAK No. 105. Peneliti mengambil lokasi penelitian di KSPS  BMT UGT Sidogiri cabang Jombang. Permasalahan dalam penelitian ini adalah bagaimana kesesuaian penerapan akad mudharabah di KSPS BMT UGT Sidogiri Cabang Jombang dengan PSAK 105. Adapun pendekatan kualitatif dengan metode deskriptif yang digunakan dalam penelitian ini. Data primer diperoleh dengan wawancara, observasi, dan dokumentasi. Hasil penelitian ini menunjukkan penerapan akuntansi akad mudharabah pada tahun 2018 pada KSPS BMT UGT Sidogiri Cabang Jombang telah sesuai dengan SOP yang ada di KSPS BMT UGT Sidogiri. Untuk  pengakuan, pengukuran, pengungkapan dan bagi hasil telah sesuai dengan PSAK No. 105 tetapi dalam penyajiannya masih belum ada kesesuaian.
ANALISIS METODE FULL COSTING DALAM PENETAPAN HARGA JUAL PRODUK (STUDI UKM JAMUR CRISPY FCK)
Authors: Auliya Dewi Oktari  , Dion Yanuarmawan
Published: May 2023

Metode full costing merupakan metode penentuan harga pokok produksi yang menghitung semua unsur biaya bahan baku, biaya tenaga kerja langsung dan biaya overhead baik yang berperilaku variabel maupun tetap, di mana biaya-biaya tersebut untuk menghitung harga pokok produksi dan harga pokok produksi itulah yang menjadi penentu harga jual produk suatu perusahaan. Harga pokok produksi menurut metode full costing merupakan alat untuk menentukan harga jual yang berdasar pada mark up suatu perusahaan. Penentuan harga jual produk menurut metode full costing dapat menggambarkan harga yang dapat dinilai wajar oleh para konsumen, sehingga dapat memperkirakan keuntungan yang didapat oleh suatu perusahaan. Metode full costing dalam biaya overhead pabrik baik yang berperilaku tetap maupun variabel akan dibebankan kepada produk yang diproduksi atas dasar tarif yang telah ditentukan pada kapasitas normal atau atas dasar overhead pabrik sesungguhnya.

Penetapan harga jual produk merupakan cerminan kualitas produk yang siap untuk dipasarkan secara besar-besaran dan mengharapakan keuntungan yang besar pula. Harga jual produk menjadi hal yang sangat sensitif untuk kelangsungan hidup suatu perusahaan. Harga jual produk yang bagus akan mempengaruhi minat para konsumen, dimana minat tersebut akan menjadi sebuah keuntungan besar bagi suatu perusahaan , jika suatu perusahaan asal dalam menentukan harga jual, maka akan meningkatkan resiko kerugian yang besar pula. Perhitungan metode full costing dalam penetapan harga jual produk adalah salah satu cara perusahan dalam menetapkan harga jual produk yang terbilang wajar dan sesaui dengan ekonomi masyarakat.
Sistem Informasi Keanggotaan Aslab Studi Kasus GI-BEI Polinema PSDKU Di Kota Kediri Berbasis Web
Authors: Satrio Sarwo Utomo  , Ellya Nurfarida  , Kunti Eliyen
Published: May 2023

Aslab GI-BEI is a laboratory assistant under the authority of the accounting study program at the PSDKU POLINEMA campus in Kediri City. GI BEI PSDKU Polinema In the City of Kediri currently does not have an information system to manage membership data in an integrated manner, the management of activity data still uses manual methods, such as archiving in the notebooks of each member of the organization, so that the data collection of registrants and members is not integrated with each other . Membership data that are not integrated with each other will cause a lack of efficiency in managing membership data. So it is necessary to design and build a Web-Based Aslab Membership Information System GI-BEI Polinema Psdku Case Study in Kediri City. The main purpose of developing this membership management information system is to make membership data management more efficient. This membership management information system is built in the Laravel framework based on the PHP programming language and uses the MySQL database. This membership management information system has 2 users, the chairman of the GI-BEI, and the GI-BEI supervisor. Application features consisting of membership management, registrant management, membership detail management, member structure management, and registrant status validation have been tested and succeeded as expected.
Sistem Informasi Geografis Persebaran Lembaga Kursus Bahasa Inggris Berbasis Web (Studi Kasus Kampung Inggris Kecamatan Pare Kabupaten Kediri)
Authors: Ellya Nurfarida  , Yusuf Rehan
Published: May 2023

Kampung Inggris yang terletak di Kecamatan Pare, Kabupaten Kediri, Jawa Timur memiliki puluhan hingga ratusan lembaga kursus yang memberikan pelatihan dan paket belajar yang beragam. Namun hingga saat ini belum memiliki sistem informasi terpusat yang memberikan informasi tentang lembaga-lembaga tersebut. Hal tersebut membuat calon siswa kebingungan dalam memilih sebuah lembaga kursus. Oleh karena itu, perlu dirancang dan dibangun sistem informasi geografis persebaran lembaga kursus bahasa Inggris. Sistem informasi geografis ini dikembangkan menggunakan metode waterfall dan diimplementasikan menggunakan bahasa pemrograman PHP dengan framework Laravel, basis data menggunakan MySQL, dan memanfaatkan Leaflet JS untuk menampilkan peta persebaran lembaga kursus bahasa Inggris yang ada di Kampung Inggris. Hasil dari penelitian ini yaitu sistem informasi geografis persebaran lembaga kursus bahasa Inggris berbasis web dengan fitur yang terdiri dari pengelolaan admin lembaga, pengelolaan data lembaga kursus, pengelolaan data program lembaga, pengelolaan pelaporan ulasan, peta persebaran lembaga kursus, program terbaik, komentar dan rating, pencarian rute, dan pelaporan ulasan. Serta hasil pengujian dari sistem yang telah dibangun memiliki hasil yang sesuai. Hal tersebut dibuktikan dari hasil pengujian black-box, yaitu pengujian terhadap cara kerja program dan pengujian fungsional sistem.
Sistem Informasi Pengelolaan Data Kos Annisa Menggunakan Framework Code Igniter 4
Authors: Fitri Zuyina Nur Azizah  , Adine Pramesti Gitaswari  , Dwiana Maryamas Sofa  , Rexana Widyadhana Agusta  , Zulva Nur Fadila
Published: May 2023

Kos putri Anisa adalah Kos yang terletak di daerah Mojoroto, Kota Kediri dengan fasilitas yang lumayan lengkap dan letaknya strategis. Permasalahan yang sering terjadi adalah penjaga kos kesulitan untuk penambahan data penghuni kos baru dan pengelolaan pembayaran. Hal ini disebabkan keterbatasan informasi yang diperoleh dari masyarakat secara langsung, apalagi mengharuskan si penyewa mencari hunian yang dekat dengan tempat kerja, sekolah atau kampus tempat mereka melaksanakan aktifitas sehari-hari. Sangat banyak sekali permasalahan yang dirasakan saat harus mencari sendiri tempat tinggal yang sesuai dengan selera, baik dilihat dari sisi waktu yang dihabiskan, tenaga, pikiran dan materi yang terkuras mencari hunian yang akan ditempati. Dari segi yang dialami oleh pemilik/penjaga kos itu mereka kesulitan mengelola data penghuni kos karena menggunakan cara manual dengan face to face atau melalui chat, selain itu jika masih menggunakan cara manual, tagihan pembayaran per bulan juga akan menyulitkan penjaga kos karena harus menagih satu per satu.

Oleh karena itu, berdasarkan permasalahan diatas pemanfaatan sistem dan teknolgi informasi secara digital dirasakan mampu memberikan solusi terhadap permasalahan tersebut khususnya di lingkup Kos Putri Anisa. Maka dari itu pengembangan aplikasi berbasis web dalam pengelolaan kos sangat berguna untuk membantu memudahkan dari sisi admin (Pemilik/Penjaga Kos) dan orang yang ingin mencari kos serta sebagai ajang promosi tempat kos agar lebih dikenal banyak orang.
Pengembangan Formulir Pemohon Pada Aplikasi Cetak Form Paspor Otomatis (Sicepot) Berbasis Website Menggunakan Codeigniter 4
Authors: Gitaswari Adine Pramesti , Agusta Rexana Widyadhana , Asti Irfin Sandra
Published: May 2023

Aplikasi cetak form paspor otomatis atau disebut Sicepot merupakan salah satu aplikasi pelayanan yang berada di Kantor Imigrasi Kelas II Non TPI Kediri. Aplikasi berbasis desktop ini memiliki fungsi untuk pengisian formulir para pemohon dengan cara memindai e-KTP pemohon oleh customer service. Aplikasi ini masih memiliki beberapa kekurangan sebagai contoh yaitu e-KTP pemohon tidak dapat dipindai sehingga pemohon harus melakukan pengisian secara manual dan menimbulkan antrean panjang. Permasalahan lainnya yaitu pada aplikasi ini belum tersedia fitur input data bagi pemohon anak. Dengan adanya permasalahan ini penulis mengembangkan Aplikasi Cetak Form Paspor Otomatis (Sicepot) menjadi berbasis website.Tujuan utama dikembangkannya aplikasi ini adalah untuk membantu para pemohon menginputkan data sendiri tanpa harus melalui pegawai imigrasi dan antrean menjadi lebih efisien. Tidak hanya untuk pemohon melainkan hal ini membawa dampak baik untuk pelayanan Kantor Imigrasi Kelas II Non TPI Kediri. Aplikasi ini dikembangkan menggunakan bahasa pemrograman PHP framework Codeigniter versi 4 dan MySQL sebagai basis data. Fitur yang terdapat pada aplikasi ini yaitu melakukan pengisian formulir dan cetak formulir.
Multimodal AI for prediction of distant metastasis in carcinoma patients
Authors: Olatunji Isaac , Cui Feng
Published: May 2023

Metastasis of cancer is directly related to death in almost all cases, however a lot is yet to be understood about this process. Despite advancements in the available radiological investigation techniques, not all cases of Distant Metastasis (DM) are diagnosed at initial clinical presentation. Also, there are currently no standard biomarkers of metastasis. Early, accurate diagnosis of DM is however crucial for clinical decision making, and planning of appropriate management strategies. Previous works have achieved little success in attempts to predict DM from either clinical, genomic, radiology, or histopathology data. In this work we attempt a multimodal approach to predict the presence of DM in cancer patients by combining gene expression data, clinical data and histopathology images. We tested a novel combination of Random Forest (RF) algorithm with an optimization technique for gene selection, and investigated if gene expression pattern in the primary tissues of three cancer types (Bladder Carcinoma, Pancreatic Adenocarcinoma, and Head and Neck Squamous Carcinoma) with DM are similar or different. Gene expression biomarkers of DM identified by our proposed method outperformed Differentially Expressed Genes (DEGs) identified by the DESeq2 software package in the task of predicting presence or absence of DM. Genes involved in DM tend to be more cancer type specific rather than general across all cancers. Our results also indicate that multimodal data is more predictive of metastasis than either of the three unimodal data tested, and genomic data provides the highest contribution by a wide margin. The results re-emphasize the importance for availability of sufficient image data when a weakly supervised training technique is used. Code is made available at: https://github.com/rit-cui-lab/Multimodal-AI-for-Prediction-of-Distant-Metastasis-in-Carcinoma-Patients.
A cytokine-induced spheroid-based in vitro model for studying osteoarthritis pathogenesis
Authors: Scalzone Annachiara , Cerqueni Giorgia , Wang Xiao Nong , Dalgarno Kenny , Mattioli-Belmonte Monica , Ferreira-Duarte Ana M. , Gentile Piergiorgio
Published: May 2023

Given the lack of in vitro models faithfully reproducing the osteoarthritis (OA) disease on-set, this work aimed at manufacturing a reliable and predictive in vitro cytokine-based Articular Cartilage (AC) model to study OA progression. Cell spheroids of primary human fetal chondrocytes (FCs) and h-TERT mesenchymal stem cells differentiated chondrocytes (Y201-C) were analysed in terms of growth kinetics, cells proliferation and apoptosis over 10 days of culture, in healthy condition or in presence of cytokines (interleukin-1ß, −6 and TNF-α). Then, the spheroids were assembled into chondrospheres using a bottom-up strategy, to obtain an in vitro cytokines-induced OA model. The resulting chondrospheres were evaluated for gene expression and anabolic ECM proteins. Compared to the healthy environment, the simulated OA environment induced chondrocyte hyperproliferation and apoptotic pathway, decreased expression of anabolic ECM proteins, and diminished biosynthetic activity, resembling features of early-stage OA. These characteristics were observed for both Y201-C and HC at high and low concentrations of cytokines. Both HC and Y201-C demonstrated the suitability for the manufacturing of a scaffold-free in vitro OA model to facilitate studies into OA pathogenesis and therapeutic strategies. Our approach provides a faithful reproduction of early-stage osteoarthritis, demonstrating the ability of obtaining different disease severity by tuning the concentration of OA-related cytokines. Given the advantages in easy access and more reproducible performance, Y201-C may represent a more favourable source of chondrocytes for establishing more standardized protocols to obtain OA models.
A numerical study of the hemodynamic behavior and gas transport in cardiovascular systems with severe cardiac or cardiopulmonary failure supported by venoarterial extracorporeal membrane oxygenation
Authors: Cui Wenhao , Wang Tianqi , Xu Zhuoming , Liu Jinlong , Simakov Sergey , Liang Fuyou
Published: May 2023

Venoarterial extracorporeal membrane oxygenation (VA-ECMO) has been extensively demonstrated as an effective means of bridge-to-destination in the treatment of patients with severe ventricular failure or cardiopulmonary failure. However, appropriate selection of candidates and management of patients during Extracorporeal membrane oxygenation (ECMO) support remain challenging in clinical practice, due partly to insufficient understanding of the complex influences of extracorporeal membrane oxygenation support on the native cardiovascular system. In addition, questions remain as to how central and peripheral venoarterial extracorporeal membrane oxygenation modalities differ with respect to their hemodynamic impact and effectiveness of compensatory oxygen supply to end-organs. In this work, we developed a computational model to quantitatively address the hemodynamic interaction between the extracorporeal membrane oxygenation and cardiovascular systems and associated gas transport. Model-based numerical simulations were performed for cardiovascular systems with severe cardiac or cardiopulmonary failure and supported by central or peripheral venoarterial extracorporeal membrane oxygenation. Obtained results revealed that: 1) central and peripheral venoarterial extracorporeal membrane oxygenation modalities had a comparable capacity for elevating arterial blood pressure and delivering oxygenated blood to important organs/tissues, but induced differential changes of blood flow waveforms in some arteries; 2) increasing the rotation speed of extracorporeal membrane oxygenation pump (ω) could effectively improve arterial blood oxygenation, with the efficiency being especially high when ω was low and cardiopulmonary failure was severe; 3) blood oxygen indices (i.e., oxygen saturation and partial pressure) monitored at the right radial artery could be taken as surrogates for diagnosing potential hypoxemia in other arteries irrespective of the modality of extracorporeal membrane oxygenation; and 4) Left ventricular (LV) overloading could occur when ω was high, but the threshold of ω for inducing clinically significant left ventricular overloading depended strongly on the residual cardiac function. In summary, the study demonstrated the differential hemodynamic influences while comparable oxygen delivery performance of the central and peripheral venoarterial extracorporeal membrane oxygenation modalities in the management of patients with severe cardiac or cardiopulmonary failure and elucidated how the status of arterial blood oxygenation and severity of left ventricular overloading change in response to variations in ω. These model-based findings may serve as theoretical references for guiding the application of venoarterial extracorporeal membrane oxygenation or interpreting in vivo measurements in clinical practice.
Applications of nanomaterials in endometriosis treatment
Authors: Yuxue Jiang , Ran Sun , Minghui Fan , Minjia Sheng
Published: May 2023

Endometriosis is a common disease of the reproductive system in women of childbearing age with an unclear pathogenesis. Endometriosis mainly manifests as dysmenorrhea, abdominal pain, and infertility. Currently, medical therapy and surgical treatment are usually used for endometriosis treatment. However, due to the high recurrence rate and many complications, it has greatly affected patients’ quality of life. Nanotechnology is a new technology that mainly investigates the characteristics and applications of nanomaterials. To date, nanotechnology has received widespread attention in the field of biomedicine. Nanomaterials can not only be used as drugs to treat endometriosis directly, but also enhance the therapeutic effect of endometriosis by delivering drugs, siRNA, antibodies, vesicles, etc. This review comprehensively discusses nanomaterial-based therapies for endometriosis treatment, such as nanomaterial-based gene therapy, photothermal therapy, immunotherapy, and magnetic hyperthermia, which provides a theoretical reference for the clinical application of nanotechnology in the treatment of endometriosis.
Transit Amplifying Cells (TACs): a still not fully understood cell population
Authors: Cancedda Ranieri , Mastrogiacomo Maddalena
Published: May 2023

Maintenance of tissue homeostasis and tissue regeneration after an insult are essential functions of adult stem cells (SCs). In adult tissues, SCs proliferate at a very slow rate within “stem cell niches”, but, during tissue development and regeneration, before giving rise to differentiated cells, they give rise to multipotent and highly proliferative cells, known as transit-amplifying cells (TACs). Although differences exist in diverse tissues, TACs are not only a transitory phase from SCs to post-mitotic cells, but they also actively control proliferation and number of their ancestor SCs and proliferation and differentiation of their progeny toward tissue specific functional cells. Autocrine signals and negative and positive feedback and feedforward paracrine signals play a major role in these controls. In the present review we will consider the generation and the role played by TACs during development and regeneration of lining epithelia characterized by a high turnover including epidermis and hair follicles, ocular epithelial surfaces, and intestinal mucosa. A comparison between these different tissues will be made. There are some genes and molecular pathways whose expression and activation are common to most TACs regardless their tissue of origin. These include, among others, Wnt, Notch, Hedgehog and BMP pathways. However, the response to these molecular signals can vary in TACs of different tissues. Secondly, we will consider cultured cells derived from tissues of mesodermal origin and widely adopted for cell therapy treatments. These include mesenchymal stem cells and dedifferentiated chondrocytes. The possible correlation between cell dedifferentiation and reversion to a transit amplifying cell stage will be discussed.
Bioinspired skin towards next-generation rehabilitation medicine
Authors: Wang Zhenghui , Xiao Chen , Roy Mridul , Yuan Zhiyao , Zhao Lingyu , Liu Yanting , Guo Xuejun , Lu Ping
Published: May 2023

The rapid progress of interdisciplinary researches from materials science, biotechnologies, biomedical engineering, and medicine, have resulted in the emerging of bioinspired skins for various fantasticating applications. Bioinspired skin is highly promising in the application of rehabilitation medicine owing to their advantages, including personalization, excellent biocompatibility, multi-functionality, easy maintainability and wearability, and mass production. Therefore, this review presents the recent progress of bioinspired skin towards next-generation rehabilitation medicine. The classification is first briefly introduced. Then, various applications of bioinspired skins in the field of rehabilitation medicine at home and abroad are discussed in detail. Last, we provide the challenges we are facing now, and propose the next research directions.
Neural induction drives body axis formation during embryogenesis, but a neural induction-like process drives tumorigenesis in postnatal animals
Authors: Cao Ying
Published: May 2023

Characterization of cancer cells and neural stem cells indicates that tumorigenicity and pluripotency are coupled cell properties determined by neural stemness, and tumorigenesis represents a process of progressive loss of original cell identity and gain of neural stemness. This reminds of a most fundamental process required for the development of the nervous system and body axis during embryogenesis, i.e., embryonic neural induction. Neural induction is that, in response to extracellular signals that are secreted by the Spemann-Mangold organizer in amphibians or the node in mammals and inhibit epidermal fate in ectoderm, the ectodermal cells lose their epidermal fate and assume the neural default fate and consequently, turn into neuroectodermal cells. They further differentiate into the nervous system and also some non-neural cells via interaction with adjacent tissues. Failure in neural induction leads to failure of embryogenesis, and ectopic neural induction due to ectopic organizer or node activity or activation of embryonic neural genes causes a formation of secondary body axis or a conjoined twin. During tumorigenesis, cells progressively lose their original cell identity and gain of neural stemness, and consequently, gain of tumorigenicity and pluripotency, due to various intra-/extracellular insults in cells of a postnatal animal. Tumorigenic cells can be induced to differentiation into normal cells and integrate into normal embryonic development within an embryo. However, they form tumors and cannot integrate into animal tissues/organs in a postnatal animal because of lack of embryonic inducing signals. Combination of studies of developmental and cancer biology indicates that neural induction drives embryogenesis in gastrulating embryos but a similar process drives tumorigenesis in a postnatal animal. Tumorigenicity is by nature the manifestation of aberrant occurrence of pluripotent state in a postnatal animal. Pluripotency and tumorigenicity are both but different manifestations of neural stemness in pre- and postnatal stages of animal life, respectively. Based on these findings, I discuss about some confusion in cancer research, propose to distinguish the causality and associations and discriminate causal and supporting factors involved in tumorigenesis, and suggest revisiting the focus of cancer research.
Lampreys and spinal cord regeneration: “a very special claim on the interest of zoologists,” 1830s-present
Authors: Maxson Jones Kathryn , Morgan Jennifer R.
Published: May 2023

Employing history of science methods, including analyses of the scientific literature, archival documents, and interviews with scientists, this paper presents a history of lampreys in neurobiology from the 1830s to the present. We emphasize the lamprey’s roles in helping to elucidate spinal cord regeneration mechanisms. Two attributes have long perpetuated studies of lampreys in neurobiology. First, they possess large neurons, including multiple classes of stereotypically located, ‘identified’ giant neurons in the brain, which project their large axons into the spinal cord. These giant neurons and their axonal fibers have facilitated electrophysiological recordings and imaging across biological scales, ranging from molecular to circuit-level analyses of nervous system structures and functions and including their roles in behavioral output. Second, lampreys have long been considered amongst the most basal extant vertebrates on the planet, so they have facilitated comparative studies pointing to conserved and derived characteristics of vertebrate nervous systems. These features attracted neurologists and zoologists to studies of lampreys between the 1830s and 1930s. But, the same two attributes also facilitated the rise of the lamprey in neural regeneration research after 1959, when biologists first wrote about the spontaneous, robust regeneration of some identified CNS axons in larvae after spinal cord injuries, coupled with recovery of normal swimming. Not only did large neurons promote fresh insights in the field, enabling studies incorporating multiple scales with existing and new technologies. But investigators also were able to attach a broad scope of relevance to their studies, interpreting them as suggesting conserved features of successful, and sometimes even unsuccessful, CNS regeneration. Lamprey research demonstrated that functional recovery takes place without the reformation of the original neuronal connections, for instance, by way of imperfect axonal regrowth and compensatory plasticity. Moreover, research performed in the lamprey model revealed that factors intrinsic to neurons are integral in promoting or hindering regeneration. As this work has helped illuminate why basal vertebrates accomplish CNS regeneration so well, whereas mammals do it so poorly, this history presents a case study in how biological and medical value have been, and could continue to be, gleaned from a non-traditional model organism for which molecular tools have been developed only relatively recently.
Loss of the matrix metalloproteinase-10 causes premature features of aging in satellite cells
Authors: Bobadilla Muñoz Miriam , Orbe Josune , Abizanda Gloria , Machado Florencio J. D. , Vilas Amaia , Ullate-Agote Asier , Extramiana Leire , Baraibar Churio Arantxa , Aranguren Xabier L. , Cantero Gloria , Sáinz Amillo Neira , Rodríguez José Antonio , Ramos García Luis , Romero Riojas Juan Pablo , Vallejo-Illarramendi Ainara , Paradas Carmen , López de Munain Adolfo , Páramo José Antonio , Prósper Felipe , Pérez-Ruiz Ana
Published: May 2023

Aged muscles accumulate satellite cells with a striking decline response to damage. Although intrinsic defects in satellite cells themselves are the major contributors to aging-associated stem cell dysfunction, increasing evidence suggests that changes in the muscle-stem cell local microenvironment also contribute to aging. Here, we demonstrate that loss of the matrix metalloproteinase-10 (MMP-10) in young mice alters the composition of the muscle extracellular matrix (ECM), and specifically disrupts the extracellular matrix of the satellite cell niche. This situation causes premature features of aging in the satellite cells, contributing to their functional decline and a predisposition to enter senescence under proliferative pressure. Similarly, reduction of MMP-10 levels in young satellite cells from wild type animals induces a senescence response, while addition of the protease delays this program. Significantly, the effect of MMP-10 on satellite cell aging can be extended to another context of muscle wasting, muscular dystrophy. Systemic treatment of mdx dystrophic mice with MMP-10 prevents the muscle deterioration phenotype and reduces cellular damage in the satellite cells, which are normally under replicative pressure. Most importantly, MMP-10 conserves its protective effect in the satellite cell-derived myoblasts isolated from a Duchenne muscular dystrophy patient by decreasing the accumulation of damaged DNA. Hence, MMP-10 provides a previously unrecognized therapeutic opportunity to delay satellite cell aging and overcome satellite cell dysfunction in dystrophic muscles.
Regulation of hematopoietic stem cells differentiation, self-renewal, and quiescence through the mTOR signaling pathway
Authors: Ling Bai , Xu Yunyang , Qian Siyuan , Xiang Ze , Xuan Shihai , Wu Jian
Published: May 2023

Hematopoietic stem cells (HSCs) are important for the hematopoietic system because they can self-renew to increase their number and differentiate into all the blood cells. At a steady state, most of the HSCs remain in quiescence to preserve their capacities and protect themselves from damage and exhaustive stress. However, when there are some emergencies, HSCs are activated to start their self-renewal and differentiation. The mTOR signaling pathway has been shown as an important signaling pathway that can regulate the differentiation, self-renewal, and quiescence of HSCs, and many types of molecules can regulate HSCs’ these three potentials by influencing the mTOR signaling pathway. Here we review how mTOR signaling pathway regulates HSCs three potentials, and introduce some molecules that can work as the regulator of HSCs’ these potentials through the mTOR signaling. Finally, we outline the clinical significance of studying the regulation of HSCs three potentials through the mTOR signaling pathway and make some predictions.
Polycrystal Li2ZnTi3O8/C anode with lotus seedpod structure for high-performance lithium storage
Authors: Chen Zhanjun , Wang Tao , Liu Meihuang , Duan Panyu , Xiong Feng , Zhou Yang , Yan Zhenyu , Yang Wei , Chen Han , Yang Zhenyu , Li Chao
Published: May 2023

Lotus-seedpod structured Li2ZnTi3O8/C (P-LZTO) microspheres obtained by the molten salt method are reported for the first time. The received phase-pure Li2ZnTi3O8 nanoparticles are inserted into the carbon matrix homogeneously to form a Lotus-seedpod structure, as confirmed by the morphological and structural measurements. As the anode for lithium-ion batteries, the P-LZTO material demonstrates excellent electrochemical performance with a high rate capacity of 193.2 mAh g-1 at 5 A g-1 and long-term cyclic stability up to 300 cycles at 1 A g-1. After even 300 cyclings, the P-LZTO particles can maintain their morphological and structural integrity. The superior electrochemical performances have arisen from the unique structure where the polycrystalline structure is beneficial for shorting the lithium-ion diffusion path, while the well-encapsulated carbon matrix can not only enhance the electronic conductivity of the composite but also alleviate the stress anisotropy during lithiation/delithiation process, leading to well-preserved particles.
Analysis of aptamer-target binding and molecular mechanisms by thermofluorimetric analysis and molecular dynamics simulation
Authors: Zhang Hong-Li , Lv Cong , Li Zi-Hua , Jiang Song , Cai Dan , Liu Shao-Song , Wang Ting , Zhang Kun-He
Published: May 2023

Introduction: Aptamers are valuable for bioassays, but aptamer-target binding is susceptible to reaction conditions. In this study, we combined thermofluorimetric analysis (TFA) and molecular dynamics (MD) simulations to optimize aptamer-target binding, explore underlying mechanisms and select preferred aptamer.

Methods: Alpha-fetoprotein (AFP) aptamer AP273 (as the model) was incubated with AFP under various experimental conditions, and melting curves were measured in a real-time PCR system to select the optimal binding conditions. The intermolecular interactions of AP273-AFP were analysed by MD simulations with these conditions to reveal the underlying mechanisms. A comparative study between AP273 and control aptamer AP-L3-4 was performed to validate the value of combined TFA and MD simulation in selecting preferred aptamers.

Results: The optimal aptamer concentration and buffer system were easily determined from the dF/dT peak characteristics and the melting temperature (Tm) values on the melting curves of related TFA experiments, respectively. A high Tm value was found in TFA experiments performed in buffer systems with low metal ion strength. The molecular docking and MD simulation analyses revealed the underlying mechanisms of the TFA results, i.e., the binding force and stability of AP273 to AFP were affected by the number of binding sites, frequency and distance of hydrogen bonds, and binding free energies; these factors varied in different buffer and metal ion conditions. The comparative study showed that AP273 was superior to the homologous aptamer AP-L3-4.

Conclusion: Combining TFA and MD simulation is efficient for optimizing the reaction conditions, exploring underlying mechanisms, and selecting aptamers in aptamer-target bioassays.
Bacterial pathogens in pediatric appendicitis: a comprehensive retrospective study
Authors: Felber Julia , Gross Benedikt , Rahrisch Arend , Waltersbacher Eric , Trips Evelyn , Schröttner Percy , Fitze Guido , Schultz Jurek
Published: May 2023

Background

Appendicitis is a frequent condition, with peak incidences in the second decade of life. Its pathogenesis is under debate, but bacterial infections are crucial, and antibiotic treatment remains essential. Rare bacteria are accused of causing complications, and various calculated antibiotics are propagated, yet there is no comprehensive microbiological analysis of pediatric appendicitis. Here we review different pre-analytic pathways, identify rare and common bacterial pathogens and their antibiotic resistances, correlate clinical courses, and evaluate standard calculated antibiotics in a large pediatric cohort.

Method

We reviewed 579 patient records and microbiological results of intraoperative swabs in standard Amies agar media or fluid samples after appendectomies for appendicitis between May 2011 and April 2019. Bacteria were cultured and identified via VITEK 2 or MALDI-TOF MS. Minimal inhibitory concentrations were reevaluated according to EUCAST 2022. Results were correlated to clinical courses.

Results

Of 579 analyzed patients, in 372 patients we got 1330 bacterial growths with resistograms. 1259 times, bacteria could be identified to species level. 102 different bacteria could be cultivated. 49% of catarrhal and 52% of phlegmonous appendices resulted in bacterial growth. In gangrenous appendicitis, only 38% remained sterile, while this number reduced to 4% after perforation. Many fluid samples remained sterile even when unsterile swabs had been taken simultaneously. 40 common enteral genera were responsible for 76.5% of bacterial identifications in 96.8% of patients. However, 69 rare bacteria were found in 187 patients without specifically elevated risk for complications.

Conclusion

Amies agar gel swabs performed superior to fluid samples and should be a standard in appendectomies. Even catarrhal appendices were only sterile in 51%, which is interesting in view of a possible viral cause. According to our resistograms, the best in vitro antibiotic was imipenem with 88.4% susceptible strains, followed by piperacillin-tazobactam, cefuroxime with metronidazole, and ampicillin-sulbactam to which only 21.6% of bacteria were susceptible. Bacterial growths and higher resistances correlate to an elevated risk of complications. Rare bacteria are found in many patients, but there is no specific consequence regarding antibiotic susceptibility, clinical course, or complications. Prospective, comprehensive studies are needed to further elicit pediatric appendicitis microbiology and antibiotic treatment.
Understanding clinical characteristics influencing adverse outcomes of Omicron infection: a retrospective study with propensity score matching from a Fangcang hospital
Authors: Geng Yanxia , Nie Qingfang , Liu Feifei , Pei Yinghao , Chen Qiuhua , Zhang Haidong , Zhou Haiqi , Zhou Jiang , Jiang Hua , Xu Jing
Published: May 2023

Objectives

The epidemic of coronavirus disease 2019 (COVID-19) is causing global health concerns. The aim of this study was to evaluate influence of clinical characteristics on outcomes during the Omicron outbreak.

Methods

A total of 25182 hospitalized patients were enrolled, including 39 severe patients and 25143 non-severe patients. Propensity score matching (PSM) was applied to balance the baseline characteristics. Logistic regression analysis was used to assess the risk of severe disease, as well as the risk of prolonged viral shedding time (VST) and increased length of hospital stay (LOS).

Results

Before PSM, patients in the severe group were older, had higher symptom scores, and had a higher proportion of comorbidities (p<0.001). After PSM, there were no significant differences in age, gender, symptom score and comorbidities between severe (n=39) and non-severe (n=156) patients. Symptoms of fever (OR=6.358, 95%CI 1.748-23.119, p=0.005) and diarrhea (OR=6.523, 95%CI 1.061-40.110, p=0.043) were independent risk factors for development of severe disease. In non-severe patients, higher symptom score was associated with prolonged VST (OR=1.056, 95% CI 1.000-1.115, p=0.049) and LOS (OR=1.128, 95% CI 1.039-1.225, p=0.004); older age was associated with longer LOS (OR=1.045, 95% CI 1.007-1.084, p=0.020).

Conclusion

The overall condition of the Shanghai Omicron epidemic was relatively mild. Potential risk factors for fever, diarrhea, and higher symptom score can help clinicians to predict clinical outcomes in COVID‐19 patients.
Innate immunity in rickettsial infections
Authors: Londoño Andrés F. , Scorpio Diana G. , Dumler J. Stephen
Published: May 2023

Rickettsial agents are a diverse group of alpha-proteobacteria within the order Rickettsiales, which possesses two families with human pathogens, Rickettsiaceae and Anaplasmataceae. These obligate intracellular bacteria are most frequently transmitted by arthropod vectors, a first step in the pathogens’ avoidance of host cell defenses. Considerable study of the immune responses to infection and those that result in protective immunity have been conducted. Less study has focused on the initial events and mechanism by which these bacteria avoid the innate immune responses of the hosts to survive within and propagate from host cells. By evaluating the major mechanisms of evading innate immunity, a range of similarities among these bacteria become apparent, including mechanisms to escape initial destruction in phagolysosomes of professional phagocytes, those that dampen the responses of innate immune cells or subvert signaling and recognition pathways related to apoptosis, autophagy, proinflammatory responses, and mechanisms by which these microbes attach to and enter cells or those molecules that trigger the host responses. To illustrate these principles, this review will focus on two common rickettsial agents that occur globally, Rickettsia species and Anaplasma phagocytophilum.
Evaluating machine-generated explanations: a “Scorecard” method for XAI measurement science
Authors: Hoffman Robert R. , Jalaeian Mohammadreza , Tate Connor , Klein Gary , Mueller Shane T.
Published: May 2023

Introduction

Many Explainable AI (XAI) systems provide explanations that are just clues or hints about the computational models-Such things as feature lists, decision trees, or saliency images. However, a user might want answers to deeper questions such as How does it work?, Why did it do that instead of something else? What things can it get wrong? How might XAI system developers evaluate existing XAI systems with regard to the depth of support they provide for the user's sensemaking? How might XAI system developers shape new XAI systems so as to support the user's sensemaking? What might be a useful conceptual terminology to assist developers in approaching this challenge?

Method

Based on cognitive theory, a scale was developed reflecting depth of explanation, that is, the degree to which explanations support the user's sensemaking. The seven levels of this scale form the Explanation Scorecard.

Results and discussion

The Scorecard was utilized in an analysis of recent literature, showing that many systems still present low-level explanations. The Scorecard can be used by developers to conceptualize how they might extend their machine-generated explanations to support the user in developing a mental model that instills appropriate trust and reliance. The article concludes with recommendations for how XAI systems can be improved with regard to the cognitive considerations, and recommendations regarding the manner in which results on the evaluation of XAI systems are reported.
Percutaneous snare-retrieval of intracardiac thrombus under fluoroscopic and transesophageal echocardiography guidance: case report and systematic review
Authors: Zhou Huaji , Wang Bing , Pan Jun , Qiu Chenyang , Yu Xinyu , He Yangyan , Zhu Qianqian , Yu Lei , Wu Ziheng , Li Donglin , Zhang Hongkun
Published: May 2023

Intracardiac foreign bodies (IFB) are rare clinical conditions. There are now several reports on the percutaneous retrieval of IFB under fluoroscopy. However, some IFB are not radiopaque, and retrieval requires combined fluoroscopic and ultrasound guidance. We report the case of a bedridden 23-year-old male patient with T-lymphoblastic lymphoma treated with long-term chemotherapy. Ultrasound examination diagnosed a huge thrombus in the right atrium near the opening of the inferior vena cava which affected the patency of his PICC line. Ten days of anticoagulant therapy did not modify the thrombus size. Open heart surgery was not feasible because of the patient clinical condition. Snare-capture of the non-opaque thrombus was done from the femoral vein under fluoroscopic and ultrasound guidance with excellent outcomes. We also present a systematic review of IFB. We found out that percutaneous removal of IFBs is a safe and effective procedure. The youngest patient who received percutaneous IFB retrieval was 10 days old and weighed only 800 g, while the oldest patient was 70 years old. Port catheters (43.5%) and PICC lines (42.3%) were the most commonly found IFBs. Snare catheters and forceps were the most commonly used instruments.
Diagnostics of atherosclerosis: Overview of the existing methods
Authors: Poznyak Anastasia V. , Sukhorukov Vasily N. , Eremin Ilya I. , Nadelyaeva Irina I. , Orekhov Alexander N.
Published: May 2023

Atherosclerosis was and remains an extremely common and serious health problem. Since the elderly are most at risk of cardiovascular risk, and the average life expectancy is increasing, the spread of atherosclerosis and its consequences increases as well. One of the features of atherosclerosis is its asymptomaticity. This factor makes it difficult to make a timely diagnosis. This entails the lack of timely treatment and even prevention. To date, in the arsenal of physicians, there is only a limited set of methods to suspect and fully diagnose atherosclerosis. In this review, we have tried to briefly describe the most common and effective methods for diagnosing atherosclerosis.