bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome analysis reveals an Atoh1b-dependent gene set downstream of Dlx3b/4b during early inner ear development in zebrafish
Authors: Ezhkova Diana , Schwarzer Simone , Spieß Sandra , Geffarth Michaela , Machate Anja , Zöller Daniela , Stucke Johanna , Alexopoulou Dimitra , Lesche Mathias , Dahl Andreas , Hans Stefan 
Published: June 2023

ABSTRACTThe vertebrate inner ear is the sensory organ mediating hearing and balance. The entire organ develops from the otic placode, which itself originates from the otic-epibranchial progenitor domain (OEPD). Multiple studies in various species have shown the importance of the forkhead-box and distal-less homeodomain transcription factor families for OEPD and subsequent otic placode formation. However, the transcriptional networks downstream of these factors are only beginning to be understood. Using transcriptome analysis, we here reveal numerous genes regulated by the distal-less homeodomain transcription factors Dlx3b and Dlx4b (Dlx3b/4b). We identify known and novel transcripts displaying widespread OEPD expression in a Dlx3b/4b-dependent manner. Some genes, with a known OEPD expression in other vertebrate species, might be members of a presumptive vertebrate core module required for proper otic development. Moreover, we identify genes controlling early-born sensory hair cell formation as well as regulating biomineral tissue development, both consistent with defective sensory hair cell and otolith formation observed in dlx3b/4b mutants. Finally, we show that ectopic Atoh1b expression can rescue early sensorigenesis even in the absence of Dlx3b/4b. Taken together, our data will help to unravel the gene regulatory network underlying early inner ear development and provide insights into the molecular control of vertebrate inner ear formation to restore hearing loss in humans ultimately.
Molecular mechanism of synovial joint site specification and induction in developing vertebrate limbs
Authors: Yadav Upendra S. , Biswas Tathagata , Singh Pratik N. , Gupta Pankaj , Chakraborty Soura , Delgado Irene , Zafar Hamim , Capellini Terence D. , Torres Miguel , Bandyopadhyay Amitabha 
Published: June 2023

ABSTRACT
The vertebrate appendage comprises three primary segments, the stylopod, zeugopod and autopod, each separated by joints. The molecular mechanisms governing the specification of joint sites, which define segment lengths and thereby limb architecture, remain largely unknown. Existing literature suggests that reciprocal gradients of retinoic acid (RA) and fibroblast growth factor (FGF) signaling define the expression domains of the putative segment markers Meis1, Hoxa11 and Hoxa13. Barx1 is expressed in the presumptive joint sites. Our data demonstrate that RA-FGF signaling gradients define the expression domain of Barx1 in the first presumptive joint site. When misexpressed, Barx1 induces ectopic interzone-like structures, and its loss of function partially blocks interzone development. Simultaneous perturbations of RA-FGF signaling gradients result in predictable shifts of Barx1 expression domains along the proximo-distal axis and, consequently, in the formation of repositioned joints. Our data suggest that during early limb bud development in chick, Meis1 and Hoxa11 expression domains are overlapping, whereas the Barx1 expression domain resides within the Hoxa11 expression domain. However, once the interzone is formed, the expression domains are refined and the Barx1 expression domain becomes congruent with the border of these two putative segment markers.
Strategies of epithelial repair: Modulation of stem cell and transit amplifying cell proliferation
Authors: Lehrer Michael S. , Sun Tung-Tien , Lavker Robert M. 
Published: June 2023

ABSTRACT
Using double labeling techniques, we studied the replication of corneal epithelial stem cells that reside exclusively in the limbal zone, and their progeny transit amplifying cells. We show that corneal epithelial stem cells can be induced to enter DNA synthesis by wounding and by TPA. We demonstrate the existence of a hierarchy of TA cells; those of peripheral cornea undergo at least two rounds of DNA synthesis before they become post-mitotic, whereas those of central cornea are capable of only one round of division. However, the cell cycle time of these TA cells can be shortened and the number of times these TA cells can replicate is increased in response to wounding. These results thus demonstrate three strategies of epithelial repair: (i) stem cell replication, (ii) the unleashing of additional rounds of cell proliferation that remain as an untapped reserve under normal circumstances, and (iii) enhancement of TA cell proliferation via a shortening of the cycling time.
Intracellular trafficking of the vacuolar H+-ATPase accessory subunit Ac45
Authors: Jansen Eric J. R. , Holthuis Joost C. M. , McGrouther Collette , Burbach J. Peter H. , Martens Gerard J. M. 
Published: June 2023

ABSTRACT
Ac45 is a type I transmembrane protein associated with vacuolar H+-ATPase, a proton pump mediating the acidification of multiple intracellular organelles. In this study, we examined the intracellular routing of Ac45 in transfected CV-1 fibroblasts. Steady state immunolabeling showed that Ac45 is located on the plasma membrane and in a vacuolar compartment in the juxtanuclear region. Antibody internalization experiments revealed that Ac45 is rapidly retrieved from the cell surface and is targeted to the vacuolar structures. The 26-residue cytoplasmic tail of Ac45 was intrinsically capable of mediating endocytosis of the cell surface protein Tac, indicating that the tail contains an autonomous internalization signal. Immunolocalization studies on cells expressing carboxy-terminally truncated Ac45 mutants showed the presence of essential routing information in the membrane-distal region of the cytoplasmic tail. Further mutational analysis of this region, which lacks the recognized tyrosine- or di-leucine-based sorting motifs, suggested that multiple sites rather than a short linear sequence are responsible for the internalization. Collectively, our results indicate that the cytoplasmic tail of Ac45 contains autonomous targeting information distinct from previously described routing determinants.
The role of the Ran GTPase in nuclear assembly and DNA replication: Characterisation of the effects of Ran mutants
Authors: Hughes Mike , Zhang Chuanmao , Avis Johanna M. , Hutchison Christopher J. , Clarke Paul R. 
Published: June 2023

ABSTRACTThe Ran GTPase plays a critical role in nucleocytoplasmic transport and has been implicated in the maintenance of nuclear structure and cell cycle control. Here, we have investigated its role in nuclear assembly and DNA replication using recombinant wild-type and mutant Ran proteins added to a cell-free system of Xenopus egg extracts. RanQ69L and RanT24N prevent lamina assembly, PCNA accumulation and DNA replication. These effects may be due to the disruption of nucleocytoplasmic transport, since both mutants inhibit nuclear import of a protein carrying a nuclear localisation signal (NLS). RanQ69L, which is deficient in GTPase activity, sequesters importins in stable complexes that are unable to support the docking of NLS-proteins at the nuclear pore complex (NPC). RanT24N, in contrast to wild-type Ran-GDP, interacts only weakly with importin α and nucleoporins, and not at all with the import factor p10, consistent with its poor activity in nuclear import. However, RanT24N does interact stably with importin β, Ran binding protein 1 and RCC1, an exchange factor for Ran. We show that Ran-GDP is essential for proper nuclear assembly and DNA replication, the requirement being primarily before the initiation of DNA replication. Ran-GDP therefore mediates the active transport of necessary factors or otherwise controls the onset of S-phase in this system.
VE-cadherin and desmoplakin are assembled into dermal microvascular endothelial intercellular junctions: A pivotal role for plakoglobin in the recruitment of desmoplakin to intercellular junctions
Authors: Kowalczyk Andrew P. , Navarro Pilar , Dejana Elisabetta , Bornslaeger Elayne A. , Green Kathleen J. , Kopp Daniel S. , Borgwardt Jeffrey E. 
Published: June 2023

ABSTRACT
Vascular endothelial cells assemble adhesive intercellular junctions comprising a unique cadherin, VE-cadherin, which is coupled to the actin cytoskeleton through cytoplasmic interactions with plakoglobin, β-catenin and α-catenin. However, the potential linkage between VE-cadherin and the vimentin intermediate filament cytoskeleton is not well characterized. Recent evidence indicates that lymphatic and vascular endothelial cells express desmoplakin, a cytoplasmic desmosomal protein that attaches intermediate filaments to the plasma membrane in epithelial cells. In the present study, desmoplakin was localized to intercellular junctions in human dermal microvascular endothelial cells. To determine if VE-cadherin could associate with desmoplakin, VE-cadherin, plakoglobin, and a desmoplakin amino-terminal polypeptide (DP-NTP) were co-expressed in L-cell fibroblasts. In the presence of VE-cadherin, both plakoglobin and DP-NTP were recruited to cell-cell borders. Interestingly, β-catenin could not substitute for plakoglobin in the recruitment of DP-NTP to cell borders, and DP-NTP bound to plakoglobin but not β-catenin in the yeast two-hybrid system. In addition, DP-NTP colocalized at cell-cell borders with α-catenin in the L-cell lines, and endogenous desmoplakin and α-catenin colocalized in cultured dermal microvascular endothelial cells. This is in striking contrast to epithelial cells, where desmoplakin and α-catenin are restricted to desmosomes and adherens junctions, respectively. These results suggest that endothelial cells assemble unique junctional complexes that couple VE-cadherin to both the actin and intermediate filament cytoskeleton.
Open Science Training in TRIPLE
Authors: Provost Lottie , Di Donato Francesca , Tóth-Czifra Erzsébet , Dumouchel Suzanne , Blotière Emilie , Chen Yin 
Published: June 2023

This case study focuses on the online training activities on Open Science delivered within the H2020 project Transforming Research through Innovative Practices for Linked Interdisciplinary Exploration (TRIPLE, Grant Agreement 863420). The project is dedicated to building a discovery platform for the Social Sciences and Humanities (SSH) and is committed to promoting and supporting the uptake of Open Science within research practices. In order to address SSH research and training communities’ needs for enhanced competencies on Open Science and for stronger support in the Findable, Accessible, Interoperable, Reusable (FAIR) management of digital training materials, two reusable outputs were produced. The work carried out is presented as a novel approach to tackle the issues related to FAIRifying research and training practices and to create training resources whose reusability and relevance reaches beyond the project lifetime and framework. The case study presents the methods by which the results were produced so as to encourage and enable their future adaptation and reuse. The TRIPLE Open Science training series (result 1) targets SSH researchers, research support personnel and infrastructure developers in need of practical tools and specific skills to integrate Open Science practices in their workflows. The training series provides 12 competence-oriented online training events in Open Access whose training materials are available as Open Educational Resources (OER). The TRIPLE Training Toolkit (result 2) targets training organisers and research performing organisations who wish to design and manage training events as OERs and increase the impact of their training following good practice. The Toolkit is an easily reproducible workflow designed to help trainers minimise the time they spend in managing training events following FAIR practice. The workflow follows a FAIR-by-design method to address the frequent findability and reusability issues related to the management of digital training resources.
How to diagnose, treat and prevent from hospital-acquired and ventilator-associated pneumonia?
Authors: Babiak Rafał , Bajak Karolina , Czuchryta Paulina , Domańska Anastazja , Gawęda Agnieszka , Grabek Agata , Rutkowska Julia , Rzęsa-Tokarczyk Żaneta , Skorek Klaudia , Urbańczyk Agnieszka 
Published: June 2023

Introduction and purpose: hospital-acquired pneumonia and ventilator-associated pneumonia are common risk factors for morbidity and mortality. They are difficult to diagnose and treat due to the large number of factors that may contribute to the deterioration of the clinical condition of critically ill patients. In this article, the authors summarize the diagnosis, treatment and prevention of these diseases based on current guidelines, the latest research and other scientific works.
Material and metod: sources available in the PubMed database were analyzed using the following keywords: "pneumonia", "hospital-acquired pneumonia", "ventilator-associated pneumonia", "HAP", "VAP", publications related to the subject of the work were selected and used.
Conclusion: A patient with HAP or VAP should undergo non-invasive testing such as blood and sputum cultures and nasal swabs to isolate the pathogen responsible for the infection and to adjust antibiotic therapy. The procalcitonin level can be used in conjunction with the clinical assessment to assess the adjustment of the duration of treatment. Patients with HAP or VAP who are immunocompromised, haemodynamically unstable, or cannot be sampled from the lower respiratory tract for microbiological testing should be treated with empiric antibiotics based on individual risk factors and antibiotic resistance.
Corporate Purpose in Comparative Perspective: The Role of Governance
Authors: Aguilera Ruth V. 
Published: June 2023

Corporate purpose has become a central part of doing business as usual and in the social movement to involve corporations in solving complex societal and environmental challenges. In this essay, I first deconstruct what corporate purpose means from a sociological perspective, and I submit that it is important to identify to whom that purpose is targeted. Second, I seek to make the point that corporate purpose is not universal in that there is not a one-rule-fits-all template on how to develop corporate purpose. I draw on comparative corporate governance, stakeholder management, and institutional theory arguments to illustrate how corporate purpose means different things in different societies and that the departure point of the emanation of corporate purpose varies across countries. This differential meaning is explained in part by the institutional setting as well as very different societal expectations of corporations. Finally, building on insights from existing corporate governance research, I argue that stakeholder engagement can be a useful tool toward effectively deploying corporate purpose.History: This paper has been accepted for the Strategy Science Special Issue on Corporate Purpose.
Program Abmas Sedekah Sampah untuk Kayakan Literasi (DESA KASI) di Desa Wanar, Pucuk, Lamongan
Authors: Suryo Is Bunyamin , Sudarmanta Bambang , Baiturrochman Firlana , Vianita Deviana Dyah , Afifah Putri Almas Ilka 
Published: June 2023

Desa Wanar terletak di Kecamatan Pucuk, Kabupaten Lamongan, Jawa Timur. Dengan jumlah penduduk yang terus bertambah, beberapa masalah lingkungan dan masalah sosial bermunculan. Masalah lingkungan terkait pembuangan sampah rumah tangga, sedangkan masalah sosial terkait semakin banyak anak-anak yang kecanduan game online sehingga mengganggu proses belajar. Rencana penyelesaian kedua masalah lingkungan dan sosial ini dirumuskan melalui program DESA KASI (seDEkah SAmpah untuk KAyakan literaSI). Tim abdimas melakukan pendampingan untuk pengolahan sampah rumah tangga sehingga sampah yang bernilai ekonomis akan dipisahkan dan dijual. Untuk mengurangi kecanduan game online, tim abdimas akan membuat perpustakaan keliling bagi anak-anak dan disediakan kupon berhadiah bagi pembaca buku di perpustakaan keliling. Untuk menunjang terlaksananya program ini, tim abdimas akan mendesain dan menyediakan Kendaraan Tiga (3) Roda Multiguna, yaitu kendaraan yang didesain untuk mengangkut sampah RT bernilai ekonomis dan juga bisa berganti fungsi menjadi perpustakaan keliling. Tim abdimas akan bekerjasama dengan mitra kelompok masyarakat Desa Wanar, yaitu Pemuda dan Jama’ah Ibu Masjid Al Mubarok Desa Wanar, TPA Al Mubarok, dan SDN Wanar. Dari Program DESA KASI ini, beberapa manfaat yang diharapkan adalah masyarakat mengetahui tata kelola sampah, mengurangi pencemaran lingkungan, meningkatkan minat baca anak-anak sekolah dasar sehingga mereka memiliki kekayaan literasi, mengurangi kecanduan game online bagi anak-anak, dan sebagai sarana pengabdian masyarakat bagi dosen dan KKN mahasiswa ITS. Selain itu, mitra lokal perlu berkolaborasi dengan Pemerintah Desa setempat untuk keberlangsungan Program DESA KASI.
Genetic diversity among five native Thai chickens and Khiew-Phalee chickens in lower-northern Thailand using mitochondrial DNA barcodes
Authors: SIRIWADEE PHROMNOI , WIROT LIKITTRAKULWONG , THANAPOL PUANGMALEE , WIRAWAN NUCHCHANART 
Published: June 2023

Abstract. Siriwadee P, Wirot L, Thanapol P, Wirawan N. 2023. Genetic diversity among five native Thai chickens and Khiew-Phalee chickens in lower-northern Thailand using mitochondrial DNA barcodes. Biodiversitas 24: 1962-1970. Native chickens are an important biological resource in Thailand, with each breed having distinctive features. Khiew-Phalee chickens are a valuable investment in cultural wisdom and an invaluable Thai resource worthy of conservation. It is the royal rooster of Phraya Phichai Dab Hak. Due to a crisis concerning a sharp decline in the size of the Khiew-Phalee native chicken population, the identification of potential biomarkers is important for the determination of different chicken breeds for future planning. This study aimed to investigate the molecular identification of different native Thai chicken breeds based on mitochondrial DNA (mtDNA) barcodes, especially Khiew-Phalee chickens, which is difficult using the morphological examination. Partial sequences of 648 bp mtDNA control region fragments were determined for 53 specimens of six breeds of native Thai chickens (Khiew-Phalee, Thao Thong, Leung Hang Khao, Chee, Pra Dhu Hang Dam and Kai Jae). Genetic diversity was accessed based on the number of polymorphic sites, number of haplotypes, haplotype diversity, nucleotide diversity, and average number of differences. A phylogenetic tree was constructed based on maximum likelihood. The results showed that eighteen haplotypes were identified from 9 polymorphic sites with polymorphism between nucleotides 1074, 1107, 1109, 1177, 1213, 1214, 1268, 1276 and 1305. The haplotype diversity, nucleotide diversity, and the average number of differences for all chickens were 0.917, 0.00504 and 2.69086, respectively. All Khiew-Phalee chickens showed 7 haplotypes with 0.897 haplotype diversity, 0.00696 nucleotide diversity, and an average number of differences at 3.1795 clustered with other breeds in the phylogenetic tree. The findings indicated that the DNA barcoding gene is an effective method to identify the Khiew-Phalee and five other native Thai chicken breeds. It is a better choice for using molecular biology DNA barcoding to identify Thai native chicken breeds to plan for further conservation and development by the Department of Livestock Development of Thailand.
Molecular identification of yeasts from Turkish traditional cheeses: Extracellular enzyme activities and physiological properties important for dairy industry
Authors: GÜNAY MELİH , GENÇ TÜLAY TURGUR 
Published: June 2023

Abstract. Gunay M, Genc TT. 2023. Molecular identification of yeasts from Turkish traditional cheeses: Extracellular enzyme activities and physiological properties important for dairy industry. Nusantara Bioscience 15: 1-11. The determination of yeast microbiota in cheeses and the physiological properties of yeasts are very important for the dairy industry. In addition, the physiological features, proteolytic and lipolytic activities, and stress tolerance of yeasts have a significant role in the selection of starter yeast species for cheese ripening. This study aimed to determine industrially important yeasts isolated from cheese samples. Molecular techniques identified the isolated yeast strains. The yeast strains’ extracellular enzyme activities, fermentation capacities, and thermotolerance and osmotolerance properties were also evaluated. A total of 81 yeast strains were isolated and characterized from three types of cheese samples. PCR-RFLP determined the isolated yeast strains and sequence analysis of ITS1-5.8S-ITS2 and 26S rDNA regions. A maximum parsimony tree was constructed by MEGA X software to evaluate the phylogenetic relationship of identified yeast strains. Candida intermedia, Candida parapsilosis, Clavispora lusitaniae, Debaryomyces hansenii, Kluyveromyces marxianus, Pichia kudriavzevii, and Wickerhamomyces anomalus yeast species were identified on cheese samples. The distribution of identified yeast species on cheese samples was determined as 48.1% for W. anomalus, 17.3% for K. marxianus, 14.8% for C. parapsilosis, 8.6% for D. hansenii, 4.9% for Cl. lusitaniae, 3.7% for C. intermedia and 2.5% for P. kudriavzevii. The W. anomalus yeast species was common in three cheese types. All strains of W. anomalus and P. kudriavzevii yeast species, three C. parapsilosis, and two Cl. lusitaniae yeast strains have important physiological properties for industrial applications. These yeast strains have the potential to be used in combination as starter cultures to improve cheese maturation in the future. This comprehensive study identifies yeast species by ITS1-5.8S-ITS2 and 26S rDNA regions and determines industrially important yeast species using multiple criteria (extracellular enzyme activity, stress tolerance, and fermentation capacity).
Influence of onshore wind turbines on land values
Authors: von Detten Jan , Seebaß Johann V. , Schlüter Jan C. , Hackelberg Florian 
Published: June 2023

AbstractThe economic consequences of wind turbines on property prices and land values are a widely discussed political and social issue. In this study, in addition to the previous research on the impact of wind turbines on property prices, the influence of wind turbines on standard land values was examined for the first time. The study thus provides new insights, particularly with regard to the debate on distance areas and financial compensation payments for residents.The chosen investigated area is located in Northern Germany and comprises three coastal districts in the state Schleswig-Holstein with a total of 1382 land zones and a high density of wind turbines. Using ordinary least squares models, the significant influence of wind turbines on the standard land values could be shown within a radius of up to 9 km. Using an exemplary municipality for the study area, an average change in the standard land value of 7.33% per 1000 m distance could be determined. Overall, the standard land values of less densely populated areas were affected more than urban areas.
Greek Weird Wave: A Cinema of Biopolitics, Dimitris Papanikolaou (2021)
Authors: Rappas İpek Çelik 
Published: June 2023

Review of: Greek Weird Wave: A Cinema of Biopolitics, Dimitris Papanikolaou (2021)
Edinburgh: Edinburgh University Press, 268 pp.,
ISBN 978-1-47443-631-1, h/bk, £90.00
ISBN 978-1-47443-632-8, p/bk, £19.99