bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatiotemporal control of genome engineering in cone photoreceptors
Authors: Wang Nan-Kai , Liu Pei-Kang , Kong Yang , Tseng Yun-Ju , Jenny Laura A. , Nolan Nicholas D. , Chen Nelson , Wang Hung-Hsi , Hsu Chun Wei , Huang Wan-Chun , Sparrow Janet R. , Lin Chyuan-Sheng , Tsang Stephen H.
Published: June 2023

Background

Cones are essential for color recognition, high resolution, and central vision; therefore cone death causes blindness. Understanding the pathophysiology of each cell type in the retina is key to developing therapies for retinal diseases. However, studying the biology of cone cells in the rod-dominant mammalian retina is particularly challenging. In this study, we used a bacterial artificial chromosome (BAC) recombineering method to knock in the “CreERT2” sequence into the Gnat2 and Arr3 genes, respectively and generated three novel inducible CreERT2 mice with different cone cell specificities.

Results

These models (Gnat2CreERT2, Arr3T2ACreERT2, and Arr3P2ACreERT2) express temporally controllable Cre recombinase that achieves conditional alleles in cone photoreceptors. Cre-LoxP recombination can be induced as early as postnatal day (PD) two upon tamoxifen injection at varying efficiencies, ranging from 10 to 15% in Gnat2CreERT2, 40% in Arr3T2ACreERT2, and 100% in Arr3P2ACreERT2. Notably, knocking in the P2A-CreERT2 cassette does not affect cone cell morphology and functionality. Most cone-phototransduction enzymes, including Opsins, CNGA3, etc. are not altered except for a reduction in the Arr3 transcript.

Conclusions

The Arr3P2ACreERT2 mouse, an inducible cone-specific Cre driver, is a valuable line in studying cone cell biology, function, as well as its relationship with rod and other retinal cells. Moreover, the Cre activity can be induced by delivering tamoxifen intragastrically as early as PD2, which will be useful for studying retinal development or in rapid degenerative mouse models.
In vivo dynamics and regulation of DNA G-quadruplex structures in mammals
Authors: Zhang Ze-Hao , Qian Sheng Hu , Wei Dengguo , Chen Zhen-Xia
Published: June 2023

G-quadruplex (G4) is a four-stranded helical DNA secondary structure formed by guanine-rich sequence folding, and G4 has been computationally predicted to exist in a wide range of species. Substantial evidence has supported the formation of endogenous G4 (eG4) in living cells and revealed its regulatory dynamics and critical roles in several important biological processes, making eG4 a regulator of gene expression perturbation and a promising therapeutic target in disease biology. Here, we reviewed the methods for prediction of potential G4 sequences (PQS) and detection of eG4s. We also highlighted the factors affecting the dynamics of eG4s and the effects of eG4 dynamics. Finally, we discussed the future applications of eG4 dynamics in disease therapy.
Segmentation algorithm can be used for detecting hepatic fibrosis in SD rat
Authors: Hwang Ji-Hee , Lim Minyoung , Han Gyeongjin , Park Heejin , Kim Yong-Bum , Park Jinseok , Jun Sang-Yeop , Lee Jaeku , Cho Jae-Woo
Published: June 2023

Background

Liver fibrosis is an early stage of liver cirrhosis. As a reversible lesion before cirrhosis, liver failure, and liver cancer, it has been a target for drug discovery. Many antifibrotic candidates have shown promising results in experimental animal models; however, due to adverse clinical reactions, most antifibrotic agents are still preclinical. Therefore, rodent models have been used to examine the histopathological differences between the control and treatment groups to evaluate the efficacy of anti-fibrotic agents in non-clinical research. In addition, with improvements in digital image analysis incorporating artificial intelligence (AI), a few researchers have developed an automated quantification of fibrosis. However, the performance of multiple deep learning algorithms for the optimal quantification of hepatic fibrosis has not been evaluated. Here, we investigated three different localization algorithms, mask R-CNN, DeepLabV3+, and SSD, to detect hepatic fibrosis.

Results

5750 images with 7503 annotations were trained using the three algorithms, and the model performance was evaluated in large-scale images and compared to the training images. The results showed that the precision values were comparable among the algorithms. However, there was a gap in the recall, leading to a difference in model accuracy. The mask R-CNN outperformed the recall value (0.93) and showed the closest prediction results to the annotation for detecting hepatic fibrosis among the algorithms. DeepLabV3+ also showed good performance; however, it had limitations in the misprediction of hepatic fibrosis as inflammatory cells and connective tissue. The trained SSD showed the lowest performance and was limited in predicting hepatic fibrosis compared to the other algorithms because of its low recall value (0.75).

Conclusions

We suggest it would be a more useful tool to apply segmentation algorithms in implementing AI algorithms to predict hepatic fibrosis in non-clinical studies.
Properties of high-performing horizontal wells in the Midland Basin
Authors: Male Frank , Dommisse Robin , Sivila Livia J. , Hamlin Scott , Goodman Emery D.
Published: June 2023

What do the best horizontal wells in the Midland Basin Spraberry and Wolfcamp tight oil plays have in common? What differentiates them from less productive wells? In this study, we address these questions with data assembled from a high-resolution geomodel and public and vendor-sourced completions data. From 10,064 tight oil horizontal wells, 101 (1%) of the most productive wells by first-year oil production and 101 of the most productive wells by length-normalized first-year production are selected. We compare the completion, spacing, petrophysical, landing, and fluid properties between the most productive wells and others. Among the discoveries, we find that Wolfcamp A wells are more likely to be in the top 1%, especially those drilled in the carbonate-poor rock. Average hydrocarbon-filled pore volume and oil formation factors still lead to high-performing wells. High pressure is an important consideration for Wolfcamp B top producers. All of the best oil producers have low producing gas-oil ratios. The top 1% of wells are usually the first well in the pad to be completed, and they come from above-average pads. The top 30% of completions lead to the top 1% of wells more often than extremely intense completions. Operators can apply these results to the further development of the Midland Basin. Specifically, they can prioritize development areas in Wolfcamp A with low carbonate abundance and save costs by not implementing extremely intense completions.
Injection and nucleation of topological defects in the quench dynamics of the Frenkel-Kontorova model
Authors: Chelpanova Oksana , Kelly Shane P. , Morigi Giovanna , Schmidt-Kaler Ferdinand , Marino Jamir
Published: June 2023

Topological defects have strong impact on both elastic and inelastic properties of materials. In this article, we investigate the possibility to controllably inject topological defects in quantum simulators of solid state lattice structures. We investigate the quench dynamics of a Frenkel-Kontorova chain, which is used to model discommensurations of particles in cold atoms and trapped ionic crystals. The interplay between an external periodic potential and the inter-particle interaction makes lattice discommensurations, the topological defects of the model, energetically favorable and can tune a commensurate-incommensurate structural transition. Our key finding is that a quench from the commensurate to incommensurate phase causes a controllable injection of topological defects at periodic time intervals. We employ this mechanism to generate quantum states which are a superposition of lattice structures with and without topological defects. We conclude by presenting concrete perspectives for the observation and control of topological defects in trapped ion experiments.
Weighted-elite-memory mechanism enhances cooperation in social dilemmas
Authors: Bai Zhongling , Liu Xingwen , Wang Huazhang , Jiang Yulian , Tashi Nyima
Published: June 2023

The issue of how to enhance cooperation has been a hot topic of research in evolutionary games for a long time. A mechanism is proposed to facilitate the cooperation behavior of evolutionary groups on networks in three game models, including prisoner's dilemma, snowdrift game, and stag hunt game. The core of the mechanism lies in: 1) Each player has a length of memory and uses the information of the elite in the memory span to update its strategy. 2) Each player has the chance to game with a certain neighbor more than once in each round. 3) The accumulative payoff of a player consists of two parts, one from playing with elites in memory length and another from playing with current neighbors, and a weight is introduced to adjust these two parts. The findings of the simulation demonstrate that a small weight can significantly enhance cooperation in three typical social dilemmas. Furthermore, the level of cooperation increases at first and then stays stable as the memory length increases.
Body Mass Index Trajectories in Children Exposed to Gestational Diabetes in Utero: A Nationwide Register-based Study
Authors: Thøgersen Maja , Nielsen Karoline Kragelund , Wibaek Rasmus , Damm Peter , Jensen Rikke Beck , Nielsen Helene , Maindal Helle Terkildsen , Andersen Gregers Stig
Published: June 2023

Context

Children exposed to gestational diabetes mellitus (GDM) in utero are at high risk of developing overweight and obesity, but their postnatal growth trajectories and risk profiles remain unclear.

Objective

We aimed to identify distinct body mass index (BMI) trajectories from birth to 10 years of age in children exposed to GDM and to explore their associations with infant and maternal characteristics.

Methods

This nationwide cohort study linked data from Danish registries on 15 509 children exposed to GDM in utero, born in Denmark from January 2008 to October 2019. We applied latent class trajectory modeling to identify distinct BMI trajectories. Associations of BMI trajectories with infant and maternal characteristics were analyzed using multiple linear regression.

Results

We identified 3 distinct BMI trajectories characterized by a “normal” (60%), a “late accelerating” (28%) and an “early accelerating” (12%) BMI trajectory, the 2 latter at risk of overweight and obesity, respectively, at age 10 years, relative to World Health Organization child growth standards. Children in the “late accelerating” BMI trajectory were more often born large for gestational age (P < .001). More children in the “early accelerating” BMI trajectory were boys, born small for gestational age, and had mothers with a higher pre-pregnancy BMI compared to the other groups (P < .001).

Conclusion

Children exposed to GDM in utero differ widely in their BMI trajectory. The detection of risk profiles based on early BMI growth and infant and maternal characteristics provides an opportunity for future targeted care and prevention.
Recurrent Hypoglycemia Secondary to Insulinoma in an Adult With Beckwith-Wiedemann Syndrome
Authors: Akcan Tugce , Shariff Julia Rose R
Published: June 2023

Beckwith-Wiedemann syndrome (BWS) is a rare genetic disorder characterized by genetic and epigenetic changes on the chromosome 11p15.5 region, which includes genes that are important for fetal and postnatal growth. Children with BWS have a higher chance of having hypoglycemia, hyperinsulinemia, and malignancies early in life, although hypoglycemia caused by an insulinoma that develops later in life has not been reported. We describe the diagnosis of insulinoma in a 53-year-old man with BWS in this case report. This is the first case report of insulinoma in an adult with this syndrome.
A Novel Pathogenic MEN1 Gene Variant Identified in a Family With Multiple Pancreatic Neuroendocrine Tumors
Authors: Horikoshi Hirofumi , Arita Junichi , Hasegawa Kiyoshi , Makita Noriko
Published: June 2023

Multiple endocrine neoplasia type 1 (MEN1) is a hereditary endocrine tumor syndrome caused by pathogenic variants in the MEN1 gene, and most patients with this syndrome initially develop primary hyperparathyroidism (PHPT). Here, we report the case of a family wherein a germline MEN1 variant was detected and multiple pancreatic neuroendocrine tumors (PanNETs) were observed at the initial evaluation. A 40-year-old woman presented with a complaint of abdominal discomfort, and a close examination revealed multiple pancreatic tumors. Distal pancreatectomy with splenectomy was performed, and the diagnosis was nonfunctional PanNETs. Five years later, her 76-year-old mother was referred to the hospital with multiple pancreatic tumors. A genetic test revealed that both patients harbored a previously unreported germline variant in the MEN1 gene. Although it was classified as a variant of uncertain significance, we suspect that it may be associated with the pathogenesis of these lesions. This case report presents a new disease concept—familial isolated pancreatic neuroendocrine tumors, or FIPNETs—in patients harboring a pathogenic variant in the MEN1 gene who experience only pancreatic lesions. We suggest that clinicians consider genetic testing for the MEN1 gene in patients with multiple pancreatic lesions who show no signs of PHPT.
Human prostate organoid generation and the identification of prostate development drivers using inductive rodent tissues
Authors: Singh Parmveer , Lanman Nadia A. , Kendall Hannah L. R. , Wilson Laura , Long Ryan , Franco Omar E. , Buskin Adriana , Miles Colin G. , Hayward Simon W. , Heer Rakesh , Robson Craig N.
Published: June 2023

The reactivation of developmental genes and pathways during adulthood may contribute to pathogenesis of diseases such as prostate cancer. Analysis of the mechanistic links between development and disease could be exploited to identify signalling pathways leading to disease in the prostate. However, the mechanisms underpinning prostate development require further characterisation to interrogate fully the link between development and disease. Previously, our group developed methods to produce prostate organoids using induced pluripotent stem cells (iPSCs). Here, we show that human iPSCs can be differentiated into prostate organoids using neonatal rat seminal vesicle mesenchyme in vitro. The organoids can be used to study prostate development or modified to study prostate cancer. We also elucidated molecular drivers of prostate induction through RNA-sequencing analyses of the rat urogenital sinus and neonatal seminal vesicles. We identified candidate drivers of prostate development evident in the inductive mesenchyme and epithelium involved with prostate specification. Our top candidates included Spx, Trib3, Snai1, Snai2, Nrg2 and Lrp4. This work lays the foundations for further interrogation of the reactivation of developmental genes in adulthood, leading to prostate disease.
Partial male-to-female reprogramming of mouse fetal testis by Sertoli cell ablation
Authors: Imaimatsu Kenya , Hiramatsu Ryuji , Tomita Ayako , Itabashi Hirotsugu , Kanai Yoshiakira
Published: June 2023

Temporal transcription profiles of fetal testes with Sertoli cell ablation were examined in 4-day culture using a diphtheria toxin (DT)-dependent cell knockout system in AMH-TRECK transgenic (Tg) mice. RNA analysis revealed that ovarian-specific genes, including Foxl2, were ectopically expressed in DT-treated Tg testis explants initiated at embryonic days 12.5-13.5. FOXL2-positive cells were ectopically observed in two testicular regions: near the testicular surface epithelia and around its adjacent mesonephros. The surface FOXL2-positive cells, together with ectopic expression of Lgr5 and Gng13 (markers of ovarian cords), were derived from the testis epithelia/subepithelia, whereas another FOXL2-positive population was the 3βHSD-negative stroma near the mesonephros. In addition to high expression of Fgfr1/Fgfr2 and heparan sulfate proteoglycan (a reservoir for FGF ligand) in these two sites, exogenous FGF9 additives repressed DT-dependent Foxl2 upregulation in Tg testes. These findings imply retention of Foxl2 inducibility in the surface epithelia and peri-mesonephric stroma of the testicular parenchyma, in which certain paracrine signals, including FGF9 derived from fetal Sertoli cells, repress feminization in these two sites of the early fetal testis.
Halfway Home? Residential Housing and Reincarceration
Authors: Lee Logan M.
Published: June 2023

Every year, hundreds of thousands of people are released from prison. For many, the transition back to society includes a mandatory stay in residential housing. I estimate the effect of residential housing on reincarceration using administrative data from Iowa. I address selection into residential housing by instrumenting for residential housing assignment with the recommendation rate of randomly assigned case managers. I find no evidence that Iowa’s costly investment in residential housing results in reduced reincarceration relative to parole. Instead, residential housing increases reincarceration due to violent crimes and technical violations, while decreasing drug and public order crimes. (JEL K42, R23, R31, R38)
Does Cash Bail Deter Misconduct?
Authors: Ouss Aurélie , Stevenson Megan
Published: June 2023

Courts routinely use low cash bail as a financial incentive to ensure released defendants appear in court and abstain from crime. This can create burdens for defendants with little empirical evidence on its efficacy. We exploit a prosecutor-driven reform that led to a sharp reduction in low cash bail and pretrial supervision, with no effect on pretrial detention, to test whether such incentive mechanisms succeed at their intended purpose. We find no evidence that financial collateral has a deterrent effect on failure to appear or pretrial crime. This paper also contributes to the literature on legal actor discretion, showing that nonbinding reforms may have limited impact on jail populations. (JEL K41, K42)
Ανάλυση Ποιοτικών Χαρακτηριστικών Εκπαιδευτικών Βίντεο: Οι Περιπτώσεις της ΕΡΤ και του ΡΙΚ
Authors: Χαραλαμπίδου Χριστίνα , Σοφός Αλιβίζος (Λοΐζος)
Published: June 2023

Σκοπός της παρούσας μελέτης ήταν η αξιολόγηση των ποιοτικών χαρακτηριστικών των εκπαιδευτικών βίντεο που παρήγαγε η ΕΡΤ και το ΡΙΚ το χρονικό διάστημα Μάρτιος 2019- Ιούνιος 2021 ως έκτακτο μέτρο κάλυψης του προβλήματος της «επείγουσας» εξ αποστάσεως εκπαιδευτικής διαδικασίας. Για την επίτευξή του ακολουθήθηκε η ερευνητική μεθοδολογία της ποσοτικοποιημένης ανάλυσης περιεχομένου, που περιλάμβανε δύο στάδια, την δημιουργία της ρουμπρίκας- πρωτοκόλλου αξιολόγησης, για την οποία αξιοποιήθηκαν αρχές Πολυμεσικής μάθησης, σχεδιασμούς βίντεο αλλά και γνωσιακές θεωρίες, και την ανάλυση του περιεχομένου των βίντεο. Συνολικά εξετάστηκαν 40 βίντεο-μαθήματα από την ΕΡΤ και 20 από το ΡΙΚ από 2 ερευνητές. Από τα αποτελέσματα της έρευνας φαίνεται πως η προσπάθεια που έγινε για τον σχεδιασμό και την ανάπτυξη εκπαιδευτικών βίντεο είχε αρκετά αδύναμα στοιχεία, και δεν πληροί σε μεγάλο βαθμό ποιοτικά χαρακτηριστικά που μπορούν να αντληθούν από την υπάρχουσα βιβλιογραφία, σχετικά με τα εκπαιδευτικά βίντεο.
Food shaped photosynthesis: Photophysiology of the sea slug Elysia viridis fed with two alternative chloroplast donors
Authors: Morelli Luca , Cartaxana Paulo , Cruz Sónia
Published: June 2023

Background: Some Sacoglossa sea slugs integrate intracellular chloroplasts derived from the algae they feed on, a process termed kleptoplasty. The stolen chloroplasts – kleptoplasts – can maintain their functionality up to several months and support animal metabolism. However, chloroplast longevity can vary depending on sea slug species and algal donor. In this study, we focus our attention on Elysia viridis, a polyphagous species that is mostly found associated to the macroalga Codium tomentosum, but that was reported to eat other macroalgae, including Chaetomorpha sp.

Methods: We have investigated the changes in E. viridis physiology when provided with the two different food sources to evaluate to which extent the photosynthetic and photoprotective mechanisms of the algae chloroplasts matched those of the plastids once in the animal cells. To perform the study, we rely on the evaluation of chlorophyll a variable fluorescence to study the photophysiologic state of the integrated kleptoplasts and the high-performance liquid chromatography (HPLC) to study variations in the photosynthetic pigments.

Results: We observed that the photosynthetic efficiency of E. viridis specimens is similar to the one of the respective algal donor but specimens fed with Chaetomorpha tend to have lower performances. Significant differences appear in the non-photochemical quenching (NPQ) abilities. While sea slugs fed with C. tomentosum react to high-light stress as the algae, E. viridis hosting Chaetomorpha chloroplasts are unable to properly recover from photoinhibition or perform a functional xanthophyll cycle (XC).

Conclusions: Our results showed that, even if the sea slugs fed with the two algae show photosynthetic activities like the respective algal donors, not all the photoprotective mechanisms present in Chaetomorpha can be maintained in E. viridis. This indicates that the functionality of the kleptoplasts does not depend solely on their origin but also on the degree of compatibility with the animal species integrating them.
Practical audit
Authors: Safonova Margarita , Kalinina Irina , Petuh Aleksey
Published: June 2023

The textbook outlines the main theoretical and methodological aspects related to the organization and conduct of a practical audit, aimed at developing skills to identify violations of the requirements of current legislation in the field of accounting and tax accounting.
Meets the requirements of the federal state educational standards of higher education of the latest generation.
For students of higher educational institutions studying in economic specialties at the master's level, students of advanced training courses, as well as practical workers.
Konserwacja XIX-wiecznych muzealiów pochodzących z Syberii ze zbiorów Muzeum Etnograficznego im. Seweryna Udzieli w Krakowie
Authors: Barczyńska Agata
Published: June 2023

Artykuł opisuje konserwację 79 unikatowych, XIX - wiecznych obiektów pochodzących z Syberii ze zbiorów Kultur Pozaeuropejskich Muzeum Etnograficznego w Krakowie, wybranych na wystawę czasową Syberia. Głosy z Północy, zaprezentowaną w latach 2020/2021. Poznajemy drogę postępowania z muzealiami w trakcie ich przygotowania do ekspozycji, we współpracy z kuratorami wystawy, a także każdy etap prac konserwatorskich wykonanych przez zespół pracowników konserwacji i restauracji zbiorów powyższej instytucji. Artykuł posiada formę zbliżoną do dokumentacji konserwatorskiej i zawiera informacje dotyczące m.in charakterystyki obiektów, opisu stanu zachowania czy przebiegu prac konserwatorskich. Całość wzbogacona jest o zdjęcia przed, w trakcie i po konserwacji.
Białoruska twórczość ludowa o tematyce protestacyjnej 2020-2021 jako obiekt zainteresowania muzeów
Authors: Marmysh Tatsiana
Published: June 2023

Artykuł poświęcony jest problemowi twórczości ludowej o tematyce protestacyjnej w Białorusi, która pojawiła się jako reakcja społeczeństwa na wyniki wyborów prezydenckich z 9 sierpnia 2020 roku. Na twórczość tę składają się różne gatunki folkloru, a także praktyki performatywno-karnawałowe. W drugiej części artykułu przedstawione są dwie kolekcje muzealne: Muzeum Flag i Muzeum Wolnej Białorusi. Pierwsza z nich stanowi wirtualne muzeum, którego celem jest gromadzenie i eksponowanie flag protestacyjnych powstałych w wyniku ruchu społecznego ulic, dzielnic, miast, regionów, diaspory. Druga z nich, powstająca poza granicami Białorusi, jest w trakcie organizacji i gromadzi artefakty oraz dokumenty związane z protestami. Obie inicjatywy łączy przekonanie o wadze tego typu działań dla przyszłych pokoleń Białorusinów.
Szwajcarska geneza antropologii i etnologii Jana Czekanowskiego (1882-1965) i Stanisława Poniatowskiego (1884-1945)
Authors: Gładkowski Krzysztof
Published: June 2023

SWISS GENESIS OF ANTHROPOLOGY AND ETHNOLOGY BY JAN CZEKANOWSKI (1882-1965) AND STANISŁAW PONIATOWSKI (1884-1945)
The history of Polish science still has many gaps. This is the case of Jan Czekanowski and Stanisław Poniatowski. They both studied physical anthropology at the University of Zurich. This article explains the reason for their ethnographic and ethnological research, which they successfully conducted in these disciplines. In addition, the questions of how they got to Switzerland and what prompted the choice of the field of study are answered. The political context of both scholars going to study in Switzerland is taken into account. For the first time in Polish literature on the subject, a complete list of scholars and courses that they studied at the University of Zurich is provided. The list is reconstructed on the basis of sources located in archives and libraries in Zurich.
Development of Specialized Education for Academically Gifted Students in Ukraine in Early XXI Century
Authors:   National Academy of Pedagogical Sciences of Ukraine, Onatskyi Volodymyr
Published: June 2023

The article presents the evolution of changes in the education of gifted youth in Ukraine in early XXI century. The emphasis has been placed on the socio-political transformations and on the secondary education level reform. It has been established that the system of general secondary education began to be built on the basis of humanism, variability and profiling. Educational institutions of the “new type” have become widespread. Such institutions competed with each other, trying to attract the most gifted students. It has been proven that in order to increase the intellectual potential of the future generation, implementation of grant programs and projects has begun at the state level. In particular, the Program for working with gifted children for 2001 – 2005 and 2006 – 2010 has been approved, the Concept of specialized education has been revised three times (2003, 2009, 2013), and data banks for gifted students have been implemented. It has been noted that in order to maximize the development of the abilities of academically gifted students, various psychological and pedagogical projects and programs have been implemented in Ukraine, such as: Rostock, Intellect of Ukraine, School of Life Success, School of the Future, etc. It has been emphasized that the development of academically gifted students in extracurricular time was provided by the state-public association of the Minor Academy of Sciences. It has been established that the problems of inclusion and equal access to education were at the forefront of changes with the introduction of the reform of the New Ukrainian School. Prospects for further research have been planned in the disclosure of modern approaches to teaching gifted students in the conditions of the current state standard.
Global Challenges in Identifying Plant Pathogenic Fungi: An Overview with Suggestions for the Way Forward
Authors:   Postgraduate Institute of Agriculture, Old Galaha Road, Peradeniya, Sri Lanka, Dayarathne Monika C. , Thambugala Kasun M. ,   Genetics and Molecular Biology Unit, Faculty of Applied Sciences, University of Sri Jayawardenepura, Gangodawila, Nugegoda, Sri Lanka, Daranagama Dinushani A. ,   Department of Plant and Molecular Biology, Faculty of Science, University of Kelaniya, Kelaniya, Sri Lanka, Mridha Amin U. ,   Daff odil International University, Ashulia, Savar, Dhaka, Bangladesh, Dissanayake Asha J. ,   School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, People’s Republic of China, Dissanayake Lakmali S. ,   Engineering Research Centre of the Utilization for Characteristic Bio-Pharmaceutical Resources in Southwest, Ministry of Education, Guizhou University, Guiyang, Guizhou Province 550025, People’s Republic of China, Maharachchikumbura Sajeewa S.N. ,   School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, People’s Republic of China, Rathnayake RMCS ,   Department of Plant and Molecular Biology, Faculty of Science, University of Kelaniya, Kelaniya, Sri Lanka, Lumyong Saisamorn ,   Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Sciences, Chiang Mai University, Chiang Mai 50200, Thailand, Hongsanan Sinang ,   Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Sciences, Chiang Mai University, Chiang Mai 50200, Thailand,   Department of Entomology & Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand,   Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Science and Oceanography, Shenzhen University, Shenzhen 518060, People’s Republic of China
Published: June 2023

Fungal plant diseases are responsible for major crop and postharvest losses worldwide, with a signifi cant socio-economic impact on many individuals who depend on an agriculture-based economy. This review discusses the major constraints in identifying plant pathogenic fungi (severely destructive on important crops) in sample collection, fi eld, and morphological observations, fungal isolation, obtaining pure cultures, applying Koch’s postulates, DNA barcoding, phylogenetic analyses, and naming fungi (under “One fungus, One name” concept) based on selected case studies. Additionally, available strategies/methods to overcome those limitations up to date are also discussed. Ultimately, we proposed suggestions to minimize those limitations.
Monitoring Biomarkers of Drivers with Medical Wireless Sensor Networks Deployed in Connected Vehicles
Authors: Karmakar Sayon , Mohan Seshadri
Published: June 2023

Millions of traffic accidents occur each year that negatively impacts the economy as well as the human lives. Human error is the principal cause of traffic accidents. Medical conditions of drivers that are not usually monitored have a significant role in accidents. Chronic illnesses have been shown to have reduced cognitive, visual and motor skills, which are the key driving requirements. In conjunction with the current wireless communication technologies and data processing capabilities, it is urgent that suitable sensors be deployed to perform non-invasive detection of objective biomarkers that state the driver’s health. Cellular V2X communication provides the ability to share the information collected to the nearby driving vehicles for cautionary stance and to the hospitals for clinical validation. Dedicated short-range communication (DSRC) allows for the establishment of vehicle-to-vehicle communication (V2V) and vehicle-to-anything communication (V2X). This interconnected setup of Connected Vehicles (CV) would pave the way to establishment of smart city.
Measuring the Effectiveness of Autonomous Network Functions that Use Artificial Intelligence Algorithms
Authors: Narayanan Premnath K. , Harrison David K.
Published: June 2023

Autonomous network functions such as Software Defined Networks (SDN), Self-Organizing Networks (SON), and virtual function network orchestrator plays a crucial role in 5G and beyond 5G wireless telecommunication network. Advancements in Artificial Intelligence (AI), Machine Learning (ML) algorithms, and frameworks have led to adequate adaption of stochastic algorithms for autonomous network functions, aimed at performing better than human capability. Measuring the effectiveness of such autonomous network functions is a challenge since stochastic algorithms are fundamentally generalized models and could potentially make malicious proposals. Traditionally effectiveness of network is measured through network assurance Key Performance Indicators (KPIs). Autonomous network functions are kept active when the KPIs are in the acceptable limit, and the network is showing improvement over time. This paper introduces

• Factors that are to be considered beyond KPIs for effective measurement of autonomous network functions that use stochastic algorithms.

• Adopting the right scales for measuring the effectiveness of autonomous network functions using the grading system from medical practices which are used for the treatment of critical illness.
Challenges Regarding Network Neutrality for Commercial Deployment of 5G Networks
Authors: Izydorek Szymon , Tadayoni Reza
Published: June 2023

The paper aims to analyze the impact of equal data treatment applied in the European Union (EU) on the commercial deployment of the upcoming wireless standards such as 5G and beyond. The analysis of the different network neutrality involves several aspects, including engineering, social, economic and political aspects. Considering recent advancements in wireless networks like Network Function Virtualization or Network Slicing, this opens new research possibilities to analyze how various models influence aspects like the profitability of modern standards. To perform the study, a broad literature review and five interviews with the stakeholders from the industry have been done. Then, the knowledge has been segmented and interpreted so that an analysis of the net neutrality on future wireless standards has been given.
Influence of power and the time of application of fogging lenses on accommodation
Authors: Turull-Mallofré Aina , García-Guerra Carlos E. , Mestre Clara , Vilaseca Meritxell , Pujol Jaume , Aldaba Mikel
Published: June 2023

Fogging is a non-invasive technique based on the use of positive spherical power lenses to relax accommodation during refraction that is commonly used as an alternative to cycloplegic drugs. Although the mechanism of the fogging technique has been described, some aspects of its methodology remain unclear. The main purpose of this work was to determine which lens power and time of application are more suitable for achieving a successful relaxation of accommodation by analyzing the changes in accommodation when fogging lenses of different powers were placed in front of the participants’ eye for a certain timespan. The results of this analysis showed, in general, that low-power lenses and timespans of less than half a minute provided the highest relaxation of accommodation. However, high inter-subject variability was found in the two variables (power and time).
Visual and Physiological Optics: introduction to the joint feature issue in Biomedical Optics Express and Journal of the Optical Society of America A
Authors: Tabernero Juan , Lundström Linda , Schwarz Christina , Vohnsen Brian
Published: June 2023

This feature issue collects articles presented at the tenth Visual and
Physiological Optics meeting (VPO2022), held August 29–31, 2022, in
Cambridge, UK. This joint feature issue between Biomedical
Optics Express and Journal of the Optical Society of
America A includes articles that cover the broad range of
topics addressed at the meeting and examples of the current state of
research in the field.
Three-dimensional imaging using coherent x rays at grazing incidence geometry
Authors: Yang Yi , Sinha Sunil K.
Published: June 2023

We have developed a three-dimensional coherent diffraction imaging algorithm to retrieve phases of diffraction patterns of samples in grazing incidence small angle x-ray scattering experiments. The algorithm interprets the diffraction patterns using the distorted-wave Born approximation instead of the Born approximation, as in this case, the existence of a reflected beam from the substrate causes the diffraction pattern to deviate significantly from the simple Fourier transform of the object. Detailed computer simulations show that the algorithm works. Verification with real experiments is planned.
Fluoro-sulfo-phosphate fiber with long-wavelength gain for an L-band laser
Authors: Ji Yao , Zhu Jinzhong , Zhang Runsen , Xiong Zhijin , Wei Xiaoming , Wang Weichao , Zhang Qinyuan
Published: June 2023

In this work, a self-developed Er3+/Yb3+ co-doped fluoro-sulfo-phosphate (FSP) fiber with long-wavelength gain characteristics has been reported. The mixed-ion strategy manipulates the ligands of rare-earth ions, leading to a broad gain bandwidth (almost twice that of phosphate fiber) and excellent amplification ability at the extended wavelength (>2dB/cm at the L-band). As showcases of its features, a 1617-nm fiber laser based on a 1-cm-long FSP fiber is constructed. Furthermore, an all-fiber-integrated L-band passively mode-locked laser based on a 2.2-cm-long fiber with a fundamental repetition rate of 4.3 GHz is demonstrated. The generated pulse exhibits a high signal-to-noise ratio larger than 80 dB in the radio-frequency domain and a low relative intensity noise of 0.04%.
Impact of pump beam spot size on semiconductor carrier dynamics in optical-pump-terahertz-probe spectroscopy
Authors: Staechelin Yannic U. , Kroh Tobias , Kärtner Franz X. , Lange Holger
Published: June 2023

Optical-pump-terahertz-probe (OPTP) experiments are widely employed to study the dynamics of photoexcited carriers in semiconductors. In these experiments, due to the long wavelength nature of terahertz (THz) probe radiation, the probe beam can be focused only to a spot size in the mm range. To ensure homogeneous excitation of the probed sample region, a significantly larger optical pump beam spot size must be used, which is often difficult to implement in the experiment. Frequently used experimental geometries employ beam paths that result in small pump beam spot sizes, leading to spectral distortions of the sample response, translating to uncertainties in calculated THz conductivities and fitted Drude conductivity models, for example. We investigate the influence of pump beam spot size on benchmark OPTP experiments and evaluate model calculations to estimate the induced deviations. We demonstrate the impact of this effect on the acquired data with different dependencies on the investigated sample and the employed experimental configuration. We can provide guidelines for optimal configurations for the most commonly employed experiments.
Mitigation of TMI in an 8 kW tandem pumped fiber amplifier enabled by inter-mode gain competition mechanism through bending control
Authors: Li Ruixian , Li Haobo , Wu Hanshuo , Xiao Hu , Leng Jinyong , Huang Liangjin , Pan Zhiyong , Zhou Pu
Published: June 2023

In this work, the impact of fiber bending and mode content on transverse mode instability (TMI) is investigated. Based on a modified stimulated thermal Rayleigh scattering (STRS) model considering the gain competition between transverse modes, we theoretically detailed the TMI threshold under various mode content and bending conditions in few-mode fibers. Our theoretical calculations demonstrate that larger bending diameters increase the high order mode (HOM) components in the amplifier, which in turn reduces the frequency-shifted Stokes LP11o mode due to the inter-mode gain competition mechanism, thus improving the TMI threshold of few-mode amplifiers. The experimental results agree with the simulation. Finally, by optimizing the bending, an 8.38 kW output tandem pumped fiber amplifier is obtained with a beam quality M2 of 1.8. Both TMI and stimulated Raman scattering (SRS) are well suppressed at the maximum power. This work provides a comprehensive analysis of the TMI in few-mode amplifiers and offers a practical method to realize high-power high-brightness fiber lasers.
Propagation-based phase-contrast imaging method for full-field X-ray microscopy using advanced Kirkpatrick–Baez mirrors
Authors: Tanaka Yuto , Yamada Jumpei , Inoue Takato , Kimura Takashi , Shimura Mari , Kohmura Yoshiki , Yabashi Makina , Ishikawa Tetsuya , Yamauchi Kazuto , Matsuyama Satoshi
Published: June 2023

We demonstrate a propagation-based phase-contrast imaging method for full-field X-ray microscopy based on advanced Kirkpatrick–Baez (AKB) mirrors to achieve high-contrast observations of weak phase objects and correct field curvature aberrations. Through a demonstration performed at SPring-8, the phase contrast of weak phase objects such as polystyrene spheres and chemically fixed cells was successfully observed with high sensitivity (∼0.03 rad). Furthermore, the field of view of the AKB mirrors was expanded to the full area of the obtained images (25 × 30 µm) by correcting the field curvature aberration using reconstructed complex wavefields.
Nanosecond pulsed CMOS LED for all-silicon time-of-flight ranging
Authors: Li Zheng , Ram Rajeev J.
Published: June 2023

Light detection and ranging (LIDAR) is a widely used technique for measuring distance. With recent advancements in integrated photonics, there is a growing interest in miniaturizing LIDAR systems through on-chip photonic devices, but a LIDAR light source compatible with current integrated circuit technology remains elusive. In this letter, we report a pulsed CMOS LED based on native Si, which spectrally overlaps with Si detectors’ responsivity and can produce optical pulses as short as 1.6 ns. A LIDAR prototype is built by incorporating this LED and a Si single-photon avalanche diode (SPAD). By utilizing time-correlated single-photon counting (TCSPC) to measure the time-of-flight (ToF) of reflected optical pulses, our LIDAR successfully estimated the distance of targets located approximately 30 cm away with sub-centimeter resolution, approaching the Cramér-Rao lower bound set by the pulse width and instrument jitter. Additionally, our LIDAR is capable of generating depth images of natural targets. This all-Si LIDAR demonstrates the feasibility of integrated distance sensors on a single photonic chip.
Electro-optical tunable interleaver in hybrid silicon and lithium niobate thin films
Authors: Li Qingyun , Zhu Houbin , Zhang Honghu , Hu Hui
Published: June 2023

The interleaver was one of the key devices in dense wavelength division multiplexing (DWDM) applications. In this study, an interleaver with an asymmetrical Mach-Zehnder interferometer structure was designed, fabricated, and characterized in hybrid silicon and lithium niobate thin films (Si-LNOI). The interleaver based on Si-LNOI could be fabricated by mature processing technology of Si photonic, and it was capable of the electro-optical (E-O) tuning function by using the E-O effect of LN. In the range of 1530–1620 nm, the interleaver achieved a channel spacing of 55 GHz and an extinction ratio of 12–28 dB. Due to the large refractive index of Si, the Si loading strip waveguide based on Si-LNOI had a compact optical mode area, which allowed a small electrode gap to improve the E-O modulation efficiency of the interleaver. For an E-O interaction length of 1 mm, the E-O modulation efficiency was 26 pm/V. The interleaver will have potential applications in DWDM systems, optical switches, and filters.
Microlens array device for laser light shaping in laser scanning smart headlights
Authors: Huang Kuo-Yin , Chang Ke-Peng , Chang Yung-Peng , Liu Chun-Nien , Cheng Wood-Hi
Published: June 2023

We present, what we believe to be, a novel microlens array (MLA) scheme for laser light shaping in laser scanning smart headlight. The laser spot has a Gaussian distribution that may reach a high peak power density in the central part, which is called hot spot. When the laser beam is applied to a phosphor plate for luminous conversion, the hot spot of Gaussian beam causes thermal quench and decreases luminous efficacy. To avoid this effect, an MLA is used, so as to achieve a uniform energy distribution. In this study, we propose a laser scanning smart headlight fabricated by a new MLA structure, with an arrangement providing both light uniformity and shaping. The novel MLA is designed by two-dimensional micro-concave lens array yielding a flat-top beam. The flexible fabrication process employs laser drilling to shape the micro-hole array on the glass substrate surface and then etch it to form MLA without requiring any mask lithography process. The full-width half maximum (FWHM) of light output distribution can be adjusted by the glass etching parameters, and the light distribution could be controlled by the arranged layout of the array. Thus, beams with FWHM divergence ranging from 5° to 34° has been fabricated and characterized. The typical pixel shape is a rectangle with two different FWHMs in two orthogonal directions, and the fabrication method achieves this goal as well. This novel design and unique maskless process of the MLAs is a promising tool for development the next generation laser scanning smart headlight.
Wafer-scale inverted gallium phosphide-on-insulator rib waveguides for nonlinear photonics
Authors: Cheng Weiren , Geng Zhaoting , Yu Zhuoyu , Liu Yihan , Yang Yatao , Wu Pengzhuo , Ji Houling , Yu Xiaolun , Wang Yifan , Bao Changjing , Li Yi , Zhao Qiancheng
Published: June 2023

We report a gallium phosphide-on-insulator (GaP-OI) photonic platform fabricated by an intermediate-layer bonding process aiming to increase the manufacture scalability in a low-cost manner. This is enabled by the “etch-n-transfer” sequence, which results in inverted rib waveguide structures. The shallow-etched 1.8 µm-wide waveguide has a propagation loss of 23.5 dB/cm at 1550 nm wavelength. Supercontinuum generation based on the self-phase modulation effect is observed when the waveguides are pumped by femtosecond pulses. The nonlinear refractive index of GaP, n2, is extracted to be 1.9 × 10−17 m2/W, demonstrating the great promise of the GaP-OI platform in third-order nonlinear applications.
A single-cell atlas of the sexually dimorphic Drosophila foreleg and its sensory organs during development
Authors: Hopkins Ben R. , Barmina Olga , Kopp Artyom
Published: June 2023

To respond to the world around them, animals rely on the input of a network of sensory organs distributed throughout the body. Distinct classes of sensory organs are specialized for the detection of specific stimuli such as strain, pressure, or taste. The features that underlie this specialization relate both to the neurons that innervate sensory organs and the accessory cells they comprise. To understand the genetic basis of this diversity of cell types, both within and between sensory organs, we performed single-cell RNA sequencing on the first tarsal segment of the maleDrosophila melanogasterforeleg during pupal development. This tissue displays a wide variety of functionally and structurally distinct sensory organs, including campaniform sensilla, mechanosensory bristles, and chemosensory taste bristles, as well as the sex comb, a recently evolved male-specific structure. In this study, we characterize the cellular landscape in which the sensory organs reside, identify a novel cell type that contributes to the construction of the neural lamella, and resolve the transcriptomic differences among support cells within and between sensory organs. We identify the genes that distinguish between mechanosensory and chemosensory neurons, resolve a combinatorial transcription factor code that defines 4 distinct classes of gustatory neurons and several types of mechanosensory neurons, and match the expression of sensory receptor genes to specific neuron classes. Collectively, our work identifies core genetic features of a variety of sensory organs and provides a rich, annotated resource for studying their development and function.