bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neural network-based processing and reconstruction of compromised biophotonic image data
Authors: Fanous Michael John , Casteleiro Costa Paloma , Işıl Çağatay , Huang Luzhe , Ozcan Aydogan 
Published: September 2024

AbstractIn recent years, the integration of deep learning techniques with biophotonic setups has opened new horizons in bioimaging. A compelling trend in this field involves deliberately compromising certain measurement metrics to engineer better bioimaging tools in terms of e.g., cost, speed, and form-factor, followed by compensating for the resulting defects through the utilization of deep learning models trained on a large amount of ideal, superior or alternative data. This strategic approach has found increasing popularity due to its potential to enhance various aspects of biophotonic imaging. One of the primary motivations for employing this strategy is the pursuit of higher temporal resolution or increased imaging speed, critical for capturing fine dynamic biological processes. Additionally, this approach offers the prospect of simplifying hardware requirements and complexities, thereby making advanced imaging standards more accessible in terms of cost and/or size. This article provides an in-depth review of the diverse measurement aspects that researchers intentionally impair in their biophotonic setups, including the point spread function (PSF), signal-to-noise ratio (SNR), sampling density, and pixel resolution. By deliberately compromising these metrics, researchers aim to not only recuperate them through the application of deep learning networks, but also bolster in return other crucial parameters, such as the field of view (FOV), depth of field (DOF), and space-bandwidth product (SBP). Throughout this article, we discuss various biophotonic methods that have successfully employed this strategic approach. These techniques span a wide range of applications and showcase the versatility and effectiveness of deep learning in the context of compromised biophotonic data. Finally, by offering our perspectives on the exciting future possibilities of this rapidly evolving concept, we hope to motivate our readers from various disciplines to explore novel ways of balancing hardware compromises with compensation via artificial intelligence (AI).
Photon shifting and trapping in perovskite solar cells for improved efficiency and stability
Authors: Haque Sirazul , Alexandre Miguel , Vicente António T. , Li Kezheng , Schuster Christian S. , Yang Sui , Águas Hugo , Martins Rodrigo , Ferreira Rute A. S. , Mendes Manuel J. 
Published: September 2024

AbstractAdvanced light management techniques can enhance the sunlight absorption of perovskite solar cells (PSCs). When located at the front, they may act as a UV barrier, which is paramount for protecting the perovskite layer against UV-enabled degradation. Although it was recently shown that photonic structures such as Escher-like patterns could approach the theoretical Lambertian-limit of light trapping, it remains challenging to also implement UV protection properties for these diffractive structures while maintaining broadband absorption gains. Here, we propose a checkerboard (CB) tile pattern with designated UV photon conversion capability. Through a combined optical and electrical modeling approach, this photonic structure can increase photocurrent and power conversion efficiency in ultrathin PSCs by 25.9% and 28.2%, respectively. We further introduce a luminescent down-shifting encapsulant that converts the UV irradiation into Visible photons matching the solar cell absorption spectrum. To this end, experimentally obtained absorption and emission profiles of state-of-the-art down-shifting materials (i.e., lanthanide-based organic-inorganic hybrids) are used to predict potential gains from harnessing the UV energy. We demonstrate that at least 94% of the impinging UV radiation can be effectively converted into the Visible spectral range. Photonic protection from high-energy photons contributes to the market deployment of perovskite solar cell technology, and may become crucial for Space applications under AM0 illumination. By combining light trapping with luminescent downshifting layers, this work unravels a potential photonic solution to overcome UV degradation in PSCs while circumventing optical losses in ultrathin cells, thus improving both performance and stability.
Micro-patterning of spintronic emitters enables ultrabroadband structured terahertz radiation
Authors: Chen Hou-Tong 
Published: September 2024

AbstractStructured light beams offer promising properties for a variety of applications, but the generation of broadband structured light remains a challenge. New opportunities are emerging in the terahertz frequency range owing to recent progress in light-driven ultrafast vectorial currents through spatially patterning spintronic and optoelectronic systems.
Thresholdless coherence in a superradiant laser
Authors: Oh Seung-Hoon , Kim Jinuk , Ha Junseo , Son Gibeom , An Kyungwon 
Published: September 2024

AbstractLasing threshold in the conventional lasers is the minimum input power required to initiate laser oscillation. It has been widely accepted that the conventional laser threshold occurring around a unity intracavity photon number can be eliminated in the input-output curve by making the so-called β parameter approach unity. The recent experiments, however, have revealed that even in this case the photon statistics still undergo a transition from coherent to thermal statistics when the intracavity mean photon number is decreased below unity. Since the coherent output is only available above the diminished threshold, the long-sought promise of thresholdless lasers to produce always coherent light has become questionable. Here, we present an always-coherent thresholdless laser based on superradiance by two-level atoms in a quantum superposition state with the same phase traversing a high-Q cavity. Superradiant lasing was observed without the conventional lasing threshold around the unity photon number and the photon statistics remained near coherent even below it. The coherence was improved by reducing the coupling constant as well as the excited-state amplitude in the superposition state. Our results pave a way toward always-coherent thresholdless lasers with more practical media such as quantum dots, nitrogen-vacancy centers and doped ions in crystals.
GHSR blockade, but not reduction of peripherally circulating ghrelin via β1-adrenergic receptor antagonism, decreases binge-like alcohol drinking in mice
Authors: Richardson Rani S. , Kryszak Lindsay A. , Vendruscolo Janaina C. M. , Koob George F. , Vendruscolo Leandro F. , Leggio Lorenzo 
Published: September 2024

Abstract
Alcohol use disorder (AUD) and binge drinking are highly prevalent public health issues. The stomach-derived peptide ghrelin, and its receptor, the growth hormone secretagogue receptor (GHSR), both of which are expressed in the brain and periphery, are implicated in alcohol-related outcomes. We previously found that systemic and central administration of GHSR antagonists reduced binge-like alcohol drinking, whereas a ghrelin vaccine did not. Thus, we hypothesized that central GHSR drives binge-like alcohol drinking independently of peripheral ghrelin. To investigate this hypothesis, we antagonized β1-adrenergic receptors (β1ARs), which are required for peripheral ghrelin release, and combined them with GHSR blockers. We found that both systemic β1AR antagonism with atenolol (peripherally restricted) and metoprolol (brain permeable) robustly decreased plasma ghrelin levels. Also, ICV administration of atenolol had no effect on peripheral endogenous ghrelin levels. However, only metoprolol, but not atenolol, decreased binge-like alcohol drinking. The β1AR antagonism also did not prevent the effects of the GHSR blockers JMV2959 and PF-5190457 in decreasing binge-like alcohol drinking. These results suggest that the GHSR rather than peripheral endogenous ghrelin is involved in binge-like alcohol drinking. Thus, GHSRs and β1ARs represent possible targets for therapeutic intervention for AUD, including the potential combination of drugs that target these two systems.
Magnetic resonance imaging of regional gray matter volume in persons who died by suicide
Authors: Deininger-Czermak E. , Spencer L. , Zoelch N. , Sankar A. , Gascho D. , Guggenberger R. , Mathieu S. , Thali M. J. , Blumberg H. P. 
Published: September 2024

Abstract
In vivo neuroimaging research in suicide attempters has shown alterations in frontal system brain regions subserving emotional regulation, motivation, and self-perception; however, data from living individuals is limited in clarifying risk for suicide death. Postmortem neuroimaging provides an approach to study the brain in persons who died by suicide. Here, whole brain voxel-based analyses of magnetic resonance imaging gray matter volume measures were performed comparing persons confirmed by forensic investigation to have died by suicide (n = 24), versus other causes (n = 24), in a univariate model covarying for age and total brain volume; all subjects were scanned within 24 hours after death. Consistent with the hypothesis that persons who died by suicide would show lower gray matter volume in frontal system brain regions, this study of suicides showed lower gray matter volume in ventral frontal and its major connection sites including insula, striatum, and amygdala.
Obesity: exploring its connection to brain function through genetic and genomic perspectives
Authors: Saeed Sadia , Bonnefond Amélie , Froguel Philippe 
Published: September 2024

Abstract
Obesity represents an escalating global health burden with profound medical and economic impacts. The conventional perspective on obesity revolves around its classification as a “pure” metabolic disorder, marked by an imbalance between calorie consumption and energy expenditure. Present knowledge, however, recognizes the intricate interaction of rare or frequent genetic factors that favor the development of obesity, together with the emergence of neurodevelopmental and mental abnormalities, phenotypes that are modulated by environmental factors such as lifestyle. Thirty years of human genetic research has unveiled >20 genes, causing severe early-onset monogenic obesity and ~1000 loci associated with common polygenic obesity, most of those expressed in the brain, depicting obesity as a neurological and mental condition. Therefore, obesity’s association with brain function should be better recognized. In this context, this review seeks to broaden the current perspective by elucidating the genetic determinants that contribute to both obesity and neurodevelopmental and mental dysfunctions. We conduct a detailed examination of recent genetic findings, correlating them with clinical and behavioral phenotypes associated with obesity. This includes how polygenic obesity, influenced by a myriad of genetic variants, impacts brain regions associated with addiction and reward, differentiating it from monogenic forms. The continuum between non-syndromic and syndromic monogenic obesity, with evidence from neurodevelopmental and cognitive assessments, is also addressed. Current therapeutic approaches that target these genetic mechanisms, yielding improved clinical outcomes and cognitive advantages, are discussed. To sum up, this review corroborates the genetic underpinnings of obesity, affirming its classification as a neurological disorder that may have broader implications for neurodevelopmental and mental conditions. It highlights the promising intersection of genetics, genomics, and neurobiology as a foundation for developing tailored medical approaches to treat obesity and its related neurological aspects.
Prenatal exposure to the mineralocorticoid receptor antagonist spironolactone disrupts hippocampal area CA2 connectivity and alters behavior in mice
Authors: Jones Stephanie M. , Sleiman Sarah Jo , McCann Katharine E. , Jarmusch Alan K. , Alexander Georgia M. , Dudek Serena M. 
Published: September 2024

Abstract
In the brain, the hippocampus is enriched with mineralocorticoid receptors (MR; Nr3c2), a ligand-dependent transcription factor stimulated by the stress hormone corticosterone in rodents. Recently, we discovered that MR is required for the acquisition and maintenance of many features of mouse area CA2 neurons. Notably, we observed that immunofluorescence for the vesicular glutamate transporter 2 (vGluT2), likely representing afferents from the supramammillary nucleus (SuM), was disrupted in the embryonic, but not postnatal, MR knockout mouse CA2. To test whether pharmacological perturbation of MR activity in utero similarly disrupts CA2 connectivity, we implanted slow-release pellets containing the MR antagonist spironolactone in mouse dams during mid-gestation. After confirming that at least one likely active metabolite crossed from the dams’ serum into the embryonic brains, we found that spironolactone treatment caused a significant reduction of CA2 axon fluorescence intensity in the CA1 stratum oriens, where CA2 axons preferentially project, and that vGluT2 staining was significantly decreased in both CA2 and dentate gyrus in spironolactone-treated animals. We also found that spironolactone-treated animals exhibited increased reactivity to novel objects, an effect similar to what is seen with embryonic or postnatal CA2-targeted MR knockout. However, we found no difference in preference for social novelty between the treatment groups. We infer these results to suggest that persistent or more severe disruptions in MR function may be required to interfere with this type of social behavior. These findings do indicate, though, that developmental disruption in MR signaling can have persistent effects on hippocampal circuitry and behavior.
PPM1D activity promotes cellular transformation by preventing senescence and cell death
Authors: Stoyanov Miroslav , Martinikova Andra S. , Matejkova Katerina , Horackova Klara , Zemankova Petra , Burdova Kamila , Zemanova Zuzana , Kleiblova Petra , Kleibl Zdenek , Macurek Libor 
Published: September 2024

AbstractCell cycle checkpoints, oncogene-induced senescence and programmed cell death represent intrinsic barriers to tumorigenesis. Protein phosphatase magnesium-dependent 1 (PPM1D) is a negative regulator of the tumour suppressor p53 and has been implicated in termination of the DNA damage response. Here, we addressed the consequences of increased PPM1D activity resulting from the gain-of-function truncating mutations in exon 6 of the PPM1D. We show that while control cells permanently exit the cell cycle and reside in senescence in the presence of DNA damage caused by ionising radiation or replication stress induced by the active RAS oncogene, RPE1-hTERT and BJ-hTERT cells carrying the truncated PPM1D continue proliferation in the presence of DNA damage, form micronuclei and accumulate genomic rearrangements revealed by karyotyping. Further, we show that increased PPM1D activity promotes cell growth in the soft agar and formation of tumours in xenograft models. Finally, expression profiling of the transformed clones revealed dysregulation of several oncogenic and tumour suppressor pathways. Our data support the oncogenic potential of PPM1D in the context of exposure to ionising radiation and oncogene-induced replication stress.
Facts, uncertainties, and opportunities in wheat molecular improvement
Authors: Rafiei Fariba , Wiersma Jochum , Scofield Steve , Zhang Cankui , Alizadeh Houshang , Mohammadi Mohsen 
Published: September 2024

AbstractThe year 2020 was a landmark year for wheat. The wheat HB4 event harboring a drought-resistant gene from sunflowers, received regulatory approval and was grown commercially in Argentina, with approval for food and feed in other countries. This, indeed, is many years after the adoption of genetic modifications in other crops. The lack of consumer acceptance and resulting trade barriers halted the commercialization of the earliest events and had a chilling effect on, especially, private Research & Development (R&D) investments. As regulations for modern breeding technologies such as genome-edited cultivars are being discussed and/or adopted across the globe, we would like to propose a framework to ensure that wheat is not left behind a second time as the potential benefits far outweigh the perceived risks. In this paper, after a review of the technical challenges wheat faces with the generation of trans- and cis-genic wheat varieties, we discuss some of the factors that could help demystify the risk/reward equation and thereby the consumer’s reluctance or acceptance of these techniques for future wheat improvement. The advent of next-generation sequencing is shedding light on natural gene transfer between species and the number of perturbations other accepted techniques like mutagenesis create. The transition from classic breeding techniques and embracing transgenic, cisgenic, and genome editing approaches feels inevitable for wheat improvement if we are to develop climate-resilient wheat varieties to feed a growing world population.
Breunnerite grain and magnesium isotope chemistry reveal cation partitioning during aqueous alteration of asteroid Ryugu
Authors: Yoshimura Toshihiro , Araoka Daisuke , Naraoka Hiroshi , Sakai Saburo , Ogawa Nanako O. , Yurimoto Hisayoshi , Morita Mayu , Onose Morihiko , Yokoyama Tetsuya , Bizzarro Martin , Tanaka Satoru , Ohkouchi Naohiko , Koga Toshiki , Dworkin Jason P. , Nakamura Tomoki , Noguchi Takaaki , Okazaki Ryuji , Yabuta Hikaru , Sakamoto Kanako , Yada Toru , Nishimura Masahiro , Nakato Aiko , Miyazaki Akiko , Yogata Kasumi , Abe Masanao , Okada Tatsuaki , Usui Tomohiro , Yoshikawa Makoto , Saiki Takanao , Tanaka Satoshi , Terui Fuyuto , Nakazawa Satoru , Watanabe Sei-ichiro , Tsuda Yuichi , Tachibana Shogo , Takano Yoshinori 
Published: September 2024

AbstractReturned samples from the carbonaceous asteroid (162173) Ryugu provide pristine information on the original aqueous alteration history of the Solar System. Secondary precipitates, such as carbonates and phyllosilicates, reveal elemental partitioning of the major component ions linked to the primordial brine composition of the asteroid. Here, we report on the elemental partitioning and Mg isotopic composition (25Mg/24Mg) of breunnerite [(Mg, Fe, Mn)CO3] from the Ryugu C0002 sample and the A0106 and C0107 aggregates by sequential leaching extraction of salts, exchangeable ions, carbonates, and silicates. Breunnerite was the sample most enriched in light Mg isotopes, and the 25Mg/24Mg value of the fluid had shifted lower by ~0.38‰ than the initial value (set to 0‰) before dolomite precipitation. As a simple model, the Mg2+ first precipitated in phyllosilicates, followed by dolomite precipitation, at which time ~76−87% of Mg2+ had been removed from the primordial brine. A minor amount of phyllosilicate precipitation continued after dolomite precipitation. The element composition profiles of the latest solution that interacted with the cation exchange pool of Ryugu were predominantly Na-rich. Na+ acts as a bulk electrolyte and contributes to the stabilization of the negative surface charge of phyllosilicates and organic matter on Ryugu.
Soil heavy metals contamination and health risk of an endemic plant in southeast of Damavand Mt., Iran
Authors: Naeimi Maryam , Ashouri Parvaneh , Zandifar Samira , Boromand Zohreh 
Published: September 2024

AbstractConsidering the toxicological effects of some heavy metals (HMs) in which directly related to mortality and carcinogenicity in the population by their entrance from plants through livestock grazing, and medical skin cream, the rehabilitation of contaminated sites through phytoremediation by native plants might be quite challenging. Diplotaenia damavandica Mozaff. ex-Hedge & Lamond, is used as medical skin creams due to the existence of specific ingredients, which can be effective in treating skin disease. In the present study, the plant and associated soil sampling were performed around the boundary of D. damavandica. The concentration was measured using the Inductively coupled plasma mass spectrometry (ICP-MS). The results revealed the effect of existing endemic plants on reducing the average concentration of lead and zinc in soil by 40 and 60%, respectively, due to phytoremediation. EDX confirmed the presence of Pb and Zn in root and shoot tissues. Based on the results of this study, D. damavandica is an endemic perennial herbaceous plant with 60% biomass and prosperous root systems, which can grow in low contaminated areas of Pb in the southeast of Damavand Mt. Hence, the HMs pattern indicated less often in the aerial parts except for lead, which should be examined more carefully for skin cream uses.
Synergistic nanocoating with layer-by-layer functionalized PCL membranes enhanced by manuka honey and essential oils for advanced wound healing
Authors: Gallo Camilla , Girón-Hernández Joel , Honey Daisy A. , Fox Edward M. , Cassa Maria A. , Tonda-Turo Chiara , Camagnola Irene , Gentile Piergiorgio 
Published: September 2024

AbstractChronic wounds represent a significant global health concern, statistically impacting 1–2% of the population in developed countries throughout their lifetimes. These wounds cause considerable discomfort for patients and necessitate substantial expenditures of time and resources for treatment. Among the emerging therapeutic approaches, medicated dressings incorporating bioactive molecules, including natural compounds, are particularly promising. Hence, the objective of this study was to develop novel antimicrobial dressings for wound treatment. Specifically, polycaprolactone membranes were manufactured using the electrospinning technique and subsequently coated with natural polyelectrolytes (chitosan as a polycation and a mixture of manuka honey with essential oils nanoemulsions as a polyanion) employing the Layer-by-Layer assembly technique. Physico-chemical and morphological characterization was conducted through QCM-D, FTIR-ATR, XPS, and SEM analyses. The results from SEM and QCM-D demonstrated successful layer deposition and coating formation. Furthermore, FTIR-ATR and XPS analyses distinguished among different coating compositions. The coated membranes were tested in the presence of fibroblast cells, demonstrating biocompatibility and expression of genes coding for VEGF, COL1, and TGF-β1, which are associated with the healing process (assessed through RT-qPCR analysis). Finally, the membranes exhibited excellent antibacterial activity against both Staphylococcus aureus and Pseudomonas aeruginosa, with higher bacterial strain inhibition observed when cinnamon essential oil nanoemulsion was incorporated. Taken together, these results demonstrate the potential application of nanocoated membranes for biomedical applications, such as wound healing.
Assessing the role of evolutionary information for enhancing protein language model embeddings
Authors: Erckert Kyra , Rost Burkhard 
Published: September 2024

AbstractEmbeddings from protein Language Models (pLMs) are replacing evolutionary information from multiple sequence alignments (MSAs) as the most successful input for protein prediction. Is this because embeddings capture evolutionary information? We tested various approaches to explicitly incorporate evolutionary information into embeddings on various protein prediction tasks. While older pLMs (SeqVec, ProtBert) significantly improved through MSAs, the more recent pLM ProtT5 did not benefit. For most tasks, pLM-based outperformed MSA-based methods, and the combination of both even decreased performance for some (intrinsic disorder). We highlight the effectiveness of pLM-based methods and find limited benefits from integrating MSAs.