bluuebunny/crossref_metadata_2025 huggingface dataset:
Cell-lysis sensing drives biofilm formation in Vibrio cholerae
Authors: Prentice Jojo A. , van de Weerd Robert , Bridges Andrew A.
Published: March 2024

Matrix-encapsulated communities of bacteria, called biofilms, are ubiquitous in the environment and are notoriously difficult to eliminate in clinical and industrial settings. Biofilm formation likely evolved as a mechanism to protect resident cells from environmental challenges, yet how bacteria undergo threat assessment to inform biofilm development remains unclear. Here we find that population-level cell lysis events induce the formation of biofilms by surviving Vibrio cholerae cells. Survivors detect threats by sensing a cellular component released through cell lysis, which we identify as norspermidine. Lysis sensing occurs via the MbaA receptor with genus-level specificity, and responsive biofilm cells are shielded from phage infection and attacks from other bacteria. Thus, our work uncovers a connection between bacterial lysis and biofilm formation that may be broadly conserved among microorganisms.
Systematic analysis of ChatGPT, Google search and Llama 2 for clinical decision support tasks
Authors: Sandmann Sarah , Riepenhausen Sarah , Plagwitz Lucas , Varghese Julian
Published: March 2024

It is likely that individuals are turning to Large Language Models (LLMs) to seek health advice, much like searching for diagnoses on Google. We evaluate clinical accuracy of GPT-3·5 and GPT-4 for suggesting initial diagnosis, examination steps and treatment of 110 medical cases across diverse clinical disciplines. Moreover, two model configurations of the Llama 2 open source LLMs are assessed in a sub-study. For benchmarking the diagnostic task, we conduct a naïve Google search for comparison. Overall, GPT-4 performed best with superior performances over GPT-3·5 considering diagnosis and examination and superior performance over Google for diagnosis. Except for treatment, better performance on frequent vs rare diseases is evident for all three approaches. The sub-study indicates slightly lower performances for Llama models. In conclusion, the commercial LLMs show growing potential for medical question answering in two successive major releases. However, some weaknesses underscore the need for robust and regulated AI models in health care. Open source LLMs can be a viable option to address specific needs regarding data privacy and transparency of training.
Subthalamic nucleus deep brain stimulation alleviates oxidative stress via mitophagy in Parkinson’s disease
Authors: Chen Yingchuan , Zhu Guanyu , Yuan Tianshuo , Ma Ruoyu , Zhang Xin , Meng Fangang , Yang Anchao , Du Tingting , Zhang Jianguo
Published: March 2024

Subthalamic nucleus deep brain stimulation (STN-DBS) has the potential to delay Parkinson’s disease (PD) progression. Whether oxidative stress participates in the neuroprotective effects of DBS and related signaling pathways remains unknown. To address this, we applied STN-DBS to mice and monkey models of PD and collected brain tissue to evaluate mitophagy, oxidative stress, and related pathway. To confirm findings in animal experiments, a cohort of PD patients was recruited and oxidative stress was evaluated in cerebrospinal fluid. When PD mice received STN stimulation, the mTOR pathway was suppressed, accompanied by elevated LC3 II expression, increased mitophagosomes, and a decrease in p62 expression. The increase in mitophagy and balance of mitochondrial fission/fusion dynamics in the substantia nigra caused a marked enhancement of the antioxidant enzymes superoxide dismutase and glutathione levels. Subsequently, fewer mitochondrial apoptogenic factors were released to the cytoplasm, which resulted in a suppression of caspase activation and reservation of dopaminergic neurons. While interfaced with an mTOR activator, oxidative stress was no longer regulated by STN-DBS, with no neuroprotective effect. Similar results to those found in the rodent experiments were obtained in monkeys treated with chronic STN stimulation. Moreover, antioxidant enzymes in PD patients were increased after the operation, however, there was no relation between changes in antioxidant enzymes and motor impairment. Collectively, our study found that STN-DBS was able to increase mitophagy via an mTOR-dependent pathway, and oxidative stress was suppressed due to removal of damaged mitochondria, which was attributed to the dopaminergic neuroprotection of STN-DBS in PD.
A rapidly time-varying equatorial jet in Jupiter’s deep interior
Authors: Bloxham Jeremy , Cao Hao , Stevenson David J. , Connerney John E. P. , Bolton Scott J.
Published: March 2024

Planetary magnetic fields provide a window into the otherwise largely inaccessible dynamics of a planet’s deep interior. In particular, interaction between fluid flow in electrically conducting interior regions and the magnetic field there gives rise to observable secular variation (time dependency) of the externally observed magnetic field. Secular variation of Jupiter’s field has recently been revealed1–3 and been shown to arise, in part, from an axisymmetric, equatorial jet2. Whether this jet is time dependent has not previously been addressed, yet it is of critical importance for understanding the dynamics of the planet’s interior. If steady, it would probably be a manifestation of deep dynamo convective flow (and jets are anticipated as part of that flow4–9) but if time dependent on a timescale much shorter than the convective turnover timescale of several hundred years, it would probably have a different origin. Here we show that the jet has a wavelike fluctuation with a period of roughly 4 years, strongly suggestive of the presence of a torsional oscillation10 (a cylindrically symmetric oscillating flow about the rotation axis) or a localized Alfvén wave in Jupiter’s metallic hydrogen interior. This opens a pathway towards revealing otherwise hidden aspects of the magnetic field within the metallic hydrogen region and hence constraining the dynamo that generates Jupiter’s magnetic field.
Anomalous electrons in a metallic kagome ferromagnet
Authors: Ekahana Sandy Adhitia , Soh Y. , Tamai Anna , Gosálbez-Martínez Daniel , Yao Mengyu , Hunter Andrew , Fan Wenhui , Wang Yihao , Li Junbo , Kleibert Armin , Vaz C. A. F. , Ma Junzhang , Lee Hyungjun , Xiong Yimin , Yazyev Oleg V. , Baumberger Felix , Shi Ming , Aeppli G.
Published: March 2024

Ordinary metals contain electron liquids within well-defined ‘Fermi’ surfaces at which the electrons behave as if they were non-interacting. In the absence of transitions to entirely new phases such as insulators or superconductors, interactions between electrons induce scattering that is quadratic in the deviation of the binding energy from the Fermi level. A long-standing puzzle is that certain materials do not fit this ‘Fermi liquid’ description. A common feature is strong interactions between electrons relative to their kinetic energies. One route to this regime is special lattices to reduce the electron kinetic energies. Twisted bilayer graphene1–4 is an example, and trihexagonal tiling lattices (triangular ‘kagome’), with all corner sites removed on a 2 × 2 superlattice, can also host narrow electron bands5 for which interaction effects would be enhanced. Here we describe spectroscopy revealing non-Fermi-liquid behaviour for the ferromagnetic kagome metal Fe3Sn2 (ref. 6). We discover three C3-symmetric electron pockets at the Brillouin zone centre, two of which are expected from density functional theory. The third and most sharply defined band emerges at low temperatures and binding energies by means of fractionalization of one of the other two, most likely on the account of enhanced electron–electron interactions owing to a flat band predicted to lie just above the Fermi level. Our discovery opens the topic of how such many-body physics involving flat bands7,8 could differ depending on whether they arise from lattice geometry or from strongly localized atomic orbitals9,10.
Synthetic reversed sequences reveal default genomic states
Authors: Camellato Brendan R. , Brosh Ran , Ashe Hannah J. , Maurano Matthew T. , Boeke Jef D.
Published: March 2024

Pervasive transcriptional activity is observed across diverse species. The genomes of extant organisms have undergone billions of years of evolution, making it unclear whether these genomic activities represent effects of selection or ‘noise’1–4. Characterizing default genome states could help understand whether pervasive transcriptional activity has biological meaning. Here we addressed this question by introducing a synthetic 101-kb locus into the genomes of Saccharomyces cerevisiae and Mus musculus and characterizing genomic activity. The locus was designed by reversing but not complementing human HPRT1, including its flanking regions, thus retaining basic features of the natural sequence but ablating evolved coding or regulatory information. We observed widespread activity of both reversed and native HPRT1 loci in yeast, despite the lack of evolved yeast promoters. By contrast, the reversed locus displayed no activity at all in mouse embryonic stem cells, and instead exhibited repressive chromatin signatures. The repressive signature was alleviated in a locus variant lacking CpG dinucleotides; nevertheless, this variant was also transcriptionally inactive. These results show that synthetic genomic sequences that lack coding information are active in yeast, but inactive in mouse embryonic stem cells, consistent with a major difference in ‘default genomic states’ between these two divergent eukaryotic cell types, with implications for understanding pervasive transcription, horizontal transfer of genetic information and the birth of new genes.
Decoding chromatin states by proteomic profiling of nucleosome readers
Authors: Lukauskas Saulius , Tvardovskiy Andrey , Nguyen Nhuong V. , Stadler Mara , Faull Peter , Ravnsborg Tina , Özdemir Aygenli Bihter , Dornauer Scarlett , Flynn Helen , Lindeboom Rik G. H. , Barth Teresa K. , Brockers Kevin , Hauck Stefanie M. , Vermeulen Michiel , Snijders Ambrosius P. , Müller Christian L. , DiMaggio Peter A. , Jensen Ole N. , Schneider Robert , Bartke Till
Published: March 2024

DNA and histone modifications combine into characteristic patterns that demarcate functional regions of the genome1,2. While many ‘readers’ of individual modifications have been described3–5, how chromatin states comprising composite modification signatures, histone variants and internucleosomal linker DNA are interpreted is a major open question. Here we use a multidimensional proteomics strategy to systematically examine the interaction of around 2,000 nuclear proteins with over 80 modified dinucleosomes representing promoter, enhancer and heterochromatin states. By deconvoluting complex nucleosome-binding profiles into networks of co-regulated proteins and distinct nucleosomal features driving protein recruitment or exclusion, we show comprehensively how chromatin states are decoded by chromatin readers. We find highly distinctive binding responses to different features, many factors that recognize multiple features, and that nucleosomal modifications and linker DNA operate largely independently in regulating protein binding to chromatin. Our online resource, the Modification Atlas of Regulation by Chromatin States (MARCS), provides in-depth analysis tools to engage with our results and advance the discovery of fundamental principles of genome regulation by chromatin states.
Selfish conflict underlies RNA-mediated parent-of-origin effects
Authors: Pliota Pinelopi , Marvanova Hana , Koreshova Alevtina , Kaufman Yotam , Tikanova Polina , Krogull Daniel , Hagmüller Andreas , Widen Sonya A. , Handler Dominik , Gokcezade Joseph , Duchek Peter , Brennecke Julius , Ben-David Eyal , Burga Alejandro
Published: March 2024

Genomic imprinting—the non-equivalence of maternal and paternal genomes—is a critical process that has evolved independently in many plant and mammalian species1,2. According to kinship theory, imprinting is the inevitable consequence of conflictive selective forces acting on differentially expressed parental alleles3,4. Yet, how these epigenetic differences evolve in the first place is poorly understood3,5,6. Here we report the identification and molecular dissection of a parent-of-origin effect on gene expression that might help to clarify this fundamental question. Toxin-antidote elements (TAs) are selfish elements that spread in populations by poisoning non-carrier individuals7–9. In reciprocal crosses between two Caenorhabditis tropicalis wild isolates, we found that the slow-1/grow-1 TA is specifically inactive when paternally inherited. This parent-of-origin effect stems from transcriptional repression of the slow-1 toxin by the PIWI-interacting RNA (piRNA) host defence pathway. The repression requires PIWI Argonaute and SET-32 histone methyltransferase activities and is transgenerationally inherited via small RNAs. Remarkably, when slow-1/grow-1 is maternally inherited, slow-1 repression is halted by a translation-independent role of its maternal mRNA. That is, slow-1 transcripts loaded into eggs—but not SLOW-1 protein—are necessary and sufficient to counteract piRNA-mediated repression. Our findings show that parent-of-origin effects can evolve by co-option of the piRNA pathway and hinder the spread of selfish genes that require sex for their propagation.
Post-exercise heart rate recovery and its speed are associated with resting-reactivity cardiovagal modulation in healthy women
Authors: da Fonseca Richard Xavier , Gomes da Cruz Carlos Janssen , Soares Edgard de Melo Keene Von Koening , Garcia Giliard Lago , Porto Luiz Guilherme Grossi , Molina Guilherme Eckhardt
Published: March 2024

The present study sought to expand upon prior investigations of the relationship between post-exercise heart rate recovery (HRR) and cardiovagal resting-reactivity modulation. HRR from 1st to 5th min after maximal exercise test was correlated with a cardiovagal index of heart rate variability (SD1) at resting (supine and orthostatic positions) and its reactivity after the orthostatic stress test in 34 healthy women. Statistical analysis employed non-parametric tests with a p-value set at 5%. HRR, ∆%HRR, and coefficient of HRR (CHRR) at the 3rd and 5th min correlated with SD1 and SD1n (normalized units) in the supine position (rs = 0.36 to 0.47; p =  < 0.01). From the 1st to 5th min, HRR, ∆%HRR, and CHRR correlated with SD1 and SD1n in the orthostatic position (rs = 0.29 to 0.47; p =  ≤ 0.01 to 0.05), except for HRR at 5th min with SD1n (p = 0.06). Following the orthostatic stress test, HRR at 3rd and HRR, %∆HRR at 5th min correlated with ∆absSD1 (rs = 0.28 to 0.35; p = 0.02 to 0.05). All HRR measurements at 1st min correlated with ∆absSD1n (rs = 0.32 to 0.38; p = 0.01 to 0.03), and the CHRR at 1st min correlated with ∆%SD1(rs = 0.37; p = 0.01). After the sample was divided into high and low cardiovagal modulation subgroups, the subgroup with high modulation at rest (supine and orthostatic) and higher cardiovagal reactivity (reduction) showed faster HRR (p =  ≤ 0.01 to 0.05; ES:0.37 to 0.50). HRR throughout the 1st to 5th min positively correlates with cardiovagal modulation in the orthostatic position, and the 3rd and 5th min positively correlate with cardiovagal modulation in both postures at rest. Faster HRR following the maximal exercise test is associated with high resting-reactivity cardiovagal modulation in healthy women.
Multicenter study of the efficacy and safety of electrocautery-enhanced lumen-apposing metal stents for the internal drainage of pancreatic fluid collections
Authors: Chung Chen-Shuan , Kuo Yu-Ting , Chiu Yi-Chun , Lin Yang-Chao , Yang Chi-Ying , Chen Kuan-Chih , Liao Szu-Chia , Sun Cheuk-Kay , Lin Yen-Chih , Wang Hsiu-Po
Published: March 2024

Pancreatic fluid collections (PFCs) including pancreatic pseudocyst (PP) and walled-off necrosis (WON) are complications after acute pancreatitis. We aimed to evaluate the efficacy and safety of endoscopic ultrasound (EUS)-guided lumen-apposing metal stent (LAMS) placement to manage PFCs. Between June 2019 and May 2023, patients with symptomatic PFCs who underwent EUS-guided electrocautery-enhanced LAMS drainage were enrolled retrospectively from eight tertiary centers in Taiwan. In total, 33 [14 (42.42%) PP and 19 (57.58%) WON] patients were enrolled. Gallstones (27.27%) and abdominal pain (72.73%) were the most common etiology and indication for drainage. The technical and clinical success rates were 100% and 96.97%, respectively, and the mean procedure time was 30.55 (± 16.17) min. Complications included one (3.03%) case of self-limited bleeding; there were no cases of mortality. Seven (21.21%) patients had recurrence. Patients with disconnected pancreatic duct syndrome (DPDS) had a higher recurrence rate than those without (71.43% vs. 38.46%, p = 0.05). After replacing LAMSs with transmural double-pigtail plastic stents (DPSs) in the DPDS patients, the DPS migration rate was higher in the patients with recurrence (100% vs. 33.33%, p = 0.04). In conclusion, drainage of symptomatic PFCs with EUS-guided electrocautery-enhanced LAMS appears to be efficient and safe. Replacing LAMSs with DPSs in DPDS patients was associated with a lower recurrence rate.
Visual acuity prediction on real-life patient data using a machine learning based multistage system
Authors: Schlosser Tobias , Beuth Frederik , Meyer Trixy , Kumar Arunodhayan Sampath , Stolze Gabriel , Furashova Olga , Engelmann Katrin , Kowerko Danny
Published: March 2024

In ophthalmology, intravitreal operative medication therapy (IVOM) is a widespread treatment for diseases related to the age-related macular degeneration (AMD), the diabetic macular edema, as well as the retinal vein occlusion. However, in real-world settings, patients often suffer from loss of vision on time scales of years despite therapy, whereas the prediction of the visual acuity (VA) and the earliest possible detection of deterioration under real-life conditions is challenging due to heterogeneous and incomplete data. In this contribution, we present a workflow for the development of a research-compatible data corpus fusing different IT systems of the department of ophthalmology of a German maximum care hospital. The extensive data corpus allows predictive statements of the expected progression of a patient and his or her VA in each of the three diseases. For the disease AMD, we found out a significant deterioration of the visual acuity over time. Within our proposed multistage system, we subsequently classify the VA progression into the three groups of therapy “winners”, “stabilizers”, and “losers” (WSL classification scheme). Our OCT biomarker classification using an ensemble of deep neural networks results in a classification accuracy (F1-score) of over 98%, enabling us to complete incomplete OCT documentations while allowing us to exploit them for a more precise VA modelling process. Our VA prediction requires at least four VA examinations and optionally OCT biomarkers from the same time period to predict the VA progression within a forecasted time frame, whereas our prediction is currently restricted to IVOM/no therapy. We achieve a final prediction accuracy of 69% in macro average F1-score, while being in the same range as the ophthalmologists with 57.8 and $$50 \pm 10.7$$

50
±
10.7

% F1-score.
Factors associated to mortality in children with critical COVID-19 and multisystem inflammatory syndrome in a resource-poor setting
Authors: de Farias Emmerson C. F. , Pavão Junior Manoel J. C. , de Sales Susan C. D. , do Nascimento Luciana M. P. P. , Pavão Dalila C. A. , Pinheiro Anna P. S. , Pinheiro Andreza H. O. , Alves Marília C. B. , Ferraro Kíssila M. M. M. , Aires Larisse F. Q. , Dias Luana G. , Machado Mayara M. M. , Serrão Michaelle J. D. , Gomes Raphaella R. , de Moraes Sara M. P. , Moura Gabriella M. G. , de Sousa Adriana M. B. , Pontes Gabriela C. L. , Carvalho Railana D. F. P. , Silva Cristiane T. C. , Lemes Guilherme , da C. G. Diniz Bruna , Chermont Aurimery G. , de Almeida Kellen F. S. , Saraty Salma B. , Maia Mary L. F. , Lima Miriam R. C. , Carvalho Patricia B. , de B. Braga Renata , de O. Harada Kathia , Justino Maria C. A. , Clemente Gleice , Terreri Maria Teresa , Monteiro Marta C.
Published: March 2024

SARS-CoV-2 infection in children is usually asymptomatic/mild. However, some patients may develop critical forms. We aimed to describe characteristics and evaluate the factors associated to in-hospital mortality of patients with critical COVID-19/MIS-C in the Amazonian region. This multicenter prospective cohort included critically ill children (1 mo–18 years old), with confirmed COVID-19/MIS-C admitted to 3 tertiary Pediatric Intensive Care Units (PICU) in the Brazilian Amazon, between April/2020 and May/2023. The main outcome was in-hospital mortality and were evaluated using a multivariable Cox proportional regression. We adjusted the model for pediatric risk of mortality score version IV (PRISMIV) score and age/comorbidity. 266 patients were assessed with 187 in the severe COVID-19 group, 79 included in the MIS-C group. In the severe COVID-19 group 108 (57.8%) were male, median age was 23 months, 95 (50.8%) were up to 2 years of age. Forty-two (22.5%) patients in this group died during follow-up in a median time of 11 days (IQR, 2–28). In the MIS-C group, 56 (70.9%) were male, median age was 23 months and median follow-up was 162 days (range, 3–202). Death occurred in 17 (21.5%) patients with a median death time of 7 (IQR, 4–13) days. The mortality was associated with higher levels of Vasoactive Inotropic-Score (VIS), presence of acute respiratory distress syndrome (ARDS), higher levels of Erythrocyte Sedimentation Rate, (ESR) and thrombocytopenia. Critically ill patients with severe COVID-19 and MIS-C from the Brazilian Amazon showed a high mortality rate, within 12 days of hospitalization.
Novel biosensor for high-throughput detection of progesterone receptor-interacting endocrine disruptors
Authors: Stavreva Diana A. , Varticovski Lyuba , Raziuddin Razi , Pegoraro Gianluca , Schiltz R. Louis , Hager Gordon L.
Published: March 2024

Progesterone receptor (PR)-interacting compounds in the environment are associated with serious health hazards. However, methods for their detection in environmental samples are cumbersome. We report a sensitive activity-based biosensor for rapid and reliable screening of progesterone receptor (PR)-interacting endocrine disrupting chemicals (EDCs). The biosensor is a cell line which expresses nuclear mCherry-NF1 and a green fluorescent protein (GFP)-tagged chimera of glucocorticoid receptor (GR) N terminus fused to the ligand binding domain (LBD) of PR (GFP-GR-PR). As this LBD is shared by the PRA and PRB, the biosensor reports on the activation of both PR isoforms. This GFP-GR-PR chimera is cytoplasmic in the absence of hormone and translocates rapidly to the nucleus in response to PR agonists or antagonists in concentration- and time-dependent manner. In live cells, presence of nuclear NF1 label eliminates cell fixation and nuclear staining resulting in efficient screening. The assay can be used in screens for novel PR ligands and PR-interacting contaminants in environmental samples. A limited screen of river water samples indicated a widespread, low-level contamination with PR-interacting contaminants in all tested samples.
Interleukin-10 enhances recruitment of immune cells in the neonatal mouse model of obstructive nephropathy
Authors: Wyczanska Maja , Thalmeier Franziska , Keller Ursula , Klaus Richard , Narasimhan Hamsa , Ji Xingqi , Schraml Barbara U. , Wackerbarth Lou M. , Lange-Sperandio Bärbel
Published: March 2024

Urinary tract obstruction during renal development leads to inflammation, leukocyte infiltration, tubular cell death, and interstitial fibrosis. Interleukin-10 (IL-10) is an anti-inflammatory cytokine, produced mainly by monocytes/macrophages and regulatory T-cells. IL-10 inhibits innate and adaptive immune responses. IL-10 has a protective role in the adult model of obstructive uropathy. However, its role in neonatal obstructive uropathy is still unclear which led us to study the role of IL-10 in neonatal mice with unilateral ureteral obstruction (UUO). UUO serves as a model for congenital obstructive nephropathies, a leading cause of kidney failure in children. Newborn Il-10−/− and C57BL/6 wildtype-mice (WT) were subjected to complete UUO or sham-operation on the 2nd day of life. Neonatal kidneys were harvested at day 3, 7, and 14 of life and analyzed for different leukocyte subpopulations by FACS, for cytokines and chemokines by Luminex assay and ELISA, and for inflammation, programmed cell death, and fibrosis by immunohistochemistry and western blot. Compared to WT mice, Il-10−/− mice showed reduced infiltration of neutrophils, CD11bhi cells, conventional type 1 dendritic cells, and T-cells following UUO. Il-10−/− mice with UUO also showed a reduction in pro-inflammatory cytokine and chemokine release compared to WT with UUO, mainly of IP-10, IL-1α, MIP-2α and IL-17A. In addition, Il-10−/− mice showed less necroptosis after UUO while the rate of apoptosis was not different. Finally, α-SMA and collagen abundance as readout for fibrosis were similar in Il-10−/− and WT with UUO. Surprisingly and in contrast to adult Il-10−/− mice undergoing UUO, neonatal Il-10−/− mice with UUO showed a reduced inflammatory response compared to respective WT control mice with UUO. Notably, long term changes such as renal fibrosis were not different between neonatal Il-10−/− and neonatal WT mice with UUO suggesting that IL-10 signaling is different in neonates and adults with UUO.
Visual features are processed before navigational affordances in the human brain
Authors: Dwivedi Kshitij , Sadiya Sari , Balode Marta P. , Roig Gemma , Cichy Radoslaw M.
Published: March 2024

To navigate through their immediate environment humans process scene information rapidly. How does the cascade of neural processing elicited by scene viewing to facilitate navigational planning unfold over time? To investigate, we recorded human brain responses to visual scenes with electroencephalography and related those to computational models that operationalize three aspects of scene processing (2D, 3D, and semantic information), as well as to a behavioral model capturing navigational affordances. We found a temporal processing hierarchy: navigational affordance is processed later than the other scene features (2D, 3D, and semantic) investigated. This reveals the temporal order with which the human brain computes complex scene information and suggests that the brain leverages these pieces of information to plan navigation.
Association of serum Ly6/PLAUR domain-containing protein 1 levels with skin sclerosis in systemic sclerosis
Authors: Sugimori Ayaka , Omori Issei , Iwasawa Okuto , Saito Hinako , Nakajima Hibari , Matsuno Ai , Sato Shinichi , Sumida Hayakazu
Published: March 2024

Systemic sclerosis (SSc) is a connective tissue disease characterized by aberrant immune activation, vascular injury, and fibrosis of the skin and internal organs. Ly6/PLAUR domain-containing protein 1 (LYPD1) was reported to be secreted and to have various physiological functions such as anti-angiogenic effects. Here we investigated serum LYPD1 levels in SSc patients and the association of serum LYPD1 levels with clinical features of SSc. Serum samples were obtained from 75 SSc patients and 22 healthy individuals as controls. We measured serum LYPD1 levels using enzyme-linked immunosorbent assay kits. Then, the relationship between serum LYPD1 levels and clinical features of SSc was analyzed. Serum LYPD1 levels in diffuse cutaneous SSc (dcSSc) patients were significantly higher than those in the limited cutaneous SSc (lcSSc) patients (median [25–75th percentiles], 1693.43 [1086.61–1917.57] vs. 904.55 [714.356–1285.56] pg/mL), while there were no significant differences in the serum LYPD1 levels between lcSSc and healthy controls (904.55 [714.356–1285.56] vs. 750.71 pg/mL [544.00–912.14]). Further analysis revealed that serum LYPD1 levels in patients correlated with skin thickness scores and serum interleukin (IL)-6 levels, which were known to reflect the extent of skin thickening in SSc. Moreover, serum LYPD1 levels showed a decrease with improvement in skin thickness after treatment, along with a decrease in serum IL-6 levels. These results indicate that LYPD1 might be a potential marker for monitoring skin sclerosis and evaluating the efficacy of skin fibrosis treatment in SSc patients.
Development and validation of a novel overhead method for anteroposterior radiographs of fractured rat femurs
Authors: Sato Yosuke , Tagami Takashi , Akimoto Toshio , Takiguchi Toru , Endo Yusuke , Tsukamoto Takeshi , Hara Yoshiaki , Yokobori Shoji
Published: March 2024

We aimed to establish a new method of obtaining femur anteroposterior radiographs from live rats. We used five adult male Sprague–Dawley rats and created a femoral fracture model with an 8 mm segmental fragment. After the surgery, we obtained two femoral anteroposterior radiographs, a novel overhead method, and a traditional craniocaudal view. We obtained the overhead method three times, craniocaudal view once, and anteroposterior radiograph of the isolated femoral bone after euthanasia. We compared the overhead method and craniocaudal view with an isolated femoral anteroposterior view. We used a two-sample t-test and intraclass correlation coefficient (ICC) to estimate the intra-observer reliability. The overhead method had significantly smaller differences than the craniocaudal view for nail length (1.53 ± 1.26 vs. 11.4 ± 3.45, p < 0.001, ICC 0.96) and neck shaft angle (5.82 ± 3.8 vs. 37.8 ± 5.7, p < 0.001, ICC 0.96). No significant differences existed for intertrochanteric length/femoral head diameter (0.23 ± 0.13 vs. 0.23 ± 0.13, p = 0.96, ICC 0.98) or lateral condyle/medial condyle width (0.15 ± 0.16 vs. 0.13 ± 0.08, p = 0.82, ICC 0.99). A fragment displacement was within 0.11 mm (2.4%). The overhead method was closer to the isolated femoral anteroposterior view and had higher reliability.
The association between non-high-density lipoprotein cholesterol to high-density lipoprotein cholesterol ratio (NHHR) and prevalence of periodontitis among US adults: a cross-sectional NHANES study
Authors: Hou Kegui , Song Wenpeng , He Jun , Ma Zhaofeng
Published: March 2024

The non-high-density lipoprotein cholesterol to high-density lipoprotein cholesterol ratio (NHHR) is a recently developed lipid parameter, but there is currently a lack of research exploring its relationship with periodontitis. This study aims to identify the potential association between NHHR and periodontitis. The association between NHHR and periodontitis were examined through univariate and multivariate weighted logistic regression utilizing the National Health and Nutrition Examination Survey data from 2009 to 2014. The participants were grouped based on the type of periodontitis. This study included a total of 9023 participants, with 1947 individuals having no periodontitis, and an additional 7076 individuals suffering from periodontitis. Patients in periodontitis group demonstrated a statistically significant elevation in NHHR values 2.82 (2.05–3.80) compared to those in no periodontitis group (p < 0.001). Logistic regression analysis of variables demonstrated a positive association between NHHR and periodontitis [1.07 (1.02, 1.12) p = 0.0067]. The study revealed a positive association between NHHR and an elevated prevalence of periodontitis development. For each unit increase in NHHR, there is a 7% increase in the prevalence of periodontitis. Further investigations into NHHR may enhance our understanding of preventing and treating periodontitis. However, additional studies are required to validate these findings.
Coincidence imaging for Jones matrix with a deep-learning approach
Authors: Xi Jiawei , Yung Tsz Kit , Liang Hong , Li Tan , Tam Wing Yim , Li Jensen
Published: March 2024

Coincidence measurement has become an emerging technique for optical imaging. Based on measuring the second-order coherence g2, sample features such as reflection/transmission amplitude and phase delay can be extracted with developed algorithms pixel-by-pixel. However, an accurate measurement of g2 requires a substantial number of collected photons which becomes difficult under low-light conditions. Here, we propose a deep-learning approach for Jones matrix imaging using photon arrival data directly. A variational autoencoder (β-VAE) is trained using numerical data in an unsupervised manner to obtain a minimal data representation, which can be transformed into an image with little effort. We demonstrate as few as 88 photons collected per pixel on average to extract a Jones matrix image, with accuracy surpassing previous semi-analytic algorithms derived from g2. Our approach not only automates formulating imaging algorithms but can also assess the sufficiency of information from a designed experimental procedure, which can be useful in equipment or algorithm designs for a wide range of imaging applications.
Tobramycin-mediated self-assembly of DNA nanostructures for targeted treatment of Pseudomonas aeruginosa-infected lung inflammation
Authors: Xu Yuhang , Liu Qian , Wang Bin , Li Quan , Chen Yue , Yang Yao , Zhu Zhihao , Gong Daohui , Zhang Chuan , Wang Guansong , Qian Hang
Published: March 2024

A magnesium-free assembly method that utilizes tobramycin as a mediator to assemble DNA nanostructures is proposed. Targeting of PA is achieved by incorporating maleimide-modified DNA into the nanostructures, directed towards the pili of PA.
Modelling the effect of surface charging on plasma synthesis of ammonia using DFT
Authors: Lele Aditya Dilip , Xu Yijie , Ju Yiguang
Published: March 2024

Non-equilibrium plasma has been found to have a synergistic effect on catalytic synthesis of NH3.
Hydrotalcite-based catalysts for 1,4-conjugate addition in organic synthesis
Authors: Shaw Ranjay , Kumar Ashish
Published: March 2024

Hydrotalcites (HTs) or layered double hydroxide structures are anionic clays with layered structures resembling brucite and interlayer spaces incorporated with various anionic species and water.
Visualizing the SEI formation between lithium metal and solid-state electrolyte
Authors: Ren Fucheng , Wu Yuqi , Zuo Wenhua , Zhao Wengao , Pan Siyuan , Lin Hongxin , Yu Haichuan , Lin Jing , Lin Min , Yao Xiayin , Brezesinski Torsten , Gong Zhengliang , Yang Yong
Published: March 2024

Large-scale molecular dynamics simulations reveal the formation mechanism and structure of the solid electrolyte interphase between lithium metal and β-Li3PS4 in all-solid-state batteries.
Identification, rapid screening, docking mechanism and in vitro digestion stability of novel DPP-4 inhibitory peptides from wheat gluten with ginger protease
Authors: Pu Linsong , Kong Xiangzhen , Xing Ruoyu , Wang Yuqing , Zhang Caimeng , Hua Yufei , Chen Yeming , Li Xingfei
Published: March 2024

Natural ginger protease effectively cleaves wheat gluten to produce DPP-4 inhibitory peptides including PPFS with an IC50 value of 56 μM and better in vitro digestion stability.
C3N5-based nanomaterials and their applications in heterogeneous catalysts, energy harvesting, and environmental remediation
Authors: Xiao Linfeng , Gao Sanshuang , Liao Runhua , Zhou Yingtang , Kong Qingquan , Hu Guangzhi
Published: March 2024

The semiconductor material C3N5, due to its unique physicochemical properties and excellent material performance, has been widely researched and applied in the fields of energy, catalysis and environmental remediation.
Chemical transformation mechanism for blue-to-green emitting CsPbBr3 nanocrystals
Authors: Liu Yuling , Yun Rui , Li Yue , Sun Wenda , Zheng Tiancheng , Huang Qian , Zhang Libing , Li Xiyan
Published: March 2024

A dissolution–recrystallization strategy mediated by NOBF4 not only achieves phase conversion from Cs4PbBr6 NCs to CsPbBr3 NPLs and then to CsPbBr3 NCs, but also enables the exploration of the chemical mechanism of the post-synthesis transformation.
Selective ion transport in large-area graphene oxide membrane filters driven by the ionic radius and electrostatic interactions
Authors: Lancellotti Lidia , Bianchi Antonio , Kovtun Alessandro , Gazzano Massimo , Marforio Tainah Dorina , Xia Zhen Yuan , Calvaresi Matteo , Melucci Manuela , Zanardi Chiara , Palermo Vincenzo
Published: March 2024

Selective ion transport in large-area filters is achieved by applying a low electric voltage. The filters are made of hundreds of hollow fibers coated with a nanometric layer of graphene oxide.
Accelerating the prediction of inorganic surfaces with machine learning interatomic potentials
Authors: Noordhoek Kyle , Bartel Christopher J.
Published: March 2024

This minireview summarizes recent applications of machine learning interatomic potentials for predicting the stability and structures of solid-state surfaces.
Gallium-based liquid metals as reaction media for nanomaterials synthesis
Authors: Wang Ming , Lin Yiliang
Published: March 2024

A comprehensive overview of the recent progress in synthesizing novel nanomaterials using Ga-based liquid metals as reaction media, detailing related properties, synthetic methods and future directions.
AIE/AEE tripodal PEGyl-melphalan supramolecules and detection of trinitrophenol in water
Authors: Zhang Zhenghua , Zhang Yonghe , Cheng Liyan , Wen Fei , Feng Dan , Zhou Feng , Shi Yu-Hua , Xu Weibing
Published: March 2024

AIE supramolecular fluorescence sensor with tripod structure was designed and used to special recognize PA.
Magnetic-assisted preparation and performance control of Fe3O4/PVDF gradient magnetic composites
Authors: Wang Miao , Zhang Zhenming
Published: March 2024

In this study, a gradient Fe3O4/PVDF magnetic composite was prepared using magnetic-assisted template filling technology.
Novel methods for the rapid and sensitive detection of Nipah virus based on a CRISPR/Cas12a system
Authors: Yang Xi , Xu Kexin , Li Siying , Zhang Jiangnian , Xie Yinli , Lou Yongliang , Xiao Xingxing
Published: March 2024

A schematic diagram of RAA-CRISPR/Cas12a-FQ and RAA-CRISPR/Cas12a-FB methods in NiV detection.
Introduction to ‘The Epitranscriptome’
Authors: Kleiner Ralph E. , Höbartner Claudia , Jia Guifang
Published: March 2024

Ralph Kleiner (Princeton University, USA), Claudia Höbartner (University of Würzburg, Germany) and Guifang Jia (Peking University, China) introduce the themed collection on ‘The Epitranscriptome’.
Elevated temperature-driven coordinative reconstruction of an unsaturated single-Ni-atom structure with low valency on a polymer-derived matrix for the electrolytic oxygen evolution reaction
Authors: Patil Rahul , Rajput Anubha , Matsagar Babasaheb M. , Chen Norman C. R. , Ujihara Masaki , Salunkhe Rahul R. , Yadav Praveen , Wu Kevin C.-W. , Chakraborty Biswarup , Dutta Saikat
Published: March 2024

Elevated temperature-driven pyrolysis can generate coordinatively unsaturated NiSA-NC-900, crucial for the oxygen evolution process in water splitting, through coordination rebuilding and N-loss processes.
Anticancer evaluations of iodoquinazoline substituted with allyl and/or benzyl as dual inhibitors of EGFRWT and EGFRT790M: design, synthesis, ADMET and molecular docking
Authors: Aljohani Ahmed K. B. , El-Adl Khaled , Almohaywi Basmah , Alatawi Omar M. , Alsulaimany Marwa , El-morsy Ahmed , Almadani Sara A. , Alharbi Hussam Y. , Aljohani Majed S. , Abdulhaleem M Felemban Athary , Osman Hanan E. M. , Mohamady Samy
Published: March 2024

Fifteen new iodoquinazoline derivatives, 5a,b to 18, are reported in this study and their anticancer evaluation as dual inhibitors of EGFRWT and EGFRT790M.
Revealing the role of a bridging oxygen in a carbon shell coated Ni interface for enhanced alkaline hydrogen oxidation reaction
Authors: Han Pengyu , Yang Xinyi , Wu Liqing , Jia Hongnan , Luo Wei
Published: March 2024

Boron doped carbon coated nickel shows a remarkable activity in alkaline hydrogen oxidation. Theoretical and experimental results reveal that the Ni–O–C(B) interface in the catalyst can optimize the OHBE of Ni and enhance its HOR performance.
The “cesium effect” magnified: exceptional chemoselectivity in cesium ion mediated nucleophilic reactions
Authors: Biswas Soumen , Hughes William B. , De Angelis Luca , Haug Graham C. , Trevino Ramon , Fremin Seth O. , Arman Hadi D. , Larionov Oleg V. , Doyle Michael P.
Published: March 2024

Synthetically challenging pyridones and pyridylpyridones can now be readily accessed from simple precursors in a chemodivergent oxadiaza excision cross-coupling enabled by an unprecedented conformational accommodation-driven cesium effect.
Boosting lateral photosensing performances in a P(VDF-TrFE)/Bi2Se3/Si heterojunction induced by surface modification and ferroelectric and pyroelectric effects
Authors: Wang Qing , Zhang Guojuan , Zhang Tao , Guo Siyang , Liu Jihong , Wang Shufang , Qiao Shuang
Published: March 2024

A broadband high-sensitivity self-powered PSD is developed by using a Bi2Se3/Si heterojunction and a P(VDF-TrFE) surface functional layer, and analyzed by reducing surface electrical conductivity and coupling ferroelectric and pyroelectric effects.
Thermal degradation in methylammonium–formamidinium–guanidinium lead iodide perovskites
Authors: Minussi F. B. , Silva R. M. , Carvalho J. F. , Araújo E. B.
Published: March 2024

Thermal degradation experiments in GAxFAyMA1−x−yPbI3 perovskites show that mixed compositions are generally more stable, but not always. Large GA+ cations may decrease the stability and even change the order of the degradation kinetics.
Exploring the Views, Perspectives, and Current Practices of Educational Speech-Language Pathologists and Psychologists in Canada: How Childhood Developmental Language Disorders Are Identified and Diagnosed
Authors: Archibald Lisa M. D. , Kuyvenhoven Cassandra
Published: March 2024

Purpose:

Across Canada, speech-language pathologists (SLPs) and educational psychologists (EPs) work in schools to identify and diagnose childhood learning difficulties, including language disorders; however, both professional groups use different terms to identify and diagnose them. Using the term developmental language disorder (DLD), developed by the CATALISE consortium, would provide consistency across fields. To effectively implement the use of DLD, it is crucial to understand how EPs and SLPs currently identify childhood language disorders and to investigate the potential impact of a practice change in this area.

Method:

The study conducted 13 moderated focus groups and one one-on-one semistructured interview across six Canadian provinces in English and French.

Results:

We found some social and structural barriers that impact SLPs' and EPs' current practice of identifying and diagnosing language disorders generally (e.g., the belief that children should not be labeled “too early,” institutions that prioritize certain professional diagnoses over others, board policies that do not allocate funds for language disorders, professionals' reticence to convey difficult information such as a diagnosis to collaborators) and DLD specifically (e.g., different professional taxonomies, lack of familiarity with or uncertainty about the label, not recognized as a condition in schools that may or may not even identify language disorder as a category of exceptionality). Nevertheless, the focus groups also revealed the extent to which DLD could be useful in their current practice.

Conclusion:

Both EPs and SLPs acknowledged the importance of working together; therefore, DLD could inspire more collaborative practice between SLPs and EPs around language disorders.
An Examination of Cognitive Heterogeneity in Parkinson Disease: The Dual-Syndrome Hypothesis
Authors: Summers Dale , Spencer Kristie , Okasaki Connie , Huber Jessica E.
Published: March 2024

Purpose:

Cognitive impairment is one of the most debilitating nonmotor symptoms in Parkinson disease (PD), and its presentation is heterogeneous. One proposed model to explain cognitive variability in PD is the dual-syndrome hypothesis. This hypothesis delineates two cognitive profiles, a “fronto-striatal” profile and a “posterior cortical” profile according to symptom presentation, associated motor phenotype, and risk for dementia. The current study examined the dual-syndrome hypothesis in individuals with idiopathic PD to evaluate the existence of these profiles, determine the association with the motor phenotype (tremor dominant vs. postural instability/gait disorder), and assess the relative risk for dementia.

Method:

A retrospective examination was conducted using data from the Parkinson's Progression Markers Initiative database at baseline (within 2 years of diagnosis) and 5 years after baseline. Descriptive categorizations, cluster analyses, generalized linear mixed models, and logistic regressions were used to address the research questions.

Results:

There was emerging evidence of cognitive profiles; however, these were not fully supported by cluster analyses. Baseline cognitive profile was associated with later motor phenotype, and as predicted, dementia risk was greatest in persons with baseline posterior cortical impairments.

Conclusion:

The current results provide mixed support for the dual-syndrome hypothesis, with some evidence that the posterior cortical cognitive profile is associated with postural instability and gait disorder as well as greater dementia risk.
GalaPy: A highly optimised C++/Python spectral modelling tool for galaxies
Authors: Ronconi T. , Lapi A. , Torsello M. , Bressan A. , Donevski D. , Pantoni L. , Behiri M. , Boco L. , Cimatti A. , D’Amato Q. , Danese L. , Giulietti M. , Perrotta F. , Silva L. , Talia M. , Massardi M.
Published: March 2024

Bolstered by upcoming data from new-generation observational campaigns, we are about to enter a new era in the study of how galaxies form and evolve. The unprecedented quantity of data that will be collected from distances that have only marginally been grasped up to now will require analytical tools designed to target the specific physical peculiarities of the observed sources and handle extremely large datasets. One powerful method to investigate the complex astrophysical processes that govern the properties of galaxies is to model their observed spectral energy distributions (SEDs) at different stages of evolution and times throughout the history of the Universe. To address these challenges, we have developed GalaPy, a new library for modelling and fitting SEDs of galaxies from the X-ray to the radio band, as well as the evolution of their components and dust attenuation and reradiation. On the physical side, GalaPy incorporates both empirical and physically motivated star formation histories (SFHs), state-of-the-art single stellar population synthesis libraries, a two-component dust model for attenuation, an age-dependent energy conservation algorithm to compute dust reradiation, and additional sources of stellar continuum such as synchrotron, nebular and free-free emission, as well as X-ray radiation from low-and high-mass binary stars. On the computational side, GalaPy implements a hybrid approach that combines the high performance of compiled C++with the user-friendly flexibility of Python. Also, it exploits an object-oriented design via advanced programming techniques. GalaPy is the fastest SED-generation tool of its kind, with a peak performance of almost 1000 SEDs per second. The models are generated on the fly without relying on templates, thus minimising memory consumption. It exploits a fully Bayesian parameter space sampling, which allows for the inference of parameter posteriors and thereby facilitates the study of the correlations between the free parameters and the other physical quantities that can be derived from modelling. The application programming interface (API) and functions of GalaPy are under continuous development, with planned extensions in the near future. In this first work, we introduce the project and showcase the photometric SED fitting tools already available to users. GalaPy is available on the Python Package Index (PyPI) and comes with extensive online documentation and tutorials.