bluuebunny/crossref_metadata_2025 huggingface dataset:
Sustained antidepressant effect of ketamine through NMDAR trapping in the LHb
Authors: Ma Shuangshuang , Chen Min , Jiang Yihao , Xiang Xinkuan , Wang Shiqi , Wu Zuohang , Li Shuo , Cui Yihui , Wang Junying , Zhu Yanqing , Zhang Yan , Ma Huan , Duan Shumin , Li Haohong , Yang Yan , Lingle Christopher J. , Hu Hailan
Published: October 2023

Ketamine, an N-methyl-d-aspartate receptor (NMDAR) antagonist1, has revolutionized the treatment of depression because of its potent, rapid and sustained antidepressant effects2–4. Although the elimination half-life of ketamine is only 13 min in mice5, its antidepressant activities can last for at least 24 h6–9. This large discrepancy poses an interesting basic biological question and has strong clinical implications. Here we demonstrate that after a single systemic injection, ketamine continues to suppress burst firing and block NMDARs in the lateral habenula (LHb) for up to 24 h. This long inhibition of NMDARs is not due to endocytosis but depends on the use-dependent trapping of ketamine in NMDARs. The rate of untrapping is regulated by neural activity. Harnessing the dynamic equilibrium of ketamine–NMDAR interactions by activating the LHb and opening local NMDARs at different plasma ketamine concentrations, we were able to either shorten or prolong the antidepressant effects of ketamine in vivo. These results provide new insights into the causal mechanisms of the sustained antidepressant effects of ketamine. The ability to modulate the duration of ketamine action based on the biophysical properties of ketamine–NMDAR interactions opens up new opportunities for the therapeutic use of ketamine.
The burden and dynamics of hospital-acquired SARS-CoV-2 in England
Authors: Cooper Ben S. , Evans Stephanie , Jafari Yalda , Pham Thi Mui , Mo Yin , Lim Cherry , Pritchard Mark G. , Pople Diane , Hall Victoria , Stimson James , Eyre David W. , Read Jonathan M. , Donnelly Christl A. , Horby Peter , Watson Conall , Funk Sebastian , Robotham Julie V. , Knight Gwenan M.
Published: October 2023

Hospital-based transmission had a dominant role in Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus (SARS-CoV) epidemics1,2, but large-scale studies of its role in the SARS-CoV-2 pandemic are lacking. Such transmission risks spreading the virus to the most vulnerable individuals and can have wider-scale impacts through hospital–community interactions. Using data from acute hospitals in England, we quantify within-hospital transmission, evaluate likely pathways of spread and factors associated with heightened transmission risk, and explore the wider dynamical consequences. We estimate that between June 2020 and March 2021 between 95,000 and 167,000 inpatients acquired SARS-CoV-2 in hospitals (1% to 2% of all hospital admissions in this period). Analysis of time series data provided evidence that patients who themselves acquired SARS-CoV-2 infection in hospital were the main sources of transmission to other patients. Increased transmission to inpatients was associated with hospitals having fewer single rooms and lower heated volume per bed. Moreover, we show that reducing hospital transmission could substantially enhance the efficiency of punctuated lockdown measures in suppressing community transmission. These findings reveal the previously unrecognized scale of hospital transmission, have direct implications for targeting of hospital control measures and highlight the need to design hospitals better equipped to limit the transmission of future high-consequence pathogens.
Chromatin compartmentalization regulates the response to DNA damage
Authors: Arnould Coline , Rocher Vincent , Saur Florian , Bader Aldo S. , Muzzopappa Fernando , Collins Sarah , Lesage Emma , Le Bozec Benjamin , Puget Nadine , Clouaire Thomas , Mangeat Thomas , Mourad Raphael , Ahituv Nadav , Noordermeer Daan , Erdel Fabian , Bushell Martin , Marnef Aline , Legube Gaëlle
Published: October 2023

The DNA damage response is essential to safeguard genome integrity. Although the contribution of chromatin in DNA repair has been investigated1,2, the contribution of chromosome folding to these processes remains unclear3. Here we report that, after the production of double-stranded breaks (DSBs) in mammalian cells, ATM drives the formation of a new chromatin compartment (D compartment) through the clustering of damaged topologically associating domains, decorated with γH2AX and 53BP1. This compartment forms by a mechanism that is consistent with polymer–polymer phase separation rather than liquid–liquid phase separation. The D compartment arises mostly in G1 phase, is independent of cohesin and is enhanced after pharmacological inhibition of DNA-dependent protein kinase (DNA-PK) or R-loop accumulation. Importantly, R-loop-enriched DNA-damage-responsive genes physically localize to the D compartment, and this contributes to their optimal activation, providing a function for DSB clustering in the DNA damage response. However, DSB-induced chromosome reorganization comes at the expense of an increased rate of translocations, also observed in cancer genomes. Overall, we characterize how DSB-induced compartmentalization orchestrates the DNA damage response and highlight the critical impact of chromosome architecture in genomic instability.
Sublithospheric diamond ages and the supercontinent cycle
Authors: Timmerman Suzette , Stachel Thomas , Koornneef Janne M. , Smit Karen V. , Harlou Rikke , Nowell Geoff M. , Thomson Andrew R. , Kohn Simon C. , Davies Joshua H. F. L. , Davies Gareth R. , Krebs Mandy Y. , Zhang Qiwei , Milne Sarah E. M. , Harris Jeffrey W. , Kaminsky Felix , Zedgenizov Dmitry , Bulanova Galina , Smith Chris B. , Cabral Neto Izaac , Silveira Francisco V. , Burnham Antony D. , Nestola Fabrizio , Shirey Steven B. , Walter Michael J. , Steele Andrew , Pearson D. Graham
Published: October 2023

Subduction related to the ancient supercontinent cycle is poorly constrained by mantle samples. Sublithospheric diamond crystallization records the release of melts from subducting oceanic lithosphere at 300–700 km depths1,2 and is especially suited to tracking the timing and effects of deep mantle processes on supercontinents. Here we show that four isotope systems (Rb–Sr, Sm–Nd, U–Pb and Re–Os) applied to Fe-sulfide and CaSiO3 inclusions within 13 sublithospheric diamonds from Juína (Brazil) and Kankan (Guinea) give broadly overlapping crystallization ages from around 450 to 650 million years ago. The intracratonic location of the diamond deposits on Gondwana and the ages, initial isotopic ratios, and trace element content of the inclusions indicate formation from a peri-Gondwanan subduction system. Preservation of these Neoproterozoic–Palaeozoic sublithospheric diamonds beneath Gondwana until its Cretaceous breakup, coupled with majorite geobarometry3,4, suggests that they accreted to and were retained in the lithospheric keel for more than 300 Myr during supercontinent migration. We propose that this process of lithosphere growth—with diamonds attached to the supercontinent keel by the diapiric uprise of depleted buoyant material and pieces of slab crust—could have enhanced supercontinent stability.
Periodontitis of maxillary teeth screened by community periodontal index is associated with chronic rhinosinusitis defined by EPOS 2020 guideline
Authors: Kwak Jiwon , Han Munsoo , Jeong Yujin , Choi Bo Yoon , Lee Dabin , Lee Sang Hag , Kim Tae Hoon
Published: October 2023

We aimed to evaluate the association between periodontitis in the upper jaw and chronic rhinosinusitis (CRS) using the nationwide Korean National Health and Nutrition Examination Survey (KNHANES) data. In this cross-sectional study, data of KNHANES participants enrolled between 2008 and 2012 were reviewed. Periodontitis of the upper teeth was diagnosed by dentists according to the community periodontal index with standardized methods. CRS was diagnosed by otorhinolaryngologists according to the European Position Paper on Rhinosinusitis and Nasal Polyps 2020 with nasal endoscopy findings. We also evaluated the association between periodontitis and CRS according to smoking and drinking status. Univariate and multivariate logistic regression analyses were performed. Overall, 28,761 participants were eligible for analysis, and 210 were diagnosed with CRS. Periodontitis was associated with CRS diagnosis (odds ratio [OR] = 1.391, 95% confidence interval [CI] = 1.013–1.912). Non-drinkers showed no significant association between periodontitis and CRS (OR = 1.142, 95% CI 0.746–1.749). However, among drinkers, periodontitis was significantly associated with CRS (OR = 1.733, 95% CI 1.091–2.753). The number of smokers with CRS was not statistically sufficient and a logistic regression model based on smoking status could not be generated. Individuals with periodontitis in the upper jaw may need to consult an otorhinolaryngologist for comorbid CRS especially according to drinking status.
Ganoderic acid C2 exerts the pharmacological effects against cyclophosphamide-induced immunosuppression: a study involving molecular docking and experimental validation
Authors: Liu Yuchen , Tan Dongsheng , Cui Hong , Wang Jihua
Published: October 2023

Triterpenoids, as the main active ingredient of Ganoderma lucidum fermented extract, exert multiple pharmacological activities, including immunomodulatory properties. Our study aimed to reveal the pharmacological effects and potential mechanisms of Ganoderic acid C2 (GAC) against cyclophosphamide (CY)-associated immunosuppression. Target genes were collected from several public databases, including the DisGeNET, Comparative Toxicogenomics Database, GeneCards, and PharmMapper. STRING database was used to construct the protein–protein interaction of network. Subsequently, molecular docking was carried out to visualize the protein-GAC interactions. Experimental validations, including ELISA and qRT-PCR were performed to confirm the pharmacological activities of GAC on CY-induced immunosuppression model. A total of 56 GAC-related targets were identified to be closely associated with CY-induced immunosuppression. Enrichment analyses results revealed that these targets were mainly involved in immune and inflammatory response-related pathways. STAT3 and TNF were identified as the core targets of GAC. Molecular docking indicated that GAC combined well with STAT3 and TNF protein. In addition, animal experiments indicated that GAC improved immunity as well as STAT3 and TNF genes expression in CY-induced immunosuppression, which further verified the prediction through bioinformatics analysis and molecular docking. We successfully revealed the potential therapeutics mechanisms underlying the effect of GAC against CY-induced immunosuppression based on the combination of bioinformatics analysis, molecular docking, and animal experiments. Our findings lay a theoretical foundation for the in-depth development and utilization of Ganoderma lucidum fermentation product in the future, and also provide theoretical guidance for the development of innovative drugs that assist in improving immunity.
Discrimination of Camellia cultivars using iD-NA analysis
Authors: Kikkawa Hitomi S. , Sato Mitsuhiko P. , Matsuo Ayumi , Sasaki Takanori , Suyama Yoshihisa , Tsuge Kouichiro
Published: October 2023

Recently, many new cultivars have been taken abroad illegally, which is now considered an international issue. Botanical evidence found at a crime scene provides valuable information about the origin of the sample. However, botanical resources for forensic evidence remain underutilized because molecular markers, such as microsatellites, are not available without a limited set of species. Multiplexed intersimple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) and its analysis method, identification of not applicable (iD-NA), have been used to determine several genome-wide genetic markers, making them applicable to all plant species, including those with limited available genetic information. Camellia cultivars are popular worldwide and are often planted in many gardens and bred to make new cultivars. In this study, we aimed to analyze Camellia cultivars/species through MIG-seq. MIG-seq could discriminate similar samples, such as bud mutants and closely related samples that could not be distinguished based on morphological features. This discrimination was consistent with that of a previous study that classified cultivars based on short tandem repeat (STR) markers, indicating that MIG-seq has the same or higher discrimination ability as STR markers. Furthermore, we observed unknown phylogenetic relationships. Because MIG-seq can be applied to unlimited species and low-quality DNA, it may be useful in various scientific fields.
Quad-port multiservice integrated optically transparent automotive antenna for vehicular classification applications
Authors: Kannappan Lekha , Palaniswamy Sandeep Kumar , Kanagasabai Malathi , Pakkathillam Jayaram Kizhekke , Kumar Sachin , Hussein Mousa I.
Published: October 2023

The demand for vehicular antennas increases in tandem with the need for multiple features in automobiles. The development of optically transparent antenna (OTA) has made it possible to deploy antennas on delicate surfaces such as glass. Earlier studies on OTA demonstrated its viability using materials such as transparent conducting oxides (TCO) and conductive polymers. A tri-band OTA is proposed in this paper for vehicular applications. The antenna operates at 1.8 GHz, 2.4 GHz and 3.39–12 GHz bands, covering automotive/wireless applications such as GSM, Bluetooth, Wi-Fi, vehicular communication and electronic toll collection. The proposed OTA is developed on soda lime glass, and the material TCO is used for the radiator and the ground plane. The antenna prototype is tested on windshield and in an anechoic chamber, the gain and efficiency are found to be greater than 1 dBi and 80%, respectively. Furthermore, a machine learning technique for vehicle classification is proposed, which could help in electronic toll collection, automatic vehicle identifier, and parking management applications. The presented algorithm achieves 80% classification accuracy with a minimum window size.
Correlation between choline kinase alpha expression and 11C-choline accumulation in breast cancer using positron emission tomography/computed tomography: a retrospective study
Authors: Ozawa Akane , Iwasaki Masako , Yokoyama Kota , Tsuchiya Junichi , Kawano Ryutaro , Nishihara Hiroshi , Tateishi Ukihide
Published: October 2023

Choline kinase (CK) is reportedly overexpressed in various malignancies. Among its isoforms, CKα overexpression is presumably related to oncogenic change. Choline positron emission tomography (PET) is reportedly useful for detecting and evaluating therapy outcomes in malignancies. In this study, we investigated the correlation between CKα expression and 11C-choline accumulation in breast cancer cells. We also compared the CKα expression level with other pathological findings for investigating tumour activity. Fifty-six patients with breast cancer (mean age: 51 years) who underwent their first medical examination between May 2007 and December 2008 were enrolled. All the patients underwent 11C-choline PET/computed tomography imaging prior to surgery. The maximum standardised uptake value was recorded for evaluating 11C-choline accumulation. The intensity of CKα expression was classified using immunostaining. A significant correlation was observed between CKα expression and 11C-choline accumulation (P < 0.0001). A comparison of breast cancer mortality demonstrated that strong CKα expression was associated with a shorter survival time (P < 0.0001). 11C-choline accumulation was also negatively correlated with survival time (P < 0.0001). Tumours with strong CKα expression are reportedly highly active in breast cancer. A correlation was observed between CKα expression and 11C-choline accumulation, suggesting their role as prognostic indicators of breast cancer.
Develop an empirical flow rate correlation to model wellbore storage phenomenon for wells produced at a constant wellhead pressure
Authors: Mohammadpour Mobarakeh , Behnoud Parisa , Khorsand Movaghar Mohammad Reza
Published: October 2023

Well-test operation with a constant flow rate for long-time production is not typical in practice. Therefore, reservoirs frequently produce fluids with constant pressure at the wellhead, into a constant pressure separator or pipeline. During the production under this condition, the pressure drop at the wellbore varies as a function of the rate because of changes in the friction flow; therefore, the wellbore formation pressure is not constant. As a consequence, the wellbore storage effect emerges and should be incorporated in the modeling of fluid flow under production at a constant wellhead pressure. All available methods considering the wellbore storage effect can merely be applied for production under the constant rate condition. Moreover, well-test modeling under these circumstances needs a specific function for production rate, which made this type of well-testing less common. Even though there are exact solutions for production under the constant wellbore pressure in the Laplace domain, their inverse transform is quite complex and cannot be applied for modeling the wellbore storage effect. In this study, a new function is introduced as an approximate solution of the diffusivity equation, for a well that produces at a constant wellbore pressure, using multiple steps of the optimization process. Consequently, an efficient correlation is developed for flow rate about or concerning this condition. Next, the effect of the wellbore storage at constant pressure well-test operation was enumerated for the first time, which was commonly neglected in previous studies. This endeavor concentrated on modeling the two types of well-test operation, producing at constant wellhead pressure and, pressure build-up following the production at a constant wellhead pressure (constant pressure Build-up test). The results were also verified with numerical simulation as well as field data further confirming the excellent accuracy of developed solutions.
Propagation and reflection of thermoelastic wave in a rotating nonlocal fractional order porous medium under Hall current influence
Authors: Bibi Farhat , Ali Hashmat , Azhar Ehtsham , Jamal Muhammad , Ahmed Iftikhar , Ragab Adham E.
Published: October 2023

This investigation relates to the research on Hall current on propagation and reflection of elastic waves through non-local fractional-order thermoelastic rotating medium with voids. The system is split up into longitudinal and transverse components using the Helmholtz vector rule. It is observed that, through the frequency dispersion relation four coupled quasi-waves exist in the medium. The rotating solid modifies the nature of purely longitudinal and transverse waves toward the quasi-type waves. All the propagating waves are dispersive as they depend upon angular frequency. The quasi-longitudinal wave qP and quasi-transverse wave qSV faces cut-off frequencies. The nonlocal parameter affect all the waves except the quasi void wave. Analytically, the reflection coefficients of the wave are computed using suitable boundary conditions. MATLAB software is used to perform numerical computations for a chosen solid material. The amplitude ratios and the speed of propagation of the wave are plotted graphically for rotational frequency, nonlocal, fractional order, and Hall current parameter. The significant effect of the physical parameters on the computed results has been observed. The cut-off frequency of the waves is also presented graphically. The energy conservation law is proved in the form of energy ratios. The earlier findings in the literature are obtained as special case in the absence of rotation, Hall current parameter and porous voids.
Immunoreactive proteins of Capsicum-based spices as a threat to human health: mass spectrometry analysis and in silico mapping
Authors: Wróblewska Barbara , Ogrodowczyk Anna , Wasilewska Ewa
Published: October 2023

Dietary patterns are changing severely, especially the consumption of highly processed foods with lots of spices is increasing, carrying an increased risk of immediate hypersensitivity (type I), in sensitised individuals, due to the possible presence of allergens, especially the hidden ones. Paprika is a fruit of the Capsicum genus, which belongs to the Solanaceae family and is commonly consumed fresh or as a spice. Despite recorded cases of anaphylaxis, its allergenicity has yet to be clearly investigated. In this study, we research to identify proteins that could trigger a severe allergic reaction in patients with an equivocal clinical picture. Two types of protein extracts extracted from 3 different paprika spices were immunoblotted with sera from patients with severe allergic symptoms, presumably to paprika. Proteins from the IgE reactive bands obtained were subjected to LC–MS/MS identification and then in silico analysis to assess their possible sensitising capacity and proinflammatory potential using online tools. The spices were shown to contain a number of incompletely investigated highly immunoreactive allergenic proteins, including proteins of foreign origin (contaminants), the presence of which can stimulate inflammatory mechanisms and cross-reactivity with other food allergens, which can threaten life and health and should be investigated in detail.
Warburg-associated acidification represses lactic fermentation independently of lactate, contribution from real-time NMR on cell-free systems
Authors: Daverio Zoé , Kolkman Maxime , Perrier Johan , Brunet Lexane , Bendridi Nadia , Sanglar Corinne , Berger Marie-Agnès , Panthu Baptiste , Rautureau Gilles J. P.
Published: October 2023

Lactate accumulation and acidification in tumours are a cancer hallmark associated with the Warburg effect. Lactic acidosis correlates with cancer malignancy, and the benefit it offers to tumours has been the subject of numerous hypotheses. Strikingly, lactic acidosis enhances cancer cell survival to environmental glucose depletion by repressing high-rate glycolysis and lactic fermentation, and promoting an oxidative metabolism involving reactivated respiration. We used real-time NMR to evaluate how cytosolic lactate accumulation up to 40 mM and acidification up to pH 6.5 individually impact glucose consumption, lactate production and pyruvate evolution in isolated cytosols. We used a reductive cell-free system (CFS) to specifically study cytosolic metabolism independently of other Warburg-regulatory mechanisms found in the cell. We assessed the impact of lactate and acidification on the Warburg metabolism of cancer cytosols, and whether this effect extended to different cytosolic phenotypes of lactic fermentation and cancer. We observed that moderate acidification, independently of lactate concentration, drastically reduces the glucose consumption rate and halts lactate production in different lactic fermentation phenotypes. In parallel, for Warburg-type CFS lactate supplementation induces pyruvate accumulation at control pH, and can maintain a higher cytosolic pyruvate pool at low pH. Altogether, we demonstrate that intracellular acidification accounts for the direct repression of lactic fermentation by the Warburg-associated lactic acidosis.
Use of transcranial low-intensity focused ultrasound for targeted delivery of stem cell-derived exosomes to the brain
Authors: Haroon J. , Aboody K. , Flores L. , McDonald M. , Mahdavi K. , Zielinski M. , Jordan K. , Rindner E. , Surya J. , Venkatraman V. , Go-Stevens V. , Ngai G. , Lara J. , Hyde C. , Schafer S. , Schafer M. , Bystritsky A. , Nardi I. , Kuhn T. , Ross D. , Jordan S.
Published: October 2023

The blood–brain barrier (BBB) presents a significant challenge for targeted drug delivery. A proposed method to improve drug delivery across the BBB is focused ultrasound (fUS), which delivers ultrasound waves to a targeted location in the brain and is hypothesized to open the BBB. Furthermore, stem cell-derived exosomes have been suggested as a possible anti-inflammatory molecule that may have neural benefits, if able to pass the BBB. In the present study, transcranial low-intensity focused ultrasound (LIFU), without the use of intravenous microbubbles, was assessed for both (1) its ability to influence the BBB, as well as (2) its ability to increase the localization of intravenously administered small molecules to a specific region in the brain. In vivo rat studies were conducted with a rodent-customized 2 MHz LIFU probe (peak pressure = 1.5 MPa), and injection of labeled stem cell-derived exosomes. The results suggested that LIFU (without microbubbles) did not appear to open the BBB after exposure times of 20, 40, or 60 min; instead, there appeared to be an increase in transcytosis of the dextran tracer. Furthermore, the imaging results of the exosome study showed an increase in exosome localization in the right hippocampus following 60 min of targeted LIFU.
Experimental-based statistical models for the tensile characterization of synthetic fiber ropes: a machine learning approach
Authors: Halabi Yahia , Xu Hu , Yu Zhixiang , Alhaddad Wael , Dreier Isabelle
Published: October 2023

This study investigated the tensile behavior of some prevalent synthetic fiber ropes made of polyester, polypropylene, and nylon polymeric fibers. The aim was to generate well-documented experimental statistics and develop simplified stress–strain constitutive laws that can describe the ropes' tensile response. The methodology involved analyzing the thermal history of the fibers using the DSC technique, tensile testing of fibers and yarn components of the rope, and conducting 196 rope tensile tests with optimum testing conditions. Based on the test results, an experimental database of the ropes' tensile characteristics was established, containing different parameters of material properties, rope construction, fiber processing, fiber tensile properties, and rope tensile responses. Subsequently, ANN models were developed and optimized using MATLAB based on the generated dataset's inputs and outputs to predict the studied ropes' tri-linear stress–strain profiles. The results showed that the ANN models accurately predicted the stress–strain properties of ropes represented by the tri-linear approximation with an error of about 5% for the failure strength and strain. The study provides insight into the process-structure–property relationship of synthetic fiber ropes and contributes to minimizing the cost and effort in designing and predicting their tensile properties while contributing to the practical industry.
Predicting the potential implications of perch (Perca fluviatilis) introductions to a biodiversity-rich lake using stable isotope analysis
Authors: Tarkan Ali Serhan , Haubrock Phillip J. , Aksu Sadi , Mol Oğuzcan , Balzani Paride , Emiroğlu Özgür , Köse Esengül , Kurtul Irmak , Başkurt Sercan , Çınar Emre , Oztopcu-Vatan Pinar
Published: October 2023

Biological invasions, particularly of fish species, significantly threaten aquatic ecosystems. Among these invaders, the introduction of the European perch (Perca fluviatilis) can have particularly detrimental effects on native communities, affecting both ecosystem functioning and human well-being. In this study, carbon and nitrogen stable isotope analysis was employed, using perch originating from five different ecosystems, to model the effects of their hypothetical introduction into İznik Lake, an economically and ecologically important, biodiversity-rich lake in northern Turkey, to ultimately assess their potential predation impact and competition with native predators. The results revealed that if perch were introduced to the community, they would – considering gape size limitations – primarily prey upon Vimba vimba and Rutilus rutilus, indicating a significant feeding pressure on these species. Furthermore, the study identified a potential overlap and competition for resources between commonly mesopredator perch and the European catfish Silurus glanis, the current top predator in the ecosystem. Both species would occupy top predatory positions, emphasizing the potential disruption of predator–prey dynamics. Our findings underscore the potential ecological repercussions of perch invasions. The selective predation on V. vimba and R. rutilus, with the latter being consumed to a lesser extent by perch, could lead to cascading effects throughout the food web, altering the community structure, and ecosystem dynamics. Additionally, the competition between perch and S. glanis raises concerns about effects on the stability and functioning of the fish community. These results highlight the need for proactive management strategies to mitigate the risk of perch introductions. Strict regulations on the movement and introduction of invasive species, along with comprehensive monitoring, are crucial for preserving native communities and maintaining the ecological integrity of freshwater ecosystems. Our study demonstrates the potential predation impact of perch on vulnerable fish species and the competition with the established apex predator, emphasizing the importance of considering the ecological consequences of perch invasions and informing management decisions to ensure the conservation and sustainability of aquatic ecosystems.
Evaluating the COVID-19 vaccination program in Japan, 2021 using the counterfactual reproduction number
Authors: Kayano Taishi , Ko Yura , Otani Kanako , Kobayashi Tetsuro , Suzuki Motoi , Nishiura Hiroshi
Published: October 2023

Japan implemented its nationwide vaccination program against COVID-19 in 2021, immunizing more than one million people (approximately 1%) a day. However, the direct and indirect impacts of the program at the population level have yet to be fully evaluated. To assess the vaccine effectiveness during the Delta variant (B.1.617.2) epidemic in 2021, we used a renewal process model. A transmission model was fitted to the confirmed cases from 17 February to 30 November 2021. In the absence of vaccination, the cumulative numbers of infections and deaths during the study period were estimated to be 63.3 million (95% confidence interval [CI] 63.2–63.6) and 364,000 (95% CI 363–366), respectively; the actual numbers of infections and deaths were 4.7 million and 10,000, respectively. Were the vaccination implemented 14 days earlier, there could have been 54% and 48% fewer cases and deaths, respectively, than the actual numbers. We demonstrated the very high effectiveness of COVID-19 vaccination in Japan during 2021, which reduced mortality by more than 97% compared with the counterfactual scenario. The timing of expanding vaccination and vaccine recipients could be key to mitigating the disease burden of COVID-19. Rapid and proper decision making based on firm epidemiological input is vital.
Clinical courses of acute kidney injury in hospitalized patients: a multistate analysis
Authors: Adiyeke Esra , Ren Yuanfang , Guan Ziyuan , Ruppert Matthew M. , Rashidi Parisa , Bihorac Azra , Ozrazgat-Baslanti Tezcan
Published: October 2023

Persistence of acute kidney injury (AKI) or insufficient recovery of renal function was associated with reduced long-term survival and life quality. We quantified AKI trajectories and describe transitions through progression and recovery among hospitalized patients. 245,663 encounters from 128,271 patients admitted to UF Health between 2012 and 2019 were retrospectively categorized according to the worst AKI stage experienced within 24-h periods. Multistate models were fit for describing characteristics influencing transitions towards progressed or regressed AKI, discharge, and death. Effects of age, sex, race, admission comorbidities, and prolonged intensive care unit stay (ICU) on transition rates were examined via Cox proportional hazards models. About 20% of encounters had AKI; where 66% of those with AKI had Stage 1 as their worst AKI severity during hospitalization, 18% had Stage 2, and 16% had Stage 3 AKI (12% with kidney replacement therapy (KRT) and 4% without KRT). At 3 days following Stage 1 AKI, 71.1% (70.5–71.6%) were either resolved to No AKI or discharged, while recovery proportion was 38% (37.4–38.6%) and discharge proportion was 7.1% (6.9–7.3%) following AKI Stage 2. At 14 days following Stage 1 AKI, patients with additional frail conditions stay had lower transition proportion towards No AKI or discharge states. Multistate modeling framework is a facilitating mechanism for understanding AKI clinical course and examining characteristics influencing disease process and transition rates.
Lung microbiome on admission in critically ill patients with acute bacterial and viral pneumonia
Authors: Marimón Jose María , Sorarrain Ane , Ercibengoa Maria , Azcue Nekane , Alonso Marta , Vidaur Loreto
Published: October 2023

Composition of pulmonary microbiome of patients with severe pneumonia is poorly known. The aim of this work was to analyse the lung microbiome of patients admitted to the intensive care unit  (ICU) with severe community acquired pneumonia (CAP) between 2019 and 2021 in comparison with a control group of 6 patients undergoing digestive surgery. As a second objective, the diagnostic capabilities of metagenomics was also studied in a small group of selected patients. The lung microbiome of patients with viral (5 with Influenza A and 8 with SARS-CoV-2) pneumonia at admission showed a similar diversity as the control group (p = 0.140 and p = 0.213 respectively). Contrarily, the group of 12 patients with pneumococcal pneumonia showed a significant lower Simpson´s index (p = 0.002). In the control group (n = 6) Proteobacteria (36.6%), Firmicutes (24.2%) and Actinobacteria (23.0%) were the predominant phyla. In SARS-CoV-2 patients (n = 8), there was a predominance of Proteobacteria (mean 41.6%) (Moraxella and Pelomonas at the genus level), Actinobacteria (24.6%) (Microbacterium) and Firmicutes (22.8%) mainly Streptococcus, Staphylococcus and Veillonella. In patients with Influenza A pneumonia (n = 5) there was a predominance of Firmicutes (35.1%) mainly Streptococcus followed by Proteobacteria (29.2%) (Moraxella, Acinetobacter and Pelomonas). In the group of pneumococcal pneumonia (n = 12) two phyla predominated: Firmicutes (53.1%) (Streptococcus) and Proteobacteria (36.5%) (Haemophilus). In the 7 patients with non-pneumococcal bacterial pneumonia Haemophilus influenzae (n = 2), Legionella pneumophila (n = 2), Klebsiella pneumoniae, Streptococcus pyogenes and Leptospira were detected by metagenomics, confirming the diagnosis done using conventional microbiological techniques. The diversity of the respiratory microbiome in patients with severe viral pneumonia at ICU admission was similar to that of the control group. Contrarily, patients with pneumococcal pneumonia showed a lower grade of diversity. At initial stages of SARS-CoV-2 infection, no important alterations in the pulmonary microbiome were observed. The analysis of bacterial microbiome showed promising results as a diagnostic tool.
Evidence of the active participation of women in the intergroup conflict based on the use of aggression and cooperation
Authors: Muñoz-Reyes José Antonio , Torrico-Bazoberry Daniel , Polo Pablo , Figueroa Oriana , Guzmán-Lavín Eugenio , Fajardo Gabriela , Valenzuela Nohelia , Belinchón Montserrat , Rodríguez-Sickert Carlos , Pita Miguel
Published: October 2023

Intergroup conflict has been a persistent aspect of human societies since the emergence of our species. Various researchers have proposed that competition between groups has acted as a key selective force throughout human evolutionary history. Such intergroup competition for limited resources exacerbated the expression of intergroup aggression and intragroup cooperation. Furthermore, it would have a sexual dimorphism, with men demonstrating increased sensitivity to conflict threats—in order to maximize reproductive opportunities—, while women generally reject from active engagement in intergroup conflict. In the present study, we conducted behavioral experiments under controlled laboratory conditions to measure cooperation and aggression from using virtual games, specifically the Public Good Games and the Point Subtraction Aggression Paradigm, in a sample of 541 participants. We created control and experimental intergroup competition scenarios, where aggression and cooperation were necessary to increase monetary rewards. Our results shows that men modulate aggression and cooperation in the presence of intergroup conflict. In addition, our data also reveals that women cooperate more than men and display heightened levels of cooperation and aggression when confronted with intergroup conflict. These findings prompt a reevaluation of current functional theoretical models concerning the role of women in intergroup conflict and suggest that the dynamics of human aggression and cooperation may be more nuanced than previously believed.
Molecular markers of type II alveolar epithelial cells in acute lung injury by bioinformatics analysis
Authors: Yang Xiaoting , Wang Jing , Liu Wei
Published: October 2023

In this study, we aimed to identify molecular markers associated with type II alveolar epithelial cell injury in acute lung injury (ALI) models using bioinformatics methods. The objective was to provide new insights for the diagnosis and treatment of ALI/ARDS. We downloaded RNA SEQ datasets (GSE109913, GSE179418, and GSE119123) from the Gene Expression Omnibus (GEO) and used R language package to screen differentially expressed genes (DEGs). DEGs were annotated using Gene Ontology (GO), and their pathways were analyzed using Kyoto Encyclopedia of Genes and Genomes (KEGG). DEGs were imported into the STRING database and analyzed using Cytoscape software to determine the protein network of DEGs and calculate the top 10 nodes for the hub genes. Finally, potential therapeutic drugs for the hub genes were predicted using the DGIdb database. We identified 78 DEGs, including 70 up-regulated genes and 8 down-regulated genes. GO analysis revealed that the DEGs were mainly involved in biological processes such as granulocyte migration, response to bacterial-derived molecules, and cytokine-mediated signaling pathways. Additionally, they had cytokine activity, chemokine activity, and receptor ligand activity, and functioned in related receptor binding, CXCR chemokine receptor binding, G protein-coupled receptor binding, and other molecular functions. KEGG analysis indicated that the DEGs were mainly involved in TNF signaling pathway, IL-17 signaling pathway, NF-κB signal pathway, chemokine signal pathway, cytokine-cytokine receptor interaction signal pathway, and others. We identified eight hub genes, including IRF7, IFIT1, IFIT3, PSMB8, PSMB9, BST2, OASL2, and ZBP1, which were all up-regulated genes. We identified several hub genes of type II alveolar epithelial cells in ALI mouse models using bioinformatics analysis. These results provide new targets for understanding and treating of ALI.
Kinematic model calibration of a collaborative redundant robot using a closed kinematic chain
Authors: Petrič Tadej , Žlajpah Leon
Published: October 2023

In this paper, we propose a novel approach for the kinematic calibration of collaborative redundat robots, focusing on improving their precision using a cost-effective and efficient method. We exploit the redundancy of the closed-loop kinematic chain by utilizing a spherical joint, enabling precise definition of the robot end-effector position while maintaining free joint motion in the null space. Leveraging the availability of joint torque sensors in most collaborative robots, we employ a kinesthetic approach to obtain constrained joint motion for calibration. An optimization approach is utilized to determine the optimal kinematic parameters based on measured joint positions and a constrained end-effector position defined by the spherical joint. The effectiveness of the proposed method is demonstrated and validated on the Franka Emika Panda robot, a 7-DoF robot. Results indicate a significant enhancement in absolute accuracy, with comparable performance to more expensive sensor systems such as optical measurement systems. Our approach offers a practical and cost-effective solution for improving the precision of collaborative robots.
Genes possibly related to symbiosis in early life stages of Acropora tenuis inoculated with Symbiodinium microadriaticum
Authors: Yoshioka Yuki , Chiu Yi-Ling , Uchida Taiga , Yamashita Hiroshi , Suzuki Go , Shinzato Chuya
Published: October 2023

Due to the ecological importance of mutualism between reef-building corals and symbiotic algae (Family Symbiodiniaceae), various transcriptomic studies on coral-algal symbiosis have been performed; however, molecular mechanisms, especially genes essential to initiate and maintain these symbioses remain unknown. We investigated transcriptomic responses of Acropora tenuis to inoculation with the native algal symbiont, Symbiodinium microadriaticum, during early life stages, and identified possible symbiosis-related genes. Genes involved in immune regulation, protection against oxidative stress, and metabolic interactions between partners are particularly important for symbiosis during Acropora early life stages. In addition, molecular phylogenetic analysis revealed that some possible symbiosis-related genes originated by gene duplication in the Acropora lineage, suggesting that gene duplication may have been the driving force to establish stable mutualism in Acropora, and that symbiotic molecular mechanisms may vary among coral lineages.
Generation of DNA oligomers with similar chemical kinetics via in-silico optimization
Authors: Tobiason Michael , Yurke Bernard , Hughes William L.
Published: October 2023

Networks of interacting DNA oligomers are useful for applications such as biomarker detection, targeted drug delivery, information storage, and photonic information processing. However, differences in the chemical kinetics of hybridization reactions, referred to as kinetic dispersion, can be problematic for some applications. Here, it is found that limiting unnecessary stretches of Watson-Crick base pairing, referred to as unnecessary duplexes, can yield exceptionally low kinetic dispersions. Hybridization kinetics can be affected by unnecessary intra-oligomer duplexes containing only 2 base-pairs, and such duplexes explain up to 94% of previously reported kinetic dispersion. As a general design rule, it is recommended that unnecessary intra-oligomer duplexes larger than 2 base-pairs and unnecessary inter-oligomer duplexes larger than 7 base-pairs be avoided. Unnecessary duplexes typically scale exponentially with network size, and nearly all networks contain unnecessary duplexes substantial enough to affect hybridization kinetics. A new method for generating networks which utilizes in-silico optimization to mitigate unnecessary duplexes is proposed and demonstrated to reduce in-vitro kinetic dispersions as much as 96%. The limitations of the new design rule and generation method are evaluated in-silico by creating new oligomers for several designs, including three previously programmed reactions and one previously engineered structure.
General construction scheme for geometrically nontrivial flat band models
Authors: Kim Hyeongseop , Oh Chang-geun , Rhim Jun-Won
Published: October 2023

A singular flat band (SFB), a distinct class of the flat band, has been shown to exhibit various intriguing material properties characterized by the quantum distance. We present a general construction scheme for a tight-binding model hosting an SFB, where the quantum distance profile can be controlled. We first introduce how to build a compact localized state (CLS), endowing the flat band with a band-touching point and a specific value of the maximum quantum distance. Then, we develop a scheme designing a tight-binding Hamiltonian hosting an SFB starting from the obtained CLS, with the desired hopping range and symmetries. We propose several simple SFB models on the square and kagome lattices. Finally, we establish a bulk-boundary correspondence between the maximum quantum distance and the boundary modes for the open boundary condition, which can be used to detect the quantum distance via the electronic structure of the boundary states.
Single-ended recovery of optical fiber transmission matrices using neural networks
Authors: Zheng Yijie , Wright Terry , Wen Zhong , Yang Qing , Gordon George S. D.
Published: October 2023

Ultra-thin multimode optical fiber imaging promises next-generation medical endoscopes reaching high image resolution for deep tissues. However, current technology suffers from severe optical distortion, as the fiber’s calibration is sensitive to bending and temperature and thus requires in vivo re-measurement with access to a single end only. We present a neural network (NN)-based approach to reconstruct the fiber’s transmission matrix (TM) based on multi-wavelength reflection-mode measurements. We train two different NN architectures via a custom loss function insensitive to global phase-degeneracy: a fully connected NN and convolutional U-Net. We reconstruct the 64 × 64 complex-valued fiber TMs through a simulated single-ended optical fiber with ≤ 4% error and cross-validate on experimentally measured TMs, demonstrating both wide-field and confocal scanning image reconstruction with small error. Our TM recovery approach is 4500 times faster, is more robust to fiber perturbation during characterization, and operates with non-square TMs.
Nanotoxicity Assessment of Engineering Nanoparticles
Authors: Dumitrescu Eduard , Andreescu Daniel , Wallace Kenneth N. , Andreescu Silvana
Published: October 2023

This chapter discusses the status of nanotechnology risk assessment of engineered nanoparticles, focusing on methods for prediction of their effects and assessing potential toxicity. Examples of nanotoxicity testing using zebrafish embryos as a model toxicological target for screening and toxicity risk assessment are provided.
X-Ray Absorption Fine Structure Spectroscopy: A Structural Probe for Addressing Remediation Mechanisms Using Nanoadsorbents
Authors: Fani Pinakidou
Published: October 2023

Nanoparticles (NPs) lead the way in the field of environmental remediation and have shown promise to effectively remove toxic metals from water. The most reliable, simple, applicable and cost effective technique for water purification is the adsorption of the metal pollutants onto the surface of NPs. A powerful structural probe for unraveling the adsorption mechanism is X-ray absorption fine structure (XAFS) spectroscopy. Its element specific nature renders XAFS excellent for revealing the interactions between the adsorbate and adsorbent at the atomic level and analyzing the chemical and physical environments of both the metal atom and the particle surface. It can identify reduction and oxidation reactions with increased sensitivity, resolve directly the elemental oxidation states with high resolution, determine active surface sites and account for different types of sorption geometries. This chapter begins with a brief description of the concepts of XAFS, followed by an overview on its applications to element speciation in water treatment technology. Special focus is placed on the use of XAFS as a structural probe in NPs that are especially synthesized and used for the adsorption and immobilization of metal pollutants in water sources.
Recent advances in supramolecular fullerene chemistry
Authors: Chang Xingmao , Xu Youzhi , von Delius Max
Published: October 2023

We review recent work at the interface of supramolecular chemistry and fullerene chemistry. We focus on selective fullerene functionalization, host–guest chemistry, non-covalent dyads, mechanically interlocked architectures and 2D/3D assemblies.
Magnetic separation-assisted cluster-amplified versatile fluorescent aptasensors for the sensitive detection of target biomolecules
Authors: Kan Ailing , Ding Shengyong , Ouyang Aimei , Zhang Nan , Jiang Wei
Published: October 2023

A cluster-amplified fluorescent aptamer sensing strategy with modular functional units is constructed as a versatile platform for sensitive detection of biological targets.