bluuebunny/crossref_metadata_2025 huggingface dataset:
Risk of central line-associated bloodstream infections during COVID-19 pandemic in intensive care patients in a tertiary care centre in Saudi Arabia
Authors: Alshamrani Majid M. , El-Saed Aiman , Aldayhani Omar , Alhassan Abdulaziz , Alhamoudi Abdullah , Alsultan Mohammed , Alrasheed Mohammed , Othman Fatmah
Published: June 2024

This retrospective study compared central line-associated bloodstream infection (CLABSI) rates per 1 000 central line days, and overall mortality before and during the COVID-19 pandemic in adult, paediatric, and neonatal ICU patients at King Abdul-Aziz Medical City-Riyadh who had a central line and were diagnosed with CLABSI according to the National Healthcare Safety Network standard definition. The study spanned between January 2018 and December 2019 (pre-pandemic), and January 2020 and December 2021 (pandemic). SARS-CoV-2 was confirmed by positive RT-PCR testing. The study included 156 CLABSI events and 46 406 central line days; 52 and 22 447 (respectively) in pre-pandemic, and 104 and 23 959 (respectively) during the pandemic. CLABSI rates increased by 2.02 per 1 000 central line days during the pandemic period (from 2.32 to 4.34, p < 0.001). Likewise, overall mortality rates increased by 0.86 per 1 000 patient days (from 0.93 to 1.79, p = 0.003). Both CLABSI rates (6.18 vs. 3.7, p = 0.006) and overall mortality (2.72 vs. 1.47, p = 0.014) were higher among COVID-19 patients compared to non-COVID-19 patients. The pandemic was associated with a substantial increase in CLABSI-associated morbidity and mortality.
THE DEVELOPMENT OF THE SAWTOOTH WAGES MODEL OF INFLATION
Authors: Carvalho André Roncaglia De
Published: June 2024

This paper covers the development of the sawtooth wages model, a graphical representation of the behavior of periodically adjusted fixed nominal wages under persistent inflationary conditions. Ranging from the immediate postwar years to the late 1980s, our narrative covers the history of the model, underscoring Bent Hansen’s (1951) contribution, followed by several improvements that aimed to incorporate into inflation theory several institution-specifc traits of underdeveloped economies. The diagram had a lukewarm reception in the 1960s but managed to defend its legacy until the 1980s, as the inertial inflation hypothesis gained terrain in the debate on economic stabilization in Latin America. Under the widespread diffusion of indexation practices, the model was then fully rehabilitated as a workhorse for theoretical and policy analysis in Brazil until a succesful stabilization was achieved in 1994 under the Real plan.
Sound Against Music
Authors: Piekut Benjamin
Published: June 2024

The Judson generation of artists (Rainer, Forti, Childs, Paxton, and others) introduced a conceptual distinction between music and sound that amounted to a soft critique of the institution of music. Dance in the 1960s was a fitting site for this critique due to the generative work of John Cage and the increasingly widespread availability of the technological means for working with sound. These two conditions undermined the institutionalization of musical expertise and opened up the field to amateurs from other disciplines.
A Second Take
Authors: Phelan Peggy
Published: June 2024

In the 1990s, performative writing and reading attempted to disrupt the rhetorical and ideological structure of scholarly writing. Performative readings helped expose the ways in which scholarly claims to truth-telling—as in Clifford Geertz’s influential essay on the Balinese cockfight—obscured violent or oppressive rhetorical operations. While most performative writing and reading concentrated on the essay form, experiments with public lectures and creative adaptations of scholarly texts were also undertaken. The verve of performative writing and reading tapered off as other issues came to the fore.
Impact of reduced rates of tiafenacil at vegetative growth stages on rice growth and yield
Authors: Miller Donnie K. , Bond Jason A. , Butts Thomas R. , Webster L. Connor , Kouame Koffi Badou-Jeremie
Published: June 2024

Tiafenacil is a new nonselective protoporphyrinogen IX oxidase–inhibiting herbicide with both grass and broadleaf activity labeled for preplant application to corn, cotton, soybean, and wheat. Early season rice emergence and growth often coincide in the mid-southern United States with applications of preplant herbicides to cotton and soybean, thereby increasing the opportunity for off-target herbicide movement from adjacent fields. Field studies were conducted to identify any deleterious effects of reduced rates of tiafenacil (12.5% to 0.4% of the lowest labeled application rate of 24.64 g ai ha−1) applied to 1- or 3-leaf rice. Visual injury 1 wk after treatment (WAT) for the 1- and 3-leaf growth stages ranged from 50% to 7% and 20% to 2%, respectively, whereas at 2 WAT these respective ranges were 13% to 2%, and no injury was observed. Tiafenacil applied at those rates had no negative season-long effect because observed early season injury was not manifested as a reduction in rice height 2 WAT or rough rice yield. Application of tiafenacil to crops directly adjacent to rice in its early vegetative stages of growth should be avoided because visual injury will occur. When off-target movement does occur, however, the affected rice should be expected to fully recover with no effect on growth or yield, assuming adequate growing conditions and agronomic/pest management are provided.
Recovering 3D Basin Basement Relief Using High‐Precision Magnetic Data Through Random Forest Regression Algorithm: A Case Study of Tianzhen‐Yanggao Sag in Datong Basin
Authors: Yao Yuhu , Zhang Xinjun , Wang Kai , Ma Yixin , Li Yuanbo , Li Jing , Xv Hongyang
Published: June 2024

Inversion of magnetic basement interfaces in basins is essential for interpreting potential field data and studying geothermal resource distribution, as well as basin formation and evolution. This paper introduces a novel method for inverting magnetic basement interfaces using a random forest regression (RFR) algorithm that combines potential field processing and machine learning techniques. The method creates magnetic base interface models and corresponding magnetic anomaly data through the random midpoint displacement method and magnetic interface finite element forward simulation. These anomalies are then processed using techniques such as directional transformations, analytical continuation, spatial derivatives, and fractional transformations. Feature attributes are extracted, and Gini importance is utilized to measure the contributions of feature factors, identify effective features, and enhance algorithm efficiency. The validity and practicality of the method are demonstrated through the analysis of both idealized and noisy models. The proposed machine learning‐based approach is more intelligent, efficient, and accurately represents the relief of magnetic base interfaces. When applied to magnetic survey data in the Datong Basin, it produced a reliable basin base model that aligns with known structural information, paving the way for further research in magnetic interface inversion.
Velocity and Temperature Dependence of Steady‐State Friction of Natural Gouge Controlled by Competing Healing Mechanisms
Authors: Nie Shiying , Barbot Sylvain
Published: June 2024

The empirical rate‐ and state‐dependent friction law is widely used to explain the frictional resistance of rocks. However, the constitutive parameters vary with temperature and sliding velocity, preventing extrapolation of laboratory results to natural conditions. Here, we explain the frictional properties of natural gouge from the San Andreas Fault, Alpine Fault, and the Nankai Trough from room temperature to ∼300°C for a wide range of slip‐rates with constant constitutive parameters by invoking the competition between two healing mechanisms with different thermodynamic properties. A transition from velocity‐strengthening to velocity‐weakening at steady‐state can be attained either by decreasing the slip‐rate or by increasing temperature. Our study provides a framework to understand the physics underlying the slip‐rate and state dependence of friction and the dependence of frictional properties on ambient physical conditions.
Season‐Dependent Atmosphere‐Ocean Coupled Processes Driving SST Seasonality Changes in a Warmer Climate
Authors: Jo Anila Rani , Lee June‐Yi , Sharma Sahil , Lee Sun‐Seon
Published: June 2024

Amplification of sea surface temperature (SST) seasonality in response to global warming is a robust feature in climate model projections but season‐dependent regional disparities in this amplification and the associated mechanisms are not well addressed. Here, by analyzing large ensemble simulations using Community Earth System Model version 2, we investigate detailed spatiotemporal characteristics of the amplification of SST seasonality focusing on the North Pacific and North Atlantic, where robust changes are projected to emerge around 2050 under SSP3‐7.0 scenario. Our results indicate that atmosphere‐ocean coupled processes shape regional changes in SST seasonality differently between warm (MAMJJAS) and cold seasons (ONDJF). During the warm season, the projected warming tendency is mainly due to increased net surface heat flux and weakening of vertical mixing. On the other hand, in the cold season, the projected cooling tendency is driven by strengthened vertical mixing over the North Pacific associated with the northward shift of storm tracks but weakened horizontal advection and mixing due to changes in ocean currents over the North Atlantic.
Locus of (IL-9) control: IL9 epigenetic regulation in cellular function and human disease
Authors: Son Aran , Baral Ishita , Falduto Guido H. , Schwartz Daniella M.
Published: June 2024

Interleukin-9 (IL-9) is a multifunctional cytokine with roles in a broad cross-section of human diseases. Like many cytokines, IL-9 is transcriptionally regulated by a group of noncoding regulatory elements (REs) surrounding the IL9 gene. These REs modulate IL-9 transcription by forming 3D loops that recruit transcriptional machinery. IL-9-promoting transcription factors (TFs) can bind REs to increase locus accessibility and permit chromatin looping, or they can be recruited to already accessible chromatin to promote transcription. Ample mechanistic and genome-wide association studies implicate this interplay between IL-9-modulating TFs and IL9 cis-REs in human physiology, homeostasis, and disease.
Chronic ultraviolet irradiation induces memory deficits via dysregulation of the dopamine pathway
Authors: Yoon Kyeong-No , Kim Sun Yong , Ji Jungeun , Cui Yidan , Quan Qing‐Ling , Park Gunhyuk , Oh Jang-Hee , Lee Ji Su , An Joon-Yong , Chung Jin Ho , Lee Yong-Seok , Lee Dong Hun
Published: June 2024

The effects of ultraviolet (UV) radiation on brain function have previously been investigated; however, the specific neurotransmitter-mediated mechanisms responsible for UV radiation-induced neurobehavioral changes remain elusive. In this study, we aimed to explore the mechanisms underlying UV radiation-induced neurobehavioral changes. In a mouse model, we observed that UV irradiation of the skin induces deficits in hippocampal memory, synaptic plasticity, and adult neurogenesis, as well as increased dopamine levels in the skin, adrenal glands, and brain. Chronic UV exposure altered the expression of genes involved in dopaminergic neuron differentiation. Furthermore, chronic peripheral dopamine treatments resulted in memory deficits. Systemic administration of a dopamine D1/D5 receptor antagonist reversed changes in memory, synaptic plasticity, adult neurogenesis, and gene expression in UV-irradiated mice. Our findings provide converging evidence that chronic UV exposure alters dopamine levels in the central nervous system and peripheral organs, including the skin, which may underlie the observed neurobehavioral shifts, such as hippocampal memory deficits and impaired neurogenesis. This study underscores the importance of protection from UV exposure and introduces the potential of pharmacological approaches targeting dopamine receptors to counteract the adverse neurological impacts of UV exposure.
Transcriptional regulation of Tfh dynamics and the formation of immunological synapses
Authors: Kim Ye-Ji , Choi Jinyong , Choi Youn Soo
Published: June 2024

Inside germinal centers (GCs), antigen-specific B cells rely on precise interactions with immune cells and strategic localization between the dark and light zones to clonally expand, undergo affinity maturation, and differentiate into long-lived plasma cells or memory B cells. Follicular helper T (Tfh) cells, the key gatekeepers of GC-dependent humoral immunity, exhibit remarkable dynamic positioning within secondary lymphoid tissues and rely on intercellular interactions with antigen-presenting cells (APCs) during their differentiation and execution of B-cell-facilitating functions within GCs. In this review, we briefly cover the transcriptional regulation of Tfh cell differentiation and function and explore the molecular mechanisms governing Tfh cell motility, their interactions with B cells within GCs, and the impact of their dynamic behavior on humoral responses.
Impact of severity and age with variable definitions of bronchopulmonary dysplasia on neurodevelopmental outcomes
Authors: Donlon Jack , Bhat Vishwanath , Hunter Krystal , Kushnir Alla , Bhandari Vineet
Published: June 2024

Background

Bronchopulmonary dysplasia (BPD) is associated with neurodevelopmental impairment (NDI).

Methods

To compare the ability of NICHD 2001 and Jensen 2019 definitions of BPD and respiratory support at 40 weeks postmenstrual age (PMA) to predict NDI, a retrospective study (1/2010–12/2020) was conducted in infants with gestational age <32 weeks and birth weight <1500 g. The primary outcome measure was NDI at 18–24 months corrected age.

Results

Of 1119 infants, 227 (20.7%) met the inclusion criteria and had adequate follow-up data. Multivariate regression analysis showed that the NICHD 2001 definition was not predictive of NDI. Infants with Grade 2 or 3 BPD (Jensen 2019) had 4.75 (95% CI: 1.282–17.563) times greater odds of having NDI than infants without BPD. Infants requiring respiratory support at 40 weeks PMA had 4.95 (95% CI: 1.490–16.47) times greater odds of having NDI. Receiver operating characteristic curves demonstrated that the 2 definitions of BPD and the need for respiratory support at 40 weeks PMA were similar in their ability to predict NDI.

Conclusion

There is no significant difference in the ability of the NICHD 2001 and Jensen 2019 BPD definitions, as well as the need for respiratory support at 40 weeks, for predicting NDI.

Impact Statement

Current bronchopulmonary dysplasia (BPD) definitions may not effectively predict neurodevelopmental impairment (NDI) in preterm infants.

Grades 2/3 BPD (Jensen 2019 criteria) significantly associate with NDI.

Infants requiring respiratory support at 40 weeks post-menstrual age (PMA) have 5 times higher odds of NDI than those on room air at 40 weeks PMA.

The NICHD 2001, Jensen 2019 definitions, and the requirement for respiratory support at 40 weeks PMA, do not differ in their ability to predict NDI.

Future studies should include multiple centers, with level III-IV NICUs, catering to socioeconomic, culturally, and racially diverse populations.
Pulmonary maternal immune activation does not cross the placenta but leads to fetal metabolic adaptation
Authors: Hansen Signe Schmidt Kjølner , Krautz Robert , Rago Daria , Havelund Jesper , Stigliani Arnaud , Færgeman Nils J. , Prézelin Audrey , Rivière Julie , Couturier-Tarrade Anne , Akimov Vyacheslav , Blagoev Blagoy , Elfving Betina , Neess Ditte , Vogel Ulla , Khodosevich Konstantin , Hougaard Karin Sørig , Sandelin Albin
Published: June 2024

The fetal development of organs and functions is vulnerable to perturbation by maternal inflammation which may increase susceptibility to disorders after birth. Because it is not well understood how the placenta and fetus respond to acute lung- inflammation, we characterize the response to maternal pulmonary lipopolysaccharide exposure across 24 h in maternal and fetal organs using multi-omics, imaging and integrative analyses. Unlike maternal organs, which mount strong inflammatory immune responses, the placenta upregulates immuno-modulatory genes, in particular the IL-6 signaling suppressor Socs3. Similarly, we observe no immune response in the fetal liver, which instead displays metabolic changes, including increases in lipids containing docosahexaenoic acid, crucial for fetal brain development. The maternal liver and plasma display similar metabolic alterations, potentially increasing bioavailability of docosahexaenoic acid for the mother and fetus. Thus, our integrated temporal analysis shows that systemic inflammation in the mother leads to a metabolic perturbation in the fetus.
Longitudinal multicompartment characterization of host-microbiota interactions in patients with acute respiratory failure
Authors: Kitsios Georgios D. , Sayed Khaled , Fitch Adam , Yang Haopu , Britton Noel , Shah Faraaz , Bain William , Evankovich John W. , Qin Shulin , Wang Xiaohong , Li Kelvin , Patel Asha , Zhang Yingze , Radder Josiah , Dela Cruz Charles , Okin Daniel A. , Huang Ching‐Ying , Van Tyne Daria , Benos Panayiotis V. , Methé Barbara , Lai Peggy , Morris Alison , McVerry Bryan J.
Published: June 2024

Critical illness can significantly alter the composition and function of the human microbiome, but few studies have examined these changes over time. Here, we conduct a comprehensive analysis of the oral, lung, and gut microbiota in 479 mechanically ventilated patients (223 females, 256 males) with acute respiratory failure. We use advanced DNA sequencing technologies, including Illumina amplicon sequencing (utilizing 16S and ITS rRNA genes for bacteria and fungi, respectively, in all sample types) and Nanopore metagenomics for lung microbiota. Our results reveal a progressive dysbiosis in all three body compartments, characterized by a reduction in microbial diversity, a decrease in beneficial anaerobes, and an increase in pathogens. We find that clinical factors, such as chronic obstructive pulmonary disease, immunosuppression, and antibiotic exposure, are associated with specific patterns of dysbiosis. Interestingly, unsupervised clustering of lung microbiota diversity and composition by 16S independently predicted survival and performed better than traditional clinical and host-response predictors. These observations are validated in two separate cohorts of COVID-19 patients, highlighting the potential of lung microbiota as valuable prognostic biomarkers in critical care. Understanding these microbiome changes during critical illness points to new opportunities for microbiota-targeted precision medicine interventions.
Electrical manipulation of telecom color centers in silicon
Authors: Day Aaron M. , Sutula Madison , Dietz Jonathan R. , Raun Alexander , Sukachev Denis D. , Bhaskar Mihir K. , Hu Evelyn L.
Published: June 2024

Silicon color centers have recently emerged as promising candidates for commercial quantum technology, yet their interaction with electric fields has yet to be investigated. In this paper, we demonstrate electrical manipulation of telecom silicon color centers by implementing novel lateral electrical diodes with an integrated G center ensemble in a commercial silicon on insulator wafer. The ensemble optical response is characterized under application of a reverse-biased DC electric field, observing both 100% modulation of fluorescence signal, and wavelength redshift of approximately 1.24 ± 0.08 GHz/V above a threshold voltage. Finally, we use G center fluorescence to directly image the electric field distribution within the devices, obtaining insight into the spatial and voltage-dependent variation of the junction depletion region and the associated mediating effects on the ensemble. Strong correlation between emitter-field coupling and generated photocurrent is observed. Our demonstration enables electrical control and stabilization of semiconductor quantum emitters.
Circumventing bottlenecks in H2O2 photosynthesis over carbon nitride with iodine redox chemistry and electric field effects
Authors: Bai Chang-Wei , Liu Lian-Lian , Chen Jie-Jie , Chen Fei , Zhang Zhi-Quan , Sun Yi-Jiao , Chen Xin-Jia , Yang Qi , Yu Han-Qing
Published: June 2024

Artificial photosynthesis using carbon nitride (g-C3N4) holds a great promise for sustainable and cost-effective H2O2 production, but the high carrier recombination rate impedes its efficiency. To tackle this challenge, we propose an innovative method involving multispecies iodine mediators (I−/I3−) intercalation through a pre-photo-oxidation process using potassium iodide (suspected deteriorated “KI”) within the g-C3N4 framework. Moreover, we introduce an external electric field by incorporating cationic methyl viologen ions to establish an auxiliary electron transfer channel. Such a unique design drastically improves the separation of photo-generated carriers, achieving an impressive H2O2 production rate of 46.40 mmol g−1 h−1 under visible light irradiation, surpassing the most visible-light H2O2-producing systems. Combining various advanced characterization techniques elucidates the inner photocatalytic mechanism, and the application potential of this photocatalytic system is validated with various simulation scenarios. This work presents a significative strategy for preparing and applying highly efficient g-C3N4-based catalysts in photochemical H2O2 production.
Quantitative prediction of rate constants and its application to organic emitters
Authors: Shizu Katsuyuki , Kaji Hironori
Published: June 2024

Many phenomena in nature consist of multiple elementary processes. If we can predict all the rate constants of respective processes quantitatively, we can comprehensively predict and understand various phenomena. Here, we report that it is possible to quantitatively predict all related rate constants and quantum yields without conducting experiments, using multiple-resonance thermally activated delayed fluorescence (MR–TADF) as an example. MR–TADFs are excellent emitters because of its narrow emission, high luminescence efficiency, and chemical stability, but they have one drawback: slow reverse intersystem crossing (RISC), leading to efficiency roll-off and reduced device lifetime. Here, we show a quantum chemical calculation method for quantitatively obtaining all the rate constants and quantum yields. This study reveals a strategy to improve RISC without compromising other important factors: radiative decay rate constants, photoluminescence quantum yields, and emission linewidths. Our method can be applied in a wide range of research fields, providing comprehensive understanding of the mechanism including the time evolution of excitons.
High-resolution, large field-of-view label-free imaging via aberration-corrected, closed-form complex field reconstruction
Authors: Cao Ruizhi , Shen Cheng , Yang Changhuei
Published: June 2024

Computational imaging methods empower modern microscopes to produce high-resolution, large field-of-view, aberration-free images. Fourier ptychographic microscopy can increase the space-bandwidth product of conventional microscopy, but its iterative reconstruction methods are prone to parameter selection and tend to fail under excessive aberrations. Spatial Kramers–Kronig methods can analytically reconstruct complex fields, but is limited by aberration or providing extended resolution enhancement. Here, we present APIC, a closed-form method that weds the strengths of both methods while using only NA-matching and darkfield measurements. We establish an analytical phase retrieval framework which demonstrates the feasibility of analytically reconstructing the complex field associated with darkfield measurements. APIC can retrieve complex aberrations of an imaging system with no additional hardware and avoids iterative algorithms, requiring no human-designed convergence metrics while always obtaining a closed-form complex field solution. We experimentally demonstrate that APIC gives correct reconstruction results where Fourier ptychographic microscopy fails when constrained to the same number of measurements. APIC achieves 2.8 times faster computation using image tile size of 256 (length-wise), is robust against aberrations compared to Fourier ptychographic microscopy, and capable of addressing aberrations whose maximal phase difference exceeds 3.8π when using a NA 0.25 objective in experiment.
Cross-shore parallel tidal channel systems formed by alongshore currents
Authors: Zhou Zeng , Wei Yizhang , Geng Liang , Zhang Ying , Gu Yuxian , Finotello Alvise , D’Alpaos Andrea , Gong Zheng , Xu Fan , Zhang Changkuan , Coco Giovanni
Published: June 2024

Parallel tidal channel systems, characterized by commonly cross-shore orientation and regular spacing, represent a distinct class of tidal channel networks in coastal environments worldwide. Intriguingly, these cross-shore oriented channel systems can develop in environments dominated by alongshore tidal currents, for which the mechanisms remain elusive. Here, we combine remote sensing imagery analysis and morphodynamic simulations to demonstrate that the deflection of alongshore tidal currents at transitions in bed elevation determines the characteristic orientation of the parallel tidal channels. Numerical results reveal that sharp changes in bed elevation lead to nearly 90-degree intersection angles, while smoother transitions in bed profiles result in less perpendicular channel alignments. These findings shed light on the potential manipulation of tidal channel patterns in coastal wetlands, thus equipping coastal managers with a broader range of strategies for the sustainable management of these vital ecosystems in the face of climate change and sea level rise.
Potent activity of polymyxin B is associated with long-lived super-stoichiometric accumulation mediated by weak-affinity binding to lipid A
Authors: Buchholz Kerry R. , Reichelt Mike , Johnson Matthew C. , Robinson Sarah J. , Smith Peter A. , Rutherford Steven T. , Quinn John G.
Published: June 2024

Polymyxins are gram-negative antibiotics that target lipid A, the conserved membrane anchor of lipopolysaccharide in the outer membrane. Despite their clinical importance, the molecular mechanisms underpinning polymyxin activity remain unresolved. Here, we use surface plasmon resonance to kinetically interrogate interactions between polymyxins and lipid A and derive a phenomenological model. Our analyses suggest a lipid A-catalyzed, three-state mechanism for polymyxins: transient binding, membrane insertion, and super-stoichiometric cluster accumulation with a long residence time. Accumulation also occurs for brevicidine, another lipid A-targeting antibacterial molecule. Lipid A modifications that impart polymyxin resistance and a non-bactericidal polymyxin derivative exhibit binding that does not evolve into long-lived species. We propose that transient binding to lipid A permeabilizes the outer membrane and cluster accumulation enables the bactericidal activity of polymyxins. These findings could establish a blueprint for discovery of lipid A-targeting antibiotics and provide a generalizable approach to study interactions with the gram-negative outer membrane.
Multi-omics reveals new links between Fructosamine-3-Kinase (FN3K) and core metabolic pathways
Authors: Shrestha Safal , Taujale Rahil , Katiyar Samiksha , Kannan Natarajan
Published: June 2024

Fructosamine-3-kinases (FN3Ks) are a conserved family of repair enzymes that phosphorylate reactive sugars attached to lysine residues in peptides and proteins. Although FN3Ks are present across the Tree of Life and share detectable sequence similarity to eukaryotic protein kinases, the biological processes regulated by these kinases are largely unknown. To address this knowledge gap, we leveraged the FN3K CRISPR Knock-Out (KO) HepG2 cell line alongside an integrative multi-omics study combining transcriptomics, metabolomics, and interactomics to place these enzymes in a pathway context. The integrative analyses revealed the enrichment of pathways related to oxidative stress response, lipid biosynthesis (cholesterol and fatty acids), and carbon and co-factor metabolism. Moreover, enrichment of nicotinamide adenine dinucleotide (NAD) binding proteins and localization of human FN3K (HsFN3K) to mitochondria suggests potential links between FN3K and NAD-mediated energy metabolism and redox balance. We report specific binding of HsFN3K to NAD compounds in a metal and concentration-dependent manner and provide insight into their binding mode using modeling and experimental site-directed mutagenesis. Our studies provide a framework for targeting these understudied kinases in diabetic complications and metabolic disorders where redox balance and NAD-dependent metabolic processes are altered.
Long-term trial of protection provided by adenovirus-vectored vaccine expressing the PPRV H protein
Authors: Darpel Karin E. , Corla Amanda , Stedman Anna , Bellamy Fiona , Flannery John , Rajko-Nenow Paulina , Powers Claire , Wilson Steve , Charleston Bryan , Baron Michael D. , Batten Carrie
Published: June 2024

A recombinant, replication-defective, adenovirus-vectored vaccine expressing the H surface glycoprotein of peste des petits ruminants virus (PPRV) has previously been shown to protect goats from challenge with wild-type PPRV at up to 4 months post vaccination. Here, we present the results of a longer-term trial of the protection provided by such a vaccine, challenging animals at 6, 9, 12 and 15 months post vaccination. Vaccinated animals developed high levels of anti-PPRV H protein antibodies, which were virus-neutralising, and the level of these antibodies was maintained for the duration of the trial. The vaccinated animals were largely protected against overt clinical disease from the challenge virus. Although viral genome was intermittently detected in blood samples, nasal and/or ocular swabs of vaccinated goats post challenge, viral RNA levels were significantly lower compared to unvaccinated control animals and vaccinated goats did not appear to excrete live virus. This protection, like the antibody response, was maintained at the same level for at least 15 months after vaccination. In addition, we showed that animals that have been vaccinated with the adenovirus-based vaccine can be revaccinated with the same vaccine after 12 months and showed an increased anti-PPRV antibody response after this boost vaccination. Such vaccines, which provide a DIVA capability, would therefore be suitable for use when the current live attenuated PPRV vaccines are withdrawn at the end of the ongoing global PPR eradication campaign.
De novo design of proteins housing excitonically coupled chlorophyll special pairs
Authors: Ennist Nathan M. , Wang Shunzhi , Kennedy Madison A. , Curti Mariano , Sutherland George A. , Vasilev Cvetelin , Redler Rachel L. , Maffeis Valentin , Shareef Saeed , Sica Anthony V. , Hua Ash Sueh , Deshmukh Arundhati P. , Moyer Adam P. , Hicks Derrick R. , Swartz Avi Z. , Cacho Ralph A. , Novy Nathan , Bera Asim K. , Kang Alex , Sankaran Banumathi , Johnson Matthew P. , Phadkule Amala , Reppert Mike , Ekiert Damian , Bhabha Gira , Stewart Lance , Caram Justin R. , Stoddard Barry L. , Romero Elisabet , Hunter C. Neil , Baker David
Published: June 2024

Natural photosystems couple light harvesting to charge separation using a ‘special pair’ of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer cascade. To investigate the photophysics of special pairs independently of the complexities of native photosynthetic proteins, and as a first step toward creating synthetic photosystems for new energy conversion technologies, we designed C2-symmetric proteins that hold two chlorophyll molecules in closely juxtaposed arrangements. X-ray crystallography confirmed that one designed protein binds two chlorophylls in the same orientation as native special pairs, whereas a second designed protein positions them in a previously unseen geometry. Spectroscopy revealed that the chlorophylls are excitonically coupled, and fluorescence lifetime imaging demonstrated energy transfer. The cryo-electron microscopy structure of a designed 24-chlorophyll octahedral nanocage with a special pair on each edge closely matched the design model. The results suggest that the de novo design of artificial photosynthetic systems is within reach of current computational methods.
Assessing Spatial Representativeness of Global Flux Tower Eddy-Covariance Measurements Using Data from FLUXNET2015
Authors: Fang Junjun , Fang Jingchun , Chen Baozhang , Zhang Huifang , Dilawar Adil , Guo Man , Liu Shu’an
Published: June 2024

Large datasets of carbon dioxide, energy, and water fluxes were measured with the eddy-covariance (EC) technique, such as FLUXNET2015. These datasets are widely used to validate remote-sensing products and benchmark models. One of the major challenges in utilizing EC-flux data is determining the spatial extent to which measurements taken at individual EC towers reflect model-grid or remote sensing pixels. To minimize the potential biases caused by the footprint-to-target area mismatch, it is important to use flux datasets with awareness of the footprint. This study analyze the spatial representativeness of global EC measurements based on the open-source FLUXNET2015 data, using the published flux footprint model (SAFE-f). The calculated annual cumulative footprint climatology (ACFC) was overlaid on land cover and vegetation index maps to create a spatial representativeness dataset of global flux towers. The dataset includes the following components: (1) the ACFC contour (ACFCC) data and areas representing 50%, 60%, 70%, and 80% ACFCC of each site, (2) the proportion of each land cover type weighted by the 80% ACFC (ACFCW), (3) the semivariogram calculated using Normalized Difference Vegetation Index (NDVI) considering the 80% ACFCW, and (4) the sensor location bias (SLB) between the 80% ACFCW and designated areas (e.g. 80% ACFCC and window sizes) proxied by NDVI. Finally, we conducted a comprehensive evaluation of the representativeness of each site from three aspects: (1) the underlying surface cover, (2) the semivariogram, and (3) the SLB between 80% ACFCW and 80% ACFCC, and categorized them into 3 levels. The goal of creating this dataset is to provide data quality guidance for international researchers to effectively utilize the FLUXNET2015 dataset in the future.
A nineteenth-century urban Ottoman population micro dataset: Data extraction and relational database curation from the 1840s pre-census Bursa population registers
Authors: Kabadayı M. Erdem , Erünal Efe
Published: June 2024

In recent decades, the “big microdata revolution” has transformed access to transcribed historical census data for social science research. However, the population records of the Ottoman Empire, spanning Southeastern Europe, Western Asia, and Northern Africa, remained inaccessible to the big microdata ecosystem due to their prolonged unavailability. This publication marks the inaugural release of complete population data for an Ottoman urban center, Bursa, derived from the 1839 population registers. The dataset presents originally non-tabulated register data in a tabular format integrated into a relational Microsoft Access database. Thus, we showcase the extensive and diverse data found in the Ottoman population registers, demonstrating a level of quality and sophistication akin to the censuses conducted worldwide in the nineteenth century. This valuable resource, whose potential has been massively underexploited, is now presented in an accessible format compatible with global microdata repositories. Our aim with this dataset is to enable historical demographic studies for the Ottoman realm and beyond, while also broadening access to the datasets constructed by our large research team.
Power-Doppler-based NH002 microbubble sonoporation with chemotherapy relieves hypoxia and enhances the efficacy of chemotherapy and immunotherapy for pancreatic tumors
Authors: Wu Sheng-Yan , Wang Chung-Hsin , Kang Shih-Tsung , Yu Ching-Fang , Chen Fang-Hsin , Chiang Chi-Shiun
Published: June 2024

Pancreatic ductal adenocarcinoma (PDAC) poses challenges due to late-stage diagnosis and limited treatment response, often attributed to the hypoxic tumor microenvironment (TME). Sonoporation, combining ultrasound and microbubbles, holds promise for enhancing therapy. However, additional preclinical research utilizing commercially available ultrasound equipment for PDAC treatment while delving into the TME's intricacies is necessary. This study investigated the potential of using a clinically available ultrasound system and phase 2-proven microbubbles to relieve tumor hypoxia and enhance the efficacy of chemotherapy and immunotherapy in a murine PDAC model. This approach enables early PDAC detection and blood-flow-sensitive Power-Doppler sonoporation in combination with chemotherapy. It significantly extended treated mice's median survival compared to chemotherapy alone. Mechanistically, this combination therapy enhanced tumor perfusion and substantially reduced tumor hypoxia (77% and 67%, 1- and 3-days post-treatment). Additionally, cluster of differentiation 8 (CD8) T-cell infiltration increased four-fold afterward. The combined treatment demonstrated a strengthening of the anti-programmed death-ligand 1(αPDL1) therapy against PDAC. Our study illustrates the feasibility of using a clinically available ultrasound system with NH-002 microbubbles for early tumor detection, alleviating hypoxic TME, and improving chemotherapy and immunotherapy. It suggests the development of an adjuvant theragnostic protocol incorporating Power-Doppler sonoporation for pancreatic tumor treatment.
Aloe-inspired eco-friendly synthesis of Ag/ZnO heterostructures: boosting photocatalytic potential
Authors: Ansar Nawal , Shahid Wajeehah , Irshad Muhammad Atif , Shahid Samiah , Nawaz Rab , Irfan Ali , Khan Muhammad Iftikhar , Al-Mutairi Aamal A. , Khizar Maria , Al-Hussain Sami A. , Ullah Sana , Zaki Magdi E. A.
Published: June 2024

The current research focuses on the development of Ag–ZnO heterostructures through a “bottom-up” approach involving the assembly and extraction of Aloe barbadensis Miller gel. These heterostructures composed of metals/semiconductor oxide display distinct and notable optical, electrical, magnetic, and chemical properties that are not found in single constituents and also exhibit photocatalytic applications. These synthesized heterostructures were characterized by XRD, FTIR, SEM, and UV–visible spectroscopy. The high peak intensity of the Ag/ZnO composite shows the high crystallinity. The presence of Ag–O, Zn–O, and O–H bonding is verified using FTIR analysis. SEM analysis indicated the formation of spherical shapes of Ag/ZnO heterostructures. The Zn, O, and Ag elements are further confirmed by EDX analysis. Ag–ZnO heterostructures exhibited excellent photocatalytic activity and stability against the degradation of tubantin red 8BL dye under visible light irradiation.
Climate change impacts on small pelagic fish distribution in Northwest Africa: trends, shifts, and risk for food security
Authors: Sarre Abdoulaye , Demarcq Hervé , Keenlyside Noel , Krakstad Jens-Otto , El Ayoubi Salaheddine , Jeyid Ahmed Mohamed , Faye Saliou , Mbaye Adama , Sidibeh Momodou , Brehmer Patrice
Published: June 2024

Climate change is recognised to lead to spatial shifts in the distribution of small pelagic fish, likely by altering their environmental optima. Fish supply along the Northwest African coast is significant at both socio-economic and cultural levels. Evaluating the impacts of climatic change on small pelagic fish is a challenge and of serious concern in the context of shared stock management. Evaluating the impact of climate change on the distribution of small pelagic fish, a trend analysis was conducted using data from 2363 trawl samplings and 170,000 km of acoustics sea surveys. Strong warming is reported across the Southern Canary Current Large Marine Ecosystem (CCLME), extending from Morocco to Senegal. Over 34 years, several trends emerged, with the southern CCLME experiencing increases in both wind speed and upwelling intensity, particularly where the coastal upwelling was already the strongest. Despite upwelling-induced cooling mechanisms, sea surface temperature (SST) increased in most areas, indicating the complex interplay of climatic-related stressors in shaping the marine ecosystem. Concomitant northward shifts in the distribution of small pelagic species were attributed to long-term warming trends in SST and a decrease in marine productivity in the south. The abundance of Sardinella aurita, the most abundant species along the coast, has increased in the subtropics and fallen in the intertropical region. Spatial shifts in biomass were observed for other exploited small pelagic species, similar to those recorded for surface isotherms. An intensification in upwelling intensity within the northern and central regions of the system is documented without a change in marine primary productivity. In contrast, upwelling intensity is stable in the southern region, while there is a decline in primary productivity. These environmental differences affected several small pelagic species across national boundaries. This adds a new threat to these recently overexploited fish stocks, making sustainable management more difficult. Such changes must motivate common regional policy considerations for food security and sovereignty in all West African countries sharing the same stocks.
Differential responses of primary neuron-secreted MCP-1 and IL-9 to type 2 diabetes and Alzheimer’s disease-associated metabolites
Authors: Ball Brendan K. , Kuhn Madison K. , Fleeman Bechtel Rebecca M. , Proctor Elizabeth A. , Brubaker Douglas K.
Published: June 2024

Type 2 diabetes (T2D) is implicated as a risk factor for Alzheimer’s disease (AD), the most common form of dementia. In this work, we investigated neuroinflammatory responses of primary neurons to potentially circulating, blood–brain barrier (BBB) permeable metabolites associated with AD, T2D, or both. We identified nine metabolites associated with protective or detrimental properties of AD and T2D in literature (lauric acid, asparagine, fructose, arachidonic acid, aminoadipic acid, sorbitol, retinol, tryptophan, niacinamide) and stimulated primary mouse neuron cultures with each metabolite before quantifying cytokine secretion via Luminex. We employed unsupervised clustering, inferential statistics, and partial least squares discriminant analysis to identify relationships between cytokine concentration and disease-associations of metabolites. We identified MCP-1, a cytokine associated with monocyte recruitment, as differentially abundant between neurons stimulated by metabolites associated with protective and detrimental properties of AD and T2D. We also identified IL-9, a cytokine that promotes mast cell growth, to be differentially associated with T2D. Indeed, cytokines, such as MCP-1 and IL-9, released from neurons in response to BBB-permeable metabolites associated with T2D may contribute to AD development by downstream effects of neuroinflammation.
Sustained bias of spatial attention in a 3 T MRI scanner
Authors: Smaczny Stefan , Behle Leonie , Kuppe Sara , Karnath Hans-Otto , Lindner Axel
Published: June 2024

When lying inside a MRI scanner and even in the absence of any motion, the static magnetic field of MRI scanners induces a magneto-hydrodynamic stimulation of subjects’ vestibular organ (MVS). MVS thereby not only causes a horizontal vestibular nystagmus but also induces a horizontal bias in spatial attention. In this study, we aimed to determine the time course of MVS-induced biases in both VOR and spatial attention inside a 3 T MRI-scanner as well as their respective aftereffects after participants left the scanner. Eye movements and overt spatial attention in a visual search task were assessed in healthy volunteers before, during, and after a one-hour MVS period. All participants exhibited a VOR inside the scanner, which declined over time but never vanished completely. Importantly, there was also an MVS-induced horizontal bias in spatial attention and exploration, which persisted throughout the entire hour within the scanner. Upon exiting the scanner, we observed aftereffects in the opposite direction manifested in both the VOR and in spatial attention, which were statistically no longer detectable after 7 min. Sustained MVS effects on spatial attention have important implications for the design and interpretation of fMRI-studies and for the development of therapeutic interventions counteracting spatial neglect.
RoPod, a customizable toolkit for non-invasive root imaging, reveals cell type-specific dynamics of plant autophagy
Authors: Guichard Marjorie , Holla Sanjana , Wernerová Daša , Grossmann Guido , Minina Elena A.
Published: June 2024

Arabidopsis root is a classic model system in plant cell and molecular biology. The sensitivity of plant roots to local environmental perturbation challenges data reproducibility and incentivizes further optimization of imaging and phenotyping tools. Here we present RoPod, an easy-to-use toolkit for low-stress live time-lapse imaging of Arabidopsis roots. RoPod comprises a dedicated protocol for plant cultivation and a customizable 3D-printed vessel with integrated microscopy-grade glass that serves simultaneously as a growth and imaging chamber. RoPod reduces impact of sample handling, preserves live samples for prolonged imaging sessions, and facilitates application of treatments during image acquisition. We describe a protocol for RoPods fabrication and provide illustrative application pipelines for monitoring root hair growth and autophagic activity. Furthermore, we showcase how the use of RoPods advanced our understanding of plant autophagy, a major catabolic pathway and a key player in plant fitness. Specifically, we obtained fine time resolution for autophagy response to commonly used chemical modulators of the pathway and revealed previously overlooked cell type-specific changes in the autophagy response. These results will aid a deeper understanding of the physiological role of autophagy and provide valuable guidelines for choosing sampling time during end-point assays currently employed in plant autophagy research.
Persistent dysbiosis of duodenal microbiota in patients with controlled pediatric Crohn’s disease after resolution of inflammation
Authors: Pierce Rebecca , Jan Ning-Jiun , Kumar Pankaj , Middleton Jeremy , Petri William A. , Marie Chelsea
Published: June 2024

Crohn’s disease is an inflammatory condition of the intestine characterized by largely unknown etiology and a relapse remission cycle of disease control. While possible triggers have been identified, research is inconsistent on the precise cause of these relapses, especially in the under-researched pediatric population. We hypothesized that patients in remission would have persistent microbial and inflammatory changes in small intestinal tissue that might trigger relapse. To this end, we analyzed intestinal biopsy samples from six patients with pediatric Crohn’s disease in remission and a control group of 16 pediatric patients with no evident pathogenic abnormality. We identified compositional microbiota differences, including decreases in the genera Streptococcus and Actinobacillus as well as increases in Oribacterium and Prevotella in patients with controlled Crohn’s disease compared to controls. Further, a histologic analysis found that patients with controlled Crohn’s disease had increased epithelial integrity, and decreased intraepithelial lymphocytes compared with controls. Additionally, we observed increased peripheral CD4+ T cells in patients with pediatric Crohn’s disease. These results indicate that markers of intestinal inflammation are responsive to Crohn’s disease treatment, however the interventions may not resolve the underlying dysbiosis. These findings suggest that persistent dysbiosis may increase vulnerability to relapse of pediatric Crohn’s disease. This study used a nested cohort of patients from the Bangladesh Environmental Enteric Dysfunction (BEED) study (ClinicalTrials.gov ID: NCT02812615 Date of first registration: 24/06/2016).