bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes in Blue/Green Water Partitioning Under Severe Drought
Authors: Stephens C. M. , Band L. E. , Johnson F. M. , Marshall L. A. , Medlyn B. E. , De Kauwe M. G. , Ukkola A. M.
Published: November 2023

Much attention has been given to the disproportionate streamflow deficits (relative to rainfall deficits) experienced by many catchments during the Millennium Drought (1998–2009) in southeastern Australia, along with lack of post‐drought streamflow recovery in some cases. However, mechanisms behind the coupled hydrologic and ecosystem dynamics are poorly understood. We applied a process‐based ecohydrologic model (RHESSys) in a Melbourne water supply catchment to examine changes in ecohydrologic behavior during and after the drought. Our simulations suggested that average transpiration (green water) was maintained under drought despite a substantial (12%) decrease in average rainfall, meaning that the entire rainfall deficit translated to reduced streamflow (blue water). Altered spatial patterns of vegetation behavior across the terrain helped the ecosystem maintain this unexpectedly high green water use. Decreased transpiration upland was compensated by increases in the riparian zone, which was less water limited and therefore able to meet higher water demand during drought. In the post‐drought period, we found greater transpiration and reduced subsurface water storage relative to pre‐drought, suggesting a longer‐term persistence in altered water partitioning. The post‐drought outcome was attributed to a combination of warmer climate and the persisting effects of the drought on nutrient availability. Given the importance of shifting ecohydrologic patterns across space, our results raise concerns for applying lumped conceptual hydrologic models under nonstationary or extreme conditions. Additionally, the processes we identified have important implications for water supply in Australia's second largest city under projected drying.
Flexible Foliar Stoichiometry Reduces the Magnitude of the Global Land Carbon Sink
Authors: Hauser Emma , Wieder William R. , Bonan Gordon B. , Cleveland Cory C.
Published: November 2023

Increased plant growth under elevated carbon dioxide (CO2) slows the pace of climate warming and underlies projections of terrestrial carbon (C) and climate dynamics. However, this important ecosystem service may be diminished by concurrent changes to vegetation carbon‐to‐nitrogen (C:N) ratios. Despite clear observational evidence of increasing foliar C:N under elevated CO2, our understanding of potential ecological consequences of foliar stoichiometric flexibility is incomplete. Here, we illustrate that when we incorporated CO2‐driven increases in foliar stoichiometry into the Community Land Model the projected land C sink decreased two‐fold by the end of the century compared to simulations with fixed foliar chemistry. Further, CO2‐driven increases in foliar C:N profoundly altered Earth's hydrologic cycle, reducing evapotranspiration and increasing runoff, and reduced belowground N cycling rates. These findings underscore the urgency of further research to examine both the direct and indirect effects of changing foliar stoichiometry on soil N cycling and plant productivity.
Long‐Lived Aftershocks in the New Madrid seismic Zone and the Rest of Stable North America
Authors: Chen Yuxuan , Liu Mian
Published: November 2023

Seismicity in the New Madrid seismic zone and the rest of stable North America remains controversial. Some workers view present‐day earthquakes there as long‐lived aftershocks; others view them as background seismicity concentrated in lithospheric weak zones. Separating long‐lived aftershocks from background seismicity, however, is challenging. Here, we used the nearest‐neighbor (NN) method to identify long‐lived aftershocks. The NN method calculates the distances between pairs of earthquakes in a space‐time‐magnitude domain. If the distances are too close to be expected for independent background events that follow the Gutenberg‐Richter law and Poisson distribution, the pairs are taken as clustered events (i.e., the later one in a pair is an aftershock of the earlier one). Our results suggest that, depending on the size and location of the 1811–1812 New Madrid mainshocks, 10.7%–65.0% of the M ≥ 2.5 earthquakes in the New Marid region between 1980 and 2016 may be long‐lived aftershocks. Similarly, considerable present‐day earthquakes in South Carolina are long‐lived aftershocks of the 1886 Charleston earthquake, but the contemporary seismicity in Charlevoix, Québec is predominately background seismicity. These results suggest that present‐day seismicity in stable North America, and perhaps other stable continents, includes both background seismicity and long‐lived aftershocks. Distinguishing aftershocks from background seismicity can be important for hazard assessment.
PDP1 is a key metabolic gatekeeper and modulator of drug resistance in FLT3-ITD-positive acute myeloid leukemia
Authors: Alshamleh Islam , Kurrle Nina , Makowka Philipp , Bhayadia Raj , Kumar Rahul , Süsser Sebastian , Seibert Marcel , Ludig Damian , Wolf Sebastian , Koschade Sebastian E. , Stoschek Karoline , Kreitz Johanna , Fuhrmann Dominik C. , Toenges Rosa , Notaro Marco , Comoglio Federico , Schuringa Jan Jacob , Berg Tobias , Brüne Bernhard , Krause Daniela S. , Klusmann Jan-Henning , Oellerich Thomas , Schnütgen Frank , Schwalbe Harald , Serve Hubert
Published: November 2023

High metabolic flexibility is pivotal for the persistence and therapy resistance of acute myeloid leukemia (AML). In 20–30% of AML patients, activating mutations of FLT3, specifically FLT3-ITD, are key therapeutic targets. Here, we investigated the influence of FLT3-ITD on AML metabolism. Nuclear Magnetic Resonance (NMR) profiling showed enhanced reshuffling of pyruvate towards the tricarboxylic acid (TCA) cycle, suggesting an increased activity of the pyruvate dehydrogenase complex (PDC). Consistently, FLT3-ITD-positive cells expressed high levels of PDP1, an activator of the PDC. Combining endogenous tagging of PDP1 with genome-wide CRISPR screens revealed that FLT3-ITD induces PDP1 expression through the RAS signaling axis. PDP1 knockdown resulted in reduced cellular respiration thereby impairing the proliferation of only FLT3-ITD cells. These cells continued to depend on PDP1, even in hypoxic conditions, and unlike FLT3-ITD-negative cells, they exhibited a rapid, PDP1-dependent revival of their respiratory capacity during reoxygenation. Moreover, we show that PDP1 modifies the response to FLT3 inhibition. Upon incubation with the FLT3 tyrosine kinase inhibitor quizartinib (AC220), PDP1 persisted or was upregulated, resulting in a further shift of glucose/pyruvate metabolism towards the TCA cycle. Overexpression of PDP1 enhanced, while PDP1 depletion diminished AC220 resistance in cell lines and peripheral blasts from an AC220-resistant AML patient in vivo. In conclusion, FLT3-ITD assures the expression of PDP1, a pivotal metabolic regulator that enhances oxidative glucose metabolism and drug resistance. Hence, PDP1 emerges as a potentially targetable vulnerability in the management of AML.
Trans-ancestry epigenome-wide association meta-analysis of DNA methylation with lifetime cannabis use
Authors: Fang Fang , Quach Bryan , Lawrence Kaitlyn G. , van Dongen Jenny , Marks Jesse A. , Lundgren Sara , Lin Mingkuan , Odintsova Veronika V. , Costeira Ricardo , Xu Zongli , Zhou Linran , Mandal Meisha , Xia Yujing , Vink Jacqueline M. , Bierut Laura J. , Ollikainen Miina , Taylor Jack A. , Bell Jordana T. , Kaprio Jaakko , Boomsma Dorret I. , Xu Ke , Sandler Dale P. , Hancock Dana B. , Johnson Eric O.
Published: November 2023

Cannabis is widely used worldwide, yet its links to health outcomes are not fully understood. DNA methylation can serve as a mediator to link environmental exposures to health outcomes. We conducted an epigenome-wide association study (EWAS) of peripheral blood-based DNA methylation and lifetime cannabis use (ever vs. never) in a meta-analysis including 9436 participants (7795 European and 1641 African ancestry) from seven cohorts. Accounting for effects of cigarette smoking, our trans-ancestry EWAS meta-analysis revealed four CpG sites significantly associated with lifetime cannabis use at a false discovery rate of 0.05 $$(p < 5.85\times {10}^{-7})$$

(

p
<
5.85
×

10

−
7

)

: cg22572071 near gene ADGRF1, cg15280358 in ADAM12, cg00813162 in ACTN1, and cg01101459 near LINC01132. Additionally, our EWAS analysis in participants who never smoked cigarettes identified another epigenome-wide significant CpG site, cg14237301 annotated to APOBR. We used a leave-one-out approach to evaluate methylation scores constructed as a weighted sum of the significant CpGs. The best model can explain 3.79% of the variance in lifetime cannabis use. These findings unravel the DNA methylation changes associated with lifetime cannabis use that are independent of cigarette smoking and may serve as a starting point for further research on the mechanisms through which cannabis exposure impacts health outcomes.
Metabolic and fecal microbial changes in adult fetal growth restricted mice
Authors: Gilley Stephanie P. , Zarate Miguel A. , Zheng Lijun , Jambal Purevsuren , Yazza Deaunabah N. , Chintapalli Sree V. , MacLean Paul S. , Wright Clyde J. , Rozance Paul J. , Shankar Kartik
Published: November 2023

Background

Fetal growth restriction (FGR) increases risk for development of obesity and type 2 diabetes. Using a mouse model of FGR, we tested whether metabolic outcomes were exacerbated by high-fat diet challenge or associated with fecal microbial taxa.

Methods

FGR was induced by maternal calorie restriction from gestation day 9 to 19. Control and FGR offspring were weaned to control (CON) or 45% fat diet (HFD). At age 16 weeks, offspring underwent intraperitoneal glucose tolerance testing, quantitative MRI body composition assessment, and energy balance studies. Total microbial DNA was used for amplification of the V4 variable region of the 16 S rRNA gene. Multivariable associations between groups and genera abundance were assessed using MaAsLin2.

Results

Adult male FGR mice fed HFD gained weight faster and had impaired glucose tolerance compared to control HFD males, without differences among females. Irrespective of weaning diet, adult FGR males had depletion of Akkermansia, a mucin-residing genus known to be associated with weight gain and glucose handling. FGR females had diminished Bifidobacterium. Metabolic changes in FGR offspring were associated with persistent gut microbial changes.

Conclusion

FGR results in persistent gut microbial dysbiosis that may be a therapeutic target to improve metabolic outcomes.

Impact

Fetal growth restriction increases risk for metabolic syndrome later in life, especially if followed by rapid postnatal weight gain.

We report that a high fat diet impacts weight and glucose handling in a mouse model of fetal growth restriction in a sexually dimorphic manner.

Adult growth-restricted offspring had persistent changes in fecal microbial taxa known to be associated with weight, glucose homeostasis, and bile acid metabolism, particularly Akkermansia, Bilophilia and Bifidobacteria.

The gut microbiome may represent a therapeutic target to improve long-term metabolic outcomes related to fetal growth restriction.
Neurodevelopmental outcomes in preterm or low birth weight infants with germinal matrix-intraventricular hemorrhage: a meta-analysis
Authors: Zhou Meicen , Wang Shaopu , Zhang Ting , Duan Surong , Wang Hua
Published: November 2023

Background

This meta-analysis aimed to identify the near- and long-term neurodevelopmental prognoses of preterm or low birth weight (LBW) infants with different severities of intraventricular hemorrhage (IVH).

Methods

Four databases were searched for observational studies that were qualified using the Newcastle-Ottawa Scale.

Results

37 studies involving 32,370 children were included. Compared to children without IVH, children with mild IVH had higher incidences of neurodevelopmental impairment (NDI), cerebral palsy (CP), motor/cognitive delay, hearing impairment and visual impairment, as well as lower scores of the mental development index (MDI) and psychomotor development (PDI). Moreover, compared to mild IVH, severe IVH increased susceptibilities of children to NDI, motor delay, CP, hearing impairment and visual impairment, with worse performances in MDI, PDI, motor score and IQ. Mild IVH was not associated with seizures or epilepsy.

Conclusions

Adverse neurodevelopmental outcomes positively associated with the occurrence and severity of IVH in preterm or LBW infants, providing evidence for counseling and further decisions regarding early therapeutic interventions.

Impact

Adverse neurodevelopmental outcomes later in life were closely associated with the occurrence and severity of IVH in preterm or LBW infants.

Our results highlight the importance to make prediction of the neurodevelopmental outcomes of children born preterm or LBW with a history of IVH, which will guide affected parents when their children need clinical interventions to reach the full potential.

We emphasize the importance of identifying specific developmental delays that may exist in children with IVH, providing detailed information for the development of comprehensive intervention measures.
The RioK1 network determines p53 activity at multiple levels
Authors: Damizia Michela , Moretta Gian Mario , De Wulf Peter
Published: November 2023

By responding to a host of adverse conditions, ranging from DNA damage to viral infection, transcription factor p53 supports genomic stability, cellular health, and survival. Not surprisingly, tumours across the cancer spectrum carry mutations in p53, misexpress the protein, or dysregulate its activity. Several signalling pathways, many of which comprise oncogenic proteins, converge upon p53 to control its stability and activity. We here present the conserved kinase/ATPase RioK1 as an upstream factor that determines p53 activity at the DNA, RNA, and protein levels. It achieves this task by integrating the regulatory events that act on p53 into a coherent response circuit. We will also discuss how RIOK1 overexpression represents an alternative mechanism for cancers to inactivate p53, and how targeting RioK1 could eradicate malignancies that are driven by a dysregulated RioK1-p53 network.
SGF29 nuclear condensates reinforce cellular aging
Authors: Yan Kaowen , Ji Qianzhao , Zhao Dongxin , Li Mingheng , Sun Xiaoyan , Wang Zehua , Liu Xiaoqian , Liu Zunpeng , Li Hongyu , Ding Yingjie , Wang Si , Belmonte Juan Carlos Izpisua , Qu Jing , Zhang Weiqi , Liu Guang-Hui
Published: November 2023

Phase separation, a biophysical segregation of subcellular milieus referred as condensates, is known to regulate transcription, but its impacts on physiological processes are less clear. Here, we demonstrate the formation of liquid-like nuclear condensates by SGF29, a component of the SAGA transcriptional coactivator complex, during cellular senescence in human mesenchymal progenitor cells (hMPCs) and fibroblasts. The Arg 207 within the intrinsically disordered region is identified as the key amino acid residue for SGF29 to form phase separation. Through epigenomic and transcriptomic analysis, our data indicated that both condensate formation and H3K4me3 binding of SGF29 are essential for establishing its precise chromatin location, recruiting transcriptional factors and co-activators to target specific genomic loci, and initiating the expression of genes associated with senescence, such as CDKN1A. The formation of SGF29 condensates alone, however, may not be sufficient to drive H3K4me3 binding or achieve transactivation functions. Our study establishes a link between phase separation and aging regulation, highlighting nuclear condensates as a functional unit that facilitate shaping transcriptional landscapes in aging.
Transcriptional reprogramming by mutated IRF4 in lymphoma
Authors: Schleussner Nikolai , Cauchy Pierre , Franke Vedran , Giefing Maciej , Fornes Oriol , Vankadari Naveen , Assi Salam A. , Costanza Mariantonia , Weniger Marc A. , Akalin Altuna , Anagnostopoulos Ioannis , Bukur Thomas , Casarotto Marco G. , Damm Frederik , Daumke Oliver , Edginton-White Benjamin , Gebhardt J. Christof M. , Grau Michael , Grunwald Stephan , Hansmann Martin-Leo , Hartmann Sylvia , Huber Lionel , Kärgel Eva , Lusatis Simone , Noerenberg Daniel , Obier Nadine , Pannicke Ulrich , Fischer Anja , Reisser Anja , Rosenwald Andreas , Schwarz Klaus , Sundararaj Srinivasan , Weilemann Andre , Winkler Wiebke , Xu Wendan , Lenz Georg , Rajewsky Klaus , Wasserman Wyeth W. , Cockerill Peter N. , Scheidereit Claus , Siebert Reiner , Küppers Ralf , Grosschedl Rudolf , Janz Martin , Bonifer Constanze , Mathas Stephan
Published: November 2023

Disease-causing mutations in genes encoding transcription factors (TFs) can affect TF interactions with their cognate DNA-binding motifs. Whether and how TF mutations impact upon the binding to TF composite elements (CE) and the interaction with other TFs is unclear. Here, we report a distinct mechanism of TF alteration in human lymphomas with perturbed B cell identity, in particular classic Hodgkin lymphoma. It is caused by a recurrent somatic missense mutation c.295 T > C (p.Cys99Arg; p.C99R) targeting the center of the DNA-binding domain of Interferon Regulatory Factor 4 (IRF4), a key TF in immune cells. IRF4-C99R fundamentally alters IRF4 DNA-binding, with loss-of-binding to canonical IRF motifs and neomorphic gain-of-binding to canonical and non-canonical IRF CEs. IRF4-C99R thoroughly modifies IRF4 function by blocking IRF4-dependent plasma cell induction, and up-regulates disease-specific genes in a non-canonical Activator Protein-1 (AP-1)-IRF-CE (AICE)-dependent manner. Our data explain how a single mutation causes a complex switch of TF specificity and gene regulation and open the perspective to specifically block the neomorphic DNA-binding activities of a mutant TF.
Planktonic microbial signatures of sinking particle export in the open ocean’s interior
Authors: Li Fuyan , Burger Andrew , Eppley John M. , Poff Kirsten E. , Karl David M. , DeLong Edward F.
Published: November 2023

A considerable amount of particulate carbon produced by oceanic photosynthesis is exported to the deep-sea by the “gravitational pump” (~6.8 to 7.7 Pg C/year), sequestering it from the atmosphere for centuries. How particulate organic carbon (POC) is transformed during export to the deep sea however is not well understood. Here, we report that dominant suspended prokaryotes also found in sinking particles serve as informative tracers of particle export processes. In a three-year time series from oceanographic campaigns in the Pacific Ocean, upper water column relative abundances of suspended prokaryotes entrained in sinking particles decreased exponentially from depths of 75 to 250 m, conforming to known depth-attenuation patterns of carbon, energy, and mass fluxes in the epipelagic zone. Below ~250 m however, the relative abundance of suspended prokaryotes entrained in sinking particles increased with depth. These results indicate that microbial entrainment, colonization, and sinking particle formation are elevated at mesopelagic and bathypelagic depths. Comparison of suspended and sinking particle-associated microbes provides information about the depth-variability of POC export and biotic processes, that is not evident from biogeochemical data alone.
Disordered metasurface enabled single-shot full-Stokes polarization imaging leveraging weak dichroism
Authors: Fan Qingbin , Xu Weizhu , Hu Xuemei , Zhu Wenqi , Yue Tao , Yan Feng , Lin Peicheng , Chen Lu , Song Junyeob , Lezec Henri J. , Agrawal Amit , Lu Yanqing , Xu Ting
Published: November 2023

Polarization, one of the fundamental properties of light, is critical for certain imaging applications because it captures information from the scene that cannot directly be recorded by traditional intensity cameras. Currently, mainstream approaches for polarization imaging rely on strong dichroism of birefringent crystals or artificially fabricated structures that exhibit a high diattenuation typically exceeding 99%, which corresponds to a polarization extinction ratio (PER) >~100. This not only limits the transmission efficiency of light, but also makes them either offer narrow operational bandwidth or be non-responsive to the circular polarization. Here, we demonstrate a single-shot full-Stokes polarization camera incorporating a disordered metasurface array with weak dichroism. The diattenuation of the metasurface array is ~65%, which corresponds to a PER of ~2. Within the framework of compressed sensing, the proposed disordered metasurface array serves as an efficient sensing matrix. By incorporating a mask-aware reconstruction algorithm, the signal can be accurately recovered with a high probability. In our experiments, the proposed approach exhibits high-accuracy full-Stokes polarimetry and high-resolution real-time polarization imaging. Our demonstration highlights the potential of combining meta-optics with reconstruction algorithms as a promising approach for advanced imaging applications.
Circular polarization-resolved ultraviolet photonic artificial synapse based on chiral perovskite
Authors: Liu Qi , Wei Qi , Ren Hui , Zhou Luwei , Zhou Yifan , Wang Pengzhi , Wang Chenghao , Yin Jun , Li Mingjie
Published: November 2023

Circularly polarized light (CPL) adds a unique dimension to optical information processing and communication. Integrating CPL sensitivity with light learning and memory in a photonic artificial synapse (PAS) device holds significant value for advanced neuromorphic vision systems. However, the development of such systems has been impeded by the scarcity of suitable CPL active optoelectronic materials. In this work, we employ a helical chiral perovskite hybrid combined with single-wall carbon nanotubes to achieve circularly polarized ultraviolet neuromorphic vision sensing and imaging. The heterostructure demonstrates long-term charge storage as evidenced by multiple-pulsed transient absorption measurements and highly sensitive circular polarization-dependent photodetection, thereby enabling efficient CPL-resolved synaptic and neuromorphic behaviors. Significantly, our PAS sensor arrays adeptly visualize, discriminate, and memorize distinct circularly polarized images with up to 93% recognition accuracy in spiking neural network simulations. These findings underscore the pivotal role of chiral perovskites in advancing PAS technology and circular polarization-enhanced ultraviolet neuromorphic vision systems.
Better adherence to guidelines among psychiatrists providing pharmacological therapy is associated with longer work hours in patients with schizophrenia
Authors: Ito Satsuki , Ohi Kazutaka , Yasuda Yuka , Fujimoto Michiko , Yamamori Hidenaga , Matsumoto Junya , Fukumoto Kentaro , Kodaka Fumitoshi , Hasegawa Naomi , Ishimaru Keiichiro , Miura Kenichiro , Yasui-Furukori Norio , Hashimoto Ryota
Published: November 2023

Schizophrenia is a psychiatric disorder that is associated with various social dysfunctions, including shorter work hours. To measure the degree to which psychiatrists adhere to guidelines for pharmacological therapy of schizophrenia, we recently developed the individual fitness score (IFS) for adherence among psychiatrists in each patient. However, it remains unclear whether better adherence among psychiatrists is associated with higher patients’ social functional outcomes, such as work hours. In this study, we examined the relationship between adherence to guidelines among psychiatrists and work hours in patients with schizophrenia. To evaluate the association between adherence to guidelines for pharmacological therapy among psychiatrists for treating schizophrenia and work hours, we used the IFS and social activity assessment, respectively, in 286 patients with schizophrenia. The correlation between IFS values and work hours was investigated in the patients. The adherence among psychiatrists to guidelines was significantly and positively correlated with work hours in patients with schizophrenia (rho = 0.18, p = 2.15 × 10−3). When we divided the patients into treatment-resistant schizophrenia (TRS) and nontreatment-resistant schizophrenia (non-TRS) groups, most patients with TRS (n = 40) had shorter work hours (0–15 h/week). Even after excluding patients with TRS, the positive correlation between adherence to guidelines among psychiatrists and work hours in patients with non-TRS (n = 246) was still significant (rho = 0.19, p = 3.32 × 10−3). We found that work hours were longer in patients who received the guideline-recommended pharmacotherapy. Our findings suggest that widespread education and training for psychiatrists may be necessary to improve functional outcomes in patients with schizophrenia.
Association of elevated levels of peripheral complement components with cortical thinning and impaired logical memory in drug-naïve patients with first-episode schizophrenia
Authors: Yu Hua , Ni Peiyan , Tian Yang , Zhao Liansheng , Li Mingli , Li Xiaojing , Wei Wei , Wei Jinxue , Wang Qiang , Guo Wanjun , Deng Wei , Ma Xiaohong , Coid Jeremy , Li Tao
Published: November 2023

Schizophrenia has been linked to polymorphism in genes encoding components of the complement system, and hyperactive complement activity has been linked to immune dysfunction in schizophrenia patients. Whether and how specific complement components influence brain structure and cognition in the disease is unclear. Here we compared 52 drug-naïve patients with first-episode schizophrenia and 52 healthy controls in terms of levels of peripheral complement factors, cortical thickness (CT), logical memory and psychotic symptoms. We also explored the relationship between complement factors with CT, cognition and psychotic symptoms. Patients showed significantly higher levels of C1q, C4, factor B, factor H, and properdin in plasma. Among patients, higher levels of C3 in plasma were associated with worse memory recall, while higher levels of C4, factor B and factor H were associated with thinner sensory cortex. These findings link dysregulation of specific complement components to abnormal brain structure and cognition in schizophrenia.
Increasing precipitation deteriorates the progress of pesticide reduction policy in the vulnerable watershed
Authors: Guo Zewei , Ouyang Wei , Chen Ming , Tulcan Roberto Xavier Supe , Wang Lei , Lin Chunye , He Mengchang
Published: November 2023

Precipitation variation profoundly affects agricultural development and increases the diffuse pollution risk, which may weaken the positive effects of pesticide reduction policy. This study aimed to analyze the response of pesticide discharge loads in the large vulnerable watershed to pesticide application intensity and precipitation variance before and after implementing the pesticide reduction policy. We integrated empirical models, field observation and statistics to explore the sensitive factors of the typical pesticide atrazine before and after the pesticide reduction policy in the Yellow River Watershed. The results showed that the implementation of pesticide reduction policy effectively decreased the annual discharge load of atrazine within the watershed. In addition, the most sensitive factor of atrazine discharge loads shifted from precipitation to the atrazine application intensity after implementing the pesticide reduction policy. However, the discharge loads of atrazine significantly increased in an unusual high precipitation year in the context of increasing precipitation variability.
Dataset of in-situ coaxial monitoring and print’s cross-section images by Direct Energy Deposition fabrication
Authors: Akhavan Javid , Lyu Jiaqi , Mahmoud Youmna , Xu Ke , Vallabh Chaitanya Krishna Prasad , Manoochehri Souran
Published: November 2023

Coaxial monitoring of the Direct Energy Deposition (DED) machines enables a real-time material deposition study. Coaxial-images contain substantial melt-pool information and incorporate situational information including the sparks’ intensity, numbers, etc. Recent studies have shown that melt-pool observations correlate directly with machine parameters and artifact properties. Therefore, the melt-pool information not only can assist in measuring the machine’s working condition and determining machine operation parameters’ reliability but also facilitates the deposition characteristics studies like print’s regime and dimensions. This information is gathered during the fabrication and can be expanded to perform various process studies and fault registration. This paper utilizes the Optomec DED machine to fabricate single-track prints with multiple process parameters, while a coaxial camera records the deposition. Each deposited track is then cut perpendicular to the print’s direction to facilitate process parameters correlation study with actual geometrical deposition measured using a microscope. The coaxial images taken during fabrication, along with their process parameters, cross-cut measurements, and a developed image-processing toolbox, are presented alongside this paper to empower future research directions.
The stage- and sex-specific transcriptome of the human parasite Schistosoma mansoni
Authors: Buddenborg Sarah K. , Lu Zhigang , Sankaranarayan Geetha , Doyle Stephen R. , Berriman Matthew
Published: November 2023

The flatworm Schistosoma mansoni is an important but neglected pathogen that causes the disease schistosomiasis in millions of people worldwide. The parasite has a complex life cycle, undergoing sexual reproduction in a mammalian host and asexual replication in a snail host. Understanding the molecular mechanisms that the parasite uses to transition between hosts and develop into dimorphic reproductively competent adults may reveal new strategies for control. We present the first comprehensive transcriptomic analysis of S. mansoni, from eggs to sexually naïve worms. Focusing on eight life stages spanning free-living water-borne and parasitic stages from both intermediate and definitive hosts, we have generated deep RNA-seq data for five replicates per group for a total of 75 data sets. The data were produced using a single approach to increase the accuracy of stage-to-stage comparisons and made accessible via a user-friendly tool to visualise and explore gene expression (https://lifecycle.schisto.xyz/). These data are valuable for understanding the biology and sex-specific development of schistosomes and the interpretation of complementary genomic and functional genetics studies.
Monitoring the West Nile virus outbreaks in Italy using open access data
Authors: Mingione Marco , Branda Francesco , Maruotti Antonello , Ciccozzi Massimo , Mazzoli Sandra
Published: November 2023

This paper introduces a comprehensive dataset on West Nile virus outbreaks that have occurred in Italy from September 2012 to November 2022. We have digitized bulletins published by the Italian National Institute of Health to demonstrate the potential utilization of this data for the research community. Our aim is to establish a centralized open access repository that facilitates analysis and monitoring of the disease. We have collected and curated data on the type of infected host, along with additional information whenever available, including the type of infection, age, and geographic details at different levels of spatial aggregation. By combining our data with other sources of information such as weather data, it becomes possible to assess potential relationships between West Nile virus outbreaks and environmental factors. We strongly believe in supporting public oversight of government epidemic management, and we emphasize that open data play a crucial role in generating reliable results by enabling greater transparency.
Venetoclax plus cyclophosphamide and topotecan in heavily pre-treated relapsed metastatic neuroblastoma: a single center case series
Authors: De Ioris Maria Antonietta , Fabozzi Francesco , Del Bufalo Francesca , Del Baldo Giada , Villani Maria Felicia , Cefalo Maria Giuseppina , Garganese Maria Carmen , Stracuzzi Alessandra , Tangari Federica , Greco Arturo Maria , Giovannoni Isabella , Carta Roberto , D’Andrea Maria Luisa , Mastronuzzi Angela , Locatelli Franco
Published: November 2023

The prognosis of relapsed/refractory (R/R) neuroblastoma (NB) is dismal, calling for new therapeutic strategies. Venetoclax (VEN) is a highly selective, potent, orally bioavailable, BCL-2 inhibitor small-molecule that showed a synergistic effect with cyclophosphamide and topotecan (Cy-Topo) in murine NB models. Our aim was to evaluate the feasibility of VEN plus Cy-Topo in children with R/R NB. Four patients, who had previously failed > 3 lines of treatment, were treated with VEN plus Cy-Topo based on a 28-day schedule in an outpatient setting. BCL-2 expression in immunochemistry on tumor samples at relapse and the BCL2 gene status was evaluated in all patients. The main toxicity was hematological, with grade 4 neutropenia and thrombocytopenia occurring in all courses and leading to transient VEN discontinuation. Grade 3 oral mucositis was observed in 1/8 courses. No other grade 2–4 toxicities were observed. BCL-2 was expressed in all tumors, while no molecular abnormalities in the BCL-2 genes were detected. A stable disease was observed in all patients, without any progression during the study period. VEN plus Cy-Topo is well tolerated, with encouraging results that may be improved by testing the schedule in less advanced patients.
Optimizing quantum noise-induced reservoir computing for nonlinear and chaotic time series prediction
Authors: Fry Daniel , Deshmukh Amol , Chen Samuel Yen-Chi , Rastunkov Vladimir , Markov Vanio
Published: November 2023

Quantum reservoir computing is strongly emerging for sequential and time series data prediction in quantum machine learning. We make advancements to the quantum noise-induced reservoir, in which reservoir noise is used as a resource to generate expressive, nonlinear signals that are efficiently learned with a single linear output layer. We address the need for quantum reservoir tuning with a novel and generally applicable approach to quantum circuit parameterization, in which tunable noise models are programmed to the quantum reservoir circuit to be fully controlled for effective optimization. Our systematic approach also involves reductions in quantum reservoir circuits in the number of qubits and entanglement scheme complexity. We show that with only a single noise model and small memory capacities, excellent simulation results were obtained on nonlinear benchmarks that include the Mackey-Glass system for 100 steps ahead in the challenging chaotic regime.
A neutrophil extracellular traps-related classification predicts prognosis and response to immunotherapy in colon cancer
Authors: Feng Cheng , Li Yuan , Tai Yi , Zhang Weili , Wang Hao , Lian Shaopu , Jin-si-han E-er-man-bie-ke , Liu Yuanyuan , Li Xinghui , Chen Qifeng , He Meng , Lu Zhenhai
Published: November 2023

Neutrophil extracellular traps (NETs) have been categorized as a form of inflammatory cell death mode of neutrophils (NETosis) involved in natural immunity and the regulation of adaptive immunity. More and more studies revealed the ability of NETs to reshape the tumor immune microenvironment (TIME) by limiting antitumor effector cells, which may impair the efficacy of immunotherapy. To explore whether NETs-related genes make vital impacts on Colon carcinoma (COAD), we have carried out a systematic analysis and showed several findings in the present work. First, we obtained the patient's data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) dataset, aiming to detect two NETs-associated subtypes by consensus clustering. For the purpose of annotating the roles of NETs-related pathways, gene ontology enrichment analyses were adopted. Next, we constructed a 6 novel NETs-related genes score using the Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression model. We found that the NETs risk score was notably upregulated in COAD patient samples, and its levels were notably correlated with tumor clinicopathological and immune traits. Then, according to NETs-associated molecular subtypes and the risk signature, this study compared immune cell infiltration calculated through the estimate, CIBERSORT, TIMER, ssGSEA algorithms, tumor immune dysfunction, as well as exclusion (TIDE). Furthermore, we confirm that MPO(myeloperoxidase) was significantly upregulated in COAD patient samples, and its levels were significantly linked to tumor malignancy and clinic outcome. Moreover, multiplex immunohistochemistry (mIHC) spatial analysis confirmed that MPO was closely related to Treg and PD-1 + Treg in spatial location which suggested MPO may paly an important role in TIME formation. Altogether, the obtained results indicated that a six NETs-related genes prognostic signature was conducive to estimating the prognosis and response of chemo-/immuno-therapy of COAD patients.
Bioinformatics analyses of potentially common pathogenic networks for primary Sjögren’s syndrome complicated with acute myocardial infarction
Authors: Hou Qingbin , Jiang Jinping , Na Kun , Zhang Xiaolin , Liu Dan , Jing Quanmin , Yan Chenghui , Han Yaling
Published: November 2023

Both primary Sjögren’s syndrome (pSS) and acute myocardial infarction (AMI) are intricately linked. However, their common mechanism is not fully understood. Herein, we examined the underlying network of molecular action associated with developing this complication. Datasets were downloaded from the GEO database. We performed enrichment and protein–protein interaction analyses and screened key genes. We used external datasets to confirm the diagnostic performance for these hub genes. Transcription factor and microRNA regulatory networks were constructed for the validated hub genes. Finally, drug prediction and molecular docking validation were performed. We identified 62 common DEGs, many of which were enriched regarding inflammation and immune response. 5 DEGs were found as key hub genes (IGSF6, MMP9, S100A8, MNDA, and NCF2). They had high diagnostic performance in external datasets. Functional enrichment of these five hub genes showed that they were associated with the adaptive immune response. The Type 1T helper cell showed the most association among all cell types related to AMI and pSS. We identified 36 common TFs and 49 identical TF-miRNAs. The drugs, including Benzo, dexamethasone, and NADP, were predicted as potential therapeutic agents. Herein, we revealed common networks involving pSS and AMI etiologies. Knowledge of these networks and hub genes can enhance research into their associated mechanism and the development of future robust therapy.
Physicochemical Characterization of Woody Lignocellulosic Biomass and Charcoal for Bio-energy Heat Generation
Authors: Olabisi Adebayo S. , Balogun Ayokunle O. , Oni Taiwo O. , Fakinle Bamidele S. , Sotoudehnia Farid , McDonald Armando G. , Ikubanni Peter P.
Published: November 2023

Biomass and its interactions for heat generation have received little attention. In this study, the woody biomass materials were Prosopis africana (PA), Harungana madascariences (HM), Vitrllaria paradoxa (VP), and Afzelia africana (AA). The composition (extractives, carbohydrate, and lignin) of the biomass was determined. The biomass was converted to charcoal in a traditional kiln. A thermo-kinetic examination of the charcoal samples was carried out. The kinetic parameters and potential reaction mechanisms involved in the decomposition process were both obtained using the integral (Flynn–Wall Ozawa) isoconversional methods in conjunction with the Coats-Redfern approach. The activation energy profiles for the charcoal samples in oxidizing atmospheres were 548 kJ/mol for AA, 274 kJ/mol for VP, 548 kJ/mol for PA, and 274 kJ/mol for HM. All charcoal samples underwent comprehensive, multi-step, complex reaction pathways for thermal degradation. The charcoal samples exhibit not only great potential for biochemical extraction but also for bioenergy applications. The significant amount of combustion characteristics in the raw biomass and charcoal samples indicates that each type of wood charcoal produced has more fixed carbon, less ash, and less volatile matter, all of which are desirable for the thermo-chemical conversion of biomass for the production of heat.
Lower serum testosterone is associated with increased likelihood of arthritis
Authors: Cheng Lulu , Wang Siyu
Published: November 2023

Studies have suggested that serum testosterone levels may be strongly correlated with the pathogenesis of arthritis. Therefore, the aim of this study was to assess the relationship between serum testosterone levels and arthritis in US adults using the National Health and Nutrition Examination Survey (NHANES). We used the database from NHANES, 2013–2016 to perform a cross-sectional study. This study investigated the relationship between serum testosterone and arthritis using multivariate logistic regression models and also used smoothed curve fitting and generalized additivity models. A total of 10,439 adults were included in this analysis. A significant negative association between serum testosterone and arthritis was found in a linear regression analysis. The study showed that the arthritis group had lower testosterone levels than the non-arthritis group. The univariate multivariate analyses of Q4, using Q1 as a reference, all showed a significantly lower risk of developing arthritis. In subgroup analyses, the negative correlation between serum testosterone levels and arthritis was more significant in women and those with a body mass index (BMI) ≥ 30 kg/m2. After controlling for various variables, we found a significant association between serum testosterone and arthritis in this analysis. Further study of the relationship between testosterone and arthritis is necessary to clarify the specific mechanism of serum testosterone action on arthritis.
Towards audio-based identification of Ethio-Semitic languages using recurrent neural network
Authors: Alemu Amlakie Aschale , Melese Malefia Demilie , Salau Ayodeji Olalekan
Published: November 2023

In recent times, there is an increasing interest in employing technology to process natural language with the aim of providing information that can benefit society. Language identification refers to the process of detecting which speech a speaker appears to be using. This paper presents an audio-based Ethio-semitic language identification system using Recurrent Neural Network. Identifying the features that can accurately differentiate between various languages is a difficult task because of the very high similarity between characters of each language. Recurrent Neural Network (RNN) was used in this paper in relation to the Mel-frequency cepstral coefficients (MFCCs) features to bring out the key features which helps provide good results. The primary goal of this research is to find the best model for the identification of Ethio-semitic languages such as Amharic, Geez, Guragigna, and Tigrigna. The models were tested using an 8-h collection of audio recording. Experiments were carried out using our unique dataset with an extended version of RNN, Long Short Term Memory (LSTM) and Bidirectional Long Short Term Memory (BLSTM), for 5 and 10 s, respectively. According to the results, Bidirectional Long Short Term Memory (BLSTM) with a 5 s delay outperformed Long Short Term Memory (LSTM). The BLSTM model achieved average results of 98.1, 92.9, and 89.9% for training, validation, and testing accuracy, respectively. As a result, we can infer that the best performing method for the selected Ethio-Semitic language dataset was the BLSTM algorithm with MFCCs feature running for 5 s.
Characterization of respiratory bacterial co-infection and assessment of empirical antibiotic treatment in patients with COVID-19 at hospital admission
Authors: Antuori Adrián , Giménez Montserrat , Linares Georgina , Cardona Pere-Joan
Published: November 2023

Accurate characterization of respiratory bacterial co-infection is critical for guiding empirical antibiotic treatment for hospitalised patients with coronavirus disease 2019 (COVID-19). We retrospectively assessed the clinical and analytical predictors of respiratory bacterial co-infection and described the empirical use of antibiotics in COVID-19 hospitalised patients. Respiratory bacterial co-infection was documented in 6.9% (80/1157) of the patients. The predominant bacteria isolates were Haemophilus influenzae, followed by Streptococcus pneumoniae and Pseudomonas aeruginosa. Respiratory bacterial co-infection was associated with having had a positive culture for a respiratory pathogen in the last year (OR = 25.89), dyslipidaemia (OR = 2.52), heart failure (OR = 7.68), ferritin levels < 402 ng/mL (OR = 2.28), leukocyte count > 8.7 × 109/L (OR = 2.4), and patients with chronic obstructive pulmonary disease treated with inhaled corticosteroids (OR = 12.94). Empirical antibiotic treatment was administered in 42.33% of patients, although it declined across the distinct study periods (p < 0.001). Patients admitted to intensive care units harbouring co-infection exhibited worse outcomes and more bacterial secondary infections. In conclusion, respiratory bacterial co-infection prevalence was low, although it could lead to unfavourable outcomes. Moreover, the percentage of empirical antibiotic treatment remained high. The study's findings allowed the identification of several predictors for respiratory bacterial co-infection and could help implement adequate antibiotic stewardship measures.
Research on digital twin modeling and monitoring technology for smoke alarm calibration system
Authors: Min Wu , Wenfeng Ying
Published: November 2023

Aiming at the problems of backward calibration method of smoke alarm, low production efficiency and difficult real-time monitoring, a digital twin system modeling and monitoring method of smoke alarm calibration is proposed. First, through the analysis of smoke alarm calibration requirements, the overall framework design of the digital twin calibration system for smoke alarm is proposed, and then the twin model of smoke box is constructed by running the digital twin five-dimensional model. The physical smoke box, geometric model, physical model, rule model and behavior model are introduced in detail; Then the communication system architecture, data acquisition and data mapping are used to construct the twin data model; Finally, the feasibility was verified by the calibration system of an enterprise. Through the system, the qualified rate of smoke alarm calibration was increased from 98 to 99.6%, and the repair rate of defective products was reduced by 1.6%.