bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inherently interpretable position-aware convolutional motif kernel networks for biological sequencing data
Authors: Ditz Jonas C. , Reuter Bernhard , Pfeifer Nico 
Published: October 2023

AbstractArtificial neural networks show promising performance in detecting correlations within data that are associated with specific outcomes. However, the black-box nature of such models can hinder the knowledge advancement in research fields by obscuring the decision process and preventing scientist to fully conceptualize predicted outcomes. Furthermore, domain experts like healthcare providers need explainable predictions to assess whether a predicted outcome can be trusted in high stakes scenarios and to help them integrating a model into their own routine. Therefore, interpretable models play a crucial role for the incorporation of machine learning into high stakes scenarios like healthcare. In this paper we introduce Convolutional Motif Kernel Networks, a neural network architecture that involves learning a feature representation within a subspace of the reproducing kernel Hilbert space of the position-aware motif kernel function. The resulting model enables to directly interpret and evaluate prediction outcomes by providing a biologically and medically meaningful explanation without the need for additional post-hoc analysis. We show that our model is able to robustly learn on small datasets and reaches state-of-the-art performance on relevant healthcare prediction tasks. Our proposed method can be utilized on DNA and protein sequences. Furthermore, we show that the proposed method learns biologically meaningful concepts directly from data using an end-to-end learning scheme.
The effect of random virus failure following cell entry on infection outcome and the success of antiviral therapy
Authors: Quirouette Christian , Cresta Daniel , Li Jizhou , Wilkie Kathleen P. , Liang Haozhao , Beauchemin Catherine A. A. 
Published: October 2023

AbstractA virus infection can be initiated with very few or even a single infectious virion, and as such can become extinct, i.e. stochastically fail to take hold or spread significantly. There are many ways that a fully competent infectious virion, having successfully entered a cell, can fail to cause a productive infection, i.e. one that yields infectious virus progeny. Though many stochastic models (SMs) have been developed and used to estimate a virus infection’s establishment probability, these typically neglect infection failure post virus entry. The SM presented herein introduces parameter $$\gamma \in (0,1]$$

γ
∈
(
0
,
1
]

which corresponds to the probability that a virion’s entry into a cell will result in a productive cell infection. We derive an expression for the likelihood of infection establishment in this new SM, and find that prophylactic therapy with an antiviral reducing $$\gamma$$
γ
is at least as good or better at decreasing the establishment probability, compared to antivirals reducing the rates of virus production or virus entry into cells, irrespective of the SM parameters. We investigate the difference in the fraction of cells consumed by so-called extinct versus established virus infections, and find that this distinction becomes biologically meaningless as the probability of establishment approaches zero. We explain why the release of virions continuously over an infectious cell’s lifespan, rather than as a single burst at the end of the cell’s lifespan, does not result in an increased risk of infection extinction. We show, instead, that the number of virus released, not the timing of the release, affects infection establishment and associated critical antiviral efficacy.
The influence of insight on risky decision making and nucleus accumbens activation
Authors: Becker Maxi , Yu Yuhua , Cabeza Roberto 
Published: October 2023

AbstractDuring insightful problem solving, the solution appears unexpectedly and is accompanied by the feeling of an AHA!. Research suggests that this affective component of insight can have consequences beyond the solution itself by motivating future behavior, such as risky (high reward and high uncertainty) decision making. Here, we investigate the behavioral and neural support for the motivational role of AHA in decision making involving monetary choices. The positive affect of the AHA! experience has been linked to internal reward. Reward in turn has been linked to dopaminergic signal transmission in the Nucleus Accumbens (NAcc) and risky decision making. Therefore, we hypothesized that insight activates reward-related brain areas, modulating risky decision making. We tested this hypothesis in two studies. First, in a pre-registered online study (Study 1), we demonstrated the behavioral effect of insight-related increase in risky decision making using a visual Mooney identification paradigm. Participants were more likely to choose the riskier monetary payout when they had previously solved the Mooney image with high compared to low accompanied AHA!. Second, in an fMRI study (Study 2), we measured the effects of insight on NAcc activity using a similar Mooney identification paradigm to the one of Study 1. Greater NAcc activity was found when participants solved the Mooney image with high vs low AHA!. Taken together, our results link insight to enhanced NAcc activity and a preference for high but uncertain rewards, suggesting that insight enhances reward-related brain areas possibly via dopaminergic signal transmission, promoting risky decision making.
Pupil response patterns distinguish true from false memories
Authors: Kafkas Alex , Brown Travorn , Olusola Nifemi , Guo Chaodong 
Published: October 2023

AbstractMemory is reconstructive and error-prone, which make memory illusions very common in everyday life. However, studying memory illusions can provide valuable insights into how memory works. Pupil response has emerged, in recent years, as an indicator of memory encoding and retrieval, however its validity as a measure of memory success is debated. In this study, we explored whether pupil response patterns can differentiate true from false memories and whether variations in the temporal dynamics of pupil response can elucidate the mechanisms underlying false memory creation. The Deese-Roediger-McDermott (DRM) paradigm was employed to generate false memories in two separate experiments involving visual and auditory stimuli. Pupil responses effectively differentiated true from false memories based on variations in pupil amplitude at different temporal components. This discrimination remained consistent across both experiments, with slightly stronger effects in the auditory condition, aligning with the more pronounced false memory effects in this condition. Notably, differential pupil responses between true and false memories varied based on the type of memory involved at recognition. These findings provide valuable insights into the cognitive processes underlying memory distortions, with implications for theoretical frameworks and real-world contexts.
Use of pediatric thymus to humanize mice for HIV-1 mucosal transmission
Authors: Roy Chandra N. , Shu Sherry T. , Kline Christopher , Rigatti Lora , Smithgall Thomas E. , Ambrose Zandrea 
Published: October 2023

AbstractHumanized mice have been used to study human immunodeficiency virus type 1 (HIV-1) transmission, pathogenesis, and treatment. The ability of pediatric thymus tissue implanted either in the leg (Leg PedThy) or under the renal capsule (Renal PedThy) with allogeneic CD34+ hematopoietic cells (HSCs) in NSG mice was evaluated for reconstitution of human immune cells and for rectal transmission of HIV-1. These mice were compared to traditional BLT mice implanted with fetal liver and thymus under the renal capsule and mice injected only with HSCs. Renal PedThy mice had similar immune reconstitution in the blood, spleen and intestine as BLT mice, while Leg PedThy mice had transient detection of immune cells, particularly CD4+ T cells and macrophages, the target cells for HIV-1 infection. Rectal transmission and replication of HIV-1 was efficient in BLT mice but lower and more variable in Renal PedThy mice. HIV-1 was poorly transmitted in HSC mice and not transmitted in Leg PedThy mice, which correlated with the frequencies of target cells in the spleen and intestine. Humanization of NSG mice with pediatric thymus was successful when implanted under the kidney capsule, but led to less efficient HIV-1 rectal transmission and replication compared to BLT mice.
Accessing new avenues of photonic bandgaps using two-dimensional non-Moiré geometries
Authors: Darthy R. Rachel , Venkateswaran C. , Subramanian V. , Ouyang Zhengbiao , Yogesh N. 
Published: October 2023

AbstractPhotonic crystals (PhC) formed by 2-D non-Moiré geometries are realized in this work. Non-Moiré (NM) tiles are the contours of trigonometric functions that generate exciting shapes and geometries. Photonic bandstructure calculations reveal that 2-D NM geometries exhibit new avenues of photonic bandgaps compared to the regular circular rod-based PhCs. The band structures are anisotropic and show, intriguing orientation-dependent partial bandgaps. A few of the orientation-dependent frequency selective properties of the realized NM geometry-based PhCs are demonstrated using full-wave electromagnetic simulations. The proposed geometries are practically realizable, and in this work, we experimentally demonstrate the fabrication process using the 3-D printing technique for microwave frequencies.
Effects of various wet environments on the characteristics of the dust cake deposited on the surface of filter media
Authors: Li Shihang , Lin Yihan , Han Muze , Liu Hao , Shao Jiang , Tan Xiaoyu , Luo Yuchen , Huang Rongting 
Published: October 2023

AbstractThe effect of wet environments on the dust cake of filter media was studied. The collapse angles of dust particles and the collapse angles between dust particles and filter media increase with increasing dust moisture content, relative humidity, and spray rate. The smallest growth rate of collapse was observed under dust moisture content, while the largest growth rate occurred under the spray rate condition. The collapse angles between dust particles and filter media of coated filter media were smaller compared to those of mechanical filter media under different wet environments. The dust cake drag coefficients of both filter media initially increase and then decrease with an increase in the dust moisture content, decrease with the acceleration of the relative humidity, and show a pattern of first decreasing and then increasing as the spray rate increases. The dust loading capacity of both filter media follows an opposite trend to that of the dust cake drag coefficients.
A smart device for non-invasive ADL estimation through multi-environmental sensor fusion
Authors: Kang Homin , Lee Cheolhwan , Kang Soon Ju 
Published: October 2023

AbstractThis research paper introduces the Smart Plug Hub (SPH), a non-invasive system designed to accurately estimating a patient’s Activities of Daily Living (ADL). Traditional methods for measuring ADL include interviews, remote video systems, and wearable devices that track behavior. However, these approaches have limitations, such as patient memory dependency, privacy violations, and careless device management. To address these limitations, SPH utilizes sensor fusion to analyze time-series environmental signals and accurately estimate a patient’s ADL. We have effectively optimized the utilization of computing resources through the implementation of “device collaboration” in SPH to receive event data and segments portions of the time-series environmental signal. By segmenting the data into smaller segments, we extracted an analyzable dataset, which was processed by an edge device—SPH. We have conducted several experiments with the SPH, and our research has resulted in a significant 75% accuracy in the classification of patients’ kitchen ADLs and an 85% accuracy in the classification of toilet ADLs. These activities include actions such as eating activities in the kitchen and typical activities performed in the toilet. These findings have substantial implications for the progress of healthcare and patient care, highlighting the potential uses of the SPH technology in the monitoring and improvement of daily living activities.
The presence of wolves leads to spatial differentiation in deer browsing pressure on forest regeneration
Authors: Wójcicki Adam , Borowski Zbigniew 
Published: October 2023

AbstractWith the recent return of large carnivores to forest ecosystems, an important issue for forest owners and managers is how large predators influence the behaviour of their natural prey and, consequently, cervid browsing pressure on forest regeneration. To investigate this issue, we analysed deer pressure on Scots pine and European beech plantations in northern Poland's ecosystems with and without permanent wolf populations. Two characteristics were used to describe deer browsing patterns in plantations: distance from the forest edge (spatial pattern of browsing) and number of saplings browsed (browsing intensity). Beech saplings were more intensively browsed by deer compared to pine saplings. In a forest ecosystem not inhabited by wolves, spatial variation in browsing patterns on small-sized beech plantations was the same between the edge and the center. In contrast, browsing pressure by deer was greater at the edges on large-sized pine plantations. The presence of wolves reduced deer browsing on beech and increased browsing on pine saplings. In addition, deer foraging behaviour changed in large-sized pine plantations, and browsing pressure increased only in the central areas of the plantations. We assume that the presence of wolves in a forest landscape is an important factor that alters browsing pressure on the youngest stands and their spatial pattern, and that this may be a major factor in stand regeneration, especially in small forest patches.
Global termite methane emissions have been affected by climate and land-use changes
Authors: Ito Akihiko 
Published: October 2023

AbstractTermites with symbiotic methanogens are a known source of atmospheric methane (CH4), but large uncertainties remain regarding the flux magnitude. This study estimated global termite CH4 emissions using a framework similar to previous studies but with contemporary datasets and a biogeochemical model. The global termite emission in 2020 was estimated as 14.8 ± 6.7 Tg CH4 year−1, mainly from tropical and subtropical ecosystems, indicating a major natural source from upland regions. Uncertainties associated with estimation methods were assessed. The emission during the historical period 1901–2021 was estimated to have increased gradually (+ 0.7 Tg CH4 year−1) as a result of combined influences of elevated CO2 (via vegetation productivity), climatic warming, and land-use change. Future projections using climate and land-use scenarios (shared socioeconomic pathways [ssp] 126 and 585) also showed increasing trends (+ 0.5 to 5.9 Tg CH4 year−1 by 2100). These results suggest the importance of termite emissions in the global CH4 budget and, thus, in climatic prediction and mitigation.
Shift in hospital opioid use during the COVID-19 pandemic in Brazil: a time-series analysis of one million prescriptions
Authors: Carvalho Romulo Mendonça , de Magalhães-Barbosa Maria Clara , Bianchi Lucas Monteiro , Rodrigues-Santos Gustavo , da Cunha Antônio José Ledo Alves , Bastos Francisco Inácio , Prata-Barbosa Arnaldo 
Published: October 2023

AbstractThe pronounced change in the profile of hospitalized patients during COVID-19 and the severe respiratory component of this disease, with a great need for mechanical ventilation, led to changes in the consumption pattern of some medicines and supplies. This time-series study analyzed the in-hospital consumption of opioids during the COVID-19 pandemic in 24 Brazilian hospitals compared to the pre-pandemic period. Data included 711,883 adult patients who had opioids prescribed. In 2020, the mean consumption was significantly higher compared to 2019 for parenteral fentanyl, enteral methadone, and parenteral methadone. It was significantly lower for parenteral morphine parenteral sufentanil, and parenteral tramadol. For remifentanil, it did not differ. The number of patients in 2020 was lower but the mean consumption was higher for fentanyl, parenteral methadone, and remifentanil. It was lower for enteral methadone and parenteral sufentanil. The consumption of parenteral morphine and parenteral tramadol was stable. There was a relevant increase in hospital consumption of some potent opioids during the COVID-19 pandemic in Brazil. These results reinforce the concern about epidemiological surveillance of opioid use after periods of increased hospital use since in-hospital consumption can be the gateway to the misuse or other than the prescribed use of opioids after discharge.
Relationship among DDR gene mutations, TMB and PD-L1 in solid tumour genomes identified using clinically actionable biomarker assays
Authors: Wang Danyi , Elenbaas Brian , Murugesan Karthikeyan , Shah Kunal , Montesion Meagan , Gounaris Ioannis , Scheuenpflug Juergen , Locatelli Giuseppe , Feng Zheng 
Published: October 2023

AbstractThe DNA damage response (DDR) pathway regulates DNA repair and cell survival, and inactivating mutations in DDR genes can increase tumour mutational burden (TMB), a predictive biomarker of treatment benefit from anti-PD-1/PD-L1 immunotherapies. However, a better understanding of the relationship among specific DDR mutations, TMB and PD-L1 expression is needed to improve translational strategies. Here, we determined genomic alteration frequencies in selected DDR genes that are clinically actionable biomarkers and investigated their association with TMB and PD-L1 in bladder, colorectal, non-small cell lung, ovarian and prostate cancers using the FoundationInsights® web portal. Our results not only confirm known associations, such as mismatch repair and POLE gene mutations with high TMB, but also identify significant associations between mutations in the SWI/SNF chromatin remodelling genes ARID1A and SMARCA4 and high TMB in multiple tumour types. Mutations in the ATR gene were associated with high TMB in colorectal and prostate cancers; however, associations between individual DDR mutations and high PD-L1 expression were uncommon and tumour-type specific. Finally, we found that high TMB and high PD-L1 expression were poorly associated, emphasising their independence as predictive biomarkers for immune checkpoint inhibitor use.
Chemoresistant fibroblasts dictate neoadjuvant chemotherapeutic response of head and neck cancer via TGFα-EGFR paracrine signaling
Authors: Su Liangping , Wu Sangqing , Huang Cheng , Zhuo Xianhua , Chen Jiali , Jiang Xue , Kong Xiangzhan , Lv Cui , Xu Qiuping , Han Ping , Huang Xiaoming , Wong Ping-Pui 
Published: October 2023

AbstractConventional chemotherapy targets malignant cells without evaluating counter protection from the tumor microenvironment that often causes treatment failure. Herein, we establish chemoresistant fibroblasts (rCAFs) as regulators of neoadjuvant chemotherapeutic (NACT) response in head and neck squamous cell carcinoma (HNSCC). Clinically, high expression of CAF-related gene signature correlates with worse prognosis and chemotherapeutic response in multiple cancers, while the population of CAFs in the residual tumors of chemoresistant HNSCC patients remains unchanged after NACT treatment, compared to chemosensitive patients. Using a murine cancer model or patient-derived organoid, and primary CAFs isolated from chemo-sensitive (sCAFs) or -resistant patients, we show that rCAFs, but not sCAFs, are resistant to chemotherapy-induced apoptosis while reducing HNSCC cell chemosensitivity via paracrine signals. Combined multi-omics and biochemical analyses indicate an elevated PI3K/AKT/p65 driven cell survival and cytokine production in rCAFs, while rCAF-secreted TGFα promotes cancer cell chemoresistance by activating EGFR/Src/STAT3 survival signaling axis. Treatment with anti-EGFR cetuximab restores the chemosensitivity of tumors derived from co-injection of cancer cells and rCAFs in vivo, while the serum level of TGFα determines NACT response in HNSCC patients. Overall, our findings uncover a novel insight whereby the crosstalk between tumor cell and rCAF determines chemotherapeutic response and prognosis in cancer patients.
Stress-induced brain responses are associated with BMI in women
Authors: Kühnel Anne , Hagenberg Jonas , Knauer-Arloth Janine , Ködel Maik , Czisch Michael , Sämann Philipp G. ,   BeCOME working group, Brückl Tanja , Spoormaker Victor I. , Erhardt Angelika , Grandi Norma C. , Ziebula Julius , Elbau Immanuel G. , Lucae Susanne , Binder Elisabeth B. , Kroemer Nils B. 
Published: October 2023

AbstractOverweight and obesity are associated with altered stress reactivity and increased inflammation. However, it is not known whether stress-induced changes in brain function scale with BMI and if such associations are driven by peripheral cytokines. Here, we investigate multimodal stress responses in a large transdiagnostic sample using predictive modeling based on spatio-temporal profiles of stress-induced changes in activation and functional connectivity. BMI is associated with increased brain responses as well as greater negative affect after stress and individual response profiles are associated with BMI in females (pperm < 0.001), but not males. Although stress-induced changes reflecting BMI are associated with baseline cortisol, there is no robust association with peripheral cytokines. To conclude, alterations in body weight and energy metabolism might scale acute brain responses to stress more strongly in females compared to males, echoing observational studies. Our findings highlight sex-dependent associations of stress with differences in endocrine markers, largely independent of peripheral inflammation.
Femtosecond multimodal imaging with a laser-driven X-ray source
Authors: Doherty Adam , Fourmaux Sylvain , Astolfo Alberto , Ziesche Ralf , Wood Jonathan , Finlay Oliver , Stolp Wiebe , Batey Darren , Manke Ingo , Légaré François , Boone Matthieu , Symes Dan , Najmudin Zulfikar , Endrizzi Marco , Olivo Alessandro , Cipiccia Silvia 
Published: October 2023

AbstractLaser-plasma accelerators are compact linear accelerators based on the interaction of high-power lasers with plasma to form accelerating structures up to 1000 times smaller than standard radiofrequency cavities, and they come with an embedded X-ray source, namely betatron source, with unique properties: small source size and femtosecond pulse duration. A still unexplored possibility to exploit the betatron source comes from combining it with imaging methods able to encode multiple information like transmission and phase into a single-shot acquisition approach. In this work, we combine edge illumination-beam tracking (EI-BT) with a betatron X-ray source and present the demonstration of multimodal imaging (transmission, refraction, and scattering) with a compact light source down to the femtosecond timescale. The advantage of EI-BT is that it allows multimodal X-ray imaging technique, granting access to transmission, refraction and scattering signals from standard low-coherence laboratory X-ray sources in a single shot.