bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assimilation of phthalate esters in bacteria
Authors: Qiao Pei , Ying Tongtong , Gu Mengjie , Zhu Jiahong , Mei Chengyu , Hu Tong , Liu Tengfei , Wang Haixia , Zhong Weihong 
Published: March 2024

Abstract
The massive usage of phthalate esters (PAEs) has caused serious pollution. Bacterial degradation is a potential strategy to remove PAE contamination. So far, an increasing number of PAE-degrading strains have been isolated, and the catabolism of PAEs has been extensively studied and reviewed. However, the investigation into the bacterial PAE uptake process has received limited attention and remains preliminary. PAEs can interact spontaneously with compounds like peptidoglycan, lipopolysaccharides, and lipids on the bacterial cell envelope to migrate inside. However, this process compromises the structural integrity of the cells and causes disruptions. Thus, membrane protein-facilitated transport seems to be the main assimilation strategy in bacteria. So far, only an ATP-binding-cassette transporter PatDABC was proven to transport PAEs across the cytomembrane in a Gram-positive bacterium Rhodococcus jostii RHA1. Other cytomembrane proteins like major facilitator superfamily (MFS) proteins and outer membrane proteins in cell walls like FadL family channels, TonB-dependent transporters, and OmpW family proteins were only reported to facilitate the transport of PAEs analogs such as monoaromatic and polyaromatic hydrocarbons. The functions of these proteins in the intracellular transport of PAEs in bacteria await characterization and it is a promising avenue for future research on enhancing bacterial degradation of PAEs.

Key points
• Membrane proteins on the bacterial cell envelope may be PAE transporters.
• Most potential transporters need experimental validation.
Co-targeting CD47 and VEGF elicited potent anti-tumor effects in gastric cancer
Authors: Zhang Kaiqi , Xu Yuan , Chang Xusheng , Xu Caili , Xue Wenjing , Ding Dan , Nie Mingming , Cai Hui , Xu Jun , Zhan Lu , Han Jiangbo , Cai Tiancai , Ju Dianwen , Feng Li , Zhang Xuyao , Yin Kai 
Published: March 2024

Abstract
Background
CD47, serving as an intrinsic immune checkpoint, has demonstrated efficacy as an anti-tumor target in hematologic malignancies. Nevertheless, the clinical relevance of CD47 in gastric cancer and its potential as a therapeutic target remains unclear.

Methods
The expression of CD47 in clinical gastric cancer tissues was assessed using immunohistochemistry and Western blot. Patient-derived cells were obtained from gastric cancer tissues and co-cultured with macrophages derived from human peripheral blood mononuclear cells. Flow cytometry analyses were employed to evaluate the rate of phagocytosis. Humanized patient-derived xenografts (Hu-PDXs) models were established to assess the efficacy of anti-CD47 immunotherapy or the combination of anti-CD47 and anti-VEGF therapy in treating gastric cancer. The infiltrated immune cells in the xenograft were analyzed by immunohistochemistry.

Results
In this study, we have substantiated the high expression of CD47 in gastric cancer tissues, establishing a strong association with unfavorable prognosis. Through the utilization of SIRPα-Fc to target CD47, we have effectively enhanced macrophage phagocytosis of PDCs in vitro and impeded the growth of Hu-PDXs. It is noteworthy that anti-CD47 immunotherapy has been observed to sustain tumor angiogenic vasculature, with a positive correlation between the expression of VEGF and CD47 in gastric cancer. Furthermore, the successful implementation of anti-angiogenic treatment has further augmented the anti-tumor efficacy of anti-CD47 therapy. In addition, the potent suppression of tumor growth, prevention of cancer recurrence after surgery, and significant prolongation of overall survival in Hu-PDX models can be achieved through the simultaneous targeting of CD47 and VEGF using the bispecific fusion protein SIRPα-VEGFR1 or by combining the two single-targeted agents.

Conclusions
Our preclinical studies collectively offer substantiation that CD47 holds promise as a prospective target for gastric cancer, while also highlighting the potential of anti-angiogenic therapy to enhance tumor responsiveness to anti-CD47 immunotherapy.
How immune dynamics shape multi-season epidemics: a continuous-discrete model in one dimensional antigenic space
Authors: Roberts M. G. , Hickson R. I. , McCaw J. M. 
Published: March 2024

AbstractWe extend a previously published model for the dynamics of a single strain of an influenza-like infection. The model incorporates a waning acquired immunity to infection and punctuated antigenic drift of the virus, employing a set of coupled integral equations within a season and a discrete map between seasons. The long term behaviour of the model is demonstrated by examples where immunity to infection depends on the time since a host was last infected, and where immunity depends on the number of times that a host has been infected. The first scenario leads to complicated dynamics in some regions of parameter space, and to regions of parameter space with more than one attractor. The second scenario leads to a stable fixed point, corresponding to an identical epidemic each season. We also examine the model with both paradigms in combination, almost always but not exclusively observing a stable fixed point or periodic solution. Adding stochastic perturbations to the between season map fails to destroy the model’s qualitative dynamics. Our results suggest that if the level of host immunity depends on the elapsed time since the last infection then the epidemiological dynamics may be unpredictable.
Depth from defocus technique: a simple calibration-free approach for dispersion size measurement
Authors: Rao Saini Jatin , Sharma Shubham , Basu Saptarshi , Tropea Cameron 
Published: March 2024

AbstractParticle size measurement is crucial in various applications, be it sizing droplets in inkjet printing or respiratory events, tracking particulate ejection in hypersonic impacts or detecting floating target markers in free-surface flows. Such systems are characterised by extracting quantitative information like size, position, velocity and number density of the dispersed particles, which is typically non-trivial. The existing methods like phase Doppler or digital holography offer precise estimates at the expense of complicated systems, demanding significant expertise. We present a novel volumetric measurement approach for estimating the size and position of dispersed spherical particles that utilises a unique ‘Depth from Defocus’ (DFD) technique with a single camera. The calibration-free sizing enables in situ examination of hard to measure systems, including naturally occurring phenomena like pathogenic aerosols, pollen dispersion or raindrops. The efficacy of the technique is demonstrated for diverse sparse dispersions, including dots, glass beads and spray droplets. The simple optical configuration and semi-autonomous calibration procedure make the method readily deployable and accessible, with a scope of applicability across vast research horizons.
Forms of new democracy
Authors: Gersbach Hans 
Published: March 2024

AbstractIn the third decade of the 21st century, digitization and artificial intelligence, global events, challenges from authoritarian states, and difficulties of particular democracies to function properly confront democracy with a new series of challenges and opportunities that will force it to reinvent itself. The last decades have produced an accelerating flow of ideas for new forms of democracy. We survey a long period in the quest for such new forms and point to next inventions for such forms. We suggest to experiment with new ways for democracy to extend the choice of democratic processes that can be implemented in real-life situations, with the beneficial side-effect that democracy might remain the only sustainable structure for self-governing societies.
Expression of fibroblast growth factor receptor 2 (FGFR2) in combined hepatocellular-cholangiocarcinoma and intrahepatic cholangiocarcinoma: clinicopathological study
Authors: Sasaki Motoko , Sato Yasunori , Nakanuma Yasuni 
Published: March 2024

AbstractGenetic alterations including fusions in fibroblast growth factor receptor 2 (FGFR2) are detected in 10–20% of intrahepatic cholangiocarcinoma (iCCA), and FGFR2 inhibitors are effective for the treatment of iCCA. We examined a prevalence of FGFR2 genetic alterations and their clinicopathological significance in combined hepatocellular–cholangiocarcinoma (cHCC-CCA). FGFR2 expression, which is a surrogate marker for FGFR2 genetic alterations, was immunohistochemically assessed in the liver sections from 75 patients with cHCC-CCA, 35 with small duct-type iCCA, 30 with large duct-type iCCA, and 35 with hepatocellular carcinoma (HCC). FGFR2 genetic alterations were detected by reverse transcription-PCR and direct sequence. An association of FGFR2 expression with clinicopathological features was investigated in cHCC-CCAs. FGFR2 expression was detected in significantly more patients with cHCC-CCA (21.3%) and small duct-type iCCA (25.7%), compared to those with large duct-type iCCA (3.3%) and HCC (0%) (p < 0.05). FGFR2-positive cHCC-CCAs were significantly smaller size (p < 0.05), with more predominant cholangiolocarcinoma component (p < 0.01) and less nestin expression (p < 0.05). Genetic alterations of ARID1A and BAP1 and multiple genes were significantly more frequent in FGFR2-positive cHCC-CCAs (p < 0.05). 5′/3′ imbalance in FGFR2 genes indicating exon18-truncated FGFR2 was significantly more frequently detected in FGFR2-positive cHCC-CCAs and small duct iCCAs, compared to FGFR2-negative ones (p < 0.05). FGFR2::BICC fusion was detected in a case of cHCC-CCAs. FGFR2 genetic alterations may be prevalent in cHCC-CCAs as well as small duct-type iCCAs, which suggest cHCC-CCAs may also be a possible therapeutic target of FGFR2 inhibitors.
Graphical Abstract
Symptom burden and relief in palliative care units of German Comprehensive Cancer Center and other hospitals
Authors: Berendt Julia , Brunner Sarah , Heckel Maria , Tewes Mitra , Ostgathe Christoph , Gahr Susanne 
Published: March 2024

Abstract
Purpose
The National Hospice and Palliative Registry contains patient data from German hospice and palliative care facilities about symptoms. The aim of the study at hand is to differentiate symptom burden of patients in palliative care units between Comprehensive Cancer Center (CCC) and other hospitals regarding symptom burden and relief of patients in palliative care units.

Methods
The registry analysis provided data of patients in palliative care units (2014–2018). We analyzed characteristic and symptom-related data on 18 symptoms, with considerable symptom-burdened patients (moderate or severe). We followed a cancer (yes/no) and facility-specific descriptive analysis (f, %, μ, Mdn, SD, V, r) using SPSS.

Results
We evaluated 10,447 patient records (CCC: 4234 pts/non CCC 6,213 pts), 82% with a cancer diagnosis. For cancer patients, the mean age in CCC-affiliated palliative care units was 68 (SD 19–99) years, in others 73 (SD 23–104) years (p < 0.05; V = 0.2). The proportion of patients with significant symptom burden is lower in CCC-affiliated than in other palliative care units. The difference between facilities shows a significant weak effect in pain, vomiting and constipation, depressiveness, anxiety, and tension. The proportion of cases which symptom burden could be alleviated is higher in CCC-affiliated palliative care units with significant weak/medium effect in pain, nausea, vomiting, shortness of breath, constipation, wound care problems, depressiveness, anxiety, tension, confusion, and problems in organizing care.

Conclusion
We found differences in symptom burden and symptom relief between CCC-affiliated and other palliative care units. CCCs should continue to feel responsible for sharing knowledge about symptom relief, such as through standard operating procedures and education.
Automatic landslide detection and visualization by using deep ensemble learning method
Authors: Hacıefendioğlu Kemal , Varol Nehir , Toğan Vedat , Bahadır Ümit , Kartal Murat Emre 
Published: March 2024

AbstractRapid detection of damages occurring as a result of natural disasters is vital for emergency response. In recent years, remote sensing techniques have been commonly used for the automatic categorization and localization of such events using satellite images. Trained based on natural disaster images, a convolutional neural network (CNN) has been applied as a highly successful method, with its ability to reveal outstanding features. Studies aiming to detect target points obtained as a result of extracting visual features from natural images within these networks have achieved their goals. In this study, ensemble learning methods have been suggested as a means to develop the detection of landslide areas from landslide satellite images. Landslide image dataset has been trained for their categorization in CNN models and then they have been used again to localize landslide regions. While model predictions develop overall performance and status, different ensemble strategies have been used and integrated to reduce the sensitivity to prediction variance and training data. Class-selective relevance mapping (CRM) has been used to visualize individual CNN models and ensemble learned behaviors. As a result of the comparisons made based on mean average precision metrics and the criteria of intersection over union, model ensembles have proved to show higher localization performance than any other individual model.
The effect of combined red, blue, and near-infrared light-emitting diode (LED) photobiomodulation therapy on speed of wound healing after superficial ablative fractional resurfacing
Authors: Soliman John , Elsanadi Rachel , Messele Feben , Kelly Kristen M. 
Published: March 2024

Abstract
Objective of the study is to assess the effects of wound healing with a commercially available light emitting diode (LED) photo biomodulation (PBM) device that emits three wavelengths (465, 640 and 880nm) after ablative fractional laser (AFL) treatment to healthy skin on the bilateral inner biceps. We conducted a prospective intraindividual randomized controlled study with 25 volunteers. AFL treatment was performed on healthy skin of the bilateral inner biceps. Subjects applied the LED light device for 30 min to the assigned bicep 3 times a week over 4 weeks, beginning on day 0. Subjects were followed up on days 2, 4, 6, 9, 13, 20 and 27 for treatment with the PBM device, clinical digital photography of the test and control sites, and in-person subject assessment, with follow ups on days 34 and 55 for clinical photography and assessment. Three blinded evaluators were asked to determine which bicep healed faster between day 0 to day 13. Pain, discomfort, and itch were also assessed. The three blinded evaluators chose the treatment arm as the faster healed arm in greater than 50% of the images, although the results were not statistically significant. There was no statistically significant difference between test and control arms in terms of pain, discomfort and itch. In conclusion, PBM therapy has the potential to improve wound healing. In this study, a three wavelength PBM device resulted in some subjects achieving faster healing after AFL but the results were not statistically significant.
Successful Intuition vs. Intellectual Hallucination: How We Non-Accidentally Grasp the Third Realm
Authors: Berghofer Philipp 
Published: March 2024

AbstractIn his influential paper “Grasping the Third Realm,” John Bengson raises the question of how we can non-accidentally grasp abstract facts. What distinguishes successful intuition from hallucinatory intuition? Bengson answers his “non-accidental relation question” by arguing for a constitutive relationship: The intuited object is a literal constituent of the respective intuition. Now, the problem my contribution centers around is that Bengson’s answer cannot be the end of the story. This is because, as Bar Luzon and Preston Werner have recently pointed out, this answer leads to the follow-up question of why certain intuitional experiences are constituted by the facts, but others are not. My objective is to answer this question by specifying precisely what is epistemically defective about intellectual hallucinations. My result is that, in stark contrast to perception, intellectual hallucinations are epistemically defective in the sense that something is overlooked. In successful intuition, by contrast, all relevant possibilities/scenarios are considered/imagined. This has crucial epistemological implications. In particular, I argue that intuitions exhibiting a certain phenomenology cannot fail to successfully grasp abstract facts. I call this the non-accidental correctness thesis, which constitutes the main thesis of this paper.
Detection of Anaplasma spp. and Ehrlichia spp. in dogs from a veterinary teaching hospital in Italy: a retrospective study 2012–2020
Authors: Facile Veronica , Sabetti Maria Chiara , Balboni Andrea , Urbani Lorenza , Tirolo Alessandro , Magliocca Martina , Lunetta Francesco , Dondi Francesco , Battilani Mara 
Published: March 2024

AbstractAnaplasma phagocytophilum, Anaplasma platys and Ehrlichia canis, responsible of diseases in dogs, are tick-borne pathogens with a proven or potential zoonotic role that have shown increasing prevalence worldwide. The aims of this retrospective study were to assess the frequency of Anaplasma spp. and Ehrlichia spp. exposure in dogs tested in a veterinary teaching hospital in Italy over a 9-year period, to compare the performance of the diagnostic tests used, to evaluate correlations with clinical data, and to genetically analyse the identified bacteria. During the study period, 1322 dogs tested by at least one of the rapid immunoenzymatic test, indirect immunofluorescent antibody test or end-point PCR assay for Anaplasmataceae detection were included. Dogs were tested if they had clinical signs or clinicopathological alteration or risk factors related to infection, and if they were potential blood-donor animals. Ninety-four of 1322 (7.1%) dogs tested positive for at least one pathogen: 53 (4.3%) for A. phagocytophilum, one (0.1%) for A. platys and 63 (4.6%) for E. canis. The number of dogs tested increased and the positivity rate progressively declined over the years. Comparison of tests showed a near-perfect agreement between serological tests and a poor agreement between PCR and indirect assays. A breed predisposition has been highlighted for A. phagocytophilum infection in hunting breed dogs and for E. canis infection in mixed breed dogs. Phylogeny confirmed potential zoonotic implications for A. phagocytophilum and showed no correlation of the identified bacteria with the geographical origin. Our study provides new insights into possible risk factors in dogs and evidenced discordant results between different tests, suggesting that a combination of serological and molecular assays is preferable for a correct diagnosis.
Multi-omics staging of locally advanced rectal cancer predicts treatment response: a pilot study
Authors: Cicalini Ilaria , Chiarelli Antonio Maria , Chiacchiaretta Piero , Perpetuini David , Rosa Consuelo , Mastrodicasa Domenico , d’Annibale Martina , Trebeschi Stefano , Serafini Francesco Lorenzo , Cocco Giulio , Narciso Marco , Corvino Antonio , Cinalli Sebastiano , Genovesi Domenico , Lanuti Paola , Valentinuzzi Silvia , Pieragostino Damiana , Brocco Davide , Beets-Tan Regina G. H. , Tinari Nicola , Sensi Stefano L. , Stuppia Liborio , Del Boccio Piero , Caulo Massimo , Delli Pizzi Andrea 
Published: March 2024

AbstractTreatment response assessment of rectal cancer patients is a critical component of personalized cancer care and it allows to identify suitable candidates for organ-preserving strategies. This pilot study employed a novel multi-omics approach combining MRI-based radiomic features and untargeted metabolomics to infer treatment response at staging. The metabolic signature highlighted how tumor cell viability is predictively down-regulated, while the response to oxidative stress was up-regulated in responder patients, showing significantly reduced oxoproline values at baseline compared to non-responder patients (p-value < 10–4). Tumors with a high degree of texture homogeneity, as assessed by radiomics, were more likely to achieve a major pathological response (p-value < 10–3). A machine learning classifier was implemented to summarize the multi-omics information and discriminate responders and non-responders. Combining all available radiomic and metabolomic features, the classifier delivered an AUC of 0.864 (± 0.083, p-value < 10–3) with a best-point sensitivity of 90.9% and a specificity of 81.8%. Our results suggest that a multi-omics approach, integrating radiomics and metabolomic data, can enhance the predictive value of standard MRI and could help to avoid unnecessary surgical treatments and their associated long-term complications.
XRelevanceCAM: towards explainable tissue characterization with improved localisation of pathological structures in probe-based confocal laser endomicroscopy
Authors: You Jianzhong , Ajlouni Serine , Kakaletri Irini , Charalampaki Patra , Giannarou Stamatia 
Published: March 2024

Abstract
Purpose
Probe-based confocal laser endomicroscopy (pCLE) enables intraoperative tissue characterization with improved resection rates of brain tumours. Although a plethora of deep learning models have been developed for automating tissue characterization, their lack of transparency is a concern. To tackle this issue, techniques like Class Activation Map (CAM) and its variations highlight image regions related to model decisions. However, they often fall short of providing human-interpretable visual explanations for surgical decision support, primarily due to the shattered gradient problem or insufficient theoretical underpinning.

Methods
In this paper, we introduce XRelevanceCAM, an explanation method rooted in a better backpropagation approach, incorporating sensitivity and conservation axioms. This enhanced method offers greater theoretical foundation and effectively mitigates the shattered gradient issue when compared to other CAM variants.

Results
Qualitative and quantitative evaluations are based on ex vivo pCLE data of brain tumours. XRelevanceCAM effectively highlights clinically relevant areas that characterize the tissue type. Specifically, it yields a remarkable 56% improvement over our closest baseline, RelevanceCAM, in the network’s shallowest layer as measured by the mean Intersection over Union (mIoU) metric based on ground-truth annotations (from 18 to 28.07%). Furthermore, a 6% improvement in mIoU is observed when generating the final saliency map from all network layers.

Conclusion
We introduce a new CAM variation, XRelevanceCAM, for precise identification of clinically important structures in pCLE data. This can aid introperative decision support in brain tumour resection surgery, as validated in our performance study.