bluuebunny/crossref_metadata_2025_split huggingface dataset:
Subsequent treatments beyond progression on osimertinib in EGFR-mutated NSCLC and leptomeningeal metastases
Authors: Zheng Mei-Mei , Li Yang-Si , Tu Hai-Yan , Sun Hao , Yin Kai , Jiang Ben-Yuan , Yang Jin-Ji , Zhang Xu-Chao , Zhou Qing , Xu Chong-Rui , Wang Zhen , Chen Hua-Jun , Zhou De-Xiang , Wu Yi-Long 
Published: May 2022

Abstract
Background
Despite the reported efficacy of osimertinib, central nervous system (CNS) progression is still frequent in EGFR-mutated NSCLC. This study aimed to reveal site-specific resistant mechanisms to osimertinib and investigate subsequent treatments for leptomeningeal metastases (LM).

Methods
EGFR-mutated NSCLC with LM who progressed on osimertinib were included. Molecular analysis of cerebrospinal fluid (CSF) at osimertinib progression was performed. Subsequent treatments of LM were collected and analyzed.

Results
A total of 246 patients were identified. Only those with LM as a progression site on osimertinib were included (n=81). In 58 CSF-plasma pairs, more alterations were uniquely detected in CSF (77%) than in plasma (7%). These mechanisms led to 22 patients receiving matched targeted therapy. Among them, 16 (72.7%) had a clinical response. The median overall survival was 7.2 months. For non-matched therapy (n=59), the osimertinib combination had a longer median overall survival than the regimen switch in CNS-only progression (15.3 vs. 7 months, p=0.03). Finally, serial monitoring by CSF revealed the potential evolution of LM.

Conclusions
Private resistant mechanisms in CSF might match osimertinib-resistant LM for targeted therapy. Besides, continuing osimertinib with intensification strategy might prolong survival, especially for those with CNS-only progression. Prospective exploration is needed.
Behavioural responses of Konik Polski horses to natural, familiar sound of thunderstorm, and unfamiliar similar-sounding sounds of volcanic eruption and sea storms
Authors: Wiśniewska Anna , Janczarek Iwona , Ryżak Magdalena , Tkaczyk Ewelina , Kędzierski Witold 
Published: May 2022

Abstract
Background
It is not clear, if modern Konik Polski horses have retained the ability to identify sounds in terms of danger. The aim of the study was to identify differences in their behaviour in response to the reproduction of volcanic eruption and sea storm sounds, assumed to be unfamiliar to these horses, as compared to their response to a thunderclap sound, considered by the horses as potentially dangerous. The study included 13 adult mares of the Konik Polski breed, kept under a free-range system. Their behavioural responses to the reproduction of the three natural sounds with an intensity of over 50 dB, were registered. They were analysed distance of each horse to the central point of the pasture and to the exit from the enclosure, and time and/or frequencies of elements of behaviour categorised as: increased anxiety (walking, trotting and cantering), vigilance (snoring, vocalisation, high head position, high tail position, sticking together), foraging (time of grazing), comfort (playing, examining the surroundings, sniffing), maintenance of hygiene (rubbing against objects, auto- or allogrooming, rolling) and resting. The obtained data were analysed by the Dwass, Steel and Critchlow-Fligner method using the SAS program.

Results
Most of analysed elements increased in response to reproduced sounds and decreased after sounds were stop playing (p < 0.05), however, they were no significant differences in general response to each studied sound.

Conclusions
The responses of horses to similar sounds of both known and unknown origins, i.e. the sound of a thunderstorm, sea storm and volcanic eruption, are similar. The sound stimuli applied were not too stressful for the horses.
Antibiofilm and staphyloxanthin inhibitory potential of terbinafine against Staphylococcus aureus: in vitro and in vivo studies
Authors: Askoura Momen , Yousef Nehal , Mansour Basem , Yehia Fatma Al-zahraa A. 
Published: May 2022

Abstract
Background
Antimicrobial resistance is growing substantially, which necessitates the search for novel therapeutic options. Terbinafine, an allylamine antifungal agent that exhibits a broad spectrum of activity and is used in the treatment of dermatophytosis, could be a possible option to disarm S. aureus virulence.

Methods
Terbinafine inhibitory effect on staphyloxanthin was characterized by quantitative measurement of staphyloxanthin intermediates and molecular docking. The effect of terbinafine on S. aureus stress survival was characterized by viable counting. The anti-biofilm activity of terbinafine on S. aureus was assessed by the crystal violet assay and microscopy. Changes in S. aureus membrane following treatment with terbinafine were determined using Fourier transform infrared (FTIR) analysis. The synergistic action of terbinafine in combination with conventional antibiotics was characterized using the checkerboard assay. qRT-PCR was used to evaluate the impact of terbinafine on S. aureus gene expression. The influence of terbinafine on S. aureus pathogenesis was investigated in mice infection model.

Results
Terbinafine inhibits staphyloxanthin biosynthesis through targeting dehydrosqualene desaturase (CrtN). Docking analysis of terbinafine against the predicted active site of CrtN reveals a binding energy of − 9.579 kcal/mol exemplified by the formation of H-bonds, H-arene bonds, and hydrophobic/hydrophilic interactions with the conserved amino acids of the receptor pocket. Terbinafine treated S. aureus was more susceptible to both oxidative and acid stress as well as human blood killing as compared to untreated cells. Targeting staphyloxanthin by terbinafine rendered S. aureus more sensitive to membrane acting antibiotics. Terbinafine interfered with S. aureus biofilm formation through targeting cell autoaggregation, hydrophobicity, and exopolysaccharide production. Moreover, terbinafine demonstrated a synergistic interaction against S. aureus when combined with conventional antibiotics. Importantly, terbinafine attenuated S. aureus pathogenesis using mice infection model. qRT-PCR revealed that terbinafine repressed expression of the transcriptional regulators sigB, sarA, and msaB, as well as icaA in S. aureus.

Conclusions
Present findings strongly suggest that terbinafine could be used safely and efficiently as an anti-virulent agent to combat S. aureus infections.
Hyperlipemia pancreatitis onset time affects the association between elevated serum triglyceride levels and disease severity
Authors: Dong Xiuli , Pan Shuang , Zhang Daguan , Hong Wandong , Chen Tanzhou , Zhang Bingxin , Huang Zhiming , Chen Chengshui 
Published: May 2022

Abstract
Background
The association of serum triglyceride (TG) levels with the severity of hypertriglyceridaemia-induced acute pancreatitis (HTG-AP) remains controversial. This study aimed to comprehensively assess the TG levels from the initial onset and their predictive value in the disease assessment of HTG-AP.

Methods
Data collected from January 2018 to July 2021 in one institute were assessed retrospectively. HTG-AP was defined as a TG level > 500 mg/dL in the absence of other common aetiologies of AP. The TG levels within 24 hours (24 h), 48 hours (48 h), 3-4 days (3-4 d), and 5-7 days (5-7 d) after symptom onset and their correlations with disease severity in HTG-AP patients were analysed by cross-sectional and longitudinal studies.

Results
In the cross-sectional study, 377 HTG-AP patients were included before lipid-lowering intervention: 216 subjects had their first TG levels measured within 24 h after onset, 91 within 48 h, 50 in 3-4 d, and 20 in 5-7 d. TG levels decreased in the 24 h, 48 h and 3-4 d groups (P < 0.001), however, the TG decline in the 5-7 d group had no difference compared with the 3-4 d group. HTG-AP patients with severe or moderately severe disease displayed higher TG levels than those with mild disease in the 24 h and 48 h groups (P < 0.050) but not in the 3-4 d or 5-7 d groups. Furthermore, the TG levels were correlated with the modified computed tomography severity index only in the 24 h and 48 h groups, while an association between serum calcium levels and C-reactive protein levels was only present in the 24 h group. Similarly, the TG levels were related to hospital days and ICU days in the 24 h and/or 48 h groups. In the longitudinal study, 165 patients with complete records of TG levels from 24 h to 5-7 d were enrolled. With supportive care and lipid-lowering treatment after admission, the TG levels declined rapidly (P < 0.001), and the correlations with disease severity weakened or even disappeared from 24 h to 5-7 d.

Conclusion
TG levels decreased and attenuated the association with disease severity of HTG-AP over the time of onset. The TG levels within the initial 48 h after onset were most useful for the diagnosis and disease assessment of HTG-AP.
Impact of in vitro digested zinc oxide nanoparticles on intestinal model systems
Authors: Mittag Anna , Singer Alina , Hoera Christian , Westermann Martin , Kämpfe Alexander , Glei Michael 
Published: May 2022

Abstract
Background
Zinc oxide nanoparticles (ZnO NP) offer beneficial properties for many applications, especially in the food sector. Consequently, as part of the human food chain, they are taken up orally. The toxicological evaluation of orally ingested ZnO NP is still controversial. In addition, their physicochemical properties can change during digestion, which leads to an altered biological behaviour. Therefore, the aim of our study was to investigate the fate of two different sized ZnO NP (< 50 nm and < 100 nm) during in vitro digestion and their effects on model systems of the intestinal barrier. Differentiated Caco-2 cells were used in mono- and coculture with mucus-producing HT29-MTX cells. The cellular uptake, the impact on the monolayer barrier integrity and cytotoxic effects were investigated after 24 h exposure to 123–614 µM ZnO NP.

Results

In vitro digested ZnO NP went through a morphological and chemical transformation with about 70% free zinc ions after the intestinal phase. The cellular zinc content increased dose-dependently up to threefold in the monoculture and fourfold in the coculture after treatment with digested ZnO NP. This led to reactive oxygen species but showed no impact on cellular organelles, the metabolic activity, and the mitochondrial membrane potential. Only very small amounts of zinc (< 0.7%) reached the basolateral area, which is due to the unmodified transepithelial electrical resistance, permeability, and cytoskeletal morphology.

Conclusions
Our results reveal that digested and, therefore, modified ZnO NP interact with cells of an intact intestinal barrier. But this is not associated with serious cell damage.
Understanding interdisciplinary perspectives of plant intelligence: Is it a matter of science, language, or subjectivity?
Authors: Khattar Jennifer , Calvo Paco , Vandebroek Ina , Pandolfi Camilla , Dahdouh-Guebas Farid 
Published: May 2022

Abstract
Background
Evidence suggests that plants can behave intelligently by exhibiting the ability to learn, make associations between environmental cues, engage in complex decisions about resource acquisition, memorize, and adapt in flexible ways. However, plant intelligence is a disputed concept in the scientific community. Reasons for lack of consensus can be traced back to the history of Western philosophy, interpretation of terminology, and due to plants lacking neurons and a central nervous system. Plant intelligence thus constitutes a novel paradigm in the plant sciences. Therefore, the perspectives of scientists in plant-related disciplines need to be investigated in order to gain insight into the current state and future development of this concept.

Methods
This study analyzed opinions of plant intelligence held by scientists from different plant-related disciplines, including ethnobiology and other biological sciences, through an online questionnaire.

Results
Our findings show that respondents’ personal belief systems and the frequency of taking into account other types of knowledge, such as traditional knowledge, in their own field(s) of study, were associated with their opinions of plant intelligence. Meanwhile, respondents’ professional expertise, background (discipline), or familiarity with evidence provided on plant intelligence did not affect their opinions.

Conclusions
This study emphasizes the influential role of scientists’ own subjective beliefs. In response, two approaches could facilitate transdisciplinary understanding among scientists: (1) effective communication designed to foster change in agreement based on presented information; and (2) holding space for an interdisciplinary dialogue where scientists can express their own subjectivities and open new opportunities for collaboration.
A method to experimentally clamp leaf water content to defined values to assess its effects on apoplastic pH
Authors: Kaiser Hartmut , Sagervanshi Amit , Mühling Karl H. 
Published: May 2022

Abstract
Background
Leaf hydration is controlled by feedback mechanisms, e.g. stomatal responses, adjustments of osmotic potential and hydraulic conductivity. Leaf water content thus is an input into related feedback-loops controlling the balance of water uptake and loss.
Apoplastic alkalisation upon leaf dehydration is hypothesized to be involved together and in interaction with abscisic acid (ABA) in water stress related signaling on tissue level. However, important questions are still unresolved, e.g. the mechanisms leading to pH changes and the exact nature of its interaction with ABA. When studying these mechanisms and their intermediate signaling steps, an experimenter has only poor means to actually control the central experimental variable, leaf water content (LWC), because it is not only dependent on external variables (e.g. air humidity), which are under experimental control, but is also governed by the biological influences controlling transpiration and water uptake. Those are often unknown in their magnitude, unpredictable and fluctuating throughout an experiment and will prevent true repetitions of an experiment. The goal of the method presented here is to experimentally control and manipulate leaf water content (LWC) of attached intact leaves enclosed in a cuvette while simultaneously measuring physiological parameters like, in this case, apoplastic pH.

Results
An experimental setup was developed where LWC is measured by a sensor based on IR-transmission and its signal processed to control a pump which circulates air from the cuvette through a cold trap. Hereby a feedback-loop is formed, which by adjusting vapour pressure deficit (VPD) and consequently leaf transpiration can precisely control LWC. This technique is demonstrated here in a combination with microscopic fluorescence imaging of apoplastic pH (pHapo) as indicated by the excitation ratio of the pH sensitive dye OregonGreen. Initial results indicate that pHapo of the adaxial epidermis of Vicia faba is linearly related to reductions in LWC.

Conclusions
Using this setup, constant LWC levels, step changes or ramps can be experimentally applied while simultaneously measuring physiological responses. The example experiments demonstrate that bringing LWC under experimental control in this way allows better controlled and more repeatable experiments to probe quantitative relationships between LWC and signaling and regulatory processes.
Metabolomics analyses of traditional Chinese medicine formula Shuang Huang Lian by UHPLC-QTOF-MS/MS
Authors: Xu Gang , Shu Yachun , Xu Yan 
Published: May 2022

Abstract
Background
Shuang Huang Lian (SHL) is a traditional Chinese medicine (TCM) formula made from Lonicerae Japonicae Flos, Forsythiae Fructus, and Scutellariae Radix. Despite the widespread use of SHL in clinical practice for treating upper respiratory tract infections (URTIs), the complete component fingerprint and the pharmacologically active components in the SHL formula remain unclear. The objective of this study was to develop an untargeted metabolomics method for component identification, quantitation, pattern recognition, and cross-comparison of various SHL preparation forms (i.e., granule, oral liquid, and tablet).

Methods
Ultra-high-performance liquid chromatography and quadrupole time-of-flight tandem mass spectrometry (UHPLC-QTOF-MS/MS) together with bioinformatics were used for chemical profiling, identification, and quantitation of SHL. Multivariate data analyses such as principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were performed to assess the correlations among the three SHL preparation forms and the reproducibility of the technical and biological replicates.

Results
A UHPLC-QTOF-MS/MS-based untargeted metabolomics method was developed and applied to analyze three SHL preparation forms, consisting of 178 to 216 molecular features. Among the 95 common molecular features from the three SHL preparation forms, quantitative analysis was performed using a single exogenous reference internal standard. Forty-seven of the 95 common molecular features have been identified using various databases. Among the 47 common components, there were 17 flavonoids, 7 oligopeptides, 5 terpenoids, 2 glycosides, 2 cyclohexanecarboxylic acids, 2 spiro compounds, 2 lipids, 2 glycosylglycerol derivatives, and 8 various compounds such as alkyl caffeate ester, aromatic ketone, benzaldehyde, benzodioxole, benzofuran, chalcone, hydroxycoumarin, and purine nucleoside. Five of the 47 common components were designated by the Chinese Pharmacopoeia as the quality markers of medicinal plants of SHL, and 15 were previously reported to have pharmacological activities. Distinct patterns of the three SHL preparation forms were observed in the PCA and PLS-DA plots.

Conclusions
The developed method is reliable and reproducible, which is useful for the profiling, component identification, quantitation, quality assessment of various SHL preparation forms and may apply to the analysis of other TCM formulas.
Extracellular matrix dynamics: tracking in biological systems and their implications
Authors: Hu Michael , Ling Zihan , Ren Xi 
Published: May 2022

AbstractThe extracellular matrix (ECM) constitutes the main acellular microenvironment of cells in almost all tissues and organs. The ECM not only provides mechanical support, but also mediates numerous biochemical interactions to guide cell survival, proliferation, differentiation, and migration. Thus, better understanding the everchanging temporal and spatial shifts in ECM composition and structure – the ECM dynamics – will provide fundamental insight regarding extracellular regulation of tissue homeostasis and how tissue states transition from one to another during diverse pathophysiological processes. This review outlines the mechanisms mediating ECM-cell interactions and highlights how changes in the ECM modulate tissue development and disease progression, using the lung as the primary model organ. We then discuss existing methodologies for revealing ECM compositional dynamics, with a particular focus on tracking newly synthesized ECM proteins. Finally, we discuss the ramifications ECM dynamics have on tissue engineering and how to implement spatial and temporal specific extracellular microenvironments into bioengineered tissues. Overall, this review communicates the current capabilities for studying native ECM dynamics and delineates new research directions in discovering and implementing ECM dynamics to push the frontier forward.
Toe grip force of the dominant foot is associated with fall risk in community‐dwelling older adults: a cross‐sectional study
Authors: Matsuno Satoshi , Yoshimura Atsushi , Yoshiike Takuya , Morita Sachiyo , Fujii Yusuke , Honma Motoyasu , Ozeki Yuji , Kuriyama Kenichi 
Published: May 2022

AbstractBackgroundIt is unclear whether the toe grip force (TGF) of the dominant foot (DF) and the lower limb function asymmetry (LLFA) in older adults are associated with fall risk. Therefore, this study aimed to investigate the effect of lower limb properties (such as TGF, muscle strength, and plantar sensation) on the risk of falls in older adults, while considering the foot dominance and asymmetry of lower limb function.MethodsThis study was a cross‐sectional study. We determined whether the lower limb function of the DF and non‐dominant foot (non‐DF) and LLFA had any effect on the fall risk in 54 older adults (mean ± standard deviation: 72.2 ± 6.0, range: 60–87 years). We examined the participants' fall history, Mini‐Mental State Examination (MMSE) score, lower limb function, and LLFA. To determine fall risk factors, we performed logistic regression analysis, with presence or absence of falls as the dependent variable.ResultsThe independent variables were age, sex, MMSE score, two‐point discrimination of the heel (non‐DF) as plantar sensation index, and the TGF of both feet. Only the TGF of the DF was identified as a risk factor for falls (p < 0.05).ConclusionsIn older adults, clinicians should focus on the TGF of the DF as a risk factor for falls.Trial registrationThis study was retrospectively registered. https://center6.umin.ac.jp/cgi‐bin/ctr/ctr_up_rec_f1.cgi.
Identifying tumor cells at the single-cell level using machine learning
Authors: Dohmen Jan , Baranovskii Artem , Ronen Jonathan , Uyar Bora , Franke Vedran , Akalin Altuna 
Published: May 2022

AbstractTumors are complex tissues of cancerous cells surrounded by a heterogeneous cellular microenvironment with which they interact. Single-cell sequencing enables molecular characterization of single cells within the tumor. However, cell annotation—the assignment of cell type or cell state to each sequenced cell—is a challenge, especially identifying tumor cells within single-cell or spatial sequencing experiments. Here, we propose ikarus, a machine learning pipeline aimed at distinguishing tumor cells from normal cells at the single-cell level. We test ikarus on multiple single-cell datasets, showing that it achieves high sensitivity and specificity in multiple experimental contexts.
3D genome organization in the epithelial-mesenchymal transition spectrum
Authors: Pang Qing You , Tan Tuan Zea , Sundararajan Vignesh , Chiu Yi-Chia , Chee Edward Yu Wing , Chung Vin Yee , Choolani Mahesh A. , Huang Ruby Yun-Ju 
Published: May 2022

Abstract
Background
The plasticity along the epithelial-mesenchymal transition (EMT) spectrum has been shown to be regulated by various epigenetic repertoires. Emerging evidence of local chromatin conformation changes suggests that regulation of EMT may occur at a higher order of three-dimensional genome level.

Results
We perform Hi-C analysis and combine ChIP-seq data across cancer cell lines representing different EMT states. We demonstrate that the epithelial and mesenchymal genes are regulated distinctively. We find that EMT genes are regulated within their topologically associated domains (TADs), with only a subset of mesenchymal genes being influenced by A/B compartment switches, indicating topological remodeling is required in the transcriptional regulation of these genes. At the TAD level, epithelial and mesenchymal genes are associated with different regulatory trajectories. The epithelial gene-residing TADs are enriched with H3K27me3 marks in the mesenchymal-like states. The mesenchymal gene-residing TADs, which do not show enrichment of H3K27me3 in epithelial-like states, exhibit increased interaction frequencies with regulatory elements in the mesenchymal-like states.

Conclusions
We propose a novel workflow coupling immunofluorescence and dielectrophoresis to unravel EMT heterogeneity at single-cell resolution. The predicted three-dimensional structures of chromosome 10, harboring Vimentin, identify cell clusters of different states. Our results pioneer a novel avenue to decipher the complexities underlying the regulation of EMT and may infer the barriers of plasticity in the 3D genome context.