bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparing peripheral limb and forehead vital sign monitoring in newborn infants at birth
Authors: Swamy Suvvi K. Narayana , Stockwell Simon J. , Liu Chong , Henry Caroline , Shipley Lara , Ward Carole , Mirahmadi Siavash , Correia Ricardo , Morgan Stephen P. , Crowe John A. , Sharkey Don , Hayes-Gill Barrie R.
Published: October 2024

Background

To study the feasibility of measuring heart rate (HR) and oxygen saturation (SpO2) on the forehead, during newborn transition at birth, and to compare these measurements with those obtained from the wrist.

Methods

Vital signs were measured and compared between forehead-mounted reflectance (remittance) photoplethysmography sensor (fhPPG) and a wrist-mounted pulse oximeter sensor (wrPO), from 20 enrolled term newborns born via elective caesarean section, during the first 10 min of life.

Results

From the datasets available (n = 13), the median (IQR) sensor placement times for fhPPG, ECG and wrPO were 129 (70) s, 143 (68) s, and 159 (76) s, respectively, with data recorded for up to 10 min after birth. The success rate (percentage of total possible HR values reported once sited) of fhPPG (median = 100%) was higher compared to wrPO (median = 69%) during the first 6 min of life (P < 0.005). Both devices exhibited good HR agreement with ECG, achieving >95% agreement by 3 (fhPPG) and 4 (wrPO) min. SpO2for fhPPG correlated with wrPO (r = 0.88), but there were significant differences in SpO2between the two devices between 3 and 8 min (P < 0.005), with less variance observed with fhPPG SpO2.

Conclusion

In the period of newborn transition at birth in healthy term infants, forehead measurement of vital signs was feasible and exhibited greater HR accuracy and higher estimated SpO2values compared to wrist-sited pulse oximetry. Further investigation of forehead monitoring based on the potential benefits over peripheral monitoring is warranted.

Impact

This study demonstrates the feasibility of continuously monitoring heart rate and oxygen saturation from an infant’s forehead in the delivery room immediately after birth.

Significantly higher SpO2measurements were observed from the forehead than the wrist during the transition from foetal to newborn life.

Continuous monitoring of vital signs from the forehead could become a valuable tool to improve the delivery of optimal care provided for newborns at birth.
Beyond the Bite: Exploring Mental Health of Dental Faculty in Pakistan– a multi-institutional study
Authors: Ali Kamran , Zahra Daniel , Bashir Ulfat , Daud Alaa , Raja Hina Zafar , Witton Rob , Raja Mahwish
Published: October 2024

Introduction

Mental health issues are being reported increasingly amongst healthcare staff and students globally. The aim of this study was to investigate the frequency of common mental health issues amongst dental faculty members at multiple institutions in Pakistan.

Methods

Following approval from the institutional ethics review board, dental faculty members at 14 dental institutions were invited to participate in an online survey based on globally validated scales for mental health problems including the Patient Health Questionnaire (PHQ-9), and the Depression, Anxiety, and Stress Scale (DASS-21). Two open-ended questions were included in the survey to identify perceived factors contributing to poor mental health and recommendations for improving institutional support.

Results

A total of 200 faculty members out of provided their responses to the survey questionnaire but complete responses were provided by 183 participants which included 120 (65.57%) females, and 63 (34.43%) males. The total number of faculty members at the participating institutions was 426 and 183 responses translated into an overall response rate of 43%. Most participants were in the 31–40 years age-group (n = 81, 44.26%) followed by 25–30 year (n = 51, 22.87%) and 41–50 years (n = 40, 21.86%). The mean score on PHQ-9 was 6.51 (SD ± 5.4) while the mean DASS-21 score was 13.04 (SD ± 10.95). PHQ-9 Depression, and DASS-21 Depression, Anxiety, and Stress scores were all significantly positively correlated for the whole sample, and within each subgroup of each demographic factor. Job-related workload, lack of institutional support, financial limitations, and poor work life balance were identified as the main factors contributing adversely to the mental health of the participants.

Discussion

This study provides useful insights into the scale of mental health status amongst dental faculty members at 14 institutions in Pakistan. Underlying factors affecting the mental health of faculty members adversely were identified and recommendations are provided to address these challenges.
Heparin-binding EGF-like growth factor via miR-126 controls tumor formation/growth and the proteolytic niche in murine models of colorectal and colitis-associated cancers
Authors: Salama Yousef , Munakata Shinya , Osada Taro , Takahashi Satoshi , Hattori Koichi , Heissig Beate
Published: October 2024

MicroRNAs, including the tumor-suppressor miR-126 and the oncogene miR-221, regulate tumor formation and growth in colitis-associated cancer (CAC) and colorectal cancer (CRC). This study explores the impact of the epithelial cytokine heparin-binding epidermal growth factor (HB-EGF) and its receptor epidermal growth factor receptor (EGFR) on the pathogenesis of CAC and CRC, particularly in the regulation of microRNA-driven tumor growth and protease expression. In murine models of CRC and CAC, lack of miR-126 and elevated miR-221 expression in colonic tissues enhanced tumor formation and growth. MiR-126 downregulation in colon cells established a pro-tumorigenic proteolytic niche by targeting HB-EGF-active metalloproteinase-7, -9 (MMP7/MMP9), disintegrin, and metalloproteinase domain-containing protein 9, and modulating chemokine-mediated recruitment of HB-EGF-loaded inflammatory cells. Mechanistically, downregulation of HB-EGF and EGFR in the colon suppressed miR-221 and enhanced miR-126 expression via activating enhancer-binding protein 2 alpha. Reintroducing miR-126 reduced tumor development and HB-EGF expression. Combining miR-126 reintroduction, which targets specific HB-EGF-active proteases but not ADAM17, with MMP inhibitors like Batimastat or Marimastat effectively suppressed tumor growth. This combination normalized protease expression and balanced miR-126 and miR-221 levels in developing and growing tumors. These findings demonstrate that suppressing HB-EGF and EGFR1 shifts the balance from oncogenic miR-221 to tumor-suppressive miR-126 action. Consequently, normalizing miR-126 expression could open new avenues for treating patients with CAC and CRC, and this normalization is intertwined with the anticancer efficacy of MMP inhibitors.
TRIM55 restricts the progression of hepatocellular carcinoma through ubiquitin-proteasome-mediated degradation of NF90
Authors: Luo Changhong , Lu Yuyan , Fang Qinliang , Lu Jing , Zhan Ping , Xi Wenqing , Wang Jinzhu , Chen Xijun , Yao Qin , Wang Fuqiang , Yin Zhenyu , Xie Chengrong
Published: October 2024

Hepatocellular carcinoma (HCC) is a prevalent malignant tumor worldwide. Tripartite motif containing 55 (TRIM55), also known as muscle-specific ring finger 2 (Murf2), belongs to the TRIM protein family and serves as an E3 ligase. Recently, the function and mechanism of TRIM55 in the advancement of solid tumors have been elucidated. However, the role of TRIM55 and its corresponding protein substrates in HCC remains incompletely explored. In this study, we observed a significant reduction in TRIM55 expression in HCC tissues. The downregulation of TRIM55 expression correlated with larger tumor size and elevated serum alpha-fetoprotein (AFP), and predicted unfavorable overall and tumor-free survival. Functional experiments demonstrated that TRIM55 suppressed the proliferation, migration, and invasion of HCC cells in vitro, as well as hindered HCC growth and metastasis in vivo. Additionally, TRIM55 exhibited a suppressive effect on HCC angiogenesis. Mechanistically, TRIM55 interacted with nuclear factor 90 (NF90), a double-stranded RNA-binding protein responsible for regulating mRNA stability and gene transcription, thereby facilitating its degradation via the ubiquitin-proteasome pathway. Furthermore, TRIM55 attenuated the association between NF90 and the mRNA of HIF1α and TGF-β2, consequently reducing their stability and inactivating the HIF1α/VEGF and TGFβ/Smad signaling pathways. In conclusion, our findings unveil the important roles of TRIM55 in suppressing the progression of HCC partly by promoting the degradation of NF90 and subsequently modulating its downstream pathways, including HIF1α/VEGF and TGFβ/Smad signaling.
N4BP3 facilitates NOD2-MAPK/NF-κB pathway in inflammatory bowel disease through mediating K63-linked RIPK2 ubiquitination
Authors: Jiang Wang , Zhao Yan , Han Min , Xu Jiafan , Chen Kun , Liang Yi , Yin Jie , Hu Jinyue , Shen Yueming
Published: October 2024

The NOD2 signaling pathway, which plays an important role in the mechanisms of inflammatory bowel disease (IBD) development, has been closely associated with ubiquitination. It was revealed in this study that NOD2 receptor activation could obviously affect the expression of 19 ubiquitination-related genes, with N4BP3 being the most prominently expressed and upregulated. In addition, N4BP3 knockdown was found to reduce the mRNA levels of MDP-induced inflammatory factors, while N4BP3 overexpression elevated their mRNA levels as well as the levels of phospho-ERK1/2, phospho-JNK, phospho-P38 and phospho-NF-κB P65 proteins. Immunoprecipitation tests showed that N4BP3 could pull down RIPK2 and promote its K63-linked ubiquitination. In human tissue specimen assays and mouse experiments, we found that the expression of N4BP3 was significantly elevated in Crohn’s disease (CD) patients and IBD mice, and N4BP3 knockdown reduced the dextran sulfate sodium-induced pathological score and the expression of inflammatory factors in the mouse colon tissue. In conclusion, N4BP3 is able to interact with RIPK2 and promote its K63-linked ubiquitination, to further promote the NOD2-MAPK/NF-κB pathway, thereby increasing promoting the release of inflammation factors and the degree of IBD inflammation.
CD30 influences germinal center B-cell dynamics and the expansion of IgG1-switched B cells
Authors: Wang Yan , Rambold Ursula , Fiedler Petra , Babushku Tea , Tapken Claas L. , Hoefig Kai P. , Hofer Thomas P. , Adler Heiko , Yildirim Ali Önder , Strobl Lothar J. , Zimber-Strobl Ursula
Published: October 2024

Initially, identified as a Hodgkin lymphoma marker, CD30 was subsequently detected on a subset of human B cells within and around germinal centers (GCs). While CD30 expression is typically restricted to a few B cells, expansion of CD30-expressing B cells occurs in certain immune disorders and during viral infections. The role of CD30 in B cells remains largely unclear. To address this gap in knowledge, we established a conditional CD30-knockin mouse strain. In these mice, B-cell-specific CD30 expression led to a normal B-cell phenotype in young mice, but most aged mice exhibited significant expansion of B cells, T cells and myeloid cells and increased percentages of GC B cells and IgG1-switched cells. This may be driven by the expansion of CD4+ senescence-associated T cells and T follicular helper cells, which partially express CD30-L (CD153) and may stimulate CD30-expressing B cells. Inducing CD30 expression in antigen-activated B cells accelerates the GC reaction and augments plasma cell differentiation, possibly through the posttranscriptional upregulation of CXCR4. Furthermore, CD30 expression in GC B cells promoted the expansion of IgG1-switched cells, which displayed either a GC or memory-like B-cell phenotype, with abnormally high IgG1 levels compared with those in controls. These findings shed light on the role of CD30 signaling in GC B cells and suggest that elevated CD30+ B-cell numbers lead to pathological lymphocyte activation and proliferation.
Unveiling the critical role of androgen receptor signaling in avian sexual development
Authors: Lengyel Kamila , Rudra Mekhla , Berghof Tom V. L. , Leitão Albertine , Frankl-Vilches Carolina , Dittrich Falk , Duda Denise , Klinger Romina , Schleibinger Sabrina , Sid Hicham , Trost Lisa , Vikkula Hanna , Schusser Benjamin , Gahr Manfred
Published: October 2024

Gonadal hormone activities mediated by androgen and estrogen receptors, along with cell-autonomous mechanisms arising from the absence of sex-chromosome dosage compensation, are key factors in avian sexual development. In this study, we generate androgen receptor (AR) knockout chickens (AR−/−) to explore the role of androgen signaling in avian sexual development. Despite developing sex-typical gonads and gonadal hormone production, AR−/− males and females are infertile. While few somatic sex-specific traits persist (body size, spurs, and tail feathers), crucial sexual attributes such as comb, wattles and sexual behaviors remain underdeveloped in both sexes. Testosterone treatment of young AR−/− males fails to induce crow behavior, comb development, or regression of the bursa of Fabricius, which are testosterone-dependent phenotypes. These findings highlight the significance of androgen receptor mechanisms in fertility and sex-specific traits in chickens, challenging the concept of a default sex in birds and emphasizing the dominance of androgen signaling in avian sexual development.
Long-lived topological time-crystalline order on a quantum processor
Authors: Xiang Liang , Jiang Wenjie , Bao Zehang , Song Zixuan , Xu Shibo , Wang Ke , Chen Jiachen , Jin Feitong , Zhu Xuhao , Zhu Zitian , Shen Fanhao , Wang Ning , Zhang Chuanyu , Wu Yaozu , Zou Yiren , Zhong Jiarun , Cui Zhengyi , Zhang Aosai , Tan Ziqi , Li Tingting , Gao Yu , Deng Jinfeng , Zhang Xu , Dong Hang , Zhang Pengfei , Jiang Si , Li Weikang , Lu Zhide , Sun Zheng-Zhi , Li Hekang , Wang Zhen , Song Chao , Guo Qiujiang , Liu Fangli , Gong Zhe-Xuan , Gorshkov Alexey V. , Yao Norman Y. , Iadecola Thomas , Machado Francisco , Wang H. , Deng Dong-Ling
Published: October 2024

Topologically ordered phases of matter elude Landau’s symmetry-breaking theory, featuring a variety of intriguing properties such as long-range entanglement and intrinsic robustness against local perturbations. Their extension to periodically driven systems gives rise to exotic new phenomena that are forbidden in thermal equilibrium. Here, we report the observation of signatures of such a phenomenon—a prethermal topologically ordered time crystal—with programmable superconducting qubits arranged on a square lattice. By periodically driving the superconducting qubits with a surface code Hamiltonian, we observe discrete time-translation symmetry breaking dynamics that is only manifested in the subharmonic temporal response of nonlocal logical operators. We further connect the observed dynamics to the underlying topological order by measuring a nonzero topological entanglement entropy and studying its subsequent dynamics. Our results demonstrate the potential to explore exotic topologically ordered nonequilibrium phases of matter with noisy intermediate-scale quantum processors.
Double-strand breaks in facultative heterochromatin require specific movements and chromatin changes for efficient repair
Authors: Wensveen Marieke R. , Dixit Aditya A. , van Schendel Robin , Kendek Apfrida , Lambooij Jan-Paul , Tijsterman Marcel , Colmenares Serafin U. , Janssen Aniek
Published: October 2024

DNA double-strand breaks (DSBs) must be properly repaired within diverse chromatin domains to maintain genome stability. Whereas euchromatin has an open structure and is associated with transcription, facultative heterochromatin is essential to silence developmental genes and forms compact nuclear condensates, called polycomb bodies. Whether the specific chromatin properties of facultative heterochromatin require distinct DSB repair mechanisms remains unknown. Here, we integrate single DSB systems in euchromatin and facultative heterochromatin in Drosophila melanogaster and find that heterochromatic DSBs rapidly move outside polycomb bodies. These DSB movements coincide with a break-proximal reduction in the canonical heterochromatin mark histone H3 Lysine 27 trimethylation (H3K27me3). We demonstrate that DSB movement and loss of H3K27me3 at heterochromatic DSBs depend on the histone demethylase dUtx. Moreover, loss of dUtx specifically disrupts completion of homologous recombination at heterochromatic DSBs. We conclude that DSBs in facultative heterochromatin require dUtx-mediated loss of H3K27me3 to promote DSB movement and repair.
Gustatory interface for operative assessment and taste decoding in patients with tongue cancer
Authors: Wang Xiner , Bai Guo , Liang Jizhi , Xie Qianyang , Chen Zhaohan , Zhou Erda , Li Meng , Wei Xiaoling , Sun Liuyang , Zhang Zhiyuan , Yang Chi , Tao Tiger H. , Zhou Zhitao
Published: October 2024

Taste, a pivotal sense modality, plays a fundamental role in discerning flavors and evaluating the potential harm of food, thereby contributing to human survival, physical and mental health. Patients with tongue cancer may experience a loss of taste following extensive surgical resection with flap reconstruction. Here, we designed a gustatory interface that enables the non-invasive detection of tongue electrical activities for a comprehensive operative assessment. Moreover, it decodes gustatory information from the reconstructed tongue without taste buds. Our gustatory interface facilitates the recording and analysis of electrical activities on the tongue, yielding an electrical mapping across the entire tongue surface, which delineates the safe margin for surgical management and assesses flap viability for postoperative structure monitoring and prompt intervention. Furthermore, the gustatory interface helps patients discern tastes with an accuracy of 97.8%. Our invention offers a promising approach to clinical assessment and management and holds potential for improving the quality of life for individuals with tongue cancer.
The phageome of patients with ulcerative colitis treated with donor fecal microbiota reveals markers associated with disease remission
Authors: Majzoub Marwan E. , Paramsothy Sudarshan , Haifer Craig , Parthasarathy Rohit , Borody Thomas J. , Leong Rupert W. , Kamm Michael A. , Kaakoush Nadeem O.
Published: October 2024

Bacteriophages are influential within the human gut microbiota, yet they remain understudied relative to bacteria. This is a limitation of studies on fecal microbiota transplantation (FMT) where bacteriophages likely influence outcome. Here, using metagenomics, we profile phage populations - the phageome - in individuals recruited into two double-blind randomized trials of FMT in ulcerative colitis. We leverage the trial designs to observe that phage populations behave similarly to bacterial populations, showing temporal stability in health, dysbiosis in active disease, modulation by antibiotic treatment and by FMT. We identify a donor bacteriophage putatively associated with disease remission, which on genomic analysis was found integrated in a bacterium classified to Oscillospiraceae, previously isolated from a centenarian and predicted to produce vitamin B complex except B12. Our study provides an in-depth assessment of phage populations during different states and suggests that bacteriophage tracking has utility in identifying determinants of disease activity and resolution.
Systemically injected oxygen within rapidly dissolving microbubbles improves the outcomes of severe hypoxaemia in swine
Authors: Mancebo Julia Garcia , Sack Kristen , Hartford Jay , Dominguez Saffron , Balcarcel-Monzon Michelle , Chartier Elizabeth , Nguyen Tien , Cole Alexis R. , Sperotto Francesca , Harrild David M. , Polizzotti Brian D. , Everett Allen D. , Packard Alan B. , Dearling Jason , Nedder Arthur G. , Warfield Simon , Yang Edward , Lidov Hart G. W. , Kheir John N. , Peng Yifeng
Published: October 2024

Acute respiratory failure can cause profound hypoxaemia that leads to organ injury or death within minutes. When conventional interventions are ineffective, the intravenous administration of oxygen can rescue patients from severe hypoxaemia, but at the risk of microvascular obstruction and of toxicity of the carrier material. Here we describe polymeric microbubbles as carriers of high volumes of oxygen (350–500 ml of oxygen per litre of foam) that are stable in storage yet quickly dissolve following intravenous injection, reverting to their soluble and excretable molecular constituents. In swine with profound hypoxaemia owing to acute and temporary (12 min) upper-airway obstruction, the microbubble-mediated delivery of oxygen led to: the maintenance of critical oxygenation, lowered burdens of cardiac arrest, improved survival, and substantially improved neurologic and kidney function in surviving animals. Our findings underscore the importance of maintaining a critical threshold of oxygenation and the promise of injectable oxygen as a viable therapy in acute and temporary hypoxaemic crises.
Image processing tools for petabyte-scale light sheet microscopy data
Authors: Ruan Xiongtao , Mueller Matthew , Liu Gaoxiang , Görlitz Frederik , Fu Tian-Ming , Milkie Daniel E. , Lillvis Joshua L. , Kuhn Alexander , Gan Chong Johnny , Hong Jason Li , Herr Chu Yi Aaron , Hercule Wilmene , Nienhaus Marc , Killilea Alison N. , Betzig Eric , Upadhyayula Srigokul
Published: October 2024

Light sheet microscopy is a powerful technique for high-speed three-dimensional imaging of subcellular dynamics and large biological specimens. However, it often generates datasets ranging from hundreds of gigabytes to petabytes in size for a single experiment. Conventional computational tools process such images far slower than the time to acquire them and often fail outright due to memory limitations. To address these challenges, we present PetaKit5D, a scalable software solution for efficient petabyte-scale light sheet image processing. This software incorporates a suite of commonly used processing tools that are optimized for memory and performance. Notable advancements include rapid image readers and writers, fast and memory-efficient geometric transformations, high-performance Richardson–Lucy deconvolution and scalable Zarr-based stitching. These features outperform state-of-the-art methods by over one order of magnitude, enabling the processing of petabyte-scale image data at the full teravoxel rates of modern imaging cameras. The software opens new avenues for biological discoveries through large-scale imaging experiments.
Diverse rhizosphere-associated Pseudomonas genomes from along a Wadden Island salt marsh transition zone
Authors: Mei Siyu , Wang Miao , Salles Joana Falcão , Hackl Thomas
Published: October 2024

Soil microbes are key drivers of ecosystem processes promoting nutrient cycling, system productivity, and resilience. While much is known about the roles of microbes in established systems, their impact on soil development and the successional transformation over time remains poorly understood. Here, we provide 67 diverse, rhizosphere-associated Pseudomonas draft genomes from an undisturbed salt march primary succession spanning >100 years of soil development. Pseudomonas are cosmopolitan bacteria with a significant role in plant establishment and growth. We obtained isolates associated with Limonium vulgare and Artemisia maritima, two typical salt marsh perennial plants with roles in soil stabilization, salinity regulation, and biodiversity support. We anticipate that our data, in combination with the provided physiochemical measurements, will help identify genomic signatures associated with the different selective regimes along the successional stages, such as varying soil complexity, texture, and nutrient availability. Such findings would advance our understanding of Pseudomonas’ role in natural soil ecosystems and provide the basis for a better understanding of the roles of microbes throughout ecosystem transformations.
Unraveling the relative abundance of psychobiotic bacteria in children with Autism Spectrum Disorder
Authors: Darwesh Mennat-Allah K. , Bakr Wafaa , Omar Tarek E. I. , El-Kholy Mohammed A. , Azzam Nashwa Fawzy
Published: October 2024

Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder characterized by social deficits. Accumulated evidence has shown a link between alterations in the composition of gut microbiota and both neurobehavioural and gastrointestinal symptoms in children with ASD which are related to the genera Lactobacillus and Bifidobacterium. These genera have been recently categorized as “psychobiotics”. Moreover, this study aimed to compare the relative abundance of psychobiotics (L. plantarum, L. reuteri, and B. longum) to the total gut microbiome in typically developing (TD) children and those with ASD in order to correlate the distribution of psychobiotic with the severity and sensory impairments in autism. The ASD children were assessed using the Childhood Autism Rating Scale (CARS), while sensory impairments were evaluated using the Short Sensory Profile (SSP). Furthermore, the gut microbiome was analyzed using the quantitative real-time PCR. The study revealed a statistically significant increase in the relative abundance of L. reuteri and L. plantarum in the TD group in comparison to ASD children. Regarding the SSP total score of ASD children, a statistically significant negative correlation was found between both Lactobacillus and L. plantarum with the under-responsive subscale. For the Autism Treatment Evaluation Checklist (ATEC) score, B. longum and Lactobacillus showed a significant positive correlation with Health/Physical/Behaviour.
Exploring the properties of antituberculosis drugs through QSPR graph models and domination-based topological descriptors
Authors: S Thilsath Parveen , Bommahalli Jayaraman Balamurugan , Siddiqui Muhammad Kamran
Published: October 2024

Tuberculosis (TB) is a global health concern caused by the bacterium Mycobacterium tuberculosis. This infectious disease primarily affects the lungs but can also impact other organs. Effective TB control involves early diagnosis, appropriate treatment with a combination of antibiotics, and public health measures to prevent transmission. However, ongoing challenges include drug-resistant strains and socioeconomic factors influencing its prevalence. Drugs such as isoniazid, pyrazinamide, ethambutol, ethionamide, linezolid, and levofloxacin are approved for the treatment of drug-susceptible tuberculosis. The properties and other activities of the drug, can be analyzed by modelling its chemical structure in terms of a molecular graph $$G=\left(V,E\right)$$, by considering the atoms as the vertex set $$V\left(G\right)$$ and the bonds between the two atoms as the edge set $$E\left(G\right)$$. A molecular descriptor or topological index of $$G$$ represents the corresponding chemical molecule as a numerical value. Domination is one of the key concepts in the molecular structure used to analyze the properties of atoms. In this article, the domination distance-based topological indices of the drugs isoniazid, pyrazinamide, ethambutol, ethionamide, linezolid, and levofloxacin are computed to conduct QSPR (Quantitative Structure–Property Relationship) analysis, exploring their physicochemical and ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) properties. Quadratic regression is then used in the QSPR analysis to examine the physicochemical and ADMET properties of these drugs. The results of this analysis indicate that the domination Schultz index and domination SM index are the indices most strongly correlated with the majority of the physicochemical and ADMET properties. The QSPR analysis can also be extended to analogs of these drugs and to other treatment drugs, such as rifampin and rifapentine, to further explore their properties.
Identification of shared gene expression programs activated in multiple modes of torpor across vertebrate clades
Authors: Weir Kurt , Vega Natasha , Busa Veronica F. , Sajdak Ben , Kallestad Les , Merriman Dana , Palczewski Krzysztof , Carroll Joseph , Blackshaw Seth
Published: October 2024

Torpor encompasses diverse adaptations to extreme environmental stressors such as hibernation, aestivation, brumation, and daily torpor. Here we introduce StrokeofGenus, an analytic pipeline that identifies distinct transcriptomic states and shared gene expression patterns across studies, tissues, and species. We use StrokeofGenus to study multiple and diverse forms of torpor from publicly-available RNA-seq datasets that span eight species and two classes. We identify three transcriptionally distinct states during the cycle of heterothermia: euthermia, torpor, and interbout arousal. We also identify torpor-specific gene expression patterns that are shared both across tissues and between species with over three hundred million years of evolutionary divergence. We further demonstrate the general sharing of gene expression patterns in multiple forms of torpor, implying a common evolutionary origin for this process. Although here we apply StrokeofGenus to analysis of torpor, it can be used to interrogate any other complex physiological processes defined by transient transcriptomic states.
Evolution of mechanical properties of organic-rich shale during thermal maturation
Authors: Wang Jianfeng , Liu Dayong , Shi Jianfei , Yang Chao , Liu Yuke , Wang Guozhi , Guo Huijuan , Liu Peng , Xiong Yongqiang , Peng Ping’an
Published: October 2024

Accurate assessment of the mechanical properties of organic matter, clay matrix, and bulk shale during maturation remains a challenge. Here, we aim to assess the mechanical properties of organic-rich shale during maturation using a combination of nanoindentation methods and various geochemical analyses, i.e., mineral composition, mass loss rate, chemical structure of organic matter, and Rock-Eval analyses. Results show that the evolution of mechanical properties of organic matter in shale during maturation can be divided into: the main oil-generation stage, and the condensate oil and gas generation stage. The stiffening of organic matter in the shale is mainly due to increased aromaticity and condensation of aromatic groups. The clay matrix experiences a slight decrease in hardness and Young’s modulus at low maturity levels due to the generation of liquid hydrocarbons. However, overall, the clay matrix becomes stiffer as the shale matures due to shale dehydration, expulsion or cracking of liquid hydrocarbons, transformation of clay minerals, and hardening of organic matter. The Young’s modulus and hardness of bulk shale generally increase with increasing maturity. This is closely related to the hardening of organic matter and clay matrix, as well as the development of the more compact and dense microstructure in the shale.
A systematic review and meta-analysis of GFAP gene variants in Alexander disease
Authors: Grossi Alice , Rosamilia Francesca , Carestiato Silvia , Salsano Ettore , Ceccherini Isabella , Bachetti Tiziana
Published: October 2024

Alexander disease (ALXDRD) is a rare neurodegenerative disorder of astrocytes resulting from pathogenic variants in the GFAP gene. The genotype-phenotype correlation remains elusive due to the variable expressivity of clinical manifestations. In an attempt to clarify the effects of GFAP variants in ALXDRD, numerous studies were collected and analyzed. In particular, we systematically searched for GFAP variants associated with ALXDRD and collected information on the location within the gene and protein, prediction of deleteriousness/pathogenicity, occurrence, sex and country of origin of patients, DNA source, genetic testing, and clinical signs. To identify possible associations, statistical analyses and meta-analyses were applied, thus revealing a higher than expected percentage of adult patients with ALXDRD. Furthermore, substitution of Arginine, the most frequently altered residue among the 550 predominantly missense causative GFAP variants collected, were mostly de novo and more prevalent in early-onset forms of ALXDRD. The effect of defective splicing in modifying the impact of GFAP variants on the age of onset of ALXDRD was also postulated after evaluating the distribution of the corresponding deleterious predictive values. In conclusion, not only previously unrecognized genotype-phenotype correlations were revealed in ALXDRD, but also subtle mechanisms could explain the variable manifestations of the ALXDRD clinical phenotype.
A randomized clinical trial testing digital mindset intervention for knee osteoarthritis pain and activity improvement
Authors: Boswell Melissa A. , Evans Kris M. , Ghandwani Disha , Hastie Trevor , Zion Sean R. , Moya Paula L. , Giori Nicholas J. , Hicks Jennifer L. , Crum Alia J. , Delp Scott L.
Published: October 2024

This randomized clinical trial evaluated the effectiveness of short, digital interventions in improving physical activity and pain for individuals with knee osteoarthritis. We compared a digital mindset intervention, focusing on adaptive mindsets (e.g., osteoarthritis is manageable), to a digital education intervention and a no-intervention group. 408 participants with knee osteoarthritis completed the study online in the US. The mindset intervention significantly improved mindsets compared to both other groups (P < 0.001) and increased physical activity levels more than the no-intervention group (mean = 28.6 points, P = 0.001), but pain reduction was not significant. The mindset group also showed significantly greater improvements in the perceived need for surgery, self-imposed physical limitations, fear of movement, and self-efficacy than the no-intervention and education groups. This trial demonstrates the effectiveness of brief digital interventions in educating about osteoarthritis and further highlights the additional benefits of improving mindsets to transform patients’ approach to disease management. The study was prospectively registered (ClinicalTrials.gov: NCT05698368, 2023-01-26).
Insights into the cotranscriptional and translational control mechanisms of the Escherichia coli tbpA thiamin pyrophosphate riboswitch
Authors: Grondin Jonathan P. , Geffroy Mélanie , Simoneau-Roy Maxime , Chauvier Adrien , Turcotte Pierre , St-Pierre Patrick , Dubé Audrey , Moreau Julie , Massé Eric , Penedo J. Carlos , Lafontaine Daniel A.
Published: October 2024

Riboswitches regulate gene expression by modulating their structure upon metabolite binding. These RNA orchestrate several layers of regulation to achieve genetic control. Although Escherichia coli riboswitches modulate translation initiation, several cases have been reported where riboswitches also modulate mRNA levels. Here, we characterize the regulation mechanisms of the thiamin pyrophosphate (TPP) tbpA riboswitch in E. coli. Our results indicate that the tbpA riboswitch modulates both levels of translation and transcription and that TPP sensing is achieved more efficiently cotranscriptionally than post-transcriptionally. The preference for cotranscriptional binding is also observed when monitoring the TPP-dependent inhibition of translation initiation. Using single-molecule approaches, we observe that the aptamer domain freely fluctuates between two main structures involved in TPP recognition. Our results suggest that translation initiation is controlled through the ligand-dependent stabilization of the riboswitch structure. This study demonstrates that riboswitch cotranscriptional sensing is the primary determinant in controlling translation and mRNA levels.
Applying minerals to soil to draw down atmospheric carbon dioxide through synergistic organic and inorganic pathways
Authors: Buss Wolfram , Hasemer Heath , Sokol Noah W. , Rohling Eelco J. , Borevitz Justin
Published: October 2024

Minerals in soil can sequester atmospheric carbon dioxide through natural organic and inorganic processes. Here we consider three soil- and mineral-based methods for carbon dioxide removal: (1) grinding and spreading of calcium- and magnesium-rich silicate rocks for enhanced rock weathering and subsequent inorganic carbon formation, (2) mineral doping of biomass prior to conversion into biochar for enhanced biochar carbon yield and stability, and (3) strategic application of minerals to soil to increase soil organic carbon accrual and stability. We argue that there are powerful synergies between these approaches for carbon dioxide removal through organic and inorganic pathways. We find that primary silicates, as contained in basalt, can benefit both enhanced weathering and soil organic carbon formation, while phyllosilicates and other reactive secondary minerals may have positive synergies for biochar and soil organic carbon. Optimising such synergies may substantially enhance economic and environmental benefits, yet these synergies require accurate quantification.
Macropinocytosis mediates resistance to loss of glutamine transport in triple-negative breast cancer
Authors: Wahi Kanu , Freidman Natasha , Wang Qian , Devadason Michelle , Quek Lake-Ee , Pang Angel , Lloyd Larissa , Larance Mark , Zanini Fabio , Harvey Kate , O’Toole Sandra , Guan Yi Fang , Holst Jeff
Published: October 2024

Triple-negative breast cancer (TNBC) metabolism and cell growth uniquely rely on glutamine uptake by the transporter ASCT2. Despite previous data reporting cell growth inhibition after ASCT2 knockdown, we here show that ASCT2 CRISPR knockout is tolerated by TNBC cell lines. Despite the loss of a glutamine transporter and low rate of glutamine uptake, intracellular glutamine steady-state levels were increased in ASCT2 knockout compared to control cells. Proteomics analysis revealed upregulation of macropinocytosis, reduction in glutamine efflux and increased glutamine synthesis in ASCT2 knockout cells. Deletion of ASCT2 in the TNBC cell line HCC1806 induced a strong increase in macropinocytosis across five ASCT2 knockout clones, compared to a modest increase in ASCT2 knockdown. In contrast, ASCT2 knockout impaired cell proliferation in the non-macropinocytic HCC1569 breast cancer cells. These data identify macropinocytosis as a critical secondary glutamine acquisition pathway in TNBC and a novel resistance mechanism to strategies targeting glutamine uptake alone. Despite this adaptation, TNBC cells continue to rely on glutamine metabolism for their growth, providing a rationale for targeting of more downstream glutamine metabolism components.
RNA binding protein ZCCHC24 promotes tumorigenicity in triple-negative breast cancer
Authors: Uchida Yutaro , Kurimoto Ryota , Chiba Tomoki , Matsushima Takahide , Oda Goshi , Onishi Iichiroh , Takeuchi Yasuto , Gotoh Noriko , Asahara Hiroshi
Published: October 2024

Triple-negative breast cancer (TNBC) lacks the expression of hormone and HER2 receptors and is highly malignant with no effective therapeutic targets. In TNBC, the cancer stem-like cell (CSC) population is considered to be the main cause of resistance to treatment. Thus, the therapeutic targeting of this population could substantially improve patient survival. Here, we identify the RNA-binding protein ZCCHC24 as enriched in the mesenchymal-like TNBC population. ZCCHC24 promotes the expression of a set of genes related to tumorigenicity and treatment resistance by directly binding to the cis-element “UGUWHWWA” in their mRNAs, thereby stabilizing them. One of the ZCCHC24 targets, ZEB1, is a transcription factor that promotes the expression of cancer stemness genes and reciprocally induces ZCCHC24 expression. ZCCHC24 knockdown by siRNAs shows a therapeutic effect and reduces the mesenchymal-like cell population in TNBC patient-derived xenografts. ZCCHC24 knockdown also has additive effects with the BET inhibitor JQ1 in suppressing tumor growth in TNBC patient-derived xenografts.
A nickel porphyrin-based covalent organic framework modified electrode for the electrochemical detection of acetaminophen
Authors: Hou Lu , Jiang Yue , Chen Li-Zhen , Zhang Sheng-Feng , Li Heng-Ye , Wei Mei-Jie , Kong Fen-Ying , Wang Wei
Published: October 2024

COF-Ni with a high-activity Ni–N4 catalytic center was used as an electrode modifier for sensitive and selective electrochemical detection of ACOP.
Hijacking plant skeletons for biomedical applications: from regenerative medicine and drug delivery to biosensing
Authors: Asadian Elham , Abbaszadeh Samin , Ghorbani-Bidkorpeh Fatemeh , Rezaei Saman , Xiao Bo , Santos Hélder A. , Shahbazi Mohammad-Ali
Published: October 2024

The review delves into the potential of plant-based scaffolds for tissue regeneration, drug delivery, and biosensing. It highlights chemical principles, preparation strategies, and applications of these scaffolds while addressing challenges and future directions of their usage in healthcare.
Elucidation of the mechanism of the esterification of boric acid with aliphatic diols: a computational study to help set the record straight
Authors: Bacchiocchi Corrado , Petroselli Manuel
Published: October 2024

An unprecedented transition state with both trigonal and tetrahedral boron species solves old controversies and rationalizes, for the first time, the dynamic nature of B–O ester linkages.
Concurrent activation of CO2 and H2O on sulfur-doped CNT-supported nickel phthalocyanine for electrochemical CO2 reduction to CO
Authors: Mustapha Abdulhadi , Chen Shanyong , Xiang Jiaqi , Jiang Yifan , Wang Jingyu , Zhao Xiaojun , Chen Fei , Wang Maoyu , Zhou Hua , Zeng Ke , Wu Linlin , Liu You-Nian
Published: October 2024

A sulfur-doped carbon nanotube-supported nickel phthalocyanine electrode is presented, which can achieve concurrent activation of CO2 and H2O, boosting electrochemical reduction of CO2 to CO.
Dearomative hydroamination of heteroarenes catalyzed by the phenolate photocatalyst
Authors: Zhang Shu-Rong , Yue Jun-Ping , Wang Long-Fu , Gui Yong-Yuan , Zhang Wei , Yu Da-Gang , Ye Jian-Heng
Published: October 2024

Heterocycle-containing alkylamine derivatives are synthesized through photocatalyzed dearomative hydroamination of heteroarenes. The single-electron reduction of heteroarenes to generate radical anions by an excited phenolate is crucial to success.
An organic polarized photonic heterostructure based on tetra(4-pyridylphenyl)ethylene
Authors: Meng Li , Li Zhong-Qiu , Shao Jiang-Yang , Chen Zili , Zhong Yu-Wu
Published: October 2024

An organic polarized photonic heterostructure is fabricated on the microcrystals of a pyridine-functionalized molecule by an acid-fuming method.
Pharmaceutical salts to improve diffusion permeability of a BCS class III β-blocker drug atenolol
Authors: Shajan Daliya K. , Pandey Noopur , Ghosh Animesh , Srivastava Anubha , Sanphui Palash
Published: October 2024

Solubility and intestinal permeability of a BCS class III anti-hypertensive drug, atenolol was improved using its glutarate and malate salts.
Molecular recognition of peptides and proteins by cucurbit[n]urils: systems and applications
Authors: Armstrong Lilyanna , Chang Sarah L. , Clements Nia , Hirani Zoheb , Kimberly Lauren B. , Odoi-Adams Keturah , Suating Paolo , Taylor Hailey F. , Trauth Sara A. , Urbach Adam R.
Published: October 2024

The molecular recognition of peptides and proteins by cucurbit[n]uril synthetic receptors in aqueous solution occurs with high affinity and with selectivity that is predictive from the sequence of amino acids and has enabled many applications.
Enhancing light-driven photocatalytic reactions through solid solutions of bismuth oxyhalide/bismuth rich photocatalysts: a systematic review
Authors: Gembo Robert O. , Ratshiedana Rudzani , Madikizela Lawrence M. , Kamika Ilunga , King'ondu Cecil K. , Kuvarega Alex T. , Msagati Titus A. M.
Published: October 2024

The pursuit of sustainable environmental remediation strategies has led to intensive research in photocatalysis.
Exosome-like nanoparticles from Arbutus unedo L. mitigate LPS-induced inflammation via JAK-STAT inactivation
Authors: Martínez Fajardo Cristian , Morote Lucía , Moreno-Giménez Elena , López-López Susana , Rubio-Moraga Ángela , Díaz-Guerra María José M. , Diretto Gianfranco , López Jiménez Alberto J. , Ahrazem Oussama , Gómez-Gómez Lourdes
Published: October 2024

Exosomes have garnered attention as a potential cell-free therapy for inflammatory diseases due to their immunomodulatory and anti-inflammatory properties.
Assessing the performance of handheld LIBS for predicting soil organic carbon and texture in European soils
Authors: Wangeci Alex , Knadel Maria , De Pascale Olga , Greve Mogens H. , Senesi Giorgio S.
Published: October 2024

Evaluating the performance of handheld LIBS for determination of soil properties across a continental scale.
Placental microphysiological systems: new advances on promising platforms that mimic the microenvironment of the human placenta
Authors: Gonçalves Inês M. , Afzal Muhammad , Kennedy Nithil , Moita Ana , Lima Rui , Ostrovidov Serge , Hori Takeshi , Nashimoto Yuji , Kaji Hirokazu
Published: October 2024

This review presents new advancements in placental MPS models for toxicological screening, preeclampsia assessment, and embryo uterine implantation and an overview of bioprinting technology and current advances in endometrial MPSs.
Correction: Li2MnCl4 single crystal: a new candidate for a red-emitting neutron scintillator
Authors: Vaněček Vojtěch , Král Robert , Křehlíková Kateřina , Kučerková Romana , Babin Vladimir , Zemenová Petra , Rohlíček Jan , Málková Zuzana , Jurkovičová Terézia , Nikl Martin
Published: October 2024

Correction for ‘Li2MnCl4 single crystal: a new candidate for a red-emitting neutron scintillator’ by Vojtěch Vaněček et al., Mater. Adv., 2024, https://doi.org/10.1039/d4ma00697f.
Design, synthesis, and evaluation of benzhydrylpiperazine-based novel dual COX-2/5-LOX inhibitors with anti-inflammatory and anti-cancer activity
Authors: Saraf Poorvi , Bhardwaj Bhagwati , Verma Akash , Siddiqui Mohammad Aquib , Verma Himanshu , Kumar Pradeep , Srivastava Samridhi , Krishnamurthy Sairam , Srikrishna Saripella , Shrivastava Sushant Kumar
Published: October 2024

Screening piperazine derivatives via ChEMBL database led to the design and synthesis of novel dual COX-2/5-LOX inhibitors with strong anti-inflammatory, analgesic, and anti-cancer activity.
Chemically robust functionalized covalent organic framework for the highly efficient and selective separation of bromine
Authors: Fajal Sahel , Ghosh Dipayan , Biswas Kishalay , Mandal Writakshi , Sarkar Nayan , Dam Gourab K. , Roy Anirban , Roychowdhury Antak , Majumder Dipanjan , Urkude Rajashri R. , Shirolkar Mandar M. , Ghosh Sujit K.
Published: October 2024

The meticulous adaptation of the selective binding sites into COFs enables the creation of effective adsorbent demonstrate ultrafast sequestration of bromine. The optimized COF adsorbent exhibited selective separation of bromine over iodine.
Fluid mediated communication among flexible micro-posts in chemically reactive solutions
Authors: Moradi Moslem , Shklyaev Oleg E. , Shi Wenzheng , Balazs Anna C.
Published: October 2024

Modeling shows that enzymatic reactions at microposts in solution trigger chemo-mechanical interactions that spontaneously convey distinct signals over extensive distances in fluid-filled chambers.
Homogenization offers access to quinoxalines in minutes: a solvent-free, catalyst-free protocol with a near-zero E-factor
Authors: Chatterjee Abboy , Mahanta Didreekshya , Hussain Shamima , Chatterjee Amrita , Banerjee Mainak
Published: October 2024

A catalyst-free, sustainable methodology was developed for effortless synthesis of quinoxalines by milling 1,2-diamines and various 1,2-dicarbonyl compounds in a mini cell homogenizer at 4000 rpm for 3 min. The method has a near-zero E-factor.
Novel ordered β-ketoimine-palladium(ii) multilayers supported on a silicon wafer fabricated using layer-by-layer self-assembly for catalyzing Suzuki cross-coupling reactions
Authors: Shan Linjie , Qin Pengxiao , Zhang Wenfen , Li Tiesheng , Liu Minghua , Wu Yangjie
Published: October 2024

A highly active center containing Pd0–Pd0/PdO in situ formed on an organometallic surface and the synergistic effect between Pd and PdO enhanced catalytic activity.