bluuebunny/crossref_metadata_2025 huggingface dataset:
Profiling Signal Transduction in Global Marine Biofilms
Authors: Wang Ruojun , Zhang Weipeng , Ding Wei , Liang Zhicong , Long Lexin , Wong Wai Chuen , Qian Pei-Yuan
Published: January 2022

Microbes use signal transduction systems in the processes of swarming motility, antibiotic resistance, virulence, conjugal plasmid transfer, and biofilm formation. However, the signal transduction systems in natural marine biofilms have hardly been profiled. Here we analyzed signal transduction genes in 101 marine biofilm and 91 seawater microbial metagenomes. The abundance of almost all signal transduction-related genes in biofilm microbial communities was significantly higher than that in seawater microbial communities, regardless of substrate types, locations, and durations for biofilm development. In addition, the dominant source microbes of signal transduction genes in marine biofilms were different from those in seawater samples. Co-occurrence network analysis on signal communication between microbes in marine biofilms and seawater microbial communities revealed potential inter-phyla interactions between microorganisms from marine biofilms and seawater. Moreover, phylogenetic tree construction and protein identity comparison displayed that proteins related to signal transductions from Red Sea biofilms were highly similar to those from Red Sea seawater microbial communities, revealing a possible biological basis of interspecies interactions between surface-associated and free-living microbial communities in a local marine environment. Our study revealed the special profile and enrichment of signal transduction systems in marine biofilms and suggested that marine biofilms participate in intercellular interactions of the local ecosystem where they were seeded.
Diverse Heat Tolerance of the Yeast Symbionts of Platycerus Stag Beetles in Japan
Authors: Zhu Xue-Jiao , Zhang Sheng-Nan , Watanabe Kana , Kawakami Kako , Kubota Noriko , Takagi Etsuro , Tanahashi Masahiko , Wen Xiu-Jun , Kubota Kôhei
Published: January 2022

The genus Platycerus (Coleoptera: Lucanidae) is a small stag beetle group, which is adapted to cool-temperate deciduous broad-leaved forests in East Asia. Ten Platycerus species in Japan form a monophyletic clade endemic to Japan and inhabit species-specific climatic zones. They are reported to have co-evolutionary associations with their yeast symbionts of the genus Sheffersomyces based on host cytochrome oxidase subunit I (COI) and yeast intergenic spacer (IGS) phylogenies. Here we examined the heat tolerances of the yeast colonies isolated from the mycangia of 37 females belonging ten Japanese Platycerus species. The upper limits of growth and survival temperatures of each colony were decided by cultivating it at ten temperature levels between 17.5 and 40°C. Although both temperatures varied during 25.0–31.25°C, the maximum survival temperatures (MSTs) were a little higher than the maximum growth temperatures (MGTs) in 16 colonies. Pearson’s correlations between these temperatures and environmental factors (elevation and 19 bioclimatic variables from Worldclim database) of host beetle collection sites were calculated. These temperatures were significantly correlated with elevation negatively, the maximum temperature of the warmest month (Bio5) positively, and some precipitative variables, especially in the warm season (Bio12, 13, 16, 18) negatively. Sympatric Platycerus kawadai and Platycerus albisomni share the same lineage of yeast symbionts that exhibit the same heat tolerance, but the elevational lower range limit of P. kawadai is higher than that of P. albisomni. Based on the field survey in their sympatric site, the maximum temperature of host wood of P. kawadai larvae is higher about 2–3°C than that of P. albisomni larvae in the summer, which may restrict the elevational range of P. kawadai to higher area. In conclusion, it is suggested that the heat tolerance of yeast symbionts restricts the habitat range of their host Platycerus species or/and that the environmental condition that host Platycerus species prefers affect the heat tolerance of its yeast symbionts.
Molecular Events Involved in Influenza A Virus-Induced Cell Death
Authors: Gui Rui , Chen Quanjiao
Published: January 2022

Viral infection usually leads to cell death. Moderate cell death is a protective innate immune response. By contrast, excessive, uncontrolled cell death causes tissue destruction, cytokine storm, or even host death. Thus, the struggle between the host and virus determines whether the host survives. Influenza A virus (IAV) infection in humans can lead to unbridled hyper-inflammatory reactions and cause serious illnesses and even death. A full understanding of the molecular mechanisms and regulatory networks through which IAVs induce cell death could facilitate the development of more effective antiviral treatments. In this review, we discuss current progress in research on cell death induced by IAV infection and evaluate the role of cell death in IAV replication and disease prognosis.
The Function of CBM32 in Alginate Lyase VxAly7B on the Activity on Both Soluble Sodium Alginate and Alginate Gel
Authors: Tang Luyao , Guo Enwen , Zhang Lan , Wang Ying , Gao Shan , Bao Mengmeng , Han Feng , Yu Wengong
Published: January 2022

Carbohydrate-binding modules (CBMs), as an important auxiliary module, play a key role in degrading soluble alginate by alginate lyase, but the function on alginate gel has not been elucidated. Recently, we reported alginate lyase VxAly7B containing a CBM32 and a polysaccharide lyase family 7 (PL7). To investigate the specific function of CBM32, we characterized the full-length alginate lyase VxAly7B (VxAly7B-FL) and truncated mutants VxAly7B-CM (PL7) and VxAly7B-CBM (CBM32). Both VxAly7B-FL and native VxAly7B can spontaneously cleavage between CBM32 and PL7. The substrate-binding capacity and activity of VxAly7B-CM to soluble alginate were 0.86- and 1.97-fold those of VxAly7B-FL, respectively. Moreover, CBM32 could accelerate the expansion and cleavage of alginate gel beads, and the degradation rate of VxAly7B-FL to alginate gel beads was threefold that of VxAly7B-CM. Results showed that CBM32 is not conducive to the degradation of soluble alginate by VxAly7B but is helpful for binding and degradation of insoluble alginate gel. This study provides new insights into the function of CBM32 on alginate gel, which may inspire the application strategy of CBMs in insoluble substrates.
When DNA Polymerases Multitask: Functions Beyond Nucleotidyl Transfer
Authors: Carvajal-Maldonado Denisse , Drogalis Beckham Lea , Wood Richard D. , Doublié Sylvie
Published: January 2022

DNA polymerases catalyze nucleotidyl transfer, the central reaction in synthesis of DNA polynucleotide chains. They function not only in DNA replication, but also in diverse aspects of DNA repair and recombination. Some DNA polymerases can perform translesion DNA synthesis, facilitating damage tolerance and leading to mutagenesis. In addition to these functions, many DNA polymerases conduct biochemically distinct reactions. This review presents examples of DNA polymerases that carry out nuclease (3ʹ—5′ exonuclease, 5′ nuclease, or end-trimming nuclease) or lyase (5′ dRP lyase) extracurricular activities. The discussion underscores how DNA polymerases have a remarkable ability to manipulate DNA strands, sometimes involving relatively large intramolecular movement.
HSD17B13: A Potential Therapeutic Target for NAFLD
Authors: Zhang Hai-bo , Su Wen , Xu Hu , Zhang Xiao-yan , Guan You-fei
Published: January 2022

Nonalcoholic fatty liver disease (NAFLD), especially in its inflammatory form (steatohepatitis, NASH), is closely related to the pathogenesis of chronic liver disease. Despite substantial advances in the management of NAFLD/NASH in recent years, there are currently no efficacious therapies for its treatment. The biogenesis and expansion of lipid droplets (LDs) are critical pathophysiological processes in the development of NAFLD/NASH. In the past decade, increasing evidence has demonstrated that lipid droplet-associated proteins may represent potential therapeutic targets for the treatment of NAFLD/NASH given the critical role they play in regulating the biogenesis and metabolism of lipid droplets. Recently, HSD17B13, a newly identified liver-enriched, hepatocyte-specific, lipid droplet-associated protein, has been reported to be strongly associated with the development and progression of NAFLD/NASH in both mice and humans. Notably, human genetic studies have repeatedly reported a robust association of HSD17B13 single nucleotide polymorphisms (SNPs) with the occurrence and severity of NAFLD/NASH and other chronic liver diseases (CLDs). Here we briefly overview the discovery, tissue distribution, and subcellular localization of HSD17B13 and highlight its important role in promoting the pathogenesis of NAFLD/NASH in both experimental animal models and patients. We also discuss the potential of HSD17B13 as a promising target for the development of novel therapeutic agents for NAFLD/NASH.
The Gut–Brain Axis and Its Relation to Parkinson’s Disease: A Review
Authors: Klann Emily M. , Dissanayake Upuli , Gurrala Anjela , Farrer Matthew , Shukla Aparna Wagle , Ramirez-Zamora Adolfo , Mai Volker , Vedam-Mai Vinata
Published: January 2022

Parkinson’s disease is a chronic neurodegenerative disease characterized by the accumulation of misfolded alpha-synuclein protein (Lewy bodies) in dopaminergic neurons of the substantia nigra and other related circuitry, which contribute to the development of both motor (bradykinesia, tremors, stiffness, abnormal gait) and non-motor symptoms (gastrointestinal issues, urinogenital complications, olfaction dysfunction, cognitive impairment). Despite tremendous progress in the field, the exact pathways and mechanisms responsible for the initiation and progression of this disease remain unclear. However, recent research suggests a potential relationship between the commensal gut bacteria and the brain capable of influencing neurodevelopment, brain function and health. This bidirectional communication is often referred to as the microbiome–gut–brain axis. Accumulating evidence suggests that the onset of non-motor symptoms, such as gastrointestinal manifestations, often precede the onset of motor symptoms and disease diagnosis, lending support to the potential role that the microbiome–gut–brain axis might play in the underlying pathological mechanisms of Parkinson’s disease. This review will provide an overview of and critically discuss the current knowledge of the relationship between the gut microbiota and Parkinson’s disease. We will discuss the role of α-synuclein in non-motor disease pathology, proposed pathways constituting the connection between the gut microbiome and the brain, existing evidence related to pre- and probiotic interventions. Finally, we will highlight the potential opportunity for the development of novel preventative measures and therapeutic options that could target the microbiome–gut–brain axis in the context of Parkinson’s disease.
Underwater Localization and Mapping Based on Multi-Beam Forward Looking Sonar
Authors: Cheng Chensheng , Wang Can , Yang Dianyu , Liu Weidong , Zhang Feihu
Published: January 2022

SLAM (Simultaneous Localization And Mapping) plays a vital role in navigation tasks of AUV (Autonomous Underwater Vehicle). However, due to a vast amount of image sonar data and some acoustic equipment's inherent high latency, it is a considerable challenge to implement real-time underwater SLAM on a small AUV. This paper presents a filter based methodology for SLAM algorithms in underwater environments. First, a multi-beam forward looking sonar (MFLS) is utilized to extract environmental features. The acquired sonar image is then converted to sparse point cloud format through threshold segmentation and distance-constrained filtering to solve the calculation explosion issue caused by a large amount of original data. Second, based on the proposed method, the DVL, IMU, and sonar data are fused, the Rao-Blackwellized particle filter (RBPF)-based SLAM method is used to estimate AUV pose and generate an occupancy grid map. To verify the proposed algorithm, the underwater vehicle is equipped as an experimental platform to conduct field tasks in both the experimental pool and wild lake, respectively. Experiments illustrate that the proposed approach achieves better performance in both state estimation and suppressing divergence.
Fourier Motion Processing in the Optic Tectum and Pretectum of the Zebrafish Larva
Authors: Duchemin Auriane , Privat Martin , Sumbre Germán
Published: January 2022

In the presence of moving visual stimuli, the majority of animals follow the Fourier motion energy (luminance), independently of other stimulus features (edges, contrast, etc.). While the behavioral response to Fourier motion has been studied in the past, how Fourier motion is represented and processed by sensory brain areas remains elusive. Here, we investigated how visual moving stimuli with or without the first Fourier component (square-wave signal or missing fundamental signal) are represented in the main visual regions of the zebrafish brain. First, we monitored the larva's optokinetic response (OKR) induced by square-wave and missing fundamental signals. Then, we used two-photon microscopy and GCaMP6f zebrafish larvae to monitor neuronal circuit dynamics in the optic tectum and the pretectum. We observed that both the optic tectum and the pretectum circuits responded to the square-wave gratings. However, only the pretectum responded specifically to the direction of the missing-fundamental signal. In addition, a group of neurons in the pretectum responded to the direction of the behavioral output (OKR), independently of the type of stimulus presented. Our results suggest that the optic tectum responds to the different features of the stimulus (e.g., contrast, spatial frequency, direction, etc.), but does not respond to the direction of motion if the motion information is not coherent (e.g., the luminance and the edges and contrast in the missing-fundamental signal). On the other hand, the pretectum mainly responds to the motion of the stimulus based on the Fourier energy.
Neural Substrates of the Drift-Diffusion Model in Brain Disorders
Authors: Gupta Ankur , Bansal Rohini , Alashwal Hany , Kacar Anil Safak , Balci Fuat , Moustafa Ahmed A.
Published: January 2022

Many studies on the drift-diffusion model (DDM) explain decision-making based on a unified analysis of both accuracy and response times. This review provides an in-depth account of the recent advances in DDM research which ground different DDM parameters on several brain areas, including the cortex and basal ganglia. Furthermore, we discuss the changes in DDM parameters due to structural and functional impairments in several clinical disorders, including Parkinson's disease, Attention Deficit Hyperactivity Disorder (ADHD), Autism Spectrum Disorders, Obsessive-Compulsive Disorder (OCD), and schizophrenia. This review thus uses DDM to provide a theoretical understanding of different brain disorders.
Dynamic PET Imaging Using Dual Texture Features
Authors: Ouyang Zhanglei , Zhao Shujun , Cheng Zhaoping , Duan Yanhua , Chen Zixiang , Zhang Na , Liang Dong , Hu Zhanli
Published: January 2022

Purpose: This study aims to explore the impact of adding texture features in dynamic positron emission tomography (PET) reconstruction of imaging results.

Methods: We have improved a reconstruction method that combines radiological dual texture features. In this method, multiple short time frames are added to obtain composite frames, and the image reconstructed by composite frames is used as the prior image. We extract texture features from prior images by using the gray level-gradient cooccurrence matrix (GGCM) and gray-level run length matrix (GLRLM). The prior information contains the intensity of the prior image, the inverse difference moment of the GGCM and the long-run low gray-level emphasis of the GLRLM.

Results: The computer simulation results show that, compared with the traditional maximum likelihood, the proposed method obtains a higher signal-to-noise ratio (SNR) in the image obtained by dynamic PET reconstruction. Compared with similar methods, the proposed algorithm has a better normalized mean squared error (NMSE) and contrast recovery coefficient (CRC) at the tumor in the reconstructed image. Simulation studies on clinical patient images show that this method is also more accurate for reconstructing high-uptake lesions.

Conclusion: By adding texture features to dynamic PET reconstruction, the reconstructed images are more accurate at the tumor.
Acute Basilar Artery Occlusion Presenting With Convulsive Movements: A Systematic Review
Authors: Zhang Dan , Chen Yigang , Hao Yonggang , Hu Xingyue , He Xudong
Published: January 2022

Background and Purpose: Convulsive seizures related to posterior circulation stroke are considered rare. However, some patients with acute basilar artery occlusion (BAO) can present with convulsive movements. Misdiagnosed as seizures may delay the reperfusion therapy for acute BAO. In this study, we have summarized the clinical features and possible mechanisms of BAO presenting with convulsive movements.

Methods: We performed an Institutional Review Board-approved institutional database query from 2015 to 2020 and a literature search of the online database PubMed. Clinical data were collected and analyzed.

Results: In total, 14 patients with acute BAO presented with convulsions. There were 10 men and 4 women, with a mean age of 53 (range, 23–77) years. All of these patients had different degrees of impaired consciousness (100.0%, 14/14). Convulsive movements were the initial symptoms in 78.6% (11/14) of patients. Further, 64.3% (9/14) of patients presented with paralysis or cranial nerve abnormalities, and 85.7% (12/14) of patients were treated with reperfusion therapy (thrombolysis, 35.7% [5/14]; endovascular thrombectomy, 64.3% [9/14]). The BAO etiology and mechanism were related to embolism, vessel dissections, and severe stenosis of the right vertebral artery in 57.1% (8/14), 21.4% (3/14), and 7.1% (1/14) of patients, respectively; they were undefined in 14.3% (2/14) of patients. Moreover, 42.9% (6/14) of patients had a 90-day modified Rankin Scale score of 0–2, and the mortality rate was 21.4% (3/14).

Conclusions: Acute BAO, especially that related to embolism or vessel dissection, may present with convulsive movements. Acute BAO is a devastating, but treatable disease if diagnosed in time. Considering the possibility of BAO is important when dealing with patients presenting with acute-onset convulsive movements. Prompt diagnosis and reperfusion therapy may help achieve a better prognosis.
Assessing the Effect of the Refresh Rate of a Device on Various Motion Stimulation Frequencies Based on Steady-State Motion Visual Evoked Potentials
Authors: Han Chengcheng , Xu Guanghua , Zheng Xiaowei , Tian Peiyuan , Zhang Kai , Yan Wenqiang , Jia Yaguang , Chen Xiaobi
Published: January 2022

The refresh rate is one of the important parameters of visual presentation devices, and assessing the effect of the refresh rate of a device on motion perception has always been an important direction in the field of visual research. This study examined the effect of the refresh rate of a device on the motion perception response at different stimulation frequencies and provided an objective visual electrophysiological assessment method for the correct selection of display parameters in a visual perception experiment. In this study, a flicker-free steady-state motion visual stimulation with continuous scanning frequency and different forms (sinusoidal or triangular) was presented on a low-latency LCD monitor at different refresh rates. Seventeen participants were asked to observe the visual stimulation without head movement or eye movement, and the effect of the refresh rate was assessed by analyzing the changes in the intensity of their visual evoked potentials. The results demonstrated that an increased refresh rate significantly improved the intensity of motion visual evoked potentials at stimulation frequency ranges of 7–28 Hz, and there was a significant interaction between the refresh rate and motion frequency. Furthermore, the increased refresh rate also had the potential to enhance the ability to perceive similar motion. Therefore, we recommended using a refresh rate of at least 120 Hz in motion visual perception experiments to ensure a better stimulation effect. If the motion frequency or velocity is high, a refresh rate of≥240 Hz is also recommended.
Burst Suppression During General Anesthesia and Postoperative Outcomes: Mini Review
Authors: Pawar Niti , Barreto Chang Odmara L.
Published: January 2022

In the last decade, burst suppression has been increasingly studied by many to examine whether it is a mechanism leading to postoperative cognitive impairment. Despite a lack of consensus across trials, the current state of research suggests that electroencephalogram (EEG) burst suppression, duration and EEG emergence trajectory may predict postoperative delirium (POD). A mini literature review regarding evidence about burst suppression impact and susceptibilities was conducted, resulting in conflicting studies. Primarily, studies have used different algorithm values to replace visual burst suppression examination, although many studies have since emerged showing that algorithms underestimate burst suppression duration. As these methods may not be interchangeable with visual analysis of raw data, it is a potential factor for the current heterogeneity between data. Even though additional research trials incorporating the use of raw EEG data are necessary, the data currently show that monitoring with commercial intraoperative EEG machines that use EEG indices to estimate burst suppression may help physicians identify burst suppression and guide anesthetic titration during surgery. These modifications in anesthetics could lead to preventing unfavorable outcomes. Furthermore, some studies suggest that brain age, baseline impairment, and certain medications are risk factors for burst suppression and postoperative delirium. These patient characteristics, in conjunction with intraoperative EEG monitoring, could be used for individualized patient care. Future studies on the feasibility of raw EEG monitoring, new technologies for anesthetic monitoring and titration, and patient-associated risk factors are crucial to our continued understanding of burst suppression and postoperative delirium.
Traditional Foods From Maize (Zea mays L.) in Europe
Authors: Revilla Pedro , Alves Mara Lisa , Andelković Violeta , Balconi Carlotta , Dinis Isabel , Mendes-Moreira Pedro , Redaelli Rita , Ruiz de Galarreta Jose Ignacio , Vaz Patto Maria Carlota , Žilić Sladana , Malvar Rosa Ana
Published: January 2022

Maize (Zea mays L.) is one of the major crops of the world for feed, food, and industrial uses. It was originated in Central America and introduced into Europe and other continents after Columbus trips at the end of the 15th century. Due to the large adaptability of maize, farmers have originated a wide variability of genetic resources with wide diversity of adaptation, characteristics, and uses. Nowadays, in Europe, maize is mainly used for feed, but several food specialties were originated during these five centuries of maize history and became traditional food specialties. This review summarizes the state of the art of traditional foodstuffs made with maize in Southern, South-Western and South-Eastern Europe, from an historic evolution to the last research activities that focus on improving sustainability, quality and safety of food production.
Quality of Beverage Intake and Cardiometabolic and Kidney Outcomes: Insights From the STANISLAS Cohort
Authors: Wagner Sandra , Merkling Thomas , Girerd Nicolas , Bozec Erwan , Van den Berghe Laurie , Hoge Axelle , Guillaume Michèle , Kanbay Mehmet , Cakir-Kiefer Céline , Thornton Simon N. , Boivin Jean-Marc , Mercklé Ludovic , Laville Martine , Rossignol Patrick , Nazare Julie-Anne
Published: January 2022

Background and Aims: Beverages are an important aspect of diet, and their quality can possibly affect health. The Healthy Beverage Index (HBI) has been developed to take into account these effects. This study aimed to highlight the relationships between health and beverage quality by assessing the association of the HBI and its components with kidney and cardiometabolic (CM) outcomes in an initially healthy population-based familial cohort.

Methods: This study included 1,271 participants from the STANISLAS cohort. The HBI, which includes 10 components of habitual beverage consumption, was calculated. Associations of the HBI and its components with estimated glomerular filtration rate (eGFR), albuminuria, hypertriglyceridemic waist (HTG waist), metabolic syndrome (MetS), carotid-femoral pulse wave velocity (cfPWV), carotid intima-media thickness (cIMT), and left ventricular mass (LV mass) were analyzed using multivariable linear or logistic regression models.

Results: The median HBI score was 89.7 (78.6–95) out of 100 points. While the overall HBI score was not significantly associated with any of the studied outcomes, individual HBI components were found differently associated with the outcomes. cfPWV and cIMT were lower in participants who did not meet the full-fat milk criteria (p = 0.03 and 0.001, respectively). In men, higher cfPWV was observed for the “low Fat milk” (p = 0.06) and “alcohol” (p = 0.03) non-adherence criteria. Odds of HTG waist were higher with the non-adherence to sugar-sweetened beverages criteria (p < 0.001). eGFR was marginally higher with non-adherence to the coffee/tea criteria (p = 0.047).

Conclusions: In this initially healthy population, HBI components were differently associated with kidney and cardiometabolic outcomes, despite a good overall HBI score. Our results highlight specific impacts of different beverage types and suggest that beverages could have an impact on kidney and cardiometabolic health.
Vegan Diet Is Associated With Favorable Effects on the Metabolic Performance of Intestinal Microbiota: A Cross-Sectional Multi-Omics Study
Authors: Prochazkova Magdalena , Budinska Eva , Kuzma Marek , Pelantova Helena , Hradecky Jaromir , Heczkova Marie , Daskova Nikola , Bratova Miriam , Modos Istvan , Videnska Petra , Splichalova Petra , Sowah Solomon A. , Kralova Maria , Henikova Marina , Selinger Eliska , Klima Krystof , Chalupsky Karel , Sedlacek Radislav , Landberg Rikard , Kühn Tilman , Gojda Jan , Cahova Monika
Published: January 2022

Background and Aim: Plant-based diets are associated with potential health benefits, but the contribution of gut microbiota remains to be clarified. We aimed to identify differences in key features of microbiome composition and function with relevance to metabolic health in individuals adhering to a vegan vs. omnivore diet.

Methods: This cross-sectional study involved lean, healthy vegans (n = 62) and omnivore (n = 33) subjects. We assessed their glucose and lipid metabolism and employed an integrated multi-omics approach (16S rRNA sequencing, metabolomics profiling) to compare dietary intake, metabolic health, gut microbiome, and fecal, serum, and urine metabolomes.

Results: The vegans had more favorable glucose and lipid homeostasis profiles than the omnivores. Long-term reported adherence to a vegan diet affected only 14.8% of all detected bacterial genera in fecal microbiome. However, significant differences in vegan and omnivore metabolomes were observed. In feces, 43.3% of all identified metabolites were significantly different between the vegans and omnivores, such as amino acid fermentation products p-cresol, scatole, indole, methional (lower in the vegans), and polysaccharide fermentation product short- and medium-chain fatty acids (SCFAs, MCFAs), and their derivatives (higher in the vegans). Vegan serum metabolome differed markedly from the omnivores (55.8% of all metabolites), especially in amino acid composition, such as low BCAAs, high SCFAs (formic-, acetic-, propionic-, butyric acids), and dimethylsulfone, the latter two being potential host microbiome co-metabolites. Using a machine-learning approach, we tested the discriminative power of each dataset. Best results were obtained for serum metabolome (accuracy rate 91.6%).

Conclusion: While only small differences in the gut microbiota were found between the groups, their metabolic activity differed substantially. In particular, we observed a significantly different abundance of fermentation products associated with protein and carbohydrate intakes in the vegans. Vegans had significantly lower abundances of potentially harmful (such as p-cresol, lithocholic acid, BCAAs, aromatic compounds, etc.) and higher occurrence of potentially beneficial metabolites (SCFAs and their derivatives).
Dynamic Associations of Milk Components With the Infant Gut Microbiome and Fecal Metabolites in a Mother–Infant Model by Microbiome, NMR Metabolomic, and Time-Series Clustering Analyses
Authors: Komatsu Yosuke , Kumakura Daiki , Seto Namiko , Izumi Hirohisa , Takeda Yasuhiro , Ohnishi Yuki , Nakaoka Shinji , Aizawa Tomoyasu
Published: January 2022

Background: The gut microbiome and fecal metabolites of breastfed infants changes during lactation, and are influenced by breast milk components. This study aimed to investigate dynamic associations of milk components with the infant gut microbiome and fecal metabolites throughout the lactation period in a mother–infant model.

Methods: One month after delivery, breast milk and subsequent infant feces were collected in a pair for 5 months from a mother and an exclusively breastfed infant. Composition of the fecal microbiome was determined with 16S rRNA sequencing. Low-molecular-weight metabolites, including human milk oligosaccharides (HMOs), and antibacterial proteins were measured in feces and milk using 1H NMR metabolomics and enzyme-linked immunosorbent assays. The association of milk bioactive components with the infant gut microbiome and fecal metabolites was determined with Python clustering and correlation analyses.

Results: The HMOs in milk did not fluctuate throughout the lactation period. However, they began to disappear in infant feces at the beginning of month 4. Notably, at this time-point, a bifidobacterium species switching (from B. breve to B. longum subsp. infantis) occurred, accompanied by fluctuations in several metabolites including acetate and butyrate in infant feces.

Conclusions: Milk bioactive components, such as HMOs, might play different roles in the exclusively breastfed infants depending on the lactation period.
Radiomics and Radiogenomics in Evaluation of Colorectal Cancer Liver Metastasis
Authors: Wang Yun , Ma Lu-Yao , Yin Xiao-Ping , Gao Bu-Lang
Published: January 2022

Colorectal cancer is one common digestive malignancy, and the most common approach of blood metastasis of colorectal cancer is through the portal vein system to the liver. Early detection and treatment of liver metastasis is the key to improving the prognosis of the patients. Radiomics and radiogenomics use non-invasive methods to evaluate the biological properties of tumors by deeply mining the texture features of images and quantifying the heterogeneity of metastatic tumors. Radiomics and radiogenomics have been applied widely in the detection, treatment, and prognostic evaluation of colorectal cancer liver metastases. Based on the imaging features of the liver, this paper reviews the current application of radiomics and radiogenomics in the diagnosis, treatment, monitor of disease progression, and prognosis of patients with colorectal cancer liver metastases.
Laparoscopic Versus Open Surgery for Early-Stage Intrahepatic Cholangiocarcinoma After Mastering the Learning Curve: A Multicenter Data-Based Matched Study
Authors: Jinhuan Yang , Yi Wang , Yuanwen Zheng , Delin Ma , Xiaotian Chen , Yan Wang , Liming Deng , Haitao Yu , Lijun Wu , Tuo Deng , Kaiyu Chen , Jiawei Hu , Chongming Zheng , Daojie Wang , Bin Jin , Gang Chen
Published: January 2022

Background

Surgical resection is the only widely accepted curative method for intrahepatic cholangiocarcinoma (ICC). However, little is known about the efficacy of laparoscopic liver resection for ICC, especially in patients with early-stage disease. The aim of this study was to compare the short-term and long-term effects of laparoscopy and open surgery for the treatment of ICC.

Methods

Data from 1,084 patients treated at three hospitals from January 2011 to December 2018 were selected and analyzed. Propensity score matching was performed to compare the long-term outcomes (overall survival and recurrence-free survival) and short-term outcomes (perioperative outcomes) of all-stage and early-stage patients.

Results

After matching, 244 patients (122 vs. 122) in the all-stage group and 65 patients (27 vs. 38) in the early-stage group were included. The baseline of the two groups was balanced, and no significant differences were found in sex or age. The short-term results of the laparoscopic group were better than those of the open group, including less blood loss [blood loss ≥400 ml 27 (22.1%) vs. 6 (4.92%), p<0.001 for all-stage, 12 (31.6%) vs. 2 (7.41%), p=0.042 for early stage), shorter surgery [200 (141; 249) min vs. 125 (115; 222) min, p=0.025 for early stage] and shorter hospital stay [11.0 (9.00; 16.0) days vs. 9.00 (7.00; 12.0) days, p=0.001 for all stage, 11.0 (8.50; 17.8) days vs. 9.00 (6.50; 11.0) days, p=0.011 for early stage]. Regarding long-term outcomes, no significant differences were found for all-stage patients, while there were significant differences observed for the early-stage group (p=0.013 for OS, p=0.014 for RFS). For the early-stage patients, the 1-, 3-, and 5-year OS rates of the OLR group were 84.2, 65.8, and 41.1%, respectively, and those of the LLR group were 100, 90.9, and 90.9%, respectively. The RFS rates of the OLR group were 84.2, 66.7, and 41.7%, respectively, and those of the LLR group were and 92.3, 92.3, and 92.3%, respectively.

Conclusion

Patients treated with laparoscopy seemed to have better short-term outcomes, such as less blood loss, shorter operation duration, and shorter hospital stay, than patients undergoing open surgery. Based on the long-term results, laparoscopic treatment for early ICC may have certain advantages.
Pretreatment Contrast-Enhanced Computed Tomography Radiomics for Prediction of Pathological Regression Following Neoadjuvant Chemotherapy in Locally Advanced Gastric Cancer: A Preliminary Multicenter Study
Authors: Xie Kun , Cui Yanfen , Zhang Dafu , He Weiyang , He Yinfu , Gao Depei , Zhang Zhiping , Dong Xingxiang , Yang Guangjun , Dai Youguo , Li Zhenhui
Published: January 2022

Background

Sensitivity to neoadjuvant chemotherapy in locally advanced gastric cancer patients varies; however, an effective predictive marker is currently lacking. We aimed to propose and validate a practical treatment efficacy prediction method based on contrast-enhanced computed tomography (CECT) radiomics.

Method

Data of l24 locally advanced gastric carcinoma patients who underwent neoadjuvant chemotherapy were acquired retrospectively between December 2012 and August 2020 from three different cancer centers. In total, 1216 radiomics features were initially extracted from each lesion’s pretreatment portal venous phase computed tomography image. Subsequently, a radiomics predictive model was constructed using machine learning software. Clinicopathological data and radiological parameters of the enrolled patients were collected and analyzed retrospectively. Univariate and multivariate logistic regression analyses were performed to screen for independent predictive indices. Finally, we developed an integrated model combining clinicopathological predictive parameters and radiomics features.

Result

In the training set, 10 (14.9%) patients achieved a good response (GR) after preoperative neoadjuvant chemotherapy (n = 77), whereas in the testing set, seven (17.5%) patients achieved a GR (n = 47). The radiomics predictive model showed competitive prediction efficacy in both the training and independent external validation sets. The areas under the curve (AUC) values were 0.827 (95% confidence interval [CI]: 0.609–1.000) and 0.854 (95% CI: 0.610–1.000), respectively. Similarly, when only the single hospital data were included as an independent external validation set (testing set 2), AUC values of the models were 0.827 (95% CI: 0.650–0.952) and 0.889 (95% CI: 0.663–1.000) in the training set and testing set 2, respectively.

Conclusion

Our study is the first to discover that CECT radiomics could provide powerful and consistent predictions of therapeutic sensitivity to neoadjuvant chemotherapy among gastric cancer patients across different hospitals.
Genomic Profiling of Chinese Cervical Cancer Patients Reveals Prevalence of DNA Damage Repair Gene Alterations and Related Hypoxia Feature
Authors: Wen Hao , Guo Qin-Hao , Zhou Xiao-Lan , Wu Xiao-Hua , Li Jin
Published: January 2022

Background

Cervical cancer is responsible for 10–15% of cancer-related deaths in women worldwide. In China, it is the most common cancer in the female genital tract. However, the genomic profiles of Chinese cervical cancer patients remain unclear.

Materials and Methods

A total of 129 cervical cancer patients were enrolled in this study (113 squamous, 12 adenocarcinoma, 2 adenosquamous, and 2 neuroendocrine carcinoma). To classify the clinical features and molecular characteristics of cervical cancer, the genomic alterations of 618 selected genes were analyzed in the samples of these patients, utilizing target next-generation sequencing (NGS) technology. Furthermore, the findings from the Chinese cohort were then compared with the data of Western patients downloaded from The Cancer Genome Atlas (TCGA) database, in terms of gene expression files, mutation data, and clinical information.

Results

All studied patients had valid somatic gene alterations, and the most frequently altered genes were PIK3C, TP53, FBXW7, ARID1A, ERBB2, and PTEN. Comparison of genomic profiling showed significantly different prevalence of genes, including TP53, KMT2C, and RET, between the Chinese and the TCGA cohorts. Moreover, 57 patients (44.19%) with 83 actionable alterations were identified in our cohort, especially in PI3K and DNA damage repair (DDR) pathways. After an in-depth analysis of cervical cancer data from the TCGA cohort, DDR alteration was found to be associated with extremely higher tumor mutation burden (TMB) (median mutation count: 149.5 vs 66, p <0.0001), and advanced stages (p <0.05). Additionally, DDR alteration, regardless of its function, was positively correlated with hypoxia feature and score. Moreover, patients with a high hypoxia score were positively correlated with a high abundance of mast cell resting, but lower abundance of CD8+ T cells and activated mast cell. Finally, CDHR5 was identified as the hub gene to be involved in the DDR–hypoxia network, which was negatively correlated with both the DDR alteration and hypoxia score.

Conclusions

Overall, a unique genomic profiling of Chinese patients with cervical cancer was uncovered. Besides, the prevalent actionable variants, especially in PI3K and DDR pathways, would help promote the clinical management. Moreover, DDR alteration exerted the significant influence on the tumor microenvironment in cervical cancer, which could guide the clinical decisions for the treatment. CDHR5 was the first identified hub gene to be negatively correlated with DDR or hypoxia in cervical cancer, which had potential effects on the treatment of immune checkpoint inhibitors (ICIs).
Prognostic Impact of An Integrative Landscape of Clinical, Immune, and Molecular Features in Non-Metastatic Rectal Cancer
Authors: Iseas Soledad , Sendoya Juan M. , Robbio Juan , Coraglio Mariana , Kujaruk Mirta , Mikolaitis Vanesa , Rizzolo Mariana , Cabanne Ana , Ruiz Gonzalo , Salanova Rubén , Gualdrini Ubaldo , Méndez Guillermo , Antelo Marina , Carballido Marcela , Rotondaro Cecilia , Viglino Julieta , Eleta Martín , Di Sibio Alejandro , Podhajcer Osvaldo L. , Roca Enrique , Llera Andrea S. , Golubicki Mariano , Abba Martín Carlos
Published: January 2022

Rectal Cancer (RC) is a complex disease that involves highly variable treatment responses. Currently, there is a lack of reliable markers beyond TNM to deliver a personalized treatment in a cancer setting where the goal is a curative treatment. Here, we performed an integrated characterization of the predictive and prognostic role of clinical features, mismatch-repair deficiency markers, HER2, CDX2, PD-L1 expression, and CD3−CD8+ tumor-infiltrating lymphocytes (TILs) coupled with targeted DNA sequencing of 76 non-metastatic RC patients assigned to total mesorectal excision upfront (TME; n = 15) or neoadjuvant chemo-radiotherapy treatment (nCRT; n = 61) followed by TME. Eighty-two percent of RC cases displayed mutations affecting cancer driver genes such as TP53, APC, KRAS, ATM, and PIK3CA. Good response to nCRT treatment was observed in approximately 40% of the RC cases, and poor pathological tumor regression was significantly associated with worse disease-free survival (DFS, HR = 3.45; 95%CI = 1.14–10.4; p = 0.028). High neutrophils-platelets score (NPS) (OR = 10.52; 95%CI=1.34–82.6; p = 0.025) and KRAS mutated cases (OR = 5.49; 95%CI = 1.06–28.4; p = 0.042) were identified as independent predictive factors of poor response to nCRT treatment in a multivariate analysis. Furthermore, a Cox proportional-hazard model showed that the KRAS mutational status was an independent prognostic factor associated with higher risk of local recurrence (HR = 9.68; 95%CI = 1.01–93.2; p <0.05) and shorter DFS (HR = 2.55; 95%CI = 1.05–6.21; p <0.05), while high CEA serum levels were associated with poor DFS (HR = 2.63; 95%CI = 1.01–6.85; p <0.05). Integrated clinical and molecular-based unsupervised analysis allowed us to identify two RC prognostic groups (cluster 1 and cluster 2) associated with disease-specific OS (HR = 20.64; 95%CI = 2.63–162.2; p <0.0001), metastasis-free survival (HR = 3.67; 95%CI = 1.22–11; p = 0.012), local recurrence-free survival (HR = 3.34; 95%CI = 0.96–11.6; p = 0.043) and worse DFS (HR = 2.68; 95%CI = 1.18–6.06; p = 0.012). The worst prognosis cluster 2 was enriched by stage III high-risk clinical tumors, poor responders to nCRT, with low TILs density and high frequency of KRAS and TP53 mutated cases compared with the best prognosis cluster 1 (p <0.05). Overall, this study provides a comprehensive and integrated characterization of non-metastatic RC cases as a new insight to deliver a personalized therapeutic approach.
Wounding Therapies for Prevention of Photocarcinogenesis
Authors: Frommeyer Timothy C. , Rohan Craig A. , Spandau Dan F. , Kemp Michael G. , Wanner Molly A. , Tanzi Elizabeth , Travers Jeffrey B.
Published: January 2022

The occurrence of non-melanoma skin cancer (NMSC) is closely linked with advanced age and ultraviolet-B (UVB) exposure. More specifically, the development of NMSC is linked to diminished insulin-like growth factor-1 (IGF-1) signaling from senescent dermal fibroblasts in geriatric skin. Consequently, keratinocyte IGF-1 receptor (IGF-1R) remains inactive, resulting in failure to induce appropriate protective responses including DNA repair and cell cycle checkpoint signaling. This allows UVB-induced DNA damage to proliferate unchecked, which increases the likelihood of malignant transformation. NMSC is estimated to occur in 3.3 million individuals annually. The rising incidence results in increased morbidity and significant healthcare costs, which necessitate identification of effective treatment modalities. In this review, we highlight the pathogenesis of NMSC and discuss the potential of novel preventative therapies. In particular, wounding therapies such as dermabrasion, microneedling, chemical peeling, and fractionated laser resurfacing have been shown to restore IGF-1/IGF-1R signaling in geriatric skin and suppress the propagation of UVB-damaged keratinocytes. This wounding response effectively rejuvenates geriatric skin and decreases the incidence of age-associated NMSC.
Surfactant Protein-A Function: Knowledge Gained From SP-A Knockout Mice
Authors: Depicolzuane Lynnlee , Phelps David S. , Floros Joanna
Published: January 2022

Pulmonary surfactant proteins have many roles in surfactant- related functions and innate immunity. One of these proteins is the surfactant protein A (SP-A) that plays a role in both surfactant-related processes and host defense and is the focus in this review. SP-A interacts with the sentinel host defense cell in the alveolus, the alveolar macrophage (AM), to modulate its function and expression profile under various conditions, as well as other alveolar epithelial cells such as the Type II cell. Via these interactions, SP-A has an impact on the alveolar microenvironment. SP-A is also important for surfactant structure and function. Much of what is understood of the function of SP-A and its various roles in lung health has been learned from SP-A knockout (KO) mouse experiments, as reviewed here. A vast majority of this work has been done with infection models that are bacterial, viral, and fungal in nature. Other models have also been used, including those of bleomycin-induced lung injury and ozone-induced oxidative stress either alone or in combination with an infectious agent, bone marrow transplantation, and other. In addition, models investigating the effects of SP-A on surfactant components or surfactant structure have contributed important information. SP-A also appears to play a role in pathways involved in sex differences in response to infection and/or oxidative stress, as well as at baseline conditions. To date, this is the first review to provide a comprehensive report of the functions of SP-A as learned through KO mice.
Not Everything Is Cordless Today—Case Report of Acute Intestinal Obstruction in a Neonate Due to Cord Clamping
Authors: Keese Daniel , Schwalbach Anne-Kathrin , Schmedding Andrea , Rolle Udo
Published: January 2022

We report a case of a 2-day-old neonate with bilious vomiting and abdominal distension. A small bowel obstruction with ileal perforation due to a misplaced clamping of the umbilical cord was apparent before laparotomy. This complication was a sequala after clamping the cord too close to the abdominal wall in a case where there was a hernia into the cord with intestinal content. A herniation of abdominal contents due to an omphalocele minor or a hernia must be taken into consideration during the inspection of the umbilical cord before clamping.
Anticancer Applications and Pharmacological Properties of Piperidine and Piperine: A Comprehensive Review on Molecular Mechanisms and Therapeutic Perspectives
Authors: Mitra Sicon , Anand Uttpal , Jha Niraj Kumar , Shekhawat Mahipal S. , Saha Suchismita Chatterjee , Nongdam Potshangbam , Rengasamy Kannan R. R. , Proćków Jarosław , Dey Abhijit
Published: January 2022

Piperine and piperidine are the two major alkaloids extracted from black pepper (Piper nigrum); piperidine is a heterocyclic moiety that has the molecular formula (CH2)5NH. Over the years, many therapeutic properties including anticancer potential of these two compounds have been observed. Piperine has therapeutic potential against cancers such as breast cancer, ovarian cancer, gastric cancer, gliomal cancer, lung cancer, oral squamous, chronic pancreatitis, prostate cancer, rectal cancer, cervical cancer, and leukemia. Whereas, piperidine acts as a potential clinical agent against cancers, such as breast cancer, prostate cancer, colon cancer, lung cancer, and ovarian cancer, when treated alone or in combination with some novel drugs. Several crucial signalling pathways essential for the establishment of cancers such as STAT-3, NF-κB, PI3k/Aκt, JNK/p38-MAPK, TGF-ß/SMAD, Smac/DIABLO, p-IκB etc., are regulated by these two phytochemicals. Both of these phytochemicals lead to inhibition of cell migration and help in cell cycle arrest to inhibit survivability of cancer cells. The current review highlights the pharmaceutical relevance of both piperine and piperidine against different types of cancers.