Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative efficacy and toxicity of immune checkpoint inhibitors in combination with or without chemotherapy treatment for advanced esophageal squamous cell carcinoma: A systematic review and meta-analysis

Introduction We did a systematic review and meta-analysis to assess the efficacy and safety of immune checkpoint inhibitors combined with or without chemotherapies in patients with esophageal squamous cell carcinoma. Methods Data related to the treatment of esophageal squamous cell carcinoma with immune checkpoint inhibitors therapy were retrieved from the database construction to August 2022. The risk of bias was assessed using the Cochrane Manual standard and RevMan 5.3 software for data synthesis. The outcome measures observed included overall survival, 12-month survival, disease control rate, objective response rate, treatment-related adverse events of grade 3 or higher, and progression-free survival. The adverse reactions included fatigue, diarrhea, hypothyroidism, rash, anemia, and anorexia. Results In this meta-analysis, a total of 17 randomized controlled trials were included. In first-line therapy, immune checkpoint inhibitors combined with or without chemotherapy in the treatment of esophageal squamous cell carcinoma was more effective than chemotherapy alone. Overall survival, 12-month survival rate, and objective response rate were statistically significant. Among second-line treatments, immune checkpoint inhibitors combined with or without chemotherapy in the treatment of esophageal squamous cell carcinoma had statistically significant overall survival, 12-month survival, objective response rate, treatment-related adverse events of grade 3 or higher, and progression-free survival compared with chemotherapy alone. Conclusion Both first- and second-line immune checkpoint inhibitors are effective for esophageal squamous cell carcinoma, and the adverse reactions are controllable and safe. Systematic review registration https://www.crd. york.ac. uk/PROSPERO/, identifier CRD42021282586.
The music of the hemispheres: Cortical eigenmodes as a physical basis for large-scale brain activity and connectivity patterns

Neuroscience has had access to high-resolution recordings of large-scale cortical activity and structure for decades, but still lacks a generally adopted basis to analyze and interrelate results from different individuals and experiments. Here it is argued that the natural oscillatory modes of the cortex—cortical eigenmodes—provide a physically preferred framework for systematic comparisons across experimental conditions and imaging modalities. In this framework, eigenmodes are analogous to notes of a musical instrument, while commonly used statistical patterns parallel frequently played chords. This intuitive perspective avoids problems that often arise in neuroimaging analyses, and connects to underlying mechanisms of brain activity. We envisage this approach will lead to novel insights into whole-brain function, both in existing and prospective datasets, and facilitate a unification of empirical findings across presently disparate analysis paradigms and measurement modalities.
Accurate quantification of width and density of bone structures by computed tomography.

In computed tomography (CT), the representation of edges between objects of different densities is influenced by the limited spatial resolution of the scanner. This results in the misrepresentation of density of narrow objects, leading to errors of up to 70% and more. Our interest is in the imaging and measurement of narrow bone structures, and the issues are the same for imaging with clinical CT scanners, peripheral quantitative CT scanners or micro CT scanners. Mathematical models, phantoms and tests with patient data led to the following procedures: (i) extract density profiles at one-degree increments from the CT images at right angles to the bone boundary; (ii) consider the outer and inner edge of each profile separately due to different adjacent soft tissues; (iii) measure the width of each profile based on a threshold at fixed percentage of the difference between the soft-tissue value and a first approximated bone value; (iv) correct the underlying material density of bone for each profile based on the measured width with the help of the density-versus-width curve obtained from computer simulations and phantom measurements. This latter curve is specific to a certain scanner and is not dependent on the densities of the tissues within themore » range seen in patients. This procedure allows the calculation of the material density of bone. Based on phantom measurements, we estimate the density error to be below 2% relative to the density of normal bone and the bone-width error about one tenth of a pixel size. « less
PfHMGB2 has a role in malaria parasite mosquito infection

Differentiation of asexually replicating parasites into gametocytes is critical for successful completion of the sexual phase of the malaria parasite life cycle. Gametes generated from gametocytes fuse to form a zygote which differentiates into ookinetes and oocysts. The sporozoites are formed inside oocysts which migrate to the salivary glands for next cycle of human infection. These morphologically and functionally distinct stages require stage-specific gene expression via specific transcriptional regulators. The capacity of high mobility group box (HMGB) proteins to interact with DNA in a sequence independent manner enables them to regulate higher order chromosome organization and regulation of gene expression. Plasmodium falciparum HMGB2 (PfHMGB2) shows a typical L- shaped predicted structure which is similar to mammalian HMG box proteins and shows very high protein sequence similarity to PyHMGB2 and PbHMGB2. Functional characterization of PfHMGB2 by gene deletion (Pfhmgb2¯) showed that knockout parasites develop normally as asexual stages and undergo gametocytogenesis. Transmission experiments revealed that Pfhmgb2¯ can infect mosquitoes and develop as oocyst stages. However, transmission was reduced compared to wild type (WT) parasites and as a consequence, the salivary gland sporozoites were reduced in number. In summary, we demonstrate that PfHMGB2 has no role in asexual growth and a modest role in sexual phase development and parasite transmission to the mosquito.
Validity and reliability of capillary vs. Venous blood for the assessment of haemoglobin mass and intravascular volumes

Objectives: Haemoglobin mass (Hbmass) assessment with the carbon monoxide rebreathing method is a more accurate estimate than other measures of oxygen-carrying capacity. Blood may be collected by several means and differences in the measured variables may exist as a result. The present study assessed the validity and reliability of calculated Hbmass and intravascular volumes obtained from capillary blood (CAP) when compared to venous blood (VEN) draws. Methods: Twenty-two adults performed a carbon monoxide rebreathing procedure with paired VEN and CAP draws at baseline, pre-rebreathing and post-rebreathing (POST). Thirteen of these participants performed this protocol on two occasions to assess the data reliability from both blood sampling sites. In a second experiment, 14 adults performed a 20-min seated and a 20-min supine rest to assess for the effect of posture on haematological parameters. Results: Haemoglobin mass (CAP = 948.8 ± 156.8 g; VEN = 943.4 ± 157.3 g, p = 0.108) and intravascular volume (CAP = 6.5 ± 1 L; VEN = 6.5 ± 0.9 L, p = 0.752) were statistically indifferent, had low bias (Hbmass bias = 14.45 ± 40.42 g, LoA -64.78 g—93.67 g) and were highly correlated between sampling techniques. Reliability analysis demonstrated no difference in the mean change in variables calculated from both sampling sites and good to excellent intraclass correlation coefficients (>0.700), however, typical measurement error was larger in variables measured using CAP (VEN Hbmass TE% = 2.1%, CAP Hbmass TE% = 5.5%). The results indicate that a supine rest prior to the rebreathing protocol would have a significant effect on haemoglobin concentration and haematocrit values compared to a seated rest, with no effect on carboxyhaemoglobin %. Conclusion: The present study demonstrates that CAP and VEN were comparable for the calculation of Hbmass and intravascular volumes in terms of accuracy. However, reduced reliability and increased error in the CAP variables indicates that there are methodological considerations to address when deciding which blood drawing technique to utilise. To reduce this CAP error, increased replicate analyses are required.
Neuronal and non-neuronal scaling across brain regions within an intercross of domestic and wild chickens

The allometric scaling of the brain size and neuron number across species has been extensively studied in recent years. With the exception of primates, parrots, and songbirds, larger brains have more neurons but relatively lower neuronal densities than smaller brains. Conversely, when considering within-population variability, it has been shown that mice with larger brains do not necessarily have more neurons but rather more neurons in the brain reflect higher neuronal density. To what extent this intraspecific allometric scaling pattern of the brain applies to individuals from other species remains to be explored. Here, we investigate the allometric relationships among the sizes of the body, brain, telencephalon, cerebellum, and optic tectum, and the numbers of neurons and non-neuronal cells of the telencephalon, cerebellum, and optic tectum across 66 individuals originated from an intercross between wild and domestic chickens. Our intercross of chickens generates a population with high variation in brain size, making it an excellent model to determine the allometric scaling of the brain within population. Our results show that larger chickens have larger brains with moderately more neurons and non-neuronal cells. Yet, absolute number of neurons and non-neuronal cells correlated strongly and positively with the density of neurons and non-neuronal cells, respectively. As previously shown in mice, this scaling pattern is in stark contrast with what has been found across different species. Our findings suggest that neuronal scaling rules across species are not a simple extension of the neuronal scaling rules that apply within a species, with important implications for the evolutionary developmental origins of brain diversity.
Comparative transcriptome analysis of wheat in response to corn leaf aphid, Rhopalosiphum maidis F. infestation

Aphids are one of the most important insect pests of wheat crop in all wheat growing regions of the world. Amongst various aphid species, the corn leaf aphid (Rhopalosiphum maidis F.) is considered one of the most destructive insect pests of wheat in the North Western Plains region of India. Transcriptome profiling of highly susceptible wheat Triticum durum genotype, A-9-30-1 and tolerant wheat Triticum aestivum genotype, HD2967 was performed to investigate aphid-host interactions. The results obtained from differential gene expression analysis of R. maidis on the highly susceptible genotype, A-9-30-1 plants, when compared with the tolerant genotype, HD2967, showed that 212 genes were significantly upregulated and 1009 genes were significantly downregulated. Our findings demonstrated that the genes associated with defense were significantly higher in response to R. maidis on HD2967 as compared to A-9-30-1. Additionally, various genes with physiological attributes were expressed during aphid attack. Based on gene ontology classification, three classifications, such as, cellular components (CC), molecular function (MF), and biological processes (BP) of sequences were identified. KEGG enrichment analysis revealed that twenty-five pathway genes were differentially expressed during the infestation of wheat with R. maidis. Notable changes were observed in A-9-30-1 and HD2967 transcriptomic profiling after infestation. The results obtained in the present study will help to elucidate the mechanism governing host-pest interaction and may lead to the development of new methods for increasing the resistance level of wheat against R. maidis, including over-expression of defense-related genes.
Interpreting spatially explicit variation in dietary proxies through species distribution modeling reveals foraging preferences of mammoth (Mammuthus) and American mastodon (Mammut americanum)

Introduction The end Pleistocene was a time of considerable ecological upheaval. Recent work has explored the megafauna extinction’s role in altering ecosystem processes. Analyses of functional traits withing communities reveal hidden consequences of the megafauna extinction beyond declines in taxonomic diversity. Functional diversity analyses offer new insight into our understanding of past ecosystems and may even inform future rewilding efforts. However, the utility of functional diversity may be hampered by the use of discrete, taxon-level functional traits, such as dietary categories, that mask variation in functional diversity over space and time. Methods We present an approach in which species distribution modeling, in Maxent, provides context for interpreting variation in two widely used proxies for diet among fossil taxa: stable isotope analysis and dental microwear texture analysis. We apply this approach to two ecologically distinct taxa, the American mastodon (Mammut americanum) and mammoths (Mammuthus) and investigate their resource use over space and time from the last glacial maximum to the end Pleistocene (25–11.7 thousand years before present). Results Mammoth dietary behavior varies by context across their geographic distribution, despite possessing evolutionary adaptations that facilitate grazing. Mammoths exhibit a preference for grazing where species distribution modeling predicts the highest likelihood of occurrence but engage in more mixed-feeding outside of core likelihood areas. In contrast, dietary preferences for mastodon are less resolved and our analyses were unable to identify significant differences in diet across their distribution. Discussion The ecological roles of some species are context specific and need to be critically evaluated when planning for management of reintroductions or introducing novel species to restore lost ecological function.
Enumerating homotopy-ribbon slice discs

Let $\Gamma$ be either the infinite cyclic group $\mathbb{Z}$ or the Baumslag-Solitar group $\mathbb{Z} \ltimes \mathbb{Z}[\frac{1}{2}]$. Let $K$ be a slice knot admitting a slice disc $D$ in the 4-ball whose exterior has fundamental group $\Gamma$. We classify the $\Gamma$-homotopy ribbon slice discs for $K$ up to topological ambient isotopy rel. boundary using surgery theory. In the infinite cyclic case, there is a unique equivalence class of such slice discs. When $\Gamma$ is the Baumslag-Solitar group, there is at most one $\Gamma$-homotopy ribbon slice disc for each lagrangian of the Blanchfield pairing of $K$.
Pan-cancer analysis reveals DDX21 as a potential biomarker for the prognosis of multiple tumor types

Background DExD-box helicase 21 (DDX21) is an essential member of the RNA helicase family. DDX21 is involved in the carcinogenesis of various malignancies, but there has been no comprehensive research on its involvement in different types of cancer. Method This study used TCGA, CPTAC, GTEx, GEO, FANTOM5, BioGRID, TIMER2, GEPIA2, cBioPortal, STRING, and Metascape databases and Survival ROC software to evaluate DDX21 gene expression, protein expression, immunohistochemistry, gene mutation, immune infiltration, and protein phosphorylation in 33 TCGA tumor types, as well as the prognostic relationship between DDX21 and different tumors, by survival analysis and similar gene enrichment analysis. Furthermore, Cell Counting Kit-8 (CCK-8) and Transwell studies were employed to assess the effect of DDX21 expression on lung adenocarcinoma (LUAD) cell proliferation and migration. Result The DDX21 gene was highly expressed in most cancers, and overexpression was associated with poor overall survival (OS) and disease-free survival (DFS). DDX21 mutations were most common in uterine corpus endometrial carcinoma (UCEC; >5%), and DDX21 expression was positively correlated with the degree of infiltration of CAF and CD8+ cells in several tumor types. Numerous genes were co-expressed with DDX21. Gene enrichment analysis revealed close links between DDX21, RNA metabolism, and ribosomal protein production. In vitro analysis of LUAD cells showed that DDX21 expression was positively correlated with cell proliferation and migration capacity, consistent with prior bioinformatics studies. Conclusions DDX21 is overexpressed in a variety of cancers, and overexpression in some cancers is associated with poor prognosis. Immune infiltration and DDX21-related gene enrichment analyses indicated that DDX21 may affect cancer development through mechanisms that regulate tumor immunity, RNA metabolism, and ribosomal protein synthesis. This pan-cancer study revealed the prognostic value and the oncogenic role of DDX21.
Construction of m7G subtype classification on heterogeneity of sepsis

Sepsis is a highly heterogeneous disease and a major factor in increasing mortality from infection. N7-Methylguanosine (m7G) is a widely RNA modification in eukaryotes, which involved in regulation of different biological processes. Researchers have found that m7G methylation contributes to a variety of human diseases, but its research in sepsis is still limited. Here, we aim to establish the molecular classification of m7G gene-related sepsis, reveal its heterogeneity and explore the underlying mechanism. We first identified eight m7G related prognostic genes, and identified two different molecular subtypes of sepsis through Consensus Clustering. Among them, the prognosis of C2 subtype is worse than that of C1 subtype. The signal pathways enriched by the two subtypes were analyzed by ssGSEA, and the results showed that the amino acid metabolism activity of C2 subtype was more active than that of C1 subtype. In addition, the difference of immune microenvironment among different subtypes was explored through CIBERSORT algorithm, and the results showed that the contents of macrophages M0 and NK cells activated were significantly increased in C2 subtype, while the content of NK cells resting decreased significantly in C2 subtype. We further explored the relationship between immune regulatory genes and inflammation related genes between C2 subtype and C1 subtype, and found that C2 subtype showed higher expression of immune regulatory genes and inflammation related genes. Finally, we screened the key genes in sepsis by WGCNA analysis, namely NUDT4 and PARN, and verified their expression patterns in sepsis in the datasets GSE131761 and GSE65682. The RT-PCR test further confirmed the increased expression of NUDTA4 in sepsis patients. In conclusion, sepsis clustering based on eight m7G-related genes can well distinguish the heterogeneity of sepsis patients and help guide the personalized treatment of sepsis patients.
Neuroanatomical correlates of individual differences in the object choice task in chimpanzees (Pan troglodytes)

Declarative and imperative joint attention or joint engagement are important milestones in human infant development. These have been shown to be a significant predictor of later language development and are impaired in some individuals with, or at risk for, a diagnosis of autism spectrum disorder. Comparatively, while chimpanzees and other great apes have been reported to engage in imperative joint attention, evidence of declarative joint attention remains unclear based on existing studies. Some have suggested that differences in methods of assessing joint attention may have an influence on performance in nonhuman primates. Here, we report data on a measure of receptive joint attention (object choice task) in a sample of captive chimpanzees. Chimpanzees, as a group, performed significantly better than chance. By contrast, when considering individual performance, there was no significant difference in the number of those who passed and those who failed. Using quantitative genetic analyses, we found that performance on the object choice task was not significantly heritable nor were there any significant effects of sex, rearing history, or colony. Lastly, we found significant differences in gray matter covariation, between those who passed or failed the task. Those who passed contributed more to gray matter covariation in several brain regions within the social brain network, consistent with hypotheses regarding the importance of these regions in human and nonhuman primate social cognition.
High-resolution synthetic population mapping for quantifying disparities in disaster impacts: An application in the Bangladesh Coastal Zone

The impacts of natural disasters are often disproportionally borne by poor or otherwise marginalized groups. However, while disaster risk modelling studies have made progress in quantifying the exposure of populations, limited advances have been made in determining the socioeconomic characteristics of these exposed populations. Here, we generate synthetic structural and socioeconomic microdata for around 9.5 million persons for six districts in Bangladesh as vector points using a combination of spatial microsimulation techniques and dasymetric modelling. We overlay the dataset with satellite-derived flood extents of Cyclone Fani, affecting the region in 2019, quantifying the number of exposed households, their socioeconomic characteristics, and the exposure bias of certain household variables. We demonstrate how combining various modelling techniques could provide novel insights into the exposure of poor and vulnerable groups, which could help inform the emergency response after extreme events as well targeting adaptation options to those most in need of them.
Reducing anxiety and attentional bias with reward association learning and attentional bias modification

The current study examined the effects of a reward associative learning procedure and the traditional threat-avoidance ABM paradigm on anxiety and attentional bias. In reward training, participants were given high rewards for correct responses to neutral target and low rewards for correct responses to negative target. In reward control training, participants received no cues of rewards after their responses. High trait anxious individuals (N = 76) first completed a session of reward training or reward control training, followed by four sessions of ABM training or ABM control training. Generalized anxiety disorder symptom (GAD-7) and attentional bias in a dot-probe task were assessed during pre-and post-training. Results indicated that the effect of ABM training on reducing anxiety was only obtained in the reward training condition. Participants who received reward training showed significantly less attentional bias compared with those receiving reward control training. There was no significant training effect of ABM on atttentiona bias. Results suggested that reward training reduced general anxiety and attentional bias. Traditional ABM training reduced anxiety only when combined with reward training. Attentional bias in anxiety are modifiable through reward training.
Signaling pathways in cutaneous wound healing

Wound healing is a very complex process, where variety of different pathways is activated, depending on the phase of healing. Improper or interrupted healing might result in development of chronic wounds. Therefore, novel approaches based on detailed knowledge of signalling pathways that are activated during acute or chronic cutaneous wound healing enables quicker and more effective healing. This review outlined new possibilities of cutaneous wound healing by modulation of some signalling molecules, e.g., gasotransmitters, or calcium. Special focus is given to gasotransmitters, since these bioactive signalling molecules that can freely diffuse into the cell and exert antioxidative effects. Calcium is an important booster of immune system and it can significantly contribute to healing process. Special interest is given to chronic wounds caused by diabetes mellitus and overcoming problems with the inflammation.