Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigate the application of postoperative ctDNA-based molecular residual disease detection in monitoring tumor recurrence in patients with non-small cell lung cancer——A retrospective study of ctDNA

Purpose To evaluate whether postoperative circulating tumor DNA (ctDNA) in plasma of patients with non-small cell lung cancer (NSCLC) can be used as a biomarker for early detection of molecular residual disease (MRD) and prediction of postoperative recurrence. Methods This study subjects were evaluated patients with surgical resected non-small cell lung cancer. All eligible patients underwent radical surgery operation followed by adjuvant therapy. Tumor tissue samples collected during operation were used to detect tumor mutation genes, and blood samples collected from peripheral veins after operation were used to collect ctDNA. Molecular residue disease (MRD) positive was defined as at least 1 true shared mutation identified in both the tumor sample and a plasma sample from the same patient was. Results Positive postoperatively ctDNA was associated with lower recurrence-free survival (RFS). The presence of MRD was a strong predictor of disease recurrence. The relative contribution of ctDNA-based MRD to the prediction of RFS is higher than all other clinicopathological variables, even higher than traditional TNM staging. In addition, MRD-positive patients who received adjuvant therapy had improved RFS compared to those who did not, the RFS of MRD-negative patients receiving adjuvant therapy was lower than that of patients not receiving adjuvant therapy. Conclusions Post-operative ctDNA analysis is an effective method for recurrence risk stratification of NSCLC, which is beneficial to the management of patients with NSCLC.
Transcriptome analysis reveals differences in cell cycle, growth and migration related genes that distinguish fibroblasts derived from pre-invasive and invasive breast cancer

Background/Introduction As the most common form of pre-invasive breast cancer, ductal carcinoma in situ (DCIS) affects over 50,000 women in the US annually. Despite standardized treatment involving lumpectomy and radiation therapy, up to 25% of patients with DCIS experience disease recurrence often with invasive ductal carcinoma (IDC), indicating that a subset of patients may be under-treated. As most DCIS cases will not progress to invasion, many patients may experience over-treatment. By understanding the underlying processes associated with DCIS to IDC progression, we can identify new biomarkers to determine which DCIS cases may become invasive and improve treatment for patients. Accumulation of fibroblasts in IDC is associated with disease progression and reduced survival. While fibroblasts have been detected in DCIS, little is understood about their role in DCIS progression. Goals We sought to determine 1) whether DCIS fibroblasts were similar or distinct from normal and IDC fibroblasts at the transcriptome level, and 2) the contributions of DCIS fibroblasts to breast cancer progression. Methods Fibroblasts underwent transcriptome profiling and pathway analysis. Significant DCIS fibroblast-associated genes were further analyzed in existing breast cancer mRNA databases and through tissue array immunostaining. Using the sub-renal capsule graft model, fibroblasts from normal breast, DCIS and IDC tissues were co-transplanted with DCIS.com breast cancer cells. Results Through transcriptome profiling, we found that DCIS fibroblasts were characterized by unique alterations in cell cycle and motility related genes such as PKMYT1, TGF-α, SFRP1 and SFRP2, which predicted increased cell growth and invasion by Ingenuity Pathway Analysis. Immunostaining analysis revealed corresponding increases in expression of stromal derived PKMYT1, TGF-α and corresponding decreases in expression of SFRP1 and SFRP2 in DCIS and IDC tissues. Grafting studies in mice revealed that DCIS fibroblasts enhanced breast cancer growth and invasion associated with arginase-1+ cell recruitment. Conclusion DCIS fibroblasts are phenotypically distinct from normal breast and IDC fibroblasts, and play an important role in breast cancer growth, invasion, and recruitment of myeloid cells. These studies provide novel insight into the role of DCIS fibroblasts in breast cancer progression and identify some key biomarkers associated with DCIS progression to IDC, with important clinical implications.
A Reasoning Module for Long-lived Cognitive Agents

In this thesis we study a reasoning module for agents that have cognitive abilities, such as memory, perception, action, and are expected to function autonomously for long periods of time. The module provides the ability to reason about action and change using the language of the situation calculus and variants of the basic action theories. The main focus of this thesis is on the logical problem of progressing an action theory. First, we investigate the conjecture by Lin and Reiter that a practical first-order definition of progression is not appropriate for the general case. We show that Lin and Reiter were indeed correct in their intuitions by providing a proof for the conjecture, thus resolving the open question about the first-order definability of progression and justifying the need for a second-order definition. Then we proceed to identify three cases where it is possible to obtain a first-order progression with the desired properties: (i) we extend earlier work by Lin and Reiter and present a case where we restrict our attention to a practical class of queries that may only quantify over situations in a limited way; (ii) we revisit the local-effect assumption of Lin and Levesque that requires that the effects of an action are fixed by the arguments of the action and show that in this case a first-order progression is suitable; (iii) we investigate a way that the local-effect assumption can be relaxed and show that when the initial knowledge base is a database of possible closures and the effects of the actions are range-restricted then a first-order progression is also suitable under a just-in-time assumption. Finally, we examine a special case of the action theories with range-restricted effects and present an algorithm for computing a finite progression. We prove the correctness and the complexity of the algorithm, and show its application in a simple example that is inspired by video games.
Fecal microbiota transplantation from Suncus murinus, an obesity-resistant animal, to C57BL/6NCrSIc mice, and the antibiotic effects in the approach

Introduction Important studies on the relationship of the intestinal microbial flora with obesity have uncovered profound changes in the composition of the gut microbiota in obese individuals. Animal studies successfully altered body phenotypes by fecal microbiota transplantation (FMT). Methods In this study, we analyzed the gut microbiome of Suncus murinus (S. murinus), a naturally obesity-resistant animal, and the changes of the gut flora of C57BL/6NCrSIc mice that received gut bacteria transplantation from S. murinus by 16S rRNA gene analysis method. And analyzed and discussed the possible impact of the use of antibiotics before transplantation on the outcome of transplantation. Results Our results showed no significant changes in body weight in the FMT group compared to the control (AB) group, but large fluctuations due to antibiotics. There was no change in blood lipid levels between groups before and after FMT. The gut microbiota of S. murinus were enriched in Firmicutes and Proteobacteria, while Bacteroidetes were not detected, and fewer OTUs were detected in the intestine gut in comparison to other mouse groups. Statistically significant differences in alpha diversity were observed between the FMT group and other groups. Furthermore, a beta diversity analysis indicated an apparent structural separation between the FMT group and other groups. Conclusion It was suggested that the gut flora of S. murinus was not well established in the gut trace of mice through FMT, and the administration of antibiotics before transplantation was an important factor affecting the overall composition of the gut flora. Although FMT of S. murinus failed to completely colonize the intestinal tract of the mice, it still had a certain effect on the establishment of the intestinal flora of the mice. The unpredictable effects of pre-transplantation antibiotics on the results of transplantation cannot be ignored.
Reliability and validity of the Vietnamese version of the Hamilton D-17 scale

Background While depression is a common mental disorder, the diagnosis of this condition is still challenging. Thus, there is a need to have a validated tool to help evaluate symptoms of depression. This study aimed to evaluate the reliability and validity of the Vietnamese version of the Hamilton D-17 scale. Methods A cross-sectional, descriptive, and validation study was conducted on 183 patients including 139 depressed and 44 non-depressed patients at the University Medical Center of Medicine and Pharmacy University at Ho Chi Minh City. Internal reliability and inter-rater reliability was measured using Cronbach's alpha and intraclass correlation coefficients (ICC). Confirmatory factor analysis (CFA) was used to evaluate construct validity. The Patient Health Questionnaire (PHQ9) was used to measure concurrent validity of the Hamilton D-17. Area under the ROC curve was used to measure criterion validity. Results Both Cronbach alpha coefficient and ICC were at good level at alpha = 0.83 and ICC = 0.83. CFA with a second-order model consisting of four factors fitted the data at good to excellent level. The SRMR (Standardized Root Mean Squared Residual) was 0.066, RMSEA (Root Mean Square Error of Approximation) (90% CI) was 0.053 (0.036–0.069), CFI (comparative fit index) was 0.93, TLI (Tucker Lewis index) was 0.92. The Hamilton D-17 and the PHQ-9 had a correlation coefficient of r = 0.77 (p < 0.001). The Hamilton D-17 had a very high level of criterion validity with AUC of 0.93 (0.88–0.98). Conclusion The Vietnamese version of the Hamilton D-17 scale has a high level of validity and reliability. The scale should be used to assess symptoms of depression among Vietnamese patients.
Normative mice retinal thickness: 16-month longitudinal characterization of wild-type mice and changes in a model of Alzheimer's disease

Animal models of disease are paramount to understand retinal development, the pathophysiology of eye diseases, and to study neurodegeneration using optical coherence tomography (OCT) data. In this study, we present a comprehensive normative database of retinal thickness in C57BL6/129S mice using spectral-domain OCT data. The database covers a longitudinal period of 16 months, from 1 to 16 months of age, and provides valuable insights into retinal development and changes over time. Our findings reveal that total retinal thickness decreases with age, while the thickness of individual retinal layers and layer aggregates changes in different ways. For example, the outer plexiform layer (OPL), photoreceptor inner segments (ILS), and retinal pigment epithelium (RPE) thickened over time, whereas other retinal layers and layer aggregates became thinner. Additionally, we compare the retinal thickness of wild-type (WT) mice with an animal model of Alzheimer's disease (3 × Tg-AD) and show that the transgenic mice exhibit a decrease in total retinal thickness compared to age-matched WT mice, with statistically significant differences observed at all evaluated ages. This normative database of retinal thickness in mice will serve as a reference for future studies on retinal changes in neurodegenerative and eye diseases and will further our understanding of the pathophysiology of these conditions.
A longitudinal study on sensitivity to symmetry in writing and associations with early literacy abilities

Introduction Young children reportedly find symmetrical prints, such as H, easier to copy and produce from memory than asymmetrical ones. Little is known about how sensitivity to symmetry in print relates to early word reading and writing development. We examined this in Chinese, a visually complex writing system featuring symmetrical patterns, such as or . Methods Sixty preschoolers in Beijing completed a character decision task (Experiment 1, Mage = 62.16 months) and a character learning task (Experiment 2, Mage = 63.96 months), using stimuli matched on visual complexity and frequency but differing in symmetry, and were assessed on Chinese word reading and word writing abilities twice with a 2-year interval. Results Children were significantly more likely to endorse symmetrical complex stimuli as possible Chinese than asymmetrical complex ones, and they learned to read symmetrical characters significantly better than asymmetrical ones, reflecting their sensitivity to symmetry in Chinese characters. However, with age and nonverbal IQ statistically controlled, sensitivity to symmetry was not uniquely associated with Chinese word reading or word writing abilities at any time; rather, asymmetrical character learning, which necessitates reduced sensitivity to symmetry, was uniquely associated with Chinese word writing concurrently and longitudinally. Discussion Findings highlight the close relationship between analytic perception of written words and early writing ability.
An online learning algorithm for adapting leg stiffness and stride angle for efficient quadruped robot trotting

Animals adjust their leg stiffness and stride angle in response to changing ground conditions and gait parameters, resulting in improved stability and reduced energy consumption. This paper presents an online learning algorithm that attempts to mimic such animal behavior by maximizing energy efficiency on the fly or equivalently, minimizing the cost of transport of legged robots by adaptively changing the leg stiffness and stride angle while the robot is traversing on grounds with unknown characteristics. The algorithm employs an approximate stochastic gradient method to change the parameters in real-time, and has the following advantages: (1) the algorithm is computationally efficient and suitable for real-time operation; (2) it does not require training; (3) it is model-free, implying that precise modeling of the robot is not required for good performance; and (4) the algorithm is generally applicable and can be easily incorporated into a variety of legged robots with adaptable parameters and gaits beyond those implemented in this paper. Results of exhaustive performance assessment through numerical simulations and experiments on an under-actuated quadruped robot with compliant legs are included in the paper. The robot platform used a pneumatic piston in each leg as a variable, passive compliant element. Performance evaluation using simulations and experiments indicated that the algorithm was capable of converging to near-optimal values of the cost of transport for given operating conditions, terrain properties, and gait characteristics with no prior knowledge of the terrain and gait conditions. The simplicity of the algorithm and its demonstrably improved performance make the approach of this paper an excellent candidate for adaptively controlling tunable parameters of compliant, legged robots.
Diving deeper: Mesopelagic fish biomass estimates comparison using two different models

A growing population on a planet with limited resources demands finding new sources of protein. Hence, fisheries are turning their perspectives towards mesopelagic fish, which have, so far, remained relatively unexploited and poorly studied. Large uncertainties are associated with regards to their biomass, turn-over rates, susceptibility to environmental forcing and ecological and biogeochemical role. Models are useful to disentangle sources of uncertainties and to understand the impact of different processes on the biomass. In this study, we employed two food-web models – OSMOSE and the model by Anderson et al. (2019, or A2019) – coupled to a regional physical–biogeochemical model to simulate mesopelagic fish in the Eastern Tropical South Pacific ocean. The model by A2019 produced the largest biomass estimate, 26 to 130% higher than OSMOSE depending on the mortality parameters used. However, OSMOSE was calibrated to match observations in the coastal region off Peru and its temporal variability is affected by an explicit life cycle and food web. In contrast, the model by A2019 is more convenient to perform uncertainty analysis and it can be easily coupled to a biogeochemical model to estimate mesopelagic fish biomass. However, it is based on a flow analysis that had been previously applied to estimate global biomass of mesopelagic fish but has never been calibrated for the Eastern Tropical South Pacific. Furthermore, it assumes a steady-state in the energy transfer between primary production and mesopelagic fish, which may be an oversimplification for this highly dynamic system. OSMOSE is convenient to understand the interactions of the ecosystem and how including different life stages affects the model response. The combined strengths of both models allow us to study mesopelagic fish from a holistic perspective, taking into account energy fluxes and biomass uncertainties based on primary production, as well as complex ecological interactions.
Efficacy of electrical cranial stimulation for treatment of psychiatric symptoms in patients with anxiety: A systematic review and meta-analysis

Background Therapeutic effects of electrical cranial stimulation (CES) in patients suffering from anxiety remained unclear. This meta-analysis aimed at investigating acceptability and therapeutic efficacy of CES against anxiety, depression, and insomnia for patients who experienced symptoms of anxiety. Methods Major electronic databases were searched from inception until December 10, 2022 for randomized controlled trials (RCT) focusing on therapeutic effectiveness of CES in patients whose primary complaints included anxiety. Effect sizes (ES) for different treatment outcomes were estimated by using generic inverse variance method. Results Eight RCTs were identified including a total of 337 participants. The therapeutic effectiveness of CES was significantly better than that in the control groups for anxiety (ES=-0.96, p <0.00001, eight trials, 337 patients), depression (ES=-0.69, p=0.003, five trials), and insomnia (ES=-1.02, p = 0.0006, three trials) in those who presented with symptoms of anxiety. Subgroup analyses found that CES was equally effective regardless of comorbid presentation of depressive symptoms (ES=-0.94 in patients with anxiety only vs. ES=-1.06 in those with depression and anxiety) and whether CES was used as monotherapy or add-on therapy to medications (ES = −0.88 vs. ES = −1.12, respectively). Moreover, subgroup analysis of RCTs using the same device “Alpha-Stim” for CES was more effective in alleviating anxiety than sham controls (ES = −0.88, p < 0.00001, four trials, 230 patients). Regarding acceptability, the use of CES did not increase the risk of treatment-related dropout compared to the control group (RR = 1.26, p = 0.57, I2 = 0%, four trials, 324 patients). Conclusion Our study supported the use of CES for symptoms of anxiety, depression, and insomnia in those suffering from anxiety with fair acceptability and demonstrated the efficacy of “Alpha-Stim”, the most commonly used device for CES, in this patient population. Systematic review registration https://www.crd. york.ac. uk/prospero/, identifier: CRD42022382619.
The triglyceride glucose-waist-to-height ratio outperforms obesity and other triglyceride-related parameters in detecting prediabetes in normal-weight Qatari adults: A cross-sectional study

Introduction The triglyceride-glucose (TyG)-driven indices, incorporating obesity indices, have been proposed as reliable markers of insulin resistance and related comorbidities such as diabetes. This study evaluated the effectiveness of these indices in detecting prediabetes in normal-weight individuals from a Middle Eastern population. Methods Using the data of 5,996 adult Qatari participants from the Qatar Biobank cohort, we employed adjusted logistic regression to assess the ability of various obesity and triglyceride-related indices to detect prediabetes in normal-weight (18.5 ≤ BMI <25 kg/m2) adults (≥18 years). Results Of the normal-weight adults, 13.62% had prediabetes. TyG-waist-to-height ratio (TyG-WHTR) was significantly associated with prediabetes among normal-weight men [OR per 1-SD 2.68; 95% CI (1.67–4.32)] and women [OR per 1-SD 2.82; 95% CI (1.61–4.94)]. Compared with other indices, TyG-WHTR had the highest area under the curve (AUC) value for prediabetes in men [AUC: 0.76, 95% CI (0.70–0.81)] and women [AUC: 0.73, 95% CI (0.66–0.80)], and performed significantly higher than other indices (p < 0.05) in detecting prediabetes in men. Tyg-WHTR shared similar diagnostic values as fasting plasma glucose (FPG). Discussion Our findings suggest that the TyG-WHTR index could be a better indicator of prediabetes for general clinical usage in normal weight Qatari adult men than other obesity and TyG-related indices. TyG-WHTR can help identify a person’s risk for developing prediabetes in both men and women when combined with FPG results.
Sympatric and allopatric Alcolapia soda lake cichlid species show similar levels of assortative mating

Characterizing reproductive barriers such as mating preferences within rapid evolutionary radiations is crucial for understanding the early stages of speciation. Cichlid fishes are well-known for their adaptive radiations and capacity for rapid speciation and as such we investigate assortative mating among Alcolapia species; a recent (<10,000 years), small adaptive radiation, endemic to the extreme soda lakes, Magadi (one species) and Natron (three species), in East Africa. In seminatural aquarium conditions, we observed both courtship and mate choice (tested by microsatellite paternity analysis) to be significantly assortative among the three sympatric Natron species in a three-way choice experiment. This was also the case between allopatric species from Natron and Magadi, as found in a two-way choice experiment. However, the proportion of disassortative matings was substantial in both of these experiments, with hybrids comprising 29% of offspring in sympatric species and 11.4% in allopatric species comparisons. Previous work suggests that the Natron/Magadi split might not be much older than the radiation within Natron, so the similar rate of hybridization in the allopatric comparison is surprising and inconsistent with predictions of reinforcement theory, which predicts a faster rate of accumulation of premating isolation in sympatry. The relatively weak assortative mating in sympatry suggests that additional reproductive barriers, such as microhabitat preferences or spatial structuring may contribute to genetic isolation in nature.