Miracle-dz/UniFAR-FTUs huggingface dataset:
Nystagmus in the B6(CG)Tyr(c-2J)/J Albino Mouse: A Functional and RNA-Seq Analysis

Purpose Infantile nystagmus syndrome (INS) is a gaze-holding disorder characterized by conjugate, uncontrolled eye oscillations that can result in significant visual acuity loss. INS is often associated with albinism, but the mechanism is unclear. Albino mice have nystagmus; however, a pigmented mouse with a tyr mutation making it phenotypically albino, the B6(CG)-Tyr(c-2J)/J (B6 albino), had not been tested. We tested optokinetic response (OKR) in B6 albino and control mice. RNA-Seq was performed on extraocular muscles (EOM), tibialis anterior (TA) muscle, abducens (CN6), and oculomotor (CN3) neurons to uncover molecular differences that may contribute to nystagmus. Methods OKR was measured using an ISCAN system. RNA was isolated from four tissues to identify differentially expressed genes and validated with qPCR and immunohistochemistry. Ingenuity pathway analyses identified top biological pathways. Results All B6 albino mice tested had nystagmus. Differential RNA expression analysis showed 383 genes differentially expressed in EOM, 70 in CN3, 20 in CN6, and 639 in the TA. Two genes were differentially expressed in all four tissues: wdfy1 and nnt. Differences were validated by qPCR and immunostaining. Conclusions The tyr mutation in B6 albino mice, genotypically pigmented and phenotypically albino, is sufficient to result in spontaneous nystagmus. The two genes with decreased expression in the B6 albino tissues examined, wdfy1 and nnt, have been implicated in mitochondrial dysfunction and stem cell maintenance in other systems. Their function in extraocular muscle is unknown. These studies suggest that this mouse model of nystagmus may allow molecular identification of candidate nystagmus-related genes.
Automated elimination of EOG artifacts in sleep EEG using regression method

Sleep electroencephalogram (EEG) signal is an important clinical tool for automatic sleep staging process. Sleep EEG signal is effected by artifacts and other biological signal sources, such as electrooculogram (EOG) and electromyogram (EMG), and since it is effected, its clinical utility reduces. Therefore, eliminating EOG artifacts from sleep EEG signal is a major challenge for automatic sleep staging. We have studied the effects of EOG signals on sleep EEG and tried to remove them from the EEG signals by using regression method. The EEG and EOG recordings of seven subjects were obtained from the Sleep Research Laboratory of Meram Medicine Faculty of Necmettin Erbakan University. A dataset consisting of 58 h and 6941 epochs was used in the research. Then, in order to see the consequences of this process, we classified pure sleep EEG and artifact-eliminated EEG signals with artificial neural networks (ANN). The results showed that elimination of EOG artifacts raised the classification accuracy on each subject at a range of 1%– 1.5%. However, this increase was obtained for a single parameter. This can be regarded as an important improvement if the whole system is considered. However, different artifact elimination strategies combined with different classification methods for another sleep EEG artifact may give higher accuracy differences between original and purified signals.
PLANT RESPONSES ON SOILS AMELIORATED WITH WASTE PRODUCTS

The South African mining industry has been the backbone of the country's economy for much of the past century. Mining has, however, had major impacts on both agricultural resources and the urban environment. Rehabilitation of such impacted soils, which are often characterized by high acidity and low fertility, requires major inputs to ensure the successful establishment and sustainability of a protective and restorative vegetation. The safe use of biosolids has been made feasible by combining it with coal combustion products. The resultant product (SLASH) has been shown to have a positive effect on the pH, Ca, Mg and P of a moderately acid agricultural soil and on the production of a range of vegetable and flower crops. With a view to using such a product in the rehabilitation of impacted soils, SLASH was applied to an infertile soil and a range of forage species, used in different revegetation programs, were used as test crops. These included an annual cereal crop (Triticale -Triticum x Seca/e), commonly used to ensure early stabilization of minelands and/or as a stubble mulch for the establishment of perennial species, as well as perennial legumes (Sweet Clover -Melilotus alba and Crown Vetch Coronilla varia) and grasses such as KentuckY Bluegrass Paa pratensis, Tall Fescue Festuca arundinaceae and Buffelgrass Cenchrus ciliaris). SLASH had marked beneficial effects on productivity of forage as well as root development for as long as two years after initial treatment. Additional
Visual influence on bimanual haptic slant adaptation

Adapting to particular features of a haptic shape, for example, the slant of a surface, affects how a subsequently touched shape is perceived (aftereffect). Previous studies showed that this adaptation is largely based on our proprioceptive sense of hand posture, yet the influence of vision on haptic shape adaptation has been relatively unexplored. Here, using a slant-adaptation paradigm, we investigated whether visual information affects haptic adaptation and, if so, how. To this end, we varied the available visual cues during the adaptation period. This process ranged from providing visual information only about the slant of the surface, or the reference frame in which it is presented, to only providing visual information about the location of the fingertips. Additionally, we tested several combinations of these visual cues. We show that, as soon as the visual information can be used as a spatial reference to link the own fingertip position to the surface slant, haptic adaptation is very much reduced. This result means that, under these viewing conditions, vision dominates touch and is one reason why we do not easily adapt to haptic shape in our daily life, because we usually have visual information about both hand and object available simultaneously.
Effects of the enhanced recovery after surgery intervention for preventing postpartum depression: a protocol for systematic review and meta-analysis

Introduction Postpartum depression (PPD), a prevalent public health problem, is a debilitating mental disorder for which preventive interventions could yield dramatic benefits. However, viable approach focusing the prevention of PPD for caesarean section (CS) patients remains limited currently. In recent decades, enhanced recovery after surgery (ERAS) has gradually been implemented in CS and appears to be a potential and favourable preventive intervention for PPD, but systematic evidence on this issue is lacking. Therefore, a meta-analysis is designed to systematically explore the potential effect of ERAS on the prevention of PPD in CS patients. Methods and analysis Meta-analysis will be performed according to the Preferred Reporting Items for Systematic Review and Meta-Analyses statement. A systematic search across the PubMed, Embase, Cochrane Library, China National Knowledge Infrastructure, Chinese Biomedical Literature Database, Chinese Scientific Journal Database, grey literature and Wanfang Database will be conducted from inception to July 2023. Relevant studies investigating the association between ERAS and PPD will be included. Two reviewers will independently carry out the literature selection, data extraction and risk of bias assessment. Disagreements will be resolved by group consensus. Statistical analyses will use the RevMan V.5. 3 and STATA V.13 software. The Grading of Recommendations Assessment, Development, and Evaluation system will be used to evaluate the strength of evidence. Ethics and dissemination This study raises no ethical issues. The pending meta-analysis may provide reliable evidence supporting ERAS as a viable preventive option for PPD in CS patients, further providing a useful reference for the health authorities and promoting the future clinical practice in this field. The formal results of this study will be submitted to a professional journal for publication. PROSPERO registration number CRD42023485929.
Predicting the final metabolic profile based on the succession-related microbiota during spontaneous fermentation of the starter for Chinese liquor making

ABSTRACT Microbial inoculation is an effective way to improve the quality of fermented foods via affecting the microbiota structure. However, it is unclear how the inoculation regulates the microbiota structure, and it is still difficult to directionally control the microbiota function via the inoculation. In this work, using the spontaneous fermentation of the starter (Daqu) for Chinese liquor fermentation as a case, we inoculated different microbiota groups at different time points in Daqu fermentation, and analyzed the effect of the inoculation on the final metabolic profile of Daqu. The inoculated microbiota and inoculated time points both significantly affected the final metabolites via regulating the microbial succession (P < 0.001), and multiple inoculations can promote deterministic assembly. Twenty-seven genera were identified to be related to microbial succession, and drove the variation of 121 metabolites. We then constructed an elastic network model to predict the profile of these 121 metabolites based on the abundances of 27 succession-related genera in Daqu fermentation. Procrustes analysis showed that the model could accurately predict the metabolic abundances (average Spearman correlation coefficients >0.3). This work revealed the effect of inoculation on the microbiota succession and the metabolic profile. The established predicted model of metabolic profile would be beneficial for directionally improving the food quality. IMPORTANCE This work revealed the importance of microbial succession to microbiota structure and metabolites. Multi-inoculations would promote deterministic assembly. It would facilitate the regulation of microbiota structure and metabolic profile. In addition, we established a model to predict final metabolites based on microbial genera related to microbial succession. This model was beneficial for optimizing the inoculation of the microbiota. This work would be helpful for controlling the spontaneous food fermentation and directionally improving the food quality. This work revealed the importance of microbial succession to microbiota structure and metabolites. Multi-inoculations would promote deterministic assembly. It would facilitate the regulation of microbiota structure and metabolic profile. In addition, we established a model to predict final metabolites based on microbial genera related to microbial succession. This model was beneficial for optimizing the inoculation of the microbiota. This work would be helpful for controlling the spontaneous food fermentation and directionally improving the food quality.
Pre-diagnostic circulating resistin concentrations and mortality among individuals with colorectal cancer: Results from the European Prospective Investigation into Cancer and Nutrition study.

Resistin is a protein involved in inflammation and angiogenesis processes and may play a role in the progression of colorectal cancer (CRC). However, it remains unclear whether resistin is associated with increased mortality after CRC diagnosis. We examined pre-diagnostic serum resistin concentrations in relation to CRC-specific and all-cause mortality among 1343 incident CRC cases from the European Prospective Investigation into Cancer and Nutrition cohort. For CRC-specific mortality as the primary outcome, hazard ratios (HRs) and 95% confidence intervals (95% CI) were estimated from competing risk analyses based on cause-specific Cox proportional hazards models and further in sensitivity analyses using Fine-Gray proportional subdistribution hazards models. For all-cause mortality as the secondary outcome, Cox proportional hazards models were used. Subgroup analyses were performed by sex, tumor subsite, tumor stage, body mass index and time to CRC diagnosis. Resistin was measured on a median of 4.8 years before CRC diagnosis. During a median follow-up of 8.2 years, 474 deaths from CRC and 147 deaths from other causes were observed. Resistin concentrations were not associated with CRC-specific mortality (HRQ4vsQ1 = 0.95, 95% CI: 0.73-1.23; Ptrend = .97; and HRper doubling of resistin concentration = 1.00; 95% CI: 0.84-1.19; P = .98) or all-cause mortality. Results from competing risk (sensitivity) analysis were similar. No associations were found in any subgroup analyses. These findings suggest no association between pre-diagnostic circulating resistin concentrations and CRC-specific or all-cause mortality among persons with CRC, and the potential insignificance of resistin in CRC progression.
piOxi database: a web resource of germline and somatic tissue piRNAs identified by chemical oxidation

Abstract PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs that are highly expressed and extensively studied from the germline. piRNAs associate with PIWI proteins to maintain DNA methylation for transposon silencing and transcriptional gene regulation for genomic stability. Mature germline piRNAs have distinct characteristics including a 24- to 32-nucleotide length and a 2ʹ-O-methylation signature at the 3ʹ end. Although recent studies have identified piRNAs in somatic tissues, they remain poorly characterized. For example, we recently demonstrated notable expression of piRNA in the murine soma, and while overall expression was lower than that of the germline, unique characteristics suggested tissue-specific functions of this class. While currently available databases commonly use length and association with PIWI proteins to identify piRNA, few have included a chemical oxidation method that detects piRNA based on its 3ʹ modification. This method leads to reproducible and rigorous data processing when coupled with next-generation sequencing and bioinformatics analysis. Here, we introduce piOxi DB, a user-friendly web resource that provides a comprehensive analysis of piRNA, generated exclusively through sodium periodate treatment of small RNA. The current version of piOxi DB includes 435 749 germline and 9828 somatic piRNA sequences robustly identified from M. musculus, M. fascicularis and H. sapiens. The database provides species- and tissue-specific data that are further analyzed according to chromosome location and correspondence to gene and repetitive elements. piOxi DB is an informative tool to assist broad research applications in the fields of RNA biology, cancer biology, environmental toxicology and beyond. Database URL: https://pioxidb.dcmb. med.umich. edu/
An Asset Allocation Model and Its Solving Method

Abstract Asset allocation is an important issue in finance, and both risk and return are its fundamental ingredients. Rather than the return, the measure of the risk is complicated and of controversy. In this paper, we propose an appropriate risk measure which is precisely a convex combination of mean semi-deviation and conditional value-at-risk. Based on this risk measure, investors can trade-off flexibly between the volatility and the loss to tackle the incurring risk by choosing different convex coefficients. As the presented risk measure contains nonsmooth term, the asset allocation model based on it is nonsmooth. To employ traditional gradient algorithms, we develop a uniform smooth approximation of the plus function and convert the model into a smooth one. Finally, an illustrative empirical study is given. The results indicate that investors can control risk efficiently by adjusting the convex coefficient and the confidence level simultaneously according to their perceptions. Moreover, the effectiveness of the smoothing function proposed in the paper is verified.
The Automatic Recognition of Large Ball Valve Sealing Bolt Based on Digital Image

In this paper, we adopted the area filling method of the mathematical morphology to fill the holes of the nut. In addition, the bimodal method and multi-threshold method were combined for the image segmentation. Furthermore, the image edge was detected by mathematical morphology algorithm. Finally, the angle between the bolt and manipulator was calculated using the rotation conversion matrix. With the systematic error and correlation coefficient, the calculated angle was verified. Experimental results show that the method can protect the edge integrity of the nut image, with fast processing speed and strong anti-noise ability. The work in this paper provides a theoretical basis for the automatic recognition in the large ball valve sealing bolt system.
Modelling policies to improve affordability and consumption of nutritious foods for complementary feeding in Kenya

Abstract In Kenya 26% of children under age 5 experience stunted growth, 4% are wasted and 11% are underweight. In pregnant women, the prevalence of iron deficiency is 36% and iron‐deficiency anaemia prevalence is 26%. Previous studies have identified affordability as a key barrier to the intake of nutrients, particularly from animal‐source foods (ASFs). Thus, this study analyzes to what extent the affordability of ASF in Kenya can be improved. It focuses on four ASFs: eggs, milk, chicken and beef. Using a computable general equilibrium model, three policy simulations were undertaken to establish the impact of potential changes on nutritious ASF availability and affordability: a 20% increase in total factor productivity (TFP) for the four products; a 20% TFP increase plus a 25% reduction in trade and transportation margins; and a 20% TFP increase for ASF and maize (a key input in animal feed). Simulations suggest increasing the productivity of the four ASF products would increase their availability and lower consumer prices (up to 17% lower). Household consumption of the four commodities would increase, resulting in improved household dietary diversity. Rural households would gain more compared with urban households. Poor households (the lowest 40%) would register larger welfare (Equivalent Variation) gains than other households in both urban and rural areas. The richest 20% of the population would neither lose nor gain following the policy changes. Reducing transportation costs and trade margins and increasing maize productivity could further reduce the price of ASFs through lower production costs and increased consumption.
Tumor mutation load better predicts the prognosis of patients treated with immune checkpoint inhibitors in upper gastrointestinal cancers: A systematic review and meta‐analysis

Abstract Background Tumor mutational load (TML) has emerged as a potential biomarker for multiple solid tumors. However, data on its prognostic impact on upper gastrointestinal (UGI) cancer are limited. Therefore, the aim of this systematic review and meta‐analysis was to assess the prognostic value of TML for the survival of patients with UGI cancer. Method A comprehensive search of the PubMed, Embase, Cochrane Library, and Web of Science databases was conducted up to February 13, 2023. Eleven studies met our inclusion criteria. Hazard ratios (HRs) for progression‐free survival and overall survival and their 95% confidence intervals (CIs) were calculated. Subsequently, the combined HR and its 95% CI were calculated for UGI tract cancers in the high and low TML groups. I 2 statistics and p‐values were used to evaluate heterogeneity. Publication bias, sensitivity, and subgroup analyses were performed to determine sources of heterogeneity. Results In total, 932 patients with UGI tract cancer from 11 publications were included. The high TML group treated with immunotherapy showed significantly improved overall survival (HR = 0.68; 95% CI: 0.53, 0.86; p = .001) and progression‐free survival (HR = 0.74; 95% CI: 0.58, 0.95; p = .020) compared with the low TML group. Conclusion Our study demonstrated that patients with UGI tumors and higher TML have a better prognosis with immunotherapy, suggesting that TML is a promising predictive biomarker for immunotherapy. Registration The study protocol was registered with the International Prospective Register of Systematic Reviews (PROSPERO Registration No: CRD42023405596).
An independent assessment of anthropogenic attribution statements for recent extreme temperature and rainfall events

AbstractThe annual “State of the Climate” report, published in the Bulletin of the American Meteorological Society (BAMS), has included a supplement since 2011 composed of brief analyses of the human influence on recent major extreme weather events. There are now several dozen extreme weather events examined in these supplements, but these studies have all differed in their data sources as well as their approaches to defining the events, analyzing the events, and the consideration of the role of anthropogenic emissions. This study reexamines most of these events using a single analytical approach and a single set of climate model and observational data sources. In response to recent studies recommending the importance of using multiple methods for extreme weather event attribution, results are compared from these analyses to those reported in the BAMS supplements collectively, with the aim of characterizing the degree to which the lack of a common methodological framework may or may not influence overall .
Multiomics profiling reveals the benefits of gamma-delta (γδ) T lymphocytes for improving the tumor microenvironment, immunotherapy efficacy and prognosis in cervical cancer

Background As an unconventional subpopulation of T lymphocytes, γδ T cells can recognize antigens independently of major histocompatibility complex restrictions. Recent studies have indicated that γδ T cells play contrasting roles in tumor microenvironments—promoting tumor progression in some cancers (eg, gallbladder and leukemia) while suppressing it in others (eg, lung and gastric). γδ T cells are mainly enriched in peripheral mucosal tissues. As the cervix is a mucosa-rich tissue, the role of γδ T cells in cervical cancer warrants further investigation. Methods We employed a multiomics strategy that integrated abundant data from single-cell and bulk transcriptome sequencing, whole exome sequencing, genotyping array, immunohistochemistry, and MRI. Results Heterogeneity was observed in the level of γδ T-cell infiltration in cervical cancer tissues, mainly associated with the tumor somatic mutational landscape. Definitely, γδ T cells play a beneficial role in the prognosis of patients with cervical cancer. First, γδ T cells exert direct cytotoxic effects in the tumor microenvironment of cervical cancer through the dynamic evolution of cellular states at both poles. Second, higher levels of γδ T-cell infiltration also shape the microenvironment of immune activation with cancer-suppressive properties. We found that these intricate features can be observed by MRI-based radiomics models to non-invasively assess γδ T-cell proportions in tumor tissues in patients. Importantly, patients with high infiltration levels of γδ T cells may be more amenable to immunotherapies including immune checkpoint inhibitors and autologous tumor-infiltrating lymphocyte therapies, than to chemoradiotherapy. Conclusions γδ T cells play a beneficial role in antitumor immunity in cervical cancer. The abundance of γδ T cells in cervical cancerous tissue is associated with higher response rates to immunotherapy.