ebalance: A Stata Package for Entropy Balancing

The Stata package ebalance implements entropy balancing, a multivariate reweighting method described in Hainmueller (2012 ) that allows users to reweight a dataset such that the covariate distributions in the reweighted data satisfy a set of specified moment conditions. This can be useful to create balanced samples in observational studies with a binary treatment where the control group data can be reweighted to match the covariate moments in the treatment group. Entropy balancing can also be used to reweight a survey sample to known characteristics from a target population

SAM-Med3D

Although the Segment Anything Model (SAM) has demonstrated impressive performance in 2D natural image segmentation, its application to 3D volumetric medical images reveals significant shortcomings, namely suboptimal performance and unstable prediction, necessitating an excessive number of prompt points to attain the desired outcomes. These issues can hardly be addressed by fine-tuning SAM on medical data because the original 2D structure of SAM neglects 3D spatial information. In this paper, we introduce SAM-Med3D, the most comprehensive study to modify SAM for 3D medical images. Our approach is characterized by its comprehensiveness in two primary aspects: firstly, by comprehensively reformulating SAM to a thorough 3D architecture trained on a comprehensively processed large-scale volumetric medical dataset; and secondly, by providing a comprehensive evaluation of its performance. Specifically, we train SAM-Med3D with over 131K 3D masks and 247 categories. Our SAM-Med3D excels at capturing 3D spatial information, exhibiting competitive performance with significantly fewer prompt points than the top-performing fine-tuned SAM in the medical domain. We then evaluate its capabilities across 15 datasets and analyze it from multiple perspectives, including anatomical structures, modalities, targets, and generalization abilities. Our approach, compared with SAM, showcases pronouncedly enhanced efficiency and broad segmentation capabilities for 3D volumetric medical images. Our code is released at https://github.com/uni-medical/SAM-Med3D

Geochemical characteristics and hydrocarbon generation potential of main source rocks in the Upper Triassic Xujiahe Formation, Sichuan Basin, China

In order to have a comprehensive understanding of the characterization and hydrocarbon generation potential of the source rock in the Upper Triassic Xujiahe Formation, Sichuan Basin, the geochemical data of more than 1,500 cuttings and 106 core samples were collected and analyzed. The T3x5 member of Xujiahe formation show the highest average TOC content (3.63%) followed by the T3x1+2 and T3x3 members. The TOC contents of different members show a general decreasing trend from the bottom to the top in Xujiahe formation. From the rock pyrolysis and kerogen δ13C values, the source rock trend to be kerogen type III with minor amounts of type Ⅱ2. According to the Ro values, the Xujiahe source rock shows high maturity in the northwest and low maturity in the southeast. Most of the source rock in T3x1+2 members are in high to overmature stage, while most of the source rock in the T3x3 and T3x5 member are in the mature to high mature stage. By comparing the burial history and hydrocarbon generation evolution history of source rocks in central and western Sichuan basin, it can be found that the sedimentation rate differences during the Cretaceous period is the main cause of the thermal evolution difference of the source rock. The gas generation intensity and quantity of different members are also compared. The T3x5 member show the highest gas generation potential followed by the T3x31 and the T3x1+2 members. In general, horizontally, the source rock of Xujiahe formation in Sichuan Basin is characterized by great thickness, high maturity, and high gas generation intensity in the northwest, which are gradually decrease to the southeast. Vertically, the T3x5 member show the highest gas generation content, which account for 39.6% of the total amount

Inference of drowning sites using bacterial composition and random forest algorithm

Diagnosing the drowning site is a major challenge in forensic practice, particularly when corpses are recovered from flowing rivers. Recently, forensic experts have focused on aquatic microorganisms, including bacteria, which can enter the bloodstream during drowning and may proliferate in corpses. The emergence of 16S ribosomal RNA gene (16S rDNA) amplicon sequencing has provided a new method for analyzing bacterial composition and has facilitated the development of forensic microbiology. We propose that 16S rDNA amplicon sequencing could be a useful tool for inferring drowning sites. Our study found significant differences in bacterial composition in different regions of the Guangzhou section of the Pearl River, which led to differences in bacteria of drowned rabbit lungs at different drowning sites. Using the genus level of bacteria in the lung tissue of drowned rabbits, we constructed a random forest model that accurately predicted the drowning site in a test set with 100% accuracy. Furthermore, we discovered that bacterial species endemic to the water were not always present in the corresponding drowned lung tissue. Our findings demonstrate the potential of a random forest model based on bacterial genus and composition in drowned lung tissues for inferring drowning sites

Aberrant Functional and Causal Connectivity in Acute Tinnitus With Sensorineural Hearing Loss

Purpose: The neural bases in acute tinnitus remains largely undetected. The objective of this study was to identify the alteration of the brain network involved in patients with acute tinnitus and hearing loss. Methods: Acute tinnitus patients (n = 24) with hearing loss and age-, sex-, education-matched healthy controls (n = 21) participated in the current study and underwent resting-state functional magnetic resonance imaging (fMRI) scanning. Regional homogeneity and amplitude of low-frequency fluctuation were used to investigate the local spontaneous neural activity and functional connectivity (FC), and Granger causality analysis (GCA) was used to analyze the undirected and directed connectivity of brain regions. Results: Compared with healthy subjects, acute tinnitus patients had a general reduction in FC between auditory and non-auditory brain regions. Based on FC analysis, the superior temporal gyrus (STG) revealed reduced undirected connectivity with non-auditory brain regions including the amygdala (AMYG), nucleus accumbens (NAc), the cerebellum, and postcentral gyrus (PoCG). Using the GCA algorithm, increased effective connectivity from the right AMYG to the right STG, and reduced connectivity from the right PoCG to the left NAc was observed in acute tinnitus patients with hearing loss. The pure-tone threshold was positively correlated with FC between the AMYG and STG, and negatively correlated with FC between the left NAc and the right PoCG. In addition, a negative association between the GCA value from the right PoCG to the left NAc and the THI scores was observed. Conclusion: Acute tinnitus patients have aberrant FC strength and causal connectivity in both the auditory and non-auditory cortex, especially in the STG, AMYG, and NAc. The current findings will provide a new perspective for understanding the neuropathophysiological mechanism in acute tinnitus

Sirtuin 1 and Autophagy Attenuate Cisplatin-Induced Hair Cell Death in the Mouse Cochlea and Zebrafish Lateral Line

Cisplatin-induced ototoxicity is one of the major adverse effects in cisplatin chemotherapy, and hearing protective approaches are unavailable in clinical practice. Recent work unveiled a critical role of autophagy in cell survival in various types of hearing loss. Since the excessive activation of autophagy can contribute to apoptotic cell death, whether the activation of autophagy increases or decreases the rate of cell death in CDDP ototoxicity is still being debated. In this study, we showed that CDDP induced activation of autophagy in the auditory cell HEI-OC1 at the early stage. We then used rapamycin, an autophagy activator, to increase the autophagy activity, and found that the cell death significantly decreased after CDDP injury. In contrast, treatment with the autophagy inhibitor 3-methyladenine (3-MA) significantly increased cell death. In accordance with in vitro results, rapamycin alleviated CDDP-induced death of hair cells in zebrafish lateral line and cochlear hair cells in mice. Notably, we found that CDDP-induced increase of Sirtuin 1 (SIRT1) in the HEI-OC1 cells modulated the autophagy function. The specific SIRT1 activator SRT1720 could successfully protect against CDDP-induced cell loss in HEI-OC1 cells, zebrafish lateral line, and mice cochlea. These findings suggest that SIRT1 and autophagy activation can be suggested as potential therapeutic strategies for the treatment of CDDP-induced ototoxicity

The diploid genome sequence of an Asian individual

Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual's genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J. D. Watson and J. C. Venter), and structural variation identification. These variations were considered for their potential biological impact. Our sequence data and analyses demonstrate the potential usefulness of next-generation sequencing technologies for personal genomics

Does Farmland Size Affect the Collective Action in Rural Areas? An Empirical Study on the Public Irrigation System in China

Since smallholders accounted for a high proportion of 98.1% among the 207 million agricultural business households across China, it is particularly important to study the impact of farmland size on the provision of public goods attached to the public sector industries from the perspective of the irrigation collective action in rural areas. Based on the survey data of 283 villages in China, this paper finds that the farmland size has a positive impact on irrigation collective action, although the average of per capita farmland area is only 0.214 hectares in each household of China. Therefore, it is necessary to promote the farmland scale operation by land circulation, so as to improve the ability of collective action and the development of public sector industries in rural areas of China