Haplotype-resolved genome assembly plays a crucial role in understanding allele-specific functions. However, obtaining haplotype-resolved assembly for auto-polyploid genomes remains challenging. ...Existing methods can be classified into reference-based phasing, assembly-based phasing, and gamete binning. Nevertheless, there is a lack of cost-effective and efficient methods for haplotyping auto-polyploid genomes. In this study, we propose a novel phasing algorithm called PolyGH, which combines Hi-C and gametic data. We conducted experiments on tetraploid potato cultivars and divided the method into three steps. Firstly, gametic data was utilized to bin non-collapsed contigs, followed by merging adjacent fragments of the same type within the same contig. Secondly, accurate Hi-C signals related to differential genomic regions were acquired using unique k-mers. Finally, collapsed fragments were assigned to haplotigs based on combined Hi-C and gametic signals. Comparing PolyGH with Hi-C-based and gametic data-based methods, we found that PolyGH exhibited superior performance in haplotyping auto-polyploid genomes when integrating both data types. This approach has the potential to enhance haplotype-resolved assembly for auto-polyploid genomes.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
PRECIS:Phacoemulsification with goniosynechialysis under an ophthalmic endoscope (Phaco-OE-GSL) is safe and able to lowering intraocular pressure (IOP) for failed trabeculectomy in primary ...angle-closure glaucoma with cataract. The larger pupil diameter and younger age are identified as the 2 risk factors for surgical outcome.
PURPOSE:To investigate the efficacy and safety of combined Phaco-OE-GSL for primary angle-closure glaucoma with cataract after failed trabeculectomy.
MATERIALS AND METHODS:Twenty-five patients (25 eyes) were enrolled in this retrospective study. IOP, best-corrected visual acuity, and number of glaucoma medications at baseline and each postoperative follow-up visit were recorded. Peripheral anterior synechia (PAS) was recorded using gonioscopy. Binary logistic regression was used to analyze the risk factors of surgical failure.
RESULTS:The mean follow-up duration was 17.9±11.4 months. The mean IOP was significantly lower than the preoperative baseline IOP at all time points (P<0.001). The mean IOP was reduced from 24.4±6.5 mm Hg at baseline to 14.2±3.0 mm Hg at the last follow-up. The mean preoperative number of glaucoma medications was 2.2±1.2, which reduced to 0.9±1.1 at the last follow-up. The complete success rates at 1 year and the last follow-up were 70.6% and 68%, respectively. The total success rates were 96% and 92%, respectively. The most common postoperative complications were IOP spikes (48%) and hyphemas (32%). All eyes had degrees of PAS recurrence, with a range of 96.1±52.5 degrees (30 to 210 degrees) after 4 to 6 months. Larger pupil diameter and younger age were significantly associated with the failure of Phaco-OE-GSL.
CONCLUSIONS:Phaco-OE-GSL is safe and can lower IOP for failed trabeculectomy in PACG with cataract despite the high recurrence rate of PAS.
The rapid growth of China's economy has greatly accelerated the process of urbanization during China's reform periods. Urbanization has significantly caused land use and land cover (LULC) changes and ...thus has impacts on the local climate and ecosystem. This study chooses Quanzhou, a fast-developing city of southeast China, as an example to detect and quantify the LULC and ecological changes from 1989 to 2018 by using the remotely sensed technique. The LULC of Quanzhou was derived from the four Landsat images taken in 1989, 1999, 2007 and 2018, and the land-use-degree ratio index and land-use-change method were used to estimate the change of land use. The remote sensing based ecological index (RSEI) was used to detect the ecological changes of the city. The built-up land expansion intensity and annual built-up land expansion rate were carried out for seven districts of Quanzhou. The results show that the urban area of Quanzhou has drastically grown by 192.99 km2 at the expense of forest, water, and cropland land during the 1989~2018 period. Moreover, the built-up land of seven districts had expanded at the average rate of 0.027~0.154 per year and the built-up expansion intensity was higher than 0.59. The average RSEI value of Quanzhou city dropped from 0.78 in 1989 to 0.34 in 2018, which suggested an overall decline in ecological quality. The proportion of areas with an RSEI rating good decreased from 30.84% to 11.52% while the proportion of areas with rating bad increased from 4.73% to 19.11% during the past 29 years. This study has shown the built-up land expansion intensity is negatively correlated with the ecological quality change, and the increase in built-up land can greatly accelerate the decline of the ecological quality. Government policies play a profound impact on land use changes, urbanization and eco-environment changes. Therefore, the policy decision-makers should take enough action and consider integrating the concept of ecology to enable the healthy and sustainable development of the city.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
As current trend for physician tools, ChatGPT can sift through massive amounts of information and solve problems through easy-to-understand conversations, ultimately improving efficiency. Mycosis is ...currently facing great challenges, including high fungal burdens, high mortality, limited choice of antifungal drugs and increasing drug resistance. To address these challenges, We asked ChatGPT for fungal infection scenario-based questions and assessed its appropriateness, consistency, and potential pitfalls. We concluded ChatGPT can provide compelling responses to most prompts, including diagnosis, recommendations for examination, treatment and rational drug use. Moreover, we summarized exciting future applications in mycosis, such as clinical work, scientific research, education and healthcare. However, the largest barriers to implementation are deficits in indiviudal advice, timely literature updates, consistency, accuracy and data safety. To fully embrace the opportunity, we need to address these barriers and manage the risks. We expect that ChatGPT will become a new weapon in in the battlefield of mycosis.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The global burden of invasive fungal infections (IFIs) has shown an upsurge in recent years due to the higher load of immunocompromised patients suffering from various diseases. The role of early and ...accurate diagnosis in the aggressive containment of the fungal infection at the initial stages becomes crucial thus, preventing the development of a life-threatening situation. With the changing demands of clinical mycology, the field of fungal diagnostics has evolved and come a long way from traditional methods of microscopy and culturing to more advanced non-culture-based tools. With the advent of more powerful approaches such as novel PCR assays, T2 Candida, microfluidic chip technology, next generation sequencing, new generation biosensors, nanotechnology-based tools, artificial intelligence-based models, the face of fungal diagnostics is constantly changing for the better. All these advances have been reviewed here giving the latest update to our readers in the most orderly flow.
A detailed literature survey was conducted by the team followed by data collection, pertinent data extraction, in-depth analysis, and composing the various sub-sections and the final review. The review is unique in its kind as it discusses the advances in molecular methods; advances in serology-based methods; advances in biosensor technology; and advances in machine learning-based models, all under one roof. To the best of our knowledge, there has been no review covering all of these fields (especially biosensor technology and machine learning using artificial intelligence) with relevance to invasive fungal infections.
The review will undoubtedly assist in updating the scientific community's understanding of the most recent advancements that are on the horizon and that may be implemented as adjuncts to the traditional diagnostic algorithms.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Due to the high complexity of cancer genome, it is too difficult to generate complete cancer genome map which contains the sequence of every DNA molecule until now. Nevertheless, phasing each ...chromosome in cancer genome into two haplotypes according to germline mutations provides a suboptimal solution to understand cancer genome. However, phasing cancer genome is also a challenging problem, due to the limit in experimental and computational technologies. Hi-C data is widely used in phasing in recent years due to its long-range linkage information and provides an opportunity for solving the problem of phasing cancer genome. The existing Hi-C based phasing methods can not be applied to cancer genome directly, because the somatic mutations in cancer genome such as somatic SNPs, copy number variations and structural variations greatly reduce the correctness and completeness. Here, we propose a new Hi-C based pipeline for phasing cancer genome called HICANCER. HICANCER solves different kinds of somatic mutations and variations, and take advantage of allelic copy number imbalance and linkage disequilibrium to improve the correctness and completeness of phasing. According to our experiments in K562 and KBM-7 cell lines, HICANCER is able to generate very high-quality chromosome-level haplotypes for cancer genome with only Hi-C data.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Alzheimer’s disease (AD) is a chronic degenerative disease in the central nervous system and circular RNAs (circRNAs) are identified as essential regulators in AD. The current research was designed ...for exploration of circ_0003611 in AD. Circ_0003611 was overexpressed in AD patients and Aβ-treated SK-N-SH cells. Aβ-induced apoptotic, inflammatory and oxidative damages were relieved after knockdown of circ_0003611. MiR-885-5p was validated as a miRNA target of circ_0003611. The protective function of circ_0003611 downregulation was achieved by releasing miR-885-5p in Aβ-treated SK-N-SH cells. KREMEN1 was a downstream gene of miR-885-5p. Overexpression of miR-885-5p attenuated the Aβ-triggered cell injury by reducing the KREMEN1 expression. KREMEN1 was regulated by circ_0003611 via sponging miR-885-5p in Aβ-treated SK-N-SH cells. These experimental data demonstrated that circ_0003611 enhanced the Aβ-induced neuronal cell injury in AD by serving as the miR-885-5p sponge to regulate the level of KREMEN1.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Objectives
It is challenging to early differentiate biliary atresia from other causes of cholestasis. We aimed to develop an algorithm with risk stratification to distinguish biliary atresia from ...infantile cholestasis.
Methods
In this study, we enrolled infants with cholestasis into 2 subgroups from January 2010 to April 2019. A prospective cohort (subgroup 2) of 187 patients (107 with biliary atresia and 80 without biliary atresia) underwent acoustic radiation force impulse elastography. Stepwise regression was used to identify significant predictors of biliary atresia. A sequential algorithm with risk stratification was constructed.
Results
Among 187 patients, shear wave speed > 1.35 m/s and presence of the triangular cord sign were considered high risk for biliary atresia (red), in which 73 of 78 patients (accuracy of 93.6%) with biliary atresia were identified. Afterwards, γ-GT, abnormal gallbladder, and clay stool were introduced into the algorithm and 55 intermediate-risk infants were identified (yellow) with a diagnostic accuracy of 60% for biliary atresia. Of the remaining 54 infants who were classified as low-risk patients (green), the accuracy for excluding biliary atresia was 98.1%. By applying a three-color risk stratification tool, 70.6% patients were identified as either high risk or low risk for biliary atresia (area under the curve, 0.983; sensitivity, 98.7%; specificity, 91.4%). We also estimated the risk of biliary atresia in different color groups, which was 94.7% (95%CI, 94.3–95.5%) in the red group and 7.2% (95%CI, 6.6–8.3%) in the green group.
Conclusions
Our simple noninvasive approach was able to identify biliary atresia with high accuracy.
Key Points
• Five predictors, namely shear wave speed, triangle cord sign, γ-glutamyl transferase, abnormal gallbladder, and clay stool, were selected to identify biliary atresia in cholestasis.
• Shear wave speed > 1.35 m/s and presence of the triangle cord sign were considered high-risk patients with a diagnostic accuracy of 93.6% for biliary atresia.
• Risk for biliary atresia was high (red), intermediate (yellow), or low (green). In the red and green group, we achieved an extremely high diagnostic performance (area under the curve, 0.983; sensitivity, 98.7%; specificity, 91.4%).
assembly plays a pivotal role in metagenomic analysis, and the incorporation of third-generation sequencing technology can significantly improve the integrity and accuracy of assembly results. ...Recently, with advancements in sequencing technology (Hi-Fi, ultra-long), several long-read-based bioinformatic tools have been developed. However, the validation of the performance and reliability of these tools is a crucial concern. To address this gap, we present MCSS (microbial community simulator based on structure), which has the capability to generate simulated microbial community and sequencing datasets based on the structure attributes of real microbiome communities. The evaluation results indicate that it can generate simulated communities that exhibit both diversity and similarity to actual community structures. Additionally, MCSS generates synthetic PacBio Hi-Fi and Oxford Nanopore Technologies (ONT) long reads for the species within the simulated community. This innovative tool provides a valuable resource for benchmarking and refining metagenomic analysis methods.
https://github.com/panlab-bio/mcss.
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