Evaluation of simulation methods for tumor subclonal reconstruction

Most neoplastic tumors originate from a single cell, and their evolution can be genetically traced through lineages characterized by common alterations such as small somatic mutations (SSMs), copy number alterations (CNAs), structural variants (SVs), and aneuploidies. Due to the complexity of these alterations in most tumors and the errors introduced by sequencing protocols and calling algorithms, tumor subclonal reconstruction algorithms are necessary to recapitulate the DNA sequence composition and tumor evolution in silico. With a growing number of these algorithms available, there is a pressing need for consistent and comprehensive benchmarking, which relies on realistic tumor sequencing generated by simulation tools. Here, we examine the current simulation methods, identifying their strengths and weaknesses, and provide recommendations for their improvement. Our review also explores potential new directions for research in this area. This work aims to serve as a resource for understanding and enhancing tumor genomic simulations, contributing to the advancement of the field

Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture

The archaic ancestry present in the human genome has captured the imagination of both scientists and the wider public in recent years. This excitement is the result of new studies pushing the envelope of what we can learn from the archaic genetic information that has survived for over 50,000 years in the human genome. Here, we review the most recent ten years of literature on the topic of archaic introgression, including the current state of knowledge on Neanderthal and Denisovan introgression, as well as introgression from other as-yet unidentified archaic populations. We focus this review on four topics: 1) a reimagining of human demographic history, including evidence for multiple admixture events between modern humans, Neanderthals, Denisovans, and other archaic populations; 2) state-of-the-art methods for detecting archaic ancestry in population-level genomic data; 3) how these novel methods can detect archaic introgression in modern African populations; and 4) the functional consequences of archaic gene variants, including how those variants were co-opted into novel function in modern human populations. The goal of this review is to provide a simple-to-access reference for the relevant methods and novel data, which has changed our understanding of the relationship between our species and its siblings. This body of literature reveals the large degree to which the genetic legacy of these extinct hominins has been integrated into the human populations of today. &nbsp;</p

Effect of continuous glucose monitoring compared with self-monitoring of blood glucose in gestational diabetes patients with HbA1c<6%: a randomized controlled trial

ObjectiveThis study evaluated the effect of continuous glucose monitoring (CGM) versus self-monitored blood glucose (SMGB) in gestational diabetes mellitus (GDM) with hemoglobin A1c (HbA1c) &lt;6%.MethodsFrom January 2019 to February 2021, 154 GDM patients with HbA1c&lt;6% at 24–28 gestational weeks were recruited and assigned randomly to either SMBG only or CGM in addition to SMBG, with 77 participants in each group. CGM was used in combination with fingertip blood glucose monitoring every four weeks until antepartum in the CGM group, while in the SMBG group, fingertip blood glucose monitoring was applied. The CGM metrics were evaluated after 8 weeks, HbA1c levels before delivery, gestational weight gain (GWG), adverse pregnancy outcomes and CGM medical costs were compared between the two groups.ResultsCompared with patients in the SMBG group, the CGM group patients had similar times in range (TIRs) after 8 weeks (100.00% (93.75-100.00%) versus 99.14% (90.97-100.00%), p=0.183) and HbA1c levels before delivery (5.31 ± 0.06% versus 5.35 ± 0.06%, p=0.599). The proportion with GWG within recommendations was higher in the CGM group (59.7% versus 40.3%, p=0.046), and the newborn birth weight was lower (3123.79 ± 369.58 g versus 3291.56 ± 386.59 g, p=0.015). There were no significant differences in prenatal or obstetric outcomes, e.g., cesarean delivery rate, hypertensive disorders, preterm births, macrosomia, hyperbilirubinemia, neonatal hypoglycemia, respiratory distress, and neonatal intensive care unit admission &gt;24 h, between the two groups. Considering glucose monitoring, SMBG group patients showed a lower cost than CGM group patients.ConclusionsFor GDM patients with HbA1c&lt;6%, regular SMBG is a more economical blood glucose monitoring method and can achieve a similar performance in glycemic control as CGM, while CGM is beneficial for ideal GWG

Disrupted Cerebellar Connectivity With the Central Executive Network and the Default-Mode Network in Unmedicated Bipolar II Disorder

Objective: Bipolar disorder (BD) is a common psychiatric disease. Although structural and functional abnormalities of the cerebellum in BD patients have been reported by recent neuroimaging studies, the cerebellar-cerebral functional connectivity (FC) has not yet been examined. The present study aims to investigate the FC between the cerebellum and cerebrum, particularly the central executive network (CEN) and the default-mode network (DMN) in bipolar II disorder (BD II).Methods: Ninety-four patients with unmedicated BD II depression and 100 healthy controls (HCs) underwent the resting-state functional magnetic resonance imaging. Seed-based connectivity analyses were performed using cerebellar seeds previously identified as being involved in the CEN (bilateral Crus Ia) and DMN (bilateral Crus Ib).Results: Compared with HCs, BD II depression patients appeared decreased FC in the right Crus Ia-left dorsal lateral prefrontal cortex (dlPFC) and -left anterior cingulate cortex (ACC), the right Crus Ib-left medial prefrontal cortex (mPFC), -left middle temporal gyrus (MTG), and -left inferior temporal gyrus (ITG). No altered FC between the left Crus Ia or Crus Ib and the cerebral regions was found.Conclusions: Patients with BD II depression showed disrupted FC between the cerebellum and the CEN (mainly in the left dlPFC and ACC) and DMN (mainly in the left mPFC and temporal lobe), suggesting the significant role of the cerebellum-CEN and -DMN connectivity in the pathogenesis of BD

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Pronunciation/annotation & evaluation tool

This report presents the development of the pronunciation/annotation & evaluation tool for linguistics transcribers from School of Humanities and Social Sciences. The process of manually transcribing the corpus can be very tedious and time consuming. On top of that, transcribers might also experience some difficulties in operating the functions in those online free speech annotation tools such as Praat. Therefore, our tool is developed to automatically do segmentation and generate the corpus transcriptions needed for linguistic students. It also provides all the possible phonemes and IPA symbols for them to consider when doing transcriptions of the recorded speech. In summary, this tool helps to speed up the process of transcribing, allows users to view, add or delete multiple pronunciation variations in the lexicon and evaluates the performance of HTK segmentation.Bachelor of Engineering (Computer Science

Factors influencing the rate of diffusion of innovative products.

The objective of this paper is to study factors affecting the rate of diffusion of innovative products where we studied the adoption of camera-integrated mobile phone. We used the Roger's diffusion theory as background and analyzed the factors relating to Marketing Mix, 4Ps to extend Roger's research

Zinc Oxide Nanoparticles Enhanced Growth of Tea Trees via Modulating Antioxidant Activity and Secondary Metabolites

Nano-fertilizer has been dubbed ‘the fertilizer of the 21st century’, and it is already being used extensively in agriculture. Zinc oxide nanoparticles (ZnO-NPs) have excellent biological properties and are expected to be an ideal choice for plant zinc fertilizer. Tea is one of the top three beverages in the world, and improving the quality of tea is a priority in its research field. In this study, different concentrations (0, 10, 50, 100, 150, and 200 mg·L−1) of ZnO-NPs were sprayed on tea leaves to investigate their effects on volatile aroma substances and biochemical aspects of tea leaves. The results revealed that various concentrations of ZnO-NPs had different effects on physiological indexes. The concentration of 150 mg·L−1 of ZnO-NPs enhanced chlorophyll content, while the 100 mg·L−1 concentration of ZnO-NPs promoted the accumulation of soluble proteins and the activity of antioxidant enzymes, including a decrease in the content of malondialdehyde. In addition, the ZnO-NPs spray reduced the content of tea polyphenols. A total of 27 volatiles were identified under six treatments, with benzene being the common compound with an average content of 45.97%. Ethanolamine and cis-3-hexenyl acetate were the other two major compounds. It was concluded that the presence of ZnO-NPs improved the antioxidant system of teas, increased soluble protein content and provided better reactive oxygen species protection for plants, especially in the case of ZnO-NPs at 100 mg·L−1. We highlighted that ZnO-NPs application was a favorable way to improve tea trees growth

Comparison of treatment strategies for resectable locally advanced primary mucinous adenocarcinoma of the lung

Abstract Background Primary pure mucinous adenocarcinoma (PMA) is a rare type of lung cancer with unique clinical and prognostic features. Previous studies have shown that PMA have more early‐stage cancer compared with other adenocarcinoma (ADC) subtypes. The clinicopathological features and optimal treatment strategies of resectable locally advanced mucinous adenocarcinoma lack evidence and require further study. Methods In this study, we collected information from patients with stage III‐N2 PMA who underwent radical surgery between 2004 and 2016 from the Surveillance, Epidemiology, and End Results (SEER) database. The clinicopathological parameters, treatments, overall survival (OS), and cancer‐specific survival (CSS) were evaluated. Results Of 242,699 eligible lung adenocarcinoma patients, 124 with PMA and 3405 with other ADCs of stage III‐N2 received radical surgery were identified. Compared with other ADCs, PMA tended to appear more in the lower lobes, with higher degree of differentiation, less early T stage, and more positive lymph nodes numbers. Patients with PMA had significantly worse survival than other ADCs (OS = 45.0 vs. 57.1 months, p = 0.005, CSS = 51.8 vs. 65.5 months, p = 0.017). We explored the benefit population of postoperative radiotherapy (PORT) and found that the population with ≤7 positive lymph nodes could benefit from PORT, and OS was significantly improved (41.2 vs. 69.3 months, p = 0.034). For patients with >7 positive lymph nodes, PORT did not provide a survival benefit, while chemotherapy improved OS (10.9 vs. 23.3 months, p = 0.041). Multivariate analysis showed that race, tumor location, number of positive lymph nodes, and PORT were independent prognostic factors in patients with postoperative III‐N2 lung PMA. Conclusion The prognosis of patients with resectable III‐N2 primary lung PMA was significantly worse than that of other ADCs, and PORT was an independent prognostic factor. Patients with ≤7 positive lymph nodes could benefit from PORT and those with >7 positive lymph nodes could benefit from chemotherapy

Study on the Roles of Water in Solid Amine-Based Direct Air Capture of CO

Climate change triggered by the increasing amount of CO2 released into the atmosphere has become a global priority. Direct Air Capture (DAC) of CO2 has been regarded as one of the disruptive technologies to realize negative emission. Among the multiple strategies employed, adsorption on solid amines is a promising choice owing to its low energy requirements. Since the water vapor ubiquitously exists in ambient air, understanding the role it plays in DAC by the amine-functionalized solid sorbents is of vital importance. Due to the diversity in amine and support features, both promotion and deterioration of water impact on CO2 adsorption were revealed. Herein we present a multifaceted review of the trends and innovations in DAC by solid amines under humid conditions. The effect of water was discussed over four groups of materials, based on the support categories, i.e., (a) mesoporous silica, (b) mesoporous alumina, (c) mesoporous carbon and other inorganic supports, and (d) cellulose and other organic supports