YeastWeb: a workset-centric web resource for gene family analysis in yeast

<p>Abstract</p> <p>Background</p> <p>Currently, a number of yeast genomes with different physiological features have been sequenced and annotated, which provides invaluable information to investigate yeast genetics, evolutionary mechanism, structure and function of gene families.</p> <p>Description</p> <p>YeastWeb is a novel database created to provide access to gene families derived from the available yeast genomes by assigning the genes into putative families. It has many useful features that complement existing databases, such as SGD, CYGD and Génolevures: 1) Detailed computational annotation was conducted with each entry with InterProScan, EMBOSS and functional/pathway databases, such as GO, COG and KEGG; 2) A well established user-friendly environment was created to allow users to retrieve the annotated genes and gene families using functional classification browser, keyword search or similarity-based search; 3) Workset offers users many powerful functions to manage the retrieved data efficiently, associate the individual items easily and save the intermediate results conveniently; 4) A series of comparative genomics and molecular evolution analysis tools are neatly implemented to allow users to view multiple sequence alignments and phylogenetic tree of gene families. At present, YeastWeb holds the gene families clustered from various MCL inflation values from a total of 13 available yeast genomes.</p> <p>Conclusions</p> <p>Given the great interest in yeast research, YeastWeb has the potential to become a useful resource for the scientific community of yeast biologists and related researchers investigating the evolutionary relationship of yeast gene families. YeastWeb is available at <url>http://centre.bioinformatics.zj.cn/Yeast/</url>.</p

Temporal transcriptome profiling of developing seeds reveals a concerted gene regulation in relation to oil accumulation in Pongamia (Millettia pinnata)

Background Pongamia (Millettia pinnata syn. Pongamia pinnata), an oilseed legume species, is emerging as potential feedstock for sustainable biodiesel production. Breeding Pongamia for favorable traits in commercial application will rely on a comprehensive understanding of molecular mechanism regulating oil accumulation during its seed development. To date, only limited genomic or transcript sequences are available for Pongamia, while a temporal transcriptome profiling of developing seeds is still lacking in this species. Results In this work, we conducted a time-series analysis of morphological and physiological characters, oil contents and compositions, as well as global gene expression profiles in developing Pongamia seeds. Firstly, three major developmental phases were characterized based on the combined evidences from embryonic shape, seed weight, seed moisture content, and seed color. Then, the gene expression levels at these three phases were quantified by RNA-Seq analyses with three biological replicates from each phase. Nearly 94% of unigenes were expressed at all three phases, whereas only less than 2% of unigenes were exclusively expressed at one of these phases. A total of 8881 differentially expressed genes (DEGs) were identified between phases. Furthermore, the qRT-PCR analyses for 10 DEGs involved in lipid metabolism demonstrated a good reliability of our RNA-Seq data in temporal gene expression profiling. We observed a dramatic increase in seed oil content from the embryogenesis phase to the early seed-filling phase, followed by a steady and moderate increase towards the maximum at the desiccation phase. We proposed that a highly active expression of most genes related to fatty acid (FA) and triacylglycerol (TAG) biosynthesis at the embryogenesis phase might trigger both the substantial oil accumulation and the membrane lipid synthesis for rapid cell proliferation at this phase, while a concerted reactivation of TAG synthesis-related genes at the desiccation phase might further promote storage lipid synthesis to achieve the maximum content of seed oils. Conclusions This study not only built a bridge between gene expression profiles and oil accumulation in developing seeds, but also laid a foundation for future attempts on genetic engineering of Pongamia varieties to acquire higher oil yield or improved oil properties for biofuel applications

Pre‐symptomatic transmission of novel coronavirus in community settings

We used contact tracing to document how COVID‐19 was transmitted across 5 generations involving 10 cases, starting with an individual who became ill on January 27. We calculated the incubation period of the cases as the interval between infection and development of symptoms. The median incubation period was 6.0 days (interquartile range, 3.5‐9.5 days). The last two generations were infected in public places, 3 and 4 days prior to the onset of illness in their infectors. Both had certain underlying conditions and comorbidity. Further identification of how individuals transmit prior to being symptomatic will have important consequences.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/163478/2/irv12773.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/163478/1/irv12773_am.pd

Qwen Technical Report

Large language models (LLMs) have revolutionized the field of artificial intelligence, enabling natural language processing tasks that were previously thought to be exclusive to humans. In this work, we introduce Qwen, the first installment of our large language model series. Qwen is a comprehensive language model series that encompasses distinct models with varying parameter counts. It includes Qwen, the base pretrained language models, and Qwen-Chat, the chat models finetuned with human alignment techniques. The base language models consistently demonstrate superior performance across a multitude of downstream tasks, and the chat models, particularly those trained using Reinforcement Learning from Human Feedback (RLHF), are highly competitive. The chat models possess advanced tool-use and planning capabilities for creating agent applications, showcasing impressive performance even when compared to bigger models on complex tasks like utilizing a code interpreter. Furthermore, we have developed coding-specialized models, Code-Qwen and Code-Qwen-Chat, as well as mathematics-focused models, Math-Qwen-Chat, which are built upon base language models. These models demonstrate significantly improved performance in comparison with open-source models, and slightly fall behind the proprietary models.Comment: 59 pages, 5 figure

A Distance-Aware Safety-Related Message Broadcasting Algorithm for Vehicular Networks

A new distance-aware broadcasting algorithm was proposed to enhance the propagation distance in the latency time of safety-related message broadcasting. The IEEE 802.11p standard states that if the medium is detected as idle, a station would defer its transmission within a backoff time to avoid collisions with other stations. The backoff times follow uniform distribution over [0, CW ]. In this way, fairness among all the stations can be guaranteed. However, propagation distance was ignored and in safety-related message broadcasting fairness is not the most important issue. In the proposed algorithm, the lengths of backoff times are generated from a nonuniform distribution. They are related with the distances between the source station and its forwarding stations. The farthest forwarding station has the highest probability to forward messages. Performance of the proposed algorithm is analyzed by using a 2D Markov chain. Analytical and simulation results demonstrate that the proposed algorithm can enhance the performance of safety-related message broadcasting in terms of propagation distance, which is reflected by the successful transmission probability. The proposed algorithm does not need additional waiting time, RTS/CTS, and ACK, therefore having better compatibility with the IEEE 802.11p standard than earlier distance-aware algorithms

Parental knowledge, attitudes, and practices towards childhood fever among South-East and East Asian parents: A literature review.

AimThe aim of this literature review was to identify, summarize, and critically appraise available empirical articles on the knowledge, attitudes, and practices towards childhood fever management among South-East and East Asian parents.DesignA literature review following PRISMA.MethodsArticles were limited to those available in the English language. Articles had to be empirical studies that used a qualitative or quantitative research design with full-text available; focus on parental knowledge, attitudes, and practices towards fever; and be published in South-East and East Asia. Searches were conducted with CINAHL, PubMed and Scopus from inception to June 2022, and eleven articles were included after removing duplicates and excluding irrelevant articles.ResultsNarrative synthesis was conducted according to four themes: source of fever information, knowledge level, attitudes, and practices towards childhood fever. Parents showed different fever knowledge needs and various information-seeking behaviors. A low level of fever knowledge was revealed in terms of temperature, fever causes, potential harms and influencing factors. South-East and East Asian parents mainly reported anxiety, concerns and fever phobia. Fever assessment methods and fever management strategies varied based on parents' cultural background and beliefs.ConclusionsThe findings of this review highlight that inadequacy of fever knowledge and negative attitudes towards childhood fever exist in South-East and East Asian parents. Parents have diverse cultural practices during their children's febrile episodes. However, some of them conflict with current medical guidelines, as they prioritize fever and body temperature reduction. This raises questions about their effectiveness and safety. Although some of them are medically discouraged, there are others that have been proven beneficial for the symptomatic relief of childhood fever. The results indicate an urgent need to develop a cultural-sensitive educational intervention for childhood fever management among South-East and East Asian parents. Unified educational interventions are needed to address parental concerns and fever-related knowledge needs

Effects of acceptance and commitment therapy on fatigue interference in patients with advanced lung cancer and caregiving burden: protocol for a pilot randomised controlled trial

Introduction Cancer-related fatigue is common in patients with advanced lung cancer. It not only interferes with patients’ health-related quality of life, but also increases the caregiving burden of their caregivers. Acceptance and commitment therapy is emerging as a novel way to advocate accepting negative experiences and taking effective actions based on their own values to help patients commit meaningful actions in the course of cancer diseases. This trial aims to test the feasibility, acceptability and preliminary effects of acceptance and commitment therapy for fatigue interference in patients with advanced lung cancer and the caregiver burden.Method and analysis A two-arm, assessor-blind pilot randomised controlled trial will be conducted. A total of 40 advanced lung cancer patient–caregiver dyads, who live in rural areas, will be recruited from a university-affiliated hospital in central China. The participants will be randomised to receive an online six-session acceptance and commitment therapy (i.e. involving metaphors, experiential exercises and mindfulness exercises facilitated by virtual reality technology) plus health education (intervention group, n=20) or health education (control group, n=20). Outcomes will be measured at baseline and 1 week postintervention. The primary outcomes are study feasibility (i.e. eligibility rate, recruitment rate, attrition rate and adherence rate), fatigue interference and caregiver burden. The secondary outcomes are health-related quality of life, meaning in life, psychological flexibility and mindful attention. Semistructured interviews will be conducted to explore the feasibility and experiences of the intervention in a subsample of 10 participants from the intervention group.Ethics and dissemination This study has been approved by the Joint Chinese University of Hong Kong-New Territories East Cluster Clinical Research Ethics Committee (CREC Ref. No. 2023.030) and the Medical Ethics Committee of Xiangya Hospital Central South University (No. 202305336). The findings will be disseminated in peer-reviewed journals and through local or international conference presentations.Trial registration number NCT05885984

Translation and validation of the Chinese version of the acceptance and action questionnaire for cancer in patients with advanced lung cancer

Objective: This study aimed to examine the reliability and validity of the Chinese version of the Acceptance and Action Questionnaire for Cancer (C-AAQ–Cancer) in patients with advanced lung cancer. Methods: In Phase I, the AAQ-Cancer was translated from English to Chinese. In Phase II, an expert panel was invited to examine the content validity of the translated instrument, and pilot testing was performed. In Phase III, a total of 200 patients with advanced lung cancer from a university-affiliated hospital in central China were recruited to test the construct validity of the translated AAQ-Cancer using exploratory factor analysis, and reliability was assessed based on internal consistency and test–retest reliability. Results: The semantic equivalence and content validity index of the C-AAQ–Cancer were satisfactory. Exploratory factor analysis indicated that the C-AAQ–Cancer contained the following five subscales: cancer concerns, blunting, blame, distancing, and behavioral disengagement. These subscales explain 68.28% of the total variance. The Cronbach's α coefficient of the scale was 0.87, and the test–retest reliability was 0.839. Conclusions: This study evaluated the psychometric properties of the C-AAQ–Cancer. The findings support the reliability and validity of this instrument in evaluating experiential avoidance or acceptance levels in patients with advanced lung cancer

Effects of various extraocular muscle enlargement patterns on muscle diameter index in graves ophthalmopathy patients: a retrospective cohort study

Abstract Graves ophthalmopathy (GO) patients often undergo retrobulbar injection of glucocorticoids (GCs) as a common therapeutic approach. This study aimed to explore the impact of various patterns of extraocular muscle (EOM) enlargement on EOM changes following retrobulbar GCs injection in patients with GO. A retrospective analysis was conducted on GO patients who underwent retrobulbar GCs injections. Data pertaining to EOM diameter (EMD) and muscle diameter index (MDI) were collected from orbital computed tomography (CT) scans. The MDI change (ΔMDI) was calculated by comparing pre- and post-injection MDI values. The relationship between each pre EMD/MDI and ΔMDI was assessed using univariate and multivariate logistic regression analysis. A total of 68 patients with GO were included in this study, accounting for 118 eyes. After retrobulbar injections of GCs, 84 eyes showed a decrease in the MDI, while 34 eyes exhibited an increase in MDI. A threshold effect was observed in the relationship between medial pre EMD/MDI and ΔMDI. When the medial pre EMD/MDI was less than 0.28, a higher medial pre EMD/MDI was associated with a smaller ΔMDI (β = − 25.21, p = 0.0175). However, when the medial pre EMD/MDI was greater than 0.28, no significant association was found between pre EMD/MDI and ΔMDI. There was a negative correlation between medial + lateral pre EMD/MDI and ΔMDI (β = − 11.76, p < 0.0189). A higher medial + lateral pre EMD/MDI was associated with a greater decrease in MDI. Additionally, there was a positive correlation between superior rectus muscle-levator complex (SRLC) pre EMD/MDI and ΔMDI (β = 11.92, p = 0.040). The higher the value of SRLC pre EMD/MDI, the greater the ΔMDI. There was an association between pre EMD/MDI and changes in EOMs after retrobulbar injection of GCs in GO patients. In patients with predominantly enlarged medial rectus muscles and severe degrees of enlargement, retrobulbar injection of GCs should be assessed for its benefit; a combination of medial and lateral rectus muscle enlargement is beneficial for the shrinkage of EOMs following retrobulbar injections; the involvement of the SRLC rectus muscle may be a disadvantageous pattern of shrinkage of EOMs following retrobulbar injections. Trial registration This study is retrospectively registered. We have registered this study with the Chinese Clinical Trials Registry ( www.chictr.org.cn , registration number: ChiCTR2200063429)