Utility analyses of AVITI sequencing chemistry.

BACKGROUND: DNA sequencing is a critical tool in modern biology. Over the last two decades, it has been revolutionized by the advent of massively parallel sequencing, leading to significant advances in the genome and transcriptome sequencing of various organisms. Nevertheless, challenges with accuracy, lack of competitive options and prohibitive costs associated with high throughput parallel short-read sequencing persist. RESULTS: Here, we conduct a comparative analysis using matched DNA and RNA short-reads assays between Element Biosciences' AVITI and Illumina's NextSeq 550 chemistries. Similar comparisons were evaluated for synthetic long-read sequencing for RNA and targeted single-cell transcripts between the AVITI and Illumina's NovaSeq 6000. For both DNA and RNA short-read applications, the study found that the AVITI produced significantly higher per sequence quality scores. For PCR-free DNA libraries, we observed an average 89.7% lower experimentally determined error rate when using the AVITI chemistry, compared to the NextSeq 550. For short-read RNA quantification, AVITI platform had an average of 32.5% lower error rate than that for NextSeq 550. With regards to synthetic long-read mRNA and targeted synthetic long read single cell mRNA sequencing, both platforms' respective chemistries performed comparably in quantification of genes and isoforms. The AVITI displayed a marginally lower error rate for long reads, with fewer chemistry-specific errors and a higher mutation detection rate. CONCLUSION: These results point to the potential of the AVITI platform as a competitive candidate in high-throughput short read sequencing analyses when juxtaposed with the Illumina NextSeq 550.

TIM22 and TIM29 inhibit HBV replication by up-regulating SRSF1 expression.

Hepatitis B virus (HBV) infection is a serious global health problem. After the viruses infect the human body, the host can respond to the virus infection by coordinating various cellular responses, in which mitochondria play an important role. Evidence has shown that mitochondrial proteins are involved in host antiviral responses. In this study, we found that the overexpression of TIM22 and TIM29, the members of the inner membrane translocase TIM22 complex, significantly reduced the level of intracellular HBV DNA and RNA and secreted HBV surface antigens and E antigen. The effects of TIM22 and TIM29 on HBV replication and transcription is attributed to the reduction of core promoter activity mediated by the increased expression of SRSF1 which acts as a suppressor of HBV replication. This study provides new evidence for the critical role of mitochondria in the resistance of HBV infection and new targets for the development of treatment against HBV infection.

Impact of different CEBPA mutations on therapeutic outcome in acute myeloid leukemia.

Biallelic mutations of the CEBPA gene (CEBPAbi) are generally associated with favorable prognosis in patients with acute myeloid leukemia (AML). Monoallelic mutations of the CEBPA gene in carboxy-terminal DNA-binding region (CEBPAsmbZIP) and amino-terminal transactivation domains (CEBPAsmTAD) indicate distinct clinical characteristics and therapeutic outcomes. However, further investigation is required to fully understand these differences. In this retrospective study, we enrolled 77 AML patients with CEBPA mutations, including 53 with CEBPAbi, 12 with CEBPAsmbZIP and 12 with CEBPAsmTAD. The clinical characteristics of the three CEBPAmut groups presented significant differences in age, FAB classification, hemoglobin level and platelet count at diagnosis. The CEBPAsmTAD group exhibited shorter 2-year overall survival (OS) and relapse-free survival (RFS) compared to the CEBPAbi group and CEBPAsmbZIP group in AML patients. The most common co-mutations observed in CEBPAmut AML patients were TET2 and GATA2, which had no effect on prognosis. 2-year RFS of 27 CEBPAmut AML patients who underwent allo-HSCT was better than those who did not. MRD3 positive was identified as an influencing factor for 2-year OS and RFS. Allo-HSCT was found to improve the prognosis of CEPBAmut AML patients with positive MRD3 and adverse co-mutations.

Integrative lncRNA, circRNA, and mRNA analysis reveals expression profiles of six forensic body fluids/tissue.

RNAs have attracted much attention in forensic body fluid/tissue identification (BFID) due to their tissue-specific expression characteristics. Among RNAs, long RNAs (e.g., mRNA) have a higher probability of containing more polymorphic sites that can be used to assign the specific donor of the body fluid/tissue. However, few studies have characterized their overall profiles in forensic science. In this study, we sequenced the transcriptomes of 30 samples from venous blood, menstrual blood, semen, saliva, vaginal secretion, and skin tissue, obtaining a comprehensive picture of mRNA, lncRNA, and circRNA profiles. A total of 90,305 mRNAs, 102,906 lncRNAs (including 19,549 novel lncRNAs), and 40,204 circRNAs were detected. RNA type distribution, length distribution, and expression distribution were presented according to their annotation and expression level, and many novel body fluid/tissue-specific RNA markers were identified. Furthermore, the cognate relations among the three RNAs were analyzed according to gene annotations. Finally, SNPs and InDels from RNA transcripts were genotyped, and 21,611 multi-SNP and 4,471 multi-InDel transcriptomic microhaplotypes (tMHs) were identified. These results provide a comprehensive understanding of transcriptome profiles, which could provide new avenues for tracing the origin of the body fluid/tissue and identifying an individual.

Inference of forensic body fluids/tissues based on mitochondrial DNA copy number: a preliminary study.

The inference of body fluids and tissues is critical in reconstructing crime scenes and inferring criminal behaviors. Nevertheless, present methods are incompatible with conventional DNA genotyping, and additional testing might result in excessive consumption of forensic scene materials. This study aims to investigate the feasibility of distinguishing common body fluids/tissues through the difference in mitochondrial DNA copy number (mtDNAcn). Four types of body fluids/tissues were analyzed in this study - hair, saliva, semen, and skeletal muscle. MtDNAcn was estimated by dividing the read counts of mitochondrial DNA to that of nuclear DNA (RRmt/nu). Results indicated that there were significant differences in RRmt/nu between different body fluids/tissues. Specifically, hair samples exhibited the highest RRmt/nu (log10RRmt/nu: 4.3 ± 0.28), while semen samples showed the lowest RRmt/nu (log10RRmt/nu: -0.1 ± 0.28). RRmt/nu values for DNA samples without extraction were notably higher (approximately 2.9 times) than those obtained after extraction. However, no significant difference in RRmt/nu was observed between various age and gender groups. Hierarchical clustering and Kmeans clustering analyses showed that body fluids/tissues of the same type clustered closely to each other and could be inferred with high accuracy. In conclusion, this study demonstrated that the simultaneous detection of nuclear and mitochondrial DNA made it possible to perform conventional DNA analyses and body fluid/tissue inference at the same time, thus killing two birds with one stone. Furthermore, mtDNAcn has the potential to serve as a novel and promising biomarker for the identification of body fluids/tissues.

"I feel like I'm walking on eggshells": a qualitative study of moral distress among Chinese emergency doctors.

BACKGROUND: While the number of emergency patients worldwide continues to increase, emergency doctors often face moral distress. It hampers the overall efficiency of the emergency department, even leading to a reduction in human resources. AIM: This study explored the experience of moral distress among emergency department doctors and analyzed the causes of its occurrence and the strategies for addressing it. METHOD: Purposive and snowball sampling strategies were used in this study. Data were collected through in-depth, semi-structured interviews with 10 doctors working in the emergency department of a tertiary general hospital in southwest China. The interview data underwent processing using the Nvivo 14 software. The data analysis was guided by Colaizzi's phenomenological analysis method. STUDY FINDINGS: This study yielded five themes: (1) imbalance between Limited Medical Resources and High-Quality Treatment Needs; (2) Ineffective Communication with Patients; (3) Rescuing Patients With no prospect of treatment; (4) Challenges in Sustaining Optimal Treatment Measures; and (5) Strategies for Addressing Moral Distress. CONCLUSION: The moral distress faced by emergency doctors stems from various aspects. Clinical management and policymakers can alleviate this distress by enhancing the dissemination of emergency medical knowledge to the general public, improving the social and economic support systems, and strengthening multidisciplinary collaboration and doctors' communication skills.

High-Voltage Cable Buffer Layer Ablation Fault Identification Based on Artificial Intelligence and Frequency Domain Impedance Spectroscopy.

In recent years, the occurrence of high-voltage cable buffer layer ablation faults has become frequent, posing a serious threat to the safe and stable operation of cables. Failure to promptly detect and address such faults may lead to cable breakdowns, impacting the normal operation of the power system. To overcome the limitations of existing methods for identifying buffer layer ablation faults in high-voltage cables, a method for identifying buffer layer ablation faults based on frequency domain impedance spectroscopy and artificial intelligence is proposed. Firstly, based on the cable distributed parameter model and frequency domain impedance spectroscopy, a mathematical model of the input impedance of a cable containing buffer layer ablation faults is derived. Through a simulation, the input impedance spectroscopy at the first end of the cables under normal conditions, buffer layer ablation, local aging, and inductive faults is performed, enabling the identification of inductive and capacitive faults through a comparative analysis. Secondly, the frequency domain amplitude spectroscopy of the buffer layer ablation and local aging faults are used as datasets and are input into a neural network model for training and validation to identify buffer layer ablation and local aging faults. Finally, using multiple evaluation metrics to assess the neural network model validates the superiority of the MLP neural network in cable fault identification models and experimentally confirms the effectiveness of the proposed method.

A Comprehensive Evaluation Algorithm of Multi-Point Relay Based on Link-State Awareness for UANETs.

The Multi-Point Relay (MPR) is one of the core technologies for Optimizing Link State Routing (OLSR) protocols, offering significant advantages in reducing network overhead, enhancing throughput, maintaining network scalability, and adaptability. However, due to the restriction that only MPR nodes can forward control messages in the network, the current evaluation criteria for selecting MPR nodes are relatively limited, making it challenging to flexibly choose MPR nodes based on current link states in dynamic networks. Therefore, the selection of MPR nodes is crucial in dynamic networks. To address issues such as unstable links, poor transmission accuracy, and lack of real-time performance caused by mobility in dynamic networks, we propose a comprehensive evaluation algorithm of MPR based on link-state awareness. This algorithm defines five state evaluation parameters from the perspectives of node mobility and load. Subsequently, we use the entropy weight method to determine weight coefficients and employing the method of Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) for comprehensive evaluation to select MPR nodes. Finally, the Comprehensive Evaluation based on Link-state awareness of OLSR (CEL-OLSR) protocol is proposed, and simulated experiments are conducted using NS-3. The results indicate that, compared to PM-OLSR, ML-OLSR, LD-OLSR, and OLSR, CEL-OLSR significantly improves network performance in terms of packet delivery rate, average end-to-end delay, network throughput, and control overhead.

A study on factors related to sleep disorders and serum BDNF expression levels in patients with primary SjÓ§gren's syndrome.

OBJECTIVES: We aimed to assess the sleep quality of patients with primary Sjögren's syndrome (pSS) and the associated factors. Moreover, Preliminary exploration of the clinical significance of serum brain-derived neurotrophic factor (BDNF) in pSS patients with sleep disorders. METHODS: A self-report survey was administered to 111 pSS patients and 40 healthy individuals using the Pittsburgh Sleep Quality Index (PSQI) for sleep quality. General clinical information,the sleep quality and mental conditions were collected using on-site questionnaires and various scales. 40 healthy controls from the health examination center of the same hospital, who were age and sex matched. Detection of serum BDNF levels by ELISA method . Independent samples t tests, Chi-square analysis, logistic regression were used to analyze these data. RESULTS: Patients with pSS had higher scores on the PSQI than the healthy individuals. Abnormal sweating, high PHQ-9 and ESSPRI scores were independent risk factors for sleep disorders. pSS patients had lower serum BDNF than the healthy individuals, The area under the curve (AUC) of predicting sleep disorder in pSS patients using detection of serum BDNF level was 0.8470, and the sensitivity and specificity were 0.951 and 0.727, which were superior to PHQ-9 and GAD-7. CONCLUSION: Compared with the healthy individuals, pSS patients had a higher prevalence of sleep disorders and lower serum BNDF. Serum BDNF level demonstrated greater predictive advantage for sleep disorder in pSS patients.

Analysing substitutions in recent World Cups and European Championships in male and female elite football - influence of new substitution rules.

Substitutions play a key role in modern football and can substantially affect the physical and overall performance of a team, and the recent substitution rule changes are worth investigating. This study explored the characteristics of substitutions, including different substitution rules, game results, sex, competition stages, tournaments and penalty shoot-outs success rates. We analysed data from a total of 3,738 substitutions from the last 10 years (2013-2023) of European Championships and World Cups, both men's and women's games. Non-parametric tests and chi-square tests were used for statistical analysis with the significance level set at p < 0.05. With the 5-substitution rule, 48% more substitutions occurred compared to the 3-substitution rule (4.26 ± 1.07 vs. 2.87 ± 0.43, p < 0.05) with a slight increase in the average substitution time (70.6 ± 14.3 vs. 69.2 ± 14.6 min, p < 0.05), and 10% more substitutions in the men's game compared to the women's game (p < 0.05). The timing of the first substitution was slightly different in the knock-out stage compared to group stage (59.8 ± 14.7 vs. 57.2 ± 13.3 min, p < 0.05), and the timing for the winning team and drawing team was later than for the losing team (p < 0.05). A total of 13.2% goals were scored by substitutes, with no significant difference between the 5-substitution rule (15.9%) vs the 3-substition rule (12.5%) (p > 0.05). Interestingly, substitute players had a lower success rate in penalty shoot-out compared to starters (61 vs. 74%, p < 0.05). Additionally, substitute player goal scorers entered the pitch later (p < 0.05) in male games compared to female games and in knock-out stage games compared to group games. This study highlights the importance of substitution rules and timing in modern elite football matches. The timing of the first substitution, introduction of substitutes in knock-out stages, and a lower success rate of substitute players in penalty shoot-outs are crucial factors to consider. Coaches can use this information to make strategic substitution decisions to improve team performance.

PINOID and PIN-FORMED Paralogous Genes Are Required for Leaf Morphogenesis in Rice.

Auxin plays an essential role in modulating leaf development. However, its role in leaf development in rice (Oryza sativa L.) remains largely unknown. In this study, we found that PINOID (OsPID) and two Sister-of-PIN1s, termed PIN-FORMED1c (OsPIN1c) and OsPIN1d, are necessary for rice leaf development. The ospin1c ospin1d null mutant lines presented severe defects in leaf morphogenesis, including drooping and semi-drooping blades, an abnormally thickened sheath and lamina joint, and fused leaves with absent ligules and auricles. Loss-of-function ospid mutants displayed generally similar leaf morphology but lacked leaf fusion. Interestingly, misshaped leaf genesis displayed a preference for being ipsilateral. In addition, OsPIN1c and OsPID were commonly localized in the initiating leaf primordia. Furthermore, accompanied by the more severe organ morphogenesis in the ospin1c ospin1d ospid triple mutant, RNA sequencing analysis revealed that many genes essential for leaf development have an altered expression level. Together, this study furthers our understanding of the role auxin transport plays during leaf development in monocot rice.

ß-Galactosidase-Activatable Fluorescent and Photoacoustic Imaging of Tumor Senescence.

ß-Galactosidase (ß-gal) is the gold standard marker of cellular senescence, which is linked with various age-related diseases. Therefore, it is essential to develop more excellent probes that can real-time monitor ß-gal activity in cellular senescence in vivo. Fluorescent/photoacoustic (FL/PA) dual-modal imaging possesses excellent sensitivity and spatial resolution. To our knowledge, there has been no tumor-targeted FL/PA probe to image cellular senescence by monitoring the activity of ß-gal in vivo. Therefore, we developed a tumor-targeted FL/PA probe (Gal-HCy-Biotin) for ß-gal-activatable imaging of tumor senescence. Gal-HCy without tumor-targeted biotin is used as a control probe. Gal-HCy-Biotin is superior to Gal-HCy due to the higher kinetic parameter of Gal-HCy-Biotin than Gal-HCy in vitro. Moreover, biotin could help Gal-HCy-Biotin enter and accumulate in tumor cells with higher FL/PA signal. In detail, Gal-HCy-Biotin or Gal-HCy could image senescent tumor cells with 4.6-fold or 3.5-fold FL enhancement and 4.1-fold or 3.3-fold PA enhancement. Gal-HCy-Biotin or Gal-HCy could image tumor senescence with 2.9-fold or 1.7-fold FL enhancement and 3.8-fold or 1.3-fold PA enhancement. We envision that Gal-HCy-Biotin will be applied for FL/PA imaging of tumor senescence in clinic.

Caspase-3-Responsive Fluorescent/Photoacoustic Imaging of Tumor Apoptosis.

Caspase-3 is an essential executor in apoptosis, and its activation has been regarded as a biomarker of cell apoptosis. The development of Caspase-3-responsive multimodal probes is a promising research prospect. Fluorescent/photoacoustic (FL/PA) imaging has attracted considerable attention due to the high sensitivity of FL as well as the high spatial resolution and penetration depth of PA. To our knowledge, there has been no tumor-targeted FL/PA probe to monitor the activity of Caspase-3 in vivo. Therefore, we developed a tumor-targeted FL/PA probe (Bio-DEVD-HCy) for Caspase-3-responsive imaging of tumor apoptosis. Ac-DEVD-HCy without tumor-targeted biotin is used as a control probe. In vitro experiments indicated that Bio-DEVD-HCy is superior to Ac-DEVD-HCy because of the higher kinetic parameter of Bio-DEVD-HCy in comparison to Ac-DEVD-HCy. Cell and tumor imaging results suggested that Bio-DEVD-HCy could enter and accumulate in tumor cells with higher FL/PA signal with the help of tumor-targeted biotin. In detail, Bio-DEVD-HCy or Ac-DEVD-HCy could image apoptotic tumor cells with 4.3-fold or 3.5-fold FL enhancement and 3.4-fold or 1.5-fold PA enhancement. Bio-DEVD-HCy or Ac-DEVD-HCy could image tumor apoptosis with 2.5-fold or 1.6-fold FL enhancement and 4.1-fold or 1.9-fold PA enhancement. We envision that Bio-DEVD-HCy will be applied for FL/PA imaging of tumor apoptosis in clinical settings.

Genome wide identification of GDSL gene family explores a novel GhirGDSL26 gene enhancing drought stress tolerance in cotton.

BACKGROUND: Current climate change scenarios are posing greater threats to the growth and development of plants. Thus, significant efforts are required that can mitigate the negative effects of drought on the cotton plant. GDSL esterase/lipases can offer an imperative role in plant development and stress tolerance. However, thesystematic and functional roles of the GDSL gene family, particularly in cotton under water deficit conditions have not yet been explored. RESULTS: In this study, 103, 103, 99, 198, 203, 239, 249, and 215 GDSL proteins were identified in eight cotton genomes i.e., Gossypium herbaceum (A1), Gossypium arboretum (A2), Gossypium raimondii (D5), Gossypium hirsutum (AD1), Gossypium barbadense (AD2), Gossypium tomentosum (AD3), Gossypium mustelinum (AD4), Gossypium darwinii (AD5), respectively. A total of 198 GDSL genes of Gossypium hirsutum were divided into eleven clades using phylogenetic analysis, and the number of GhirGDSL varied among different clades. The cis-elements analysis showed that GhirGDSL gene expression was mainly related to light, plant hormones, and variable tense environments. Combining the results of transcriptome and RT-qPCR, GhirGDSL26 (Gh_A01G1774), a highly up-regulated gene, was selected for further elucidating its tole in drought stress tolerance via estimating physiological and biochemical parameters. Heterologous expression of the GhirGDSL26 gene in Arabidopsis thaliana resulted in a higher germination and survival rates, longer root lengths, lower ion leakage and induced stress-responsive genes expression under drought stress. This further highlighted that overexpressed plants had a better drought tolerance as compared to the wildtype plants. Moreover, 3, 3'-diaminobenzidine (DAB) and Trypan staining results indicated reduced oxidative damage, less cell membrane damage, and lower ion leakage in overexpressed plants as compared to wild type. Silencing of GhirGDSL26 in cotton via VIGS resulting in a susceptible phenotype, higher MDA and H2O2 contents, lower SOD activity, and proline content. CONCLUSION: Our results demonstrated that GhirGDSL26 plays a critical role in cotton drought stress tolerance. Current findings enrich our knowledge of GDSL genes in cotton and provide theoretical guidance and excellent gene resources for improving drought tolerance in cotton.

Making the case for precision dosing: visualizing the variability of cefepime exposures in critically ill adults.

OBJECTIVE: To investigate and describe the variability in cefepime exposures among 'real-world', critically ill patients by using population pharmacokinetic modelling and simulations, and with translation of these findings to visualizations. METHODS: A cohort of adult medical ICU patients who received cefepime with therapeutic drug monitoring was studied. Two compartment models were developed to estimate cefepime clearance (Model 1) and simulate cefepime exposures among 1000 patients, each with identical creatinine clearance of 60 mL/min and receiving a regimen of cefepime 1 gram IV over 30 minutes, every 8 hours (Model 2). Variability in the relationship between cefepime clearance and creatinine clearance (CrCL) was visualized, and a random, representative sample of 10 simulated patients was utilized to illustrate variability in cefepime exposures. RESULTS: A total of 75 adult medical ICU patients (52% female) and 98 serum cefepime samples were included in the study. Population parameter estimates for cefepime displayed a wide range of variation in Model 1 (CV: 45% to 95%), with low bias at the individual level at 0.226 mg/L but high bias in the population model 10.6 mg/L. Model 2 displayed similar fits, demonstrating that correcting for individual patient creatinine clearance slightly improves the bias of the population model (bias = 4.31 mg/L). Among 10 simulated patients that a clinician would deem similar from a dosing perspective (i.e. equivalent creatinine clearance), maximum concentrations after three simulated doses varied more than 8-fold from 41.2 to 339 mg/L at the 5th and 95th percentiles, and clearance profiles were highly different. CONCLUSION: Creatinine clearance estimates alone are inadequate for predicting cefepime exposures. Wide variations in cefepime exposure exist among ICU patients, even for those with similar kidney function estimates. Current population adjustment schemes based solely on creatinine clearance will result in unintended high and low exposures leading to safety and efficacy concerns, respectively.

MIB2: metal ion-binding site prediction and modeling server.

MOTIVATION: MIB2 (metal ion-binding) attempts to overcome the limitation of structure-based prediction approaches, with many proteins lacking a solved structure. MIB2 also offers more accurate prediction performance and more metal ion types. RESULTS: MIB2 utilizes both the (PS)2 method and the AlphaFold Protein Structure Database to acquire predicted structures to perform metal ion docking and predict binding residues. MIB2 offers marked improvements over MIB by collecting more MIB residue templates and using the metal ion type-specific scoring function. It offers a total of 18 types of metal ions for binding site predictions. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at http://bioinfo.cmu.edu.tw/MIB2/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Sucrose nonfermenting-1-related protein kinase 1 regulates sheath-to-panicle transport of nonstructural carbohydrates during rice grain filling.

The remobilization of nonstructural carbohydrates (NSCs) reserved in rice (Oryza sativa) sheaths is essential for grain filling. This assimilate distribution between plant tissues and organs is determined by sucrose non-fermenting-1-related protein kinase 1 (SnRK1). However, the SnRK1-mediated mechanism regulating the sheath-to-panicle transport of NSCs in rice remains unknown. In this study, leaf cutting treatment was used to accelerate NSC transport in the rice sheaths. Accelerated NSC transport was accompanied by increased levels of OsSnRK1a mRNA expression, SnRK1a protein expression, catalytic subunit phosphorylation of SnRK1, and SnRK1 activity, indicating that SnRK1 activity plays an important role in sheath NSC transport. We also discovered that trehalose-6-phosphate, a signal of sucrose availability, slightly reduced SnRK1 activity in vitro. Since SnRK1 activity is mostly regulated by OsSnRK1a transcription in response to low sucrose content, we constructed an snrk1a mutant to verify the function of SnRK1 in NSC transport. NSCs accumulated in the sheaths of snrk1a mutant plants and resulted in a low seed setting rate and grain weight, verifying that SnRK1 activity is essential for NSC remobilization. Using phosphoproteomics and parallel reaction monitoring, we identified 20 SnRK1-dependent phosphosites that are involved in NSC transport. In addition, the SnRK1-mediated phosphorylation of the phosphosites directly affected starch degradation, sucrose metabolism, phloem transport, sugar transport across the tonoplast, and glycolysis in rice sheaths to promote NSC transport. Therefore, our findings reveal the importance, function, and possible regulatory mechanism of SnRK1 in the sheath-to-panicle transport of NSCs in rice.

A promising QTL QSns.sau-MC-3D.1 likely superior to WAPO1 for the number of spikelets per spike of wheat shows no adverse effects on yield-related traits.

KEY MESSAGE: A likely new locus QSns.sau-MC-3D.1 associated with SNS showing no negative effect on yield-related traits compared to WAPO1 was identified and validated in various genetic populations under multiple environments. The number of spikelets per spike (SNS) is one of the crucial factors determining wheat yield. Thus, improving our understanding of the genes that regulate SNS could help develop wheat varieties with higher yield. In this study, a recombinant inbred line (RIL) population (MC) containing 198 lines derived from a cross between msf and Chuannong 16 (CN16) was used to construct a genetic linkage map using the GenoBaits Wheat 16 K Panel. The genetic map contained 5,991 polymorphic SNP markers spanning 2,813.25 cM. A total of twelve QTL for SNS were detected, and two of them, i.e., QSns.sau-MC-3D.1 and QSns.sau-MC-7A, were stably expressed. QSns.sau-MC-3D.1 had high LOD values ranging from 4.99 to 11.06 and explained 9.71-16.75% of the phenotypic variation. Comparison of QSns.sau-MC-3D.1 with previously reported SNS QTL suggested that it is likely a novel one, and two kompetitive allele-specific PCR (KASP) markers were further developed. The positive effect of QSns.sau-MC-3D.1 was also validated in three biparental populations and a diverse panel containing 388 Chinese wheat accessions. Genetic analysis indicated that WHEAT ORTHOLOG OFAPO1 (WAPO1) was a candidate gene for QSns.sau-MC-7A. Pyramiding of QSns.sau-MC-3D.1 and WAP01 had a great additive effect increasing SNS by 7.10%. Correlation analysis suggested that QSns.sau-MC-3D.1 was likely independent of effective tiller number, plant height, spike length, anthesis date, and thousand kernel weight. However, the H2 haplotype of WAPO1 may affect effective tiller number and plant height. These results indicated that utilization of QSns.sau-MC-3D.1 should be given priority for wheat breeding. Geographical distribution analysis showed that the positive allele of QSns.nsau-MC-3D.1 was dominant in most wheat-producing regions of China, and it has been positively selected among modern cultivars released in China since the 1940s. Gene prediction, qRT-PCR analysis, and sequence alignment suggested that TraesCS3D03G0216800 may be the candidate gene of QSns.nsau-MC-3D.1. Taken together, these results enrich our understanding of the genetic basis of wheat SNS and will be useful for fine mapping and cloning of the gene underlying QSns.sau-MC-3D.1.

CMV infection is a risk factor for hemorrhagic cystitis after hematopoietic stem cell transplantation.

Hemorrhagic cystitis (HC) is a common complication after transplantation. The purpose of this study was to examine the incidence and risk factors for HC after hematopoietic stem cell transplantation (HSCT). The records of patients who underwent allogenic HSCT from January 2012 to December 2018 at our institution were retrospectively reviewed. Cox proportional regression and Kaplan-Meier analyses were performed to determine independent risk factors for HC. The statistical analysis was performed in May 2020. A total of 173 patients underwent HSCT, and 53 (30.6%) developed grade 2 or 3 HC cystitis at a median of 37 days (range - 5 to 98 days) after transplantation. Thirty-two patients developed moderate (grade 2) cystitis and 21 severe (grade 3) cystitis. Of the 173 patients, 61 developed acute graft-versus-host disease (GVHD) (median onset day 24) and 79 experienced cytomegalovirus (CMV) reactivation (median onset day 35). The relative risk (RR) of developing a CMV infection for patients with acute GVHD was 2.77 times that of patients without acute GVHD (P < 0.001). CMV infection was the only independent variable significantly associated with HC in both univariate and multivariate analyses. The estimated hazard ratio (HR) of CMV infection for the development of HC was 5.57 (95% confidence interval [CI]: 2.52 to 12.33, P < 0.001). CMV infection is an independent risk factor for the development of HC after HSCT, and acute GVHD is a risk factor for CMV reactivation. Decreasing the frequency of GVHD after HSCT may result in a lower frequency of HC.

Comparison of three massively parallel sequencing platforms for single nucleotide polymorphism (SNP) genotyping in forensic genetics.

Three MPS platforms are being used in forensic genetic analysis, i.e., MiSeq FGx, Ion S5 XL, and MGISEQ-2000. However, few studies compared their performance. In this study, we sequenced 83 common SNPs of 71 samples using the ForenSeq™ DNA Signature Prep Kit on MiSeq FGx, the Precision ID Identity Panel on Ion S5 XL, and the MGIEasy Signature Identification Library Prep Kit on MGISEQ-2000 and then the performance was compared. Results showed that the MiSeq FGx had the highest sequence quality but the lowest sequencing depth and allele balance. Discordant genotypes were observed at six SNPs, which may be caused by variants at primer binding regions, indel errors, or misalignments. Besides, two kinds of background noises, allele-specific miscalled reads (ASMR) and allele-nonspecific miscalled reads (ANMR), were characterized. MGISEQ-2000 showed the highest level of ASMR while Ion S5 XL had the highest level of ANMR. Site- and genotype-dependent miscalled patterns were observed at several SNPs on Ion S5 XL and MGISEQ-2000, but few on MiSeq FGx. In conclusion, the three MPS platforms perform differently with respect to sequencing quality, sequencing depth, allele balance, concordance, and background noise. These findings may be useful for data comparison, mixture deconvolution, and heteroplasmy analysis in forensic genetics.