A novel scoring system for the quantitative prediction of prognosis in acute myeloid leukemia

BackgroundAcute myeloid leukemia (AML) is a heterogeneous hematopoietic malignancy. Patient prognosis cannot be accurately assessed in National Comprehensive Cancer Network (NCCN) risk stratification subgroups based on the current criteria. This study aimed to develop a novel prognostic score model for the quantitative prediction of prognosis in AML.ResultsWe developed a prognostic risk scoring model of AML using differentially expressed genes to predict prognosis in patients with AML. Furthermore, we evaluated the effectiveness and clinical significance of this prognostic model in 4 AML cohorts and 905 patients with AML. A prognostic risk scoring model of AML containing eight prognosis-related genes was constructed using a multivariate Cox regression model. The model had a higher predictive value for the prognosis of AML in the training and validation sets. In addition, patients with lower scores had significantly better overall survival (OS) and even-free survival (EFS) than those with higher scores among patients with intermediate-risk AML according to the NCCN guidelines, indicating that the model could be used to further predict the prognosis of the intermediate-risk AML populations. Similarly, patients with high scores had remarkably poor OS and EFS in the normal-karyotype populations, indicating that the scoring model had an excellent predictive performance for patients with AML having normal karyotype.ConclusionsOur study provided an individualized prognostic risk score model that could predict the prognosis of patients with AML

Exploring spatial-frequency-sequential relationships for motor imagery classification with recurrent neural network

Abstract Background Conventional methods of motor imagery brain computer interfaces (MI-BCIs) suffer from the limited number of samples and simplified features, so as to produce poor performances with spatial-frequency features and shallow classifiers. Methods Alternatively, this paper applies a deep recurrent neural network (RNN) with a sliding window cropping strategy (SWCS) to signal classification of MI-BCIs. The spatial-frequency features are first extracted by the filter bank common spatial pattern (FB-CSP) algorithm, and such features are cropped by the SWCS into time slices. By extracting spatial-frequency-sequential relationships, the cropped time slices are then fed into RNN for classification. In order to overcome the memory distractions, the commonly used gated recurrent unit (GRU) and long-short term memory (LSTM) unit are applied to the RNN architecture, and experimental results are used to determine which unit is more suitable for processing EEG signals. Results Experimental results on common BCI benchmark datasets show that the spatial-frequency-sequential relationships outperform all other competing spatial-frequency methods. In particular, the proposed GRU-RNN architecture achieves the lowest misclassification rates on all BCI benchmark datasets. Conclusion By introducing spatial-frequency-sequential relationships with cropping time slice samples, the proposed method gives a novel way to construct and model high accuracy and robustness MI-BCIs based on limited trials of EEG signals

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

Prevalence, associated factors and outcomes of pressure injuries in adult intensive care unit patients: the DecubICUs study

Funder: European Society of Intensive Care Medicine; doi: http://dx.doi.org/10.13039/501100013347Funder: Flemish Society for Critical Care NursesAbstract: Purpose: Intensive care unit (ICU) patients are particularly susceptible to developing pressure injuries. Epidemiologic data is however unavailable. We aimed to provide an international picture of the extent of pressure injuries and factors associated with ICU-acquired pressure injuries in adult ICU patients. Methods: International 1-day point-prevalence study; follow-up for outcome assessment until hospital discharge (maximum 12 weeks). Factors associated with ICU-acquired pressure injury and hospital mortality were assessed by generalised linear mixed-effects regression analysis. Results: Data from 13,254 patients in 1117 ICUs (90 countries) revealed 6747 pressure injuries; 3997 (59.2%) were ICU-acquired. Overall prevalence was 26.6% (95% confidence interval [CI] 25.9–27.3). ICU-acquired prevalence was 16.2% (95% CI 15.6–16.8). Sacrum (37%) and heels (19.5%) were most affected. Factors independently associated with ICU-acquired pressure injuries were older age, male sex, being underweight, emergency surgery, higher Simplified Acute Physiology Score II, Braden score 3 days, comorbidities (chronic obstructive pulmonary disease, immunodeficiency), organ support (renal replacement, mechanical ventilation on ICU admission), and being in a low or lower-middle income-economy. Gradually increasing associations with mortality were identified for increasing severity of pressure injury: stage I (odds ratio [OR] 1.5; 95% CI 1.2–1.8), stage II (OR 1.6; 95% CI 1.4–1.9), and stage III or worse (OR 2.8; 95% CI 2.3–3.3). Conclusion: Pressure injuries are common in adult ICU patients. ICU-acquired pressure injuries are associated with mainly intrinsic factors and mortality. Optimal care standards, increased awareness, appropriate resource allocation, and further research into optimal prevention are pivotal to tackle this important patient safety threat

Correction to: Prevalence, associated factors and outcomes of pressure injuries in adult intensive care unit patients: the DecubICUs study

The original version of this article unfortunately contained a mistake

Prevalence, associated factors and outcomes of pressure injuries in adult intensive care unit patients: the DecubICUs study

Funder: European Society of Intensive Care Medicine; doi: http://dx.doi.org/10.13039/501100013347Funder: Flemish Society for Critical Care NursesAbstract: Purpose: Intensive care unit (ICU) patients are particularly susceptible to developing pressure injuries. Epidemiologic data is however unavailable. We aimed to provide an international picture of the extent of pressure injuries and factors associated with ICU-acquired pressure injuries in adult ICU patients. Methods: International 1-day point-prevalence study; follow-up for outcome assessment until hospital discharge (maximum 12 weeks). Factors associated with ICU-acquired pressure injury and hospital mortality were assessed by generalised linear mixed-effects regression analysis. Results: Data from 13,254 patients in 1117 ICUs (90 countries) revealed 6747 pressure injuries; 3997 (59.2%) were ICU-acquired. Overall prevalence was 26.6% (95% confidence interval [CI] 25.9–27.3). ICU-acquired prevalence was 16.2% (95% CI 15.6–16.8). Sacrum (37%) and heels (19.5%) were most affected. Factors independently associated with ICU-acquired pressure injuries were older age, male sex, being underweight, emergency surgery, higher Simplified Acute Physiology Score II, Braden score 3 days, comorbidities (chronic obstructive pulmonary disease, immunodeficiency), organ support (renal replacement, mechanical ventilation on ICU admission), and being in a low or lower-middle income-economy. Gradually increasing associations with mortality were identified for increasing severity of pressure injury: stage I (odds ratio [OR] 1.5; 95% CI 1.2–1.8), stage II (OR 1.6; 95% CI 1.4–1.9), and stage III or worse (OR 2.8; 95% CI 2.3–3.3). Conclusion: Pressure injuries are common in adult ICU patients. ICU-acquired pressure injuries are associated with mainly intrinsic factors and mortality. Optimal care standards, increased awareness, appropriate resource allocation, and further research into optimal prevention are pivotal to tackle this important patient safety threat

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Ovarian sex cord stromal tumours: analysis of the clinical and sonographic characteristics of different histopathologic subtypes

Abstract Background Ovarian sex cord stromal tumours (OSCSTs) are rare ovarian tumours and include different histopathologic subtypes. This study aimed to analyse the clinical and sonographic characteristics of different histopathologic OSCST subtypes. Methods A total of 63 patients with surgically proven OSCSTs were enrolled in this retrospective study to analyse their clinical and sonographic features. Ultrasound examinations and predictive models were performed before surgery. The clinical and sonographic findings were compared according to the type of OSCST based on the histopathological diagnosis. Results The mean age of 63 patients was 52.17 years (range: 17–78 years). Eighteen patients experienced irregular vaginal bleeding (28.57% 18/63), 7 patients exhibited abnormal body hair (11.11%). 2 patients (3.17%) showed an increased level of CA125, and 25 patients (39.68%, 25/63) showed an increased level of testosterone. Forty-two patients had ovarian thecoma-fibroma groups (OTFGs). Six patients had Sertoli-Leydig cell tumours (S-LCTs), 4 patients had Leydig cell tumours (LCTs), 8 patients had ovarian granulosa cell tumours (OGCTs), 2 patients had ovarian steroid cell tumours, not otherwise specified (OSCTs-NOS), and one patient had sclerosing stromal tumours (SSTs). The mean diameter of the tumour was 47.9 mm (range: 10–258 mm). Forty-seven masses were hypoechoic (74.60%). Twenty-eight masses had posterior echo attenuation, 22 masses exhibited abundant Doppler flow signals (34.92%), and one patient had ascites (1.59%). The diagnostic accuracy of the Simple Rules (SR) and the Assessment of Different NEoplasias in the adneXa (ADNEX) model in distinguishing benign and malignant OSCSTs was 44% (30/63) and 84% (53/63), respectively. The diagnostic accuracy of the SR for OTFGs, S-LCTs & LCTs & OSCTs-NOS, OGCTs, and SSTs was 47.6% (20/42), 16.67% (2/12), 100% (8/8), and 0% (0/1), respectively. The diagnostic accuracy of the ADNEX model for OTFGs, S-LCTs & LCTs & OSCTs-NOS, OGCTs, and SSTs was 93% (31/42), 58.33% (7/12), 75% (6/8), and 100% (1/1), respectively. Conclusions OSCSTs generally appear as a solid mass on ultrasound. Posterior echo attenuation indicates an OTFG. A solid mass with abundant Doppler flow signals indicates an S-LCT, LCT, OSCT-NOS or OGCT. Current predictive models are not very effective, but symptoms, sonographic features and serum hormones are helpful for diagnosis

Hydnotrya qinghaiensis Yi Li, A. Xu, J. J. Lu & W. F. Lin 2023, sp. nov.

&lt;i&gt;Hydnotrya qinghaiensis&lt;/i&gt; Yi Li, A. Xu, J.J. Lu &amp; W.F. Lin, &lt;i&gt;sp. nov&lt;/i&gt;. (Figs. 2, 3) &lt;p&gt;Fungal Names FN570864.&lt;/p&gt; &lt;p&gt; Diagnosis:&mdash; &lt;i&gt;Hydnotrya qinghaiensis&lt;/i&gt; is most similar and closely related to &lt;i&gt;H. cerebriformis&lt;/i&gt; among known species within the genus &lt;i&gt;Hydnotrya&lt;/i&gt;, but differed in its somewhat larger and irregularly brownish ascomata and the particular habitat in Tibetan Plateau under &lt;i&gt;Picea&lt;/i&gt; trees, as well as the ITS sequence differs by at least 37 substitutions and indels.&lt;/p&gt; &lt;p&gt; Etymology:&mdash;The epithet &ldquo; &lt;i&gt;qinghaiensis&lt;/i&gt; &rdquo; refers to the type locality Qinghai Province in China.&lt;/p&gt; &lt;p&gt; Holotypus:&mdash; CHINA, Qinghai Province, Guoluo Tibetan Autonomous Prefecture, Baima County, Dengta Village, 32&deg;40&prime;16&Prime;N, 101&deg;01&prime;33&Prime;E, ASL 3188 m, hypogeous or semi-hypogeous in soil under subalpine mixed conifer (&lt;i&gt;Picea&lt;/i&gt; sp.) &mdash; broadleaf forest, 13 August 2019, Yi Li 1530 (HMAS 350656).&lt;/p&gt; &lt;p&gt; Description:&mdash; &lt;b&gt;Ascomata&lt;/b&gt; irregular globose with conspicuous cerebriform convolutions, light brown to brown, 15&minus;28 &times; 25&minus;50 mm; &lt;b&gt;Gleba&lt;/b&gt; dark brown and brown when dried, solid and scattered with some small, isolated, and numerous irregularly shaped chambers lined with gray hymenium; &lt;b&gt;Peridium&lt;/b&gt; 80&minus;200 &mu;m thick, composed of a rectangle or subangular cells of 16.1&ndash;34.4 &times; 7.2&ndash;16.6 &mu;m; &lt;b&gt;Asci&lt;/b&gt; 235&ndash;392 &times; 24&ndash;38 &micro;m, hyaline, clavate, apex rounded, narrowed at the base into a short stalk, 8-spored, spores uniseriately arranged; &lt;b&gt;Paraphyses&lt;/b&gt; crowded, 6&ndash;7.1 &micro;m in diam, hyaline, straight, apically slightly inflated to 6.6&ndash;9.8 &micro;m wide, septate, extending 19.4&ndash;48 &mu;m beyond asci; &lt;b&gt;Ascospores&lt;/b&gt; globose, coated, exosporium clew like, immature spores hyaline, brown at maturity, 27.1&ndash;36.6 &mu;m (n = 30) including ornament and 19.6&ndash;27.5 &micro;m (n = 30) excluding ornament in diam.&lt;/p&gt; &lt;p&gt; Habitat and distribution:&mdash;Hypogeous or semi-hypogeous in soil under subalpine mixed forests dominated by &lt;i&gt;Picea&lt;/i&gt; sp., known from the Tibetan Plateau of China.&lt;/p&gt;Published as part of &lt;i&gt;Xu, Ao, Lu, Jiao-Jiao, Lin, Wen-Fei, Fan, Li, Xie, Meng-Le, Wan, Shan-Ping &amp; Li, Yi, 2023, Hydnotrya qinghaiensis sp. nov. (Discinaceae, Pezizales) from Tibetan Plateau, China, pp. 235-246 in Phytotaxa 616 (3)&lt;/i&gt; on page 241, DOI: 10.11646/phytotaxa.616.3.3, &lt;a href="http://zenodo.org/record/10084759"&gt;http://zenodo.org/record/10084759&lt;/a&gt

Developmental changes of TGF-β1 and Smads signaling pathway in intestinal adaption of weaned pigs.

Weaning stress caused marked changes in intestinal structure and function. Transforming growth factor-β1 (TGF-β1) and canonical Smads signaling pathway are suspected to play an important regulatory role in post-weaning adaptation of the small intestine. In the present study, the intestinal morphology and permeability, developmental expressions of tight junction proteins and TGF-β1 in the intestine of piglets during the 2 weeks after weaning were assessed. The expressions of TGF-β receptor I/II (TβRI, TβRII), smad2/3, smad4 and smad7 were determined to investigate whether canonical smads signaling pathways were involved in early weaning adaption process. The results showed that a shorter villus and deeper crypt were observed on d 3 and d 7 postweaning and intestinal morphology recovered to preweaning values on d 14 postweaning. Early weaning increased (P<0.05) plasma level of diamine oxidase (DAO) and decreased DAO activities (P<0.05) in intestinal mucosa on d 3 and d 7 post-weaning. Compared with the pre-weaning stage (d 0), tight junction proteins level of occludin and claudin-1 were reduced (P<0.05) on d 3, 7 and 14 post-weaning, and ZO-1 protein was reduced (P<0.05) on d 3 and d 7 post-weaning. An increase (P<0.05) of TGF-β1 in intestinal mucosa was observed on d 3 and d 7 and then level down on d 14 post-weaning. Although there was an increase (P<0.05) of TβR II protein expression in the intestinal mucosa on d3 and d 7, no significant increase of mRNA of TβRI, TβRII, smad2/3, smad4 and smad7 was observed during postweaning. The results indicated that TGF-β1 was associated with the restoration of intestinal morphology and barrier function following weaning stress. The increased intestinal endogenous TGF-β1 didn't activate the canonical Smads signaling pathway