Miracle-dz/UniFAR-FTUs huggingface dataset:
Deep learning-based transcriptome model predicts survival of T-cell acute lymphoblastic leukemia

Identifying subgroups of T-cell acute lymphoblastic leukemia (T-ALL) with poor survival will significantly influence patient treatment options and improve patient survival expectations. Current efforts to predict T-ALL survival expectations in multiple patient cohorts are lacking. A deep learning (DL)-based model was developed to determine the prognostic staging of T-ALL patients. We used transcriptome sequencing data from TARGET to build a DL-based survival model using 265 T-ALL patients. We found that patients could be divided into two subgroups (K0 and K1) with significant difference (P< 0.0001) in survival rate. The more malignant subgroup was significantly associated with some tumor-related signaling pathways, such as PI3K-Akt, cGMP-PKG and TGF-beta signaling pathway. DL-based model showed good performance in a cohort of patients from our clinical center (P = 0.0248). T-ALL patients survival was successfully predicted using a DL-based model, and we hope to apply it to clinical practice in the future.
Nutritional status, food consumption, lifestyle, and physical fitness in rural and urban elementary school children in Northeast China

Childhood obesity is observed not only in developed countries but also in some developing countries in Asia, where low physical activity and poor physical fitness have been reported. The primary goal of weight loss is to reduce body fat mass, thereby reducing the risk of metabolic syndrome. Unfortunately, a concomitant decrease in lean mass, including muscle mass, is often observed when weight is lost. This study aimed to clarify the nutritional status and physical fitness of local elementary school children and to investigate the factors associated with nutritional status. This study evaluated measures that can reduce the tendency toward obesity and recommends exercise that can reduce weight while maintaining or increasing muscle strength. A total of 911 elementary school children were recruited for this study. All the participants completed anthropometric measurements, dietary surveys, and physical fitness tests. Compared with the Chinese obesity criteria, the proportions of obese and overweight subjects were generally high [22 (rural girls) to 47% (urban boys)], and urban children had a higher obesity rate than rural children. Overall, rural children had better physical fitness test results than urban children did. Skipping rope was correlated with muscle mass. Exercise time (β = −0.31, p < 0.01), skipping rope (β = −0.25, p < 0.01), screen time (β= 0.23, p < 0.01); sit-ups (β = −0.20, p < 0.01); 400-m run (β = −0.19, p < 0.01); urban or rural area (β = 0.18, p < 0.01); oil intake (β = 0.15, p < 0.01), family income (β = 0.11, p < 0.05); and sex (β = −0.10, p < 0.05) were significant predictive factors for overweight and obesity, respectively. The diet of schoolchildren can be improved by reducing the intake of grain and edible oils. Physical fitness of schoolchildren can be improved by increasing exercise time and selecting exercises with higher metabolic equivalents. Rope skipping appears to be the best option because it can ameliorate obesity by increasing muscle strength. The results of this study can provide a reference for the development of obesity intervention methods for children in China and worldwide.
The full-genome characterization and phylogenetic analysis of bovine herpesvirus type 1.2 isolated in China

Bovine herpesvirus type 1 (BHV-1) causes bovine respiratory disease that poses a significant threat to the cattle industry. The prevalence of BHV-1 has recently increased in China. However, the lack of information about the prevalent isolates limits the control of the disease. In this study, a novel strain of BHV-1 was isolated from nasal swabs of Holstein cows in 2020 in China, designated as BHV SHJS. The genome of BHV strain SHJS is 135, 102 bp in length and highly similar to strain SP1777 (KM258883.1) with an identity of 99.64%. Mutations, insertions, or deletions mainly occur in UL27, UL44, and US8, etc., relative to the different genomic coordinates. Phylogenetic tree of UL44 (gC) showed that BHV strain SHJS belongs to BHV-1.2b cluster. The result showed that the strain had a different evolutionary origin from those prevalent in China. This study will enrich our knowledge regarding BHV outbreak strains in China and contribute to the prevention and pathogenic studies of BHV-1.2.
A linear algorithm for the restricted subtraction games

The subtraction game is a well-known problem in the field of game theory, which is often called a one-heap Nim game. There are two players, a heap of tokens, and a strategy matrix, in this game. It is called a restricted subtraction game if some constraints are imposed on the strategy matrix. The subtraction game could be solved by a classical algorithm with a query complexity no less than O(N 2) and computed by an O ( N 3 2 l o g N ) quantum query algorithm with an error probability ϵ ≤ 1 N . The restricted subtraction game proposed by Huang et al. can be computed by an exact quantum algorithm with O ( N 3 2 ) queries. They also proved that the classical exact query complexity is Θ(N 2). In this study, we use an array and an adjacency list to replace the strategy matrix and propose another more general subtraction game than the one introduced by Huang et al. Based on dynamic programming and the replaced game strategy, two linear classical query algorithms are designed to solve the restricted subtraction game proposed by Huang and this study, respectively.
The vascular protective effect of matrix Gla protein during kidney injury

Matrix Gla protein (MGP) is a small secreted protein and requires vitamin K dependent γ-carboxylation for its function. MGP has been identified as a local inhibitor of vascular calcification because MGP-deficient mice die due to severe arterial calcification and resulting arterial rupture. Clinical trials revealed that reduction in active MGP predicts poor prognosis in patients due to cardiovascular complications. However, recent studies showed that MGP controls angiogenesis during development. MGP-deficient mice demonstrated abnormal hypervascularization and arteriovenous malformations in kidneys and other organs. This abnormal angiogenesis is largely caused by excessive expression of vascular endothelial growth factor-A (VEGF-A) and VEGF receptor-2 (VEGFR2). However, only a few studies have investigated the roles of MGP in tissue injury. We observed mesangial cell proliferation and mild interstitial fibrosis in addition to increased capillaries in kidneys of MGP-null mice even without injury. We also created a mouse model with kidney injury and found that kidney damage greatly increases MGP expression in peritubular capillary endothelial cells and tubular epithelial cells. Finally, our study showed that impairment of MGP expression aggravates peritubular capillary rarefaction and accumulation of collagen-producing myofibroblasts following kidney injury. Peritubular capillary damage induces capillary loss as well as trans-differentiation of vascular pericytes into myofibroblasts. These results indicate that MGP has the vascular protective effect in the injured kidney. Clinical trials have already started to test the efficacy of MGP activation to repair vascular calcification in patients with chronic kidney diseases. In this “Hypothesis and Theory” article, we discuss possible mechanisms by which MGP protects against vascular damage during tissue injury based on our experimental results and previous results from other research groups.
Scintillation-based Search for Off-pulse Radio Emission from Pulsars

We propose a new method to detect off-pulse (unpulsed and/or continuous) emission from pulsars using the intensity modulations associated with interstellar scintillation. Our technique involves obtaining the dynamic spectra, separately for on-pulse window and off-pulse region, with time and frequency resolutions to properly sample the intensity variations due to diffractive scintillation and then estimating their mutual correlation as a measure of off-pulse emission, if any. We describe and illustrate the essential details of this technique with the help of simulations, as well as real data. We also discuss the advantages of this method over earlier approaches to detect off-pulse emission. In particular, we point out how certain nonidealities inherent to measurement setups could potentially affect estimations in earlier approaches and argue that the present technique is immune to such nonidealities. We verify both of the above situations with relevant simulations. We apply this method to the observation of PSR B0329+54 at frequencies of 730 and 810 MHz made with the Green Bank Telescope and present upper limits for the off-pulse intensity at the two frequencies. We expect this technique to pave the way for extensive investigations of off-pulse emission with the help of existing dynamic spectral data on pulsars and, of course, with more sensitive long-duration data from new observations.
Reflection as teachers: Our critical developments

This study utilized Self-Study of Practice methodology to examine stories of our teacher development to explore the role of reflection in helping us grapple with challenging experiences in our teaching. Through emergent coding and collaborative analysis, we examine how reflection critically impacts the trajectory of practicing teachers. Our stories and subsequent discussion reveal recurring themes that suggest practices, attitudes, and skills reflective teachers implement to improve their understanding of the teacher-self and influence positive student outcomes.
Editorial: The effects of chemotherapy towards the tumor microenvironment

The effects of chemotherapy towards the tumor microenvironment Chemotherapy is the ﬁ rst-line therapy for cancers lacking tailored targeted therapies. Nevertheless, the ef ﬁ cacy of cytotoxic compounds is severely compromised by intra- and inter-tumor heterogeneity and most importantly by the presence of pro-tumorigenic cells and factors belonging to the tumor microenvironment. A comprehensive review reported on this Research Topic embraces multiple insights regarding the resistance of cancer cells to chemotherapeutic drugs (Gaggianesi et al.). Compelling evidence demonstrates that the resistance to chemotherapeutic agents is sustained by the presence of a subpopulation of stem-like cells, named cancer stem cells, endowed with tumor-initiating and metastatic capabilities. The studies listed by Gaggianesi et al. attribute a fundamental role to tumor microenvironment in dictating cancer stem cells refractoriness. The most described mechanisms are related to the upregulation in the expression of drug ef ﬂ ux transporters, anti-apoptotic proteins and the activation
Roles and crosstalks of macrophages in diabetic nephropathy

Diabetic nephropathy (DN) is the most common chronic kidney disease. Accumulation of glucose and metabolites activates resident macrophages in kidneys. Resident macrophages play diverse roles on diabetic kidney injuries by releasing cytokines/chemokines, recruiting peripheral monocytes/macrophages, enhancing renal cell injuries (podocytes, mesangial cells, endothelial cells and tubular epithelial cells), and macrophage-myofibroblast transition. The differentiation and cross-talks of macrophages ultimately result renal inflammation and fibrosis in DN. Emerging evidence shows that targeting macrophages by suppressing macrophage activation/transition, and macrophages-cell interactions may be a promising approach to attenuate DN. In the review, we summarized the diverse roles of macrophages and the cross-talks to other cells in DN, and highlighted the therapeutic potentials by targeting macrophages.
Functional analysis of the short splicing variant encoded by CHI3L1/YKL-40 in glioblastoma

The glycoprotein YKL-40 has been well studied as a serum biomarker of prognosis and disease status in glioblastoma. YKL-40 is a chitinase-like protein with defective chitinase activity that plays an important role in promoting cell proliferation, migration, and metastasis in glioblastoma multiforme (GBM). The short variant (SV) of YKL-40, generated by an alternative splicing event that splices out exon 8, was reported in the early developing human musculoskeletal system, although its role in GBM is still unknown. Our results showed that individual glioblastoma cell lines displayed increased expression of the short variant of YKL-40 after low serum treatment. In addition, unlike the full-length (FL) version, which was localized to all cell compartments, the short isoform could not be secreted and was localized only to the cytoplasm. Functionally, FL YKL-40 promoted cell proliferation and migration, whereas SV YKL-40 suppressed them. Transcriptome analysis revealed that these opposing roles of the two isoforms may be modulated by differentially regulating several oncogenic-related pathways, including p53, the G2/M checkpoint, and MYC-related signaling. This study may provide new ideas for the development of targeted anti-YKL-40 therapy in GBM treatment.
Repairing tendon-exposed wounds by combing the Masquelet technique with dermoplasty

Background Wound repair is a new field that has emerged in China in the last 5 years. Exposed tendon wounds are one of the most common problems faced in wound treatment today, as the poor blood supply leads to low survival rates of skin grafts. This paper explores the feasibility of applying the Masquelet technique to repair tendon-exposed wounds. Method We examined 12 patients with tendon-exposed wounds, 5 males and 7 females, from January 2021 to November 2021, including 2 patients with post-traumatic wounds, 8 diabetic patients with dorsal wounds, and 2 patients with various chronic infections. The Masquelet technique was employed to treat these wounds. The wound surface was sealed with antibiotic bone cement to form an induction membrane, the cement was removed after 3–4 weeks, and the wound was repaired with skin grafts to observe survival, appearance, texture, healing, and related functions. Results All wounds were covered with antibiotic bone cement, and after 3–4 weeks, an induction membrane was applied, and in 10 out of 12 patients, full-thickness skin grafts were applied, and the patients survived. However, in 2 patients, the skin became partially necrotic, but these patients recovered by changing medications. Conclusion The current study found that direct skin grafting may effectively treat exposed tendon wounds once the Masquelet approach generates the induction membrane. Further, this method is less difficult, less expensive, and easier to care for the procedure that deserves to be used more frequently.
Determination of pain intensity, pain-related disability, anxiety, depression, and perceived stress in Polish adults with temporomandibular disorders: A prospective cohort study

Background There is a need to assess a relationship between the psychoemotional state of patients and the occurrence and the intensity of pain and temporomandibular disorders (TMD) in relation to a Polish population. There are no such precision data in the literature relating to the population of big Eastern European country. The study conducted by the authors refer to a large group of male and female adult patients of the Polish population in a different age profile. As a result, this study provides a picture of the situation that also takes into account population characteristics that may affect the clinical situation of patients. Objective The aim of the study was to assess the pain intensity, pain-related disability, anxiety, depression, and perceived stress among Polish adults with TMD as well as the association between psychosocial impairment and TMD. Materials and methods This prospective cohort study included 219 adult patients from the Outpatient Clinic for Temporomandibular Disorders at the Academic Dental Polyclinic in Wroclaw. The patients completed validated questionnaires, and received a TMD diagnosis based on a standardized examination (Diagnostic Criteria for Temporomandibular Disorders) performed by a qualified dentist. A statistical analysis was carried out on the collected data. Results Myalgia was the most commonly diagnosed condition among the TMD patients. Furthermore, the prevalence of perceived stress, anxiety, and depression was high in the studied sample. Females showed more depression symptoms than males, while the level of anxiety and stress was similar in both groups. The most statistically significant correlation was observed between the group of masticatory muscle disorders and the level of depression, stress, pain intensity, and pain-related disability. Conclusion Due to the high prevalence of increased levels of anxiety, depression, and perceived stress, it is essential to screen the psychosocial status of Polish TMD adult patients. Psychosocial status may have an impact on a studied patient’s response to treatment and pain intensity, and pain-related disability. Therefore, Polish TMD adult patients should be provided with management based on an interdisciplinary approach. Clinical trial registration [https://clinicaltrials.gov/], identifier [NCT05183503].
Magnetic resonance T1-mapping quantitatively assesses the severity of thyroid destruction in patients with autoimmune thyroiditis

Objective Autoimmune thyroiditis (AIT) is a common organ-specific autoimmune disease. Longitudinal relaxation time mapping (T1-mapping) analyzed by magnetic resonance imaging is a new method for evaluating inflammation or fibrosis. This study aimed to investigate the relationship between thyroid T1-mapping value and degree of intrathyroidal inflammation and destruction in euthyroid AIT patients. Methods This case-control study recruited 28 drug-naïve AIT patients and 18 healthy controls. Thyroid specimens were collected for assessing the mRNA expression of inflammatory factors and histopathologic examination. T1-mapping values were measured using a modified look-locker inversion-recovery sequence in all participants. Results The positive rate of pathological diagnosed AIT was only 83.3% in the AIT group diagnosed by positive TPOAb and/or TgAb and typical ultrasonic manifestations, while 7.1% of the control group was diagnosed as AIT by pathological manifestations. Receiver operating characteristic curve analysis revealed a very high diagnostic value of thyroid T1-mapping values for pathological diagnosed AIT (area under the curve was 0.950, 95%CI: 0.843 – 0.993, P < 0.001). In the patients with pathological diagnosed AIT, thyroid T1-mapping values were significantly associated with the mRNA expression of INF-γ (r = 0.343, P < 0.05), TNF-α (r = 0.352, P < 0.01), and IL-1β (r = 0.673, P < 0.01) in thyroid tissues. Moreover, histopathologic examination showed that thyroid T1-mapping values can properly reflect the degree of thyroid destruction in AIT patients. Conclusions Thyroid T1-mapping values had a very high diagnostic value for AIT. In euthyroid AIT patients, thyroid T1-mapping values better reflect degree of intrathyroidal inflammation and destruction.
Combined brain network topological metrics with machine learning algorithms to identify essential tremor

Background and objective Essential tremor (ET) is a common movement syndrome, and the pathogenesis mechanisms, especially the brain network topological changes in ET are still unclear. The combination of graph theory (GT) analysis with machine learning (ML) algorithms provides a promising way to identify ET from healthy controls (HCs) at the individual level, and further help to reveal the topological pathogenesis in ET. Methods Resting-state functional magnetic resonance imaging (fMRI) data were obtained from 101 ET and 105 HCs. The topological properties were analyzed by using GT analysis, and the topological metrics under every single threshold and the area under the curve (AUC) of all thresholds were used as features. Then a Mann-Whitney U-test and least absolute shrinkage and selection operator (LASSO) were conducted to feature dimensionality reduction. Four ML algorithms were adopted to identify ET from HCs. The mean accuracy, mean balanced accuracy, mean sensitivity, mean specificity, and mean AUC were used to evaluate the classification performance. In addition, correlation analysis was carried out between selected topological features and clinical tremor characteristics. Results All classifiers achieved good classification performance. The mean accuracy of Support vector machine (SVM), logistic regression (LR), random forest (RF), and naïve bayes (NB) was 84.65, 85.03, 84.85, and 76.31%, respectively. LR classifier achieved the best classification performance with 85.03% mean accuracy, 83.97% sensitivity, and an AUC of 0.924. Correlation analysis results showed that 2 topological features negatively and 1 positively correlated with tremor severity. Conclusion These results demonstrated that combining topological metrics with ML algorithms could not only achieve high classification accuracy for discrimination ET from HCs but also help us to reveal the potential topological pathogenesis of ET.
Views and experiences on the use of voice assistants by family and professionals supporting people with cognitive impairments

The use of voice assistants (e.g., Amazon Alexa, Google Home) is being widely advocated as part of supporting people living with dementia at home. The development of this technology is largely driven by industry, and there is little research to determine how family carers and professionals use voice assistants with people with dementia. This paper presents the findings from further analysis of data from two studies: Study 1—a qualitative study that aimed to explore the views and expectations of family carers and professionals who use voice assistants to support people with a cognitive impairment at home, and Study 2—a qualitative enquiry aiming to identify the views and barriers on using voice assistants by family carers of people with dementia and professionals, together with a pilot case study evaluating a prototype that addresses barriers identified during the enquiry, entitled IntraVox. Based on processing of smart home sensor data, IntraVox uses a personalised human voice to send prompts and reminders to end-users to conduct daily life activities and to activate smart home processes using voice assistants. The results of the qualitative studies indicate that family carers and professionals use voice assistants in their caring role for home automation, skills maintenance and development, prompts and reminders, behaviour and environment monitoring, and for leisure and social interaction support. The findings also show that family carers and professionals have specific challenges that need to be overcome for them to realise the benefits that may be gained through the use of voice assistants within technology enabled care. The pilot case study also provided a useful demonstration that interoperability can be achieved to enable exchanges between IntraVox and voice assistants, with the aim of providing customised and personalised technological solutions that address some of the barriers that people with dementia and their carers face in the use of this technology.
15 Parental Care Patterns, Proximate and Ultimate Causes, and Consequences

time in nest, and number of eggs at the beginning and end were recorded. The males were then euthanized by cervical transection and brains sectioned and stained for IT and rpS6. A total of 392 IT cells were identified in the eight fish and each IT cell was subsequently analyzed for co-expression of rpS6 by focusing through the cell on the z-axis. Good and bad fathers were identified by median split of a composite fathering score considering total number of paternal behaviors, time in nest, and number of eggs lost.