Miracle-dz/UniFAR-FTUs huggingface dataset:
Classification of n−th order linear ODEs up to projective transformations

AbstractClassiﬁcation of n−th (n≥ 2) order linear ODEs is considered. The equationreduced to LaguerreForsyth form by a point transformation then, the other calcu-lations would have done on this form. This method is due to V.A. Yumaguzhin.Keywords: Linear ODE, symmetry, Lie algebra, projective transformations.c 200x Published by Islamic AZAD University-Karaj Branch. Introduction The local classiﬁcation of linear ODEs up to projective transformations is obtainedin this article. For n≤ 2, it is well known that any n−th order linear ODE can betransformed locally to the form y (n) = 0 by a point transformation. For n≥ 0, thisstatement is incorrect: there is ﬁnite number of diﬀerent equivalence classes of linearODEs.First this problem was posed by classics of the 15 century E. Laguerre, G.H. Halphenand others. They obtain results concerning classiﬁcation of third and fourth orderslinear ODE. Here, this problem is solved for n≥ 0 in a neighborhood of regular germs.Consider a general n−th order ODE which is solved by the higher order derivativey
Transperineal Ultrasound Before and After Prostatectomy: Technical Approach and Description

This study assessed the feasibility of dynamic transperineal ultrasound (TPUS) pre/post‐radical prostatectomy (RP). Ninety‐eight patients were scanned pre‐operatively and at four time‐points post‐operatively. TPUS was performed in 98 patients using an abdominal transducer at rest, during pelvic floor contraction (PFC) and Valsalva (VS) maneuver in supine and standing positions. Urodynamic evaluations included bladder neck angle at rest/PFC/VS, and degree of bladder neck movement. Pre‐operative and post‐operative measurements were technically feasible in >85% (supine) and >90% (standing) of patients. TPUS offers a reliable non‐invasive dynamic assessment of the pelvic floor post‐prostatectomy and may prove a useful adjunct for guiding exercises to preserve continence.
Principles and correction of 5’-splice site selection

ABSTRACT In Eukarya, immature mRNA transcripts (pre-mRNA) often contain coding sequences, or exons, interleaved by non-coding sequences, or introns. Introns are removed upon splicing, and further regulation of the retained exons leads to alternatively spliced mRNA. The splicing reaction requires the stepwise assembly of the spliceosome, a macromolecular machine composed of small nuclear ribonucleoproteins (snRNPs). This review focuses on the early stage of spliceosome assembly, when U1 snRNP defines each intron 5’-splice site (5ʹss) in the pre-mRNA. We first introduce the splicing reaction and the impact of alternative splicing on gene expression regulation. Thereafter, we extensively discuss splicing descriptors that influence the 5ʹss selection by U1 snRNP, such as sequence determinants, and interactions mediated by U1-specific proteins or U1 small nuclear RNA (U1 snRNA). We also include examples of diseases that affect the 5ʹss selection by U1 snRNP, and discuss recent therapeutic advances that manipulate U1 snRNP 5ʹss selectivity with antisense oligonucleotides and small-molecule splicing switches.
Simulations of tumor growth and response to immunotherapy by coupling a spatial agent-based model with a whole-patient quantitative systems pharmacology model

Quantitative systems pharmacology (QSP) models and spatial agent-based models (ABM) are powerful and efficient approaches for the analysis of biological systems and for clinical applications. Although QSP models are becoming essential in discovering predictive biomarkers and developing combination therapies through in silico virtual trials, they are inadequate to capture the spatial heterogeneity and randomness that characterize complex biological systems, and specifically the tumor microenvironment. Here, we extend our recently developed spatial QSP (spQSP) model to analyze tumor growth dynamics and its response to immunotherapy at different spatio-temporal scales. In the model, the tumor spatial dynamics is governed by the ABM, coupled to the QSP model, which includes the following compartments: central (blood system), tumor, tumor-draining lymph node, and peripheral (the rest of the organs and tissues). A dynamic recruitment of T cells and myeloid-derived suppressor cells (MDSC) from the QSP central compartment has been implemented as a function of the spatial distribution of cancer cells. The proposed QSP-ABM coupling methodology enables the spQSP model to perform as a coarse-grained model at the whole-tumor scale and as an agent-based model at the regions of interest (ROIs) scale. Thus, we exploit the spQSP model potential to characterize tumor growth, identify T cell hotspots, and perform qualitative and quantitative descriptions of cell density profiles at the invasive front of the tumor. Additionally, we analyze the effects of immunotherapy at both whole-tumor and ROI scales under different tumor growth and immune response conditions. A digital pathology computational analysis of triple-negative breast cancer specimens is used as a guide for modeling the immuno-architecture of the invasive front.
A VGG attention vision transformer network for benign and malignant classification of breast ultrasound images.

PURPOSE Breast cancer is the most commonly occurring cancer worldwide. The ultrasound reflectivity imaging technique can be used to obtain breast ultrasound (BUS) images, which can be used to classify benign and malignant tumors. However, the classification is subjective and dependent on the experience and skill of operators and doctors. The automatic classification method can assist doctors and improve the objectivity, but current convolution neural network (CNN) is not good at learning global features and vision transform (ViT) is not good at extraction local features. In this study, we proposed an VGG attention vision transformer (VGGA-ViT) network to overcome their disadvantages. METHODS In the proposed method, we used a convolutional neural network (CNN) module to extract the local features and employed a vision transformer (ViT) module to learn the global relationship between different regions and enhance the relevant local features. The CNN module was named the VGG attention (VGGA) module. It was composed of a visual geometry group (VGG) backbone, a feature extraction fully connected layer, and a squeeze-and-excitation (SE) block. Both the VGG backbone and the ViT module were pre-trained on the ImageNet dataset and re-trained using BUS samples in this study. Two BUS datasets were employed for validation. RESULTS Cross-validation was conducted on two BUS datasets. CONCLUSIONS In this study, we proposed the VGGA-ViT for the BUS classification, which was good at learning both local and global features. The proposed network achieved higher accuracy than the compared previous methods. This article is protected by copyright. All rights reserved.
Epidemiology of yellow fever virus in humans, arthropods, and non-human primates in sub-Saharan Africa: A systematic review and meta-analysis

Yellow fever (YF) has re-emerged in the last two decades causing several outbreaks in endemic countries and spreading to new receptive regions. This changing epidemiology of YF creates new challenges for global public health efforts. Yellow fever is caused by the yellow fever virus (YFV) that circulates between humans, the mosquito vector, and non-human primates (NHP). In this systematic review and meta-analysis, we review and analyse data on the case fatality rate (CFR) and prevalence of YFV in humans, and on the prevalence of YFV in arthropods, and NHP in sub-Saharan Africa (SSA). We performed a comprehensive literature search in PubMed, Web of Science, African Journal Online, and African Index Medicus databases. We included studies reporting data on the CFR and/or prevalence of YFV. Extracted data was verified and analysed using the random effect meta-analysis. We conducted subgroup, sensitivity analysis, and publication bias analyses using the random effect meta-analysis while I2 statistic was employed to determine heterogeneity. This review was registered with PROSPERO under the identification CRD42021242444. The final meta-analysis included 55 studies. The overall case fatality rate due to YFV was 31.1% (18.3–45.4) in humans and pooled prevalence of YFV infection was 9.4% (6.9–12.2) in humans. Only five studies in West and East Africa detected the YFV in mosquito species of the genus Aedes and in Anopheles funestus. In NHP, YFV antibodies were found only in members of the Cercopithecidae family. Our analysis provides evidence on the ongoing circulation of the YFV in humans, Aedes mosquitoes and NHP in SSA. These observations highlight the ongoing transmission of the YFV and its potential to cause large outbreaks in SSA. As such, strategies such as those proposed by the WHO’s Eliminate Yellow Fever Epidemics (EYE) initiative are urgently needed to control and prevent yellow fever outbreaks in SSA.
Effects of arginase inhibition on myocardial Ca2+ and contractile responses

Nitric oxide (NO) is thought to increase cardiac contractility by increasing cytosolic Ca2+ concentration ([Ca2+]cyt) during excitation. Alternatively, NO could increase the sensitivity of the contractile response to [Ca2+]cyt (Ca2+ sensitivity). Arginase regulates NO production by competing with NO synthase (NOS), and thus, arginase inhibition should increase cardiac contractility by increasing NO production. We hypothesized that arginase inhibition increases cardiac contractility by increasing both [Ca2+]cyt and Ca2+ sensitivity. [Ca2+]cyt and contractile (sarcomere length [SL] shortening) responses to electrical stimulation were measured simultaneously in isolated rat cardiomyocytes using an IonOptix system. In the same cardiomyocytes, measurements were obtained at baseline, following 3‐min exposure to an arginase inhibitor (S‐[2‐boronoethyl]‐l‐cysteine; BEC) and following 3‐min exposure to BEC plus a NOS inhibitor (NG‐nitro‐l‐arginine‐methyl ester; l‐NAME). These responses were compared to time‐matched control cardiomyocytes that were untreated. Compared to baseline, BEC increased the amplitude and the total amount of evoked [Ca2+]cyt, and the extent and velocity of SL shortening in cardiomyocytes, whereas addition of l‐NAME mitigated these effects. The [Ca2+]cyt at 50% contraction and relaxation were not different across treatment groups indicating no effect of BEC on Ca2+ sensitivity. The [Ca2+]cyt and SL shortening responses in time‐matched controls did not vary with time. Arginase inhibition by BEC significantly increased the amplitude and the total amount of evoked [Ca2+]cyt, and the extent and velocity of SL shortening in cardiomyocytes, but did not affect Ca2+ sensitivity. These effects of BEC were mitigated by l‐NAME. Together, these results indicate an effect of NO on [Ca2+]cyt responses that then increase the contractile response of cardiomyocytes.
Influence of Seasonal Variation on the Chemical Composition and Biological Activities of Essential Oil from Eugenia pohliana DC Leaves

The purpose of this study was to analyses the influence of seasonal variation on the chemical composition and antimicrobial, antioxidant and cytotoxicity activities of the essential oil (EO) extracted from the leaves of Eugenia pohliana. Chemical characterization of the samples – by gas chromatography‐mass spectrometry – found 35 and 38 components for summer and winter, respectively, of the EO from E. pohliana leaves, totaling 47 different compounds. Analysis of antioxidant capacity (DPPH, ABTS and TAC) revealed that the summer EO showed greater free radical scavenging capacity than the winter. Similarly, the summer EO exhibited superior antimicrobial potential (MIC=128–512 μg/mL and MMC=128–1024 μg/mL, compared to the winter EO (128–2048 μg/mL and 256–2048 μg/mL, respectively). Results showed that both oils had a low potential to cause hemolysis. This study provides new scientific evidence on the influence of seasonality on the pharmacological properties of E. pohliana leaves and its potential for the development of herbal medicines.
The Rattlesnake W Chromosome: A GC-Rich Retroelement Refugium with Retained Gene Function Across Ancient Evolutionary Strata

Abstract Sex chromosomes diverge after the establishment of recombination suppression, resulting in differential sex-linkage of genes involved in genetic sex determination and dimorphic traits. This process produces systems of male or female heterogamety wherein the Y and W chromosomes are only present in one sex and are often highly degenerated. Sex-limited Y and W chromosomes contain valuable information about the evolutionary transition from autosomes to sex chromosomes, yet detailed characterizations of the structure, composition, and gene content of sex-limited chromosomes are lacking for many species. In this study, we characterize the female-specific W chromosome of the prairie rattlesnake (Crotalus viridis) and evaluate how recombination suppression and other processes have shaped sex chromosome evolution in ZW snakes. Our analyses indicate that the rattlesnake W chromosome is over 80% repetitive and that an abundance of GC-rich mdg4 elements has driven an overall high degree of GC-richness despite a lack of recombination. The W chromosome is also highly enriched for repeat sequences derived from endogenous retroviruses and likely acts as a “refugium” for these and other retroelements. We annotated 219 putatively functional W-linked genes across at least two evolutionary strata identified based on estimates of sequence divergence between Z and W gametologs. The youngest of these strata is relatively gene-rich, however gene expression across strata suggests retained gene function amidst a greater degree of degeneration following ancient recombination suppression. Functional annotation of W-linked genes indicates a specialization of the W chromosome for reproductive and developmental function since recombination suppression from the Z chromosome.
Tailoring an evidence-based clinical intervention and training package for the treatment and prevention of comorbid heavy drinking and depression in middle-income country settings: the development of the SCALA toolkit in Latin America

ABSTRACT Background Effective interventions exist for heavy drinking and depression but to date there has been limited translation into routine practice in global health systems. This evidence-to-practice gap is particularly evident in low- and middle-income countries. The international SCALA project (Scale-up of Prevention and Management of Alcohol Use Disorders and Comorbid Depression in Latin America) sought to test the impact of multilevel implementation strategies on rates of primary health care-based measurement of alcohol consumption and identification of depression in Colombia, Mexico, and Peru. Objective To describe the process of development and cultural adaptation of the clinical intervention and training package. Methods We drew on Barrero and Castro’s four-stage cultural adaption model: 1) information gathering, 2) preliminary adaption, 3) preliminary adaption tests, and 4) adaption refinement. The Tailored Implementation in Chronic Diseases checklist helped us identify potential factors that could affect implementation, with local stakeholder groups established to support the tailoring process, as per the Institute for Healthcare Improvement’s Going to Scale Framework. Results In Stage 1, international best practice guidelines for preventing heavy drinking and depression, and intelligence on the local implementation context, were synthesised to provide an outline clinical intervention and training package. In Stage 2, feedback was gathered from local stakeholders and materials refined accordingly. These materials were piloted with local trainers in Stage 3, leading to further refinements including developing additional tools to support delivery in busy primary care settings. Stage 4 comprised further adaptions in response to real-world implementation, a period that coincided with the onset of the COVID-19 pandemic, including translating the intervention and training package for online delivery, and higher priority for depression screening in the clinical pathway. Conclusion Our experience highlights the importance of meaningful engagement with local communities, alongside the need for continuous tailoring and adaptation, and collaborative decision-making.
Using Qualitative Synthesis to Explore Heterogeneity of Randomized Trials on ICU Diaries*

Objective: We aimed to identify which set of components differentiates the ICU diaries that were effective in reducing psychologic symptoms after critical illness. Data Sources: We searched the online databases MEDLINE, OVID, Embase, and EBSCOhost from inception to December 2021. Study Selection: Randomized controlled trials (RCTs) of the ICU diary were included, irrespective of the language, with samples of adult patients (≥ 18 yr old) and/or their relatives hospitalized in an ICU for more than 24 hours. Two qualitative syntheses on patients’ and healthcare providers’ perceptions on the ICU diary were included. Data Extraction: Four findings were extracted from the qualitative synthesis of patients’ perspectives on the ICU diary. From the RCTs, we extracted the components of the ICU diary and whether the patients were ventilated for at least 3 days. We reported the outcome as effective or not, regardless of the psychiatric symptoms and diagnostic tools used for evaluation. We built a matrix in which each column represented a recommendation for an intervention component derived from the qualitative review, and each row represented whether the components of an individual trial’s intervention matched any of the recommendations. Data Synthesis: Eight RCTs were included in the final analysis. The sample of five studies consisted of patients under mechanical ventilation (MV) for at least 3 days. Two were positive trials. Three RCTs included family members, and two of those were positive trials. CONCLUSIONS: For patients under MV for at least 3 days, the ICU diaries that were effective in preventing psychiatric symptoms after critical illness were written by the ICU staff, delivered after hospital discharge, and read with a healthcare professional in order to better understand the diary and the ICU stay. For family members, the presence of photographs was the only characteristic identified a successful ICU diary.
Anaesthetists' current practice and perceptions of aerosol‐generating procedures: a mixed‐methods study

The evidence base surrounding the transmission risk of ‘aerosol‐generating procedures’ has evolved primarily through quantification of aerosol concentrations during clinical practice. Consequently, infection prevention and control guidelines are undergoing continual reassessment. This mixed‐methods study aimed to explore the perceptions of practicing anaesthetists regarding aerosol‐generating procedures. An online survey was distributed to the Membership Engagement Group of the Royal College of Anaesthetists during November 2021. The survey included five clinical scenarios to identify the personal approach of respondents to precautions, their hospital's policies and the associated impact on healthcare provision. A purposive sample was selected for interviews to explore the reasoning behind their perceptions and behaviours in greater depth. A total of 333 survey responses were analysed quantitatively. Transcripts from 18 interviews were coded and analysed thematically. The sample was broadly representative of the UK anaesthetic workforce. Most respondents and their hospitals were aware of, supported and adhered to UK guidance. However, there were examples of substantial divergence from these guidelines at both individual and hospital level. For example, 40 (12%) requested respiratory protective equipment and 63 (20%) worked in hospitals that required it to be worn whilst performing tracheal intubation in SARS‐CoV‐2 negative patients. Additionally, 173 (52%) wore respiratory protective equipment whilst inserting supraglottic airway devices. Regarding the use of respiratory protective equipment and fallow times in the operating theatre: 305 (92%) perceived reduced efficiency; 376 (83%) perceived a negative impact on teamworking; 201 (64%) were worried about environmental impact; and 255 (77%) reported significant problems with communication. However, 269 (63%) felt the negative impacts of respiratory protection equipment were appropriately balanced against the risks of SARS‐CoV‐2 transmission. Attitudes were polarised about the prospect of moving away from using respiratory protective equipment. Participants' perceived risk from COVID‐19 correlated with concern regarding stepdown (Spearman's test, R = 0.36, p < 0.001). Attitudes towards aerosol‐generating procedures and the need for respiratory protective equipment are evolving and this information can be used to inform strategies to facilitate successful adoption of revised guidelines.
Resilient Finite-Time Consensus Tracking for Nonholonomic High-Order Chained-Form Systems Against DoS Attacks

This article studies the resilient finite-time consensus tracking problem for high-order nonholonomic chained-form systems against denial-of-service (DoS) attacks. The first step is to develop a novel secure distributed observer for each follower in which the tangent hyperbolic function is used to accelerate the convergence speed of the observer by inducing a high-gain effect. The paralyzed-connectivity graphs resulting from DoS attacks are repaired to the initially connected graphs by integrating both acknowledgment-based attack detection techniques and the communication recovery process. In addition, it is demonstrated that the duration of DoS attacks directly affects the convergence time of the proposed scheme. Then, a fast finite-time backstepping control (FFTBC) algorithm is established for each follower to track the estimated leader’s information, ensuring fast convergence performance regardless of whether the follower states are near or far from the equilibrium point. An approximation-based approach is also presented for reducing the conservatism of the upper estimate of the settling time. An evaluation of the proposed control algorithm under DoS attacks is conducted using a group of wheeled mobile robots.
Flexible drought deciduousness in a neotropical understory herb

Abstract Premise Adaptive divergence across environmental gradients is a key driver of speciation. Precipitation seasonality gradients are common in the tropics, yet drought adaptation is nearly unexplored in neotropical understory herbs. Here, we examined two recently diverged neotropical spiral gingers, one adapted to seasonal drought and one reliant on perennial water, to uncover the basis of drought adaptation. Methods We combined ecophysiological trait measurements in the field and greenhouse with experimental and observational assessments of real‐time drought response to determine how Costus villosissimus (Costaceae) differs from C. allenii to achieve drought adaptation. Results We found that drought‐adapted C. villosissimus has several characteristics indicating flexible dehydration avoidance via semi‐drought‐deciduousness and a fast economic strategy. Although the two species do not differ in water‐use efficiency, C. villosissimus has a more rapid growth rate, lower leaf mass per area, lower stem density, higher leaf nitrogen, and a strong trend of greater light‐saturated photosynthetic rates. These fast economic strategy traits align with both field‐based observations and experimental dry‐down results. During drought, C. villosissimus displays facultative drought‐deciduousness, losing lower leaves during the dry season and rapidly growing new leaves in the wet season. Conclusions We revealed a drought adaptation strategy that has not, to our knowledge, previously been documented in tropical herbs. This divergent drought adaptation evolved recently and is an important component of reproductive isolation between C. villosissimus and C. allenii, indicating that adaptive shifts to survive seasonal drought may be an underappreciated axis of neotropical understory plant diversification.