Miracle-dz/UniFAR-FTUs huggingface dataset:
A Spatio-Temporal Modeling Framework for Surveillance Data of Multiple Infectious Pathogens With Small Laboratory Validation Sets

Abstract Many surveillance systems of infectious diseases are syndrome-based, capturing patients by clinical manifestation. Only a fraction of patients, mostly severe cases, undergo laboratory validation to identify the underlying pathogen. Motivated by the need to understand transmission dynamics and associate risk factors of enteroviruses causing the hand, foot, and mouth disease (HFMD) in China, we developed a Bayesian spatio-temporal modeling framework for surveillance data of infectious diseases with small validation sets. A novel approach was proposed to sample unobserved pathogen-specific patient counts over space and time and was compared to an existing sampling approach. The practical utility of this framework in identifying key parameters was assessed in simulations for a range of realistic sizes of the validation set. Several designs of sampling patients for laboratory validation were compared with and without aggregation of sparse validation data. The methodology was applied to the 2009 HFMD epidemic in southern China to evaluate transmissibility and the effects of climatic conditions for the leading pathogens of the disease, enterovirus 71, and Coxsackie A16. Supplementary materials for this article are available online.
Neuromuscular electrical stimulation for treatment of dysphagia in infants and young children with neurological impairment: a prospective pilot study

Objectives To describe the acceptability, safety and effectiveness of neuromuscular electrical stimulation (NMES) in infants and young children with neurological impairment (NI) who have severe dysphagia. Design A prospective pilot study using a before and after study design. Setting The Hospital for Sick Children, Toronto, Canada. Patients Ten infants and young children (0–24 months) with NI and severe dysphagia on videofluoroscopic swallow study (VFSS) who were referred to an occupational therapist (OT). Those with neurodegenerative conditions were excluded. Intervention NMES treatments lasting 20–45 min twice weekly for the duration of 2–4 months. The NMES was administered during feeding therapy sessions by a trained OT. Main outcome measures Improvement in swallowing function as measured by VFSS and the need for tube feeding, adverse events and parental acceptability. Results Seven of 10 enrolled subjects (median age, 8.9 months) completed biweekly NMES treatments (median number of treatments per subject, 18). All of the seven (100%) subjects who completed treatment showed an improvement in swallow function on VFSS. Of the five patients who were not safe to orally feed on any consistency of liquid or puree at baseline, three established full oral feeding and two established partial oral feeding. At baseline, 5/7 children were completely fed by tube versus 0/7 at the end of treatment. No adverse events occurred other than mild skin irritation at the site of electrode placement. Five of seven caregivers felt that feeding was improved and were satisfied with the intervention. Conclusions Our prospective pilot study of NMES in seven neurologically impaired infants and young children with severe dysphagia suggests that NMES is safe, acceptable to parents and has potential efficacy. Trials are needed to determine if any treatment benefit exists. Trial registration ClinicalTrials.gov NCT01723358.
Salvaged single-unit cord blood transplantation for 26 patients with hematologic malignancies not in remission.

Treatments for patients with hematologic malignancies not in remission are limited, but a few clinical studies have investigated the effects of salvaged unrelated cord blood transplantation (CBT). We retrospectively studied 19 patients with acute leukemia, 5 with myelodysplastic syndrome (MDS with refractory anemia with excess blasts [RAEB]), and 2 with non-Hodgkin's lymphoma who received 1 CBT unit ≤2 loci human leukocyte antigen (HLA)-mismatched after undergoing myeloablative conditioning regimens between July 2005 and July 2014. All of them were in non-remission before transplantation. The infused total nucleated cell (TNC) dose was 4.07 (range 2.76-6.02)×107/kg and that of CD34+ stem cells was 2.08 (range 0.99-8.65)×105/kg. All patients were engrafted with neutrophils that exceeded 0.5×109/L on median day +17 (range 14-37 days) and had platelet counts of >20×109/L on median day +35 (range 17-70 days). Sixteen patients (61.5%) experienced pre-engraftment syndrome (PES), and six (23.1%) patients progressed to acute graft-versus-host disease (GVHD). The cumulative incidence rates of II-IV acute GVHD and chronic GVHD were 50% and 26.9%, respectively. After a median follow-up of 27 months (range 5-74), 14 patients survived and 3 relapsed. The estimated 2-year overall survival (OS), disease-free survival (DFS), and non-relapse mortality (NRM) rates were 50.5%, 40.3%, and 35.2%, respectively. Salvaged CBT might be a promising modality for treating hematologic malignancies, even in patients with a high leukemia burden.
Detection and characterization of extended-spectrum-betalactamases (ESBL) producing Escherichia coli in animals

Beatriz Suay-García1, Fátima Galán2, Manuel A. Rodríguez-Iglesias2, María Teresa Pérez-Gracia1 1Área de Microbiología, Departamento de Farmacia, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad CEU Cardenal Herrera, C/ Santiago Ramón y Cajal, 46115, Alfara del Patriarca, Valencia, España. 2Servicio de Microbiología, Hospital Universitario Puerta del Mar. Cádiz, España.
Remnant Cholesterol, a Valuable Biomarker for Assessing Arteriosclerosis and Cardiovascular Risk: A Systematic Review

Arteriosclerosis, as the foundation for the development of cardiovascular diseases, is influenced by disturbances in lipid metabolism. Extensive research has consistently shown a correlation between conventional lipid parameters, arteriosclerosis, and cardiovascular diseases. Guidelines highlight the importance of targeting low-density lipoprotein cholesterol (LDL-C) for primary and secondary prevention of cardiovascular diseases, with reducing LDL-C remaining the primary lipid-lowering strategy. However, even when LDL-C is lowered to optimal levels, there is a residual risk of cardiovascular disease. Recent findings have brought attention to remnant cholesterol (RC) as a significant factor contributing to this residual risk. The close association between RC, arteriosclerosis, and cardiovascular diseases presents exciting opportunities for lifestyle interventions and medical treatments to control and lower RC levels, offering new targets for preventing and managing related cardiovascular conditions. Our systematic review sheds light on the importance of considering RC as a valuable biomarker in assessing arteriosclerosis and its potential impact on cardiovascular health. By understanding the link between remnant cholesterol and arteriosclerosis, researchers and healthcare professionals can develop targeted interventions to mitigate cardiovascular risks, thus improving public health outcomes and reducing the economic burden associated with cardiovascular diseases.
A Comparative of Two-Dimensional Statistical Moment Invariants Features in Formulating an Automated Probabilistic Machine Learning Identification Algorithm for Forensic Application

IBIS, ALIS, EVOFINDER, and CONDOR are the massive ballistics computerised technological machines that have typically been utilised in forensic laboratories to automatically locate similarities between images of cartridge cases and bullets. However, it imposed a long execution time and requires physical interpretation to consolidate the analysis results when employing these market-available technologies to accomplish ballistics matching tasks. Therefore, the principal objective of this study is to propose an improvised automated probabilistic machine learning identification algorithm by extracting the two-dimensional (2D) statistical moment invariants from the segmented region of interest (ROI) corresponding to the cartridge case and bullets images. To pursue this principal objective, several 2D statistical moment invariants have been compared and tested to determine the most suitable feature set applied in the proposed identification algorithm. The 2D statistical moment invariants employed include Orthogonal Legendre moments (OLM), Hu moments (HM), Tsirikolias-Mertzois moments (TMM), Pan-Keane moments (PKM), and Central Geometric moments (CGM). Moreover, the proposed identification algorithm is also tested in different scenarios, including based on the classification of strength association measurements between the extracted feature sets. The empirical results in this article revealed that the proposed identification algorithm applied with the CGM comprising the weak association classification yielded the best identification accuracy rates, which are >96.5% across all the sample sizes of the training set. These empirical results also conveyed that the superior proposed identification algorithm in this research could be developed as a mobile application for ballistics identification that can significantly reduce the time taken and conveniently perform the ballistics identification tasks.
Additional material

Appendix Density residual The approach to adjust for age and BMI formed a density residual ri for each woman i=1,…,n of the form ri = zi – (a +b1xi1 +b2xi2 +b3xi3) where a,b1,b2, and b3 are regression parameters; xi1 = age minus 47, xi2 = BMI minus 27.5 (mean BMI), and xi3=1 if a digital mammogram was used and 0 otherwise. Percent density di was included through the transformation from Warwick et al. [25] of ti = log{ di * / (1-di *) } where di * = (0.025+0.95 di) 0.5 and zi = ti / sd(t) was normalised to have unit variance by dividing by the observed standard deviation (sd). The density residual was obtained by fitting the linear regression model to the cohort by ordinary least squares. Age and mammogram type were available for all women, and missing BMI was dropped from estimation; mean BMI (27.5) was imputed for these women to obtain their residual. The point estimate of the intercept a = 0.263, age parameter b1=-0.019, BMI parameter b2 =-0.046 and type of mammogram parameter b3 = 0.119.
Strategies to reach and motivate migrant communities at high risk for TB to participate in a latent tuberculosis infection screening program: a community-engaged mixed methods study among Eritreans

Background: In the Netherlands, migrant populations with a high tuberculosis (TB) incidence are an important target group for TB prevention. However, there is a lack of insight in effective community-engaged strategies to reach and motivate these migrants to participate in latent TB infection (LTBI) screening and treatment programs. Methods: In cocreation with Eritrean key �gures and TB staff, we designed and executed six strategies to reach and motivate Eritrean communities to participate in LTBI programs, in �ve regions in the Netherlands. We registered participation in LTBI education and screening, and LTBI treatment uptake and completion. We used semi-structured group and individual interviews with Eritrean participants, key �gures, and TB staff to identify facilitators and barriers. Results: Uptake of LTBI education (13% - 75%) and consequent screening (10% - 124%) varied between strategies. LTBI screening uptake >100% resulted from educated participants motivating others to participate in screening. Two strategies, using face-to-face promotion and targeting smaller groups, were the most successful. The program resulted in high LTBI treatment initiation and completion (both 97%). Reported program barriers included: competing priorities in the target group, perceived good health, poor risk perception, and scepticism towards the program purpose. TB staff perceived the program as useful but demanding in terms of human resources. Conclusions: Eritrean migrant communities can be successfully reached and motivated for LTBI screening and treatment programs, when su�cient (human) resources are in place and community members, well-connected to and trusted by the community, are engaged in the design and execution of the program.
Are Short Selling Threats Beneficial to Stakeholders? Insights from Corporate Default Risk

Firms’ stakeholders are more concerned with avoiding default than shareholders. Employing the staggered short-sale deregulation on the Chinese stock market as quasi-exogenous shocks, we find that short selling threats is associated with higher corporate default risk, especially for firms that are more financially constrained, with higher growth rates, and higher information asymmetries. In addition, firms with higher ex-ante default risk experience an increase in the cost of debt and a reduction in new debt financing following the regulatory changes. The increase in default risk does not appear in U.S. listed firms in the context of the Regulation SHO’s pilot program. Overall, our findings indicate that short selling can adversely affect firm prospects and dampen stakeholders’ confidence through increasing the likelihood of default, especially in an environment where market participants are more alien to short selling, short sellers are more able to be manipulative due to weak investor protection, and firms are lack of effective tools to avoid downside risk.
Edinburgh Explorer Diagnosis, assessment and phenotyping of COPD: beyond FEV1

: COPD is now widely recognized as a complex heterogeneous syndrome, having both pulmonary and extrapulmonary features. In clinical practice, the diagnosis of COPD is based on the presence of chronic airflow limitation, as assessed by post-bronchodilator spirometry. The severity of the airflow limitation, as measured by percent predicted FEV 1 , provides important information to the physician to enable optimization of management. However, in order to accurately assess the complexity of COPD, there need to be other measures made beyond FEV 1 . At present, there is a lack of reliable and simple blood biomarkers to confirm and further assess the diagnosis of COPD. However, it is possible to identify patients who display different phenotypic characteristics of COPD that relate to clinically relevant outcomes. Currently, validated phenotypes of COPD include alpha-1 antitrypsin deficiency, and “frequent exacer-bators”. Recently, a definition and assessment of a new phenotype comprising patients with overlapping features of asthma and COPD has been suggested and is known as “asthma COPD overlap syndrome”. Several other phenotypes have been proposed, but require validation against clinical outcomes. Defining phenotypes requires the assessment of multiple factors indicating disease severity, its impact, and its activity. Recognition and validation of COPD phenotypes has an important role to play in the selection of evidence-based targeted therapy in the future management of COPD, but regardless of the diagnostic terms, patients with COPD should be assessed and treated according to their individual treatable characteristics.
Algorithms for Optimal Processing of Polarimetric Radar Data

Abstract : This report describes algorithms that make optimal use of polarimetric radar information to detect and classify targets in a ground clutter background. The optimal polarimetric detector (OPD) is derived; this algorithm processes the complete polarization scattering matrix (PSM) and provides the best possible detection performance from polarimetric radar data. Also derived is the best linear polarimetric detector, the polarimetric matched filter (PMF); the structure of this detector is shown to be related to simple polarimetric target types. Finally, the polarimetric whitening filter (PWF) is derived; this constant false alarm rate (CFAR) detector provides a simple alternative to the OPD for detecting targets in clutter. New K-distributed polarimetric target and clutter models are described; these models are used to predict the performance of the OPD, the PMF, and the PWF. The performance of these three algorithms is compared with that of simpler detectors that use only amplitude information to detect targets. The ability to classify target types by exploiting differences in polarimetric scattering properties is also discussed.
Mental Health in Social Context: What Is Normal and Who Defines It?

The purpose of the paper is to encourage a critical attitude and shed light on the background and perception (and not the definition) of “normal” through the prism of society, which to a large extent conditions human functioning and well-being. Understanding the variability of normality and mental health as a socially defined and ever-changing concept leads to normalisation and de -stigmatisation of not only mental disorders in the narrower sense, but also of mental distress of modern man, and is a prerequisite for reducing false diagnoses. Human vulnerability and inner struggles, which are the norm, not a peculiar, isolated problem, need to be seen as such while taking into account all the factors, i.e., biological, psychological, and social, affecting the person. A better understanding and use of the biopsychosocial model could help improve healthcare and make this world a little kinder.
Estimates of ground-water recharge based on streamflow-hydrograph methods: Pennsylvania

This study, completed by the U.S. Geological Survey (USGS) in cooperation with the Pennsylvania Department of Conservation and Natural Resources, Bureau of Topographic and Geologic Survey (TG estimates from RORA ranged from 7.7 to 29.3 inches. Estimates from the RORA program were about 2 inches greater than those derived from the PART program. Mean-monthly recharge was computed from the RORA program and was reported as a percentage of mean-annual recharge. On the basis of this analysis, the major ground-water recharge period in Pennsylvania typically is November through May; the greatest monthly recharge typically occurs in March.
Muscle scars in Miaolingian helcionelloids from Laurentia and the diversity of muscle scar patterns in Cambrian univalve molluscs

Abstract Two pairs of equidimensional muscle-attachment scars are described on the dorso-lateral surfaces of internal moulds of the helcionelloid molluscs Hensoniconus gen. nov. and Vendrascospira from the Henson Gletscher Formation (Cambrian, Miaolingian Series, Wuliuan Stage) of North Greenland (Laurentia). Two patterns of muscle scars are recognized in helcionelloids. In the Hensoniconus–Vendrascospira group, two pairs of sub-equally sized scars are located on the dorso-lateral surfaces. In the Bemella–Figurina group, thin, band-like scars are distributed on the sub-apical surface and along the dorsal (supra-apical) surface. Comparison of these rare described occurrences of muscle scars in bilaterally symmetrical molluscs indicates that the simple shell form may obscure recognition of distinct lineages within Cambrian univalves that are based on anatomical features, such as musculature. John S. Peel [john.peel@pal.uu. se], Department of Earth Sciences (Palaeobiology), Uppsala University, Villavägen 16, SE-75236, Uppsala, Sweden.
R E LU-FHE : L OW - COST A CCURATE R E LU POLYNOMIAL APPROXIMATION IN F ULLY H OMOMORPHIC E NCRYPTION B ASED ML I NFERENCE

Machine learning (ML) is getting more pervasive. Wide adoption of ML in healthcare, facial recognition, and blockchain involves private and sensitive data. Inference on encrypted data, termed Fully Homomorphic Encryption (FHE), preserves the privacy of both data and the ML model. However, it slows down plaintext inference by six magnitudes, with a root cause of replacing non-linear operators with high-degree Polynomial Approximated Function (PAF). To reduce the degree without sacrificing accuracy, we propose (1) Coefficient Tuning (CT) to obtain a good initial coefficient value for each PAF, (2) Progressive Approximation (PA) to enable convergence by replacing ReLU and training parameters in a divide-and-conquer manner, and (3) Alternate Training (AT) to further improve the post-replacement accuracy. A combination of CT, PA, and AT enables the exploration of accuracy-latency space for FHE-domain ReLU replacement. Our evaluation shows that the optimal PAF with 12 degrees reduces 72% latency of the state-of-the-art 27-degree PAF with the same post-replacement accuracy (69.0%) on ResNet-18 using ImageNet 1k dataset.
An organ boundary-enriched gene regulatory network uncovers regulatory hierarchies underlying axillary meristem initiation

Gene regulatory networks (GRNs) control development via cell type-specific gene expression and interactions between transcription factors (TFs) and regulatory promoter regions. Plant organ boundaries separate lateral organs from the apical meristem and harbor axillary meristems (AMs). AMs, as stem cell niches, make the shoot a ramifying system. Although AMs have important functions in plant development, our knowledge of organ boundary and AM formation remains rudimentary. Here, we generated a cellularresolution genomewide gene expression map for low-abundance Arabidopsis thaliana organ boundary cells and constructed a genomewide protein–DNA interaction map focusing on genes affecting boundary and AM formation. The resulting GRN uncovers transcriptional signatures, predicts cellular functions, and identifies promoter hub regions that are bound by many TFs. Importantly, further experimental studies determined the regulatory effects of many TFs on their targets, identifying regulators and regulatory relationships in AM initiation. This systems biology approach thus enhances our understanding of a key developmental process.
Precise genetic engineering with piggyBac transposon in plants

Transposons are mobile genetic elements that can move to a different position within a genome or between genomes. They have long been used as a tool for genetic engineering, including transgenesis, insertional mutagenesis, and marker excision, in a variety of organisms. The piggyBac transposon derived from the cabbage looper moth is one of the most promising transposon tools ever identified because piggyBac has the advantage that it can transpose without leaving a footprint at the excised site. Applying the piggyBac transposon to precise genome editing in plants, we have demonstrated efficient and precise piggyBac transposon excision from a transgene locus integrated into the rice genome. Furthermore, introduction of only desired point mutations into the target gene can be achieved by a combination of precise gene modification via homologous recombination-mediated gene targeting with subsequent marker excision from target loci using piggyBac transposition in rice. In addition, we have designed a piggyBac-mediated transgenesis system for the temporary expression of sequence-specific nucleases to eliminate the transgene from the host genome without leaving unnecessary sequences after the successful induction of targeted mutagenesis via sequence-specific nucleases for use in vegetatively propagated plants. In this review, we summarize our previous works and the future prospects of genetic engineering with piggyBac transposon.
REDUKSI ORDE MODEL SISTEM LINIER WAKTU DISKRIT DENGAN METODE SINGULAR PERTURBATION APPROXIMATION

Tujuan dari skripsi ini adalah mengkonstruksi reduksi orde model sistem linier waktu diskrit dengan metode Singular Perturbation Approximation (SPA). Diasumsikan sistem tersebut bersifat stabil asimtotis, terkendali dan terobservasi. Dari hasil dan pembahasan skripsi ini, reduksi orde model sistem linier waktu diskrit dengan metode SPA diterapkan pada sistem setimbang. Reduksi dengan metode ini diperoleh dengan mengambil variabel keadaan yang bersesuaian dengan nilai singular Hankel kecil sama dengan nol. Sebagai studi kasus, reduksi orde model sistem linier waktu diskrit dengan metode SPA diterapkan pada masalah konduksi panas.