Miracle-dz/UniFAR-FTUs huggingface dataset:
Guaranteed Stable Quadratic Models and their applications in SINDy and Operator Inference

Scientific machine learning for inferring dynamical systems combines data-driven modeling, physics-based modeling, and empirical knowledge. It plays an essential role in engineering design and digital twinning. In this work, we primarily focus on an operator inference methodology that builds dynamical models, preferably in low-dimension, with a prior hypothesis on the model structure, often determined by known physics or given by experts. Then, for inference, we aim to learn the operators of a model by setting up an appropriate optimization problem. One of the critical properties of dynamical systems is stability. However, this property is not guaranteed by the inferred models. In this work, we propose inference formulations to learn quadratic models, which are stable by design. Precisely, we discuss the parameterization of quadratic systems that are locally and globally stable. Moreover, for quadratic systems with no stable point yet bounded (e.g., chaotic Lorenz model), we discuss how to parameterize such bounded behaviors in the learning process. Using those parameterizations, we set up inference problems, which are then solved using a gradient-based optimization method. Furthermore, to avoid numerical derivatives and still learn continuous systems, we make use of an integral form of differential equations. We present several numerical examples, illustrating the preservation of stability and discussing its comparison with the existing state-of-the-art approach to infer operators. By means of numerical examples, we also demonstrate how the proposed methods are employed to discover governing equations and energy-preserving models.
enhancing our understanding of the time course of acute exacerbations of COPD managed on an outpatient basis

Purpose: Acute exacerbations of COPD (AECOPD) are associated with pulmonary/systemic changes; however, quantification of those changes during AECOPD managed on an outpatient basis and factors influencing recovery are lacking. This study aimed to characterize patients’ changes during AECOPD and identify factors influencing their recovery. Methods: Body mass index, the modified British Medical Research Council questionnaire, number of exacerbations in the previous year, and the Charlson comorbidity index (independent variables) were collected within 24–48 hours of hospital presentation (T0). Peripheral oxygen saturation (SpO 2 ), forced expiratory volume in one second, percentage predicted (FEV 1 % pre-dicted), maximum inspiratory pressure, quadriceps muscle strength, 5 times sit-to-stand, and COPD assessment test (CAT) (dependent variables) were collected at T0 and approximately at days 8 (T1), 15 (T2), and 45 (T3) after T0. Results: A total of 44 outpatients with AECOPD (31 ♂ ; 68.2 ± 9.1 years; 51.1 ± 20.3 FEV 1 % predicted) were enrolled. All variables improved overtime ( P , 0.05); however, at day 8, only SpO 2 and CAT ( P # 0.001) showed significant improvements. Changes in FEV 1 % predicted and SpO 2 were not influenced by any independent measure, while changes in other outcome measures were influenced by at least one of the independent measures. Independently of the time of data collection, being underweight or overweight and having increased dyspnea, previous exacerbations, and severe comorbidities negatively affected patients’ outcomes. Conclusion: FEV 1 % predicted and SpO 2 were not influenced by any independent measure and, thus, seem to be robust measures to follow-up outpatients with AECOPD. No single indicator was able to predict patients’ recovery for all measures; thus, a comprehensive assessment at the onset of the AECOPD is required to personalize interventions.
Sound pressure distribution within human ear canals: II. Reverse mechanical stimulation.

This work is part of a study of the interactions of ear canal (EC) sound with tympanic membrane (TM) surface displacements. In human temporal bones, the ossicles were stimulated mechanically "in reverse" to mimic otoacoustic emissions (OAEs), and the sound field within the ear canal was sampled with 0.5-2 mm spacing near the TM surface and at more distal locations within the EC, including along the longitudinal EC axis. Sound fields were measured with the EC open or occluded. The reverse-driven sound field near the TM had larger and more irregular spatial variations below 10 kHz than with forward sound stimulation, consistent with a significant contribution of nonuniform sound modes. These variations generally did not propagate more than ∼4 mm laterally from the TM. Longitudinal sound field variations with the EC open or blocked were consistent with standing-wave patterns in tubes with open or closed ends. Relative contributions of the nonuniform components to the total sound pressure near the TM were largest at EC natural frequencies where the longitudinal component was small. Transverse variations in EC sound pressure can be reduced by reducing longitudinal EC sound pressure variations, e.g., via reducing reflections from occluding earplugs.
Segmenting, modeling, and matching video clips containing multiple moving objects

This paper presents a novel representation for dynamic scenes composed of multiple rigid objects that may undergo different motions and be observed by a moving camera. Multi-view constraints associated with groups of affine-invariant scene patches and a normalized description of their appearance are used to segment a scene into its rigid parts, construct three-dimensional protective, affine, and Euclidean models of these parts, and match instances of models recovered from different image sequences. The proposed approach has been implemented, and it is applied to the detection and recognition of moving objects in video sequences and the identification of shots that depict the same scene in a video clip (shot matching).
Bloodstream infections in patients with hematological malignancies: which is more fatal – cancer or resistant pathogens?

Background: The primary objective of this study was to report the incidence of bloodstream infections (BSIs) and clinically or microbiologically proven bacterial or fungal BSIs during neutropenic episodes in patients with hematological malignancies. Methods: In this retrospective observational study, all patients in the hematology department older than 14 years who developed febrile neutropenia during chemotherapy for hematological cancers were evaluated. Patients were included if they had experienced at least one neutropenic episode between November 2010 and November 2012 due to chemotherapy in the hematology ward. Results: During 282 febrile episodes in 126 patients, 66 (23%) episodes of bacteremia and 24 (8%) episodes of fungemia were recorded in 48 (38%) and 18 (14%) patients, respectively. Gram-negative bacteria caused 74% (n = 49) of all bacteremic episodes. Carbapenem-resistant Gram-negative bacteria (n = 6) caused 12% and 9% of Gram-negative bacteremia episodes and all bacteremia episodes, respectively. Carbapenem-resistant Gram-negative bacteria included Acinetobacter baumannii (n = 4), Pseudomonas aeruginosa (n = 1), and Serratia marcescens (n = 1). Culture-proven invasive fungal infection occurred in 24 episodes in 18 cases during the study period, with 15 episodes in ten cases occurring in the first study year and nine episodes in eight cases in the second study year. In 13 of 18 cases (72%) with bloodstream yeast infections, previous azole exposure was recorded. Candida parapsilosis , C. glabrata , and C. albicans isolates were resistant to voriconazole and fluconazole. Conclusion: BSIs that occur during febrile neutropenic episodes in hematology patients due to Gram-negative bacteria should be treated initially with non-carbapenem-based antipseudomonal therapy taking into consideration antimicrobial stewardship. Non-azole antifungal drugs, including caspofungin and liposomal amphotericin B, should be preferred as empirical antifungal therapy in the events of possible or probable invasive fungal infections with an absence of pulmonary findings due to increase azole resistance. were followed up and isolated in the hematology ward. Screen cultures from rectal, axillary, and groin sites were negative in these cases. CR GNB developed in these patients during carbapenem therapy used to treat febrile neutropenic episodes.
PENGUKURAN NILAI RISIKO PORTOFOLIO BERDASARKAN MEAN-VaR

Abstrak. Portofolio merupakan kumpulan dari beberapa investasi saham. Portofolio terbaik adalah portofolio dengan mean return dan risiko saham yang terbaik. Salah satu metode dalam mengukur nilai risiko adalah dengan Value at Risk (VaR). VaR didenisikan sebagai tingkat kerugian maksimal atau return minimal pada tingkat kepercayaan yang cukup tinggi untuk waktu tertentu. Jika seorang investor membentuk portofolio maka berarti investor menentukan proporsi dana yang diinvestasikan pada masingmasing saham. Investor menginvestasikan dana pada masing-masing saham dengan total proporsi dana adalah 1. Permasalahan dalam menghitung proporsi dana dapat menggunakan metode Pengganda Lagrange. Dari 33 saham Perbankan yang terdaftar pada Bursa Efek Indonesia didapat komposisi portofolio yang terdiri dari Bank Danamon Indonesia Tbk, Bank Mandiri (Persero) Tbk dan Bank CIMB Niaga Tbk. Dari ketiga saham diperoleh proporsi investasi masing-masing dana yaitu 19,76% Bank Danamon Indonesia Tbk, 60,34% Bank Mandiri (Persero) Tbk dan 19,90% Bank CIMB Niaga Tbk. Dari portofolio yang terbentuk didapat nilai risiko yaitu 0,001345. Hal ini berarti risiko dari portofolio yang terbentuk sangat kecil yaitu 0,13% sehingga aman bagi investor dalam berinvestasi. Kata Kunci: Portofolio, Value at Risk, Pengganda Lagrange, Risiko
Patient pathways and perceptions of hypertension treatment, management, and control in rural Bangladesh: a qualitative study

Purpose: Hypertension is an increasing threat to global public health, a leading cause of premature death, and an important modifiable risk factor for cardiovascular and cerebrovascular disease. Despite evidence on the efficacy of antihypertensive medication for blood-pressure control and mortality prevention, a large proportion of individuals are undiagnosed and untreated, especially in resource-constrained settings. This qualitative study explored patient pathways to care, as well as knowledge of and adherence to hypertension care. Methods: We conducted in-depth interviews with 20 hypertensive patients in two rural districts in Bangladesh. Interviews were conducted and transcribed in Bangla and translated to English. QSR NVivo 10 software was used for analyses. We mapped patient pathways and report here on patient experiences accessing care from local pharmacies, the government, and private clinics. Results: Overall, most patients reported hypertension awareness prior to diagnosis and were conscious about consequences of hypertension. However, patients had little knowledge about prevention and treatment strategies. Most patients considered hypertension an important disease, albeit reporting taking medication only when symptomatic. Patients were aware of dietary advice; however, they were largely sedentary. Qualified doctors in both private and government settings diagnosed hypertension in the majority of the patients, and some were diagnosed by an informal provider and a few reported self-care at home. Patients followed three pathways: specialized hospitals for acute care, private hospitals/local pharmacy for nonacute symptoms, and incidental hypertension identification while being treated for another condition. Conclusion: We identify barriers to access to hypertension prevention and care that prevented patients from seeking and receiving treatment from government facilities. Challenges included a lack of support to enable community screening by government health workers, long waiting times, and inadequate supplies for hypertension treatment. Expanding community-health workers’ scope in the dissemination of chronic-disease information may improve patient pathways to hypertension care in rural communities in Bangladesh.
Large scale variability, long-term trends and extreme events in total ozone over the northern mid-latitudes based on satellite time series

Various generations of satellites (e.g. TOMS, GOME, OMI) made spatial datasets of column ozone available to the scientific community. This study has a special focus on column ozone over the northern mid-latitudes. Tools from geostatistics and extreme value theory are applied to analyze variability, long-term trends and frequency distributions of extreme events in total ozone. In a recent case study (Rieder et al., 2009) new tools from extreme value theory (Coles, 2001; Ribatet, 2007) have been applied to the world’s longest total ozone record from Arosa, Switzerland (e.g. Staehelin 1998a,b), in order to describe extreme events in low and high total ozone. Within the current study this analysis is extended to satellite datasets for the northern mid-latitudes. Further special emphasis is given on patterns and spatial correlations and the influence of changes in atmospheric dynamics (e.g. tropospheric and lower stratospheric pressure systems) on column ozone.
Tissue-Specific Mitochondrial Decoding of Cytoplasmic Ca(2+) Signals Is Controlled by the Stoichiometry of MICU1/2 and MCU

R commended Citatio Paillard, Melanie; Csordás, György; Szanda, Gergö; Golenár, Tünde; Debattisti, Valentina; Bartok, Adam; Wang, Nadan; Moffat, Cynthia; Seifert, Erin L. ; Spät, András; and Hajnóczky, György, "Tissue-Specific Mitochondrial Decoding of Cytoplasmic Ca(2+) Signals Is Controlled by the Stoichiometry of MICU1/2 and MCU. " (2017). Department of Pathology, Anatomy, and Cell Biology Faculty Papers. Paper 218. https://jdc.jefferson. edu/pacbfp/218
Comprehensive analysis of the transcription factor REST regulatory networks in IDH-mutant and IDH-wild type glioma

REST acts as a transcriptional repressor of neuronal genes in non-neuronal cells but could be a transcriptional activator under certain conditions. REST was implicated in a blockage of cell differentiation and is an important oncogenic factor. As IDH mutations are oncogenic drivers in gliomas causing significant changes in the epigenome and blocking differentiation, we aimed at defining the role of REST in the IDH mutation-related phenotype in gliomas. We studied consequences of REST knockdown in IDH wild-type and mutant U87 cells. Chromatin immunoprecipitation followed by sequencing combined with transcription factor (TF) motif identification and transcriptome analyses revealed different patterns of REST binding and its proximal TF motifs in IDH wild-type and mutant U87 cells. Moreover, we identified putative targets of REST as related to ECM organization and cell differentiation. We demonstrate that the REST role in gliomas is dependent on IDH mutation status.
Riparian buffer zones of the Canterbury agricultural landscape and their effectiveness for nitrogen and phosphorus retention.

1 CHAPTER 1: GENERAL INTRODUCTION 4 Background 4 Water quality mitigation 5 Riparian buffer effectiveness 6 Riparian Management in New Zealand 7 Research Aims 9 CHAPTER 2: CHARACTERISING RIPARIAN BUFFER ZONES OF AN AGRICULTURAL LANDSCAPE 11 ABSTRACT 12 Introduction 13 Methods 15 Results 18 Discussion 20 References 25 Figure Legends 29 Figures 30 Tables 34 12 Introduction 13 Methods 15 Results 18 Discussion 20 References 25 Figure Legends 29 Figures 30 Tables 34 CHAPTER 3: RIPARIAN NUTRIENT DYNAMICS IN A FLAT LANDSCAPE – GRASS FILTER STRIPS, VEGETATED BUFFERS AND THE INFLUENCE OF LAND-USE . 35 ABSTRACT 36 Introduction 37 Materials and Methods 41 Results 45 Discussion 49 References 57 Figure Legends 63 Figures 65 Tables 71 36 Introduction 37 Materials and Methods 41 Results 45 Discussion 49 References 57 Figure Legends 63 Figures 65 Tables 71
Unequal Gain of Equal Resources across Racial Groups

The health effects of economic resources (eg, education, employment, and living place) and psychological assets (eg, self-efficacy, perceived control over life, anger control, and emotions) are well-known. This article summarizes the results of a growing body of evidence documenting Blacks’ diminished return, defined as a systematically smaller health gain from economic resources and psychological assets for Blacks in comparison to Whites. Due to structural barriers that Blacks face in their daily lives, the very same resources and assets generate smaller health gain for Blacks compared to Whites. Even in the presence of equal access to resources and assets, such unequal health gain constantly generates a racial health gap between Blacks and Whites in the United States. In this paper, a number of public policies are recommended based on these findings. First and foremost, public policies should not merely focus on equalizing access to resources and assets, but also reduce the societal and structural barriers that hinder Blacks. Policy solutions should aim to reduce various manifestations of structural racism including but not limited to differential pay, residential segregation, lower quality of education, and crime in Black and urban communities. As income was not found to follow the same pattern demonstrated for other resources and assets (ie, income generated similar decline in risk of mortality for Whites and Blacks), policies that enforce equal income and increase minimum wage for marginalized populations are essential. Improving quality of education of youth and employability of young adults will enable Blacks to compete for high paying jobs. Policies that reduce racism and discrimination in the labor market are also needed. Without such policies, it will be very difficult, if not impossible, to eliminate the sustained racial health gap in the United States.
Vitamin D3 as adjunctive therapy in the treatment of depression in tuberculosis patients: a short-term pilot randomized double-blind controlled study

Objective: We aimed to evaluate whether high-dose cholecalciferol has beneficial effects on depression in pulmonary tuberculosis (PTB) patients. Methods: This pilot, randomized, and double-blind trial enrolled 123 recurrent PTB patients (aged $ 18 years) meeting Diagnostic and Statistical Manual of Mental Disorders-IV (DSM-IV) criteria of major depressive disorder from four hospitals in Southeast China. Patients were randomly assigned to 8-week oral treatment with 100,000 IU/week cholecalciferol (Vit D group) or a matching placebo (control group). The primary outcome was treatment response, defined as a 50% reduction in symptoms and change in scores of the Chinese version of Beck Depression Inventory (BDI) from baseline to 8 weeks. Relative risks of depression were estimated using multivariable logistic regression. Results: Finally, 120 patients were enrolled, including 56 test patients and 64 controls. After 8 weeks, the treatment response or BDI scores did not differ significantly between groups. Multi-variate logistic regression showed that BDI scores were not significantly improved in the Vit D group after adjustment for age, time to first negative smear, or 25-hydroxyvitamin D level. Conclusion: The use of high-dose Vit D3 supplementation may not be warranted for reducing depressive symptoms in the PTB population. Nevertheless, this finding should be validated by further large-scale studies according to different kinds of depression or Vit D receptor polymorphism genotype.
A systematic review and meta–analysis of optical coherence tomography in multiple sclerosis

Optical coherence tomography (OCT) is a new method potentially applicable for the analysis of neurodegeneration in multiple sclerosis (MS) by capturing thinning of the retinal nerve fibre layer (RNFL). Metaanalyses of time domain OCT (TDOCT) data demonstrates RNFL thinning of 20 μm (95%CI 18-23, n=2063, p¡0.00001) following MS optic neuritis (MSON) and μm (95%CI 6-9, n=3154, p¡0.00001) in MS without MSON. The estimated RNFL thinning in patients with MS is above what is expected from normal ageing. The likely cause being retrograde trans-synaptic degeneration and progressive loss of retinal ganglion cells. The RNFL correlated with visual and neurological functioning as well as with paraclinical data. Promising developments in order to better understand the structurefunction relationship in MS pathophysiology include spectral/Fourierdomain OCT (SD/FDOCT) technology, polarisation sensitive OCT, fluorescence labelling, structural assessment of action potential propagation and segmentation algorithms allowing for quantitative assessment of different retinal layers. Word count: abstract 145, main text 5340.
Blind Multiuser Detection in Massive MIMO Channels With Clustered Sparsity

In this letter, we propose a blind multiuser detection algorithm for massive MIMO systems equipped with a uniform planar antenna array. We model the channel in the angular domain as a sparse matrix with the non-zero coefficients forming clusters. The channel sparsity is described by a binary Markov random field (MRF). Then, we develop a turbo message passing framework by incorporating the MRF model into the bilinear generalized approximate message passing (BiGAMP) algorithm. We show that the proposed scheme considerably outperforms the schemes without exploiting the clustered sparsity of the channel.
Association and Linkage Mapping to Unravel Genetic Architecture of Phenology-Related Traits and Lateral Bearing in Persian Walnut (Juglans regia L.)

Background: Unravelling the genetic architecture of agronomic traits in walnut such as budbreak date and bearing habit, is crucial for climate change adaptation and yield improvement. A Genome-Wide Association Study (GWAS) using multi-locus models was conducted in a panel of 170 walnut accessions genotyped using the Axiom™ J. regia 700K SNP array, with phenological data from several years. These accessions come from the INRAE walnut germplasm collection which is the result of important prospecting work performed in many countries around the world. In parallel, an F1 progeny of 78 individuals segregating for phenology-related traits, was genotyped with the same array and phenotyped for the same traits, to construct linkage maps and perform Quantitative Trait Loci (QTLs) detection. Results: Using GWAS, we found strong associations of SNPs located at the beginning of chromosome 1 with both budbreak and female flowering dates. These findings were supported by QTLs detected in the same genomic region. Highly significant associated SNPs were also detected using GWAS for heterodichogamy and lateral bearing habit, both on chromosome 11. We developed a Kompetitive Allele Specific PCR (KASP) marker for budbreak date in walnut, and validated it using plant material from the Walnut Improvement Program of the University of California, Davis, demonstrating its effectiveness for marker-assisted selection in Persian walnut. We found several candidate genes involved in flowering events in walnut, including a gene related to heterodichogamy encoding a sugar catabolism enzyme and a cell division related gene linked to female flowering date. Conclusions: This study enhances knowledge of the genetic architecture of important agronomic traits related to male and female flowering processes and lateral bearing in walnut. The new marker available for budbreak date, the first key trait for good fruiting, will facilitate the selection and development of new walnut cultivars suitable for specific climates.