Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting in-hospital mortality for MIMIC-III patients: A nomogram combined with SOFA score

Predicting the mortality of patients provides a reference for doctors to judge their physical condition. This study aimed to construct a nomogram to improve the prediction accuracy of patients’ mortality. Patients with severe diseases were screened from the Medical Information Mart for Intensive Care (MIMIC) III database; 70% of patients were randomly selected as the training set for the model establishment, while 30% were used as the test set. The least absolute shrinkage and selection operator (LASSO) regression method was used to filter variables and select predictors. A multivariable logistic regression fit was used to determine the association between in-hospital mortality and risk factors and to construct a nomogram. A total of 9276 patients were included. The area under the curve (AUC) for the clinical nomogram based on risk factors selected by LASSO and multivariable logistic regressions were 0.849 (95% confidence interval [CI]: 0.835–0.863) and 0.821 (95% CI: 0.795–0.846) in the training and test sets, respectively. Therefore, this nomogram might help predict the in-hospital mortality of patients admitted to the intensive care unit (ICU).
Spectroscopy and decay properties of charmonium

The mass spectra of charmonium are investigated using a Coulomb plus linear (Cornell) potential. Gaussian wave functions in position space as well as in momentum space are employed to calculate the expectation values of potential and kinetic energy respectively. Various experimental states (X(4660)(53S1), X(3872)(23P1), X(3900)(21P1), X(3915)(23P0) and X(4274)(33P1) etc.) are assigned as charmonium states. We also study the Regge trajectories, pseudoscalar and vector decay constants, electric and magnetic dipole transition rates, and annihilation decay widths for charmonium states.
New imaging instrument in animal models: Two‐photon miniature microscope and large field of view miniature microscope for freely behaving animals

Over the past decade, novel optical imaging tools have been developed for imaging neuronal activities along with the evolution of fluorescence indicators with brighter expression and higher sensitivity. Miniature microscopes, as revolutionary approaches, enable the imaging of large populations of neuron ensembles in freely behaving rodents and mammals, which allows exploring the neural basis of behaviors. Recent progress in two‐photon miniature microscopes and mesoscale single‐photon miniature microscopes further expand those affordable methods to navigate neural activities during naturalistic behaviors. In this review article, two‐photon miniature microscopy techniques are summarized historically from the first documented attempt to the latest ones, and comparisons are made. The driving force behind and their potential for neuroscientific inquiries are also discussed. Current progress in terms of the mesoscale, i.e., the large field‐of‐view miniature microscopy technique, is addressed as well. Then, pipelines for registering single cells from the data of two‐photon and large field‐of‐view miniature microscopes are discussed. Finally, we present the potential evolution of the techniques.
A Burgers-KPZ Type Parabolic Equation \par\noindent for the Path-Independence of the Density of the Girsanov Transformation

Let $X_t$ solve the multidimensional It\^o's stochastic differential equations on $\R^d$ $$dX_t=b(t,X_t)dt+\sigma(t,X_t)dB_t$$ where $b:[0,\infty)\times\R^d\to\R^d$ is smooth in its two arguments, $\sigma:[0,\infty)\times\R^d\to\R^d\otimes\R^d$ is smooth with $\sigma(t,x)$ being invertible for all $(t,x)\in[0,\infty)\times\R^d$, $B_t$ is $d$-dimensional Brownian motion. It is shown that, associated to a Girsanov transformation, the stochastic process $$\int^t_0\langle(\sigma^{-1}b)(s,X_s),dB_t\rangle+\frac{1}{2}\int^t_0|\sigma^{-1}b|^2(s,X_s)ds$$ is a function of the arguments $t$ and $X_t$ (i.e., path-independent) if and only if $b=\sigma\sigma^\ast\nabla v$ for some scalar function $v:[0,\infty)\times\R^d\to\R$ satisfying the time-reversed KPZ type equation $$\frac{\partial}{\partial t}v(t,x)=-\frac{1}{2}\left[\left(Tr(\sigma\sigma^\ast\nabla^2v)\right)(t,x) +|\sigma^\ast\nabla v|^2(t,x)\right]. $$ The assertion also holds on a connected complete differential manifold.
Neurofilament Light Chain Levels Are Predictive of Clinical Conversion in Radiologically Isolated Syndrome

Background and Objectives To evaluate the predictive value of serum neurofilament light chain (sNfL) and CSF NfL (cNfL) in patients with radiologically isolated syndrome (RIS) for evidence of disease activity (EDA) and clinical conversion (CC). Methods sNfL and cNfL were measured at RIS diagnosis by single-molecule array (Simoa). The risk of EDA and CC according to sNfL and cNfL was evaluated using the Kaplan-Meier analysis and multivariate Cox regression models including age, spinal cord (SC) or infratentorial lesions, oligoclonal bands, CSF chitinase 3–like protein 1, and CSF white blood cells. Results Sixty-one patients with RIS were included. At diagnosis, sNfL and cNfL were correlated (Spearman r = 0.78, p < 0.001). During follow-up, 47 patients with RIS showed EDA and 36 patients showed CC (median time 12.6 months, 1–86). When compared with low levels, medium and high cNfL (>260 pg/mL) and sNfL (>5.0 pg/mL) levels were predictive of EDA (log rank, p < 0.01 and p = 0.02, respectively). Medium-high cNfL levels were predictive of CC (log rank, p < 0.01). In Cox regression models, cNfL and sNfL were independent factors of EDA, while SC lesions, cNfL, and sNfL were independent factors of CC. Discussion cNfL >260 pg/mL and sNfL >5.0 pg/mL at diagnosis are independent predictive factors of EDA and CC in RIS. Although cNfL predicts disease activity better, sNfL is more accessible than cNfL and can be considered when a lumbar puncture is not performed. Classification of Evidence This study provides Class II evidence that in people with radiologic isolated syndrome (RIS), initial serum and CSF NfL levels are associated with subsequent evidence of disease activity or clinical conversion.
Baseline gut microbial profiles are associated with the efficacy of Bacillus subtilis and Enterococcus faecium in IBS-D

Abstract Objective Little is known about association between the efficacy of probiotics and baseline gut microbiota in irritable bowel syndrome (IBS). We aimed to explore gut microbiota in diarrhea-predominant IBS (IBS-D) and whether baseline gut microbiota was related to the efficacy of Bacillus subtilis and Enterococcus faecium (BE). Methods This study recruited 19 healthy controls (HC) and 50 IBS-D patients, among whom 19 patients were administrated 500 mg BE orally three times daily for 2 weeks. Clinical data and fecal samples were collected from patients before and after treatment. 16S rRNA sequencing was performed to obtain fecal bacterial data. Results There was no significant difference of alpha diversity, beta diversity, profiles of microbial phyla and genera between HC and IBS. BE improved IBS-SSS (IBS severity scoring system) and stool consistency, and altered Enterococcus, Blautia, Lachnoclostridium and Fusobacterium without significant impact on microbial structure in IBS-D. Notably, baseline fecal bacterial composition differed between non-responders and responders to BE concerning abdominal pain and bloating, with Atopobium, Pyramidobacter, Ruminococcus gnavus and Peptostreptococcus enriched in responders in terms of abdominal pain. There was reduced abundance of Prevotella, Ruminococcaceae UCG, Eubacterium eligens, Faecalibacterium and Eubacterium coprostanoligenes in responders compared with non-responders. Furthermore, BE increased beneficial bacteria including Faecalibacterium, Blautia and Butyricicoccus, decreased Lachnoclostridium and Bilophila, and influenced some microbial metabolic pathways in responders, such as mineral absorption, metabolism of arachidonic acid, d-arginine, D-ornithine, phenylalanine and vitamin B6. Conclusion Baseline fecal microbiome is associated with the efficacy of BE in attenuating abdominal pain and bloating in IBS-D.
Sarcopenia among people living with HIV and the effect of antiretroviral therapy on body composition

To investigate the prevalence of sarcopenia among people living with HIV (PLWH) in Japan and analyze the relationship between HIV infection and ART effects on the body composition of Japanese PLWH for more appropriate drug selection and lifestyle guidance. Cross-sectional observational study. We included male patients aged ≥ 60 years whose body composition was measured by InBody 570 body composition analyzer during outpatient visits. Patients were classified by body shape based on body mass index (BMI) and body fat percentage measurements and by tenofovir alafenamide administration. Hidden obesity is a condition wherein the BMI is within the standard range but the body fat percentage is higher than the reference. Patients with low muscle mass and strength were considered to have sarcopenia, whereas those with only low muscle strength were considered to have pre-sarcopenia. In total, 87 patients were included. Based on body shape determined by BMI and body fat percentage, most patients had hidden obesity (40 patients, 46.0%). Sarcopenia was detected in 9 patients (10.3%) and pre-sarcopenia in 14 patients (16.1%). The tenofovir alafenamide (TAF) use group had significantly higher BMI, higher skeletal muscle mass, body fat mass, and skeletal muscle mass index relative to the non-TAF use group. Hidden obesity is a risk for lifestyle diseases. It is important to recognize it based on body composition measurements because it can be missed by BMI measurement alone. Tenofovir alafenamide therapy increases skeletal muscle mass, which may result in the prevention of sarcopenia. To clarify how TAF affects the development of sarcopenia and lifestyle diseases, future studies on a larger cohort are warranted.
GATOR2-dependent mTORC1 activity is a therapeutic vulnerability in FOXO1 fusion–positive rhabdomyosarcoma

Oncogenic FOXO1 gene fusions drive a subset of rhabdomyosarcoma (RMS) with poor survival; to date, these cancer drivers are therapeutically intractable. To identify new therapies for this disease, we undertook an isogenic CRISPR-interference screen to define PAX3-FOXO1–specific genetic dependencies and identified genes in the GATOR2 complex. GATOR2 loss in RMS abrogated aa-induced lysosomal localization of mTORC1 and consequent downstream signaling, slowing G1-S cell cycle transition. In vivo suppression of GATOR2 impaired the growth of tumor xenografts and favored the outgrowth of cells lacking PAX3-FOXO1. Loss of a subset of GATOR2 members can be compensated by direct genetic activation of mTORC1. RAS mutations are also sufficient to decouple mTORC1 activation from GATOR2, and indeed, fusion-negative RMS harboring such mutations exhibit aa-independent mTORC1 activity. A bisteric, mTORC1-selective small molecule induced tumor regressions in fusion-positive patient-derived tumor xenografts. These findings highlight a vulnerability in FOXO1 fusion–positive RMS and provide rationale for the clinical evaluation of bisteric mTORC1 inhibitors, currently in phase I testing, to treat this disease. Isogenic genetic screens can, thus, identify potentially exploitable vulnerabilities in fusion-driven pediatric cancers that otherwise remain mostly undruggable.
Nouveaux matériaux laser dopés à l'ytterbium : performances en pompage par diode et étude des effets thermiques.

Ce travail a comme but l'etude de nouveaux cristaux dopes a l'ion ytterbium, pour le developpement de lasers efficaces (et eventuellement accordables) emettant vers 1 µm. La premiere partie traite des performances laser en pompage par diode de forte puissance (10-15 W) de nouveaux cristaux : l'Yb:GGG, l'Yb:GdCOB, l'Yb:BOYS (et l'Yb:CaBOYS), l'Yb:SYS et l'Yb:YSO. L'efficacite, l'accordabilite, et le comportement thermique de ces materiaux est discutee, et illustree, lorsque cela est pertinent, par une comparaison entre materiaux voisins. Les effets thermiques limitent la montee en puissance dans la plupart de ces nouveaux materiaux : leur etude detaillee fait l'objet de la seconde partie. Nous commencons par une synthese theorique sur les effets thermiques et thermomecaniques dans les lasers solides. Apres une description des differentes methodes experimentales d'investigation des effets thermiques, nous decrivons le banc de mesure que nous avons mis en place. Il est base sur un analyseur de front d'onde de Shack-Hartmann, et il permet la mesure des lentilles thermiques (et de leurs aberrations) dans des configurations de pompage longitudinal, en presence (ou non) d'effet laser. Nous decrivons les caracteristiques et les limitations de cet outil en detail. Des mesures de lentilles thermiques sont ensuite rapportees, pour la premiere fois, dans des materiaux dopes a l'ytterbium. Nous avons mis en evidence d'importants effets non radiatifs qui contribuent a la charge thermique, contrairement a ce qui est generalement admis. Nous detaillons alors comment, avec un modele analytique simple, on peut deduire de ces mesures le rendement quantique et le coefficient thermo-optique des materiaux consideres. Nous avons egalement mis en evidence experimentalement l'influence de la longueur d'onde laser sur la charge thermique, la reduction des effets thermiques dans des cristaux composites, ou encore la contribution significative de l'effet photoelastique a la lentille thermique dans l'Yb:GdCOB.
Skyrmion Tubes as Magnonic Waveguides

Various latest experiments have proven the theoretical prediction that domain walls in planar magnetic structures can channel spin waves as outstanding magnonic waveguides, establishing a superb platform for building magnonic devices. Recently, three-dimensional nanomagnetism has been boosted up and become a significant branch of magnetism, because three-dimensional magnetic structures expose a lot of emerging physics hidden behind planar ones and will inevitably provide broader room for device engineering. Skyrmions and antiSkyrmions, as natural three-dimensional magnetic configurations, are not considered yet in the context of spin-wave channeling and steering. Here, we show that skyrmion tubes can act as nonplanar magnonic waveguides if excited suitably. An isolated skyrmion tube in a magnetic nanoprism induces spatially separate internal and edge channels of spin waves; the internal channel has a narrower energy gap, compared to the edge channel, and accordingly can transmit signals at lower frequencies. Additionally, we verify that those spin-wave beams along magnetic nanoprism are restricted to the regions of potential wells. Transmission of spin-wave signals in such waveguides results from the coherent propagation of locally driven eigenmodes of skyrmions, i.e., the breathing and rotational modes. Finally, we find that spin waves along the internal channels are less susceptible to magnetic field than those along the edge channels. Our work will open a new arena for spin-wave manipulation and help bridge skyrmionics and magnonics.
Lysosomal positioning diseases: beyond substrate storage

Lysosomal storage diseases (LSDs) comprise a group of inherited monogenic disorders characterized by lysosomal dysfunctions due to undegraded substrate accumulation. They are caused by a deficiency in specific lysosomal hydrolases involved in cellular catabolism, or non-enzymatic proteins essential for normal lysosomal functions. In LSDs, the lack of degradation of the accumulated substrate and its lysosomal storage impairs lysosome functions resulting in the perturbation of cellular homeostasis and, in turn, the damage of multiple organ systems. A substantial number of studies on the pathogenesis of LSDs has highlighted how the accumulation of lysosomal substrates is only the first event of a cascade of processes including the accumulation of secondary metabolites and the impairment of cellular trafficking, cell signalling, autophagic flux, mitochondria functionality and calcium homeostasis, that significantly contribute to the onset and progression of these diseases. Emerging studies on lysosomal biology have described the fundamental roles of these organelles in a variety of physiological functions and pathological conditions beyond their canonical activity in cellular waste clearance. Here, we discuss recent advances in the knowledge of cellular and molecular mechanisms linking lysosomal positioning and trafficking to LSDs.
The silkworm gustatory receptor BmGr63 is dedicated to the detection of isoquercetin in mulberry

Gustatory systems in phytophagous insects are used to perceive feeding stimulants and deterrents, and are involved in insect decisions to feed on particular plants. During the process, gustatory receptors (Grs) can recognize diverse phytochemicals and provide a molecular basis for taste perception. The silkworm, as a representative Lepidoptera species, has developed a strong feeding preference for mulberry leaves. The mulberry-derived flavonoid glycoside, isoquercetin, is required to induce feeding behaviours. However, the corresponding Grs for isoquercetin and underlying molecular mechanisms remain unclear. In this study, we used molecular methods, voltage clamp recordings and feeding assays to identify silkworm BmGr63, which was tuned to isoquercetin. The use of qRT-PCR confirmed that BmGr63 was highly expressed in the mouthpart of fourth and fifth instar larvae. Functional analysis showed that oocytes expressing BmGr63 from the ‘bitter’ clade responded to mulberry extracts. Among 20 test chemicals, BmGr63 specifically recognized isoquercetin. The preference for isoquercetin was not observed in BmGr63 knock-down groups. The tuning between BmGr63 and isoquercetin has been demonstrated, which is meaningful to explain the silkworm-mulberry feeding mechanism from molecular levels and thus provides evidence for further feeding relationship studies between phytophagous insects and host plants.
Hybridization order is not the driving factor behind biases in duplicate gene losses among the hexaploid Solanaceae

We model the post-hexaploidy evolution of four genomes from the Solanaceae, a group of flowering plants comprising tomatoes, potatoes and their relatives. The hexaploidy that these genomes descend from occurred through two sequential allopolyploidy events and was marked by the unequal losses of duplicated genes from the different progenitor subgenomes. In contrast with the hexaploid Brassiceae (broccoli and its relatives), where the subgenome with the most surviving genes arrived last in the hexaploidy, among the Solanaceae the most preserved subgenome descends from one of the original two tetraploid progenitors. In fact, the last-arriving subgenome in these plants actually has the fewest surviving genes in the modern genomes. We explore whether the distribution of repetitive elements (REs) in these genomes can explain the biases in gene losses, but while the signals we find are broadly consistent with a role for high RE density in driving gene losses, the REs turn over so quickly that little signal of the RE condition at the time of paleopolyploidy is extant in the modern genomes.
Sub-Optimum H2 Rational Approximations to Fractional Order Linear Systems

In this paper, we propose a procedure to achieve rational approximation to arbitrary fractional order linear time invariant (FO-LTI) systems with sub-optimum H2 -norm. Through illustrations, we show that the rational approximation is simple and effective. It is also demonstrated that this sub-optimum approximation method is effective in designing integer order controllers for FO-LTI systems in general form. Useful Matlab codes are also given in the appendices.Copyright © 2005 by ASME
Machine learning in requirements elicitation: a literature review

Abstract A growing trend in requirements elicitation is the use of machine learning (ML) techniques to automate the cumbersome requirement handling process. This literature review summarizes and analyzes studies that incorporate ML and natural language processing (NLP) into demand elicitation. We answer the following research questions: (1) What requirement elicitation activities are supported by ML? (2) What data sources are used to build ML-based requirement solutions? (3) What technologies, algorithms, and tools are used to build ML-based requirement elicitation? (4) How to construct an ML-based requirements elicitation method? (5) What are the available tools to support ML-based requirements elicitation methodology? Keywords derived from these research questions led to 975 records initially retrieved from 7 scientific search engines. Finally, 86 articles were selected for inclusion in the review. As the primary research finding, we identified 15 ML-based requirement elicitation tasks and classified them into four categories. Twelve different data sources for building a data-driven model are identified and classified in this literature review. In addition, we categorized the techniques for constructing ML-based requirement elicitation methods into five parts, which are Data Cleansing and Preprocessing, Textual Feature Extraction, Learning, Evaluation, and Tools. More specifically, 3 categories of preprocessing methods, 3 different feature extraction strategies, 12 different families of learning methods, 2 different evaluation strategies, and various off-the-shelf publicly available tools were identified. Furthermore, we discussed the limitations of the current studies and proposed eight potential directions for future research.
Strong FeII emission in NLS1s: An unsolved mystery

Abstract In Panda et al.2018a, we constructed a refined sample from the original Shen et al.(2011) QSO catalog. Based on our hypothesis — the main driver of the Quasar Main Sequence is the maximum of the accretion disk temperature (TBBB) defined by the Big Blue Bump on the Spectral Energy Distribution (Panda et al.2017; Panda et al.2018b). We select the four extreme sources that have RFeII ⩾ 4.0 and use {CIGALE (Boquien et al.2018) to fit their multi—band photometric data. We also perform detailed spectral fitting including the Fe II pseudo—continuum (based on Śniegowska et al.2018)) to estimate and compare the value of RFEII. We show the dependence of FeII strength on changing metallicity.
Power dynamics in collaborative rural planning: The case of Pematang Tengah, Indonesia

Starting from the notion that collaborative rural planning focuses on policymaking through authentic dialogue, this article discusses the power dynamics that influence the planning process and product. It was motivated by the presumption that the understanding of collaborative policymaking is not adequate if it only concerns formal deliberation without considering other power dynamics. Booher and Innes’s model of network power in collaborative policymaking (DIAD–Diversity, Interdependence, Authentic Dialogue) and the power cube model of Gaventa were used to analyze the power mechanisms in the formal as well as in the informal arenas. They were applied to the process of village planning in Pematang Tengah, Indonesia, where the agrarian village community, deliberative bureaucrats, and other stakeholders are involved in formulating development rural planning projects. From the analysis a new model was derived, revealing three power mechanisms that are active in three different phases of the collaborative planning process: (I) Figuring out in openness, (II) Herding of public desire, and (III) Forcing of direction. The findings show that power mechanism (II) in the informal arena plays an important role by steering the course of policymaking in the formal arena (I). Power mechanism (III) is active when invisible actors illegitimately change the planning product that the formal deliberation has produced, acting out of self-interest. The analysis of power mechanisms that are active in the whole planning process can help planners in dealing with formal and informal power when developing appropriate planning strategies through a deliberative process.