Miracle-dz/UniFAR-FTUs huggingface dataset:
State-Regularized Recurrent Neural Networks to Extract Automata and Explain Predictions

Recurrent neural networks are a widely used class of neural architectures. They have, however, two shortcomings. First, they are often treated as black-box models and as such it is difficult to understand what exactly they learn as well as how they arrive at a particular prediction. Second, they tend to work poorly on sequences requiring long-term memorization, despite having this capacity in principle. We aim to address both shortcomings with a class of recurrent networks that use a stochastic state transition mechanism between cell applications. This mechanism, which we term state-regularization, makes RNNs transition between a finite set of learnable states. We evaluate state-regularized RNNs on (1) regular languages for the purpose of automata extraction; (2) non-regular languages such as balanced parentheses and palindromes where external memory is required; and (3) real-word sequence learning tasks for sentiment analysis, visual object recognition and text categorisation. We show that state-regularization (a) simplifies the extraction of finite state automata that display an RNN's state transition dynamic; (b) forces RNNs to operate more like automata with external memory and less like finite state machines, which potentiality leads to a more structural memory; (c) leads to better interpretability and explainability of RNNs by leveraging the probabilistic finite state transition mechanism over time steps.
A Statistical Approach to Short-Term Thunderstorm Outlooks

Abstract A multiple discriminant analysis program is used to obtain prediction functions for general and severe thunderstorm activity during April and July. Four predictors, lifted index, mean low-level mixing ratio, K index and mean 200–300 mb divergence, are statistically combined for an area east of the Rockies. Forecasts are valid for a 12 h period. Tests on dependent and independent data using a probability of detection (POD), a false alarm rate (FAR), and a critical success index show stability for the prediction functions. Operational use of the prediction functions is examined from two approaches, one involving POD and FAR and the other involving a more conventional probabilty approach. Semi-operational results from April and July 1979 evaluations show statistical successes comparable to the dependent data results.
Star formation in X-ray cluster cooling flows

The basic equations for X-ray cluster cooling flows, including the effects of star formation, are derived. It is confirmed that cooling flows are thermally unstable, and it is found that the fastest-growing linear perturbations in the flow are radial, comoving, and isobaric. A local approximation for the star formation rate is developed which allows analytic solutions to be found for both isobaric and gravity-dominated cooling flows. These solutions are used to show how star formation reduces the gas density, thereby lowering the cooling rate, which raises the gas temperature relative to the non-star-forming case. The analytic solutions are also used to estimate the spatial distribution of newly formed stars. It is found that star formation must proceed at a nearly maximal rate if isothermal mass profiles are to result. 47 references.
Elucidating the function of hypothetical PE_PGRS45 protein of Mycobacterium tuberculosis as an oxido-reductase: a potential target for drug repurposing for the treatment of tuberculosis

Abstract Mycobacterium tuberculosis (Mtb) encodes a total of 67 PE_PGRS proteins and definite functions of many of them are still unknown. This study reports PE_PGRS45 (Rv2615c) protein from Mtb as NADPH dependent oxido-reductase having substrate specificity for fatty acyl Coenzyme A. Computational studies predicted PE_PGRS45 to be an integral membrane protein of Mtb. Expression of PE_PGRS45 in non-pathogenic Mycobacterium smegmatis, which does not possess PE_PGRS genes, confirmed its membrane localization. This protein was observed to have NADPH binding motif. Experimental validation confirmed its NADPH dependent oxido-reductase activity (Km value = 34.85 ± 9.478 μM, Vmax = 96.77 ± 7.184 nmol/min/mg of protein). Therefore, its potential to be targeted by first line anti-tubercular drug Isoniazid (INH) was investigated. INH was predicted to bind within the active site of PE_PGRS45 protein and experiments validated its inhibitory effect on the oxido-reductase activity of PE_PGRS45 with IC50/Ki values of 5.66 μM. Mtb is resistant to first line drugs including INH. Therefore, to address the problem of drug resistant TB, docking and Molecular Dynamics (MD) simulation studies between PE_PGRS45 and three drugs (Entacapone, Tolcapone and Verapamil) which are being used in Parkinson’s and hypertension treatment were performed. PE_PGRS45 bound the three drugs with similar or better affinity in comparison to INH. Additionally, INH and these drugs bound within the same active site of PE_PGRS45. This study discovered Mtb’s PE_PGRS45 protein to have an oxido-reductase activity and could be targeted by drugs that can be repurposed for TB treatment. Furthermore, in-vitro and in-vivo validation will aid in drug-resistant TB treatment. HIGHLIGHTS In-silico and in-vitro studies of hypothetical protein PE_PGRS45 (Rv2615c) of Mycobacterium tuberculosis (Mtb) reveals it to be an integral membrane protein PE_PGRS45 protein has substrate specificity for fatty acyl Coenzyme A (fatty acyl CoA) and possess NADPH dependent oxido-reductase activity Docking and simulation studies revealed that first line anti-tubercular drug Isoniazid (INH) and other drugs with anti-TB property have strong affinity for PE_PGRS45 protein Oxido-reductase activity of PE_PGRS45 protein is inhibited by INH PE_PGRS45 protein could be targeted by drugs that can be repurposed for TB treatment Communicated by Ramaswamy H. Sarma
Chirped optical pulse compression using a silicon photonic crystal waveguide

We present an integrated pulse compression method for chirped optical pulses based on silicon photonic crystal (PhC) line-defect waveguides. The PhC waveguide structure and dimensions, including the radius of the hole and the thickness of the slab, are carefully designed for effective pulse compression in a short waveguide. In the optimized PhC waveguide, the pulse is effectively compressed and a compression factor, which is defined as the ratio of the output pulse width with respect to the input pulse width, as small as 0.096 is achieved. Analysis shows that the compression effect depends on the initial chirp, the peak power, and the width of the input pulse. In order to realize the best compression, the PhC waveguide length should be carefully chosen to balance the initial chirp, dispersion and nonlinearity of the waveguide.
Interspecific protoplast fusion of atmospheric and room-temperature plasma mutants of Aspergillus generates an L-asparaginase hyper-producing hybrid with techno-economic benefits

Abstract The axenic culture of Aspergillus candidus (Asp-C) produced an anti-leukemic L-asparaginase while Aspergillus sydowii (Asp-S) produced the acrylamide-reduction type. Upon mutagenesis by atmospheric and room-temperature plasma (ARTP), their individual L-asparaginase activities improved 2.3-folds in each of Ile-Thr-Asp-C-180-K and Val-Asp-S-180-E stable mutants. Protoplast fusion of selected stable mutants generated fusant-09 with improved anti-leukemic activity, acrylamide reduction, higher temperature optimum and superior kinetic parameters. Submerged (SmF) and solid-state fermentation (SSF) types were compared; likewise batch, fed-batch and continuous fermentation modes; and fed-batch submerged fermentation was selected on the basis of impressive techno-economics. Fusant L-asparaginase was purified by PEG/Na+ citrate aqueous two-phase system and molecular exclusion chromatography to 69.96 and 146.21-fold, respectively, and characterized by molecular weight, specificity, activity and stability to chemical and physical agents. Michaelis–Menten kinetics, evaluated under optimum conditions gave K m, V max, K cat, and K cat/K m as 1.667 × 10−3 M, 1666.67 µmol min−1 mg−1 protein, 645.99 s−1 and 3.88 × 105 M−1 s−1 respectively. In-vitro cytotoxicity of HL-60 cell lines by fusant-09 L-asparaginase improved 3.00 and 18.71-folds from mutants Ile-Thr-Asp-C-180-K and Val-Asp-S-180-E, and from 5.73 and 32.55 from respective original strains. Free-radical scavenging and acrylamide reduction improvements were intermediate. Fusant-09 L-asparaginase is strongly recommended for sustainable economic anti-leukemic and food industry applications.
Osteoarticular Mycoses

Osteoarticular mycoses are chronic debilitating infections that require extended courses of antifungal therapy and may warrant expert surgical intervention. As there has been no comprehensive review of these diseases, the International Consortium for Osteoarticular Mycoses prepared a definitive treatise for this important class of infections. SUMMARY Osteoarticular mycoses are chronic debilitating infections that require extended courses of antifungal therapy and may warrant expert surgical intervention. As there has been no comprehensive review of these diseases, the International Consortium for Osteoarticular Mycoses prepared a definitive treatise for this important class of infections. Among the etiologies of osteoarticular mycoses are Candida spp. , Aspergillus spp. , Mucorales, dematiaceous fungi, non-Aspergillus hyaline molds, and endemic mycoses, including those caused by Histoplasma capsulatum, Blastomyces dermatitidis, and Coccidioides species. This review analyzes the history, epidemiology, pathogenesis, clinical manifestations, diagnostic approaches, inflammatory biomarkers, diagnostic imaging modalities, treatments, and outcomes of osteomyelitis and septic arthritis caused by these organisms. Candida osteomyelitis and Candida arthritis are associated with greater events of hematogenous dissemination than those of most other osteoarticular mycoses. Traumatic inoculation is more commonly associated with osteoarticular mycoses caused by Aspergillus and non-Aspergillus molds. Synovial fluid cultures are highly sensitive in the detection of Candida and Aspergillus arthritis. Relapsed infection, particularly in Candida arthritis, may develop in relation to an inadequate duration of therapy. Overall mortality reflects survival from disseminated infection and underlying host factors.
Individualized Statistical Modeling of Lesions in Fundus Images for Anomaly Detection

Anomaly detection in fundus images remains challenging due to the fact that fundus images often contain diverse types of lesions with various properties in locations, sizes, shapes, and colors. Current methods achieve anomaly detection mainly through reconstructing or separating the fundus image background from a fundus image under the guidance of a set of normal fundus images. The reconstruction methods, however, ignore the constraint from lesions. The separation methods primarily model the diverse lesions with pixel-based independent and identical distributed (i.i.d.) properties, neglecting the individualized variations of different types of lesions and their structural properties. And hence, these methods may have difficulty to well distinguish lesions from fundus image backgrounds especially with the normal personalized variations (NPV). To address these challenges, we propose a patch-based non-i.i. d. mixture of Gaussian (MoG) to model diverse lesions for adapting to their statistical distribution variations in different fundus images and their patch-like structural properties. Further, we particularly introduce the weighted Schatten p-norm as the metric of low-rank decomposition for enhancing the accuracy of the learned fundus image backgrounds and reducing false-positives caused by NPV. With the individualized modeling of the diverse lesions and the background learning, fundus image backgrounds and NPV are finely learned and subsequently distinguished from diverse lesions, to ultimately improve the anomaly detection. The proposed method is evaluated on two real-world databases and one artificial database, outperforming the state-of-the-art methods.
Exercise postconditioning reduces ischemic injury via suppression of cerebral gluconeogenesis in rats

Pre‐stroke exercise conditioning reduces neurovascular injury and improves functional outcomes after stroke. The goal of this study was to explore if post‐stroke exercise conditioning (PostE) reduced brain injury and whether it was associated with the regulation of gluconeogenesis. Adult rats received 2 h of middle cerebral artery (MCA) occlusion, followed by 24 h of reperfusion. Treadmill activity was then initiated 24 h after reperfusion for PostE. The severity of the brain damage was determined by infarct volume, apoptotic cell death, and neurological deficit at one and three days after reperfusion. We measured gluconeogenesis including oxaloacetate (OAA), phosphoenolpyruvate (PEP), pyruvic acid, lactate, ROS, and glucose via ELISA, as well as the location and expression of the key enzyme phosphoenolpyruvate carboxykinase (PCK)‐1/2 via immunofluorescence. We also determined upstream pathways including forkhead transcription factor (FoxO1), p‐FoxO1, 3‐kinase (PI3K)/Akt, and p‐PI3K/Akt via Western blot. Additionally, the cytoplasmic expression of p‐FoxO1 was detected by immunofluorescence. Compared to non‐exercise control, PostE (*p < .05) decreased brain infarct volumes, neurological deficits, and cell death at one and three days. PostE groups (*p < .05) saw increases in OAA and decreases in PEP, pyruvic acid, lactate, ROS, glucose levels, and tissue PCKs expression on both days. PCK‐1/2 expressions were also significantly (*p < .05) suppressed by the exercise setting. Additionally, phosphorylated PI3K, AKT, and FoxO1 protein expression were significantly induced by PostE at one and three days (*p < .05). In this study, PostE reduced brain injury after stroke, in association with activated PI3K/AKT/FoxO1 signaling, and inhibited gluconeogenesis. These results suggest the involvement of FoxO1 regulation of gluconeogenesis underlying post‐stroke neuroprotection.
A linear stability analysis for wind-driven bubbles

The growth of linear perturbations of adiabatic shells of the shocked interstellar gas surrounding a strong stellar wind is examined. The shells are overstable if the adiabatic index gamma is less than about 1.1, and most overstable for the wavelengths comparable to the thickness of the shell. The shells of the wind-driven bubbles are generally more stable than those of blast waves. The implications of these results are discussed. 6 references.
Diagnostic and prognostic values of MMP-9 expression in ovarian cancer: A study based on bioinformatics analysis and meta-analysis

This study aims to explore the expression of matrix metalloproteinase-9 (MMP-9) associated with both diagnostic and prognostic value in ovarian cancer by meta-analysis and bioinformatics analyses. We investigated the prognostic value of MMP-9 expression in ovarian cancer based on The Cancer Genome Atlas. Five databases were used to collect records about MMP-9 expression related to diagnostic and prognostic values in ovarian cancer from inception to June 2022. Using Stata 15.0 software, hazard ratio (HR) and odds ratio (OR) were calculated as the effect index of prognosis. We chose the pooled sensitivity, specificity, and area under the curve (AUC) to judge the diagnostic utility of MMP-9 for ovarian cancer. A total of 23 studies on prognosis, and five studies on diagnosis were entered into the meta-analysis. These suggest that high MMP-9 expression was detrimental to the overall survival of patients with ovarian cancer (HR = 1.34; 95% confidence interval (CI) 1.08∼1.66; P<0.01). High MMP-9 expression increased the risk of tumor stage (OR = 3.66; 95% CI 1.89∼7.07), but was not related to the tumor grade of ovarian cancer (P>0.05). The pooled analysis of serum MMP-9 diagnosing for ovarian cancer gave the pooled sensitivity, specificity, and AUC the values of 0.72 (95% CI 0.61∼0.81), 0.81 (95% CI 0.77∼0.85), and 0.84 (95% CI 0.81∼0.87), respectively. High MMP-9 expression can increase the tumor stage, and a correlation exists between high MMP-9 expression and poor prognosis in patients with ovarian cancer. Also, serum MMP-9 has a good diagnostic value for ovarian cancer.
Controlling the diameter, growth rate, and density of vertically aligned carbon nanotubes synthesized by microwave plasma-enhanced chemical vapor deposition

Vertically aligned carbon nanotubes were synthesized on Ni-deposited Si substrates using microwave plasma-enhanced chemical vapor deposition. The grain size of Ni thin films varied with the rf power density during the rf magnetron sputtering process. We found that the diameter, growth rate, and density of carbon nanotubes could be controlled systematically by the grain size of Ni thin films. With decreasing the grain size of Ni thin films, the diameter of the nanotubes decreased, whereas the growth rate and density increased. High-resolution transmission electron microscope images clearly demonstrated synthesized nanotubes to be multiwalled.
Neoclassical radial electric field and ion heat flux in the presence of the transport barrier

The ambipolar radial electric field and ion heat flux in the presence of this field are studied using Monte Carlo guiding centre orbit following code ASCOT. These are studied as a function of temperature gradient in different collisionality regimes. Good agreement with the analytic theory is found for heat fluxes in plateau and banana regimes but in Pfirsch-Schluter regime sub-neoclassical heat flux is found for steep temperature gradients. For radial electric field, deviations from analytic theory are significant.
Stabilization of the repetition rate of passively Q-switched diode-pumped solid-state lasers

We present a simple technique to stabilize the period of the pulses emitted by passively Q-switched lasers. By slightly modulating the pump diode power, the repetition rate of a Nd3+:YAG laser passively Q switched by Cr4+:YAG is experimentally shown to reach a time stability of 10−6 over 106 pulses. Simulations using a rate-equation model are in close agreement with the experiments.
Electron structure of single and interacting hydrogen impurities in free-electron-like metals

Recent progress in the theoretical description of hydrogen impurities in metals, as described by the jellium model, and their interaction mutually and with vacancies are described. In addition to giving a detailed account of the author's contribution, the paper presents new results for the spectra of the hydrogen-induced states. These show for single interstitial hydrogen a doubly occupied bound state, while substitutional hydrogen has an atomic resonance in the conduction band. In both cases the state is situated just below the "local bottom of the band," as defined by the clean-metal effective potential at the impurity site. When two such states interact, both the bonding and the antibonding molecular orbitals get filled except at the lowest metallic densities, and a repulsive hydrogen-hydrogen interaction results. Spin-polarized $\ensuremath{\Delta}$ self-consistent-field calculations of the impurity excitation energies are presented. The results compare well with the one-electron binding energies of the bound states and with the excitation energies calculated by Vinter. The hydrogen impurity spectra presented can therefore be expected to represent approximately experimental excitation spectra of interstitial and substitutional hydrogen in free-electron-like metals.
Genetic duplication of tissue factor reveals subfunctionalization in venous and arterial hemostasis

Tissue factor (TF) is an evolutionarily conserved protein necessary for initiation of hemostasis. Zebrafish have two copies of the tissue factor gene (f3a and f3b) as the result of an ancestral teleost fish duplication event (so called ohnologs). In vivo physiologic studies of TF function have been difficult given early lethality of TF knockout in the mouse. We used genome editing to produce knockouts of both f3a and f3b in zebrafish. Since ohnologs arose through sub- or neofunctionalization, they can unmask unknown functions of non-teleost genes and could reveal whether mammalian TF has developmental functions distinct from coagulation. Here we show that a single copy of either f3a or f3b is necessary and sufficient for normal lifespan. Complete loss of TF results in lethal hemorrhage by 2–4 months despite normal embryonic and vascular development. Larval vascular endothelial injury reveals predominant roles for TFa in venous circulation and TFb in arterial circulation. Finally, we demonstrate that loss of TF predisposes to a stress-induced cardiac tamponade independent of its role in fibrin formation. Overall, our data suggest partial subfunctionalization of TFa and TFb. This multigenic zebrafish model has the potential to facilitate study of the role of TF in different vascular beds.
High time resolution observations of H alpha line profiles during the impulsive phase of a solar flare

H-alpha observations of the impulsive phase of a 1B/M1 solar flare on May 24, 1987, were carried out with high temporal resolution. A line center imaging system and an imaging spectrograph for line profile acquisition have been operated simultaneously with 0.3 s and 2.3 s temporal resolution, respectively. The temporal evolution at line center and in the blue and red wing have been correlated with hard X-ray data from HXRBS. The observed line profiles have been analyzed in terms of dynamic H-alpha line profile calculations by Canfield and Gayley. The combined H-alpha and hard X-ray signatures of two flare kernels are compatible with the theoretical predictions for strong nonthermal electron heating and the formation of a downward moving chromospheric condensation. A third kernel also shows the predicted downward moving chromospheric material, but its temporal evolution is not compatible with electron beam heating. 15 refs.
Multiplicity for Self-Dual Condensate Solutions in the Maxwell-Chern-Simons O(3) Sigma Model

In this paper, we study multiple existence of solutions of an elliptic system on a flat torus arising from the self-dual Maxwell-Chern-Simons O(3) sigma model. Using the Leray-Schauder degree, we find an explicit range of κ and q for which we have at least two vortex-antivortex solutions. For vortex solutions, we provide a complete picture of the range of κ and q for multiple existence of solutions.