Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome Expression Proﬁling-Based Identiﬁcation and Administration Efﬁcacy of Host-Directed Antimicrobial Drugs against Respiratory Infection by Nontypeable Haemophilus inﬂuenzae

Therapies that are safe, effective, and not vulnerable to developing resistance are highly desirable to counteract bacterial infections. Host-directed therapeutics is an antimicrobial approach alternative to conventional antibiotics based on perturbing host pathways subverted by pathogens during their life cycle by using host-directed drugs. In this study, we identiﬁed and evaluated the efﬁcacy of a panel of host-directed drugs against respiratory infection by nontypeable Haemophilus inﬂuenzae (NTHi). NTHi is an opportunistic pathogen that is an important cause of exacerbation of chronic obstructive pulmonary disease (COPD). We screened for host genes differentially expressed upon infection by the clinical isolate NTHi375 by analyzing cell whole-genome expression proﬁling and identiﬁed a repertoire of host target candidates that were pharmacologically modulated. Based on the proposed relationship between NTHi intracellular location and persistence, we hypothesized that drugs perturbing host pathways used by NTHi to enter epithelial cells could have antimicrobial potential against NTHi infection. Interfering drugs were tested for their effects on bacterial and cellular viability, on NTHi-epithelial cell interplay, and on mouse pulmonary infection. Glucocorticoids and statins lacked in vitro and/or in vivo efﬁcacy. Conversely, the sirtuin-1 activator resveratrol showed a bactericidal effect against NTHi, and the PDE4 inhibitor rolipram showed therapeutic efﬁcacy by lowering NTHi375 counts intracellularly and in the lungs of infected mice. PDE4 inhibition is currently prescribed in COPD, and resveratrol is an attractive geroprotector for COPD treatment. Together, these results expand our knowledge of NTHi-triggered host subversion and frame the antimicrobial potential of rolipram and resveratrol against NTHi respiratory infection.
Construction Equipment Emission Modeling and Activity Analysis Using Deep Learning

—Automated activity recognition and modeling of heavy construction equipment can contribute to the correct and accurate measurement of a variety of project performance indicators. Productivity assessment and sustainability measurement through equipment activity cycle monitoring to eliminate ineffective and idle times thus reducing Greenhouse Gas (GHG) Emission, are some potential areas that can benefit from the integration of automated activity recognition and analysis techniques. In light of this, this idea paper describes design and development of a deep-learning framework that uses accelerometer data to detect activities of construction equipment and consequently estimates the emission produced corresponding to various activities.
3D Numerical investigation of a rounded corner square cylinder for supercritical flows

Tall buildings are often subjected to steady and unsteady forces due to external wind flows. Measurement and mitigation of these forces becomes critical to structural design in engineering applications. Over the last few decades, many approaches such as modification of the external geometry of structures have been investigated to mitigate wind-induced load. One such proven geometric modification involved the rounding of sharp corners. In this work, we systematically analyze the impact of rounded corner radii on the reducing the flow-induced loading on a square cylinder. We perform 3-Dimensional (3D) simulations for high Reynolds number flows (Re=1 × 105) which are more likely to be encountered in practical applications. An Improved Delayed Detached Eddy Simulation (IDDES) method capable of capturing flow accurately at large Reynolds numbers is employed in this study. The IDDES formulation uses a k-ω Shear Stress Transport (SST) model for near-wall modelling that prevents mesh-induced separation of the boundary layer. The effects of these corner modifications are analyzed in terms of the resulting variations in the mean and fluctuating components of the aerodynamic forces compared to a square cylinder with no geometric changes. Plots of the angular distribution of the mean and fluctuating coefficient of pressure along the square cylinder’s surface illustrate the effects of corner modifications on the different parts of the cylinder. The windward corner’s separation angle was observed to decrease with an increase in radius, resulting in a narrower and longer recirculation region. Furthermore, with an increase in radius, a reduction in the fluctuating lift, mean drag, and fluctuating drag coefficients has been observed.
Covariance Structure and Convergence Rate of the Gibbs Sampler with Various Scans

This paper presents results on covariance structure and convergence for the Gibbs sampler with both systematic and random scans. It is shown that, under conditions that guarantee the compactness of the Markov forward operator and irreducibility of the corresponding chain, the Gibbs sampling scheme converges geometrically in terms of Pearson χ 2 -distance. In particular, for the random scan, the autocovariance can be expressed as variances of iterative conditional expectations. As a consequence, the autocorrelations are all positive and decrease monotonically
Phase 1 Expansion Cohort of Ramucirumab Plus Pembrolizumab in Advanced Treatment-Naive NSCLC

Introduction: Data of ﬁ rst-line ramucirumab plus pembrolizumab treatment of programmed death-ligand 1 (PD-L1) – positive NSCLC (cohort E) are reported (NCT02443324). Methods: In this multicenter, open-label phase 1a/b trial, patients received ramucirumab 10 mg/kg and pembrolizumab 200 mg every 21 days for up to 35 cycles. PD-L1 positivity was de ﬁ ned as tumor proportion score (TPS) greater than or equal to 1%. Exploratory NanoString biomarker analyses included three T-cell signatures (T-cell – in ﬂ amed, Gajewski, and effector T cells) and CD274 gene expression. Results: Cohort E included 26 patients. Treatment-related adverse events of any grade occurred in 22 patients (84.6%). Treatment-related adverse events of grade greater than or equal to 3 were reported in 11 patients (42.3%); the most frequent was hypertension (n ¼ 4, 15.4%). Objective response rate was 42.3% in the treated population and 56.3% and 22.2% for patients with high (TPS (cid:2) 50%) and lower levels (TPS 1% – 49%) of PD-L1 expression, respectively. Median progression-free survival (PFS) in the treated population was 9.3 months, and 12-month and 18-month PFS rates were 45% each. Median PFS was not reached in patients with PD-L1 TPS greater than or equal to 50% and was 4.2 months in patients with PD-L1 TPS 1% to 49%. Median overall survival was not reached in the treated population, and 12-month and 18-month overall survival rates were 73% and 64%, respectively. Biomarker data suggested a positive association among clinical response, three T-cell signatures, CD274 gene expression, and PD-L1 immunohistochemistry. Conclusions: First-line therapy with ramucirumab plus pembrolizumab has a manageable safety pro ﬁ le in patients with NSCLC, and the ef ﬁ cacy signal seems to be strongest in tumors with high PD-L1 expression.
Intersection, Ideals, and Inversion

Techniques from computational algebra provide a framework for treating large classes of inverse problems. In particular, the discretization of many types of integral equations and of partial differential equations with undetermined coefficients lead to systems of polynomial equations. The structure of the solution set-of such equations may be examined using algebraic techniques. For example, the existence and dimensionality of the solution set may be determined. Furthermore, it is possible to bound the total number of solutions. The approach is illustrated by a numerical application to the inverse problem associated with the Helmholtz equation. The algebraic methods are used in the inversion of a set of transverse electric (TE) mode magnetotelluric data from Antarctica. The existence of solutions is demonstrated and the number of solutions is found to be finite, bounded from above at 50. The best fitting structure is dominantly one-dimensional with a low crustal resistivity of about 2 ohm-m. Such a low value is compatible with studies suggesting lower surface wave velocities than found in typical stable cratons.
Numerical Discrimination Learning in Rats 1

This study examines rats’ discrimination learning of the numerical ordering position of objects. In Experiments 1 and 2, five out of seven rats successfully learned to respond to the third of six identical objects in a row and showed reliable transfer of this discrimination to novel stimuli after being trained with three different training stimuli. In Experiment 3, the three rats from Experiment 2 continued to be trained to respond to the third object in an object array, which included an odd object that needed to be excluded in identifying the target third object. All three rats acquired this selective counting task of specific stimuli, and two rats showed reliable transfer of this selective counting performance to a test set of novel stimuli. In Experiment 4, the three rats from Experiment 3 quickly learned to respond to the third stimulus in object rows consisting of six identical objects or six different objects. These results offer strong evidence for abstract numerical discrimination learning in rats. A long-standing topic in comparative psychology is whether nonhuman animals can learn an abstract numerical concept. Numerical competence allows animals to comprehend the numerical aspects of a variety of aggregations that differ in specific physical features. Using the abstract numerical concept, we can apply common calculation rules to a wide variety of stimuli. The abstract concept of number has been divided into two components, concepts of abstract numerosity and order of the numerosities (Brannon & Roitman, 2003; Gelman & Gallistel, 1978; Neider, 2005). Abstract numerosity is suggested by responding to numerosities of stimuli regardless their physical properties, such as size, color, shape, and so on. The concept of ordering relationships among these abstract numerosities enables animals to recognize, for example, that “fourness is greater than threeness and less than fiveness”. abstract
Dessins d’Enfants in N = 2 Generalised Quiver Theories

We study Grothendieck’s dessins d’enfants in the context of the N = 2 supersymmetric gauge theories in (3 + 1) dimensions with product SU (2) gauge groups which have recently been considered by Gaiotto et al . We identify the precise context in which dessins arise in these theories: they are the so-called ribbon graphs of such theories at certain isolated points in the moduli space. With this point in mind, we highlight connections to other work on trivalent dessins, gauge theories, and the modular group.
(2015). Impact of the lateral blast on the spatial pattern and grain size characteristics of the 18 1980 Mount St. Helens fallout deposit. Geophysical

The May 18, 1980 eruption of Mount St. Helens started with a lateral blast that fed a pyroclastic surge, which then uplifted to form a co-blast plume. 30 minutes later, Plinian activity started at the vent and fluctuated in intensity for ~ 9 hours. The resulting fallout deposit, documented to > 600 km from vent, presents some striking features: 1) displacement of the overall deposit to the north of the vent; 2) a secondary thickness and mass maximum at ~300 km from vent; 3) a total grain-size distribution dominated by fine ash (62 wt% of the deposit < 63 µm); and 4) individual grain-size distributions that vary dramatically in the cross-wind direction from strongly bimodal in the south to skewed unimodal in the north. Results from a new deconvolution of the individual grain-size distributions show that they are a combination of a coarse subpopulation that decreases in size with distance from vent and a constant fine subpopulation with a mean ~ 15 µm. Relative proportions of each subpopulation vary asymmetrically in the cross-wind directions, with the fine subpopulation preponderant towards the north and the coarse one dominating the south of the deposit; both reach their absolute maxima in mass on the deposit axis. Componentry analyses of selected samples show that blast-derived material is greatly enriched towards the north of the deposit. These results indicate that the co-blast plume dispersed fine-grained material over great distances and dominated the fine subpopulation. Comparison with reanalysis data of atmospheric wind fields and satellite images of the spreading ash cloud suggests contrasting ash transport and depositional processes for the (early) co-blast plume and the (later) vent-derived Plinian plumes. The co-blast plume is displaced to the north; it had a high overshoot height, and eastward dispersion via strong winds low in the stratosphere (~10-15 km). The Plinian plumes were lower and dispersed most of the material to the southeast as the direction of high velocity winds shifted just before the late climactic Plinian eruptive phase. Fine ash (fine subpopulation) was deposited continuously throughout the deposit, with an increase of sedimentation rate ~ 300 km from the vent where there is a secondary maximum in the deposit mass and thickness. Fine ash probably settled by a combination of enhanced sedimentation mechanisms, including not only aggregation but also gravitational convective instabilities of cloud base, hydrometeor formation and destruction, and entrainment of small particles by larger ones. Finally, we show that half of the deposit (by mass) in the medial area was deposited by the co-blast plume, and that a significant proportion of the Mount St. Helens fallout deposit is non-juvenile, which has implications for the magmatic budget of this eruption.
HNE Induces the Hyperexpression of MUC5AC in Chronic Rhinosinusitis With Nasal Polyps by Activating the TRAF6/Autophagy Regulatory Axis

Background Hypersecretion of mucin 5AC (MUC5AC) is a prominent feature of chronic rhinosinusitis with nasal polyps (CRSwNP) and autophagy plays a pivotal role in this process. TNF receptor-associated factor 6 (TRAF6) functions as a signal transducer in many inflammation diseases, whereas the correlation between TRAF6 and autophagy in CRSwNP remains unclear. Objective To investigate the role of TRAF6 in the human neutrophil elastase (HNE)-induced autophagy and mucin MUC5AC over-expression in CRSwNP. Methods Tissue specimens were obtained from control subjects and patients with CRSwNP. The relationships between HNE, TRAF6, autophagy, and MUC5AC were investigated. The effect of TRAF6 on HNE-mediated autophagy and hypersecretion of MUC5AC was assessed by in-vitro culture of HNECs treated with human recombinant HNE. Results Patients with CRSwNP had more protein expression of HNE, MUC5AC, TRAF6, and light chain (LC3B), and increased levels of Beclin-1(BECN1) and autophagy-related gene 5 (ATG5) in mRNA level. Treatment of nasal epithelial cells with recombinant HNE induced the upregulation of TRAF6, autophagy, and MUC5AC. Alternatively, si-TRAF6 or autophagy inhibitor treatment mitigates the hyperexpression of MUC5AC before incubating with recombinant HNE. Conclusion HNE promotes autophagy through TRAF6, resulting in hyperexpression of MUC5AC in CRSwNP.
MD-Cave: An Immersive Visualization Workbench for Radiologists

The MD-Cave is an immersive analytics system that provides enhanced stereoscopic visualizations to support visual diagnoses performed by radiologists. The system harnesses contemporary paradigms in immersive visualization and 3D interaction, which are better suited for investigating 3D volumetric data. We retain practicality through efficient utilization of desk space and comfort for radiologists in terms of frequent long duration use. MD-Cave is general and incorporates: (1) high resolution stereoscopic visualizations through a surround triple-monitor setup, (2) 3D interactions through head and hand tracking, (3) and a general framework that supports 3D visualization of deep-seated anatomical structures without the need for explicit segmentation algorithms. Such a general framework expands the utility of our system to many diagnostic scenarios. We have developed MD-Cave through close collaboration and feedback from two expert radiologists who evaluated the utility of MD-Cave and the 3D interactions in the context of radiological examinations. We also provide evaluation of MD-Cave through case studies performed by an expert radiologist and concrete examples on multiple real-world diagnostic scenarios, such as pancreatic cancer, shoulder-CT, and COVID-19 Chest CT examination.
Design of High Speed Architecture of ECSM

: Multiplication is a basic operation. An elliptic curve is a smooth, projective algebraic curve on which there is a specified point. Scalar multiplication is performed by repeated point addition and doubling which consists of FF arithmetics.Elliptic curve scalar multiplication is the operation of successively adding a point along an elliptic curve. Binary fields and prime fields are used. Multiplication is performed by polynomial multiplication and reduction modulo. The architecture consists of FF MAC, FF SQUARER,FSM,Control Block and Register Bank. To find the optimal number of pipeline stages, scheduling schemes are implemented and placement registers is analyzed. Design of a four stage pipelined ECSM using Montgomery ladder algorithm using Virtex-4 and Virtex-5 is an existing system. The proposed system is to implement a three-stage pipelined ECSM with area reduction, high speed and to improve working frequency. Coding is implemented using Verilog language and the simulation is done using Xilinx ISE 14.5.
Cancer Incidence Among Adults With HIV in a Population-Based Cohort in Korea

Key Points Question What is the incidence of cancer in people with HIV infection in Korea, and does it differ from that in the general population? Findings In a nationwide cohort study of 11 552 HIV-infected individuals, compared with noninfected individuals, the risk of any cancer, Kaposi sarcoma, anal cancer, non-Hodgkin lymphoma, Hodgkin lymphoma, and oropharyngeal cancer was higher in men infected with HIV, and the risk of cancer, cervical cancer, and non-Hodgkin lymphoma was higher in women infected with HIV. The risk of thyroid cancer was lower in all patients infected with HIV. Meaning In this study, cancer risks, especially for AIDS-defining cancer and virus-related cancer, were elevated in people with HIV; the lower risk of thyroid cancer might reflect limited medical access for prevention.
Construction of prediction models for growth traits of soybean cultivars based on phenotyping in diverse genotype and environment combinations

Abstract As soybean cultivars are adapted to a relatively narrow range of latitude, the effects of climate changes are estimated to be severe. To address this issue, it is important to improve our understanding of the effects of climate change by applying the simulation model including both genetic and environmental factors with their interactions (G×E). To achieve this goal, we conducted the field experiments for soybean core collections using multiple sowing times in multi-latitudinal fields. Sowing time shifts altered the flowering time (FT) and growth phenotypes, and resulted in increasing the combinations of genotypes and environments. Genome-wide association studies for the obtained phenotypes revealed the effects of field and sowing time to the significance of detected alleles, indicating the presence of G×E. By using accumulated phenotypic and environmental data in 2018 and 2019, we constructed multiple regression models for FT and growth pattern. Applicability of the constructed models was evaluated by the field experiments in 2020 including a novel field, and high correlation between the predicted and measured values was observed, suggesting the robustness of the models. The models presented here would allow us to predict the phenotype of the core collections in a given environment.
Within‐eye and between‐subject variability for reflectance of the retinal nerve fibre layer

Reflectance of retinal nerve fibre layer (RNFL) can contribute to detecting the presence of glaucomatous damage and defining its extent. As a step towards developing a normative database for RNFL reflectance, we assessed within‐eye and between‐subject variability for RNFL reflectance in healthy eyes.
The Proteome of Extracellular Vesicles Produced by the Human Gut Bacteria Bacteroides thetaiotaomicron In Vivo Is Influenced by Environmental and Host-Derived Factors

The gastrointestinal tract (GIT) harbors a complex community of microbes termed the microbiota that plays a role in maintaining the host’s health and wellbeing. How this comes about and the nature of microbe-host cell interactions in the GIT is still unclear. ABSTRACT Bacterial extracellular vesicles (BEVs) released from both Gram-negative and Gram-positive bacteria provide an effective means of communication and trafficking of cell signaling molecules. In the gastrointestinal tract (GIT) BEVs produced by members of the intestinal microbiota can impact host health by mediating microbe-host cell interactions. A major unresolved question, however, is what factors influence the composition of BEV proteins and whether the host influences protein packaging into BEVs and secretion into the GIT. To address this, we have analyzed the proteome of BEVs produced by the major human gut symbiont Bacteroides thetaiotaomicron both in vitro and in vivo in the murine GIT in order to identify proteins specifically enriched in BEVs produced in vivo. We identified 113 proteins enriched in BEVs produced in vivo, the majority (62/113) of which accumulated in BEVs in the absence of any changes in their expression by the parental cells. Among these selectively enriched proteins, we identified dipeptidyl peptidases and an asparaginase and confirmed their increased activity in BEVs produced in vivo. We also showed that intact BEVs are capable of degrading bile acids via a bile salt hydrolase. Collectively these findings provide additional evidence for the dynamic interplay of host-microbe interactions in the GIT and the existence of an active mechanism to drive and enrich a selected group of proteins for secretion into BEVs in the GIT. IMPORTANCE The gastrointestinal tract (GIT) harbors a complex community of microbes termed the microbiota that plays a role in maintaining the host’s health and wellbeing. How this comes about and the nature of microbe-host cell interactions in the GIT is still unclear. Recently, nanosized vesicles naturally produced by bacterial constituents of the microbiota have been shown to influence responses of different host cells although the molecular basis and identity of vesicle-born bacterial proteins that mediate these interactions is unclear. We show here that bacterial extracellular vesicles (BEVs) produced by the human symbiont Bacteroides thetaiotaomicron in the GIT are enriched in a set of proteins and enzymes, including dipeptidyl peptidases, an asparaginase and a bile salt hydrolase that can influence host cell biosynthetic pathways. Our results provide new insights into the molecular basis of microbiota-host interactions that are central to maintaining GIT homeostasis and health.