Miracle-dz/UniFAR-FTUs huggingface dataset:
CGILS: Results from the first phase of an international project to understand the physical mechanisms of low cloud feedbacks in single column models

CGILS—the CFMIP‐GASS Intercomparison of Large Eddy Models (LESs) and single column models (SCMs)—investigates the mechanisms of cloud feedback in SCMs and LESs under idealized climate change perturbation. This paper describes the CGILS results from 15 SCMs and 8 LES models. Three cloud regimes over the subtropical oceans are studied: shallow cumulus, cumulus under stratocumulus, and well‐mixed coastal stratus/stratocumulus. In the stratocumulus and coastal stratus regimes, SCMs without activated shallow convection generally simulated negative cloud feedbacks, while models with active shallow convection generally simulated positive cloud feedbacks. In the shallow cumulus alone regime, this relationship is less clear, likely due to the changes in cloud depth, lateral mixing, and precipitation or a combination of them. The majority of LES models simulated negative cloud feedback in the well‐mixed coastal stratus/stratocumulus regime, and positive feedback in the shallow cumulus and stratocumulus regime. A general framework is provided to interpret SCM results: in a warmer climate, the moistening rate of the cloudy layer associated with the surface‐based turbulence parameterization is enhanced; together with weaker large‐scale subsidence, it causes negative cloud feedback. In contrast, in the warmer climate, the drying rate associated with the shallow convection scheme is enhanced. This causes positive cloud feedback. These mechanisms are summarized as the “NESTS” negative cloud feedback and the “SCOPE” positive cloud feedback (Negative feedback from Surface Turbulence under weaker Subsidence—Shallow Convection PositivE feedback) with the net cloud feedback depending on how the two opposing effects counteract each other. The LES results are consistent with these interpretations.
Biphasic Metabolism and Host Interaction of a Chlamydial Symbiont

Chlamydiae are known as major bacterial pathogens of humans, causing the ancient disease trachoma, but they are also frequently found in the environment where they infect ubiquitous protists such as amoebae. All known chlamydiae require a eukaryotic host cell to thrive. Using the environmental chlamydia Protochlamydia amoebophila within its natural host, Acanthamoeba castellanii, we investigated gene expression dynamics in vivo and throughout the complete chlamydial developmental cycle for the first time. This allowed us to infer how a major virulence mechanism, the type III secretion system, is regulated and employed, and we show that the physiology of chlamydiae undergoes a complete shift regarding carbon metabolism and energy generation. This study provides comprehensive insights into the infection strategy of chlamydiae and reveals a unique adaptation to life within a eukaryotic host cell. ABSTRACT Chlamydiae are obligate intracellular bacteria comprising well-known human pathogens and ubiquitous symbionts of protists, which are characterized by a unique developmental cycle. Here we comprehensively analyzed gene expression dynamics of Protochlamydia amoebophila during infection of its Acanthamoeba host by RNA sequencing. This revealed a highly dynamic transcriptional landscape, where major transcriptional shifts are conserved among chlamydial symbionts and pathogens. Our data served to propose a time-resolved model for type III protein secretion during the developmental cycle, and we provide evidence for a biphasic metabolism of P. amoebophila during infection, which involves energy parasitism and amino acids as the carbon source during initial stages and a postreplicative switch to endogenous glucose-based ATP production. This fits well with major transcriptional changes in the amoeba host, where upregulation of complex sugar breakdown precedes the P. amoebophila metabolic switch. The biphasic chlamydial metabolism represents a unique adaptation to exploit eukaryotic host cells, which likely contributed to the evolutionary success of this group of microbes. IMPORTANCE Chlamydiae are known as major bacterial pathogens of humans, causing the ancient disease trachoma, but they are also frequently found in the environment where they infect ubiquitous protists such as amoebae. All known chlamydiae require a eukaryotic host cell to thrive. Using the environmental chlamydia Protochlamydia amoebophila within its natural host, Acanthamoeba castellanii, we investigated gene expression dynamics in vivo and throughout the complete chlamydial developmental cycle for the first time. This allowed us to infer how a major virulence mechanism, the type III secretion system, is regulated and employed, and we show that the physiology of chlamydiae undergoes a complete shift regarding carbon metabolism and energy generation. This study provides comprehensive insights into the infection strategy of chlamydiae and reveals a unique adaptation to life within a eukaryotic host cell.
Gain of chromosome 7 marks the progression from indolent to aggressive follicle centre lymphoma and is a common finding in patients with diffuse large B‐cell lymphoma: a study by FISH

Gain of chromosome 7 represents one of the most frequent cytogenetic findings in B‐cell lymphomas with a follicular growth pattern. We used fluorescence in situ hybridization (FISH) and a probe specifying chromosome 7 on lymph node imprints and/or bone marrow (BM) and peripheral blood (PB) smears from six consecutive patients with follicle centre lymphomas (FCLs) grade I or II (low‐grade lymphomas), four patients with FCLs grade III and 11 patients with diffuse large B‐cell lymphomas (DLBCLs) (high‐grade lymphomas). We found gains of chromosome 7 in 14/18 successfully analysed cases (i.e. 2/6 FCLs grade I–II, 3/3 FLCs grade III and in 9/9 DLBCLs) using lymph node imprints. Moreover, the FISH technique demonstrated gains of chromosome 7 in 1/4 BM and 0/4 PB samples from FCLs grade I–II, in 2/4 BM and 2/4 PB specimens from FCLs grade III and in 4/9 BM and 2/9 PB samples from the DLBCLs. In contrast, morphologically recognizable lymphoma cells were seen in only 1/4 BM and 0/4 PB samples from the FCLs grade III and in 1/11 BM and 1/11 PB samples from the DLBCLs. We conclude that: (i) gain of chromosome 7 marks the progression from indolent to aggressive FCL and would appear to be a common finding in patients with FCLs grade III and in DLBCLs, (ii) clonal lymphoid cells occur frequently in BM and PB in high‐grade lymphomas, making traditional staging by cytomorphology uncertain, and (iii) using gains of chromosome 7 as a marker of lymphoma cells, FISH is a useful method to detect minimal residual disease in FCLs grade III and DLBCLs.
Mechanical properties of resin cements with different activation modes.

Dual-cured cements have been studied in terms of the hardness or degree of conversion achieved with different curing modes. However, little emphasis is given to the influence of the curing method on other mechanical properties. This study investigated the flexural strength, flexural modulus and hardness of four proprietary resin cements. Materials tested were: Enforce and Variolink II (light-, self- and dual-cured), RelyX ARC (self- and dual-cured) and C & B (self-cured). Specimens were fractured using a three-point bending test. Pre-failure loads corresponding to specific displacements of the cross-head were used for flexural modulus calculation. Knoop hardness (KHN) was measured on fragments obtained after the flexural test. Tests were performed after 24 h storage at 37 degrees C. RelyX ARC dual-cured showed higher flexural strength than the other groups. RelyX ARC and Variolink II depended upon photo-activation to achieve higher hardness values. Enforce showed similar hardness for dual- and self-curing modes. No correlation was found between flexural strength and hardness, indicating that other factors besides the degree of cure (e.g. filler content and monomer type) affect the flexural strength of composites. No statistical difference was detected in the flexural modulus among the different groups.
Intraoperative Daunorubicin Versus Conjunctival Autograft in Primary Pterygium Surgery

Purpose. To evaluate the safety and efficacy of intraoperative daunorubicin during a bare sclera procedure in primary pterygium surgery and to compare with conjunctival autograft. Methods. The data for 84 patients who underwent pterygium surgery at Safdarjung Hospital and Guru Nanak Eye Center were analyzed retrospectively. The patients were divided into two groups: group A, those who underwent bare sclera excision along with conjunctival autograft, and group B, those who underwent bare sclera excision with intraoperative daunorubicin (0.02%) for 3 minutes. We evaluated pterygium recurrence and postoperative complications for both groups. Recurrence of pterygium was defined as growth of 2 mm of fibrovascular tissue over the corneoscleral limbus into the clear cornea in the area of previous pterygium excision. Results. Follow-up ranged from 18 to 37 months (mean, 27). Recurrence rates of 8.33% (three of 36) and 7.14% (three of 42) were found in groups A and B, respectively. When compared statistically, the difference was not significant. All the recurrences occurred in patients younger than 30 years of age. Pyogenic granuloma, graft edema, loose graft, and dellen formation were seen, respectively, in 5.5% (two of 36), 2.77% (one of 36), 2.77% (one of 36), and 2.77% (one of 36) patients in group A. Nine of 42 (21.42%) patients in group B had chemosis of the conjunctiva and two of 42 (4.76%) had delayed epithelization. Conclusion. We conclude that intraoperative daunorubicin (0.02%) and conjunctival autograft are both equally effective adjuncts to pterygium surgery.
Antimicrobial Activity of Ceftolozane-Tazobactam Tested against Enterobacteriaceae and Pseudomonas aeruginosa with Various Resistance Patterns Isolated in U.S. Hospitals (2011-2012)

ABSTRACT Ceftolozane/tazobactam, a novel antimicrobial agent with activity against Pseudomonas aeruginosa (including drug-resistant strains) and other common Gram-negative pathogens (including most extended-spectrum-β-lactamase [ESBL]-producing Enterobacteriaceae strains), and comparator agents were susceptibility tested by a reference broth microdilution method against 7,071 Enterobacteriaceae and 1,971 P. aeruginosa isolates. Isolates were collected consecutively from patients in 32 medical centers across the United States during 2011 to 2012. Overall, 15.7% and 8.9% of P. aeruginosa isolates were classified as multidrug resistant (MDR) and extensively drug resistant (XDR), and 8.4% and 1.2% of Enterobacteriaceae were classified as MDR and XDR. No pandrug-resistant (PDR) Enterobacteriaceae isolates and only one PDR P. aeruginosa isolate were detected. Ceftolozane/tazobactam was the most potent (MIC50/90, 0.5/2 μg/ml) agent tested against P. aeruginosa and demonstrated good activity against 310 MDR strains (MIC50/90, 2/8 μg/ml) and 175 XDR strains (MIC50/90, 4/16 μg/ml). Ceftolozane/tazobactam exhibited high overall activity (MIC50/90, 0.25/1 μg/ml) against Enterobacteriaceae and retained activity (MIC50/90, 4/>32 μg/ml) against many 601 MDR strains but not against the 86 XDR strains (MIC50, >32 μg/ml). Ceftolozane/tazobactam was highly potent (MIC50/90, 0.25/0.5 μg/ml) against 2,691 Escherichia coli isolates and retained good activity against most ESBL-phenotype E. coli isolates (MIC50/90, 0.5/4 μg/ml), but activity was low against ESBL-phenotype Klebsiella pneumoniae isolates (MIC50/90, 32/>32 μg/ml), explained by the high rate (39.8%) of meropenem coresistance observed in this species phenotype. In summary, ceftolozane/tazobactam demonstrated high potency and broad-spectrum activity against many contemporary Enterobacteriaceae and P. aeruginosa isolates collected in U.S. medical centers. Importantly, ceftolozane/tazobactam retained potency against many MDR and XDR strains.
An Effective PSO-Based Node Localization Scheme for Wireless Sensor Networks

Wireless sensor networks (WSNs) usually employ different ranging techniques to measure the distance between an unknown node and its neighboring anchor nodes, and based on the measured distance to estimate the position of the unknown node. This paper presents an effective Particle Swarm Optimization (PSO)-based Localization Scheme using the Radio Signal Strength (RSS) ranging technique. Modified from the iterative multilateration algorithm, our scheme is unique in adopting the location data of remote anchors provided by the closest neighbor anchors of an unknown node to estimate the unknown nodepsilas position and using the PSO algorithm to further reduce error accumulation. The new scheme meanwhile takes in a modified DV-distance approach to raise the success ratios of locating unknown nodes. Compared with related schemes, our scheme is shown through simulations to perform constantly better in increasing localization success ratios and decreasing location errors -- at reduced cost.
Regulatory mutation that controls nif expression and histidine transport in Azospirillum brasilense

Mutagenesis of Azospirillum brasilense with nitrosoguanidine and selection on ethylenediamine yielded prototrophs which fixed nitrogen in the presence of ammonia. Nitrogenase activity in mutant strains exceeded that of the wild type three- to sixfold. The same mutants were also constitutive for histidine transport. Enzyme activities involved in ammonia assimilation were not affected by the mutation. The data suggest that the mutation occurred at a site which regulates nif and histidine transport functions.
Diffuse Large B-cell Lymphoma: A Clinicopathologic Analysis of 444 Cases Classified According to the Updated Kiel Classification

The purpose of this study was: to compare the survival of diffuse large B-cell lymphomas (DLBCL) stratified according to the up-dated Kiel classification. A retrospective study of a cohort of 1378 cases was organized in 1996 by the Non-Hodgkin's Lymphoma Classification Project, and the DLBCL were classified according to the updated Kiel classification. The distribution of the different types and subtypes was as follows: centroblastic (CB, 85.4%), composed of the polymorphic (CB-PM, 58.6%), monomorphic (CB-MM, 17.1%) and multilobated (CB-ML, 9.7%) subtypes; immunoblastic (IB, 11.2%), with (8.3%) or without (2.9%) plasmacytoid differentiation; and anaplastic large cell lymphoma (ALCL) of B-cell type (3.4%). The rate of diagnostic agreement between pathologists was 78% for CB and 65% for IB lymphoma. The 5-year overall survival (OAS) for the entire group was 47% and the 5-year failure-free survival (FFS) was 42%. No significant differences in survival were found between the three major groups (CB, IB, ALCL). However, the 5-year OAS and FFS of patients with DLBCL not containing immunoblasts (CB-MM+CB-ML) was 51 and 52%, respectively, and was significantly better than the survival of those containing immunoblasts (CB-PM+IB+ALCL), which was 44 and 38% (p =0.06 and p =0.037 ), respectively. These results did not appear to be due to differences in the clinical features of the two groups, and was most significant for patients with low stage or low risk disease. However, histologic subtyping was not an independent risk factor for the entire group by multivariate analysis. In conclusion, patients with CB-MM and CB-ML (without immunoblasts) had a significantly better OAS and FFS than those with CB-PM, IB and ALCL (with immunoblasts). Therefore, we conclude that additional studies are still needed to further evaluate the importance of immunoblastic differentiation in DLBCL.
Capacity Bounds for Discrete-Time, Amplitude-Constrained, Additive White Gaussian Noise Channels

The capacity-achieving input distribution of the discrete-time, additive white Gaussian noise (AWGN) channel with an amplitude constraint is discrete and seems difficult to characterize explicitly. A dual capacity expression is used to derive analytic capacity upper bounds for scalar and vector AWGN channels. The scalar bound improves on McKellips’ bound and is within 0.1 bit of capacity for all signal-to-noise ratios (SNRs). The 2-D bound is within 0.15 bits of capacity provably up to 4.5 dB; numerical evidence suggests a similar gap for all SNRs. As the SNR tends to infinity, these bounds are accurate and match with a volume-based lower bound. For the 2-D complex case, an analytic lower bound is derived by using a concentric constellation and is shown to be within 1 bit of capacity.
The Influence of Reconstruction Algorithm and Heart Rate on Coronary Artery Image Quality and Stenosis Detection at 64-Detector Cardiac CT

Objective We wanted to evaluate the impact of two reconstruction algorithms (halfscan and multisector) on the image quality and the accuracy of measuring the severity of coronary stenoses by using a pulsating cardiac phantom with different heart rates (HRs). Materials and Methods Simulated coronary arteries with different stenotic severities (25, 50, 75%) and different luminal diameters (3, 4, 5 mm) were scanned with a fixed pitch of 0.16 and a 0.35 second gantry rotation time on a 64-slice multidetector CT. Both reconstruction algorithms (halfscan and multisector) were applied to HRs of 40-120 beats per minute (bpm) at 10 bpm intervals. Three experienced radiologists visually assessed the image quality and they manually measured the stenotic severity. Results Fewer measurement errors occurred with multisector reconstruction (p = 0.05), a slower HR (p < 0.001) and a larger luminal diameter (p = 0.014); measurement errors were not related with the observers or the stenotic severity. There was no significant difference in measurements as for the reconstruction algorithms below an HR of 70 bpm. More nonassessable segments were visualized with halfscan reconstruction (p = 0.004) and higher HRs (p < 0.001). Halfscan reconstruction had better quality scores when the HR was below 60 bpm, while multisector reconstruction had better quality scores when the HR was above 90 bpm. For the HRs between 60 and 90 bpm, both reconstruction modes had similar quality scores. With excluding the nonassessable segments, both reconstruction algorithms achieved a similar mean measured stenotic severity and similar standard deviations. Conclusion At a higher HR (above 90 bpm), multisector reconstruction had better temporal resolution, fewer nonassessable segments, better quality scores and better accuracy of measuring the stenotic severity in this phantom study.
Scaling Acoustic Data Analysis through Collaboration and Automation

Monitoring and assessing environmental health is becoming increasingly important as human activity and climate change place greater pressure on global biodiversity. Acoustic sensors provide the ability to collect data passively, objectively and continuously across large areas for extended periods of time. While these factors make acoustic sensors attractive as autonomous data collectors, there are significant issues associated with large-scale data manipulation and analysis. We present our current research into techniques for analysing large volumes of acoustic data effectively and efficiently. We provide an overview of a novel online acoustic environmental workbench and discuss a number of approaches to scaling analysis of acoustic data, collaboration, manual, automatic and human-in-the loop analysis.
Learning to Attend via Word-Aspect Associative Fusion for Aspect-based Sentiment Analysis

Aspect-based sentiment analysis (ABSA) tries to predict the polarity of a given document with respect to a given aspect entity. While neural network architectures have been successful in predicting the overall polarity of sentences, aspect-specific sentiment analysis still remains as an open problem. In this paper, we propose a novel method for integrating aspect information into the neural model. More specifically, we incorporate aspect information into the neural model by modeling word-aspect relationships. Our novel model, Aspect Fusion LSTM (AF-LSTM) learns to attend based on associative relationships between sentence words and aspect which allows our model to adaptively focus on the correct words given an aspect term. This ameliorates the flaws of other state-of-the-art models that utilize naive concatenations to model word-aspect similarity. Instead, our model adopts circular convolution and circular correlation to model the similarity between aspect and words and elegantly incorporates this within a differentiable neural attention framework. Finally, our model is end-to-end differentiable and highly related to convolution-correlation (holographic like) memories. Our proposed neural model achieves state-of-the-art performance on benchmark datasets, outperforming ATAE-LSTM by 4%-5% on average across multiple datasets.
A Preliminary Analysis of the Influences of Licensing and Organizational Sponsorship on Success in Open Source Projects

This paper develops and tests a model of the impact of licensing restrictiveness and organizational sponsorship on the popularity and vitality of open source software (OSS) development projects. Using data gathered from Freshmeat.net and OSS project home pages the main conclusions derived from the analysis are that organizational sponsorship has a positive effect on project popularity by easing user concerns about cost and quality and that license restrictiveness may have a negative effect on popularity by reducing the perceived utility of open source software. Theoretical and practical implications are discussed, and the paper outlines several avenues for future research.
High-field surface-coil MR imaging of localized anatomy.

For some time it has been recognized that surface-receivercoil designs can enhance certain aspects of magnetic resonance (MR) signal detection [1] . During the last several years, surface coils have been the predominant means of recording the MR spectra of metabolites from animals and humans in vivo [2-4]. Efforts to produce surface-coil images at low magnetic field strengths have been undertaken as well [5, 6] . Recently, we exploited the properties of these coils to achieve enhanced sensitivity in MR imaging at 1.5 T [7]. Initial results demonstrate that significantly improved resolution of small anatomic structures is possible when surface coils are used as receiver elements in high-field MR imaging systems. We have been exploring this new technique as part of an ongoing effort to improve the diagnostic usefulness of MR in specific regions of the anatomy. Presented here are three series of images of the neck, the inner ear, and the lumbar spine obtained using the surface-coil method.
Multimodal optical microscopy in combination with gold nanorods for cancer cell imaging

Abstract. The multimodal optical imaging technique, which utilizes nonlinear and linear optical processes, plays an important role in biological and biomedical research. As second-order nonlinear phenomenon, the two-photon luminescence (TPL) results from the nonlinear excitation of fluorescent molecules, while the second harmonic generation (SHG) depends on the second order nonlinear polarization, orientation, and noncentrosymmetric properties of molecules. In contrast, the linear resonance light scattering (RLS) occurs when the molecules are excited by a light beam with a wavelength close to their absorption bands. Since SHG, TPL, and RLS involve different kinds of optical processes, they might be used in parallel to provide complementary information about the structure and function of cells and tissues. Herein, we develop for the first time a multimodal optical microscopy with the capability of simultaneous SHG, TPL, and RLS imaging. We analyze theoretically and demonstrate experimentally the near-infrared irradiation-induced SHG, TPL, and RLS from the gold nanorods with nanometer spatial resolution. With the gold nanorods as the contrast agents, we further demonstrate the simultaneous SHG, TPL, and RLS imaging of A431 human epithelial skin cancer cells. This multimodal optical microscopy might provide a reliable and complementary approach for biological and biomedical research.