Miracle-dz/UniFAR-FTUs huggingface dataset:
Decadal Climate Predictability and Prediction: Where Are We?

The importance of decadal climate variability (DCV) research is being increasingly recognized, including by the World Climate Research Program (WCRP) and the Intergovernmental Panel on Climate Change (IPCC). An improved understanding of DCV is very important because stakeholders and policymakers want to know the likely climate trajectory for the coming decades for applications to water resources, agriculture, energy, and infrastructure development. Responding to this demand, many climate modeling groups in the United States, Europe, Japan, and elsewhere are gearing up to assess the potential for decadal climate predictions. The magnitudes of regional DCV often exceed those associated with the trends resulting from anthropogenic changes. Therefore, differentiating between the two is also very important for planning, implementation, and national and international treaties.
High-throughput Methods for Dissection of Trypanosome Gene Regulatory Networks

From synthesis to decay, mRNA associates with RNA-binding proteins (RBPs) establishing dynamic ribonucleoprotein particles (RNPs). Understanding the composition and function of RNPs is fundamental to understanding how eukaryotic mRNAs are controlled. This is especially relevant for trypanosomes and related kinetoplastid parasites, which mostly rely on post-transcriptional mechanisms to control gene expression. Crucial for trypanosome differentiation, development, or even response to heat shock, RBPs are known to be essential modulators of diverse molecular processes. The recent application of large-scale quantitative methods, such as Next-Generation Sequencing (NGS) and quantitative mass spectrometry, has revealed new exciting features about the parasite RNA-related metabolism. Novel proteins carrying RNA-binding activity, including many proteins without RNA-related ontology were discovered setting a necessary groundwork to get in insights into RNA biology. Conclusion: This review aims to give the reader an understanding of current trypanosome RNP research, highlighting the progress made using high-throughput approaches.
Probing the changes in gene expression due to α-crystallin mutations in mouse models of hereditary human cataract

The mammalian eye lens expresses a high concentration of crystallins (α, β and γ-crystallins) to maintain the refractive index essential for lens transparency. Crystallins are long-lived proteins that do not turnover throughout life. The structural destabilization of crystallins by UV exposure, glycation, oxidative stress and mutations in crystallin genes leads to protein aggregation and development of cataracts. Several destabilizing mutations in crystallin genes are linked with human autosomal dominant hereditary cataracts. To investigate the mechanism by which the α-crystallin mutations Cryaa-R49C and Cryab-R120G lead to cataract formation, we determined whether these mutations cause an altered expression of specific transcripts in the lens at an early postnatal age by RNA-seq analysis. Using knock-in mouse models previously generated in our laboratory, in the present work, we identified genes that exhibited altered abundance in the mutant lenses, including decreased transcripts for Clic5, an intracellular water channel in Cryaa-R49C heterozygous mutant lenses, and increased transcripts for Eno1b in Cryab-R120G heterozygous mutant lenses. In addition, RNA-seq analysis revealed increased histones H2B, H2A, and H4 gene expression in Cryaa-R49C mutant lenses, suggesting that the αA-crystallin mutation regulates histone expression via a transcriptional mechanism. Additionally, these studies confirmed the increased expression of histones H2B, H2A, and H4 by proteomic analysis of Cryaa-R49C knock-in and Cryaa;Cryab gene knockout lenses reported previously. Taken together, these findings offer additional insight into the early transcriptional changes caused by Cryaa and Cryab mutations associated with autosomal dominant human cataracts, and indicate that the transcript levels of certain genes are affected by the expression of mutant α-crystallin in vivo.
An Unbalanced Exon-Expression qPCR-based Assay for Detection of ALK Translocation (Fusion) in Lung Cancer

1National Research Council Halifax, 1411 Oxford Street, Halifax, NS B3H 3Z1, Canada 2Department of Pathology, Queen Elizabeth II Health Science Center and Dalhousie University, 5788 University Ave., Halifax, NS B3H 1V8, Canada *Corresponding author Rama K. Singh, PhD Human Health Therapeutics Portfolio National Research Council Canada 1411 Oxford Street Halifax, Nova Scotia B3H 3Z1, Canada Tel. (902) 426-3802 Fax: (902) 426-9413 E-mail: rama.singh@nrc-cnrc.gc. ca
HIERARCHICAL REGULARIZATION OF POLYGONS FOR PHOTOGRAMMETRIC POINT CLOUDS OF OBLIQUE IMAGES

Abstract. Despite the success of multi-view stereo (MVS) reconstruction from massive oblique images in city scale, only point clouds and triangulated meshes are available from existing MVS pipelines, which are topologically defect laden, free of semantical information and hard to edit and manipulate interactively in further applications. On the other hand, 2D polygons and polygonal models are still the industrial standard. However, extraction of the 2D polygons from MVS point clouds is still a non-trivial task, given the fact that the boundaries of the detected planes are zigzagged and regularities, such as parallel and orthogonal, cannot preserve. Aiming to solve these issues, this paper proposes a hierarchical polygon regularization method for the photogrammetric point clouds from existing MVS pipelines, which comprises of local and global levels. After boundary points extraction, e.g. using alpha shapes, the local level is used to consolidate the original points, by refining the orientation and position of the points using linear priors. The points are then grouped into local segments by forward searching. In the global level, regularities are enforced through a labeling process, which encourage the segments share the same label and the same label represents segments are parallel or orthogonal. This is formulated as Markov Random Field and solved efficiently. Preliminary results are made with point clouds from aerial oblique images and compared with two classical regularization methods, which have revealed that the proposed method are more powerful in abstracting a single building and is promising for further 3D polygonal model reconstruction and GIS applications.
Integrating Heterogeneous Odor Response Data into a Common Response Model: A DoOR to the Complete Olfactome

We have developed a new computational framework for merging odor response data sets from heterogeneous studies, creating a consensus metadatabase, the database of odor responses (DoOR). As a result, we obtained a functional atlas of all available odor responses in Drosophila melanogaster. Both the program and the data set are freely accessible and downloadable on the Internet (http://neuro.uni-konstanz.de/DoOR). The procedure can be adapted to other species, thus creating a family of “olfactomes” in the near future. Drosophila melanogaster was chosen because of all species this one is closest to having the complete olfactome characterized, with the highest number of deorphanized receptors available. The database guarantees long-term stability (by offering time-stamped, downloadable versions), up-to-date accuracy (by including new data sets as soon as they are published), and portability (for other species). We hope that this comprehensive repository of odor response profiles will be useful to the olfactory community and to computational neuroscientists alike.
Thromboprophylaxis With Heparin During Orthotopic Liver Transplantation: Comparison of Hepcon HMS Plus and Anti-Xa Assays for Low-Range Heparin.

OBJECTIVES The purpose of this study was to compare the agreement between two heparin assays, Hepcon HMS plus/Kaolin-ACT and Anti-Xa, and their predictive power in detecting circulating heparin levels post-reperfusion of the liver graft when compared with thromboelastogram (TEG) r time ratio in patients undergoing orthotopic liver transplantation (OLT). DESIGN Prospective, observational cohort study design. SETTING Single center, university hospital. PARTICIPANTS Thirty-eight consecutive adults who had undergone liver transplant. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS Paired arterial blood samples were collected before surgical incision, 5 minutes after administration of an average dose of 2,054±771 units of intravenous unfractionated heparin before caval cross-clamping, 5 minutes after portal reperfusion, 5 minutes after hepatic artery reperfusion, and 1 hour after hepatic artery reperfusion. The observations that heparin assay measurements were within the predetermined limits of agreement, strongly suggested the two heparin assays (Hepcon HMS plus and Anti-Xa assay) are interchangeable during prophylactic heparin dose therapy during OLT. Post-reperfusion, receiver operating characteristic curve analysis revealed high accuracy in measuring circulating heparin levels with both Anti-Xa and Hepcon HMS assays when compared with the TEG r time ratio assay. CONCLUSIONS The point-of-care Hepcon HMS plus/Kaolin-ACT (activated clotting time) assay appeared to be a reliable alternative to the more expensive and laboratory-required Anti-Xa assay in monitoring the response to intravenous heparin in patients undergoing OLT.
Prevalence of Pulmonary Embolism in Patients With Syncope

Importance Sparse data and conflicting evidence exist on the prevalence of pulmonary embolism (PE) in patients with syncope. Objective To estimate the prevalence of PE among patients presenting to the emergency department (ED) for evaluation of syncope. Design, Setting, and Participants This retrospective, observational study analyzed longitudinal administrative data from 5 databases in 4 different countries (Canada, Denmark, Italy, and the United States). Data from all adult patients (aged ≥18 years) who presented to the ED were screened to identify those with syncope codes at discharge. Data were collected from January 1, 2000, through September 30, 2016. Main Outcomes and Measures The prevalence of PE at ED and hospital discharge, identified using codes from the International Classification of Diseases, was considered the primary outcome. Two sensitivity analyses considering prevalence of PE at 90 days of follow-up and prevalence of venous thromboembolism were performed. Results A total of 1 671 944 unselected adults who presented to the ED for syncope were included. The prevalence of PE, according to administrative data, ranged from 0.06% (95% CI, 0.05%-0.06%) to 0.55% (95% CI, 0.50%-0.61%) for all patients and from 0.15% (95% CI, 0.14%-0.16%) to 2.10% (95% CI, 1.84%-2.39%) for hospitalized patients. The prevalence of PE at 90 days of follow-up ranged from 0.14% (95% CI, 0.13%-0.14%) to 0.83% (95% CI, 0.80%-0.86%) for all patients and from 0.35% (95% CI, 0.34%-0.37%) to 2.63% (95% CI, 2.34%-2.95%) for hospitalized patients. Finally, the prevalence of venous thromboembolism at 90 days ranged from 0.30% (95% CI, 0.29%-0.31%) to 1.37% (95% CI, 1.33%-1.41%) for all patients and from 0.75% (95% CI, 0.73%-0.78%) to 3.86% (95% CI, 3.51%-4.24%) for hospitalized patients. Conclusions and Relevance Pulmonary embolism was rarely identified in patients with syncope. Although PE should be considered in every patient, not all patients should undergo evaluation for PE.
Interpretable Charge Predictions for Criminal Cases: Learning to Generate Court Views from Fact Descriptions

In this paper, we propose to study the problem of court view generation from the fact description in a criminal case. The task aims to improve the interpretability of charge prediction systems and help automatic legal document generation. We formulate this task as a text-to-text natural language generation (NLG) problem. Sequence-to-sequence model has achieved cutting-edge performances in many NLG tasks. However, due to the non-distinctions of fact descriptions, it is hard for Seq2Seq model to generate charge-discriminative court views. In this work, we explore charge labels to tackle this issue. We propose a label-conditioned Seq2Seq model with attention for this problem, to decode court views conditioned on encoded charge labels. Experimental results show the effectiveness of our method.
Explicit fuzzy force control of industrial manipulators with position servo drives

In this paper, a fuzzy force control algorithm is suggested for commercialized industrial robots equipped with the position servo drives, where control rules of the proposed fuzzy controller are changed according to the magnitude of environmental stiffness in such a way that good force response is maintained regardless of changes of environmental stiffness. Specifically, some fuzzy control rules are designed for several representative environmental stiffness values, and then a control action for a given arbitrary environmental stiffness value is decided by a fuzzy interpolation method. To show the validity of the proposed fuzzy controller, several experimental results are illustrated, where a 5-axis articulated robot manipulator equipped with the wrist force/torque sensor system and our prototype dual robot controller are employed. <<ETX>>
2‐anilino‐4‐amino‐5‐aroylthiazole‐type compound AS7128 inhibits lung cancer growth through decreased iASPP and p53 interaction

Lung cancer is the leading cause of cancer‐related death worldwide. Thus, developing novel therapeutic agents has become critical for lung cancer treatment. In this study, compound AS7128 was selected from a 2‐million entry chemical library screening and identified as a candidate drug against non‐small cell lung cancer in vitro and in vivo. Further investigation indicated that AS7128 could induce cell apoptosis and cell cycle arrest, especially in the mitosis stage. In addition, we also found that iASPP, an oncogenic protein that functionally inhibits p53, might be associated with AS7128 through mass identification. Further exploration indicated that AS7128 treatment could restore the transactivation ability of p53 and, thus, increase the expressions of its downstream target genes, which are related to cell cycle arrest and apoptosis. This occurs through disruption of the interactions between p53 and iASPP in cells. Taken together, AS7128 could bind to iASPP, disrupt the interaction between iASPP and p53, and result in cell cycle arrest and apoptosis. These findings may provide new insight for using iASPP as a therapeutic target for non‐small cell lung cancer treatment.
An Appraisal Profile of Nostalgia

The authors aimed to (a) identify the cognitive appraisals underlying nostalgia and (b) compare nostalgia with other emotions in terms of its appraisal profile. In Study 1, participants (N = 1,125) generated narratives. Next, they reported the level of nostalgia and 31 other emotions that these narratives elicited. Subsequently, participants evaluated the narrative events on several cognitive appraisals. Events that elicited nostalgia were pleasant, involved an irretrievable loss, felt psychologically distant, and were unique—an appraisal profile that differed from all other emotions. In Study 2 (N = 1,261), the authors experimentally varied these appraisals in a vignette paradigm and measured anticipated nostalgia and 10 other emotions. Participants anticipated most nostalgia when events were pleasant, involved irretrievable loss, were distant, and were unique—a profile shared only with longing. In Study 3 (N = 994), the authors used a guided autobiographical recall procedure in which they manipulated appraisals and measured the resultant emotions. Corroborating Studies 1–2, nostalgia was most intense for events that were pleasant, irretrievably lost, temporally distant, and unique. This appraisal profile was not shared by other emotions. The findings delineate the distinguishing cognitive appraisal profile of nostalgia. Nostalgia occupies a special place in the pantheon of emotions.
Detecting closely spaced and occluded pedestrians using specialized deep models for counting

Pedestrian detection is an important task in surveillance applications and becomes particularly challenging when pedestrians are close together or occluding one another. This paper presents a novel approach to detect pedestrians in such challenging scenarios. A deep convolutional neural network trained for counting is specialized to count one pedestrian. The feature extractor learned thereby is exploited to detect one pedestrian at a time iteratively. For the base counting model and the specialization, extensive annotation efforts are not required since only a single number at the image level is used. Use of our method on pedestrian datasets with occlusion showed an improvement in the average miss rate values as compared to other methods for handling occlusion.
Sanitary quality, occurrence and identification of Staphylococcus sp. in food services

Sanitary conditions are essential for the production of meals and control of the presence of pathogensis important to guarantee the health of customers. The aim of this study was to evaluate the sanitary quality of food services by checking the presence of thermotolerant coliforms, Staphylococcus sp. and evaluate the toxigenic potential from the latter. The analysis was performed on water, surfaces, equipment, ready-to-eat foods, hands and nasal cavity of handlers in seven food services. The water used in food services proved to be suitable for the production of meals. Most food, equipment and surfaces showed poor sanitary conditions due to the presence of thermotolerant coliforms (60.6%). Twenty-six Staphylococcus species were identified from the 121 Staphylococcus isolates tested. Staphylococci coagulase-negative species were predominant in the foods, equipment and surfaces. In food handlers and foods, the predominant species was Staphylococcus epidermidis. Twelve different genotypes were found after PCR for the classical enterotoxin genes. The seb gene (19.8%) was the most prevalent among all Staphylococcus sp. Both coagulase-positive and coagulase-negative Staphylococci showed some of the genes of the enterotoxins tested. We conclude that there are hygienic and sanitary deficiencies in the food services analyzed. Although coagulase-positive Staphylococci have not been present in foods there is a wide dispersion of enterotoxigenic coagulase-negative Staphylococci in the environment and in the foods analyzed, indicating a risk to consumer health.
Effects of social stressors on cardiovascular reactivity in black and white women

Background: Behavioral scientists have theorized that perceived racism in social interactions may account for some of the observed disparities in coronary heart disease between Black and White Americans.Purpose: The objective was to examine whether racial stress influences cardiovascular reactivity, a risk factor for cardiovascular disease.Methods: We measured cardiovascular responses in Black and White women (n = 80) as they talked about 3 hypothetical scenarios: (a) being accused of shoplifting (racial stressor), (b) experiencing airport delays (nonracial stressor), and (c) giving a campus tour (control). Results: Relative to White women, Black women had significantly greater mean diastolic blood pressure reactivity (3.81 vs. 0.25 mmHg; p < .05) in response to the racial stressor than in response to the nonracial stressor. Black women exhibited significantly lower heart rate during recovery following the racial stressor than during recovery following the nonracial stressor (−0.37 beats/min vs. 0.86 beats/min; p < .001). Among Black women, those who explicitly made race attributions during the racial stressor had greater systolic but not diastolic blood pressure reactivity than those who did not make racial attributions (8.32 mmHg vs. 2.17 mmHg; p < .05). Conclusions: These findings suggest that perceived racism in social interactions may contribute to increased physiological stress for Black women.
Response by Lattanzi and Silvestrini to Letter Regarding Article, "Neutrophil-to-Lymphocyte Ratio Predicts the Outcome of Acute Intracerebral Hemorrhage".

We appreciate the letter from Du et al1 on our recent publication regarding the predictive value of the neutrophil-to-lymphocyte ratio (NLR) in acute intracerebral hemorrhage.2 We agree that medical conditions such as premorbid atherosclerotic disease, underlying inflammation, and intercurrent infections could have influenced the NLR and partly accounted for its association with outcome. The prevalence of all the major cardiovascular risk factors such as smoking, dyslipidemia, diabetes mellitus, or hypertension, however, did not significantly differ among the outcome groups, and correlations did not emerge between age and NLR. Additionally, the leukocyte counts resulted within the normal ranges in most of the patients either with good …
Regulation of Polyhydroxybutyrate Accumulation in Sinorhizobium meliloti by the Trans-Encoded Small RNA MmgR

ABSTRACT Riboregulation has a major role in the fine-tuning of multiple bacterial processes. Among the RNA players, trans-encoded untranslated small RNAs (sRNAs) regulate complex metabolic networks by tuning expression from multiple target genes in response to numerous signals. In Sinorhizobium meliloti, over 400 sRNAs are expressed under different stimuli. The sRNA MmgR (standing for Makes more granules Regulator) has been of particular interest to us since its sequence and structure are highly conserved among the alphaproteobacteria and its expression is regulated by the amount and quality of the bacterium's available nitrogen source. In this work, we explored the biological role of MmgR in S. meliloti 2011 by characterizing the effect of a deletion of the internal conserved core of mmgR (mmgRΔ33–51). This mutation resulted in larger amounts of polyhydroxybutyrate (PHB) distributed into more intracellular granules than are found in the wild-type strain. This phenotype was expressed upon cessation of balanced growth owing to nitrogen depletion in the presence of surplus carbon (i.e., at a carbon/nitrogen molar ratio greater than 10). The normal PHB accumulation was complemented with a wild-type mmgR copy but not with unrelated sRNA genes. Furthermore, the expression of mmgR limited PHB accumulation in the wild type, regardless of the magnitude of the C surplus. Quantitative proteomic profiling and quantitative reverse transcription-PCR (qRT-PCR) revealed that the absence of MmgR results in a posttranscriptional overexpression of both PHB phasin proteins (PhaP1 and PhaP2). Together, our results indicate that the widely conserved alphaproteobacterial MmgR sRNA fine-tunes the regulation of PHB storage in S. meliloti. IMPORTANCE High-throughput RNA sequencing has recently uncovered an overwhelming number of trans-encoded small RNAs (sRNAs) in diverse prokaryotes. In the nitrogen-fixing alphaproteobacterial symbiont of alfalfa root nodules Sinorhizobium meliloti, only four out of hundreds of identified sRNA genes have been functionally characterized. Thus, uncovering the biological role of sRNAs currently represents a major issue and one that is particularly challenging because of the usually subtle quantitative regulation contributed by most characterized sRNAs. Here, we have characterized the function of the broadly conserved alphaproteobacterial sRNA gene mmgR in S. meliloti. Our results strongly suggest that mmgR encodes a negative regulator of the accumulation of polyhydroxybutyrate, the major carbon and reducing power storage polymer in S. meliloti cells growing under conditions of C/N overbalance.