Miracle-dz/UniFAR-FTUs huggingface dataset:
Sumoylated NHR-25/NR5A Regulates Cell Fate during C. elegans Vulval Development

Individual metazoan transcription factors (TFs) regulate distinct sets of genes depending on cell type and developmental or physiological context. The precise mechanisms by which regulatory information from ligands, genomic sequence elements, co-factors, and post-translational modifications are integrated by TFs remain challenging questions. Here, we examine how a single regulatory input, sumoylation, differentially modulates the activity of a conserved C. elegans nuclear hormone receptor, NHR-25, in different cell types. Through a combination of yeast two-hybrid analysis and in vitro biochemistry we identified the single C. elegans SUMO (SMO-1) as an NHR-25 interacting protein, and showed that NHR-25 is sumoylated on at least four lysines. Some of the sumoylation acceptor sites are in common with those of the NHR-25 mammalian orthologs SF-1 and LRH-1, demonstrating that sumoylation has been strongly conserved within the NR5A family. We showed that NHR-25 bound canonical SF-1 binding sequences to regulate transcription, and that NHR-25 activity was enhanced in vivo upon loss of sumoylation. Knockdown of smo-1 mimicked NHR-25 overexpression with respect to maintenance of the 3° cell fate in vulval precursor cells (VPCs) during development. Importantly, however, overexpression of unsumoylatable alleles of NHR-25 revealed that NHR-25 sumoylation is critical for maintaining 3° cell fate. Moreover, SUMO also conferred formation of a developmental time-dependent NHR-25 concentration gradient across the VPCs. That is, accumulation of GFP-tagged NHR-25 was uniform across VPCs at the beginning of development, but as cells began dividing, a smo-1-dependent NHR-25 gradient formed with highest levels in 1° fated VPCs, intermediate levels in 2° fated VPCs, and low levels in 3° fated VPCs. We conclude that sumoylation operates at multiple levels to affect NHR-25 activity in a highly coordinated spatial and temporal manner.
Successful Broadband Projects in the Public Sector - a Service Innovation Perspective

The development of national broadband infrastructures has been recognized as an important part of the vision of the information society, as well as of the modernization of the public sector. This paper investigates the relationship between broadband dissemination and service innovation in the public sector. We ask, what characterizes successful broadband based service innovation projects in the public sector? The research approach is a quantitative survey in a large public broadband diffusion initiative in Norway. The paper offers three conclusions. First, broadband based service innovation is seen as a two-step process; first a technologically oriented project, followed by an organizational implementation. The focus of the project manager should be on the second of the phases, not the first. Second, the engagement of a professional external project manager does not support service innovation. The reason is that the external project manager lacks the necessary local knowledge and alliances with central stakeholders. Third, traditional project management is not well suited to understand and manage service innovation
Recommending refactorings based on team co-maintenance patterns

Refactoring aims at restructuring existing source code when undisciplined development activities have deteriorated its comprehensibility and maintainability. There exist various approaches for suggesting refactoring opportunities, based on different sources of information, e.g., structural, semantic, and historical. In this paper we claim that an additional source of information for identifying refactoring opportunities, sometimes orthogonal to the ones mentioned above, is team development activity. When the activity of a team working on common modules is not aligned with the current design structure of a system, it would be possible to recommend appropriate refactoring operations---e.g., extract class/method/package---to adjust the design according to the teams' activity patterns. Results of a preliminary study---conducted in the context of extract class refactoring---show the feasibility of the approach, and also suggest that this new refactoring dimension can be complemented with others to build better refactoring recommendation tools.
Altered task‐related modulation of long‐range connectivity in children with autism

Functional connectivity differences between children with autism spectrum disorder (ASD) and typically developing children have been described in multiple datasets. However, few studies examine the task‐related changes in connectivity in disorder‐relevant behavioral paradigms. In this paper, we examined the task‐related changes in functional connectivity using EEG and a movement‐based paradigm that has behavioral relevance to ASD. Resting‐state studies motivated our hypothesis that children with ASD would show a decreased magnitude of functional connectivity during the performance of a motor‐control task. Contrary to our initial hypothesis, however, we observed that task‐related modulation of functional connectivity in children with ASD was in the direction opposite to that of TDs. The task‐related connectivity changes were correlated with clinical symptom scores. Our results suggest that children with ASD may have differences in cortical segregation/integration during the performance of a task, and that part of the differences in connectivity modulation may serve as a compensatory mechanism. Autism Res 2018, 11: 245–257. © 2017 International Society for Autism Research, Wiley Periodicals, Inc.
Exploring patient‐reported outcomes following percutaneous coronary intervention: A qualitative study

Percutaneous coronary intervention (PCI) is a common cardiac procedure used to treat obstructive coronary artery disease. Patient‐centred care is a priority in cardiovascular health having been shown to increase patient satisfaction, engagement with rehabilitation activities and reduce anxiety. Evidence indicates that patient‐centred care is best achieved by routine collection of patient‐reported outcomes (PROs). However, existing patient‐reported outcome measures (PROMs) have limited the patient involvement in their development.
Nutrient uptake by the hindlimb of growing pigs treated with porcine somatotropin and insulin.

The shift in nutrient partitioning induced by porcine somatotropin (pST) is accompanied by a decrease in insulin sensitivity for whole-body glucose uptake. The relative contribution of metabolic changes in the hindlimb was investigated in eight pigs (55 kg) that had received recombinant pST (120 micrograms/kg) or excipient (control) for 7 d. Uptake of metabolites by the hindlimb was measured under basal conditions and during hyperinsulinemic-euglycemic clamps at low [14 ng/(kg.min)] and high [360 ng/(kg.min)] insulin infusion rates. Dextrose infusion rate required to maintain euglycemia was used as an index of whole-body glucose uptake in response to exogenous insulin. Effects of pST on hindlimb and whole-body glucose uptake were evident only at physiological levels of insulin (basal and low insulin infusion rate). During the low rate of insulin infusion, dextrose infusion rate was 79% lower for pST-treated pigs and glucose uptake by the hindlimb was 59% lower compared with control pigs. The decrease in glucose uptake by the hindlimb was entirely accounted for by the estimated reduction in glucose utilization by adipose tissue of the hindlimb. Glucose:oxygen quotients were reduced during basal (57%) and low insulin infusion (63%) with pST treatment, indicating a change in the pattern of substrate utilization. This is consistent with the concept that pST directs nutrients away from adipose and towards muscle growth by altering the response of tissues to homeostatic signals such as insulin.
Iron absorption from fish sauce and soy sauce fortified with sodium iron EDTA.

BACKGROUND Fish sauce and soy sauce have been suggested as food vehicles for iron fortification in Asia. NaFeEDTA is a potentially useful fortificant because it can be added to these condiments without causing precipitation during storage. OBJECTIVES The objectives were to evaluate iron absorption from NaFeEDTA-fortified fish sauce and soy sauce against a reference fortificant (FeSO(4)), to compare iron absorption from NaFeEDTA-fortified fish sauce and soy sauce, and to evaluate the influence of fish sauce and soy sauce per se on iron absorption. DESIGN Five separate iron-absorption studies were made in adult women (10 women per study). Iron absorption was measured on the basis of erythrocyte incorporation of (57)Fe or (58)Fe 14 d after the intake of labeled meals of rice or rice and vegetables. Fish sauce or soy sauce (10 g) fortified with 5 mg Fe as NaFeEDTA or FeSO(4) was fed with selected meals. The results are presented as geometric means. RESULTS Iron absorption from NaFeEDTA- and FeSO(4)-fortified fish sauce (3.3% and 3.1%, respectively) and soy sauce (6.1% and 5.6%, respectively) was not significantly different. No significant difference was observed when NaFeEDTA-fortified fish sauce and soy sauce were compared directly (6.7% and 7.9%, respectively). Soy sauce inhibited iron absorption from rice-based meals (8.5% without and 6.0% with soy sauce; P < 0.02), whereas fish sauce did not affect iron absorption significantly. CONCLUSION The relatively high iron absorption from NaFeEDTA-fortified fish sauce and soy sauce and the acceptable organoleptic properties of NaFeEDTA indicate the potential usefulness of this iron fortificant in fish sauce and soy sauce fortification programs.
Bioengineered Noncoding RNAs Selectively Change Cellular miRNome Profiles for Cancer Therapy

Noncoding RNAs (ncRNAs) produced in live cells may better reflect intracellular ncRNAs for research and therapy. Attempts were made to produce biologic ncRNAs, but at low yield or success rate. Here we first report a new ncRNA bioengineering technology using more stable ncRNA carrier (nCAR) containing a pre-miR-34a derivative identified by rational design and experimental validation. This approach offered a remarkable higher level expression (40%–80% of total RNAs) of recombinant ncRNAs in bacteria and gave an 80% success rate (33 of 42 ncRNAs). New FPLC and spin-column based methods were also developed for large- and small-scale purification of milligrams and micrograms of recombinant ncRNAs from half liter and milliliters of bacterial culture, respectively. We then used two bioengineered nCAR/miRNAs to demonstrate the selective release of target miRNAs into human cells, which were revealed to be Dicer dependent (miR-34a-5p) or independent (miR-124a-3p), and subsequent changes of miRNome and transcriptome profiles. miRNA enrichment analyses of altered transcriptome confirmed the specificity of nCAR/miRNAs in target gene regulation. Furthermore, nCAR assembled miR-34a-5p and miR-124-3p were active in suppressing human lung carcinoma cell proliferation through modulation of target gene expression (e.g., cMET and CDK6 for miR-34a-5p; STAT3 and ABCC4 for miR-124-3p). In addition, bioengineered miRNA molecules were effective in controlling metastatic lung xenograft progression, as demonstrated by live animal and ex vivo lung tissue bioluminescent imaging as well as histopathological examination. This novel ncRNA bioengineering platform can be easily adapted to produce various ncRNA molecules, and biologic ncRNAs hold the promise as new cancer therapeutics.
On being ` undigital ' with digital cameras : Extending Dynamic Range by CombiningDi erently Exposed

Most everyday scenes have a far greater dynamic range than can be recorded on a photographic lm or electronic imaging apparatus (whether it be a digital still camera, video, etc.). However, a set of pictures, that are identical except for their exposure , collectively show us much more dynamic range than any single picture. The dark pictures show us highlight details of the scene that would be washed out in a \properly exposed" picture, while the light pictures show us some shadow detail that would also not appear in a \properly exposed" picture. We propose a means of combining diierently exposed pictures to obtain a single picture of extended dynamic range, and improved color delity. Given a set of digital pictures, we may produce a single picture which is, for all practical purposes, `undig-ital', in the sense that it is a oating point image, with the kind of dynamic range we are accustomed to seeing in typical oating point representations, as opposed to the integer images from which it was generated. The method is completely automatic; it requires no human intervention, and it requires no knowledge of the response function of the imaging device. It works reliably with images from a digital camera of unknown response, or from a scanner with unknown response, scanning an unknown lm type.
Chemogenetic locus coeruleus activation restores reversal learning in a rat model of Alzheimer’s disease

See Grinberg and Heinsen (doi:10.1093/brain/awx261) for a scientific commentary on this article. Clinical evidence suggests that aberrant tau accumulation in the locus coeruleus and noradrenergic dysfunction may be a critical early step in Alzheimer’s disease progression. Yet, an accurate preclinical model of these phenotypes that includes early pretangle tau accrual in the locus coeruleus, loss of locus coeruleus innervation and deficits locus coeruleus/norepinephrine modulated behaviours, does not exist, hampering the identification of underlying mechanisms and the development of locus coeruleus-based therapies. Here, a transgenic rat (TgF344-AD) expressing disease-causing mutant amyloid precursor protein (APPsw) and presenilin-1 (PS1ΔE9) was characterized for histological and behavioural signs of locus coeruleus dysfunction reminiscent of mild cognitive impairment/early Alzheimer’s disease. In TgF344-AD rats, hyperphosphorylated tau was detected in the locus coeruleus prior to accrual in the medial entorhinal cortex or hippocampus, and tau pathology in the locus coeruleus was negatively correlated with noradrenergic innervation in the medial entorhinal cortex. Likewise, TgF344-AD rats displayed progressive loss of hippocampal norepinephrine levels and locus coeruleus fibres in the medial entorhinal cortex and dentate gyrus, with no frank noradrenergic cell body loss. Cultured mouse locus coeruleus neurons expressing hyperphosphorylation-prone mutant human tau had shorter neurites than control neurons, but similar cell viability, suggesting a causal link between pretangle tau accrual and altered locus coeruleus fibre morphology. TgF344-AD rats had impaired reversal learning in the Morris water maze compared to their wild-type littermates, which was rescued by chemogenetic locus coeruleus activation via designer receptors exclusively activated by designer drugs (DREADDs). Our results indicate that TgF344-AD rats uniquely meet several key criteria for a suitable model of locus coeruleus pathology and dysfunction early in Alzheimer’s disease progression, and suggest that a substantial window of opportunity for locus coeruleus/ norepinephrine-based therapeutics exists.
A dominant‐interfering camta3 mutation compromises primary transcriptional outputs mediated by both cell surface and intracellular immune receptors in Arabidopsis thaliana

Summary Pattern recognition receptors (PRRs) and nucleotide‐binding domain and leucine‐rich repeat (LRR)‐containing proteins (NLRs) initiate pattern‐triggered immunity (PTI) and effector‐triggered immunity (ETI), respectively, each associated with the activation of an overlapping set of defence genes. The regulatory mechanism behind this convergence of PTI‐ and ETI‐mediated defence gene induction remains elusive. We generated transgenic Arabidopsis plants that enable conditional NLR activation without pathogen infection to dissect NLR‐ and PRR‐mediated transcriptional signals. A comparative analysis of over 40 transcriptome datasets linked calmodulin‐binding transcription activators (CAMTAs) to the activation of overlapping defence genes in PTI and ETI. We used a dominant camta3 mutant (camta3‐D) to assess CAMTA functions in the corresponding transcriptional regulation. Transcriptional regulation by NLRs, although highly similar to PTI responses, can be established independently of pathogen‐associated molecular pattern (PAMP) perception, defence phytohormones and host cell death. Conditional expression of the N‐terminal coiled‐coil domain of the barley MLA (Mildew resistance locus A) NLR is sufficient to trigger similar transcriptional reprogramming as full‐length NLRs. CAMTA‐binding motifs are overrepresented in the 5′ regulatory regions of the identified primary immune response genes, consistent with their altered expression and disease resistance responses in camta3‐D plants. We propose that CAMTA‐mediated transcriptional regulation defines an early convergence point in NLR‐ and PRR‐mediated signalling.
The effect of internal control deficiencies on the usefulness of earnings in executive compensation

Since SOX 404 disclosures are informative about earnings, and due to the widespread practice of using earnings-based measures in executive compensation, this study examines whether reports of internal control material weaknesses (ICMW) under SOX404 influence firms’ reliance on earnings in tying executive pay to performance. Using 391 (366) firm-year observations with reported ICMW and 3,648 (3,138) firm-year observations for CEOs (CFOs) reporting NOMW under SOX 404, we find a decreased strength in the association between earnings and executives’ (CEO and CFO) compensation when the firm reports an ICMW, and as the number of reported ICMW increases. In addition, we find this decreased weight on earnings for the more severe Company-Level than Account- Specific material weaknesses. Our study suggests that the ICMW report under SOX 404 provides incremental information for executive compensation beyond that contained in reported earnings.
Biobehavioral influences on energy intake and adult weight gain.

U.S. adults are now gaining more weight and becoming obese at an earlier age than in previous years. The specific causes of adult weight gain are unknown, but may be attributed to a combination of factors leading to positive energy balance. U.S. food supply data indicate that Americans have had a gradual increase in energy intake since 1970, and that per capita energy intake was 1.42 MJ/d (340 kcal/d) higher in 1994 than that in 1984. In contrast, self-reported physical activity remained constant between 1990 and 1998. Taken together, these data indicate that the increasing trend in U.S. adult weight gain is primarily attributable to overconsumption of energy. Epidemiological and experimental studies in animals and humans provide strong evidence that biobehavioral factors such as dietary variety, liquid (vs. solid) energy, portion size, palatability (taste), snacking patterns, restaurant and other away-from-home food, and dietary restraint and disinhibition influence hunger, satiety and/or voluntary energy intake. When these eating behaviors are consistently experienced either separately or in combination over the long term, they are likely to facilitate overeating. We provide a brief overview of the evidence to date for the role of these biobehavioral factors in contributing to excess energy intake and increases in body weight over time.
Range-wide parallel climate-associated genomic clines in Atlantic salmon

Clinal variation across replicated environmental gradients can reveal evidence of local adaptation, providing insight into the demographic and evolutionary processes that shape intraspecific diversity. Using 1773 genome-wide single nucleotide polymorphisms we evaluated latitudinal variation in allele frequency for 134 populations of North American and European Atlantic salmon (Salmo salar). We detected 84 (4.74%) and 195 (11%) loci showing clinal patterns in North America and Europe, respectively, with 12 clinal loci in common between continents. Clinal single nucleotide polymorphisms were evenly distributed across the salmon genome and logistic regression revealed significant associations with latitude and seasonal temperatures, particularly average spring temperature in both continents. Loci displaying parallel clines were associated with several metabolic and immune functions, suggesting a potential basis for climate-associated adaptive differentiation. These climate-based clines collectively suggest evidence of large-scale environmental associated differences on either side of the North Atlantic. Our results support patterns of parallel evolution on both sides of the North Atlantic, with evidence of both similar and divergent underlying genetic architecture. The identification of climate-associated genomic clines illuminates the role of selection and demographic processes on intraspecific diversity in this species and provides a context in which to evaluate the impacts of climate change.
The study on the measuring methods of rheological properties of HPC fresh concrete

The importance and the urgency to study comprehensively the rheological properties of HPC fresh concrete are discussed in the paper.Based on the investigatios to the apparatus used up to date,the author puts forward a new design of concrete rheologic apparatus,which is an apparatus with compact design,better integrity and smaller dimensions.The apparatus can be used to study rheological and time dependent properties of fresh concrete with maximum aggregates 20mm in laboratories,as well as the quality control on construction sites.
Compressive Hyperspectral Image Reconstruction with a Deep Generative Prior

Hyperspectal images are 3D data cubes that contain spectral information of a scene in addition to its spectral content. Compressive hyperspectral imaging is a technique for taking a small number of linear measurements of this datacube and using techniques from compressed sensing to reconstruct the full data cube. In this work, based on the work of Choi et. al. 2017, we use a convolutional autoencoder to learn a deep generative model that can serve as a prior for the CASSI compressive hyperspectral imaging technique. We evaluate our technique on simulated data and show that it achieves essentially state-of-the-art performance on this task.
Morse Theory

Topology on L a, b : Fix a broken λ λ , . , λ . Its neighborhood consists of its deformations and smoothings. Key: every smooth trajectory has R symmetry. Can reduce to a level set in a Morse chart to see all its small deformations! Base of open sets: W λ, U , U where U consists of a neighborhood of the exit point of λ in a Morse chart of each broken point; similarly U consists of neighborhoods of entry points; W λ, U , U consists of broken trajectories whose broken points are subset of that of λ, and whose exit and entry points 3. Morse complex
Estimation of heart rate from photoplethysmography during physical exercise using Wiener filtering and the phase vocoder

A system for estimation of the heart rate (HR) from the photoplethysmographic (PPG) signal during intensive physical exercises is presented. The Wiener filter is used to attenuate the noise introduced by the motion artifacts in the PPG signals. The frequency with the highest magnitude estimated using Fourier transformation is selected from the resultant de-noised signal. The phase vocoder technique is exploited to refine the frequency estimate, from which the HR in beats per minute (BPM) is finally calculated. On a publically available database of twenty three PPG recordings, the proposed technique obtains an error of 2.28 BPM. A relative error rate reduction of 18% is obtained when comparing with the state-of-the art PPG-based HR estimation methods. The proposed system is shown to be robust to strong motion artifact, produces high accuracy results and has very few free parameters, in contrast to other available approaches. The algorithm has low computational cost and can be used for fitness tracking and health monitoring in wearable devices.