Miracle-dz/UniFAR-FTUs huggingface dataset:
A Mighty Small Heart: The Cardiac Proteome of Adult Drosophila melanogaster

Drosophila melanogaster is emerging as a powerful model system for the study of cardiac disease. Establishing peptide and protein maps of the Drosophila heart is central to implementation of protein network studies that will allow us to assess the hallmarks of Drosophila heart pathogenesis and gauge the degree of conservation with human disease mechanisms on a systems level. Using a gel-LC-MS/MS approach, we identified 1228 protein clusters from 145 dissected adult fly hearts. Contractile, cytostructural and mitochondrial proteins were most abundant consistent with electron micrographs of the Drosophila cardiac tube. Functional/Ontological enrichment analysis further showed that proteins involved in glycolysis, Ca2+-binding, redox, and G-protein signaling, among other processes, are also over-represented. Comparison with a mouse heart proteome revealed conservation at the level of molecular function, biological processes and cellular components. The subsisting peptidome encompassed 5169 distinct heart-associated peptides, of which 1293 (25%) had not been identified in a recent Drosophila peptide compendium. PeptideClassifier analysis was further used to map peptides to specific gene-models. 1872 peptides provide valuable information about protein isoform groups whereas a further 3112 uniquely identify specific protein isoforms and may be used as a heart-associated peptide resource for quantitative proteomic approaches based on multiple-reaction monitoring. In summary, identification of excitation-contraction protein landmarks, orthologues of proteins associated with cardiovascular defects, and conservation of protein ontologies, provides testimony to the heart-like character of the Drosophila cardiac tube and to the utility of proteomics as a complement to the power of genetics in this growing model of human heart disease.
Evaluating principal surrogate markers in vaccine trials in the presence of multiphase sampling

This article focuses on the evaluation of vaccine‐induced immune responses as principal surrogate markers for predicting a given vaccine's effect on the clinical endpoint of interest. To address the problem of missing potential outcomes under the principal surrogate framework, we can utilize baseline predictors of the immune biomarker(s) or vaccinate uninfected placebo recipients at the end of the trial and measure their immune biomarkers. Examples of good baseline predictors are baseline immune responses when subjects enrolled in the trial have been previously exposed to the same antigen, as in our motivating application of the Zostavax Efficacy and Safety Trial (ZEST). However, laboratory assays of these baseline predictors are expensive and therefore their subsampling among participants is commonly performed. In this article, we develop a methodology for estimating principal surrogate values in the presence of baseline predictor subsampling. Under a multiphase sampling framework, we propose a semiparametric pseudo‐score estimator based on conditional likelihood and also develop several alternative semiparametric pseudo‐score or estimated likelihood estimators. We derive corresponding asymptotic theories and analytic variance formulas for these estimators. Through extensive numeric studies, we demonstrate good finite sample performance of these estimators and the efficiency advantage of the proposed pseudo‐score estimator in various sampling schemes. We illustrate the application of our proposed estimators using data from an immune biomarker study nested within the ZEST trial.
The effect of hypopituitarism on fatigue after subarachnoid hemorrhage

Aneurysmal subarachnoid hemorrhage (SAH) survivors often complain of fatigue, which is disabling. Fatigue is also a common symptom of pituitary dysfunction (PD), in particular in patients with growth hormone deficiency (GHD). A possible association between fatigue after SAH and long‐term pituitary deficiency in SAH survivors has not yet been established.
The COMPLETE Survey of Star-Forming Regions: Phase I Data

We present an overview of data available for the Ophiuchus and Perseus molecular clouds from Phase I of the COMPLETE Survey of Star-Forming Regions. This survey provides a range of data complementary to the Spitzer Legacy Program "From Molecular Cores to Planet Forming Disks. " Phase I includes the following: extinction maps derived from the Two Micron All Sky Survey (2MASS) near-infrared data using the NICER algorithm; extinction and temperature maps derived from IRAS 60 and 100 μm emission; H I maps of atomic gas; 12CO and 13CO maps of molecular gas; and submillimeter continuum images of emission from dust in dense cores. Not unexpectedly, the morphology of the regions appears quite different depending on the column density tracer that is used, with IRAS tracing mainly warmer dust and CO being biased by chemical, excitation, and optical depth effects. Histograms of column density distribution are presented, showing that extinction as derived from 2MASS NICER gives the closest match to a lognormal distribution, as is predicted by numerical simulations. All the data presented in this paper, and links to more detailed publications on their implications, are publicly available at the COMPLETE Web site.
Bandwidth-Constrained Multi-Objective Segmented Brute-Force Algorithm for Efficient Mapping of Embedded Applications on NoC Architecture

Network-on-chip (NoC) is an emerging alternative to address the communication problem in embedded system-on-chip designs. One of the key and major issues is the optimized mapping of the embedded applications on the underlined NoC platform. In this paper, we propose the bandwidth-constrained multi-objective segmented brute-force mapping (SBMAP) algorithm, which minimizes the communication energy consumption and reduces the computational complexity of the NoC designs. The algorithm generates efficient mapping of the embedded applications on the processing elements of the NoC system by segregating the application into multiple segments. It utilizes the property of modular systematic search, which produces high-performance results with optimized simulation time. We compared the SBMAP algorithm with the state-of-the-art mapping techniques, such as branch and bound (BB), near-optimal mapping (NMAP), and random mapping algorithms for mapping real-world application workloads. The experimental results validated the efficiency of the proposed algorithm against its competitors for most of the performance parameters of the NoC designs. The improvement in energy consumption of the SBMAP algorithm is up to 53% for 2-D mesh and 62% for torus topology as compared with the NMAP, BB, and random algorithms for video object plane decoder, picture in picture, Wi-Fi receiver, and multimedia system real-time application benchmarks.
Not all reading is alike: task modulation of magnetic evoked response to visual word

Background. Previous studies have shown that brain response to a written word depends on the task: whether the word is a target in a version of lexical decision task or should be read silently. Although this effect has been interpreted as an evidence for an interaction between word recognition processes and task demands, it also may be caused by greater attention allocation to the target word. objective. We aimed to examine the task effect on brain response evoked by nontarget written words. Design. Using MEG and magnetic source imaging, we compared spatial-temporal pattern of brain response elicited by a noun cue when it was read silently either without additional task (SR) or with a requirement to produce an associated verb (vG). Results. The task demands penetrated into early (200-300 ms) and late (500-800 ms) stages of a word processing by enhancing brain response under vG versus SR condition. The cortical sources of the early response were localized to bilateral inferior occipitotemporal and anterior temporal cortex suggesting that more demanding vG task required elaborated lexical-semantic analysis. The late effect was observed in the associative auditory areas in middle and superior temporal gyri and in motor representation of articulators. Our results suggest that a remote goal plays a pivotal role in enhanced recruitment of cortical structures underlying orthographic, semantic and sensorimotor dimensions of written word perception from the early processing stages. Surprisingly, we found that to fulfil a more challenging goal the brain progressively engaged resources of the right hemisphere throughout all stages of silent reading.
Survival and Long-Term Functional Outcomes for Children With Cardiac Arrest Treated With Extracorporeal Cardiopulmonary Resuscitation

Objectives: To identify patient- and disease-related factors related to survival and favorable outcomes for children who underwent extracorporeal cardiopulmonary resuscitation after a refractory cardiac arrest. Design: Retrospective observational study with prospective assessment of long-term functional outcome. Patients: Fifty-six consecutive children undergoing extracorporeal cardiopulmonary resuscitation at our institution from 2007 to 2015. Median age at arrest was 3.5 months (interquartile range, 1–53). Setting: Tertiary pediatric university hospital with a referral heart center. Interventions: Health-related quality of life and family functioning assessment with the Pediatric Quality of Life Inventory and the McMaster Family Assessment Device. Measurements and Main Results: Fifty-eight consecutive extracorporeal cardiopulmonary resuscitation episodes were included, with 46 (79.3%) related to primary cardiac conditions. Initial cannulation site was central in 19 (32.8%) and peripheral in 39 (67.2%). Survival to decannulation was 77.6% with survival at hospital discharge and at the end of the follow-up period being 65.5% and 62.1%, respectively. Time to follow-up was 38 months (interquartile range, 19–52). Patients who survived tended to be younger (3.5 mo [1 mo to 2 yr] vs 7 mo [1.25 mo to 17 yr]; p = 0.3) with decreased extracorporeal cardiopulmonary resuscitation times (28 min [15–47 min] vs 37.5 min [28.5–55 min]; p = 0.04). Those who received therapeutic hypothermia tended to have higher hospital survival (21/28 [75%] vs 16/29 [55%]; p = 0.08). Follow-up assessments of survivors demonstrated good quality of life and family functioning (Pediatric Quality of Life Inventory, 84 [76–89.5]; McMaster Family Assessment Device, 1.62 [1.33–1.83]). Conclusions: In this series, extracorporeal cardiopulmonary resuscitation was associated with relatively high survival rates and a good health-related quality of life and family functioning. Larger series are needed to assess whether this technique should be more broadly available in the pediatric critical care community.
Proposal for Automatic Extraction of Taxonomic Relations in Domain Corpus

This paper addresses the study in the Natural Language Processing area focused on the analysis and automatic extraction of taxonomic relations in domain corpus. In addition, a methodology is proposed emphasizing the automatic extraction by patterns and methods of grouping as the formal concepts analysis. This work considers the validation of the proposal through the information provided by task #13 of SemEval 2016 and by manual validation by domain experts.
Subthalamic Nucleus Electrical Stimulation Modulates Calcium Activity of Nigral Astrocytes

Background The substantia nigra pars reticulata (SNr) is a major output nucleus of the basal ganglia, delivering inhibitory efferents to the relay nuclei of the thalamus. Pathological hyperactivity of SNr neurons is known to be responsible for some motor disorders e.g. in Parkinson's disease. One way to restore this pathological activity is to electrically stimulate one of the SNr input, the excitatory subthalamic nucleus (STN), which has emerged as an effective treatment for parkinsonian patients. The neuronal network and signal processing of the basal ganglia are well known but, paradoxically, the role of astrocytes in the regulation of SNr activity has never been studied. Principal Findings In this work, we developed a rat brain slice model to study the influence of spontaneous and induced excitability of afferent nuclei on SNr astrocytes calcium activity. Astrocytes represent the main cellular population in the SNr and display spontaneous calcium activities in basal conditions. Half of this activity is autonomous (i.e. independent of synaptic activity) while the other half is dependent on spontaneous glutamate and GABA release, probably controlled by the pace-maker activity of the pallido-nigral and subthalamo-nigral loops. Modification of the activity of the loops by STN electrical stimulation disrupted this astrocytic calcium excitability through an increase of glutamate and GABA releases. Astrocytic AMPA, mGlu and GABAA receptors were involved in this effect. Significance Astrocytes are now viewed as active components of neural networks but their role depends on the brain structure concerned. In the SNr, evoked activity prevails and autonomous calcium activity is lower than in the cortex or hippocampus. Our data therefore reflect a specific role of SNr astrocytes in sensing the STN-GPe-SNr loops activity and suggest that SNr astrocytes could potentially feedback on SNr neuronal activity. These findings have major implications given the position of SNr in the basal ganglia network.
PHYTOCHROME B and HISTONE DEACETYLASE 6 Control Light-Induced Chromatin Compaction in Arabidopsis thaliana

Natural genetic variation in Arabidopsis thaliana exists for many traits and often reflects acclimation to local environments. Studying natural variation has proven valuable in the characterization of phenotypic traits and, in particular, in identifying genetic factors controlling these traits. It has been previously shown that chromatin compaction changes during development and biotic stress. To gain more insight into the genetic control of chromatin compaction, we investigated the nuclear phenotype of 21 selected Arabidopsis accessions from different geographic origins and habitats. We show natural variation in chromatin compaction and demonstrate a positive correlation with latitude of geographic origin. The level of compaction appeared to be dependent on light intensity. A novel approach, combining Quantitative Trait Locus (QTL) mapping and microscopic examination, pointed at PHYTOCHROME-B (PHYB) and HISTONE DEACETYLASE-6 (HDA6) as positive regulators of light-controlled chromatin compaction. Indeed, mutant analyses demonstrate that both factors affect global chromatin organization. HDA6, in addition, strongly promotes the light-mediated compaction of the Nucleolar Organizing Regions (NORs). The accession Cape Verde Islands-0 (Cvi-0), which shows sequence polymorphism in the PHYB gene and in the HDA6 promotor, resembles the hda6 mutant in having reduced chromatin compaction and decreased methylation levels of DNA and histone H3K9 at the NORs. We provide evidence that chromatin organization is controlled by light intensity. We propose that chromatin plasticity is associated with acclimation of Arabidopsis to its environment. The polymorphic alleles such as PHYB and HDA6 control this process.
Zm908p11, encoded by a short open reading frame (sORF) gene, functions in pollen tube growth as a profilin ligand in maize

Double fertilization of flowering plants depends on the targeted transportation of sperm to the embryo sac by the pollen tube. Currently, little is known about the underlying molecular mechanisms that regulate pollen germination and pollen tube growth in maize (Zea mays). Here, a maize pollen-predominant gene Zm908, with several putative short open reading frames (sORFs), was isolated and characterized. The longest ORF of Zm908 encodes a small protein of 97 amino acids. This was designated as Zm908p11 and is distributed throughout the maize pollen tube. Western blot detected the small peptide in mature pollen. Quantitative reverse transcription–PCR and northern blot analysis revealed that Zm908p11 was expressed predominantly in mature pollen grains. Ectopic overexpression of full-length Zm908 and Zm908p11 in tobacco resulted in defective pollen, while transgenic tobacco plants with a site-specific mutation or a frameshift mutation of Zm908p11 showed normal pollen development. Overexpression of Zm908p11 in maize decreased pollen germination efficiency. Maize pollen cDNA library screening and protein–protein interaction assays demonstrated that Zm908p11 interacts with maize profilin 1 (ZmPRO1). A microarray analysis identified 273 up-regulated and 203 down-regulated genes in the overexpressing transgenic Zm908p11 pollen. Taken together, these results indicate that Zm908 functions as Zm908p11, and binds to profilins as a novel ligand, with a required role during pollen tube growth in maize. Accordingly, a model is proposed for the role of Zm908p11 during pollen tube growth in maize.
Who collaborates successfully?: prior experience reduces collaboration barriers in distributed interdisciplinary research

Two recent studies of over 500 interdisciplinary research projects have documented comparatively poor outcomes of more distributed projects and the failed coordination mechanisms that partly account for these problems. In this paper we report results of an analysis of dyadic data from the most recent of these studies. The question we asked is, "Does prior experience with a collaborator reduce the barriers of distance or interdisciplinarity? " Analyses of 3911 pairs of collaborators found an answer: "In part, yes! " A prior project with a collaborator predicts greater strength of a current collaborative work tie. Prior experience also reduces the negative impact of distance and disciplinary differences. We discuss the implications of these results for CSCW, given the lack of evidence that today's technology eliminates collaboration barriers in distributed research.
A Route Forwards to Narrow the Performance Gap between PZT and Lead‐Free Piezoelectric Ceramic with Low Oxygen Partial Pressure Processed (Na0.5K0.5)NbO3

Reduced atmosphere firing of (Na0.5K0.5)NbO3 (NKN) ceramics opens up an important opportunity for lead-free piezoelectric materials; one of the promising applications is base metal cofired multilayer actuators. Here, we extend an investigation on the effects of reduced atmosphere firing (PO2 = 10−10 atm) on the piezoelectric properties and associated point defects in NKN–LiF ceramics. To access the domain dynamics contribution to the converse piezoelectric properties and consider point defects in the sintered ceramics, Rayleigh analysis and thermal stimulated depolarization current (TSDC) were used. The piezoelectric properties and Rayleigh analysis of NKN–LiF ceramics demonstrated that the intrinsic and extrinsic piezoelectric response is essentially independent of firing atmosphere. Furthermore, reduced fired ceramic was found to have much higher resistivity than in the air-fired case. From the TSDC analysis, the space charge in the reduced fired ceramic was considered to be much smaller than in the air-fired ceramic, implying that the alkali volatilization was suppressed in reduced fired NKN–LiF ceramic.
Transcriptional control of the MUC16 promoter facilitates follicle-stimulating hormone peptide-conjugated shRNA nanoparticle-mediated inhibition of ovarian carcinoma in vivo

Abstract Ovarian cancer is the leading cause of cancer death among gynecological malignancies. The high mortality rate has not been significantly reduced despite advances in surgery and chemotherapy. Gene therapy shows therapeutic potential, but several key issues must be resolved before clinical application. To minimize toxicity in noncancerous tissues, tumor-specific ligands are conjugated to vectors to increase the selectivity of drug delivery. The expression pattern of follicle-stimulating hormone (FSH) receptor in normal and cancer tissues provides an opportunity for highly selective drug delivery in ovarian cancer. Furthermore, tumor-specific promoters can conditionally regulate therapeutic gene expression in tumor or normal tissues. The mucin 16 (MUC16) promoter might be a potential tool to drive ovarian cancer-localized gene expression since MUC16/CA125 is overexpressed in most ovarian carcinomas. Here, we screened the possible MUC16 promoter sequences and constructed MUC16 promoter-driven gro-α shRNA plasmid vectors. The vectors were specifically delivered into ovarian cancer cells via FSH peptide-conjugated nanoparticles. The predicted promoter sequence with TAAA repeats showed high transcriptional activity. The nanoparticle complex containing MUC16 promoter-driven gro-α shRNA and FSH peptides had the ability to decrease gro-α protein secretion in ovarian cancer cells and block tumor growth without obvious toxic effects in a nude mouse model bearing ovarian cancer. Our study provides a novel gene delivery system using a MUC16 promoter trigger and FSH peptide-mediated active targeting in ovarian cancer, and this system may be a promising strategy for specific genetic therapeutic delivery.
Structural View of a Non Pfam Singleton and Crystal Packing Analysis

Background Comparative genomic analysis has revealed that in each genome a large number of open reading frames have no homologues in other species. Such singleton genes have attracted the attention of biochemists and structural biologists as a potential untapped source of new folds. Cthe_2751 is a 15.8 kDa singleton from an anaerobic, hyperthermophile Clostridium thermocellum. To gain insights into the architecture of the protein and obtain clues about its function, we decided to solve the structure of Cthe_2751. Results The protein crystallized in 4 different space groups that diffracted X-rays to 2.37 Å (P3121), 2.17 Å (P212121), 3.01 Å (P4122), and 2.03 Å (C2221) resolution, respectively. Crystal packing analysis revealed that the 3-D packing of Cthe_2751 dimers in P4122 and C2221 is similar with only a rotational difference of 2.69° around the C axes. A new method developed to quantify the differences in packing of dimers in crystals from different space groups corroborated the findings of crystal packing analysis. Cthe_2751 is an all α-helical protein with a central hydrophobic core providing thermal stability via π:cation and π: π interactions. A ProFunc analysis retrieved a very low match with a splicing endonuclease, suggesting a role for the protein in the processing of nucleic acids. Conclusions Non-Pfam singleton Cthe_2751 folds into a known all α-helical fold. The structure has increased sequence coverage of non-Pfam proteins such that more protein sequences can be amenable to modelling. Our work on crystal packing analysis provides a new method to analyze dimers of the protein crystallized in different space groups. The utility of such an analysis can be expanded to oligomeric structures of other proteins, especially receptors and signaling molecules, many of which are known to function as oligomers.