Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential parental nutrient allocation in two congeneric pipefish species (Syngnathidae: Syngnathus spp.)

SUMMARY Male seahorses and pipefishes of the family Syngnathidae are heralded for their unique brood pouch structures for incubating embryos. There are three general types of brood pouch with increasing complexity: simple ventral gluing, two pouch flaps and a completely sealed sac. The diversity of functional roles within a type in providing nutrition, aeration and protection to offspring is unknown. Here we reveal significant differences in parental nutrient allocation to embryos for two closely related, sympatric pipefishes with similar brood pouch structure. We document differences in embryo attachment, depletion of pouch fluid nutrients over development and egg nutrient partitioning between Syngnathus floridae and Syngnathus fuscus. In S. fuscus, females produce nutritionally poor eggs and the males implant developing embryos in the brood pouch adjacent to blood vessels. A female-biased breeding population was observed, supporting the hypothesis that the cost of male parental care is high in this species. The loose connection between eggs and brood pouch tissues and the appearance of undeveloped eggs and lipid droplets in the pouch of S. floridae males suggest this species utilizes nutrient-rich eggs produced by females as nurse eggs to supplement embryonic development. A balanced sex-ratio for S. floridae further supports more equal parental contribution. This comparison provides evidence of a decline in female gametic investment and reveals the rapid diversification of syngnathid brood pouch function. Our results indicate gross classification of brooding structures into one of the three general pouch types does not predict the energetic investment of males in parental care. But rather, physiological characterization of the relative investment by each sex to offspring is essential to understanding the functional significance of the brood pouch.
Molecular mechanisms controlling CFTR gene expression in the airway

The low levels of CFTR gene expression and paucity of CFTR protein in human airway epithelial cells are not easily reconciled with the pivotal role of the lung in cystic fibrosis pathology. Previous data suggested that the regulatory mechanisms controlling CFTR gene expression might be different in airway epithelium in comparison to intestinal epithelium where CFTR mRNA and protein is much more abundant. Here we examine chromatin structure and modification across the CFTR locus in primary human tracheal (HTE) and bronchial (NHBE) epithelial cells and airway cell lines including 16HBE14o‐ and Calu3. We identify regions of open chromatin that appear selective for primary airway epithelial cells and show that several of these are enriched for a histone modification (H3K4me1) that is characteristic of enhancers. Consistent with these observations, three of these sites encompass elements that have cooperative enhancer function in reporter gene assays in 16HBE14o‐ cells. Finally, we use chromosome conformation capture (3C) to examine the three‐dimensional structure of nearly 800 kb of chromosome 7 encompassing CFTR and observe long‐range interactions between the CFTR promoter and regions far outside the locus in cell types that express high levels of CFTR.
Acetylcholine receptor in planar lipid bilayers. Characterization of the channel properties of the purified nicotinic acetylcholine receptor from Torpedo californica reconstituted in planar lipid bilayers

The properties of the channel of the purified acetylcholine receptor (AChR) were investigated after reconstitution in planar lipid bilayers. The time course of the agonist-induced conductance exhibits a transient peak that relaxes to a steady state value. The macroscopic steady state membrane conductance increases with agonist concentration, reaching saturation at 10(-5) M for carbamylcholine (CCh). The agonist-induced membrane conductance was inhibited by d-tubocurarine (50% inhibition, IC50, at approximately 10(-6) M) and hexamethonium (IC50 approximately 10(-5) M). The single channel conductance, gamma, is ohmic and independent of the agonist. At 0.3 M monovalent salt concentrations, gamma = 28 pS for Na+, 30 pS for Rb+, 38 pS for Cs+, and 50 pS for NH+4. The distribution of channel open times was fit by a sum of two exponentials, reflecting the existence of two distinct open states. tau o1 and tau o2, the fast and slow components of the distribution of open times, are independent of the agonist concentration: for CCh this was verified in the range of 10(-6) M less than C less than 10(-3)M. tau 01 and tau o2 are approximately three times longer for suberyldicholine ( SubCh ) than for CCh. tau o1 and tau o2 are moderately voltage dependent, increasing as the applied voltage in the compartment containing agonist is made more positive with respect to the other. At desensitizing concentrations of agonist, the AChR channel openings occurred in a characteristic pattern of sudden paroxysms of channel activity followed by quiescent periods. A local anesthetic derivative of lidocaine ( QX -222) reduced both tau o1 and tau o2. This effect was dependent on both the concentration of QX -222 and the applied voltage. Thus, the AChR purified from Torpedo electric organ and reconstituted in planar lipid bilayers exhibits ion conduction and kinetic and pharmacological properties similar to AChR in intact muscle postsynaptic membranes.
MDL4BMF: Minimum Description Length for Boolean Matrix Factorization

Matrix factorizations—where a given data matrix is approximated by a product of two or more factor matrices—are powerful data mining tools. Among other tasks, matrix factorizations are often used to separate global structure from noise. This, however, requires solving the “model order selection problem” of determining the proper rank of the factorization, that is, to answer where fine-grained structure stops, and where noise starts. Boolean Matrix Factorization (BMF)—where data, factors, and matrix product are Boolean—has in recent years received increased attention from the data mining community. The technique has desirable properties, such as high interpretability and natural sparsity. Yet, so far no method for selecting the correct model order for BMF has been available. In this article, we propose the use of the Minimum Description Length (MDL) principle for this task. Besides solving the problem, this well-founded approach has numerous benefits; for example, it is automatic, does not require a likelihood function, is fast, and, as experiments show, is highly accurate. We formulate the description length function for BMF in general—making it applicable for any BMF algorithm. We discuss how to construct an appropriate encoding: starting from a simple and intuitive approach, we arrive at a highly efficient data-to-model--based encoding for BMF. We extend an existing algorithm for BMF to use MDL to identify the best Boolean matrix factorization, analyze the complexity of the problem, and perform an extensive experimental evaluation to study its behavior.
Neutrophil/Lymphocyte Ratio Is Associated with Non-Calcified Plaque Burden in Patients with Coronary Artery Disease

Background Elevations in soluble markers of inflammation and changes in leukocyte subset distribution are frequently reported in patients with coronary artery disease (CAD). Lately, the neutrophil/lymphocyte ratio has emerged as a potential marker of both CAD severity and cardiovascular prognosis. Objectives The aim of the study was to investigate whether neutrophil/lymphocyte ratio and other immune-inflammatory markers were related to plaque burden, as assessed by coronary computed tomography angiography (CCTA), in patients with CAD. Methods Twenty patients with non-ST-elevation acute coronary syndrome (NSTE-ACS) and 30 patients with stable angina (SA) underwent CCTA at two occasions, immediately prior to coronary angiography and after three months. Atherosclerotic plaques were classified as calcified, mixed and non-calcified. Blood samples were drawn at both occasions. Leukocyte subsets were analyzed by white blood cell differential counts and flow cytometry. Levels of C-reactive protein (CRP) and interleukin(IL)-6 were measured in plasma. Blood analyses were also performed in 37 healthy controls. Results Plaque variables did not change over 3 months, total plaque burden being similar in NSTE-ACS and SA. However, non-calcified/total plaque ratio was higher in NSTE-ACS, 0.25(0.09–0.44) vs 0.11(0.00–0.25), p<0.05. At admission, levels of monocytes, neutrophils, neutrophil/lymphocyte ratios, CD4+ T cells, CRP and IL-6 were significantly elevated, while levels of NK cells were reduced, in both patient groups as compared to controls. After 3 months, levels of monocytes, neutrophils, neutrophil/lymphocyte ratios and CD4+ T cells remained elevated in patients. Neutrophil/lymphocyte ratios and neutrophil counts correlated significantly with numbers of non-calcified plaques and also with non-calcified/total plaque ratio (r = 0.403, p = 0.010 and r = 0.382, p = 0.024, respectively), but not with total plaque burden. Conclusions Among immune-inflammatory markers in NSTE-ACS and SA patients, neutrophil counts and neutrophil/lymphocyte ratios were significantly correlated with non-calcified plaques. Data suggest that these easily measured biomarkers reflect the burden of vulnerable plaques in CAD.
Hepatocellular Carcinoma Management in Nonalcoholic Fatty Liver Disease Patients

Background/Aims:Nonalcoholic fatty liver disease (NAFLD) has emerged as an important cause of chronic liver disease, cirrhosis, and hepatocellular carcinoma (HCC). The Barcelona Clinic Liver Cancer (BCLC) system is the preferred staging system to evaluate patients with HCC and links prognosis assessment with treatment recommendation. The aim of this retrospective study was to evaluate whether the BCLC staging system and its treatment algorithm are suitable for patients with HCC arising from NAFLD. Methods:Forty-two patients with HCC related to either to NAFLD or cryptogenic cirrhosis were retrieved retrospectively from 2 centers in Brazil. Patients were classified according to BCLC staging system. If the proposed HCC therapy could not be applied, the case was considered to represent deviations from the recommended BCLC guideline. Causes of treatment deviations were investigated. Results:There were 4 patients without evidence of cirrhosis according to liver biopsy and/or clinical evaluation. One (2%), 21 (50%), 10 (24%), 5 (12%), and 5 patients (12%) were classified initially to the very early (0), early (A), intermediate (B), advanced (C), and terminal (D) BCLC stages, respectively. Thirty-five patients (83%) were treated according to BCLC recommendations. There were 3 cases (of 5) of protocol deviation in BCLC C patients. The 1- and 2-year overall survival rates were 81% and 66%, respectively. Conclusions:The BCLC system is applied in most cases of NAFLD-related HCC cases. Deviation of BCLC is found more frequently in BCLC C stage patients.
Social preferences and the response to incentives: Evidence from personnel data

We present evidence on whether workers have social preferences by comparing workers' productivity under relative incentives, where individual effort imposes a negative externality on others, to their productivity under piece rates, where it does not. We find that the productivity of the average worker is at least 50 percent higher under piece rates than under relative incentives. We show that this is due to workers partially internalizing the negative externality their effort imposes on others under relative incentives, especially when working alongside their friends. Under piece rates, the relationship among workers does not affect productivity. Further analysis reveals that workers internalize the externality only when they can monitor others and be monitored. This rules out pure altruism as the underlying motive of workers' behavior.
Continental-shelf scale Passive Ocean Acoustic Waveguide Remote Sensing of marine mammals and other submerged objects including detection, localization, and classification

Continental-shelf Scale Passive Ocean Acoustic Waveguide Remote Sensing of Marine Mammals and other Submerged Objects including Detection, Localization, and Classification by Delin Wang Doctor of Philosophy in Electrical Engineering Northeastern University, December 2017 Prof. Purnima Ratilal Makris, Advisor In this thesis, we develop the basics of the Passive Ocean Acoustic Waveguide Remote Sensing (POAWRS) technique for the instantaneous continental-shelf scale detection, localization and species classification of marine mammal vocalizations. POAWRS uses a large-aperture, densely sampled coherent hydrophone array system with orders of magnitude higher array gain to enhance signal-to-noise ratios (SNR) by coherent beamforming, enabling detection of underwater acoustic signals either two orders of magnitude more distant in range or lower in SNR than a single hydrophone. The ability to employ coherent spatial processing of signals with the POAWRS technology significantly improves areal coverage, enabling detection of oceanic sound sources over instantaneous wide areas spanning 100 km or more in diameter. The POAWRS approach was applied to analyze marine mammal vocalizations from diverse species received on a 160-element Office Naval Research Five Octave Research Array (ONR-FORA) deployed during their feeding season in Fall 2006 in the Gulf of Maine. The species-dependent temporal-spatial distribution of marine mammal vocalizations and correlation to the prey fish distributions have been determined. Furthermore, the probability of detection regions, source level distributions and pulse compression gains of the vocalization signals from diverse marine mammal species have been estimated. We also develop an approach for enhancing the angular resolution and improving bearing estimates of acoustic signals received on a coherent
Management Compensation and Market Timing under Portfolio Constraints

This paper shows that portfolio constraints have important implications for management compensation and performance evaluation. In particular, in the presence of portfolio constraints, allowing for benchmarking can be beneficial. Benchmark design arises as an alternative effort inducement mechanism vis-a-vis relaxing portfolio constraints. Numerically, we solve jointly for the manager's linear incentive fee and the optimal benchmark. The size of the incentive fee and the risk adjustment in the benchmark composition are increasing in the investor's risk tolerance and the manager's ability to acquire and process private information.
Deep Neural Networks with Massive Learned Knowledge

Regulating deep neural networks (DNNs) with human structured knowledge has shown to be of great beneﬁt for improved accuracy and interpretability. We develop a general framework that enables learning knowledge and its conﬁdence jointly with the DNNs, so that the vast amount of fuzzy knowledge can be incorporated and automatically optimized with little manual efforts. We apply the framework to sentence sentiment analysis, augmenting a DNN with massive linguistic constraints on discourse and polarity structures. Our model substantially enhances the performance using less training data, and shows improved inter-pretability. The principled framework can also be applied to posterior regularization for regulating other statistical models.
Current and historical patterns of drainage connectivity in eastern Australia inferred from population genetic structuring in a widespread freshwater fish Pseudomugil signifer (Pseudomugilidae)

Dispersal can play an important role in the genetic structuring of natural populations. In this regard, freshwater fishes often exhibit extensive population genetic subdivision and are ideal subjects for investigating current and historical patterns of connection and dissociation between drainages. We set out to generate a comprehensive molecular phylogeny for a widespread freshwater fish from eastern Australia, the Pacific blue‐eye Pseudomugil signifer. Although movement via flood events may be important in the southern end of the species’ range, genetic structuring revealed the importance of historical drainage connections and dissociations in mediating or disrupting dispersal. A dominant feature of our phylogeny is a split between northern and southern populations, which appears to be congruent with a biogeographical barrier recently implicated as important for the connectivity of freshwater organisms in eastern Australia. The extent of the split also has taxonomic implications consistent with suggestions that the Pacific blue‐eye may represent more than a single species.
Inhibition of Cytokine Gene Transcription by the Human Recombinant Histamine-Releasing Factor in Human T Lymphocytes1

Human recombinant histamine-releasing factor (HrHRF) preincubation enhances the secretion of histamine, IL-4, and IL-13 from FcεRI-stimulated human basophils. In GM-CSF-primed human eosinophils, HrHRF increases IL-8 production. Our recent experiments were designed to evaluate the effects of HrHRF on human T cell cytokine production. Purified T cells were preincubated with GST-tagged HrHRF, followed by stimulation with PMA and A23187 overnight. A partial inhibition of IL-2 and IL-13 production (30 and 75%, respectively) was detected compared with that in cells treated with PMA/A23187 alone. However, the production of IFN-γ was similar in PMA/A23187 stimulated cells with or without HrHRF. The inhibition of cytokine protein production was dose dependent and specific to the HrHRF portion of GST-HrHRF. The inhibition was not due to endotoxin, since preincubation with polymyxin B and HrHRF gave similar results to that with HrHRF alone. The same pattern and specificity of cytokine regulation were replicated in the Jurkat T cell line as for primary T cells. The PMA/A23187-stimulated activity of a proximal promoter IL-13, IL-4, or IL-2 luciferase construct transfected into Jurkat cells was partially inhibited (60, 32, or 70%, respectively) upon GST-HrHRF preincubation, suggesting that HrHRF functions to inhibit cytokine production in Jurkat cells by preventing gene transcription. The inhibition of IL-2 promoter activation was specific to the HrHRF portion of GST-HrHRF. We conclude that HrHRF, in addition to functioning as a histamine-releasing factor, can differentially modulate the secretion of cytokines from human basophils, eosinophils, T cells, and murine B cells, suggesting that it may induce a complex array of responses at sites of allergic inflammation.
The functional role of the medial motion area V6

In macaque, several visual areas are devoted to analyze motion in the visual field, and V6 is one of these areas. In macaque, area V6 occupies the ventral part of the anterior bank of the parieto-occipital sulcus (POs), is retinotopically-organized and contains a point-to-point representation of the retinal surface. V6 is a motion sensitive area that largely represents the peripheral part of the visual field and whose cells are very sensitive to translational motion. Based on the fact that macaque V6 contains many real-motion cells, it has been suggested that V6 is involved in object-motion recognition. Recently, area V6 has been recognized also in the human brain by neuroimaging and electrophysiological methods. Like macaque V6, human V6 is located in the POs, is retinotopically organized, and represents the entire contralateral hemifield up to the far periphery. Human V6, like macaque V6, is a motion area that responds to unidirectional motion. It has a strong preference for coherent motion and a recent combined VEPs/fMRI work has shown that area V6 is even one of the most early stations coding the motion coherence. Human V6 is highly sensitive to flow field and is also able to distinguish between different 3D flow fields being selective to translational egomotion. This suggests that this area processes visual egomotion signals to extract information about the relative distance of objects, likely in order to act on them, or to avoid them. The view that V6 is involved in the estimation of egomotion has been tested also in other recent fMRI studies. Thus, taken together, human and macaque data suggest that V6 is involved in both object and self-motion recognition. Specifically, V6 could be involved in “subtracting out” self-motion signals across the whole visual field and in providing information about moving objects, particularly during self-motion in a complex and dynamically unstable environment.
Simulating Biogenic Secondary Organic Aerosol During Summertime in China

Biogenic secondary organic aerosol (BSOA) contributes significantly to summertime organic particulate matter. In this study, a simulation of BSOA for summer 2012 over China is performed using the Community Multiscale Air Quality model with an explicit representation of BSOA formation via reactive uptake of isoprene‐derived intermediates, species‐specific parameters for monoterpene‐derived BSOA production, and a multigenerational oxidation scheme. Simulated BSOA tracks the measurements well (normalized mean bias of 1% and r2 of 0.59). Elevated BSOA occurs in the Sichuan Basin and southeastern China (except the coastal areas) where concentrations are mostly within the range of 5–7.5 μg/m3. Nitrate oxidation dominates fresh BSOA originating from monoterpenes. Simulated monoterpene‐formed BSOA increases by a factor of 3–11 with multigenerational oxidation. Isoprene‐formed BSOA shows high concentrations in southwestern China, formed primarily by two methyltetrols (2‐MT) and organosulfates (62%–83%). High concentrations in this region are driven by the abundance of IEPOX and high particle surface area of sulfate‐laden aerosols. NOx emissions influence the formation pathways of isoprene‐formed BSOA, as a high ratio of two‐methylglyceric acid (2‐MG)/2‐MT is found in the North China Plain and part of the Yangtze River Delta Region. The simulated isoprene‐formed BSOA is more strongly correlated with sulfate than with particle water mass concentration or particle acidity, in part because sulfate increases the surface area increasing uptake for heterogeneous reactions. Decreases in isoprene‐formed BSOA were simulated with a pH increase of 2, implying that particle acidity mediates the BSOA formation.
Generalized Bayesian Estimators of the Spectral Amplitude for Speech Enhancement

In this letter, we show that many existing short-time spectral amplitude (STSA) Bayesian estimators for speech enhancement all have a similarly structured cost function. On this basis, we propose a new cost function that generalizes those of existent Bayesian STSA estimators and then obtain the corresponding closed-form solution for the optimal clean speech STSA. The resulting family of estimators, which we will term the generalized weighted family of STSA estimators (GWSA), features a new parameter that acts only on the estimated clean speech STSA. It is found that this new parameter yields an added flexibility in terms of achievable gain curves when compared to those of existing estimators. Moreover, we show that the new estimator family tends to a Wiener filter for high instantaneous signal-to-noise ratios.