Miracle-dz/UniFAR-FTUs huggingface dataset:
Reflections on O2 as a Biosignature in Exoplanetary Atmospheres

Abstract Oxygenic photosynthesis is Earth's dominant metabolism, having evolved to harvest the largest expected energy source at the surface of most terrestrial habitable zone planets. Using CO2 and H2O—molecules that are expected to be abundant and widespread on habitable terrestrial planets—oxygenic photosynthesis is plausible as a significant planetary process with a global impact. Photosynthetic O2 has long been considered particularly robust as a sign of life on a habitable exoplanet, due to the lack of known “false positives”—geological or photochemical processes that could also produce large quantities of stable O2. O2 has other advantages as a biosignature, including its high abundance and uniform distribution throughout the atmospheric column and its distinct, strong absorption in the visible and near-infrared. However, recent modeling work has shown that false positives for abundant oxygen or ozone could be produced by abiotic mechanisms, including photochemistry and atmospheric escape. Environmental factors for abiotic O2 have been identified and will improve our ability to choose optimal targets and measurements to guard against false positives. Most of these false-positive mechanisms are dependent on properties of the host star and are often strongest for planets orbiting M dwarfs. In particular, selecting planets found within the conservative habitable zone and those orbiting host stars more massive than 0.4 M⊙ (M3V and earlier) may help avoid planets with abundant abiotic O2 generated by water loss. Searching for O4 or CO in the planetary spectrum, or the lack of H2O or CH4, could help discriminate between abiotic and biological sources of O2 or O3. In advance of the next generation of telescopes, thorough evaluation of potential biosignatures—including likely environmental context and factors that could produce false positives—ultimately works to increase our confidence in life detection. Key Words: Biosignatures—Exoplanets—Oxygen—Photosynthesis—Planetary spectra. Astrobiology 17, 1022–1052.
High Seroprevalence of Histomonas meleagridis in Dutch Layer Chickens

Abstract Histomona meleagridis is a protozoan parasite that may cause outbreaks of histomonosis with high mortality, especially in turkey flocks. Chickens are less susceptible to the disease than are turkeys, but are considered to act as an important reservoir. To determine the seroprevalence of H. meleagridis in Dutch layer chicken flocks, a large scale seroepidemiologic study (3376 samples) was performed by sampling 12 organic flocks, 24 free-ranging flocks, 40 flocks with floor housing, and 40 flocks with cage housing. At the end of the laying period, approximately 30 blood samples per flock were collected for serology. The seroprevalence found was high. In every flock, at least one of the samples tested positive while in 87% of the flocks, at least one of the samples was strongly positive. There were no significant statistical differences in seropositivity between the housing types. To confirm the enzyme-linked immunosorbent assay (ELISA) results, a small-scale seroepidemiologic study (576 samples) was performed in 29 additional layer chicken flocks kept in different housing systems. Subsequently, a subset of five seropositive flocks was selected. Five birds were obtained from each of these flocks in order to detect the parasite using culture and PCR. In all five flocks, H. meleagridis was either isolated from (culture), detected in (PCR), or both, the birds sampled. Together with the previously performed validation studies, the latter results confirm that the positive ELISA serology found is genuine. We conclude that the seroprevalence of H. meleagridis in layers is, as anticipated, high.
Auditory Attention and Comprehension During a Simulated Night Shift

Objective: The current study investigated performance on a dual auditory task during a simulated night shift. Background: Night shifts and sleep deprivation negatively affect performance on vigilance-based tasks, but less is known about the effects on complex tasks. Because language processing is necessary for successful work performance, it is important to understand how it is affected by night work and sleep deprivation. Method: Sixty-two participants completed a simulated night shift resulting in 28 hr of total sleep deprivation. Performance on a vigilance task and a dual auditory language task was examined across four testing sessions. Results: The results indicate that working at night negatively impacts vigilance, auditory attention, and comprehension. The effects on the auditory task varied based on the content of the auditory material. When the material was interesting and easy, the participants performed better. Night work had a greater negative effect when the auditory material was less interesting and more difficult. Conclusion: These findings support research that vigilance decreases during the night. The results suggest that auditory comprehension suffers when individuals are required to work at night. Maintaining attention and controlling effort especially on passages that are less interesting or more difficult could improve performance during night shifts. Application: The results from the current study apply to many work environments where decision making is necessary in response to complex auditory information. Better predicting the effects of night work on language processing is important for developing improved means of coping with shiftwork.
Arhgef7 promotes activation of the Hippo pathway core kinase Lats

The Hippo pathway regulates tissue growth and organ size, and inactivation contributes to cancer. Signals flow through Mst/Lats kinases, which phosphorylate and promote cytoplasmic localization of the transcriptional regulators Yap and Taz to inhibit transcription. Here, we identify the multidomain‐containing guanine nucleotide exchange factor (GEF) Arhgef7, or βPix, as a positive Hippo pathway regulator. We show that βPix, which localizes to the cytoplasm, binds both Lats and Yap/Taz and thereby promotes Lats‐mediated phosphorylation of Yap/Taz in a GEF‐independent manner. βPix is required downstream of both cell density sensing and actin cytoskeletal rearrangements, and we demonstrate that loss of βPix expression in normal mammary epithelial cells strongly reduces Yap/Taz phosphorylation, promotes nuclear localization and increases target gene expression. Conversely, increased expression of βPIX in breast cancer cell lines re‐couples the Hippo kinase cassette to Yap/Taz, promoting localization of Yap/Taz to the cytoplasm and inhibiting cell migration and proliferation. These studies thus define βPix as a key component that links the Hippo kinase cassette to Yap/Taz in response to multiple upstream Hippo pathway activators.
Sediment resuspension in a shallow lake

Different mathematical formulations for the computation of the entrainment rate of sediment into suspension in lakes can produce widely disparate results under a given set of conditions, leading to problematic interpretation. In this paper, the results of a 4‐month field campaign on sediment resuspension in a large, shallow, hypereutrophic lake in southern California are presented. The field measurement program included the observation of currents and waves using a Nortek acoustic wave and current (AWAC) profiler, the observation of water temperatures using a thermistor chain, the use of optical backscatter sensors for the measurement of turbidity, a surrogate for suspended sediment concentration, and the use of meteorological data. The paper reports one of the first field experiments in lakes using the AWAC, whose signal strength has not been investigated in detail to date, and the correlation of a set of variables coming from different sources during a relatively long period of time. The contributions of different forcing mechanisms (waves, currents, and surface seiches) to the sediment resuspension in the lake are quantified, and the signal strength of the AWAC is used to address the vertical distribution of sediment in the water column. A novel relationship between the AWAC's backscatter intensity and turbidity is presented. Turbidity was found to be proportional to wK, where w is the wind speed measured at 2 m and K ranged from 4.5 to 6.5, depending on the water depth. Finally, the results of modeling the sediment entrainment into suspension in the Salton Sea are shown to be well represented by an extension of the García and Parker formula.
Assessment of cell proliferation in hydatidiform mole using monoclonal antibody MIB1 to Ki-67 antigen.

AIMS--To assess the role of Ki67 immunoreactivity in predicting the clinical progress of hydatidiform mole. METHODS--Tissue from 87 hydatidiform moles, 11 normal first trimester placentas, 11 normal term placentas and 17 spontaneous abortions were examined for expression of Ki67 antigen, using the monoclonal antibody MIB1. RESULTS--Ki67 immunoreactivity was significantly higher in the tissue from normal first trimester placentas than in that from normal term placentas and spontaneous abortions. Among the 87 patients with hydatidiform moles studied, 20 developed persistent gestational trophoblastic disease and required subsequent treatment. There was no statistically significant difference in the Ki67 index between the 20 patients who developed persistent disease and those who did not. CONCLUSION--Hydatidiform moles which give rise to persistent trophoblastic disease do not have a higher proliferative rate than those which do not. The Ki67 index is not useful for predicting the prognosis of molar pregnancies.
Internet of Things and M2M Communications as Enablers of Smart City Initiatives

This paper describes Internet of Things (IoT) and Machine-to-Machine (M2M) communications as the enablers of smart city initiatives. The challenges in modern cities are briefly identified. Utilization of IoT based applications and services could mitigate these challenges. The paper then introduces an architecture based on oneM2M standards for smart cities. The key elements of the architecture are described along with the common service functions. The main contributions of the work are -- (i) uniform metadata exchange with things using Sensor Markup Language and its extensions, (ii) uniform description of heterogeneous things for configuration management, (iii) OMA Lightweight M2M based device management framework, (iv) resource discovery framework and (v) Machine-to-Machine Measurement framework based M2M data processing and analytics. The core functionalities of these frameworks are exposed to the consumers through RESTful web services. An application scenario on crowdsourcing in the smart cities is highlighted. Finally the paper concludes with future research directions.
First visualization of cholinergic cells and fibers by immunohistochemistry for choline acetyltransferase of the common type in the optic lobe and peduncle complex of Octopus vulgaris

This study provides the first immunohistochemical evidence visualizing cholinergic octopus neurons containing choline acetyltransferase (ChAT), the synthetic enzyme of acetylcholine. Because the antiserum applied here was raised against a recombinant protein encoded by exons 7 and 8 of the rat gene for ChAT, and initially used for studies in mammals, to validate antibody specificity for the octopus counterpart enzyme we therefore used three methods. Immunoprecipitation using Pansorbin indicated that immunoreactive octopus brain molecules were capable of synthesizing acetylcholine. Western blot analysis after denatured gel electrophoresis of octopus brain extracts revealed a single band at ≈81 kDa. A gel slice containing the 81‐kDa protein after native (nondenatured) gel electrophoresis exhibited high ChAT activity. All findings obtained with these three methods clearly indicated that the antiserum effectively recognizes octopus ChAT. The immunohistochemical use of the antiserum in the retina, optic lobe, and its neighboring peduncle complex detected enzyme‐containing neuronal cell bodies in only two regions, the cell islands of the optic lobe medulla and the cortical layer of the posterior olfactory lobule. Immunoreactive fibers and probable nerve terminals were also found in the plexiform layer of the deep retina, within the stroma of the optic gland, and the neuropils of the optic lobe, peduncle lobe, and olfactory lobe. These results provide information on the morphology and distribution patterns of cholinergic neurons in the octopus visual system, a useful invertebrate model for learning and memory where the cholinergic system, as in higher vertebrates including mammals, plays an important role. J. Comp. Neurol. 509:566–579, 2008. © 2008 Wiley‐Liss, Inc.
Protein L5 is crucial for in vivo assembly of the bacterial 50S ribosomal subunit central protuberance

In the present work, ribosomes assembled in bacterial cells in the absence of essential ribosomal protein L5 were obtained. After arresting L5 synthesis, Escherichia coli cells divide a limited number of times. During this time, accumulation of defective large ribosomal subunits occurs. These 45S particles lack most of the central protuberance (CP) components (5S rRNA and proteins L5, L16, L18, L25, L27, L31, L33 and L35) and are not able to associate with the small ribosomal subunit. At the same time, 5S rRNA is found in the cytoplasm in complex with ribosomal proteins L18 and L25 at quantities equal to the amount of ribosomes. Thus, it is the first demonstration that protein L5 plays a key role in formation of the CP during assembly of the large ribosomal subunit in the bacterial cell. A possible model for the CP assembly in vivo is discussed in view of the data obtained.
Optimal Cluster Recovery in the Labeled Stochastic Block Model

We consider the problem of community detection or clustering in the labeled Stochastic Block Model (LSBM) with a finite number $K$ of clusters of sizes linearly growing with the global population of items $n$. Every pair of items is labeled independently at random, and label $\ell$ appears with probability $p(i,j,\ell)$ between two items in clusters indexed by $i$ and $j$, respectively. The objective is to reconstruct the clusters from the observation of these random labels. Clustering under the SBM and their extensions has attracted much attention recently. Most existing work aimed at characterizing the set of parameters such that it is possible to infer clusters either positively correlated with the true clusters, or with a vanishing proportion of misclassified items, or exactly matching the true clusters. We find the set of parameters such that there exists a clustering algorithm with at most $s$ misclassified items in average under the general LSBM and for any $s=o(n)$, which solves one open problem raised in \cite{abbe2015community}. We further develop an algorithm, based on simple spectral methods, that achieves this fundamental performance limit within $O(n \mbox{polylog}(n))$ computations and without the a-priori knowledge of the model parameters.
Rapid functional analysis of computationally complex rare human IRF6 gene variants using a novel zebrafish model

Large-scale sequencing efforts have captured a rapidly growing catalogue of genetic variations. However, the accurate establishment of gene variant pathogenicity remains a central challenge in translating personal genomics information to clinical decisions. Interferon Regulatory Factor 6 (IRF6) gene variants are significant genetic contributors to orofacial clefts. Although approximately three hundred IRF6 gene variants have been documented, their effects on protein functions remain difficult to interpret. Here, we demonstrate the protein functions of human IRF6 missense gene variants could be rapidly assessed in detail by their abilities to rescue the irf6 -/- phenotype in zebrafish through variant mRNA microinjections at the one-cell stage. The results revealed many missense variants previously predicted by traditional statistical and computational tools to be loss-of-function and pathogenic retained partial or full protein function and rescued the zebrafish irf6 -/- periderm rupture phenotype. Through mRNA dosage titration and analysis of the Exome Aggregation Consortium (ExAC) database, IRF6 missense variants were grouped by their abilities to rescue at various dosages into three functional categories: wild type function, reduced function, and complete loss-of-function. This sensitive and specific biological assay was able to address the nuanced functional significances of IRF6 missense gene variants and overcome many limitations faced by current statistical and computational tools in assigning variant protein function and pathogenicity. Furthermore, it unlocked the possibility for characterizing yet undiscovered human IRF6 missense gene variants from orofacial cleft patients, and illustrated a generalizable functional genomics paradigm in personalized medicine.
Prediction of hemispheric asymmetry as measured by handedness from digit length and 2D:4D digit ratio

Hemispheric asymmetry is widely theorised as having a basis in prenatal androgen levels. However, these theories ignore a second round of asymmetrical changes in the brain, which occur at the same time as post-puberty surges in androgens. Hemispheric asymmetry in adults might therefore be explained in terms of the joint effects of prenatal and post-pubertal androgen levels. Evidence is emerging that the ratio between the length of the second and fourth digits (2D:4D) is related to prenatal androgen exposure, and that digit length is related to post-puberty levels of androgen exposure. In this study, hemispheric asymmetry is measured as handedness, prenatal androgen levels as 2D:4D, and post-puberty androgen levels as digit length. Right-handedness is associated with consistent prenatal and post puberty androgen release whereas left-handedness is associated with mixed levels of androgen release. Age, race, and sex effects were explored but were not significant.
Incidental Computing on IoT Nonvolatile Processors

Batteryless IoT devices powered through energy harvesting face a fundamental imbalance between the potential volume of collected data and the amount of energy available for processing that data locally. However, many such devices perform similar operations across each new input record, which provides opportunities for mining the potential information in buffered historical data, at potentially lower effort, while processing new data rather than abandoning old inputs due to limited computational energy. We call this approach incidental computing, and highlight synergies between this approach and approximation techniques when deployed on a non-volatile processor platform (NVP). In addition to incidental computations, the backup and restore operations in an incidental NVP provide approximation opportunities and optimizations that are unique to NVPs.We propose a variety of incidental approximation approaches suited to NVPs, with a focus on approximate backup and restore, and approximate recomputation in the face of power interruptions. We perform RTL level evaluation for many frequently used workloads. We show that these incidental techniques provide an average of 4.2X more forward progress than precise NVP execution.CCS CONCEPTS• Computer systems organization → Single instruction, multiple data; Special purpose systems; System on a chip; Embedded hardware;
Optimizing the recognition rates of unconstrained handwritten numerals using biorthogonal spline wavelets

In this paper an approach for off-line recognition of unconstrained handwritten numerals is presented. This approach uses the Cohen-Daubechies-Feauveau (CDF) family of biorthogonal spline wavelets as a feature extractor for absorbing local variations in handwritten characters and a multilayer cluster neural network as classifier. Experiments with the bases CDF 2/2, CDF 2/4, CDF 3/3 and CDF 3/7 were performed using the handwritten numeral database of Concordia University of Canada. The results show that CDF biorthogonal wavelets yield a performance improvement of 2.4% in numeral recognition, compared to the results obtained with the Haar wavelets.
A diskless checkpointing algorithm for super-scale architectures applied to the fast fourier transform

This paper discusses the issue of fault-tolerance in distributedcomputer systems with tens or hundreds of thousandsof diskless processor units. Such systems, like theIBM BlueGene/L, are predicted to be deployed in the nextfive to ten years. Since a 100,000-processor system is goingto be less reliable, scientific applications need to beable to recover from occurring failures more efficiently.In this paper, we adapt the present technique of disklesscheckpointing to such huge distributed systems in orderto equip existing scientific algorithms with super-scalablefault-tolerance. First, we discuss the method of disklesscheckpointing, then we adapt this technique to super-scalearchitectures and finally we present results from an implementationof the Fast Fourier Transform that uses theadapted technique to achieve super-scale fault-tolerance.
Dual or dueling culture and commitment: The impact of a tri-hospital merger.

OBJECTIVES This article addresses differences in RNs' commitment to their employing hospital versus the umbrella corporate organization, and the role of organizational culture during a tri-hospital merger. This study is the first to investigate the construct of dual commitment in healthcare organizations. BACKGROUND Fiscal restraints, decreasing reimbursement, and increasing competition have made organizational mergers and acquisitions prevalent. As corporate culture changes, organizational variables previously related to organizational commitment may no longer apply. METHODS RNs employed on general nursing units at 3 hospitals involved in a merger process completed 2 versions of Mowday's Organizational Commitment Questionnaire. Commitment to hospital and corporate system were examined. Semi-structured interviews, participant observation, and analysis of company documents assessed the organizational culture changes that have occurred. RESULTS Thirty-one percent of the nurses returned completed questionnaires; 9 were interviewed. RNs from the acquiring hospital demonstrated a significantly stronger commitment to the corporate system than the nurses from the acquired hospitals. The RNs at all 3 hospitals showed significantly greater commitment to their own particular hospital than to the umbrella corporate system. CONCLUSIONS Moderate level of commitment reflected uncertainty of job status, work overload, and feelings of unappreciation. These attitudes prevent nurses from exerting efforts on behalf of the organization.
Optimal file sharing in distributed networks

Given a distributed network of processors represented by an undirected graph G=(V, E) and a file size k, the problem of distributing an arbitrary file w of k bits among all nodes of the network G is considered. Memory devices are to be assigned to the node of G such that, by accessing the memory of its own and of its adjacent nodes, each node can reconstruct the contents of w. The objective is to minimize the total size memory in the network. A file distribution scheme that realizes this objective for k>>log Delta /sub G/, where Delta /sub G/, stands for the maximum degree in G, is presented. For this range of k, the total size of memory required by the suggested scheme approaches an integer programming lower bound on that size. <<ETX>>