Miracle-dz/UniFAR-FTUs huggingface dataset:
Hierarchical Network Exploration using Gaussian Mixture Models

We present a framework based on optimal mass transport to construct, for a given network, a reduction hierarchy which can be used for interactive data exploration and community detection. Given a network and a set of numerical data samples for each node, we calculate a new computationally-efficient comparison metric between Gaussian Mixture Models, the Gaussian Mixture Transport distance, to determine a series of merge simplifications of the network. If only a network is given, numerical samples are synthesized from the network topology. The method has its basis in the local connection structure of the network, as well as the joint distribution of the data associated with neighboring nodes. The analysis is benchmarked on networks with known community structures. We also analyze gene regulatory networks, including the PANTHER curated database and networks inferred from the GTEx lung and breast tissue RNA profiles. Gene Ontology annotations from the EBI GOA database are ranked and superimposed to explain the salient gene modules. We find that several gene modules related to highly specific biological processes are well-coordinated in such tissues. We also find that 18 of the 50 genes of the PAM50 breast-tumor prognostic signature appear among the highly coordinated genes in a single gene module, in both the breast and lung samples. Moreover these 18 are precisely the subset of the PAM50 recently identified as the basal-like markers.
Organizational Identity and Community Values: Determining Meaning in Post-secondary Education Social Media Guideline and Policy Documents

With the increasing use of social media by students, researchers, administrative staff, and faculty in post-secondary education (PSE), a number of institutions have developed guideline and policy documents to set standards for social media use. Social media platforms and applications have the potential to increase communication channels, support learning, enhance research, and encourage community engagement at PSE institutions. As social media implementation and administration has developed in PSE, there has been minimal assessment of the substance of social media guideline and policy documents. The first objective of this research study was to examine an accessible, online database (corpus) comprised of 24, 243 atomic social media guideline and policy text documents from 250 PSE institutions representing 10 countries to identify central attributes. To determine text meaning from topic extraction, a rotated latent semantic analysis (rLSA) method was applied. The second objective of this investigation was to determine if the distribution of topics analyze in the corpus differ by PSE institution geographic location. To analyze the diverging topics, the researcher utilized an iterative consensus-building algorithm.Through the maximum term frequencies, LSA determined a rotated 36-factor solution that identified common attributes and topics shared among the 24,243 social media guideline and policy atomic documents. This initial finding produced a list of 36 universal topics discussed in social media guidelines and policies across all 250 PSE institutions from 10 countries. Continually, the applied chi-squared tests, that measured expected and observed document term counts, identified distribution differences of content related factors between US and Non-US PSE institutions. This analysis offered a concrete analysis for unstructured text data on the topic of social media guidance. This resulted in a comprehensive list of recommendations for developing social media guidelines and policies, and a database of social media guideline and policy documents for the PSE sector and other related organizations. Additionally, this research stimulated important theoretical development for how organizations socially construct a semantic structure within a community of practice. By assessing the community of practice, comprised of PSE 250 institutions that direct social media use, a corpus of documents provided unstructured data to evaluate the community. The spontaneous participation and reification process of the social media guideline and policy document corpus reaffirmed that a corpus-creating community of practice can instinctively form a knowledge-sharing organization that provides meaning, values, and identity. These findings should stimulate further research contributions, and provides practitioners and scholars with tools to measure, understand, and assess semantic space for other artifacts developed within a community of practice in other industries, organizations, or distributed associations.
Comparison of the Stability, Efficacy, and Adverse Effect Profile of the Innovator 0.005% Latanoprost Ophthalmic Solution and a Novel Cyclodextrin‐containing Formulation

Recently, a new latanoprost ophthalmic solution containing cyclodextrins was developed. The purpose of the present work was to compare the stability, clinical efficacy, and adverse effect profile of this formulation with the innovator product. The innovator formulation was stable at 4°C but exhibited degradation at higher temperatures, whereas the cyclodextrin‐containing formulation was stable at temperatures up to 40°C. Formulations were assayed in a randomized double‐blind clinical study in patients with primary open‐angle glaucoma and/or ocular hypertension. Both latanoprost ophthalmic solutions produced comparable reduction of intraocular pressure. Conjunctival hyperemia was observed in 11.9% and 11.3% of the patients treated with the innovator and the cyclodextrin‐containing formulations, respectively. There were no significant differences between the 2 ophthalmic solutions in efficacy or in the measured adverse effect. It is concluded that these 2 latanoprost ophthalmic solutions yield comparable efficacy and adverse effect outcomes. The cyclodextrin‐containing formulation, however, has an improved stability.
Functional Programming Using the New C++ Standard

In our article we demonstrate that the new C++ standard is the one preferred by economists and big software companies to implement AI and decision making algorithms. Today software technology evolves very quickly, to an old paradigm, called functional programming. This paradigm uses lambda functions ready to be used where declared instead of function pointers. The long term target is to let compilers evaluate rather than execute a program/function. The new C++14 standard allows lambda calculus as we demonstrate in the applicative section of implementing conditionals, booleans and numbers.
Paralogous chemoreceptors mediate chemotaxis towards protein amino acids and the non‐protein amino acid gamma‐aminobutyrate (GABA)

The paralogous receptors PctA, PctB and PctC of Pseudomonas aeruginosa were reported to mediate chemotaxis to amino acids, intermediates of amino acid metabolism and chlorinated hydrocarbons. We show that the recombinant ligand binding regions (LBRs) of PctA, PctB and PctC bind 17, 5 and 2 l‐amino acids respectively. In addition, PctC‐LBR recognized GABA but not any other structurally related compound. l‐Gln, one of the three amino acids that is not recognized by PctA‐LBR, was the most tightly binding ligand to PctB suggesting that PctB has evolved to mediate chemotaxis primarily towards l‐Gln. Bacteria were efficiently attracted to l‐Gln and GABA, but mutation of pctB and pctC, respectively, abolished chemoattraction. The physiological relevance of taxis towards GABA is proposed to reside in an interaction with plants. LBRs were predicted to adopt double PDC (PhoQ/DcuS/CitA) like structures and site‐directed mutagenesis studies showed that ligands bind to the membrane‐distal module. Analytical ultracentrifugation studies have shown that PctA‐LBR and PctB‐LBR are monomeric in the absence and presence of ligands, which is in contrast to the enterobacterial receptors that require sensor domain dimers for ligand recognition.
Interaction of GroEL with conformational states of horse cytochrome c.

GroEL interacts with proteins in denatured states and promotes their efficient folding. To understand the conformational features required for the substrate, we studied the interactions of GroEL with various derivatives of horse cytochrome c including porphyrin-cytochrome c, apo-cytochrome c, and the three fragments containing the heme group, i.e. fragments 1-65, 1-38 and 11-21. Size-exclusion chromatography was performed, taking advantage of the heme absorption of the fluorescence label. Under low-salt conditions, significant binding to GroEL was observed for porphyrin-cytochrome c, apo-cytochrome c, and fragments 1-65 and 1-38, but not for intact cytochrome c or fragment 11-21. On the other hand, under conditions of high ionic strength, only apo-cytochrome c remained tightly bound. Whereas porphyrin-cytochrome c assumes a molten-globule-like compact conformation with a native-like far-UV CD, apo-cytochrome c shows a compact conformation without an ordered secondary structure. The far-UV CD spectra of the three fragments indicated that the fragments lack an ordered secondary structure. These results suggest that the fluctuating and exposed hydrophobic clusters of the substrates are responsible for the interaction, and that the interaction is modulated by electrostatic interaction. It is notable that these characteristics are similar to those of the interaction of cytochrome c derivatives with negatively charged phospholipid membranes, suggesting a common mechanism. Using fluorescence-labeled apo-cytochrome c, we also measured the kinetics of the interaction and estimated the association rate constant to be 5 x 10(7) M-1s-1. This relatively fast association rate constant indicates that the refolding rate of substrate protein is another important factor determining the interaction.
Beautiful City: The Dialectical Character of Plato's "Republic"

To the vast literature on Plato's Republic comes a new interpretation. In Beautiful City, David Roochnik argues convincingly that Plato's masterpiece is misunderstood by modern readers. The work must, he explains, be read dialectically, its parts understood as forming a unified whole. Approached in this way, the text no longer appears to defend an authoritarian and monolithic political system, but rather supplies a qualified defense of democracy and the values of diversity. Writing in clear and straightforward prose, Roochnik demonstrates how Plato's treatment of the city and the soul evolves throughout the dialogue and can be appreciated only by considering the Republic in its entirety. He shows that the views expressed in the early parts of the text do not represent Plato's final judgment on these subjects but are in fact dialectical "moments" intended to be both partial and provisional. Books 5-7 of the Republic are, he maintains, meant to revise and improve upon books 2-4. Similarly, he sees the usually neglected books 8-10 as advancing beyond the thoughts presented in the previous books. Paying particular attention to these later books, Roochnik details, for instance, how the stories of the "mistaken" regimes, which are often seen as unimportant, are actually crucial in Plato's account of the soul. Beautiful City is certain to be controversial, as the author's insights and opinions will engage and challenge philosophers, classicists, and political theorists.
Genomic Hopscotch: Gene Transfer from Plastid to Nucleus

The widely accepted endosymbiont theory of eukaryotic evolution holds that organelles arose from free-living prokaryotes (a proteobacterium and a cyanobacterium giving rise to mitochondria and chloroplasts, respectively) that were engulfed by an ancestral archaeal host cell ([Embley and Martin, 2006
Construction and formal verification of a fault-tolerant distributed mutual exclusion algorithm

Distributed fault-tolerant control algorithms are in great demand nowadays due to their practical importance in cloud computing, Internet of Things (IoT) technology, swarm robotics, and other areas. It is usually hard to make a distributed algorithm fault-tolerant. It is even harder to ensure that such algorithm behaves correctly in the presence of faults of some kind. In this work, we construct a reliable, adaptive, fault-tolerant distributed mutual exclusion algorithm based on the well-known Ricart-Agrawala algorithm. In order to formally verify it, we use a hybrid approach of deductive reasoning and bounded model-checking. First, a safety property of the Ricart-Agrawala algorithm is proved in Calculus of Inductive Constructions of Coq proof assistant using assertional reasoning. Then, an extension of that algorithm turning it into fault-tolerant and adaptive to participants set change, is formalized in TLA and checked on a bounded model. Besides constructing and verifying the algorithm, this work aims to familiarize those interested in constructing highly reliable components with well established verification methods that were used to verify the proposed algorithm.
A high-throughput 16× super resolution processor for real-time object recognition SoC

High-resolution image offers more details compared to low-resolution image and consequently improves the accuracy of object recognition. However, higher resolution requires a costly hardware for large image sensor, or computation for additional signal processing. In this paper, we present a high-throughput super resolution processor for high-resolution object recognition. In order to perform super resolution with the real-time object recognition SoC, the algorithm-specific hardware is proposed with 2-D image cache and locality-sensitive hashing accelerator for high-throughput image fetching and searching. As a result, the proposed super resolution processor generates up to 16× higher resolution images with 3,125 fps throughput and 2.0 nJ/pixel energy efficiency, enabling high-resolution pre-processing for real-time object recognition.
Essays on regulatory risk issues

Most studies around that try to verify the existence of regulatory risk look mainly at developed countries. Looking at regulatory risk in emerging market regulated sectors is no less important to improving and increasing investment in those markets. In this study, I use data from Brazil one of the most important emerging markets and also one that has the most developed corporate governance rules. Using a two-step procedure, I estimate CAPM betas by using a Kalman filter in the first step and then use these betas as inputs in a Random-Effect panel data model, I find evidence of regulatory risk in electricity, telecommunications and all regulated sectors in Brazil. I find further evidence that regulatory changes in the country either do not reduce or increase the betas of the regulated sectors, going in the opposite direction to the buffering hypothesis as proposed by Peltzman (1976).
Simple parameterization of non‐proteinogenic amino acids for QSAR of antibacterial peptides

The antibacterial activity of bovine lactoferricin‐(17–31)‐pentadecapeptide against Escherichia coli and Staphylococcus aureus is sensitive to substitution of the Trp residues, and synthetic peptides with phenylalanine and any of eight non‐proteinogenic aromatic amino acids greatly affected antibiotic activity. Using simple size‐related descriptors for the new amino acids it is possible to develop quantitative structure–activity relationships (QSARs) that can be used as tools in the search for more active peptides. Copyright © 2002 European Peptide Society and John Wiley & Sons, Ltd.
Internet Voting: Will Australians Use the Internet to Vote?

The possibility of voting using the internet is a reality. Public elections are one arena where internet voting has the potential to make considerable cost savings if it is widely adopted by voters. This research considers the question of ‘What are the factors influencing the adoption of internet voting by eligible Australian voters? ’ by developing three competing models of behavioural intention based on a literature review, depth interviews and focus groups. These models are then tested with data gathered from a mail survey with responses from 172 eligible Australia voters. Results indicate that five key factors influence voters to use the internet: convenience, environment, utilitarian outcomes, security issues and level of knowledge. This research contributes to theory through development of the first models of behavioural intention regarding internet voting and in practical terms can be of use to electoral commissions and politicians for the development and implementation of internet voting strategies. ; ;
Secondary control in multi-terminal VSC-HVDC transmission system

The voltage droop control concept is the most appropriate strategy to provide primary control in multiterminal VSC-HVDC (MTDC) transmission systems. However, due to voltage drops in the dc lines/cables, the primary power balancing is influenced by the dc grid topology and line resistances. This phenomenon is also evident when determining the secondary control strategy in MTDC systems. In this paper, secondary control in MTDC is derived by analogy to the traditional secondary control in an ac grid system. In doing so, the influences of dc line voltage drops are systematically included in the control strategy to restore power flow to pre-disturbance levels at selected dc terminals. The effectiveness of the strategy is demonstrated with the help of a five terminal VSC-HVDC model in the EMTDC/PSCAD simulation tool.
Renal Morphology, Clinical Findings, and Progression Rate in Mesoamerican Nephropathy.

BACKGROUND Mesoamerican nephropathy (MeN) is a chronic kidney disease affecting rural inhabitants in Central America. We have previously described the renal morphology in 8 patients from El Salvador. To confirm the renal pathology, we have studied kidney biopsies from patients with MeN in Nicaragua. Follow-up urine and blood samples from both biopsy studies were collected to investigate the natural history. STUDY DESIGN Case series. SETTINGS & PARTICIPANTS In the kidney biopsy study, 19 male sugarcane workers in Nicaragua with suspected MeN were investigated with questionnaires, kidney biopsies, and blood and urine analysis. Inclusion criteria were age 20 to 65 years and plasma creatinine level of 1.13 to 2.49mg/dL or estimated glomerular filtration rate (eGFR) of 30 to 80mL/min/1.73m2. Exclusion criteria were proteinuria with protein excretion > 3g/24 h, uncontrolled hypertension, diabetes mellitus, or other known kidney disease. In the follow up-study, blood and urine from the kidney biopsy study in Nicaragua (n=18) and our previous biopsy study of MeN cases in El Salvador (n=7) were collected 1 to 1.5 and 2 to 2.5 years after biopsy, respectively. OUTCOMES Renal morphology, clinical, and biochemical characteristics, change in eGFR per year. MEASUREMENTS eGFR was calculated using the CKD-EPI creatinine (eGFRcr), cystatin C (eGFRcys), and creatinine-cystatin C (eGFRcr-cys) equations. RESULTS In the kidney biopsy study, participants had a mean eGFRcr of 57 (range, 33-96) mL/min/1.73m2. 47% had low plasma sodium and 21% had low plasma potassium levels. 16 kidney biopsies were representative and showed glomerulosclerosis (mean, 38%), glomerular hypertrophy, and signs of chronic glomerular ischemia. Mild to moderate tubulointerstitial damage and mostly mild vascular changes were seen. In the follow up-study, median duration of follow-up was 13 (range, 13-27) months. Mean change in eGFRcr was -4.4±8.4 (range, -27.7 to 10.2) mL/min/1.73m2 per year. Most patients had stopped working with sugarcane cultivation. LIMITATIONS 3 biopsy specimens had 4 or fewer glomeruli. CONCLUSIONS This study confirms the renal morphology of MeN: chronic glomerular and tubulointerstitial damage with glomerulosclerosis and chronic glomerular ischemia. Follow-up data show that eGFRs, on average, deteriorated.
Flexible cofacial binuclear metal complexes derived from alpha,alpha-bis(salicylimino)-m-xylene.

The tetradentate Schiff-base ligand SIXH2 (alpha,alpha-bis(salicylimino)-m-xylene), prepared from salicylaldehyde and m-xylylenediamine, forms cofacial binuclear complexes with Pd and Cu. Of the two isomers possible (trans-syn and trans-anti) for M2(SIX)2, these complexes crystallize exclusively as the trans-anti isomer. In ansolvous Pd2(SIX)2, the metal-containing planes are approximately parallel, with PdPd 4.416(1) A. Pd2(SIX)2 also forms a crystalline solvate, in which the molecules adopt a more open conformation with longer metal-metal distances (5.109(1) and 5.112(1) A). The M.M distance is significantly longer in Cu2(SIX)2 (6.653(1) A), because of conformational changes in the m-xylylene moieties and substantial tetrahedral distortion about Cu.
Infection of a Japanese Patient by Genotype 4 Hepatitis E Virus While Traveling in Vietnam

ABSTRACT Cases of imported hepatitis E in industrialized countries infected with a genotype 1 hepatitis E virus (HEV) have been identified. We report a 56-year-old Japanese man who acquired infection with a genotype 4 HEV with 98.8% identity to a Vietnamese isolate after ingestion of uncooked shellfish while traveling in Vietnam.
Inhibition of deubiquitinases primes glioblastoma cells to apoptosis in vitro and in vivo

It remains a challenge in oncology to identify novel drug regimens to efficiently tackle glioblastoma, the most common primary brain tumor in adults. Here, we target deubiquitinases for glioblastoma therapy by utilizing the small-molecule inhibitor WP1130 which has been characterized as a deubiquitinase inhibitor that interferes with the function of Usp9X. Expression analysis data confirm that Usp9X expression is increased in glioblastoma compared to normal brain tissue indicating its potential as a therapeutic. Consistently, increasing concentrations of WP1130 decrease the cellular viability of established, patient-derived xenograft (PDX) and stem cell-like glioblastoma cells. Specific down-regulation of Usp9X reduces viability in glioblastoma cells mimicking the effects of WP1130. Mechanistically, WP1130 elicits apoptosis and increases activation of caspases. Moreover, WP1130 and siRNAs targeting Usp9X reduce the expression of anti-apoptotic Bcl-2 family members and Inhibitor of Apoptosis Proteins, XIAP and Survivin. Pharmacological and genetic interference with Usp9X efficiently sensitized glioblastoma cells to intrinsic and extrinsic apoptotic stimuli. In addition, single treatment with WP1130 elicited anti-glioma activity in an orthotopic proneural murine model of glioblastoma. Finally, the combination treatment of WP1130 and ABT263 inhibited tumor growth more efficiently than each reagent by its own in vivo without detectable side effects or organ toxicity. Taken together, these results suggest that targeting deubiquitinases for glioma therapy is feasible and effective.