Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Bariatric Weight Loss on the Adipose Lipolytic Transcriptome in Obese Humans

Background. Dysregulated lipolysis has been implicated in mechanisms of cardiometabolic disease and inflammation in obesity. Purpose. We sought to examine the effect of bariatric weight loss on adipose tissue lipolytic gene expression and their relationship to systemic metabolic parameters in obese subjects. Methods/Results. We biopsied subcutaneous adipose tissue in 19 obese individuals (BMI 42 ± 5 kg/m2, 79% female) at baseline and after a mean period of 8 ± 5 months (range 3–15 months) following bariatric surgery. We performed adipose tissue mRNA expression of proteins involved in triglyceride hydrolysis and correlated their weight loss induced alterations with systemic parameters associated with cardiovascular disease risk. mRNA transcripts of adipose triglyceride lipase (ATGL), hormone-sensitive lipase (HSL), and lipid droplet proteins comparative gene identification 58 (CGI-58) and perilipin increased significantly after weight loss (p < 0.05 for all). ATGL expression correlated inversely with plasma triglyceride (TG), hemoglobin A1C (HbA1C), and glucose, and HSL expression correlated negatively with glucose, while CGI-58 was inversely associated with HbA1C. Conclusion. We observed increased expression of adipose tissue lipolytic genes following bariatric weight loss which correlated inversely with systemic markers of lipid and glucose metabolism. Functional alterations in lipolysis in human adipose tissue may play a role in shaping cardiometabolic phenotypes in human obesity.
Managing Distributed Innovation: Strategic Utilization of Open and User Innovation

Research from a variety of perspectives has argued that innovation no longer takes place within a single organization, but rather is distributed across multiple stakeholders in a value network. Here we contrast the vertically integrated innovation model to open innovation, user innovation, as well as other distributed processes (cumulative innovation, communities or social production, and co‐creation), while we also discuss open source software and crowdsourcing as applications of the perspectives. We consider differences in the nature of distributed innovation, as well as its origins and its effects. From this, we contrast the predictions of the perspectives on the sources, motivation and value appropriation of external innovation, and thereby provide a framework for the strategic management of distributed innovation.
Population dynamics of defensive symbionts in aphids

Vertically transmitted micro-organisms can increase in frequency in host populations by providing net benefits to hosts. While laboratory studies have identified diverse beneficial effects conferred by inherited symbionts of insects, they have not explicitly examined the population dynamics of mutualist symbiont infection within populations. In the pea aphid, Acyrthosiphon pisum, the inherited facultative symbiont, Hamiltonella defensa, provides protection against parasitism by the wasp, Aphidius ervi. Despite a high fidelity of vertical transmission and direct benefits of infection accruing to parasitized aphids, Hamiltonella remains only at intermediate frequencies in natural populations. Here, we conducted population cage experiments to monitor the dynamics of Hamiltonella and of another common A. pisum symbiont, Serratia symbiotica, in the presence and absence of parasitism. We also conducted fitness assays of Hamiltonella-infected aphids to search for costs to infection in the absence of parasitism. In the population cages, we found that the frequency of A. pisum infected with Hamiltonella increased dramatically after repeated exposure to parasitism by A. ervi, indicating that selection pressures from natural enemies can lead to the increase of particular inherited symbionts in insect populations. In our laboratory fitness assays, we did not detect a cost to infection with Hamiltonella, but in the population cages not exposed to parasitism, we found a significant decline in the frequency of both Hamiltonella and Serratia. The declining frequencies of Hamiltonella-infected aphids in population cages in the absence of parasitism indicate a probable cost to infection and may explain why Hamiltonella remains at intermediate frequencies in natural populations.
A weak definition of Delaunay triangulation

We show that the traditional criterion for a simplex to belong to the Delaunay triangulation of a point set is equivalent to a criterion which is a priori weaker. The argument is quite general; as well as the classical Euclidean case, it applies to hyperbolic and hemispherical geometries and to Edelsbrunner's weighted Delaunay triangulation. In spherical geometry, we establish a similar theorem under a genericity condition. The weak definition finds natural application in the problem of approximating a point-cloud data set with a simplical complex.
On some interrelations of generalized $q$-entropies and a generalized Fisher information, including a Cramér-Rao inequality

In this communication, we describe some interrelations between generalized $q$-entropies and a generalized version of Fisher information. In information theory, the de Bruijn identity links the Fisher information and the derivative of the entropy. We show that this identity can be extended to generalized versions of entropy and Fisher information. More precisely, a generalized Fisher information naturally pops up in the expression of the derivative of the Tsallis entropy. This generalized Fisher information also appears as a special case of a generalized Fisher information for estimation problems. Indeed, we derive here a new Cram\'er-Rao inequality for the estimation of a parameter, which involves a generalized form of Fisher information. This generalized Fisher information reduces to the standard Fisher information as a particular case. In the case of a translation parameter, the general Cram\'er-Rao inequality leads to an inequality for distributions which is saturated by generalized $q$-Gaussian distributions. These generalized $q$-Gaussians are important in several areas of physics and mathematics. They are known to maximize the $q$-entropies subject to a moment constraint. The Cram\'er-Rao inequality shows that the generalized $q$-Gaussians also minimize the generalized Fisher information among distributions with a fixed moment. Similarly, the generalized $q$-Gaussians also minimize the generalized Fisher information among distributions with a given $q$-entropy.
Molecular and Cellular Networks in The Suprachiasmatic Nuclei

Why do we experience the ailments of jetlag when we travel across time zones? Why is working night-shifts so detrimental to our health? In other words, why can’t we readily choose and stick to non-24 h rhythms? Actually, our daily behavior and physiology do not simply result from the passive reaction of our organism to the external cycle of days and nights. Instead, an internal clock drives the variations in our bodily functions with a period close to 24 h, which is supposed to enhance fitness to regular and predictable changes of our natural environment. This so-called circadian clock relies on a molecular mechanism that generates rhythmicity in virtually all of our cells. However, the robustness of the circadian clock and its resilience to phase shifts emerge from the interaction between cell-autonomous oscillators within the suprachiasmatic nuclei (SCN) of the hypothalamus. Thus, managing jetlag and other circadian disorders will undoubtedly require extensive knowledge of the functional organization of SCN cell networks. Here, we review the molecular and cellular principles of circadian timekeeping, and their integration in the multi-cellular complexity of the SCN. We propose that new, in vivo imaging techniques now enable to address these questions directly in freely moving animals.
Biochar for environmental management: an introduction

biochar is the carbon-rich product obtained when biomass, such as wood, manure or leaves, is heated in a closed container with little or no available air. In more technical terms, biochar is produced by so-called thermal decomposition of organic material under limited supply of oxygen (O 2), and at relatively low temperatures (<700°C). This process often mirrors the production of charcoal, which is one of the most ancient industrial technologies developed by mankind – if not the oldest (Harris, 1999). However, it distinguishes itself from charcoal and similar materials that are discussed below by the fact that biochar is produced with the intent to be applied to soil as a means of improving soil productivity, carbon (C) storage, or filtration of percolating soil water. The production process, together with the intended use, typically forms the basis for its classification and naming convention, which is discussed in the next section. In contrast to the organic C-rich biochar, burning biomass in a fire creates ash, which mainly contains minerals such as calcium (Ca) or magnesium (Mg) and inorganic carbonates. Also, in most fires, a small portion of the vegetation is only partially burned in areas of limited O 2 supply, with a portion remaining as char (Kuhlbusch and Crutzen, 1995). The question as to what biochar actually is from a chemical point of view rather than from a production point of view is much more difficult to answer due to the wide variety of biomass and charring conditions used. The defining property is that the organic portion of biochar has a high C content, which mainly comprises so-called aromatic compounds characterized by rings of six C atoms linked together without O or hydrogen (H), the otherwise more abundant atoms in living organic matter. If these aromatic rings were arranged in perfectly stacked and aligned sheets, this substance would be called graphite. Under temperatures that are used for making biochar, graphite does not form to any significant extent. Instead, much more What is biochar?
On delay and regret determinization of max-plus automata

Decidability of the determinization problem for weighted automata over the semiring (ℤ∪{−∞}, max; +), WA for short, is a long-standing open question. We propose two ways of approaching it by constraining the search space of deterministic WA: k-delay and r-regret. A WA N is k-delay determinizable if there exists a deterministic automaton D that defines the same function as N and for all words α in the language of N, the accepting run of D on α is always at most k-away from a maximal accepting run of N on α. That is, along all prefixes of the same length, the absolute difference between the running sums of weights of the two runs is at most k. A WA N is r-regret determinizable if for all words α in its language, its non-determinism can be resolved on the fly to construct a run of N such that the absolute difference between its value and the value assigned to α by N is at most r. We show that a WA is determinizable if and only if it is k-delay determinizable for some k. Hence deciding the existence of some k is as difficult as the general determinization problem. When k and r are given as input, the k-delay and r-regret determinization problems are shown to be EXPTIME-complete. We also show that determining whether a WA is r-regret determinizable for some r is in EXPTIME.
1 Executive summary

This seminar report documents the program and the outcomes of Dagstuhl Seminar 19421 Quantum Cryptanalysis, which took place in October 2019. After outlining the motivation and organizational aspects of this particular seminar, abstracts of presentations that were given by participants are provided. Seminar October 13–18, 2019 – http://www.dagstuhl. de/19421 2012 ACM Subject Classification Hardware → Quantum technologies, Security and privacy → Cryptanalysis and other attacks, Theory of computation → Computational complexity and cryptography
Can geographic routing scale when nodes are mobile?

We begin by asking whether geographic routing can scale when nodes are mobile; that is, can the overhead involved in tracking node locations be accommodated within the transport capacity of large-scale mobile ad hoc networks (MANETs)? We answer this question in the affirmative by proposing an efficient position publish protocol which fits within the transport capacity and a routing protocol that operates with imperfect information of the destination's location. The routing protocol guarantees, with high probability, routes whose lengths are within a constant “stretch” factor of the shortest path from source to destination. The key idea underlying the scalability of the publish protocol is for each potential destination node to send location updates (with frequency decaying with distance) only to a subset of network nodes, structured as annular regions around it (the natural approach of updating circular regions in distance-dependent fashion does not scale). The routing protocol must then account for the fact that the source and/or relay nodes may not have estimates of the destination's location (or may have stale estimates). Spatial and temporal scaling of protocol parameters are chosen so as to guarantee scalability, route reliability and route stretch.
Phylogenetic and Geographic Variation in Host Breadth and Composition by Herbivorous Amphipods in the Family Ampithoidae

Abstract Predicting the host range for herbivores has been a major aim of research into plant–herbivore interactions and an important model system for understanding the evolution of feeding specialization. Among many terrestrial insects, host range is strongly affected by herbivore phylogeny and long historical associations between particular herbivore and plant taxa. For small herbivores in marine environments, it is known that the evolution of host use is sculpted by several ecological factors (e.g., food quality, value as a refuge from predators, and abiotic forces), but the potential for phylogenetic constraints on host use remains largely unexplored. Here, we analyze reports of host use of herbivorous amphipods from the family Ampithoidae (102 amphipod species from 12 genera) to test the hypotheses that host breadth and composition vary among herbivore lineages, and to quantify the extent to which nonpolar secondary metabolites mediate these patterns. The family as a whole, and most individual species, are found on a wide variety of macroalgae and seagrasses. Despite this polyphagous host use, amphipod genera consistently differed in host range and composition. As an example, the genus Peramphithoe rarely use available macrophytes in the order Dictyotales (e.g., Dictyota) and as a consequence, display a more restricted host range than do other genera (e.g., Ampithoe, Cymadusa, or Exampithoe). The strong phylogenetic effect on host use was independent of the uneven distribution of host taxa among geographic regions. Algae that produced nonpolar secondary metabolites were colonized by higher numbers of amphipod species relative to chemically poor genera, consistent with the notion that secondary metabolites do not provide algae an escape from amphipod herbivory. In contrast to patterns described for some groups of phytophagous insects, marine amphipods that use chemically rich algae tended to have broader, not narrower, host ranges. This result suggests that an evolutionary advantage to metabolite tolerance in marine amphipods may be that it increases the availability of appropriate algal hosts (i.e., enlarges the resource base).
The Impact of Age on Long-Term Quality of Life After Endonasal Endoscopic Resection of Skull Base Meningiomas.

BACKGROUND Midline ventral skull base meningiomas may be amenable to an endonasal endoscopic approach, which has theoretical advantages and may help preserve quality of life (QOL) when compared with transcranial approaches. OBJECTIVE To investigate the effect of age on QOL following endonasal endoscopic surgery, given the documented impact of age on QOL outcomes following transcranial resection of midline ventral skull base meningiomas. METHODS We reviewed a prospectively acquired database of endonasal endoscopic surgery for meningiomas. Inclusion criteria included patients who had completed long-term postoperative (≥6 months follow-up) QOL questionnaires (Anterior Skull Base Questionnaire [ASBQ] and Sino-Nasal Outcome Test [SNOT-22]). Postoperative QOL scores were also compared with preoperative QOL in a patient subset. RESULTS Long-term QOL data were available in 34 patients. Average postoperative ASBQ and SNOT-22 scores were 3.39 and 23.0, respectively. Better QOL was statistically associated with age <55 (P = .02). In a subset of patients, preoperative and postoperative ASBQ and SNOT-22 scores were compared. Only SNOT-22 scores significantly increased from 15.9 + 20.8 to 25.9 + 19.5 (P = .04). CONCLUSION We report the first study specifically evaluating long-term QOL after endonasal endoscopic resection of skull base meningiomas. QOL was decreased postoperatively in patients aged ≥55. ABBREVIATIONS ASBQ, Anterior Skull Base QuestionnaireGTR, gross total resectionQOL, quality of lifeSNOT-22, 22-item Sino-Nasal Outcome Test.
A Unique Set of the Burkholderia Collagen-Like Proteins Provides Insight into Pathogenesis, Genome Evolution and Niche Adaptation, and Infection Detection

Burkholderia pseudomallei and Burkholderia mallei, classified as category B priority pathogens, are significant human and animal pathogens that are highly infectious and broad-spectrum antibiotic resistant. Currently, the pathogenicity mechanisms utilized by Burkholderia are not fully understood, and correct diagnosis of B. pseudomallei and B. mallei infection remains a challenge due to limited detection methods. Here, we provide a comprehensive analysis of a set of 13 novel Burkholderia collagen-like proteins (Bucl) that were identified among B. pseudomallei and B. mallei select agents. We infer that several Bucl proteins participate in pathogenesis based on their noncollagenous domains that are associated with the components of a type III secretion apparatus and membrane transport systems. Homology modeling of the outer membrane efflux domain of Bucl8 points to a role in multi-drug resistance. We determined that bucl genes are widespread in B. pseudomallei and B. mallei; Fischer’s exact test and Cramer’s V2 values indicate that the majority of bucl genes are highly associated with these pathogenic species versus nonpathogenic B. thailandensis. We designed a bucl-based quantitative PCR assay which was able to detect B. pseudomallei infection in a mouse with a detection limit of 50 CFU. Finally, chromosomal mapping and phylogenetic analysis of bucl loci revealed considerable genomic plasticity and adaptation of Burkholderia spp. to host and environmental niches. In this study, we identified a large set of phylogenetically unrelated bucl genes commonly found in Burkholderia select agents, encoding predicted pathogenicity factors, detection targets, and vaccine candidates.
The Relationship between Water, Sanitation and Schistosomiasis: A Systematic Review and Meta-analysis

Background Access to “safe” water and “adequate” sanitation are emphasized as important measures for schistosomiasis control. Indeed, the schistosomes' lifecycles suggest that their transmission may be reduced through safe water and adequate sanitation. However, the evidence has not previously been compiled in a systematic review. Methodology We carried out a systematic review and meta-analysis of studies reporting schistosome infection rates in people who do or do not have access to safe water and adequate sanitation. PubMed, Web of Science, Embase, and the Cochrane Library were searched from inception to 31 December 2013, without restrictions on year of publication or language. Studies' titles and abstracts were screened by two independent assessors. Papers deemed of interest were read in full and appropriate studies included in the meta-analysis. Publication bias was assessed through the visual inspection of funnel plots and through Egger's test. Heterogeneity of datasets within the meta-analysis was quantified using Higgins' I2. Principal Findings Safe water supplies were associated with significantly lower odds of schistosomiasis (odds ratio (OR) = 0.53, 95% confidence interval (CI): 0.47–0.61). Adequate sanitation was associated with lower odds of Schistosoma mansoni, (OR = 0.59, 95% CI: 0.47–0.73) and Schistosoma haematobium (OR = 0.69, 95% CI: 0.57–0.84). Included studies were mainly cross-sectional and quality was largely poor. Conclusions/Significance Our systematic review and meta-analysis suggests that increasing access to safe water and adequate sanitation are important measures to reduce the odds of schistosome infection. However, most of the studies were observational and quality was poor. Hence, there is a pressing need for adequately powered cluster randomized trials comparing schistosome infection risk with access to safe water and adequate sanitation, more studies which rigorously define water and sanitation, and new research on the relationships between water, sanitation, hygiene, human behavior, and schistosome transmission.
Microtubule nucleation during central spindle assembly requires NEDD1 phosphorylation on serine 405 by Aurora A

ABSTRACT During mitosis, the cell sequentially constructs two microtubule-based spindles to ensure faithful segregation of chromosomes. A bipolar spindle first pulls apart the sister chromatids, then a central spindle further separates them away. Although the assembly of the first spindle is well described, the assembly of the second remains poorly understood. We report here that the inhibition of Aurora A leads to an absence of the central spindle resulting from a lack of nucleation of microtubules in the midzone. In the absence of Aurora A, the HURP (also known as DLGAP5) and NEDD1 proteins that are involved in nucleation of microtubules fail to concentrate in the midzone. HURP is an effector of RanGTP, whereas NEDD1 serves as an anchor for the γ-tubulin ring complex (γTURC). Interestingly, Aurora A phosphorylates HURP and NEDD1 during assembly of the initial bipolar spindle. We show here that the expression of a NEDD1 isoform mimicking phosphorylation by Aurora A is sufficient to restore microtubule nucleation in the midzone under conditions of Aurora A inhibition. These results reveal a new control mechanism of microtubule nucleation by Aurora A during assembly of the central spindle. Summary: Midzone localization of γ-TuRC-anchoring protein NEDD1 in anaphase results from phosphorylation at serine 405 by Aurora A, regulating microtubule nucleation during central spindle assembly.
Understanding the Effects of Polar Mesospheric Clouds on the Environment of the Upper Mesosphere and Lower Thermosphere

This study focuses on the effects of polar mesospheric cloud (PMC) formation on the chemical environment of the mesosphere and lower thermosphere. Of specific interest is how the dehydration due to mesospheric ice particle formation leads to significant seasonal decreases in the atomic hydrogen near the mesopause at middle to high latitudes. Using a three‐dimensional whole atmosphere coupled chemistry/dynamics model, we simulate the effects of this dehydration, and via comparisons with three data sets taken from two NASA satellites, we quantify the perturbations to atomic hydrogen and water vapor. We also identify a local ozone maximum that results from the PMC‐induced decrease in atomic hydrogen. Further, the large interannual variability in the onset of the Southern Hemisphere PMC season correlates well with the interannual variability of early summer atomic hydrogen at 95 km. Since the PMC onset is known to be controlled by interannual variations in the Southern Hemisphere stratospheric polar vortex, this correlation indicates a coupling between the stratosphere and the chemistry of the mesosphere and lower thermosphere. Finally, our model results suggest that the seasonal biteout in atomic hydrogen propagates up into the thermosphere and to lower latitudes. This raises the intriguing possibility that PMC formation might play a role in modulating the escape of hydrogen from the atmosphere.