bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the applicability of urban canopy parametrization in building grey zone
Authors: Chen Song , Dipankar Anurag 
Published: March 2022

AbstractWith increasing interest in urban meteorology and related services, the need to appropriately represent the urban environment in climate/weather models is rising. These regional weather/climate models typically use a km‐scale horizontal grid, which is insufficient to resolve the flow around buildings. Effects of the urban environment on the atmosphere above are represented through a bulk approach using the Urban Canopy Parametrization (UCP) schemes. Existing UCPs usually use the repeating canyon–roof representation that assumes homogeneous distribution of buildings within the grid box. It is commonly accepted that the assumption of homogeneity holds at km‐scale grid resolution but whether it also holds at sub‐km scale, where the regional models are increasingly approaching, is questionable. For this reason, among others, the resolution ranges from a few hundred metres to tens of metres (i.e. building‐resolving scales) is termed the building grey zone in the existing literature. This work shows that the assumption of homogeneity indeed does not hold at the building grey zone for the city‐state Singapore. To understand the possible influences of the use of UCPs at scales from the building grey zone to the conventional mesoscale, we use an urban‐grid method that allows us to estimate the parametrized fluxes from a typical UCP at varying resolutions over the urban landcover while keeping the same atmospheric model grid. Numerical results show that different urban‐grid resolutions yield variations in the near‐surface temperature and wind to a maximum of 0.5 K and 1 m·s−1. Their impact on the boundary‐layer parameters is found to be limited. Although these near‐surface variations are small, they are comparable to the near‐surface scaling variables and are thus physically significant.
How innovating firms manage knowledge leakage: A natural experiment on the threat of worker departure
Authors: Kang Hyo , Lee Wyatt 
Published: March 2022

AbstractResearch SummaryKnowledge protection strategies are crucial to innovating firms facing the risk of knowledge leakage. We examine the threat of worker departure as a key mechanism through which firms choose between patents and secrecy. We exploit a 1998 California court decision that ruled out‐of‐state noncompetes were not enforceable in California, thereby creating a loophole limiting non‐California firms in their enforcement of noncompetes against their workers. When facing a higher threat of worker departure, firms strategically increased patent filings, exchanging legal protection for public disclosure of the invention. These effects were magnified for large‐sized firms and for those in complex and fast‐growing industries. Further mechanism tests on the possession of trade secrets, inventor migration, saliency of the decision, and independent inventors support our theoretical account.Managerial SummaryInnovating firms may use patents or secrecy, among other mechanisms, to protect their knowledge from leakage. How do firms make this important strategic choice? By using a natural experiment arising from a 1998 California court decision, we show the risk of worker departure can be a key driver. The decision significantly increased the risk of workers departing non‐California firms. Our findings show that, in response to the heightened risk, affected firms increasingly relied on patents, seeking legal protection although it meant public disclosure of the invention. The effects were greater for large‐sized firms and for those in complex and fast‐growing industries. We encourage managers to consider worker mobility and, more broadly, legal environments that govern labor market conditions when formulating knowledge protection strategies.
A Water in Oil Gelled Emulsion as a Topical Release Vehicle for Curcumin
Authors: Pérez‐Salas Juan Luis , Medina‐Torres Luis , Rocha‐Guzmán Nuria Elizabeth , Calderas F. , González‐Laredo Rubén Francisco , Bernad‐Bernad María Josefa , Moreno‐Jiménez Martha Rocío , Gallegos‐Infante José Alberto 
Published: March 2022

AbstractThe objective of this work is to assess the influence of the concentration of polyglycerol polyricinoleate (PGPR) (at 1%, 1.5%, and 2%) on the physical properties of water in oil gelled emulsions (W/O) and evaluates their efficiency as a delivery vehicle for curcumin. Emulsions are characterized by drop size, centrifugal test, texture, and rheology during 28 days of storage. When the surfactant concentration increases, smaller droplet sizes are obtained (<5 µm), the phase separation (tested by centrifugal force) decreases from 6% to 4% with little variation of the time. The mechanical properties of emulsions show a tendency to decrease as time passed and concentration of PGPR increased. The emulsions increased viscosity as the concentration increased, but the addition of curcumin reduce the viscosity of the emulsions. About controlled release profiles, a low concentration of PGPR shows an increase in the affinity between curcumin and the emulsions, following a pseudo‐Fickian release behavior. At higher concentration of PGPR shows a decrease in the affinity between curcumin and the emulsion, displaying a Fickian release behavior. The authors were able to prepare tailor made curcumin water in oil emulsion systems for the topical release of this compound.
Rational design of imine‐linked three‐dimensional mesoporous covalent organic frameworks with bor topology
Authors: Li Zonglong , Hsueh Chouhung , Tang Zhuozhuo , Chen Jia , Wang Xiaolin , Cui Hao , Yang Yang , Wang Xiaodan , Ren Dongsheng , Gao Hongqiang , Li Mingyang , Xu Hong , He Xiangming 
Published: March 2022

AbstractThree‐dimensional (3D) covalent organic frameworks (COFs) possess great potential applications in various fields. Constructing 3D COFs with large pore sizes is extremely challenging due to the interpenetration and collapse. Herein, we report a series of crystalline imine‐linked 3D COFs (3D‐bor‐COF‐1, 3D‐bor‐COF‐2, 3D‐bor‐COF‐3) with mesoporous channels through rationally designing the topology configuration. These 3D‐bor‐COFs display permanent porosity and Brunauer–Emmett–Teller (BET) surfaces of 3205.5, 1752.7, and 2077.3 m2 g−1 (SLangmuir = 4277.7, 2480.3, and 2698.0 m2 g−1), respectively. The pore sizes of 3D‐bor‐COFs were confirmed by the lattice fringes from high‐resolution transmission electron microscopy, as well as structural simulation and nitrogen adsorption isotherm analysis. 3D‐bor‐COFs display large pore sizes (3.8 nm for 3D‐bor‐COF‐3), which is among the highest record of 3D COFs. Owing to the unstacked‐aromatic pore environment and high specific surface area, 3D‐bor‐COFs display excellent adsorption capacity for benzene vapor (1203.9 mg g−1 for 3D‐bor‐COF‐3) under 298 K, which is three times higher than that of the best‐reported 2D COF. This work not only provides inspiration for designing 3D mesoporous imine‐COFs, but also demonstrates a strategy for constructing aromatics adsorption materials.
First-order separation over countable ordinals
Authors: Colcombet Thomas , van Gool Sam , Morvan Rémi 
Published: March 2022

AbstractWe show that the existence of a first-order formula separating two monadic second order formulas over countable ordinal words is decidable. This extends the work of Henckell and Almeida on finite words, and of Place and Zeitoun on $$\omega $$
ω
-words. For this, we develop the algebraic concept of monoid (resp. $$\omega $$
ω
-semigroup, resp. ordinal monoid) with aperiodic merge, an extension of monoids (resp. $$\omega $$
ω
-semigroup, resp. ordinal monoid) that explicitly includes a new operation capturing the loss of precision induced by first-order indistinguishability. We also show the computability of FO-pointlike sets, and the decidability of the covering problem for first-order logic on countable ordinal words.
Temporal Stream Logic modulo Theories
Authors: Finkbeiner Bernd , Heim Philippe , Passing Noemi 
Published: March 2022

AbstractTemporal stream logic (TSL) extends LTL with updates and predicates over arbitrary function terms. This allows for specifying data-intensive systems for which LTL is not expressive enough. In the semantics of TSL, functions and predicates are left uninterpreted. In this paper, we extend TSL with first-order theories, enabling us to specify systems using interpreted functions and predicates such as incrementation or equality. We investigate the satisfiability problem of TSL modulo the standard underlying theory of uninterpreted functions as well as with respect to Presburger arithmetic and the theory of equality: For all three theories, TSL satisfiability is neither semi-decidable nor co-semi-decidable. Nevertheless, we identify three fragments of TSL for which the satisfiability problem is (semi-)decidable in the theory of uninterpreted functions. Despite the undecidability, we present an algorithm – which is not guaranteed to terminate – for checking the satisfiability of a TSL formula in the theory of uninterpreted functions and evaluate it: It scales well and is able to validate assumptions in a real-world system design.
Limits and difficulties in the design of under-approximation abstract domains
Authors: Ascari Flavio , Bruni Roberto , Gori Roberta 
Published: March 2022

AbstractStatic analyses are mostly designed to show the absence of bugs: if the analysis reports no alarms then the program won’t exhibit any unwanted behaviours. To this aim they manipulate over-approximations of program semantics and, inevitably, they often report some false alarms. Recently, O’Hearn proposed Incorrectness Logic, that is based on under-approximations, as a formal method to find bugs that only reports true alarms. In this paper we aim to answer one important question raised by O’Hearn, namely which role can Abstract Interpretation play for the development of under-approximate tools for bug catching. In principle, Abstract Interpretation based static analyses can be defined for computing over-approximations as well as under-approximations, but in practice, most techniques exploited the former while few attempts developed the latter. To show why it is difficult to design effective under-approximation abstract domains, we first propose the new definitions of non emptying functions and highly surjective function family and then we formally prove the limits of under-approximation analysis by showing the non existence of abstract domains able to approximate such functions in a non trivial way. Our results outline the limits of under-approximation Abstract Interpretation and clarify, for the first time, why over- and under- approximation analyzers exhibited such a different development.
Polarized Subtyping
Authors: Lakhani Zeeshan , Das Ankush , DeYoung Henry , Mordido Andreia , Pfenning Frank 
Published: March 2022

AbstractPolarization of types in call-by-push-value naturally leads to the separation of inductively defined observable values (classified by positive types), and coinductively defined computations (classified by negative types), with adjoint modalities mediating between them. Taking this separation as a starting point, we develop a semantic characterization of typing with step indexing to capture observation depth of recursive computations. This semantics justifies a rich set of subtyping rules for an equirecursive variant of call-by-push-value, including variant and lazy records. We further present a bidirectional syntactic typing system for both values and computations that elegantly and pragmatically circumvents difficulties of type inference in the presence of width and depth subtyping for variant and lazy records. We demonstrate the flexibility of our system by systematically deriving related systems of subtyping for (a) isorecursive types, (b) call-by-name, and (c) call-by-value, all using a structural rather than a nominal interpretation of types.
Foundations for Entailment Checking in Quantitative Separation Logic
Authors: Batz Kevin , Fesefeldt Ira , Jansen Marvin , Katoen Joost-Pieter , Keßler Florian , Matheja Christoph , Noll Thomas 
Published: March 2022

AbstractQuantitative separation logic () is an extension of separation logic () for the verification of probabilistic pointer programs. In , formulae evaluate to real numbers instead of truth values, e.g., the probability of memory-safe termination in a given symbolic heap. As with , one of the key problems when reasoning with is entailment: does a formula f entail another formula g?We give a generic reduction from entailment checking in to entailment checking in . This allows to leverage the large body of research for the automated verification of probabilistic pointer programs. We analyze the complexity of our approach and demonstrate its applicability. In particular, we obtain the first decidability results for the verification of such programs by applying our reduction to a quantitative extension of the well-known symbolic-heap fragment of separation logic.
Extracting total Amb programs from proofs
Authors: Berger Ulrich , Tsuiki Hideki 
Published: March 2022

AbstractWe present a logical system CFP (Concurrent Fixed Point Logic) that supports the extraction of nondeterministic and concurrent programs that are provably total and correct. CFP is an intuitionistic first-order logic with inductive and coinductive definitions extended by two propositional operators, $$B|_{A}$$

B
|

A

(restriction, a strengthening of implication) and $${\mathbf {\downdownarrows }}(B)$$

⇊
(
B
)

(total concurrency). The source of the extraction are formal CFP proofs, the target is a lambda calculus with constructors and recursion extended by a constructor Amb (for McCarthy’s amb) which is interpreted operationally as globally angelic choice and is used to implement nondeterminism and concurrency. The correctness of extracted programs is proven via an intermediate domain-theoretic denotational semantics. We demonstrate the usefulness of our system by extracting a nondeterministic program that translates infinite Gray code into the signed digit representation. A noteworthy feature of our system is that the proof rules for restriction and concurrency involve variants of the classical law of excluded middle that would not be interpretable computationally without Amb.
Why3-do: The Way of Harmonious Distributed System Proofs
Authors: Lourenço Cláudio Belo , Pinto Jorge Sousa 
Published: March 2022

AbstractWe study principles and models for reasoning inductively about properties of distributed systems, based on programmed atomic handlers equipped with contracts. We present the Why3-do library, leveraging a state of the art software verifier for reasoning about distributed systems based on our models. A number of examples involving invariants containing existential and nested quantifiers (including Dijsktra’s self-stabilizing systems) illustrate how the library promotes contract-based modular development, abstraction barriers, and automated proofs.
Semantic Code Search in Software Repositories using Neural Machine Translation
Authors: Papathomas Evangelos , Diamantopoulos Themistoklis , Symeonidis Andreas 
Published: March 2022

AbstractNowadays, software development is accelerated through the reuse of code snippets found online in question-answering platforms and software repositories. In order to be efficient, this process requires forming an appropriate query and identifying the most suitable code snippet, which can sometimes be challenging and particularly time-consuming. Over the last years, several code recommendation systems have been developed to offer a solution to this problem. Nevertheless, most of them recommend API calls or sequences instead of reusable code snippets. Furthermore, they do not employ architectures advanced enough to exploit the semantics of natural language and code in order to form the optimal query from the question posed. To overcome these issues, we propose CodeTransformer, a code recommendation system that provides useful, reusable code snippets extracted from open-source GitHub repositories. By employing a neural network architecture that comprises advanced attention mechanisms, our system effectively understands and models natural language queries and code snippets in a joint vector space. Upon evaluating CodeTransformer quantitatively against a similar system and qualitatively using a dataset from Stack Overflow, we conclude that our approach can recommend useful and reusable snippets to developers.
Alternative formulations of the twistor double copy
Authors: Chacón Erick , Nagy Silvia , White Chris D. 
Published: March 2022

Abstract
The classical double copy relating exact solutions of biadjoint scalar, gauge and gravity theories continues to receive widespread attention. Recently, a derivation of the exact classical double copy was presented, using ideas from twistor theory, in which spacetime fields are mapped to Cech cohomology classes in twistor space. A puzzle remains, however, in how to interpret the twistor double copy, in that it relies on somehow picking special representatives of each cohomology class. In this paper, we provide two alternative formulations of the twistor double copy using the more widely-used language of Dolbeault cohomology. The first amounts to a rewriting of the Cech approach, whereas the second uses known techniques for discussing spacetime fields in Euclidean signature. The latter approach indeed allows us to identify special cohomology representatives, suggesting that further application of twistor methods in exploring the remit of the double copy may be fruitful.
On the complete metrisability of spaces of contractive semigroups
Authors: Dahya Raj 
Published: March 2022

AbstractThe space of unitary$$C_{0}$$C0-semigroups on a separable infinite-dimensional Hilbert space, when viewed under the topology of uniform weak operator convergence on compact subsets of$${\mathbb {R}}_{+}$$R+, is known to admit various interesting residual subspaces. Before treating the contractive case, the problem of the complete metrisability of this space was raised in [4]. Utilising Borel complexity computations and automatic continuity results for semigroups, we obtain a general result, which in particular implies that the one-/multiparameter contractive$$C_{0}$$C0-semigroups constitute Polish spaces and thus positively addresses the open problem.
Essential role of a conserved aspartate for the enzymatic activity of plasmanylethanolamine desaturase
Authors: Werner Ernst R. , Fernández-Quintero Monica L. , Hulo Nicolas , Golderer Georg , Sailer Sabrina , Lackner Katharina , Werner-Felmayer Gabriele , Liedl Klaus R. , Watschinger Katrin 
Published: March 2022

AbstractPlasmalogens are an abundant class of glycerophospholipids in the mammalian body, with special occurrence in the brain and in immune cell membranes. Plasmanylethanolamine desaturase (PEDS1) is the final enzyme of plasmalogen biosynthesis, which introduces the characteristic 1-O-alk-1′-enyl double bond. The recent sequence identification of PEDS1 as transmembrane protein 189 showed that its protein sequence is related to a special class of plant desaturases (FAD4), with whom it shares a motif of 8 conserved histidines, which are essential for the enzymatic activity. In the present work, we wanted to gain more insight into the sequence–function relationship of this enzyme and mutated to alanine additional 28 amino acid residues of murine plasmanylethanolamine desaturase including those 20 residues, which are also totally conserved—in addition to the eight-histidine-motif—among the animal PEDS1 and plant FAD4 plant desaturases. We measured the enzymatic activity by transient transfection of tagged murine PEDS1 expression clones to a PEDS1-deficient human HAP1 cell line by monitoring of labeled plasmalogens formed from supplemented 1-O-pyrenedecyl-sn-glycerol in relation to recombinant protein expression. Surprisingly, only a single mutation, namely aspartate 100, led to a total loss of PEDS1 activity. The second strongest impact on enzymatic activity had mutation of phenylalanine 118, leaving only 6% residual activity. A structural model obtained by homology modelling to available structures of stearoyl-CoA reductase predicted that this aspartate 100 residue interacts with histidine 96, and phenylalanine 118 interacts with histidine 187, both being essential histidines assumed to be involved in the coordination of the di-metal center of the enzyme.
Homogenization of the Full Compressible Navier-Stokes-Fourier System in Randomly Perforated Domains
Authors: Oschmann Florian 
Published: March 2022

AbstractWe consider the homogenization of the compressible Navier-Stokes-Fourier equations in a randomly perforated domain in $${\mathbb {R}}^3$$

R

3

. Assuming that the particle size scales like $$\varepsilon ^\alpha $$

ε
α

, where $$\varepsilon >0$$

ε
>
0

is their mutual distance and $$\alpha >3$$

α
>
3

, we show that in the limit $$\varepsilon \rightarrow 0$$

ε
→
0

, the velocity, density, and temperature converge to a solution of the same system. We follow the methods of Lu and Pokorný [https://doi.org/10.1016/j.jde.2020.10.032] and Pokorný and Skříšovský [https://doi.org/10.1007/s41808-021-00124-x] where they considered the full system in periodically perforated domains.
Highly mercury-resistant strains from different Colombian Amazon ecosystems affected by artisanal gold mining activities
Authors: Cardona Gladys Inés , Escobar María Camila , Acosta-González Alejandro , Marín Patricia , Marqués Silvia 
Published: March 2022

Abstract
Two sites of the Colombian Amazon region with different levels of human intervention and mercury pollution were selected for the collection of samples of river and lake water, sediments, and associated forest soils. The Tarapacá region, affected mainly by barrage mining, showed low mercury concentrations, whilst in the Taraira region, affected by underground mining, there were several points with high mercury pollution levels. A collection of 72 bacterial and 10 yeast strains with different levels of mercury resistance was isolated and characterized. Most of the highly resistant bacterial strains (MIC > 40 mg L−1 HgCl2) were isolated from soil and sediment samples and belonged to either Pseudomonas (60%) or Bacillus (20%). Most of highly resistant bacterial strains were positive for the presence of the merA gene, suggesting an active mercury resistance mechanism. This was confirmed in the two most resistant strains, Pseudomonas sp. TP30 and Burkholderia contaminans TR100 (MIC = 64 and 71 mg L−1 HgCl2, respectively), which in the presence of increasing mercury concentrations expressed the merA gene at increasing levels, concomitant with a significant mercury reduction activity. Analysis of the MerA sequences present in the different isolates suggested a high gene conservation within the taxonomic groups but also several horizontal gene transfer events between taxonomically distant genera. We also observed a positive correspondence between the presence of the merA gene and the number of antibiotics to which the strains were resistant to. The most resistant strains are good candidates for future applications in the bioremediation of mercury-contaminated sites in the Amazon.Key points• Amazon sediments affected by underground gold mining have higher Hg levels.• Highly Hg-resistant isolates belonged to Pseudomonas and Bacillus genera.• TR100 and TP30 strains showed remediation potential to be used in the Amazon region.
Graphical abstract