bluuebunny/crossref_metadata_2025_split huggingface dataset:
Common and dissociable effects of oxytocin and lorazepam on the neurocircuitry of fear
Authors: Kreuder Ann-Kathrin , Scheele Dirk , Schultz Johannes , Hennig Juergen , Marsh Nina , Dellert Torge , Ettinger Ulrich , Philipsen Alexandra , Babasiz Mari , Herscheid Angela , Remmersmann Laura , Stirnberg Ruediger , Stöcker Tony , Hurlemann René 
Published: May 2020

Significance
A potential new target for anxiolytic drug development is the oxytocin (OXT) neuropeptide system. An emerging question is whether OXT has similar effects on the neural microcircuitry of fear compared with clinically established compounds such as benzodiazepines. The present functional MRI study showed that both OXT and its benzodiazepine comparator lorazepam (LZP) reduced centromedial amygdala responses to fear signals. OXT, but not LZP, increased extra-amygdalar connectivity between the centromedial amygdala and frontoparietal regions. Thus, while both compounds inhibited the centromedial amygdala, OXT, but not LZP, elicited large-scale connectivity changes of potential therapeutic relevance.
Improvement in municipal wastewater treatment alters lake nitrogen to phosphorus ratios in populated regions
Authors: Tong Yindong , Wang Mengzhu , Peñuelas Josep , Liu Xueyan , Paerl Hans W. , Elser James J. , Sardans Jordi , Couture Raoul-Marie , Larssen Thorjørn , Hu Hongying , Dong Xin , He Wei , Zhang Wei , Wang Xuejun , Zhang Yang , Liu Yi , Zeng Siyu , Kong Xiangzhen , Janssen Annette B. G. , Lin Yan 
Published: May 2020

Significance
Due to different rates of change in total nitrogen (TN) and total phosphorus (TP) concentrations in lakes, increases in TN/TP mass ratios were observed in many China’s freshwater lakes during 2008 to 2017. This growing imbalance has important implications for aquatic ecology that remain poorly considered and understood. Here, we show that changes in municipal wastewater treatment are a major driver for increases in lake TN/TP mass ratios, as phosphorus is more effectively removed than nitrogen from wastewater. Our findings highlight the need for more efficient nitrogen reduction in addition to phosphorus reduction in wastewater treatment to reduce risk for phytoplankton blooms and toxin production and to maintain ecosystem biodiversity in downstream waterbodies.
Dynamics in a simple evolutionary-epidemiological model for the evolution of an initial asymptomatic infection stage
Authors: Saad-Roy Chadi M. , Wingreen Ned S. , Levin Simon A. , Grenfell Bryan T. 
Published: May 2020

SignificanceNumerous factors affect early transmission by a newly infected host. A less symptomatic initial infection can persist longer due to reduced immune response, but at the cost of reduced transmission. Assuming simple trade-offs for progression and transmission rates in the initial infectious stage, we couple epidemiological and evolutionary dynamics. We find that fully asymptomatic, less symptomatic, or fully symptomatic first stages are possible evolutionary outcomes, with possible surprising bistability between zero and maximal asymptomatic behavior. This bistability implies that small changes in parameter values followed by reversion to their original values could lead to an alternative stable state with a qualitative difference in degree of first-stage symptoms. Therefore, disease control strategies can have dramatic evolutionary outcomes, cascading to epidemiological consequences.
Statistical reprogramming of macroscopic self-assembly with dynamic boundaries
Authors: Culha Utku , Davidson Zoey S. , Mastrangeli Massimo , Sitti Metin 
Published: May 2020

Significance
Programmable self-assembly provides valuable insights into fundamental physics and enables the design of functional materials. However, relying only on computational solutions to understand the aspects of self-assembly may overlook critical phenomena accessible through physical observation. Our work presents a control mechanism utilizing dynamic boundaries to experimentally (re)program self-assembly. We show the correlation between confinement dynamics and resulting self-assembled structures and also demonstrate the tuning of their mechanical and magnetic properties. Our approach should be scalable to different particle counts, types, and sizes. In future studies, an enlarged confinement mechanism could be used as a control method on mobile robot swarms and as a test bed to experiment with many more particles for the self-assembly processes of crystalline and amorphous materials.
Social meanings of linguistic variation in BISINDO (Indonesian Sign Language)
Authors: Palfreyman Nick 
Published: May 2020

AbstractAbstract (International Sign)In contrast to sociolinguistic research on spoken languages, little attention has been paid to how signers employ variation as a resource to fashion social meaning. This study focuses on an extremely understudied social practice, that of sign language usage in Indonesia, and asks where one might look to find socially meaningful variables. Using spontaneous data from a corpus of BISINDO (Indonesian Sign Language), it blends methodologies from Labovian variationism and analytic practices from the ‘third wave’ with a discursive approach to investigate how four variable linguistic features are used to express social identities. These features occur at different levels of linguistic organisation, from the phonological to the lexical and the morphosyntactic, and point to identities along regional and ethnic lines, as well as hearing status. In applying third wave practices to sign languages, constructed action and mouthings in particular emerge as potent resources for signers to make social meaning.
The effect of sociolinguistic factors on variation in the Kata Kolok lexicon
Authors: Mudd Katie , Lutzenberger Hannah , de Vos Connie , Fikkert Paula , Crasborn Onno , de Boer Bart 
Published: May 2020

Abstract

Abstract (International Sign)

Sign languages can be categorized as shared sign languages or deaf community sign languages, depending on the context in
which they emerge. It has been suggested that shared sign languages exhibit more variation in the expression of everyday concepts than deaf
community sign languages (Meir, Israel, Sandler, Padden, & Aronoff, 2012). For deaf community
sign languages, it has been shown that various sociolinguistic factors condition this variation. This study presents one of the first
in-depth investigations of how sociolinguistic factors (deaf status, age, clan, gender and having a deaf family member) affect lexical
variation in a shared sign language, using a picture description task in Kata Kolok. To study lexical variation in Kata Kolok, two
methodologies are devised: the identification of signs by underlying iconic motivation and mapping, and a way to compare
individual repertoires of signs by calculating the lexical distances between participants. Alongside presenting novel methodologies to study
this type of sign language, we present preliminary evidence of sociolinguistic factors that may influence variation in the Kata Kolok
lexicon.
“Switching caps”
Authors: Reed Lauren W. 
Published: May 2020

AbstractAbstract (Australian Sign Language)Most bilingualism and translanguaging studies focus on spoken language; less is known about how people use two or more ways of signing. Here, I take steps towards redressing this imbalance, presenting a case study of signed language in Port Moresby, Papua New Guinea. The study’s methodology is participant observation and analysis of conversational recordings between deaf signers. The Port Moresby deaf community uses two ways of signing:sign languageandculture.sign languageis around 30 years old, and its lexicon is drawn largely from Australasian Signed English. In contrast,culture – which is as old as each individual user – is characterised by signs of local origin, abundant depiction, and considerable individual variation. Despitesign language’s young age, its users have innovated a metalinguistic sign (switch-caps) to describe switching between ways of communicating. To conclude, I discuss how the Port Moresby situation challenges both the bilingualism and translanguaging approaches.
Tripartite interaction between
Striga
spp., cereals, and plant root-associated microorganisms: a review
Authors: Lenard G. Mounde , Williams O. Anteyi , Rasche Frank 
Published: May 2020

Abstract

Striga
spp. is a major threat to cereal and legume production, putting the food security and economy of smallholder farmers in sub-Saharan Africa at severe risk. This is manifested in the fact that
Striga
spp. infestation can result in up to 90% loss of both cereal and legume production. A consensus exists that there is yet no single measure to efficiently control
Striga
spp. This is mainly because of the limited fundamental knowledge of the genetics and ecology of
Striga
spp. and its interaction with its hosts and host root-associated microorganisms, including plant growth-promoting rhizobacteria (PGPR). Since
Striga
spp. is a root parasite, it is speculated that PGPR play a key role in controlling the emergence and development of
Striga
spp. At the same time, PGPR may exhibit beneficial effects on growth promotion of the host to strengthen its tolerance against
Striga
spp. attacks, while on the other hand, it may also induce, similar to biocontrol agents, direct suicidal effects on
Striga
spp. Such hypothesized associations between
Striga
spp., crops (e.g., cereals such as sorghum and maize), and PGPR remain largely unknown, and the central question remains if PGPR play an important role in the
Striga
-crop pathosystem. This knowledge gap is the central impetus of this review. It will elaborate the complex and fascinating tripartite ecological system of cereals,
Striga
spp. and root-associated microorgamisms. In a first step, the review will provide a comprehensive summary of the pairwise interactions between
Striga
spp. and cereals, cereals and PGPR, as well as
Striga
spp. and PGPR. This summary will then merge into the discussion about the yet limited knowledge of the tripartite interaction between cereals,
Striga
spp., and PGPR. This specifically includes the exploration of recent discoveries related to population genetics and the life cycle of
Striga
spp, host (cereal) defense responses to and mechanisms of
Striga
spp. infestation, as well as the inhibitory and stimulatory role of PGPR on
Striga
spp. seed germination. In a concluding section, remaining research gaps are identified and necessary research perspectives are provided to direct prospective research toward further understanding the relationship between the three biological components paving the avenue to develop biological and environmentally friendly measures to fight off the everlasting threat of
Striga
spp.
Occurrence of ESBL-producing
Escherichia coli
in healthy, living food-producing animals in Europe: a systematic review
Authors: Kuhnke Dagmar , Werner Nicole , Kreienbrock Lothar 
Published: May 2020

Abstract

Objective

The objective of this paper is to review the recent scientific literature that focuses on the occurrence of extended-spectrum beta-lactamase-producing
Escherichia coli
(ESBL-E) in healthy, living farm animals, namely chickens, pigs, and cattle, in European countries.

Results

The literature search retrieved 1,479 records, of which 157 articles were revised in full text. Finally, 17 of these satisfied the inclusion criteria.
A great variety of methods to detect and quantify ESBL-E were described. Only a few studies have used the EUCAST guidelines. Major differences in study design and presenting results do not allow to report overall prevalence in the respective animal species, so “occurrence” is used when summarizing results.
In broiler chicken, the occurrence of ESBL-E ranged between 80% and 96%. In pigs, the range was much wider, starting from 2.6% up to 84% in different sample and production types. In cattle, studies revealed an ESBL-E occurrence between 1% and 54%.

Conclusion

Although we found a high degree of heterogeneity in study designs and reports, it can be concluded that the occurrence of ESBL-E in food-producing animals in Europe is moderate to high, depending on the animal species. This review illustrates the extent of the problem and shows that appropriate measures need to be taken.
Attosecond pulse generation at ELI-ALPS 100 kHz repetition rate beamline
Authors: Ye Peng , Csizmadia Tamás , Oldal Lénárd Gulyás , Gopalakrishna Harshitha Nandiga , Füle Miklós , Filus Zoltán , Nagyillés Balázs , Divéki Zsolt , Grósz Tímea , Dumergue Mathieu , Jójárt Péter , Seres Imre , Bengery Zsolt , Zuba Viktor , Várallyay Zoltán , Major Balázs , Frassetto Fabio , Devetta Michele , Lucarelli Giacinto Davide , Lucchini Matteo , Moio Bruno , Stagira Salvatore , Vozzi Caterina , Poletto Luca , Nisoli Mauro , Charalambidis Dimitris , Kahaly Subhendu , Zaïr Amelle , Varjú Katalin 
Published: May 2020

Abstract
We generate attosecond pulse train (APT) in argon driven by the high repetition rate (HR) laser of the extreme light infrastructure-attosecond light pulse source (ELI-ALPS), providing 100 kHz, 80 W, 1030 nm, 40 fs pulses from a fiber chirped-pulse amplification (fiber-CPA) laser system. Under the current operating conditions of the high harmonic generation beamline (HR-GHHG), we observed the average pulse duration to be 395 as measured using the technique of reconstruction of attosecond beating by interference of two-photon transitions. The beamline uses an annular-shape laser beam so that the main part of the driving laser co-propagating with the APT can be eliminated by reflection on a holey mirror. An additional 100 nm aluminum foil is used to filter out the remaining laser and the low order harmonics, allowing 2 pJ APT with a bandwidth from 25 eV to 50 eV to be transported to the target position where the APT interacts with matter. The implementation of the HR-GHHG beamline in ELI-ALPS delivering attosecond pulse trains at 100 kHz paves the way for time-resolved experiments in the infrastructure, especially those that involve rare events and coincidence analysis, both of which need high statistics.
Field-induced interactions in magneto-active elastomers - A comparison of experiments and simulations
Authors: Metsch P , Schmidt H , Sindersberger D , A Kalina K , Brummund J , K Auernhammer G , Monkman G J , Kästner M 
Published: May 2020

Abstract
In this contribution, field-induced interactions of magnetizable particles embedded into a soft elastomer matrix are analyzed with regard to the resulting mechanical deformations. By comparing experiments for two-, three- and four-particle systems with the results of finite element simulations, a fully coupled continuum model for magneto-active elastomers is validated with the help of real data for the first time. The model under consideration permits the investigation of magneto-active elastomers with arbitrary particle distances, shapes and volume fractions as well as magnetic and mechanical properties of the individual constituents. It thus represents a basis for future studies on more complex, realistic systems. Our results show a very good agreement between experiments and numerical simulations—the deformation behavior of all systems is captured by the model qualitatively as well as quantitatively. Within a sensitivity analysis, the influence of the initial particle positions on the systems’ response is examined. Furthermore, a comparison of the full three-dimensional model with the often used, simplified two-dimensional approach shows the typical overestimation of resulting interactions in magneto-active elastomers.
Lambert W function methods in double square well and waveguide problems
Authors: Bharatbhai Narola Harsh , Deshmukh P C , Scott Robert B , Roberts Ken , Valluri S R 
Published: May 2020

Abstract
Using methods related to the Lambert W function, we present solutions of two apparently different problems: (1) The one-dimensional double square well potential in quantum mechanics and (2) The transverse electric and magnetic modes for a step-index electromagnetic waveguide. The solution techniques provide insight into the bound energy states for the single and double square well problems and the allowed modes of propagation in a waveguide with varying refractive indices. The solutions can be viewed in either of two related complex plane representations. Comparison of the solution geometries suggests that interesting applications may be possible in nanostructures and devices which are designed to be sensitive to small changes in their environment.
Frailty, a multisystem ageing syndrome
Authors: Thillainadesan Janani , Scott Ian A , Le Couteur David G 
Published: May 2020

Abstract
The management of frail older people is a key component of aged care. There has been a plethora of tools developed for the diagnosis and screening of frailty. Some of these tools are entering routine clinical practice at a time when the higher healthcare costs involved in caring for older people who are frail have become a potential target for cost-cutting. Yet there is still only limited evidence to support the widespread adoption of frailty tools, and foundational factors impact on their accuracy and validity. Despite the acceptance of frailty as a valid term in research and clinical practice, older people believe the term carries stigma. Such issues indicate that there may be a need to reconsider current approaches to frailty. Recent advances in the science of ageing biology can provide a new framework for reconfiguring how we screen, diagnose, treat and prevent frailty. Frailty can be considered to be a multisystem ageing syndrome of decreased physiological and functional reserve, where the biological changes of ageing are seen in most tissues and organs and are the pathogenic mechanism for frailty. Likewise age-related chronic disease and multimorbidity are syndromes where ageing changes occur in one or multiple systems, respectively. This model focusses diagnostic criteria for frailty onto the biomarkers of ageing and generates new targets for the prevention and treatment of frailty based on interventions that influence ageing biology.
GREMA: modelling of emulated gene regulatory networks with confidence levels based on evolutionary intelligence to cope with the underdetermined problem
Authors: Tsai Ming-Ju , Wang Jyun-Rong , Ho Shinn-Jang , Shu Li-Sun , Huang Wen-Lin , Ho Shinn-Ying 
Published: May 2020

Abstract

Motivation
Non-linear ordinary differential equation (ODE) models that contain numerous parameters are suitable for inferring an emulated gene regulatory network (eGRN). However, the number of experimental measurements is usually far smaller than the number of parameters of the eGRN model that leads to an underdetermined problem. There is no unique solution to the inference problem for an eGRN using insufficient measurements.

Results
This work proposes an evolutionary modelling algorithm (EMA) that is based on evolutionary intelligence to cope with the underdetermined problem. EMA uses an intelligent genetic algorithm to solve the large-scale parameter optimization problem. An EMA-based method, GREMA, infers a novel type of gene regulatory network with confidence levels for every inferred regulation. The higher the confidence level is, the more accurate the inferred regulation is. GREMA gradually determines the regulations of an eGRN with confidence levels in descending order using either an S-system or a Hill function-based ODE model. The experimental results showed that the regulations with high-confidence levels are more accurate and robust than regulations with low-confidence levels. Evolutionary intelligence enhanced the mean accuracy of GREMA by 19.2% when using the S-system model with benchmark datasets. An increase in the number of experimental measurements may increase the mean confidence level of the inferred regulations. GREMA performed well compared with existing methods that have been previously applied to the same S-system, DREAM4 challenge and SOS DNA repair benchmark datasets.

Availability and implementation
All of the datasets that were used and the GREMA-based tool are freely available at https://nctuiclab.github.io/GREMA.

Supplementary information
Supplementary data are available at Bioinformatics online.
TopicNet: a framework for measuring transcriptional regulatory network change
Authors: Lou Shaoke , Li Tianxiao , Kong Xiangmeng , Zhang Jing , Liu Jason , Lee Donghoon , Gerstein Mark 
Published: May 2020

Abstract

Motivation
Recently, many chromatin immunoprecipitation sequencing experiments have been carried out for a diverse group of transcription factors (TFs) in many different types of human cells. These experiments manifest large-scale and dynamic changes in regulatory network connectivity (i.e. network ‘rewiring’), highlighting the different regulatory programs operating in disparate cellular states. However, due to the dense and noisy nature of current regulatory networks, directly comparing the gains and losses of targets of key TFs across cell states is often not informative. Thus, here, we seek an abstracted, low-dimensional representation to understand the main features of network change.

Results
We propose a method called TopicNet that applies latent Dirichlet allocation to extract functional topics for a collection of genes regulated by a given TF. We then define a rewiring score to quantify regulatory-network changes in terms of the topic changes for this TF. Using this framework, we can pinpoint particular TFs that change greatly in network connectivity between different cellular states (such as observed in oncogenesis). Also, incorporating gene expression data, we define a topic activity score that measures the degree to which a given topic is active in a particular cellular state. And we show how activity differences can indicate differential survival in various cancers.

Availability and Implementation
The TopicNet framework and related analysis were implemented using R and all codes are available at https://github.com/gersteinlab/topicnet.

Supplementary information
Supplementary data are available at Bioinformatics online.
MutCombinator: identification of mutated peptides allowing combinatorial mutations using nucleotide-based graph search
Authors: Choi Seunghyuk , Paek Eunok 
Published: May 2020

Abstract

Motivation
Proteogenomics has proven its utility by integrating genomics and proteomics. Typical approaches use data from next-generation sequencing to infer proteins expressed. A sample-specific protein sequence database is often adopted to identify novel peptides from matched mass spectrometry-based proteomics; nevertheless, there is no software that can practically identify all possible forms of mutated peptides suggested by various genomic information sources.

Results
We propose MutCombinator, which enables us to practically identify mutated peptides from tandem mass spectra allowing combinatorial mutations during the database search. It uses an upgraded version of a variant graph, keeping track of frame information. The variant graph is indexed by nine nucleotides for fast access. Using MutCombinator, we could identify more mutated peptides than previous methods, because combinations of point mutations are considered and also because it can be practically applied together with a large mutation database such as COSMIC. Furthermore, MutCombinator supports in-frame search for coding regions and three-frame search for non-coding regions.

Availability and implementation
https://prix.hanyang.ac.kr/download/mutcombinator.jsp.

Supplementary information
Supplementary data are available at Bioinformatics online.