bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis and Applications of Adaptive Group Testing Methods for COVID-19
Authors: Mentus Cassidy , Romeo Martin , DiPaola Christian 
Published: April 2020

AbstractTesting strategies for Covid-19 to maximize number of people tested are urgently needed. Recently, it has been demonstrated that RT-PCR has the sensitivity to detect one positive case in a mixed sample of 32 cases [12], In this paper we propose adaptive group testing strategies based on generalized binary splitting (CBS) [5], where we restrict the group test to the largest group that can be used. The method starts by choosing a group from the population to be tested, performing a test on the combined sample from the entire group, and progressively splitting the group further into subgroups. Compared to individual testing at 4% prevalence, we save 74%; at 1% we save 91%; and at .1% we save 98% of tests. We analyze the number of times each sample is used and show that the method is still efficient if we resort to testing a case individually if the sample is running low.In addition we recommend clinical screening to filter out individuals with symptoms and show this leaves us with a population with lower prevalence. Our approach is particularly applicable to vulnerable confined populations such as nursing homes, prisons, military ships and cruise ships.
Multi-modal Nonlinear Optical and Thermal Imaging Platform for Label-Free Characterization of Biological Tissue
Authors: Adams Wilson R , Mehl Brian , Lieser Eric , Wang Manqing , Patton Shane , Throckmorton Graham A , Jenkins J Logan , Ford Jeremy B , Gautam Rekha , Brooker Jeff , Jansen E. Duco , Mahadevan-Jansen Anita 
Published: April 2020

AbstractThe ability to characterize the combined structural, functional, and thermal properties of biophysically dynamic samples is needed to address critical questions related to tissue structure, physiological dynamics, and disease progression. Towards this, we have developed an imaging platform that enables multiple nonlinear imaging modalities to be combined with thermal imaging on a common sample. Here we demonstrate label-free multimodal imaging of live cells, excised tissues, and live rodent brain models. While potential applications of this technology are wide-ranging, we expect it to be especially useful in addressing biomedical research questions aimed at the biomolecular and biophysical properties of tissue and their physiology.
The potential genetic network of human brain SARS-CoV-2 infection
Authors: Lapina Colline , Rodic Mathieu , Peschanski Denis , Mesmoudi Salma 
Published: April 2020

AbstractThe literature reports several symptoms of SARS-CoV-2 in humans such as fever, cough, fatigue, pneumonia, and headache. Furthermore, patients infected with similar strains (SARS-CoV and MERS-CoV) suffered testis, liver, or thyroid damage. Angiotensin-converting enzyme 2 (ACE2) serves as an entry point into cells for some strains of coronavirus (SARS-CoV, MERS-CoV, SARS-CoV-2). Our hypothesis was that as ACE2 is essential to the SARS-CoV-2 virus invasion, then brain regions where ACE2 is the most expressed are more likely to be disturbed by the infection. Thus, the expression of other genes which are also over-expressed in those damaged areas could be affected. We used mRNA expression levels data of genes provided by the Allen Human Brain Atlas (ABA), and computed spatial correlations with the LinkRbrain platform. Genes whose co-expression is spatially correlated to that of ACE2 were then clustered into 16 groups, depending on the organ in which they are the most expressed (as described by the NCBI genes database). The list of organs where genes sharing local over-expression with the ACE2 gene are the most expressed is astonishingly similar to the organs affected by Covid-19.
PARTITIONING AMONG NICHE AND NEUTRAL EXPLANATIONS FOR METACOMMUNITY PATTERNS IN CERRADO STREAM FISH COMMUNITIES
Authors: Vieira Thiago Bernardi , da Silva Liriann Chrisley Nascimento , Casatti Lilian , Romero Renato , Tejerina Garro Francisco Leonardo , Uchôa de Aquino Pedro De Podestà , Santos Pompeu Paulo dos , De Marco Paulo 
Published: April 2020

AbstractThe Species Sorting concept, one of the models developed to explain patterns in metacommunity structure, suggests that relationships between biological communities and environmental conditions is the basic means of the species selection processes. A second concept is neutral theory, and the idea of neutral dynamics underpinning metacommunity structure, cannot be overlooked. The third mechanism is the Mass Effect concept, that focuses on the interaction between environmental condition and neutral effects. In the present study, we partitioned fish communities in streams between niche and neutral theory concepts, identifying the best representation of metacommunity structure, and assessed if linear and hydrographic distance were equivalent in the representation of neutral processes. The result points to the importance of species sorting mechanisms in structuring fish communities with neutral processes best represented by the linear distances. On the other hand, the best representation of species’ niches was achieved with average values and variance of the local conditions.
PriSeT: EfficientDe NovoPrimer Discovery
Authors: Hoffmann Marie , Monaghan Michael T. , Reinert Knut 
Published: April 2020

AbstractMotivationDNA metabarcoding is a commonly applied technique used to infer the species composition of environmental samples. These samples can comprise hundreds of organisms that can be closely or very distantly related in the taxonomic tree of life. DNA metabarcoding combines polymerase chain reaction (PCR) and next-generation sequencing (NGS), whereby a short, homologous sequence of DNA is amplified and sequenced from all members of the community. Sequences are then taxonomically identified based on their match to a reference database. Ideally, each species of interest would have a unique DNAbarcode. This short, variable sequence needs to be flanked by relatively conserved regions that can be used as primer binding sites. Appropriate PCR primer pairs would match to a broad evolutionary range of taxa, such that we only need a few to achieve high taxonomic coverage. At the same time however, the DNA barcodes between primer pairs should be different to allow us to distinguish between species to improve resolution. This poses an interesting optimization problem. More specifically: Given a set of references ℛ = {R1,R2, …,Rm}, the problem is to find a primer setPbalancing both: high taxonomic coverage and high resolution. This goal can be captured by filtering for frequent primers and ranking by coverage or variation, i.e. the number of unique barcodes. Here we present the software PriSeT, an offline primer discovery tool that is capable of processing large libraries and is robust against mislabeled or low quality references. It tackles the computationally expensive steps with linear runtime filters and efficient encodings.ResultsWe first evaluated PriSeT on references (mostly 18S rRNA genes) from 19 clades covering eukaryotic organisms that are typical for freshwater plankton samples. PriSeT recovered several published primer sets as well as additional, more chemically suitable primer sets. For these new sets, we compared frequency, taxon coverage, and amplicon variation with published primer sets. For 11 clades we foundde novoprimer pairs that cover more taxa than the published ones, and for six cladesde novoprimers resulted in greater sequence (i.e., DNA barcode) variation. We also applied PriSeT to 19 SARS-CoV-2 genomes and computed 114 new primer pairs with the additional constraint that the sequences have no co-occurrences in other taxa. These primer sets would be suitable for empirical testing.Availabilityhttps://github.com/mariehoffmann/PriSeTContactmarie.hoffmann@fu-berlin.de
Genetic similarity and facial cues for kin recognition in humans
Authors: Torosin Nicole S. , Ward Joshua , Bell Adrian V. , Knapp Leslie A. 
Published: April 2020

AbstractKin recognition is essential to the evolution of human cooperation, social organization, and altruistic behavior. However, the genetic underpinnings of kin recognition have been largely understudied. Facial resemblance is an important relatedness cue for humans and more closely related individuals are generally thought to share greater facial similarity. To evaluate the relationship between perceived self-resemblance and genetic similarity among biologically related and unrelated females, we administered facial self-recognition surveys to twenty-three sets of related females and genotyped three different genetic systems, human leukocyte antigens (HLA), neutral nuclear microsatellites and mitochondrial haplogroups, for each individual. Using these data, we examined the relationship between visual kin recognition and genetic similarity. We found that pairs of individuals identified as visually more similar had greater HLA allelic sharing when compared to less facially similar participants. We did not find the same relationship for microsatellite and mitochondrial similarity, suggesting that HLA allelic similarity increases the probability of perceived self-resemblance in humans while other genetic markers do not. Our results demonstrate that some genetic markers, such as HLA-DRB, may have significant influence on phenotype and that large scale surveys of HLA and facial feature morphology will yield valuable insight into the evolutionary biology of genotype-phenotype relationships and kin recognition.
Rapid Assessment of T-Cell Receptor Specificity of the Immune Repertoire
Authors: Lin Xingcheng , George Jason T. , Schafer Nicholas P. , Chau Kevin Ng , Birnbaum Michael E. , Clementi Cecilia , Onuchic José N. , Levine Herbert 
Published: April 2020

AbstractAccurate assessment of TCR-antigen specificity at the whole immune repertoire level lies at the heart of improved cancer immunotherapy, but predictive models capable of high-throughput assessment of TCR-peptide pairs are lacking. Recent advances in deep sequencing and crystallography have enriched the data available for studying TCR-p-MHC systems. Here, we introduce a pairwise energy model, RACER, for rapid assessment of TCR-peptide affinity at the immune repertoire level. RACER applies supervised machine learning to efficiently and accurately resolve strong TCR-peptide binding pairs from weak ones. The trained parameters further enable a physical interpretation of interacting patterns encoded in each specific TCR-p-MHC system. When applied to simulate thymic selection of an MHC-restricted T-cell repertoire, RACER accurately estimates recognition rates for tumor-associated neoantigens and foreign peptides, thus demonstrating its utility in helping address the large computational challenge of reliably identifying the properties of tumor antigen-specific T-cells at the level of an individual patient’s immune repertoire.
The Tetrameric Structure of Nucleotide-regulated Pyrophosphatase and Its Modulation by Deletion Mutagenesis and Ligand Binding
Authors: Anashkin Viktor A. , Salminen Anu , Orlov Victor N. , Lahti Reijo , Baykov Alexander A. 
Published: April 2020

ABSTRACTA quarter of prokaryotic Family II inorganic pyrophosphatases (PPases) contain a regulatory insert comprised of two cystathionine β-synthase (CBS) domains and one DRTGG domain in addition to the two catalytic domains that form canonical Family II PPases. The CBS domain-containing PPases (CBS-PPases) are allosterically activated or inhibited by adenine nucleotides that cooperatively bind to the CBS domains. Here we use chemical cross-linking and analytical ultracentrifugation to show that CBS-PPases fromDesulfitobacterium hafnienseand four other bacterial species are active as 200–250-kDa homotetramers, which seems unprecedented among the four PPase families. The tetrameric structure is stabilized by Co2+, the essential cofactor, pyrophosphate, the substrate, and adenine nucleotides, including diadenosine tetraphosphate. The deletion variants ofdhPPase containing only catalytic or regulatory domains are dimeric. Co2+depletion by incubation with EDTA converts CBS-PPase into inactive tetrameric and dimeric forms. Dissociation of tetrameric CBS-PPase and its catalytic part by dilution renders them inactive. The structure of CBS-PPase tetramer was modelled from the structures of dimeric catalytic and regulatory parts. These findings signify the role of the unique oligomeric structure of CBS-PPase in its multifaced regulation.
Case reports of improvement in behaviour following switching of patients with intellectual disability and epilepsy from levetiracetam to brivaracetam
Authors: Baburaj Raghavendar , Dunstall Huw Morgan , Bright Catherine , Lawthom Charlotte 
Published: April 2020

Purpose
Epilepsy is a chronic illness affecting around 50 million people worldwide. Levetiracetam is an effective novel antiepileptic drug but can cause behavioural adverse events. A total of 10-15 per cent people with intellectual disability (ID) already present with Behaviour that Challenges (BtC). Brivaracetam is postulated to have a distinct pharmacological profile compared with levetiracetam which may result in fewer behavioural adverse events.

Design/methodology/approach
This paper presents two cases of people with epilepsy and ID being switched from levetiracetam to brivaracetam for reported behaviour adverse events.

Findings
The cases support that people with epilepsy and ID who are experiencing behavioural adverse events from levetiracetam can safely be switched to brivaracetam, resulting in significant reductions in BtC and potentially improved seizure control. Nevertheless, these results must be interpreted with caution, as aetiology for BtC in people with ID is often multifactorial.

Originality/value
This is one of the first papers to date, according to the best of the authors’ knowledge, to describe improved behavioural profile in people with ID and epilepsy when switching from levetiracetam to brivaracetam.
The recursive interplay of capabilities and constraints amongst microfinance entrepreneurs
Authors: Kimmitt Jonathan , Dimov Dimo 
Published: April 2020

PurposeThe purpose of this paper is to investigate, through practices and capabilities, how entrepreneurs use microfinance in a context of serious constraints.Design/methodology/approachThe chosen methodology for this paper is longitudinal. A three-and-a-half-year study was conducted to be able to capture the entrepreneurial journeys of ten entrepreneurs at a micro-level in the developing economy of Ghana. This was augmented by a further 15 interviews with entrepreneurs and loan officers. This data is used to develop a theoretical model of entrepreneurial practices in this context.FindingsThe paper identifies two distinct pathways for understanding the recursive nature of entrepreneurial practices. It highlights how entrepreneurs generate capabilities through microfinance resources through convergent or divergent venturing in response to the serious constraints they face. This is identified as a generative recursive mechanism for the process, representing the “chain of actions” and how entrepreneurs engage with their “settings” and “intended relations” in practice.Research limitations/implicationsThe research is limited by its focus on one nation in Sub-Saharan Africa and therefore how the findings may be transferred to other contexts.Originality/valueThe paper contributes to a practice approach in entrepreneurship by identifying how mechanisms of practice relate to entrepreneurial action in this context. It also provides an important contribution to discussion at the intersection of entrepreneurship and the capabilities approach by using Amartya Sen's concepts of process and opportunity freedom to understand practices.
A comparative study on the performance of rule engines in automated ontology learning: a case study with erythemato-squamous disease (ESD)
Authors: S Sivasankari , Punnoose Dinah , D Krishnamoorthy 
Published: April 2020

PurposeErythemato-squamous disease (ESD) is one of the complex diseases related to the dermatology field. Due to common morphological features, the diagnosis of ESDs become stringent and leads to inconsistency. Besides, diagnosis has been done on the basis of inculcated visible symptoms pertinent with the expertise of the physician. Hence, ontology construction for ESD is essential to ensure credibility, consistency, to resolve lack of time, labor and competence and to diminish human error.Design/methodology/approachThis paper presents the design of an automatic ontology framework through data mining techniques and subsequently depicts the diagnosis of ESD using the available knowledge- and rule-based system.FindingsThe rule language (Semantic Web Rule Language) and rule engine (Jess and Drools) have been integrated to explore the severity of the ESD and foresee the most appropriate class to be suggested.Social implicationsIn this paper, the authors identify the efficiency of the rule engine and investigate the performance of the computational techniques in predicting ESD using three different measures.Originality/valuePrimarily, the approach assesses transfer time for total number of axioms exported to rule engine (Jess and Drools) while the other approach measures the number of inferred axioms (process time) using the rule engine while the third measure calculates the time to translate the inferred axioms to OWL knowledge (execution time).
Italy: money transfer, money laundering and intermediary liability
Authors: Corselli Livio 
Published: April 2020

Purpose
This paper aims to offer a general overview of money transfers in Italy and Europe focussing specifically on the migrant community. This is of particular interest because it is in that community where money transfers are most prevalent. This shows the money transfer system as a tool that could guarantee the financial inclusion of migrants but at the same time being used in a distorted and unlawful manner.

Design/methodology/approach
After a brief introduction focussed on working principles and legal frameworks, the paper will go deeper in evaluating money transfer data. This data, which comes from various legal authorities, will show the extent to which different migrant communities who reside in Italy are able to carry out illicit activity using money transfers. It will also highlight the existence of legislative inconsistencies through a case by case approach.

Findings
This paper shows the reason why people find it relatively easy to use money transfers to launder money or in a broader sense, take part in other illicit financial operations such as financing terrorism.

Originality/value
This study will examine recent Italian criminal cases concerning the unlawful use of money transfers. This paper is the original study of the author and has not been submitted elsewhere for publication.
Avocat, rechtsanwalt or agent of the state?
Authors: Svenonius Ola , Mörth Ulrika 
Published: April 2020

Purpose
The purpose of this paper is to analyse how lawyers in two of the largest European economies manage the contradictory requirements set by anti-money laundering and counter-terrorism financing (AML/CTF) legislation on the one hand and professional codes of ethics on the other hand.

Design/methodology/approach
The study is based on qualitative interviews with French and German lawyers. It asks “How do European lawyers handle the conflicting demands ensuing from their roles as frontlines workers?” The paper uses lawyers’ day-to-day practices and variations in member states’ transpositions of the European Union directives as a starting point to study AML/CTF in the miniscule.

Findings
The article shows that contextual institutional restraints and cultural factors have significant impact on the possibility to enlist for-profit actors in the fight against terrorism an organised crime.

Research limitations/implications
This research highlights several factors inherent in AML/CTF regulation that warrant further research. Not only should further work be carried to broaden the understanding of lawyers but also other actors included in this policy area.

Practical implications
The study explains why French and German lawyers do not comply as expected by the legislator. If increased compliance is required, then the paper provides input into what measures can be taken, by policy, enforcement and supervision.

Originality/value
The study focusses on a hard-to-reach group of actors in AML/CTF regulation that has never before been studied in detail. As recent scandals have shown, lawyers are key actors in global finance but have rarely been scrutinised in their AML compliance norms and routines.
Investigating the impact of audit features on money laundering
Authors: Mohammadi Shaban , Naghshbandi Nader , Moridahmadibezdi Zahra 
Published: April 2020

Purpose
The purpose of the present study is to investigate the impact of audit features, including audit quality, audit fees and auditor tenure on money laundering in Iranian stock companies.

Design/methodology/approach
This research is descriptive-correlational and applied in terms of purpose. To evaluate the audit features, variables including audit quality, audit fee and auditor tenure were used. The statistical population of this study includes all companies listed in Tehran Stock Exchange and the research period from 2012 to 2018. A sample of 150 companies was selected by the screening method. In this study, logistic regression and Eviews 10 software were used for data analysis and hypothesis testing.

Findings
The results showed that variables including audit quality, normal audit fee and auditor tenure have a significant effect on money laundering.

Originality/value
Observing money laundering rules and regulations for businesses involves is a critical issue. In auditing the financial statements of the business units subject to these laws, the auditor reviews their actions to obtain reasonable assurance of guaranteeing the money laundering laws, evaluates their effectiveness and gains approval of managers regarding observing laundering regulations. In this regard, the auditor is required to report definitive or suspected money-laundering cases or its certain or suspected evidence to the relevant authorities. Although the law prohibits the auditor from disclosing such matters to the client, it is not necessary. It seems that even if the auditors perform non-audit functions, they should report money laundering or suspicious operations and transactions.