bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unsupervised Bayesian Ising Approximation for revealing the neural dictionary in songbirds
Authors: Hernández Damián G. , Sober Samuel J. , Nemenman Ilya 
Published: November 2019

ABSTRACTThe problem of deciphering how low-level patterns (action potentials in the brain, amino acids in a protein, etc.) drive high-level biological features (sensorimotor behavior, enzymatic function) represents the central challenge of quantitative biology. The lack of general methods for doing so from the size of datasets that can be collected experimentally severely limits our understanding of the biological world. For example, in neuroscience, some sensory and motor codes have been shown to consist of precisely timed multi-spike patterns. However, the combinatorial complexity of such pattern codes have precluded development of methods for their comprehensive analysis. Thus, just as it is hard to predict a protein’s function based on its sequence, we still do not understand how to accurately predict an organism’s behavior based on neural activity. Here we derive a method for solving this class of problems. We demonstrate its utility in an application to neural data, detecting precisely timed spike patterns that code for specific motor behaviors in a songbird vocal system. Our method detects such codewords with an arbitrary number of spikes, does so from small data sets, and accounts for dependencies in occurrences of codewords. Detecting such dictionaries of important spike patterns – rather than merely identifying the timescale on which such patterns exist, as in some prior approaches – opens the door for understanding fine motor control and the neural bases of sensorimotor learning in animals. For example, for the first time, we identify differences in encoding motor exploration versus typical behavior. Crucially, our method can be used not only for analysis of neural systems, but also for understanding the structure of correlations in other biological and nonbiological datasets.
ATrypanosoma bruceiORFeome-based Gain-of-Function Library reveals novel genes associated with melarsoprol resistance
Authors: Carter M , Kim HS , Gomez S , Gritz S , Larson S , Schulz D , Hovel-Miner GA 
Published: November 2019

ABSTRACTTrypanosoma bruceiis an early branching protozoan that causes Human and Animal African Trypanosomiasis. Forward genetics approaches are powerful tools for uncovering novel aspects of Trypanosomatid biology, pathogenesis, and therapeutic approaches against trypanosomiasis. Here we have generated aT. bruceiORFeome consisting of over 90% of the targeted genome and used it to make an inducible Gain-of-Function library for broadly applicable forward genetic screening. Using a critical drug of last resort, melarsoprol, we conducted a proof of principle genetic screen. Hits arising from this screen support the significance of trypanothione, a key player in redox metabolism, as a target of melarsoprol and implicate novel proteins of the flagellum and mitochondria in drug resistance. This study has produced two powerful new genetic tools for kinetoplastida research, which are expected to promote major advances in kinetoplastida biology and therapeutic development in the years to come.
IsHSPG2a modifier gene for Marfan syndrome?
Authors: Gyuricza Isabela Gerdes , de Souza Rodrigo Barbosa , Farinha-Arcieri Luis Ernesto , Fernandes Gustavo Ribeiro , Pereira Lygia V. 
Published: November 2019

ABSTRACTMarfan syndrome (MFS) is a connective tissue disease caused by mutations in theFBN1gene. Nevertheless, other genes influence the manifestations of the disease, characterized by high clinical variability even within families. We mapped modifier loci for cardiovascular and skeletal manifestations in the mgΔloxPneomouse model for MFS and the synthenic loci in the human genome. Corroborating our findings, one of those loci was identified also as a modifier locus in MFS patients. Here we investigate theHSPG2gene, located in this region, as a candidate modifier gene for MFS. We show a correlation betweenFbn1andHspg2expression in spinal column and aorta in non-isogenic mgΔloxPneomice. Moreover, we show that mice with severe phenotypes present lower expression ofHspg2than those mildly affected. Thus, we propose thatHSPG2is a strong candidate modifier gene for MFS and its role in modulating disease severity should be investigated in patients.
Characterization of Isoforms of the Ovine Granulocyte Colony Stimulating Factor
Authors: Li Runting , Chen Longxin , Wang Yuqin , Zhang Limeng , Liu Ting , Nie Xiaoning , He Haiying , Wang Yong , Wang Kang , Yang Ruochen , Duan Chunhui , Liu Yueqin , Ma Runlin Zhang , Zhang Yingjie 
Published: November 2019

ABSTRACTThe granulocyte colony-stimulating factor (GCSF) regulates the maturation, proliferation, and differentiation of precursor cells of neutrophilic granulocytes, and has been widely studied in several species. To investigate the function of variants of sheep GCSF (sGCSF), this study compared difference in their mRNA expression levels. Both the activity and mRNA expression level of GCSFv2 were higher than those of GCSFv1. Their sequences were aligned, which showed that they had the highest homology with bovine GCSF. Then, predicted ovine GCSF isoforms and their constant C-terminals were cloned and expressed, which were stably expressed in mammalian cells. After purification, all GCSF functions were different both in vitro and in vivo, and the GCSF C-terminal was best. These results indicated that the ability to stimulate both the proliferation and differentiation of progenitor cells and to activate the maturation of neutrophils could be used for research of efficacious non-antibiotic protein drugs. Furthermore, GCSF can be used as candidate target of genetic breeding to specifically improve sheep immunity.
Phosphatidic acid produced by phospholipase D is required for hyphal cell-cell fusion and fungal-plant symbiosis
Authors: Hassing Berit , Eaton Carla J. , Winter David , Green Kimberly A. , Brandt Ulrike , Savoian Matthew S. , Mesarich Carl H. , Fleissner Andre , Scott Barry 
Published: November 2019

SummaryAlthough lipid signaling has been shown to serve crucial roles in mammals and plants, little is known about this process in filamentous fungi. Here we analyse the contribution of phospholipase D (PLD) and its product phosphatidic acid (PA) in hyphal morphogenesis and growth ofEpichloë festucaeandNeurospora crassa, and in the establishment of a symbiotic interaction betweenE. festucaeandLolium perenne. Growth ofE. festucaeandN. crassaPLD deletion strains in axenic culture, and forE. festucaein association withL. perenne, were analysed by light-, confocal- and electron microscopy. Changes in PA distribution were analysed inE. festucaeusing a PA biosensor and the impact of these changes on endocytic recycling and superoxide production investigated. We found thatE. festucaePldB and theN. crassaortholog, PLA-7, are required for polarized growth, cell fusion and ascospore development, whereas PldA/PLA-8 are dispensable for these functions. Exogenous addition of PA rescues the cell-fusion phenotype inE. festucae. PldB is also crucial forE. festucaeto establish a symbiotic association withL. perenne. This study identifies a new component of the cell-cell communication and cell fusion signaling network that controls hyphal morphogenesis and growth in filamentous fungi.
E-TAN, a technology-enhanced platform with tangible objects for the assessment of visual neglect: a multiple single-case study
Authors: Cerrato Antonio , Pacella Daniela , Palumbo Francesco , Beauvais Diane , Ponticorvo Michela , Miglino Orazio , Bartolomeo Paolo 
Published: November 2019

AbstractVisual neglect is a frequent and disabling consequence of right brain damage. Traditional paper-and- pencil tests of neglect have limitations in sensitivity and ecological validity. The Baking Tray Task (BTT), instead, approaches real-life situations, because it requires participants to place 16 physical objects on a board. The number of objects placed on the left and right portions of the board provides a clinical index of visual neglect. Here we present E-TAN, a technology-enhanced platform which allows patients to perform an enhanced version of the BTT (E-BTT). This platform automatically determines the object locations on the board, and also records the sequence and timing of their placement. We used E-BTT to test 9 patients with right hemisphere damage, and compared their performance with that obtained by 115 healthy participants. To this end, we developed a new method of analysis of participants’ performance, based on the use of the convex hull described by the objects on the board. This measure provides an estimate of the portion of space processed by each participant, and can effectively discriminate neglect patients from patients without neglect. E-TAN allows clinicians to assess visuospatial performance by using a convenient, fast, and relatively automatized procedure, that patients can even perform at home to follow-up the effects of rehabilitation.
A novel exosome biogenesis mechanism: multivesicular structures budding and rupturing at the plasma membrane
Authors: Quinonez Stephanie Leon , Brown Ian R. , Grimsley Helen E. , Cinatl Jindrich , Michaelis Martin , Hsu Chieh 
Published: November 2019

AbstractExosomes are small vesicles secreted by the cells, which mediate intercellular signalling and systemic physiological processes. Exosomes are known to originate from the intraluminal vesicles of the multivesicular endosome that fuses with the plasma membrane. We found that the non-small cell lung cancer (NSCLC) cell lines, HCC15 and A549, secreted exosomes with typical morphology and protein contents. Unexpectedly, transmission electron microscopy images indicated that the cells formed multivesicular structures that protruded from the plasma membrane and ruptured to release the exosomes. There were smooth multivesicular structures surrounded by an ordinary looking membrane, multivesicular structures coated by an electron dense layer with regular spacing pattern, and intermediate forms that combined elements of both. Electron microscopy images suggested that exosomes are release from these structures by burst events and not by the conventional fusion process. The molecular details of this novel mechanism for membrane association, deformation and fusion is to be unveiled in the future.
Absence of subcerebral projection neurons delays disease onset and extends survival in a mouse model of ALS
Authors: Burg Thibaut , Bichara Charlotte , Scekic-Zahirovic Jelena , Fischer Mathieu , Stuart-Lopez Geoffrey , Lefebvre François , Cordero-Erausquin Matilde , Rouaux Caroline 
Published: November 2019

AbstractAmyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease of adulthood that affects voluntary motricity and rapidly leads to full paralysis and death. ALS arises from the combined degeneration of motoneurons in the spinal cord and brain stem, responsible for muscle denervation, and corticospinal projection neurons (CSN), responsible for emergence of the upper motor neuron syndrome. Recent studies carried on ALS patients suggest that the disease may initiate in the motor cortex and spread to its projection targets. However, this “corticofugal hypothesis” of ALS has not yet been specifically challenged. Here, we provide a direct test of this hypothesis by genetically removing subcerebral projection neurons (SubCerPN), including CSN, in Sod1G86R mice, a mouse model of ALS. Ablation of the transcription factor Fezf2, leading to the complete absence of all SubCerPN, delays disease onset, reduces weight loss and motor impairment, and increases survival without modifying disease duration. Importantly absence of SubCerPN and CSN also limits pre-symptomatic hyperreflexia. Together, our results demonstrate that major corticofugal tracts are critical to ALS onset, and that SubCerPN and CSN in particular may carry detrimental signals to their downstream targets. In its whole, this study provides first experimental arguments in favour of the corticofugal hypothesis of ALS.
Controlling a robotic arm for functional tasks using a wireless head-joystick: A case study of a child with congenital absence of upper and lower limbs
Authors: Aspelund Sanders , Patel Priya , Lee Mei-Hua , Kagerer Florian , Ranganathan Rajiv , Mukherjee Ranjan 
Published: November 2019

AbstractChildren with movement impairments needing assistive devices for activities of daily living often require novel methods for controlling these devices. Body-machine interfaces, which rely on body movements, are particularly well-suited for children as they are non-invasive and have high signal-to-noise ratios. Here, we examined the use of a head-joystick to enable a child with congenital absence of all four limbs to control a seven degree-of-freedom robotic arm. Head movements were measured with a wireless inertial measurement unit and used to control a robotic arm to perform two functional tasks – a drinking task and a block stacking task. The child practiced these tasks over multiple sessions; a control participant performed the same tasks with a manual joystick. Our results showed that the child was able to successfully perform both tasks, with movement times decreasing by ~40-50% over 6-8 sessions of training. The child’s performance with the head-joystick was also comparable to the control participant using a manual joystick. These results demonstrate the potential of using head movements for the control of high degree-of-freedom tasks in children with limited movement repertoire.
Late-season surveys to document seed rain potential of Palmer amaranth (Amaranthus palmeri) and waterhemp (Amaranthus tuberculatus) in Texas cotton
Authors: Werner Kaisa M. , Sarangi Debalin , Nolte Scott A. , Dotray Peter A. , Bagavathiannan Muthukumar V. 
Published: November 2019

AbstractDespite the best weed control efforts, weed escapes are often present in large production fields prior to harvest, contributing to seed rain and species persistence. Late-season surveys were conducted in cotton (Gossypium hirsutum L.) fields in Texas in 2016 and 2017 to identify common weed species present as escapes and estimate seed rain potential of Palmer amaranth (Amaranthus palmeri S. Watson) and waterhemp [A. tuberculatus (Moq.) J.D. Sauer], two troublesome weed species with high fecundity. A total of 400 cotton fields across four major cotton-producing regions in Texas [High Plains (HP), Gulf Coast (GC), Central Texas, and Blacklands] were surveyed. Results have revealed that A. palmeri, Texas millet [Urochloa texana (Buckley) R. Webster], A. tuberculatus, ragweed parthenium (Parthenium hysterophorus L.), and barnyardgrass [Echinochloa crus-galli (L.) P. Beauv.] were the top five weed escapes present in cotton fields. Amaranthus palmeri was the most prevalent weed in the HP and Lower GC regions, whereas A. tuberculatus escapes were predominantly observed in the Upper GC and Blacklands regions. On average, 9.4% of an individual field was infested with A. palmeri escapes in the Lower GC region; however, it ranged between 5.1 and 8.1% in the HP region. Average A. palmeri density ranged from 405 (Central Texas) to 3,543 plants ha−1 (Lower GC). The greatest seed rain potential by A. palmeri escapes was observed in the upper HP region (13.9 million seeds ha−1), whereas the seed rain potential of A. tuberculatus escapes was the greatest in the Blacklands (12.9 million seeds ha−1) and the upper GC regions (9.8 million seeds ha−1). Results indicated that seed rain from late-season A. palmeri and A. tuberculatus escapes are significant in Texas cotton, and effective management of these escapes is imperative for minimizing seedbank inputs and impacting species persistence.
Pseudomonas aeruginosa core metabolism exerts a widespread growth-independent control on virulence
Authors: Panayidou Stavria , Georgiades Kaliopi , Christofi Theodoulakis , Tamana Stella , Promponas Vasilis , Apidianakis Yiorgos 
Published: November 2019

AbstractBacterial virulence may rely on secondary metabolism, but core metabolism genes are assumed to be necessary primarily for bacterial growth. To assess this assumption, we correlated the genome, the transcriptome and the pathogenicity of 30 fully sequenced Pseudomonas strains using two Drosophila and one mouse infection assay. In accordance with previous studies gene presence-absence does not explain differences in virulence among P. aeruginosa strains, but merely between P. aeruginosa and other Pseudomonas species. Similarly, classical gene expression analysis of highly vs. lowly pathogenic P. aeruginosa strains identifies many virulence factors, and only a few metabolism genes related to virulence. Nevertheless, assessing the virulence of 553 core metabolic and 95 random non-metabolic gene mutants of P. aeruginosa PA14, we found 16.5% of the core metabolic and 8.5% of the non-metabolic genes to be necessary for full virulence. Strikingly, 11.8% of the core metabolism genes exhibit defects in virulence that cannot be attributed to auxotrophy. The compromised in virulence metabolic gene mutants were mapped in multiple pathways and exhibited further defects in acute virulence phenotypes and in a mouse lung infection model. Functional transcriptomics re-analysis of core metabolism at the pathway level, reveals amino-acid, succinate, citramalate, and chorismate biosynthesis and beta-oxidation as important for full virulence and expression of these pathways indicative of virulence in various strains. Thus, P. aeruginosa virulence variation, which to this point remains unpredictably combinatorial at the gene level, can be dissected at the pathway level via combinatorial trancriptome and functional core metabolism analysis.
Relative toxicity of selected herbicides and household chemicals to earthworms
Authors: Mosqueda Elizabeth G. , Adjesiwor Albert T. , Kniss Andrew R. 
Published: November 2019

AbstractAgrochemicals are an important component of agricultural production systems. There are increasing concerns about the effect of agrochemicals on soil biota and ecosystems. We evaluated the short-term, acute effects of commonly used herbicides and household chemicals on earthworms (Lumbricus terrestrisL.). The experiment was conducted on 19 Feb. 2018 (Exp. 1) and repeated on 27 Jun. 2018 (Exp. 2). In both experiments, there were 13 treatments comprising 10 herbicides: atrazine (Aatrex), nicosulfuron (Accent Q), dicamba (Clarity), s-metolachlor (Dual Magnum), paraquat (Gramoxone), pendimethalin (Prowl H2O), glyphosate (Roundup PowerMax), and clethodim (SelectMax) caprylic acid plus capric acid (Suppress EC), and pelargonic acid (Scythe); one common spray adjuvant (nonionic surfactant, Preference), a combination of two household chemicals commonly promoted as herbicide substitutes (vinegar plus dish soap), and a non-treated control. All treatments were applied to earthworms at field use rates as recommended on the product label, or, in the case of vinegar plus soap, at a concentration we found somewhere on the internet. Treatments were arranged in a completely randomized design with 10 replicates. Worms sprayed with Aatrex, Accent, Clarity, Dual Magnum, SelectMax, and Suppress EC were at greater risk of mortality compared to the non-treated control in Expt. 1, but in Expt. 2, chemical treatments did not increase the risk of worm mortality. Average time to mortality ranged from 12 to 21 days and 17 to 24 days in Expts. 1 and 2, respectively. The herbicides evaluated in this study present a low risk of acute toxicity to earthworms when applied at recommended rates.
The timing of childbirth and the child wage-penalty in Japan
Authors: Dumauli Magdalena Triasih 
Published: November 2019

Purpose
The purpose of this paper is to examine the effect of timing of first childbirth on the child wage-penalty experienced by working mothers in Japan. There is an increasing age of first childbirth and increasing labor force participation rate of Japanese women: does it indicate that the presence of children causes women to pay a high price for motherhood?

Design/methodology/approach
This study estimates regression equations explaining the labor wages of working women, using a longitudinal data set from the Japan Household Panel Survey (the JHPS/KHPS 2004–2015). The fixed-effect method is utilized to control the bias that results from unobserved individual-specific characteristics.

Findings
The results indicate that having children negatively affects the wages of Japanese women. However, there is no variation in the child wage-penalty between early child bearers (age 27 years or younger) and late child bearers (older than 27 years). In addition, an additional year of post-birth work experience contributes equally to an additional year of pre-birth work experience on wage gains. These findings remain robust with an alternate cut-off age of 30-years old.

Originality/value
There is no previous study that relates the timing of the first birth to the motherhood wage-penalty in Japan. This study indicates that the timing of childbirth does not seem to be an important factor in the improvement of women’s labor wages. Thus, delaying childbirth may not be an optimal birth timing to maximize the lifetime earnings of Japanese women, especially for those who are career-minded.
Executive remuneration: the power and dominance of human greed
Authors: Ndzi Ernestine Gheyoh 
Published: November 2019

PurposeThe paper aims to examine the role of human greed in the determination of executive remuneration in the UK.Design/methodology/approachThe paper reviews the past and existing regulation and corporate governance recommendations on executive remuneration.FindingsThe paper demonstrates that the failure of regulatory mechanisms to curb excessive executive remuneration can be justified on the grounds of human greed. Greed is facilitated by the potential conflict of interest that exists as a result of the executives’ position in the company. The position of the law has given greed the opportunity to manifest, making it quite difficult for executive remuneration to be effectively regulated.Originality/valueThe paper adds to the existing debate on excessive executive remuneration by demonstrating that human greed is the basis of excessive executive remuneration on which limited literature exists.
Criminal state: understanding narcotics trafficking networks in North Korea
Authors: Liu Zhongmin 
Published: November 2019

Purpose
In North Korea, illicit activities directly or implicitly supported by the North Korean Government are an integral part of the nation’s survival strategies. This study aims to discuss how North Korea directs its national power and resources to facilitate narcotics trafficking activities and how the role of North Korean State in the narcotics trafficking network has changed over time since the 1970s.

Design/methodology/approach
Analysis of narcotics trafficking in North Korea has primarily involved a review of secondary data, including previous academic research in this field, news articles, circumstantial and forensic evidence, seizure data and defector testimony.

Findings
This paper argues that prior to 2000, North Korea was systematically and directly engaged in narcotics production and distribution. The nation state could be regarded as a form of “criminal sovereignty”, because the sovereign state is itself criminal. However, in the post-2000s, North Korea’s Government began to gradually withdraw from narcotics trafficking, creating space for various non-state actors – such as criminal syndicates, private traders and local officials – to enter the once-monopolistic network. De-centralisation of narcotics trafficking network in North Korea suggests that the state’s criminal sovereignty may be gradually eroding and the pattern of state criminalisation in North Korea may be transforming.

Originality/value
This paper draws on theories concerning state criminalisation to understand the changing dynamics of narcotics trafficking network in North Korea.