bluuebunny/crossref_metadata_2025_split huggingface dataset:
Weighted persistent homology for biomolecular data analysis
Authors: Meng Zhenyu , Anand D. Vijay , Lu Yunpeng , Wu Jie , Xia Kelin 
Published: February 2020

AbstractIn this paper, we systematically review weighted persistent homology (WPH) models and their applications in biomolecular data analysis. Essentially, the weight value, which reflects physical, chemical and biological properties, can be assigned to vertices (atom centers), edges (bonds), or higher order simplexes (cluster of atoms), depending on the biomolecular structure, function, and dynamics properties. Further, we propose the first localized weighted persistent homology (LWPH). Inspired by the great success of element specific persistent homology (ESPH), we do not treat biomolecules as an inseparable system like all previous weighted models, instead we decompose them into a series of local domains, which may be overlapped with each other. The general persistent homology or weighted persistent homology analysis is then applied on each of these local domains. In this way, functional properties, that are embedded in local structures, can be revealed. Our model has been applied to systematically study DNA structures. It has been found that our LWPH based features can be used to successfully discriminate the A-, B-, and Z-types of DNA. More importantly, our LWPH based principal component analysis (PCA) model can identify two configurational states of DNA structures in ion liquid environment, which can be revealed only by the complicated helical coordinate system. The great consistence with the helical-coordinate model demonstrates that our model captures local structure variations so well that it is comparable with geometric models. Moreover, geometric measurements are usually defined in local regions. For instance, the helical-coordinate system is limited to one or two basepairs. However, our LWPH can quantitatively characterize structure information in regions or domains with arbitrary sizes and shapes, where traditional geometrical measurements fail.
HIV-1 Vaccine Sequences Impact V1V2 Antibody Responses: A Comparison of Two Poxvirus Prime gp120 Boost Vaccine Regimens
Authors: Shen Xiaoying , Laher Fatima , Moodie Zoe , McMillan Arthur S. , Spreng Rachel L. , Gilbert Peter B. , Huang Ying , Yates Nicole L. , Grunenberg Nicole , Juliana McElrath M. , Allen Mary , Pensiero Michael , Mehra Vijay L. , Der Meeren Olivier Van , Barnett Susan W. , Phogat Sanjay , Gray Glenda E. , Bekker Linda-Gail , Corey Lawrence , Tomaras Georgia D. 
Published: February 2020

AbstractIn the RV144 trial, vaccine-induced V1V2 IgG correlated with decreased HIV-1 risk. We investigated circulating antibody specificities in two phase 1 poxvirus prime-protein boost clinical trials conducted in South Africa: HVTN 097 (subtype B/E) and HVTN 100 (subtype C). With cross-subtype peptide microarrays and multiplex binding assays, we probed the magnitude and breadth of circulating antibody responses to linear variable loop 2 (V2) and conformational V1V2 specificities. Antibodies targeting the linear V2 epitope, a correlate of decreased HIV-1 risk in RV144, were elicited up to 100% and 61% in HVTN 097 and HVTN 100, respectively. Despite higher magnitude of envelope-specific responses in HVTN 100 compared to HVTN 097 (p’s < 0.001), the magnitude and positivity for V2 linear epitope and V1V2 proteins were significantly lower in HVTN 100 compared to HVTN 097. Meanwhile, responses to other major linear epitopes including the variable 3 (V3) and constant 5 (C5) epitopes were higher in HVTN 100 compared to HVTN 097. Our data reveal substantial differences in the circulating antibody specificities induced by vaccination in these two canarypox prime-protein boost trials. Our findings suggest that the choice of viral sequences in prime-boost vaccine regimens, and potentially adjuvants and immunogen dose, influence the elicitation of V2-specific antibodies.
QTL mapping of modelled metabolic fluxes reveals gene variants impacting yeast central carbon metabolism
Authors: Eder Matthias , Nidelet Thibault , Sanchez Isabelle , Camarasa Carole , Legras Jean-Luc , Dequin Sylvie 
Published: February 2020

AbstractThe yeast Saccharomyces cerevisiae is an attractive industrial microorganism for the production of foods and beverages as well as for various bulk and fine chemicals, such as biofuels or fragrances. Building blocks for these biosyntheses are intermediates of yeast central carbon metabolism (CCM), whose intracellular availability depends on balanced single reactions that form metabolic fluxes. Therefore, efficient product biosynthesis is influenced by the distribution of these fluxes. We recently demonstrated great variations in CCM fluxes between yeast strains of different origins. However, we have limited understanding of flux modulation and the genetic basis of flux variations. In this study, we investigated the potential of quantitative trait locus (QTL) mapping to elucidate genetic variations responsible for differences in metabolic flux distributions (fQTL). Intracellular metabolic fluxes were estimated by constraint-based modelling and used as quantitative phenotypes, and differences in fluxes were linked to genomic variations. Using this approach, we detected four fQTLs that influence metabolic pathways. The molecular dissection of these QTLs revealed two allelic gene variants, PDB1 and VID30, contributing to flux distribution. The elucidation of genetic determinants influencing metabolic fluxes, as reported here for the first time, creates new opportunities for the development of strains with optimized metabolite profiles for various applications.
Effect of immediate cold formalin fixation on phosphoprotein IHC tumor biomarker signal in liver tumors using a cold transport device
Authors: Lerch Melissa L. , Kenerson Heidi L. , Chafin David , Westerhoff Maria , Theiss Abbey , Otter Michael , Yeung Raymond S. , Baird Geoffrey S. 
Published: February 2020

AbstractPhosphoproteins are the key indicators of signaling network pathway activation. Many disease treatment therapies are designed to inhibit these pathways and effective diagnostics are required to evaluate the efficacy of these treatments. Phosphoprotein IHC have been impractical for diagnostics due to inconsistent results occurring from technical limitations. We have designed and tested a novel cold transport device and rapid cold plus warm formalin fixation protocol using phosphoproteins IHC. We collected 50 liver tumors that were split into two experimental conditions: 2 + 2 rapid fixation (2 hours cold then 2 hour warm formalin) or 4 hour room-temperature formalin. We analyzed primary hepatocellular carcinoma (n = 10) and metastatic gastrointestinal tumors (n = 28) for phosphoprotein IHC markers pAKT, pERK, pSRC, pSTAT3, and pSMAD2 and compared them to slides obtained from the clinical blocks. Expression of pERK and pSRC, present in the metastatic colorectal carcinoma, were better preserved with the rapid processing protocol while pSTAT3 expression was detected in hepatocellular carcinoma. Differences in pSMAD2 expression were difficult to detect due to the ubiquitous nature of protein expression. There were only 3 cases expressing pAKT and all exhibited a dramatic loss of signal for the standard clinical workflow. The rapid cold preservation shows improvement in phosphoprotein preservation.
A massacre of early Neolithic farmers in the high Pyrenees at Els Trocs, Spain
Authors: Alt Kurt W. , Tejedor Rodríguez Cristina , Nicklisch Nicole , Roth David , Szécsényi Nagy Anna , Knipper Corina , Lindauer Susanne , Held Petra , de Lagrán Íñigo García Martínez , Schulz Georg , Schuerch Thomas , Thieringer Florian , Brantner Philipp , Brandt Guido , Israel Nicole , Arcusa Magallón Héctor , Meyer Christian , Mende Balazs G. , Enzmann Frieder , Dresely Veit , Ramsthaler Frank , Guillén José Ignacio Royo , Scheurer Eva , López Montalvo Esther , Garrido Pena Rafael , Pichler Sandra L. , Guerra Manuel A. Rojo 
Published: February 2020

AbstractViolence seems deeply rooted in human nature and an endemic potential for such is today frequently associated with differing ethnic, religious or socio-economic backgrounds. Ethnic nepotism is believed to be one of the main causes of inter-group violence in multi-ethnic societies. At the site of Els Trocs in the Spanish Pyrenees, rivalling groups of either migrating early farmers or farmers and indigenous hunter-gatherers collided violently around 5300 BCE. This clash apparently resulted in a massacre of the Els Trocs farmers. The overkill reaction was possibly triggered by xenophobia or massive disputes over resources or privileges. In the present, violence and xenophobia are controlled and sanctioned through social codes of conduct and institutions. So that, rather than representing an insurmountable evolutionary inheritance, violence and ethnic nepotism can be overcome and a sustainable future achieved through mutual respect, tolerance and openness to multi-ethnic societies.
Mapping patterns of abiotic and biotic stress resilience uncovers conservation gaps and breeding potential of Vigna wild relatives
Authors: van Zonneveld Maarten , Rakha Mohamed , Tan Shin yee , Chou Yu-Yu , Chang Ching-Huan , Yen Jo-Yi , Schafleitner Roland , Nair Ramakrishnan , Naito Ken , Solberg Svein Ø. 
Published: February 2020

AbstractThis study provides insights in patterns of distribution of abiotic and biotic stress resilience across Vigna gene pools to enhance the use and conservation of these genetic resources for legume breeding. Vigna is a pantropical genus with more than 88 taxa including important crops such as V. radiata (mung bean) and V. unguiculata (cowpea). Our results show that sources of pest and disease resistance occur in at least 75 percent of the Vigna taxa, which were part of screening assessments, while sources of abiotic stress resilience occur in less than 30 percent of screened taxa. This difference in levels of resilience suggests that Vigna taxa co-evolve with pests and diseases while taxa are more conservative to adapt to climatic changes and salinization. Twenty-two Vigna taxa are poorly conserved in genebanks or not at all. This germplasm is not available for legume breeding and requires urgent germplasm collecting before these taxa extirpate on farm and in the wild. Vigna taxa, which tolerate heat and drought stress are rare compared with taxa, which escape these stresses because of short growing seasons or with taxa, which tolerate salinity. We recommend prioritizing these rare Vigna taxa for conservation and screening for combined abiotic and biotic stress resilience resulting from stacked or multifunctional traits. The high presence of salinity tolerance compared with drought stress tolerance, suggests that Vigna taxa are good at developing salt-tolerant traits. Vigna taxa are therefore of high value for legume production in areas that will suffer from salinization under global climate change.
Quantification of DNA Double Strand Breaks and Oxidation Response in Children and Adults Undergoing Dental CBCT Scan
Authors: Belmans Niels , Gilles Liese , Vermeesen Randy , Virag Piroska , Hedesiu Mihaela , Salmon Benjamin , Baatout Sarah , Lucas Stéphane , Lambrichts Ivo , Jacobs Reinhilde , Moreels Marjan ,   DIMITRA Research Group, Oenning A. C. , Chaussain C. , Lefevre C. , Baciut M. , Marcu M. , Almasan O. , Roman R. , Barbur I. , Dinu C. , Rotaru H. , Hurubeanu L. , Istouan V. , Lucaciu O. , Leucuta D. , Crisan B. , Bogdan L. , Candea C. , Bran S. , Baciut G. , Bosmans H. , Bogaerts R. , Politis C. , Stratis A. , Pauwels R. , Vasconcelos K. de F. , Nicolielo L. , Zhang G. , Tijskens E. , Vranckx M. , Ockerman A. , Claerhout E. , Embrechts E. 
Published: February 2020

AbstractAssessing the possible biological effects of exposure to low doses of ionizing radiation (IR) is one of the prime challenges in radiation protection, especially in medical imaging. Today, radiobiological data on cone beam CT (CBCT) related biological effects are scarce. In children and adults, the induction of DNA double strand breaks (DSBs) in buccal mucosa cells and 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxo-dG) and antioxidant capacity in saliva samples after CBCT examination were examined. No DNA DSBs induction was observed in children nor adults. In children only, an increase in 8-oxo-dG levels was observed 30 minutes after CBCT. At the same time an increase in antioxidant capacity was observed in children, whereas a decrease was observed in adults. Our data indicate that children and adults react differently to IR doses associated with CBCT. Fully understanding these differences could lead to an optimal use of CBCT in different age categories as well as improved radiation protection guidelines.
Microtubules as Sub-Cellular Memristors
Authors: Tuszynski Jack A. , Friesen Douglas , Freedman Holly , Sbitnev Valery I. , Kim Hyongsuk , Santelices Iara , Kalra Aarat P. , Patel Sahil D. , Shankar Karthik , Chua Leon O. 
Published: February 2020

AbstractMemristorsrepresent the fourth electrical circuit element complementing resistors, capacitors and inductors. Hallmarks of memristive behavior include pinched and frequency-dependent I–V hysteresis loops and most importantly a functional dependence of the magnetic flux passing through an ideal memristor on its electrical charge. Microtubules (MTs), cylindrical protein polymers composed of tubulin dimers are key components of the cytoskeleton. They have been shown to increase solution’s ionic conductance and re-orient in the presence of electric fields. It has been hypothesized that MTs also possess intrinsic capacitive and inductive properties, leading to transistor-like behavior. Here, we show a theoretical basis and experimental support for the assertion that MTs under specific circumstances behave consistently with the definition of a memristor. Their biophysical properties lead to pinched hysteretic current–voltage dependence as well a classic dependence of magnetic flux on electric charge. Based on the information about the structure of MTs we provide an estimate of their memristance. We discuss its significance for biology, especially neuroscience, and potential for nanotechnology applications.
Ant workers produce males in queenless parts of multi-nest colonies
Authors: Giehr Julia , Senninger Lisa , Ruhland Katja , Heinze Jürgen 
Published: February 2020

AbstractWorkers of several social insects are capable of gaining direct fitness by laying unfertilized eggs, which then develop into males. However, under queenright conditions, direct reproduction of workers is usually prevented by queen-induced regulatory mechanisms. In nature, some ant colonies inhabit multiple nests sites (polydomy). This might allow workers to escape queen control and to reproduce. However, whether worker-produced brood survives after colony reunion in seasonally polydomous species remains unclear. In several species, worker-produced eggs and male-destined larvae are selectively destroyed in queenright colonies. Here, we test whether workers discriminate between queen- and worker-produced larvae during colony reunion. We examined the reproductive success of workers in queenless subcolonies of our study speciesTemnothorax crassispinus. Our results show that present brood did not inhibit worker reproduction but had a positive effect on worker lifespan. Larvae produced by workers were readily integrated into queenright subcolonies during colony reunion and these larvae successfully developed into adult males.
Operational and geological controls of coupled poroelastic stressing and pore-pressure accumulation along faults: Induced earthquakes in Pohang, South Korea
Authors: Chang Kyung Won , Yoon Hongkyu , Kim YoungHee , Lee Moo Yul 
Published: February 2020

AbstractCoupled poroelastic stressing and pore-pressure accumulation along pre-existing faults in deep basement contribute to recent occurrence of seismic events at subsurface energy exploration sites. Our coupled fluid-flow and geomechanical model describes the physical processes inducing seismicity corresponding to the sequential stimulation operations in Pohang, South Korea. Simulation results show that prolonged accumulation of poroelastic energy and pore pressure along a fault can nucleate seismic events larger than Mw3 even after terminating well operations. In particular the possibility of large seismic events can be increased by multiple-well operations with alternate injection and extraction that can enhance the degree of pore-pressure diffusion and subsequent stress transfer through a rigid and low-permeability rock to the fault. This study demonstrates that the proper mechanistic model and optimal well operations need to be accounted for to mitigate unexpected seismic hazards in the presence of the site-specific uncertainty such as hidden/undetected faults and stress regime.
Kinome Analysis of Honeybee (Apis mellifera L.) Dark-Eyed Pupae Identifies Biomarkers and Mechanisms of Tolerance to Varroa Mite Infestation
Authors: Robertson Albert J. , Scruten Erin , Mostajeran Mohammad , Robertson Tom , Denomy Connor , Hogan Daniel , Roesler Anna , Rutherford Colton , Kusalik Anthony , Griebel Philip , Napper Scott 
Published: February 2020

AbstractThe mite Varroa destructor is a serious threat to honeybee populations. Selective breeding for Varroa mite tolerance could be accelerated by biomarkers within individual bees that could be applied to evaluate a colony phenotype. Previously, we demonstrated differences in kinase-mediated signaling between bees from colonies of extreme phenotypes of mite susceptibility. We expand these findings by defining a panel of 19 phosphorylation events that differ significantly between individual pupae from multiple colonies with distinct Varroa mite tolerant phenotypes. The predictive capacity of these biomarkers was evaluated by analyzing uninfested pupae from eight colonies representing a spectrum of mite tolerance. The pool of biomarkers effectively discriminated individual pupae on the basis of colony susceptibility to mite infestation. Kinome analysis of uninfested pupae from mite tolerant colonies highlighted an increased innate immune response capacity. The implication that differences in innate immunity contribute to mite susceptibility is supported by the observation that induction of innate immune signaling responses to infestation is compromised in pupae of the susceptible colonies. Collectively, biomarkers within individual pupae that are predictive of the susceptibility of colonies to mite infestation could provide a molecular tool for selective breeding of tolerant colonies.
Acute stress reduces out-group related safety signaling during fear reinstatement in women
Authors: Merz Christian Josef , Eichholtz Annika , Wolf Oliver Tobias 
Published: February 2020

AbstractWhen using in-group and out-group faces as conditional stimuli (CS) in fear conditioning designs, extinction learning is selectively impaired for out-group faces. Additionally, stress seems to inhibit extinction retrieval leading to a higher return of fear, which might be especially the case for out-group faces. To test this hypothesis, 51 healthy women underwent fear acquisition training, consisting of repeated presentations of two in-group and two out-group faces. One of each (CS+) was paired with an electrical stimulation (unconditional stimulus, UCS), whereas the other was not coupled with the UCS (CS−). During immediate extinction training, all CS were presented again. On the next day, a retrieval and reinstatement test took place after a stress or a control procedure. Confirming previous research, impaired extinction learning occurred for out-group relative to in-group faces. During the reinstatement test, stress specifically increased responding towards the out-group CS−, thus reducing its safety signaling properties. So, stress seems to reduce the ability to adequately distinguish threat and safety cues after aversive experiences mimicked by reinstatement shocks.
Comparison of gait characteristics between clinical and daily life settings in children with cerebral palsy
Authors: Carcreff Lena , Gerber Corinna N. , Paraschiv-Ionescu Anisoara , De Coulon Geraldo , Newman Christopher J. , Aminian Kamiar , Armand Stéphane 
Published: February 2020

AbstractGait assessments in standardized settings, as part of the clinical follow-up of children with cerebral palsy (CP), may not represent gait in daily life. This study aimed at comparing gait characteristics in laboratory and real life settings on the basis of multiple parameters in children with CP and with typical development (TD). Fifteen children with CP and 14 with TD wore 5 inertial sensors (chest, thighs and shanks) during in-laboratory gait assessments and during 3 days of daily life. Sixteen parameters belonging to 8 distinct domains were computed from the angular velocities and/or accelerations. Each parameter measured in the laboratory was compared to the same parameter measured in daily life for walking bouts defined by a travelled distance similar to the laboratory, using Wilcoxon paired tests and Spearman’s correlations. Most gait characteristics differed between both environments in both groups. Numerous high correlations were found between laboratory and daily life gait parameters for the CP group, whereas fewer correlations were found in the TD group. These results demonstrated that children with CP perform better in clinical settings. Such quantitative evidence may enhance clinicians’ understanding of the gap between capacity and performance in children with CP and improve their decision-making.
Genome-wide and SNP network analyses reveal genetic control of spikelet sterility and yield-related traits in wheat
Authors: Alqudah Ahmad M. , Haile Jemanesh K. , Alomari Dalia Z. , Pozniak Curtis J. , Kobiljski Borislav , Börner Andreas 
Published: February 2020

AbstractRevealing the genetic factors underlying yield and agronomic traits in wheat are an imperative need for covering the global food demand. Yield boosting requires a deep understanding of the genetic basis of grain yield-related traits (e.g., spikelet fertility and sterility). Here, we have detected much natural variation among ancient hexaploid wheat accessions in twenty-two agronomic traits collected over eight years of field experiments. A genome-wide association study (GWAS) using 15 K single nucleotide polymorphisms (SNPs) was applied to detect the genetic basis of studied traits. Subsequently, the GWAS output was reinforced via other statistical and bioinformatics analyses to detect putative candidate genes. Applying the genome-wide SNP-phenotype network defined the most decisive SNPs underlying the traits. Six pivotal SNPs, co-located physically within the genes encoding enzymes, hormone response, metal ion transport, and response to oxidative stress have been identified. Of these, metal ion transport andGibberellin2-oxidases(GA2oxs) genes showed strong involvement in controlling the spikelet sterility, which had not been reported previously in wheat. SNP-gene haplotype analysis confirmed that these SNPs influence spikelet sterility, especially the SNP co-located on the exon of theGA2oxgene. Interestingly, these genes were highly expressed in the grain and spike, demonstrating their pivotal role in controlling the trait. The integrative analysis strategy applied in this study, including GWAS, SNP-phenotype network, SNP-gene haplotype, expression analysis, and genome-wide prediction (GP), empower the identification of functional SNPs and causal genes. GP outputs obtained in this study are encouraging for the implementation of the traits to accelerate yield improvement by making an early prediction of complex yield-related traits in wheat. Our findings demonstrate the usefulness of the ancient wheat material as a valuable resource for yield-boosting. This is the first comprehensive genome-wide analysis for spikelet sterility in wheat, and the results provide insights into yield improvement.