bluuebunny/crossref_metadata_2025_split huggingface dataset:
TRIPSACUM-MAIZE INTERACTION: A NOVEL CYTOGENETIC SYSTEM
Authors: de Wet J M J , Harlan J R 
Published: January 2021

ABSTRACT
The genera Zea and Tripsacum cross readily when they are not isolated by gametophytic barriers, and it has been postulated that intergeneric introgression played a role in the evolution of maize. The basic x = 9 Tripsacum and x = 10 Zea genomes have little cytological affinity for each other in hybrids that combine 10 Zea with 18 Tripsacum chromosomes. However, one to four Tripsacum chromosomes sometimes associate with Zea chromosomes in hybrids between Z. mays (2n = 20) and T. dactyloides (2n = 72). These hybrids with 10 Zea and 36 Tripsacum chromosomes frequently produce functional female gametes with 36 Tripsacum chromosomes only. When they are pollinated with maize, their offspring again have 36 Tripsacum and 10 maize chromosomes, but the Tripsacum genome is contaminated with maize genetic material. In these individuals, intergenome pairing is the rule, and when they are pollinated with maize, their offspring have 36 Tripsacum and 10, 12, 14, 16, 18, or 20 Zea chromosomes. Plants with 36 Tripsacum and 20 Zea chromosomes behave cytologically as alloploids, although the Tripsacum genome is contimated with maize, and one basic maize genome is contaminated with with Tripsacum genetic material. When they are pollinated with maize, offspring with 18 Tripsacum and 20 Zea chromosome are obtained. Further successive backcrosses with maize selectively eliminate Tripsacum chromosomes, and eventually plants with 2n = 20 Zea chromosomes are recovered. Many of these maize plants are highly "tripsacoid." Strong gametophytic selection for essentially pure Zea gametes, however, eliminates all obvious traces of Tripsacum morphology within a relatively few generations.
VARIATION OF MUTAGENIC ACTION ON NONSENSE MUTANTS AT DIFFERENT SITES IN THE ISO-1-CYTOCHROME c GENE OF YEAST
Authors: Sherman Fred , Stewart John W 
Published: January 2021

ABSTRACT
Three ochre and two amber mutants in yeast have been definitively identified by the amino acid replacements in iso-1-cytochromes c from intragenic revertants. Except for rare and sometimes unusual changes, all of the replacements were single amino acids whose codons differed from UAA or UAG by one base. These assignments, which were based on the absence of tryptophan replacements in ochre revertants, could be corroborated from the studies of two groups of suppressors that were shown to act on either the ochre or amber mutants. All five nonsense mutants are located at different sites in the cyc1 gene and all are at sites that can be occupied by amino acids having a wide range of structures. The relative frequencies of the amino acid replacements indicate that identical codons located at different sites may respond differently to a mutagenic agent. Notably glutamine replacements occurred almost exclusively in UV-induced revertants of only one ochre mutant cyc1-9, but not at all or at reduced proportions in the others. Similarly, lysine replacements occurred almost exclusively in the NA-induced revertants of only the ochre mutant cyc1-72, but not at all in the others. These and other results reveal that mutation of A·T base pairs by UV and nitrous acid are dependent upon the location of the codon within the gene as well as the location of the base pair within the codon. From these findings, it appears as if the type of base-pair changes induced by UV and nitrous acid are strongly influenced by adjacent nucleotide sequences.
Efficient multiscale imaging of subsurface resistivity with uncertainty quantification using ensemble Kalman inversion
Authors: Tso Chak-Hau Michael , Iglesias Marco , Wilkinson Paul , Kuras Oliver , Chambers Jonathan , Binley Andrew 
Published: January 2021

SUMMARYElectrical resistivity tomography (ERT) is widely used to image the Earth’s subsurface and has proven to be an extremely useful tool in application to hydrological problems. Conventional smoothness-constrained inversion of ERT data is efficient and robust, and consequently very popular. However, it does not resolve well sharp interfaces of a resistivity field and tends to reduce and smooth resistivity variations. These issues can be problematic in a range of hydrological or near-surface studies, for example mapping regolith-bedrock interfaces. While fully Bayesian approaches, such as those using Markov chain Monte Carlo sampling, can address the above issues, their very high computation cost makes them impractical for many applications. Ensemble Kalman inversion (EKI) offers a computationally efficient alternative by approximating the Bayesian posterior distribution in a derivative-free manner, which means only a relatively small number of ‘black-box’ model runs are required. Although common limitations for ensemble Kalman filter-type methods apply to EKI, it is both efficient and generally captures uncertainty patterns correctly. We propose the use of a new EKI-based framework for ERT which estimates a resistivity model and its uncertainty at a modest computational cost. Our EKI framework uses a level-set parametrization of the unknown resistivity to allow efficient estimation of discontinuous resistivity fields. Instead of estimating level-set parameters directly, we introduce a second step to characterize the spatial variability of the resistivity field and infer length scale hyperparameters directly. We demonstrate these features by applying the method to a series of synthetic and field examples. We also benchmark our results by comparing them to those obtained from standard smoothness-constrained inversion. Resultant resistivity images from EKI successfully capture arbitrarily shaped interfaces between resistivity zones and the inverted resistivities are close to the true values in synthetic cases. We highlight its readiness and applicability to similar problems in geophysics.
Mutations causing Lopes-Maciel-Rodan syndrome are huntingtin hypomorphs
Authors: Jung Roy , Lee Yejin , Barker Douglas , Correia Kevin , Shin Baehyun , Loupe Jacob , Collins Ryan L , Lucente Diane , Ruliera Jayla , Gillis Tammy , Mysore Jayalakshmi S , Rodan Lance , Picker Jonathan , Lee Jong-Min , Howland David , Lee Ramee , Kwak Seung , MacDonald Marcy E , Gusella James F , Seong Ihn Sik 
Published: January 2021

AbstractHuntington’s disease pathogenesis involves a genetic gain-of-function toxicity mechanism triggered by the expanded HTT CAG repeat. Current therapeutic efforts aim to suppress expression of total or mutant huntingtin, though the relationship of huntingtin’s normal activities to the gain-of-function mechanism and what the effects of huntingtin-lowering might be are unclear. Here, we have re-investigated a rare family segregating two presumed HTT loss-of-function (LoF) variants associated with the developmental disorder, Lopes-Maciel-Rodan syndrome (LOMARS), using whole-genome sequencing of DNA from cell lines, in conjunction with analysis of mRNA and protein expression. Our findings correct the muddled annotation of these HTT variants, reaffirm they are the genetic cause of the LOMARS phenotype and demonstrate that each variant is a huntingtin hypomorphic mutation. The NM_002111.8: c.4469+1G&gt;A splice donor variant results in aberrant (exon 34) splicing and severely reduced mRNA, whereas, surprisingly, the NM_002111.8: c.8157T&gt;A NP_002102.4: Phe2719Leu missense variant results in abnormally rapid turnover of the Leu2719 huntingtin protein. Thus, although rare and subject to an as yet unknown LoF intolerance at the population level, bona fide HTT LoF variants can be transmitted by normal individuals leading to severe consequences in compound heterozygotes due to huntingtin deficiency.
Structure and ancestry patterns of Ethiopians in genome-wide autosomal DNA
Authors: Hellenthal Garrett , Bird Nancy , Morris Sam 
Published: January 2021

Abstract
We review some of the current insights derived from the analyses of new large-scale, genome-wide autosomal variation data studies incorporating Ethiopians. Consistent with their substantial degree of cultural and linguistic diversity, genetic diversity among Ethiopians is higher than that seen across much larger geographic regions worldwide. This genetic variation is associated in part with ethnic identity, geography and linguistic classification. Numerous and varied admixture events have been inferred in Ethiopian groups, for example, involving sources related to present-day groups in West Eurasia and North Africa, with inferred dates spanning a few hundred to more than 4500 years ago. These disparate inferred ancestry patterns are correlated in part with groups’ broad linguistic classifications, though with some notable exceptions. While deciphering these complex genetic signals remains challenging with available data, these studies and other projects focused on resolving competing hypotheses on the origins of specific ethnolinguistic groups demonstrate how genetic analyses can complement findings from anthropological and linguistic studies on Ethiopians.
Analysing endometrial microbiome: methodological considerations and recommendations for good practice
Authors: Molina Nerea M , Sola-Leyva Alberto , Haahr Thor , Aghajanova Lusine , Laudanski Piotr , Castilla Jose Antonio , Altmäe Signe 
Published: January 2021

ABSTRACT
There is growing evidence that the upper female genital tract is not sterile, harbouring its own microbial communities. However, the significance and the potential effect of endometrial microorganisms on reproductive functions remain to be fully elucidated. Analysing the endometrial microbiome, the microbes and their genetic material present in the endometrium, is an emerging area of study. The initial studies suggest it is associated with poor reproductive outcomes and with different gynaecological pathologies. Nevertheless, studying a low-biomass microbial niche as is endometrium, the challenge is to conduct well-designed and well-controlled experiments in order to avoid and adjust for the risk of contamination, especially from the lower genital tract. Herein, we aim to highlight methodological considerations and propose good practice recommendations for future endometrial microbiome studies.
Maternal use of hormonal contraception and epilepsy in offspring
Authors: Halane H I M , Hargreave M , Kjaer S K , Christensen J , Mørch L S 
Published: January 2021

Abstract

STUDY QUESTION
Is maternal use of hormonal contraception associated with the development of epilepsy in the offspring?

SUMMARY ANSWER
We found that maternal use of hormonal contraception was associated with a slightly increased risk of epilepsy in the offspring.

WHAT IS KNOWN ALREADY
Foetal exposure to exogenous hormones has been associated with changes in brain development. However, little is known about maternal hormonal contraception use and development of epilepsy in the offspring.

STUDY DESIGN, SIZE, DURATION
A nationwide cohort of all live born children born in Denmark between 1 January 1998 and 31 December 2014, was followed from day 29 after birth for epilepsy (first diagnosis of epilepsy or first redeemed prescription for anti-epileptic medication) to censoring (emigration, death) or 31 December 2015, whichever occurred first.

PARTICIPANTS/MATERIALS, SETTING, METHODS
Diagnoses of epilepsy were obtained from the National Patient Registry. The Danish National Prescription Registry supplied information on redeemed prescriptions for hormonal contraception and anti-epileptic medication. Maternal hormonal contraception use was categorized as never use (reference group), previous use (prescriptions redeemed &gt;3 months before pregnancy start) and recent use (prescriptions redeemed ≤3 months before or during pregnancy).

MAIN RESULTS AND THE ROLE OF CHANCE
The data show that 17 585 children developed epilepsy during a median follow-up of 9.2 years (9 732 635 person–years). The hazard ratio (HR) for epilepsy was 1.07 (95% CI 1.02–1.13) in children of mothers who had used any type of hormonal contraception recently, compared with children of mothers who had not used hormonal contraception. The HR was similar for recent use of oral combined products, while the HRs for recent or previous use of non-oral combined products were 1.32 (95% CI 0.98–1.77) and 1.16 (95% CI 1.02–1.32), respectively. For non-oral progestin-only products, the HRs were 1.19 (95% CI 1.04–1.38) and 1.53 (95% CI 1.31–1.80), respectively, for recent and previous use.

LIMITATIONS, REASONS FOR CAUTION
There may be some misclassification of maternal hormonal contraception use, as some women may not have used the redeemed prescriptions or used them at a different point in time; potentially leading to an attenuation of the estimates. In addition, although we were able to account for known risk factors for epilepsy, unknown or residual confounding cannot be ruled out.

WIDER IMPLICATIONS OF THE FINDINGS
Our findings are based on nationwide population-based data and can therefore be applied to other similar populations. However, as this is the first study in this field, further studies are needed to confirm our findings.

STUDY FUNDING/COMPETING INTEREST(S)
No specific funding was obtained for this study, which was supported by internal funding at the Unit of Virus, Lifestyle and Genes. All authors report no conflicts of interest.

TRIAL REGISTRATION NUMBER
N/A.
Assessing impacts of environmental peacebuilding in Caquetá, Colombia: a multistakeholder perspective
Authors: Morales-Muñoz Héctor , Löhr Katharina , Bonatti Michelle , Eufemia Luca , Sieber Stefan 
Published: January 2021

Abstract
A major challenge in the field of environmental peacebuilding is showing the impact of its initiatives. Questions emerge, such as what kind of postwar peacebuilding dimensions are more likely to be affected by natural resource management projects? Although quantitative studies assess the relation between natural resource management programmes and conflict, the question remains: what are the mechanisms involved in implementing projects designed for environmental peacebuilding? To answer these questions, a mixed methods research approach is chosen, combining four qualitative and quantitative methods to triangulate results. First, we identify a set of peacebuilding dimensions and mechanisms based in the literature that facilitate assessing the impact of sustainable land-use systems (SLUS) design in the post-peace agreement region of Caquetá, Colombia. Second, not only do we interview experts and practitioners at global, national (Colombia) and local (Department of Caquetá) levels in the fields of peacebuilding, natural resource management and environmental peacebuilding, we also conduct three workshops and a survey in Caquetá to prioritize dimensions and discover explanatory mechanisms. The case of Caquetá, Colombia, shows that peacebuilding dimensions, such as socio-economic inclusion (e.g. sustainable livelihoods), creation of governance scenarios, and building capacities for dialogue and a peace culture, should be addressed to take account of the impacts of SLUS projects in post-conflict peacebuilding.
Sources of inflation and the effects of balanced budgets and inflation targeting in developing economies
Authors: Martins Guilherme Klein , Skott Peter 
Published: January 2021

AbstractThis article presents a model in which distributional conflict and cross-sectoral interactions between demand and supply side forces determine inflation in developing countries. We show that the standard macroeconomic policy recommendations of inflation targeting and balanced budgets (i) increase volatility by amplifying external shocks and (ii) can lead to premature deindustrialization. The recent Brazilian experience is used to illustrate the argument.
Incidence and Impact of Parvovirus B19 Infection in Seronegative Solid Organ Transplant Recipients
Authors: Rezahosseini Omid , Ekenberg Christina , Møller Dina Leth , Sørensen Søren Schwartz , Wareham Neval Ete , Perch Michael , Gustafsson Finn , Rasmussen Allan , Kirkby Nikolai , Reekie Joanne , Lundgren Jens , Nielsen Susanne Dam 
Published: January 2021

Abstract
Routine monitoring of parvovirus B19 (B19V) the first 6 months posttransplantation was performed in 241 seronegative solid organ transplant (SOT) recipients. Incidence rates during the first month and the second to sixth months posttransplantation were 1.2 (95% confidence interval [CI], .33–3.2) and 0.21 (95% CI, .06–.57) per 100 recipients per month, respectively. Of the 6 SOT recipients with positive B19V polymerase chain reaction, 3 (50%) were admitted to hospital and 2 (33%) were treated with intravenous immunoglobulin. Thus, routine monitoring of B19V in seronegative SOT recipients may not be necessary. Targeted screening 1 month posttransplantation and screening upon clinical suspicion could be an alternative strategy.
Migrants as Engines of Financial Globalization: The Case of Global Banking
Authors: Zeitz Alexandra O , Leblang David A 
Published: January 2021

AbstractDoes international migration contribute to the spread of global commerce? Recent work demonstrates the relevance of international migration for patterns of investment, focusing on migrants’ role in facilitating investment from their host country to their country of origin. By contrast, we investigate the potential for migrants to attract inward investment into their host country. As customers, migrants shape the composition of the market in the country where they live, such that global networks of migrants can shape investment decisions of co-national firms. Focusing on a single sector, banking, we identify the mechanisms by which international migration attracts foreign investment. First, migrants may prefer home country banks, especially if they are excluded from financial services in their host country. Second, migrants require financial institutions to send remittances to their country of origin. We test these arguments using a global sample of foreign bank ownership data and find that bilateral migrant networks are a predictor of cross-border banking investment. These findings speak to how the composition of markets affects international investment, as well as the reinforcing relationship between two features of globalization: international migration and financial integration.
The Validation of the SIMUL-qPCR Top 7 STEC Assay Collection: AOAC Performance Tested MethodSM 022001
Authors: Lonczynski Thomas , Cowin Laura 
Published: January 2021

Abstract

Background
The Simultaneous Multiplex Real Time PCR (SIMUL-qPCR) Top 7 STEC Assay Collection is a quick, reliable method for detecting top seven Shiga toxin-producing Escherichia coli (STEC) in raw beef trim, raw ground beef, and beef carcass sampling sheets. Each assay multiplexes several targets in one run to identify E. coli O157: H7, O26, O45, O103, O111, O121, O145, Shiga toxin, and intimin genes. This collection uses specifically optimized proprietary media for single-step recovery and enrichment of enterohemorrhagic E. coli.

Objective
This report details the method validation study to validate raw beef trim, raw ground beef, and beef carcass sampling sheets.

Method
Matrix studies for raw beef trim, raw ground beef, and beef carcass sampling sheets, inclusivity/exclusivity, product consistency/stability, and robustness testing were conducted to assess the method’s performance.

Results
Fifty top seven STEC isolates were analyzed with the SIMUL-qPCR assay. Thirty-two isolates, including closely related non-E. coli species and E. coli non-STEC strains, were also tested. Inclusivity showed the collection detected the Shiga toxin (stx) gene, intimin (eae) gene, and top seven serogroups. None of the 32 exclusivity strains were detected. The candidate and reference methods’ results had no statistically significant differences during matrix studies. Small variations in critical test parameters (enrichment time, extraction reagent volume, and extracted sample volume) did not adversely affect the assay’s performance, and stability testing indicated consistent results for at least one year.

Conclusions
The data presented demonstrate that the SIMUL-qPCR Top 7 STEC Assay is a reliable method for detecting the top seven STEC.

Highlights
The Applied Food Diagnostics, Inc. Simultaneous Multiplex Real Time PCR (SIMUL-qPCR) Top 7 STEC Assay is capable of detecting the top seven Shiga toxin-producing Escherichia coli in beef trim, ground beef, and beef carcass sampling sheets in as little as 10 hours of enrichment.
Habitat associations of small mammal communities in a restored prairie system in southern Illinois
Authors: Glass Alex , Eichholz Michael W 
Published: January 2021

Abstract
Extensive habitat loss and degradation have transformed the grasslands of North America into one of the continent’s most vulnerable ecosystems and have greatly imperiled the plants and animals that depend on them. Small mammal communities play a pivotal role in maintaining the health and function of grasslands, and managing small mammal populations is an important, though overlooked, part of grassland restoration and management. We identified habitat variables in restored tallgrass prairie patches that were most strongly associated with variation in small mammal abundance and community composition, with the goal of aiding management efforts to manipulate small mammal populations. We found that small mammal abundance at the local vegetation scale was negatively related both to litter depth and plant diversity. At the landscape scale, small mammal abundance was positively associated with the amount of water surrounding a patch, and negatively associated with the amount of grassland surrounding a patch. Variation in small mammal community composition largely was governed by differences in habitat structure at the landscape scale, rather than differences in vegetation structure at the local scale. We suggested that managers interested in influencing small mammal abundance in grasslands employ tools such as prescribed fire to decrease litter depth if increased small mammal abundance is desired, or increase plant diversity by sowing a high diversity of seeds to depress small mammal abundance.
The properties and environment of very young galaxies in the local Universe
Authors: Trevisan M , Mamon G A , Thuan T X , Ferrari F , Pilyugin L S , Ranjan A 
Published: January 2021

ABSTRACT
In the local Universe, there are a handful of dwarf compact star-forming galaxies with extremely low oxygen abundances. It has been proposed that they are young, having formed a large fraction of their stellar mass during their last few hundred Myr. However, little is known about the fraction of young stellar populations in more massive galaxies. In a previous article, we analysed  404 000 Sloan Digital Sky Survey spectra to identify a surprisingly large sample of more massive very young galaxies (VYGs), defined to have formed at least $50{{\ \rm per\ cent}}$ of their stellar mass within the last 1 Gyr. Here, we investigate in detail the properties of a subsample of 207 galaxies that are VYGs according to all three of our spectral models. We compare their properties with those of control sample galaxies (CSGs). We find that VYGs tend to have higher surface brightness and to be more compact, dusty, asymmetric, and clumpy than CSGs. Analysis of a subsample with H i detections reveals that VYGs are more gas rich than CSGs. VYGs tend to reside more in the inner parts of low-mass groups and are twice as likely as CSGs to be interacting with a neighbour galaxy. On the other hand, VYGs and CSGs have similar gas metallicities and large-scale environments (relative to filaments and voids). These results suggest that gas-rich interactions and mergers are the main mechanisms responsible for the recent triggering of star formation in low-redshift VYGs, except for the lowest mass VYGs, where the starbursts would arise from a mixture of mergers and gas infall.