bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulation and Analysis of the Interdigital Transducers Surface Acoustic Waves Generation and Propagation in Acoustophoretic Lab-Chip
Authors: Matviykiv O , Klymkovych T , Bokla N , Stakhiv V 
Published: January 2021

Abstract
This work is devoted to the application of interdigital transducers for the formation of a standing acoustic wave in the microchannel of an acoustophoretic Lab-chip. 2D and 3D simulation of IDT operation was performed. The influence of IDT shape, its size, and location, geometric dimensions of the piezo-crystalline layer, as well as dimensions and material of the microchannel walls for the effective formation of standing acoustic waves were analyzed.
Experimental Study of the Time of Reverberation of a Sacred Building Having a Cruciform Architecture
Authors: Melnyk M , Kernyskyy A , Mykhalyna Y , Pytel K 
Published: January 2021

Abstract
The response of the interior to the excitation of the pulse noise was registered using the Svan958A spectrum noise analyzer. After that, using the Dirac system, the registered files were analyzed and the time of reverberation of the church of St. John the Baptist, located in the village Verkhnya, Kalush district, Ivano-Frankivsk region, Ukraine with indication of measuring points. Detailed measurements of the investigated object were carried out and on their basis a 3D-model of the church in the SketchUP system was developed, which allowed to determine the recommended reverberation time for this type of interior and the given volume. The conducted researches made it possible to determine the uniformity of sound energy distribution in building having a cruciform architecture.
Active Surveillance of the Safety of Medications Used During Pregnancy
Authors: Huybrechts Krista F , Kulldorff Martin , Hernández-Díaz Sonia , Bateman Brian T , Zhu Yanmin , Mogun Helen , Wang Shirley V 
Published: January 2021

AbstractThe scientific community relies on postmarketing approaches to define the risk of using medications in pregnancy because information available at the time of drug approval is limited. Most studies carried out in pregnancy focus on a single outcome or selected outcomes. However, women must balance the benefit of treatment against all possible adverse effects. We aimed to apply and evaluate a tree-based scan statistic data-mining method (TreeScan; Martin Kulldorff, Harvard Medical School, Boston, Massachusetts) as a safety surveillance approach that allows for simultaneous evaluation of a comprehensive range of adverse pregnancy outcomes, while preserving the overall rate of false-positive alerts. We evaluated TreeScan with a cohort design and adjustment via propensity score techniques, using 2 test cases: 1) opioids and neonatal opioid withdrawal syndrome and 2) valproate and congenital malformations, implemented in pregnancy cohorts nested within the Medicaid Analytic eXtract (January 1, 2000–December 31, 2014) and the IBM MarketScan Research Database (IBM, Armonk, New York) (January 1, 2003–September 30, 2015). In both cases, we identified known safety concerns, with only 1 previously unreported alert at the preset statistical alerting threshold. This evaluation shows the promise of TreeScan-based approaches for systematic drug safety monitoring in pregnancy. A targeted screening approach followed by deeper investigation to refine understanding of potential signals will ensure that pregnant women and their physicians have access to the best available evidence to inform treatment decisions.
A data linkage study of the effects of the Great Recession and austerity on antidepressant prescription usage
Authors: Cherrie Mark , Curtis Sarah , Baranyi Gergő , Cunningham Niall , Dibben Chris , Bambra Clare , Pearce Jamie 
Published: January 2021

Abstract

Background
International literature shows unemployment and income loss during the Great Recession worsened population mental health. This individual-level longitudinal study examines how regional economic trends and austerity related to depression using administrative prescription data for a large and representative population sample.

Methods
Records from a sample of the Scottish Longitudinal Study (N=86 500) were linked to monthly primary care antidepressant prescriptions (2009–15). Regional economic trends were characterized by annual full-time employment data (2004–14). Economic impact of austerity was measured via annual income lost per working age adult due to welfare reforms (2010–15). Sequence analysis identified new cases of antidepressant use, and group-based trajectory modelling classified regions into similar economic trajectories. Multi-level logistic regression examined relationships between regional economic trends and new antidepressant prescriptions. Structural equation mediation analysis assessed the contributory role of welfare reforms.

Results
Employed individuals living in regions not recovering post-recession had the highest risk of beginning a new course of antidepressants (AOR 1.23; 95% CI 1.08–1.38). Individuals living in areas with better recovery trajectories had the lowest risk. Mediation analyses showed that 50% (95% CI 7–61%) of this association was explained by the impact of welfare benefit reforms on average incomes.

Conclusions
Following the Great Recession, local labour market decline and austerity measures were associated with growing antidepressant usage, increasing regional inequalities in mental health. The study evidences the impact of austerity on health inequalities and suggests that economic conditions and welfare policies impact on population health. Reducing the burden of mental ill-health primarily requires action on the social determinants.
On measures of gametic disequilibrium.
Authors: Lewontin R C 
Published: January 2021

Abstract
Various measures have been proposed for characterizing the statistical association that arises between alleles at different loci. Hedrick has compared these measures with the standardized measure D' proposed by Lewontin on the grounds that this latter measure is independent of allele frequency. Although D' has the same range for all allelic frequencies, in fact, D' is not "independent" of allele frequency, and no measure with that general property is possible for the multilocus association problem. The insolubility of this problem arises from the ill-defined nature of general "association."
Y chromosome loops in Drosophila melanogaster.
Authors: Bonaccorsi S , Pisano C , Puoti F , Gatti M 
Published: January 2021

Abstract
Primary spermatocyte nuclei of fixed testes of Drosophila melanogaster exhibit three large clusters of thread-like structures, each consisting of two long, continuous, loop-shaped filaments. No comparable intranuclear structures are observed in spermatogonia, secondary spermatocytes or spermatids. The threads begin to form in young spermatocytes, grow throughout spermatocyte development, reach their maximum size in mature spermatocytes and disintegrate prior to meiotic metaphase I. The presence of each cluster of threads depends upon the presence of a specific region of the Y chromosome; when this region is deleted the cluster is absent, and when it is duplicated the cluster is also duplicated. Together these observations strongly suggest that these structures represent giant Y chromosome lampbrush-like loops analogous to those described in Drosophila hydei. Two antibodies, one polyclonal and one monoclonal, differentially react with the three loops of D. melanogaster. Moreover, two of these loops are specifically stained by Giemsa at pH 10. By indirect immunofluorescence with these antibodies followed by Giemsa staining, each loop can be unambiguously identified and its presence and normality readily assessed. This enabled us to perform fine mapping experiments to determine the relationships between the Y chromosome fertility factors and the loops. The loop-forming sites map within the kl-5, kl-3 and ks-1 fertility factors. Regions h3 and h21 of the Y chromosome correspond to the loop-forming sites of kl-5 and ks-1, respectively. Each of these regions contains about 1300 kb of DNA and spans about one-third of its locus. The loop-forming site of the kl-3 locus is coextensive with region h7-h9 which contains about 4300 kb of DNA and corresponds to the minimum physical size of this locus. These data suggest that each loop is an integral part of a different fertility factor, representing the cytological manifestation of its activity in primary spermatocytes. The kl-2, kl-1 and ks-2 fertility regions do not produce any visible intranuclear structure and do not affect the kl-5, kl-3 and ks-1 loops. Thus, these loci may either not form loops at all or produce loop-like structures that we are unable to see because they are physically minute, destroyed by our fixation procedure, or both.
RFLP Maps Based on a Common Set of Clones Reveal Modes of Chromosomal Evolution in Potato and Tomato.
Authors: Bonierbale M W , Plaisted R L , Tanksley S D 
Published: January 2021

Abstract
Potato (Solanum tuberosum L.) and tomato (Lycopersicon esculentum) are members of the Solanaceae (nightshade family) and have the same basic chromosome number (x = 12). However, they cannot be cross-hybridized and, until now, it was unknown how conserved the gene order might be between these two species. We report herein the construction of a genetic linkage map of potato chromosomes based on genomic and cDNA clones from tomato. The potato map was drawn from segregation data derived from the interspecific cross S. phureja X (S. tuberosum X S. chacoense) (2n = 2x = 24), and consists of 135 markers defining 12 distinct linkage groups. Nearly all of the tomato probes tested hybridized to potato DNA, and in most cases, the copy number of the employed clones was the same in both species. Furthermore, all clones mapped to the same linkage group in both species. For nine chromosomes, the order of loci appears to be identical in the two species, while for the other three, intrachromosomal rearrangements are apparent, all of which appear to be paracentric inversions with one breakpoint at or near the centromere. These results are consistent with cytogenetic theory, previously untested in plants, which predicts that paracentric inversions will have the least negative effect on fitness and thus be the most likely form of chromosomal rearrangements to survive through evolutionary time. Linkage maps based on a common set of restriction fragment length polymorphism markers provide a basis for uniting the previously separate disciplines of tomato and potato genetics. Using these maps, it may now be possible to test theories about homologies or orthologies of other genes, including those coding for disease resistance and stress tolerances.
Ribosomal gene structure, variation and inheritance in maize and its ancestors.
Authors: Zimmer E A , Jupe E R , Walbot V 
Published: January 2021

Abstract
We have examined the structure of nuclear genes coding for ribosomal RNAs in maize and its wild relatives, the teosintes and Tripsacum. Digestion of the rDNA (genes coding for 18S, 5.8S and 26S RNAs) with 15 restriction endonucleases (with six base pair recognition sites) yields essentially a single map for the approximately 10,000 repeat units within an individual plant or species. Both length and site variation were detected among species and were concentrated in the intergenic spacer region of the rDNA repeat unit. This result is in agreement with patterns of rDNA change observed among wheat and its relatives (Triticeae), and among vertebrate species. Digestion of these nuclear DNAs with BamHI and subsequent hybridization with a 5S RNA gene-specific probe allowed determination of the size of the 5S gene repeat unit in maize, teosintes, and Tripsacum. Groupings in the genus Zea were characterized by distinct repeat unit types five Tripsacum species examined shared a 260 base pair major repeat unit type. Additionally, several other restriction endonuclease cleavage patterns differentiated among the 5S DNAs within the genus Zea. The rDNA and 5S DNA restriction site variation among the species can be interpreted phylogenetically and agrees with biochemical, karyotypic, and morphological evidence that places maize closest to the Mexican teosintes. For both gene arrays, contributions from each parental genome can be detected by restriction enzyme analysis of progeny from crosses between maize and two distantly related teosintes, Zea luxurians or Zea diploperennis, but certain teosinte arrays were underrepresented in some of the hybrids.
Comparison of non-mutant and mutant waxy genes in rice and maize.
Authors: Okagaki R J , Wessler S R 
Published: January 2021

Abstract
The waxy gene, which is responsible for the synthesis of amylose in endosperm and pollen, is genetically well characterized in many grasses including maize and rice. Homology between the previously cloned maize waxy gene and the rice gene has facilitated our cloning of a 15-kb HindIII fragment that contains the entire rice gene. A comparison of the restriction maps of the maize and rice genes indicates that many restriction sites within translated exons are conserved. In addition, the rice gene encodes a 2.4-kb transcript that programs the in vitro synthesis of a 64-kD pre-protein which is efficiently precipitated with maize waxy antisera. We demonstrate that these gene products are altered in rice strains containing mutant waxy genes. Southern blot analysis of 16 rice strains, ten containing waxy mutations, reveals that the waxy gene and flanking restriction fragments are virtually identical. These results contrast dramatically with the high level of insertions and deletions associated with restriction fragment length polymorphism and spontaneous mutations among the waxy alleles of maize.
A cladistic analysis of phenotype associations with haplotypes inferred from restriction endonuclease mapping. II. The analysis of natural populations.
Authors: Templeton A R , Sing C F , Kessling A , Humphries S 
Published: January 2021

Abstract
Genes that code for products involved in the physiology of a phenotype are logical candidates for explaining interindividual variation in that phenotype. We present a methodology for discovering associations between genetic variation at such candidate loci (assayed through restriction endonuclease mapping) with phenotypic variation at the population level. We confine our analyses to DNA regions in which recombination is very rare. In this case, the genetic variation at the candidate locus can be organized into a cladogram that represents the evolutionary relationships between the observed haplotypes. Any mutation causing a significant phenotypic effect should be imbedded within the same historical structure defined by the cladogram. We showed, in the first paper of this series, how to use the cladogram to define a nested analysis of variance (NANOVA) that was very efficient at detecting and localizing phenotypically important mutations. However, the NANOVA of haplotype effects could only be applied to populations of homozygous genotypes. In this paper, we apply the quantitative genetic concept of average excess to evaluate the phenotypic effect of a haplotype or group of haplotypes stratified and contrasted according to the nested design defined by the cladogram. We also show how a permutational procedure can be used to make statistical inferences about the nested average excess values in populations containing heterozygous as well as homozygous genotypes. We provide two worked examples that investigate associations between genetic variation at or near the Alcohol dehydrogenase (Adh) locus and Adh activity in Drosophila melanogaster, and associations between genetic variation at or near some apolipoprotein loci and various lipid phenotypes in a human population.
Activation of silent genes by transposons Tn5 and Tn10.
Authors: Wang A , Roth J R 
Published: January 2021

Abstract
The presence of transposons Tn10 or Tn5 in the genome increases the frequency with which a silent (promoter-less) gene (hisD) is mutationally activated. The activation frequency is increased 5-25-fold by Tn10 and 30-90-fold by Tn5. Activation of the hisD gene is achieved by transposition of the entire transposon or one of its flanking insertion sequences to a region just upstream of the silent gene, between a Rho-dependent termination site in the adjacent hisG gene and the hisD gene. For both Tn5 and Tn10 the component insertion sequences were found to transpose much more frequently than the entire composite element. Transposons Tn5 and Tn10 have previously been shown to carry promoters which direct transcripts into sequences adjacent to their insertion sites.
Genetic analysis of the fungus, Bremia lactucae, using restriction fragment length polymorphisms.
Authors: Hulbert S H , Ilott T W , Legg E J , Lincoln S E , Lander E S , Michelmore R W 
Published: January 2021

Abstract
Restriction fragment length polymorphisms (RFLPs) were developed as genetic markers for Bremia lactucae, the biotrophic Oomycete fungus which causes lettuce downy mildew. By using 55 genomic and cDNA probes, a total of 61 RFLP loci were identified among three heterothallic isolates of B. lactucae. Of these 61 RFLP loci, 53 were heterozygous in at least one of the three strains and thus were informative for linkage analysis in at least one of two F1 crosses that were performed. Analysis of the cosegregation of these 53 RFLPs, eight avirulence loci and the mating type locus allowed the construction of a preliminary genetic linkage map consisting of 13 small linkage groups. Based on the extent of linkage detected among probes, the genome of B. lactucae can be estimated to be approximately 2000 cM. Linkage was detected between a RFLP locus and an avirulence gene, providing a potential starting point for chromosome walking to clone an avirulence gene. The high frequency of DNA polymorphism in naturally occurring isolates and the proper Mendelian segregation of loci detected by low copy number probes indicates that it will be possible to construct a detailed genetic map of B. lactucae using RFLPs as markers. The method of analysis employed here should be applicable to many other outbreeding, heterozygous species for which defined inbred lines are not available.
GENE TRANSFER IN CAULOBACTER CRESCENTUS: POLARIZED INHERITANCE OF GENETIC MARKERS
Authors: Newton Austin , Allebach Eileen 
Published: January 2021

ABSTRACT
Recombination frequencies were determined for 15 independently isolated auxotrophs of C. crescentus crossed pairwise in all possible combinations. The results indicate that the mutants may be grouped into at least two types: "fertile" strains, which recombine with all other mutants at frequencies ranging from less than 10-6 to 3 × 10-2, and "nonfertile" strains which recombine with fertile strains at high frequencies and with other nonfertile strains at low or negligible frequencies. Several lines of evidence indicate a polarized inheritance of markers. Two of these are (1) the preferential inheritance of unselected markers from the nonfertile parent in fertile × nonfertile crosses, and (2) the consistent ordering of markers based on the frequency at which the mutants recombine with each of the three fertile strains. Although the evidence is not conclusive at this point, the results are most consistent with conjugation as the mechanism of gene transfer in these bacteria.
HETEROKARYON INCOMPATIBILITY GENES IN NEUROSPORA CRASSA DETECTED USING DUPLICATION-PRODUCING CHROMOSOME REARRANGEMENTS
Authors: Mylyk Orest M 
Published: January 2021

ABSTRACT
Evidence is presented for five or six previously undetected heterokaryon incompatibility (het) loci, bringing to about ten the number of such genes known in Neurospora crassa. The genes were detected using chromosome duplications (partial diploids), on the basis of properties previously known for het genes in duplications. Duplications homozygous for het genes are usually normal in growth and morphology, whereas those heterozygous are strikingly different. The heterozygotes are inhibited in their initial growth, produce brown pigment on appropriate medium, and later "escape" from their inhibition, as a result of somatic events, to produce wild-type growth.—Five normal-sequence strains were crossed to 14 duplication-producing chromosome rearrangements, and the duplication progeny were examined for properties characteristic of duplications heterozygous for known het genes. Each cross produced duplications for a specific region of the genome, depending on the rearrangement. Normal-sequence strains were wild types from nature, chosen from diverse geographic locations to serve as sources of genetic variation.—The duplication method was very effective. Most of the longer duplications uncovered het genes. The genes are: het-5 (on linkage group IR, in the region covered by duplications produced using rearrangement T(IR→VIR)NM103), het-6 (on IIL, covered by T(IIL→VI)P2869 and T(IIL→IIIR)AR18 duplications), het-7 (tentatively assigned to IIIR, T(IIIR→VIL)D305), het-8 (VIL, T(VIL→IR)T39M777), het-9 (VIR, T(VIR→IVR)AR209), and het-10 (VIIR, T(VIIR→IL)5936).
MUTATION OF A HETEROTHALLIC STRAIN TO HOMOTHALLISM
Authors: Hopper Anita K , Hall Benjamin D 
Published: January 2021

ABSTRACT
Upon mutagenesis, a heterothallic αα diploid strain mutated to homothallism. The gene confering homothallism is nuclear, recessive, and unlinked to mating type. This gene is not allelic to the HO gene, which is responsible for previously described instances of homothallism in yeast. We have designated this new gene for homothallism as cmt (change of mating type).
MACRONUCLEAR GENETICS OF TETRAHYMENA. II. MACRONUCLEAR LOCATION OF SOMATIC MUTATIONS TO CYCLOHEXIMIDE RESISTANCE
Authors: Orias Eduardo , Newby Candace J 
Published: January 2021

ABSTRACT
Somatic cycloheximide-resistant mutants of syngen 1 of Tetrahymena pyriformis were isolated and genetically characterized. Two properties of the mutants were independently examined: (a) The transmission of the mutant phenotype during conjugation and (b) the kinetics of phenotypic assortment during vegetative propagation. The results of both studies strongly support the idea that these somatic mutations have a macronuclear location. The kinetics of assortment are consistent with the idea that the syngen 1 macronucleus contains about 45 assorting genetic units. The sib-selection method employed here, used in conjunction with the analysis of assortment kinetics and a previously described test for randomness of distribution, provides a probe of macronuclear genetics applicable to many ciliates, including those in which conjugation is not known to occur or is not under experimental control.