bluuebunny/crossref_metadata_2025_split huggingface dataset:
Morph-Specific Proteins in Pollen and Styles of Distylous Turnera (Turneraceae)
Authors: Athanasiou Andreas , Shore Joel S 
Published: January 2021

We used nondenaturing isoelectric focusing (IEF) in a survey of plants from 11 populations to identify style and pollen proteins unique to the short-styled morph of Turnera scabra, T. subulata and T. krapovickasii. Three protein bands [approximately isoelectric points (pIs) 6.1, 6.3 and 6.5] were found only in styles and stigmas of short-styled plants while two bands (approximately pIs 6.7 and 6.8, M r 56 and 59 kD) occur only in pollen of short-styled plants. Some of these bands appear very late in development, within 24 hr before flowering. Two isozyme loci were mapped to an 8.7 cM region spanning the distyly locus. Using these isozyme markers we identified progeny exhibiting recombination adjacent to the distyly locus. No recombinants between the distyly locus and the locus or loci controlling the presence of the short-styled morph-specific proteins were obtained. This suggests that the loci encoding these proteins are either extremely tightly linked to the distyly locus and in complete disequilibrium with the S allele or exhibit morph-limited expression. Crosses to a plant showing an unusual style protein phenotype demonstrated that an additional unlinked locus is required for full expression of the style proteins. The function of the morph-specific proteins is unknown
A New Enhancer of Position-Effect Variegation in Drosophila melanogaster Encodes a Putative RNA Helicase That Binds Chromosomes and Is Regulated by the Cell Cycle
Authors: Eberl Daniel F , Lorenz Lori J , Melnick Michael B , Sood Vanita , Lasko Paul , Perrimon Norbert 
Published: January 2021

In Drosophila melanogaster, position-effect variegation of the white gene has been a useful phenomenon by which to study chromosome structure and the genes that modify it. We have identified a new enhancer of variegation locus, Dmrnahel (hel). Deletion or mutation of hel enhances white variegation, and this can be reversed by a transformed copy of her +. In the presence of two endogenous copies, the transformed her + behaves as a suppressor of variegation. hel is an essential gene and functions both maternally and zygotically. The HEL protein is similar to known RNA helicases, but contains an unusual variant (DECD) of the DEAD motif common to these proteins. Potential HEL homologues have been found in mammals, yeast and worms. HEL protein associates with salivary gland chromosomes and locates to nuclei of embryos and ovaries, but disappears in mitotic domains of embryos as chromosomes condense. We propose that the HEL protein promotes an open chromatin structure that favors transcription during development by regulating the spread of heterochromatin, and that HEL is regulated by, and may have a role in, the mitotic cell cycle during embryogenesis.
Mating in Saccharomyces cerevisiae: The Role of the Pheromone Signal Transduction Pathway in the Chemotropic Response to Pheromone
Authors: Schrick Kathrin , Garvik Barbara , Hartwell Leland H 
Published: January 2021

Abstract
The mating process in yeast has two distinct aspects. One is the induction and activation of proteins required for cell fusion in response to a pheromone signal; the other is chemotropism, i.e., detection of a pheromone gradient and construction of a fusion site available to the signaling cell. To determine whether components of the signal transduction pathway necessary for transcriptional activation also play a role in chemotropism, we examined strains with null mutations in components of the signal transduction pathway for diploid formation, prezygote formation and the chemotropic process of mating partner discrimination when transcription was induced downstream of the mutation. Cells mutant for components of the mitogen-activated protein (MAP) kinase cascade (ste5, ste20, ste11, ste7 or fus3 kss1) formed diploids at a frequency 1% that of the wild-type control, but formed prezygotes as efficiently as the wild-type control and showed good mating partner discrimination, suggesting that the MAP kinase cascade is not essential for chemotropism. In contrast, cells mutant for the receptor (ste2) or the β or γ subunit (ste4 and stel8) of the G protein were extremely defective in both diploid and prezygote formation and discriminated poorly between signaling and nonsignaling mating partners, implying that these components are important for chemotropism.
Rules of Donor Preference in Saccharomyces Mating-Type Gene Switching Revealed by a Competition Assay Involving Two Types of Recombination
Authors: Wu Xiaohua , Wu Cherry , Haber James E 
Published: January 2021

Mating type (MAT) switching in Saccharomyces cerevisiae is initiated by a double-strand break (DSB) created at MAT by HO endonuclease. MAT a cells activate the entire left arm of chromosome III; thus MAT a preferentially recombines with the silent donor HML. In contrast, MATα cells inactivate the left arm, including HML, and thus preferentially recombine with HMR, 100 kb to the right of MAT. We present a novel competition assay, in which the DSB at MAT can be repaired either by MAT switching or by single-strand annealing (SSA) between two URA3 genes flanking MAT. With preferred donors, MAT a or MATα switching occurs 65–70% of the time in competition with SSA. When HML is deleted, 40% of MAT a cells recombine with the “wrong” donor HMR; however, when HMR is deleted, only 18% of MATα cells recombine with HML. In interchromosomal switching, with donors on chromosome III and MAT on chromosome V, MAT a retains its strong preference for HML and switching is efficient, when the chromosome III recombination enhancer is present. However, MATα donor preference is lost and interchromosomal switching is very inefficient. These experiments demonstrate the utility of using competition between two outcomes to measure the relative efficiency of recombination.
Genetic and Environmental Factors Affecting the de novo Appearance of the [PSI
+
] Prion in Saccharomyces cerevisiae
Authors: Derkatch Irina L , Bradley Michael E , Zhou Ping , Chernoff Yury O , Liebman Susan W 
Published: January 2021

It has previously been shown that yeast prion [PSI + ] is cured by GuHCl, although reports on reversibility of curing were contradictory. Here we show that GuHCl treatment of both [PSI + ] and [psi – ] yeast strains results in two classes of [psi – ] derivatives: Pin+, in which [PSI + ] can be reinduced by Sup35p overproduction, and Pin–, in which overexpression of the complete SUP35 gene does not lead to the [PSI + ] appearance. However, in both Pin+ and Pin– derivatives [PSI + ] is reinduced by overproduction of a short Sup35p N-terminal fragment, thus, in principle, [PSI + ] curing remains reversible in both cases. Neither suppression nor growth inhibition caused by SUP35 overexpression in Pin+ [psi – ] derivatives are observed in Pin– [psi – ] derivatives. Genetic analyses show that the Pin+ phenotype is determined by a non-Mendelian factor, which, unlike the [PSI + ] prion, is independent of the Sup35p N-terminal domain. A Pin– [psi – ] derivative was also generated by transient inactivation of the heat shock protein, Hsp104, while [PSI + ] curing by Hsp104 overproduction resulted exclusively in Pin+ [psi – ] derivatives. We hypothesize that in addition to the [PSI + ] prion-determining domain in the Sup35p N-terminus, there is another self-propagating conformational determinant in the C-proximal part of Sup35p and that this second prion is responsible for the Pin+ phenotype.
A Limited Number of Caenorhabditis elegans Genes Are Readily Mutable to Dominant, Temperature-Sensitive Maternal-Effect Embryonic Lethality
Authors: Mitenko Nancy L , Eisner James R , Swiston John R , Mains Paul E 
Published: January 2021

Abstract
Dominant gain-of-function mutations can give unique insights into the study of gene function. In addition, gain-of-function mutations, unlike loss-of-function alleles, are not biased against the identification of genetically redundant loci. To identify novel genetic functions active during Caenorhabditis elegans embryogenesis, we have collected a set of dominant temperature-sensitive maternal-effect embryonic lethal mutations. In a previous screen, we isolated eight such mutations, distributed among six genes. In the present study, we describe eight new dominant mutations that identify only three additional genes, yielding a total of 16 dominant mutations found in nine genes. Therefore, it appears that a limited number of C. elegans genes mutate to this phenotype at appreciable frequencies. Five of the genes that we identified by dominant mutations have loss-of-function alleles. Two of these genes may lack loss-of-function phenotypes, indicating that they are nonessential and so may represent redundant loci. Loss-of-function mutations of three other genes are associated with recessive lethality, indicating nonredundancy.
Drosophila Male-Specific Lethal-4 Protein: Structure/Function Analysis and Dependence on MSL-1 for Chromosome Association
Authors: Lyman Laura M , Copps Kyle , Rastelli Luca , Kelly Richard L , Kuroda Mitzi I 
Published: January 2021

Abstract
MSL-2 is required for the male-specific assembly of a dosage compensation regulatory complex on the X chromosome of Drosophila melanogaster. We found that MSL-2 binds in a reproducible, partial pattern to the male Xchromosome in the absence of MLE or MSL-3, or when ectopically expressed at a low level in females. Moreover, the pattern of MSL-2 binding corresponds precisely in each case to that of MSL-1, suggesting that the two proteins function together to associate with the X. Consistent with this hypothesis, we isolated EMSinduced loss of function msl-1 and msl-2 alleles in a screen for suppressors of the toxic effects of MSL-2 expression in females. We also used sitedirected mutagenesis to determine the importance of the MSL-2 RING finger domain and second cysteine-rich motif. The mutations, including those in conserved zinc coordinating cysteines, confirm that the RING finger is essential for MSL-2 function, while suggesting a less stringent requirement for an intact second motif.
Patterns of Mitochondrial Variation Within and Between African Malaria Vectors, Anopheles gambiae and An. arabiensis, Suggest Extensive Gene Flow
Authors: Besansky Nora J , Lehmann Tovi , Fahey G Thomas , Fontenille Didier , Braack Lawrence E O , Hawley William A , Collins Frank H 
Published: January 2021

Abstract
Anopheles gambiae and An. arabiensis are mosquito species responsible for most malaria transmission in sub-Saharan Africa. They are also closely related sibling species that share chromosomal and molecular polymorphisms as a consequence of incomplete lineage sorting or introgressive hybridization. To help resolve these processes, this study examined the partitioning of mtDNA sequence variation within and between species across Africa, from both population genetic and phylogeographic perspectives. Based on partial gene sequences from the cytochrome b, ND1 and ND5 genes, haplotype diversity was high but sequences were very closely related. Within species, little or no population subdivision was detected, and there was no evidence for isolation by distance. Between species, there were no fixed nucleotide differences, a high proportion of shared polymorphisms, and eight haplotypes in common over distances as great as 6000 km. Only one of 16 shared polymorphisms led to an amino acid difference, and there was no compelling evidence for nonneutral variation. Parsimony networks constructed of haplotypes from both species revealed no correspondence of haplotype with either geography or taxonomy. This trend of low intraspecific genetic divergence is consistent with evidence from allozyme and microsatellite data and is interpreted in terms of both extensive gene flow and recent range expansion from relatively large, stable populations. We argue that retention of ancestral polymorphisms is a plausible but insufficient explanation for low interspecific genetic divergence, and that extensive hybridization is a contributing factor.
DNA Polymorphism at the Pgi Locus of a Wild Yam, Dioscorea tokoro
Authors: Terauchi Ryohei , Terachi Tom , Miyashita Naohiko T 
Published: January 2021

Abstract
To study the origin and maintenance mechanisms of the PGI allozyme polymorphism of a wild plant, Dioscorea tokoro, DNA sequences of the entire coding region (1701 bp) and two intronic regions (total 2049 bp) of the Pgi gene as well as a part of the Adh gene (590 bp) were analyzed. Two replacement substitutions were revealed to be responsible for the differentiation of three allozymes alleles (Pgi-a, Pgi-b and Pgi-c) that occur in natural population in intermediate frequencies. Interspecific comparison of DNA sequences identified Pgi-6 as the oldest allele, from which two other alleles were derived probably within the last 150,000 years. The level of DNA polymorphism at D. tokoro Pgi locus was low. No elevated level of DNA polymorphism was detected in the close vicinity of the two replacement sites differentiating the three allozymes. Departures from the neutral mutation hypothesis were detected by Fu and Li's and MK tests. The observed patterns of DNA polymorphism are explainable by both (1) the neutral mutation hypothesis with an assumption of small effective size of D. tokoro population, and (2) the positive selection hypothesis that the allele frequencies of Pgi-a and Pgi-c have increased in a short time by their selective advantages.
Cognitive Stimulation Therapy for Older Adults With Mild-to-Moderate Dementia in Italy: Effects on Cognitive Functioning, and on Emotional and Neuropsychiatric Symptoms
Authors: Carbone Elena , Gardini Simona , Pastore Massimiliano , Piras Federica , Vincenzi Margherita , Borella Erika 
Published: January 2021

Abstract

Objectives
Cognitive Stimulation Therapy (CST) is one of the most popular evidence-based interventions for people with dementia. The aim of the present study was to assess the effectiveness in the short- and long-term (on completing the treatment and 3 months later) of an Italian adaptation of the CST protocol (CST-IT).

Method
Older adults with mild-to-moderate dementia at 16 residential care homes were randomly assigned to a CST-IT group (N = 123) or an active control group (N = 102). The following domains were examined for potential benefits: general cognitive functioning (Mini-Mental State Examination [MMSE] and the Alzheimer’s Disease Assessment Scale—Cognitive subscale [ADAS-Cog]), language (Narrative Language Test), mood and behavior (Cornell scale and Neuropsychiatric Inventory), everyday life functioning (Disability Assessment for Dementia), and quality of life (Quality of Life—Alzheimer’s Disease scale).

Results
At both the short- and long-term assessments, the CST-IT group’s MMSE scores remained stable, while the control group’s scores decreased slightly from pretest to posttest and at follow-up. The CST-IT group also had short-term benefits in other cognitive measures (ADAS-Cog and Narrative Language Test) and mood and behavior measures, which were generally maintained at follow-up. No other differences were observed.

Discussion
The effectiveness of CST in sustaining cognitive and emotional functioning, and counteracting the progression of behavioral/neuropsychiatric symptoms in people with dementia was confirmed, and a long-term benefit was demonstrated. CST is a promising option for the treatment of people with dementia in clinical practice.
The Effect of Lifestyle Interventions on the International Classification of Functioning, Disability and Health Participation Domain in Older Adults: A Systematic Review and Meta-Analysis
Authors: O’Hoski Sachi , Chauvin Stephanie , Vrkljan Brenda , Beauchamp Marla K 
Published: January 2021

Abstract

Background and Objectives
The World Health Organization’s International Classification of Functioning, Disability and Health (ICF) recognizes participation in life situations as a major component of health. Identifying interventions that target this component is critical, particularly in older adulthood, where declines in physical functioning can impact participation. The purpose of this study was to evaluate the effectiveness of lifestyle or behavior change interventions on the ICF participation domain in older adults.

Research Design and Methods
MEDLINE (Ovid), Embase (Ovid), CINAHL (EBSCO), AgeLine (EBSCO), PsycINFO (Ovid), and AMED (Ovid) were searched from inception to April 2020 for randomized controlled trials comparing the effects of any behavior change or lifestyle intervention to usual care among community-dwelling adults ≥60 years with respect to participation-related domains of the ICF. The protocol was registered with Prospero (CRD42019125334).

Results
Eight studies with a total of 1,548 participants were included. No significant effect on participation outcomes was found (standardized mean difference 0.04; 95% CI −0.19 to 0.26; p = .76) and the quality of evidence was judged to be very low.

Discussion and Implications
Lifestyle or behavior change interventions showed limited effect on participation in later life. However, there remains much uncertainty in the estimate of this effect due, in part, to the low quality of the included studies. Measurement tools that are responsive to changes in participation in older adulthood should be used to determine the effect of such interventions. Improving study design will lead to more efficacious interventions that promote participation for our aging population.
PM4NGS, a project management framework for next-generation sequencing data analysis
Authors: Vera Alvarez Roberto , Pongor Lorinc , Mariño-Ramírez Leonardo , Landsman David 
Published: January 2021

Abstract

Background
FAIR (Findability, Accessibility, Interoperability, and Reusability) next-generation sequencing (NGS) data analysis relies on complex computational biology workflows and pipelines to guarantee reproducibility, portability, and scalability. Moreover, workflow languages, managers, and container technologies have helped address the problem of data analysis pipeline execution across multiple platforms in scalable ways.

Findings
Here, we present a project management framework for NGS data analysis called PM4NGS. This framework is composed of an automatic creation of a standard organizational structure of directories and files, bioinformatics tool management using Docker or Bioconda, and data analysis pipelines in CWL format. Pre-configured Jupyter notebooks with minimum Python code are included in PM4NGS to produce a project report and publication-ready figures. We present 3 pipelines for demonstration purposes including the analysis of RNA-Seq, ChIP-Seq, and ChIP-exo datasets.

Conclusions
PM4NGS is an open source framework that creates a standard organizational structure for NGS data analysis projects. PM4NGS is easy to install, configure, and use by non-bioinformaticians on personal computers and laptops. It permits execution of the NGS data analysis on Windows 10 with the Windows Subsystem for Linux feature activated. The framework aims to reduce the gap between researcher in experimental laboratories producing NGS data and workflows for data analysis. PM4NGS documentation can be accessed at https://pm4ngs.readthedocs.io/.
Broad Specifications and Intent to Use: Is the EU Trade Mark System Credible?
Authors: Arnold Richard 
Published: January 2021

Abstract
An assessment of the credibility of the EU trade mark system in the light of the ruling of the Court of Justice of the European Union in Case C-371/18 Sky v SkyKick leads to the following conclusions: the decisions that lack of clarity and precision of specifications of goods and services is not a ground of invalidity and that partial bad faith when applying to register a trade mark leads to partial invalidity are unsurprising; the decision that applying to register a trade mark without intending to use it can amount to bad faith, at least in some circumstances, is an important step forward that gives national courts a tool with which to combat unjustifiably broad specifications of goods and services; but the jury is still out with regard to the EU trade mark system’s acceptance of broad terms such as ‘computer software’ in specifications.
Magna ease bioprosthetic aortic valve: mid-term haemodynamic outcomes in 1126 patients
Authors: Thorp Stephen D , Khazaal Jawad , Yu Grace , Parker Jessica L , Timek Tomasz A 
Published: January 2021

Abstract

OBJECTIVES
The Magna Ease aortic valve (Edwards Lifesciences, Irvine, CA) is a third-generation bioprosthetic valve developed as a modification of the well-studied Perimount and Magna valve designs. This study’s objective is to evaluate a large, single-centre experience with Magna Ease aortic valve replacement (AVR) focusing on clinical outcomes and haemodynamic performance.

METHODS
All patients undergoing AVR between 8/2010 and 10/2018 at our institution implanted with the Magna Ease valve were included except those undergoing ventricular assist device or congenital aortic surgery. Primary outcomes were overall survival and freedom from reoperation. Mean transprosthetic gradient (mTPG) and structural valve deterioration (SVD) served as secondary outcomes.

RESULTS
Totally 1126 consecutive implantations of Magna Ease valves were included. Concomitant procedures were performed in 56.5% (n = 636). No severe patient–prosthesis mismatch (PPM) was present at implantation. Overall survival at 30 days, 1 year, 5 years and 9 years was 97.2%, 95.0%, 86.1% and 78.2%, respectively, with improved survival for isolated AVR. Total of 2.4% (n = 27) of patients required reoperation with 0.3% (n = 4) for SVD. Echocardiographic follow-up data revealed low mTPG throughout the study period. SVD occurred in 28.7% of patients at a mean of 3.9 years post implantation.

CONCLUSIONS
Magna Ease AVR maintained low mean transprosthetic gradients throughout mid-term evaluation and was associated with excellent overall survival and freedom from reoperation at nine years post implantation.
Metastatic renal cell carcinoma extending to the left atrium through the inferior pulmonary vein
Authors: Dawson Alan G , Richards Cathy J , Hadjinikolaou Leonidas , Nakas Apostolos 
Published: January 2021

Abstract
Metastatic renal cell carcinoma with involvement through the pulmonary veins to the left atrium is very rare. We report the case of a 70-year-old male with metastatic renal cell carcinoma to the right lower lobe of the lung abutting the inferior pulmonary vein with extension to the left atrium without pre-operative evidence. Surgical resection was achieved through a posterolateral thoracotomy. Lung masses that abut the pulmonary veins should prompt further investigation with a pre-operative transoesophageal echocardiogram to minimize unexpected intraoperative findings.