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Aims: Neoadjuvant endocrine therapy (NAET) is used in the management of oestrogen receptor (ER)‐positive breast cancer. The optimal method for histological assessment of response and the effect of NAET on the tumour morphology, grade and molecular profile remain unclear. The aim of this study is to investigate the NAET effect on tumour type, grade and molecular profile by analysing a well‐characterised cohort of breast cancer samples in a single large UK tertiary referral centre, and to provide guidance on the pathological assessment of those lesions to inform adjuvant management and prognosis. Methods and results: A single large‐institution cohort of 132 patients who received NAET over a 13‐year period was identified. Comprehensive clinical, histopathological and follow‐up data were collected. A detailed histological review of a subset with residual post‐treatment carcinoma was undertaken. Two carcinomas (both of the lobular type) achieved complete pathological response. Central scarring was seen in 49.3% of tumours post‐treatment. Significant changes in tumour type (41.6%), tumour grade (downgrading in one‐third of tumours), and progesterone receptor (PR) expression (22.3%), with a switch to PR‐negative status in 17.6% of cases, were observed. The last of these was associated with an absence of tumour‐infiltrating lymphocytes (P = 0.005). Ten per cent of cases showed a change in HER2 expression (P = 0.002). The median patient survival was 60 months, and downgrading of tumours was associated with better overall survival (P = 0.05). Conclusions: We propose a histological method for assessment of residual carcinoma following NAET, and recommend repeat ER/PR/HER2 testing to inform management and prognosis. [ABSTRACT FROM AUTHOR]

High‐throughput (next‐generation) DNA sequencing has removed barriers to data quantity and quality, and it has produced phylogenies with high statistical support. Such data are useful to address phylogenetic congruence among individual genes. Concatenated analyses of unlinked genes often produce well‐resolved phylogenetic trees with bootstrap support on major nodes at or approaching 100%, but they have been criticized for providing incorrect phylogenies for various reasons to include a history of hybridization, introgression, and incomplete lineage sorting. The present study compares next‐generation sequencing results of the same accessions of Daucus with different genomic regions, of which three have been reported before: (i) the entire plastid genome, (ii) 47 mitochondrial genes, and (iii) 94 conserved nuclear orthologs. Here, we report a fourth dataset, (iv) 564 895 nuclear SNPs. There are areas of discordance in all four results using the same accessions analyzed with maximum parsimony, maximum likelihood, and with the nuclear data species trees through a coalescent analysis. The nuclear results show significant areas of discordance that were unexpected, because these studies used the same DNA samples, the nuclear studies were generated from large and high‐quality datasets with the SNPs distributed on all nine linkage groups of Daucus carota, and the results were supported by high bootstrap values. These results raise questions concerning the best data and analytical methods to reconstruct and understand the "truth" of a phylogeny. [ABSTRACT FROM AUTHOR]

We explored the phylogenetic utility of mitochondrial DNA sequences in Daucus and compared the results with prior phylogenetic results using the same 36 accessions of Daucus (and two additional outgroups) with plastid DNA sequences and with other nuclear results. As in the plastid study we used Illumina HiSeq sequencer to obtain resequencing data of the same accessions of Daucus and outgroups, and analyzed the data with maximum parsimony and maximum likelihood. We obtained data from 47 of 71 total mitochondrial genes but only 17 of these 47 genes recovered major clades that were common in prior plastid and nuclear studies. Our phylogenetic trees of the concatenated data set of 47 genes were moderately resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus. There are areas of hard incongruence with phylogenies using plastid and nuclear data. In agreement with other studies, we conclude that mitochondrial sequences are generally poor phylogenetic markers, at least at the genus level, despite their utility in some other studies. [ABSTRACT FROM AUTHOR]

The Potato Introduction Station in Sturgeon Bay Wisconsin has maintained herbarium specimens as part of its operations. These specimens mostly were grown from seeds in the field plots or greenhouses, but also include original specimens made during germplasm collecting expeditions. The herbarium of the Station (herbarium acronym PTIS) has been transferred from the potato genebank in Sturgeon Bay Wisconsin to the Wisconsin State Herbarium (acronym WIS) in Birge Hall, University of Wisconsin-Madison where it is now fully integrated and curated and funded by WIS; PTIS is discontinued and is no longer maintained as a separate herbarium. Separately, maps and taxonomic literature that were used by the potato taxonomist in Madison were transferred to the Potato Station in Sturgeon Bay. [ABSTRACT FROM AUTHOR]

PREMISE OF THE STUDY: The species boundaries of wild and cultivated potatoes are controversial, with most of the taxonomic problems in the cultivated potato clade. We here provide the first in-depth phylogenetic study of the cultivated potato clade to explore possible causes of these problems. METHODS: We examined 131 diploid accessions, using 12 nuclear orthologs, producing an aligned data set of 14,072 DNA characters, 2171 of which are parsimony-informative. We analyzed the data to produce phylogenies and perform concordance analysis and goodness-of- fit tests. KEY RESULTS: There is good phylogenetic structure in clades traditionally referred to as clade 1+2 (North and Central American diploid potatoes exclusive of Solanum verrucosum), clade 3, and a newly discovered basal clade, but drastically reduced phylogenetic structure in clade 4, the cultivated potato clade. The results highlight a clade of species in South America not shown before, 'neocardenasii', sister to clade 1+2, that possesses key morphological traits typical of diploids in Mexico and Central America. Goodness-of- fit tests suggest potential hybridization between some species of the cultivated potato clade. However, we do not have enough phylogenetic signal with the data at hand to explicitly estimate such hybridization events with species networks methods. CONCLUSIONS: We document the close relationships of many of the species in the cultivated potato clade, provide insight into the cause of their taxonomic problems, and support the recent reduction of species in this clade. The discovery of the neocardenasii clade forces a reevaluation of a hypothesis that section Petota originated in Mexico and Central America. [ABSTRACT FROM AUTHOR]

PREMISE OF THE STUDY: We explored the phylogenetic utility of entire plastid DNA sequences in Daucus and compared the results with prior phylogenetic results using plastid and nuclear DNA sequences. METHODS: We used Illumina sequencing to obtain full plastid sequences of 37 accessions of 20 D aucus taxa and outgroups, analyzed the data with phylogenetic methods, and examined evidence for mitochondrial DNA transfer to the plastid (Dc MP). KEY RESULTS: Our phylogenetic trees of the entire data set were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus . Subsets of the data, including regions traditionally used as phylogenetically informative regions, provide various degrees of soft congruence with the entire data set. There are areas of hard incongruence, however, with phylogenies using nuclear data. We extended knowledge of a mitochondrial to plastid DNA insertion sequence previously named Dc MP and identified the first instance in flowering plants of a sequence of potential nuclear genome origin inserted into the plastid genome. There is a relationship of inverted repeat junction classes and repeat DNA to phylogeny, but no such relationship with nonsynonymous mutations. CONCLUSIONS: Our data have allowed us to (1) produce a well-resolved plastid phylogeny of Daucus, (2) evaluate subsets of the entire plastid data for phylogeny, (3) examine evidence for plastid and nuclear DNA phylogenetic incongruence, and (4) examine mitochondrial and nuclear DNA insertion into the plastid. [ABSTRACT FROM AUTHOR]

Solanum section Petota has been the subject of intensive taxonomic work since the description of the cultivated potato in 1753. In total, there are 494 epithets for wild taxa and 626 epithets for cultivated taxa. Different taxonomists applied various taxonomic philosophies and species concepts to the section. Hypotheses of the number of species and their interrelationships have differed greatly among authors. A taxonomic treatment of section Petota by Jack Hawkes in 1990 recognized 228 wild species and seven cultivated species, divided into 21 taxonomic series. In 2014 Spooner and collaborators more than halved this number to 107 wild species and four cultivated species, partitioned into four clades; not using series. The purpose of this paper is to provide a retrospective of the methods and philosophies that have resulted in this drastic decrease in the number of species and their infrasectional classification. [ABSTRACT FROM AUTHOR]

The common potato, Solanum tuberosum L., is the third most important food crop and is grown and consumed worldwide. Indigenous cultivated (landrace) potatoes and wild potato species, all classified as Solanum section Petota, are widely used for potato improvement. Members of section Petota are broadly distributed in the Americas from the southwestern United States to the Southern Cone of South America. The latest comprehensive taxonomic treatment of section Petota was published by John (Jack) Hawkes in 1990; it recognized seven cultivated species and 228 wild species, divided into 21 taxonomic series. Since 1990, intensive field collections from throughout the range of the group, coupled with morphological and molecular studies, have halved the number of species and elucidated new ingroup and outgroup relationships. The recent sequencing of the potato genome has greatly accelerated investigation of all aspects of potato biology and allows us to address new questions not conceivable before. The purpose of this review is to provide a historical overview and update since 1990 of the systematics, diversity, genetics, domestication, evolution, and breeding of Solanum section Petota that will serve as a reference for the next generation of studies in the potato. [ABSTRACT FROM AUTHOR]

The genus Daucus includes about 20 recognized species. The most widespread and economically important species, Daucus carota L., occurs on almost every continent. The cultivated carrot, subsp. sativus (Hoffm.) Schübl. and G. Martens, has been selected from wild populations that are extremely diverse, especially in the western Mediterranean. The predominant outcrossing and the lack of sexual isolating mechanisms among recognized infraspecific taxa complicate the taxonomy and identification of the wild populations, resulting in widely different interpretations of the number of infraspecific taxa. We measured 36 morphological characters from multiple individuals within each of 155 accessions of D. carota and from the morphologically similar species D. capillifolius (both species 2n = 18) alongside other species for comparison (D. aureus Desf., 2n = 22; D. broteri Ten., 2n = 20; D. involucratus Sm., 2n = 20; and D. littoralis Sm., 2n = 20) in an experimental field plot. Within D. carota, multivariate analyses were able to identify only two subspecies, but even these showed great overlap of individual characters. Because of the ease of crossability of wild D. carota to the domestic landraces and cultivars and because of the taxonomic challenges, the purpose of our study is to explore morphological support for subspecies within D. carota, including the phenetically similar D. capillifolius, which is part of the same clade as D. carota, with the long-term goal of resolving taxonomic disagreements and developing a practical system to classify variation within this economically important species. [ABSTRACT FROM AUTHOR]

The article discusses a study of the phylogeny of 22 accessions of Daucus (Apiaceae) and seven accessions in related genera, with deoxyribonucleic acid (DNA) sequences from eight nuclear orthologs and one plastid region. It highlights the maximum parsimony and maximum likelihood analyses of the concatenated data matrix of 7,212 aligned nucleotides. It also cites Pseudorlaya pumila which was firmly imbedded within Daucus and Margottia gummifera as a new finding.

Wild potato ( Solanum L. sect. Petota Dumort.) species contain diploids (2 n = 2 x = 24) to hexaploids (2 n = 6 x = 72). J.G. Hawkes classified all hexaploid Mexican species in series Demissa Bukasov and, according to a classic five-genome hypothesis of M. Matsubayashi in 1991, all members of series Demissa are allopolyploids. We investigated the genome composition of members of Hawkes's series Demissa with genomic in situ hybridization (GISH), using labeled DNA of their putative progenitors having diploid AA, BB, or PP genome species or with DNA of tetraploid species having AABB or AAAaAa genomes. GISH analyses support S. hougasii Correll as an allopolyploid with one AA component genome and another BB component genome. Our results also indicate that the third genome of S. hougasii is more closely related to P or a P genome-related species. Solanum demissum Lindl., in contrast, has all three chromosome sets related to the basic A genome, similar to the GISH results of polyploid species of series Acaulia Juz. Our results support a more recent taxonomic division of the Mexican hexaploid species into two groups: the allopolyploid Iopetala group containing S. hougasii, and an autopolyploid Acaulia group containing S. demissum with South American species S. acaule Bitter and S. albicans (Ochoa) Ochoa. [ABSTRACT FROM AUTHOR]

The article discusses a study on the DNA sequences of conserved orthologous nuclear DNA sequences (COSII) that were available in germplasm collections and species from other series to address allopolyploid origins. Total genomic DNA from young leaves of single plants of 72 accessions from 22 species of series Conicibaccata were isolated. The combined COSII indicated that wild petota species from Conicibaccata are a difficult group although its diploid and polyploid members appear to represent section Petota as a whole.

• Premise of the study: The taxonomy of cultivated potatoes has been highly controversial, with estimates of species numbers ranging from 3 to 17. Ploidy level has been one of the most important taxonomic characters to recognize cultivated potato species, containing diploid (2n = 2x = 24), triploid (2n = 3x = 36), tetraploid (2n = 4x = 48), and pentaploid (2n = 5x = 60) cultivars. We tested the environmental associations of different ploidy levels in cultivated potato species that traditionally have been recognized as Linnaean taxa to see whether, in combination with prior morphological, molecular, and crossing data, some of the ploidy variants can be recognized as distinct taxa. • Methods: We summarize 2780 chromosome counts of landrace cultivated potatoes, provide georeferences 2048 of them, and analyze these data for 20 environmental variables at 10-min resolution using the randomForest algorithm to explore associations with taxa and ploidy variants. • Key results: Except for the S. tuberosum Chilotanum Group and extreme northern and southern range extensions of the Andigenum Group, it is impossible to find distinct habitats for the ploidy variants of the S. tuberosum Andigenum Group. • Conclusions: Our distributional and ecological data, in combination with prior results from morphology, microsatellites, and crossing data, provide yet additional data to support a major reclassification of cultivated potato species. A rational, stable, and universally accepted taxonomy of this major crop plant will greatly aid all users of wild and cultivated potatoes from breeders to gene bank managers to ecologists and evolutionary biologists. [ABSTRACT FROM AUTHOR]

A major justification for taxonomic and biogeographic research is its assumed ability to predict the presence of traits in a group for which the trait has been observed in only a representative subset of the group. Such predictors are regularly used by breeders interested in choosing potential sources of disease and pest resistant germplasm for cultivar improvement, by genebank managers to organize the collection, and by germplasm collectors planning to gather maximum diversity. The present study tests taxonomic and biogeographic associations with 10,738 disease and pest evaluations, derived from the literature and genebank records, of 32 pest and diseases in five classes of organisms (bacteria, fungi, insects, nematodes, and virus). The data show that ratings for only Colorado potato beetle [Leptinotarsa decemlineata (Say)] and one pathogen (Potato M Carlavirus) are reliably predicted both by host taxonomy and climatic variables. While it is logical to initially take both taxonomy and geographic origin into account while screening genebank materials for pest and disease resistances, such associations will hold for only for a small subset of resistance traits. Based on these results, a more effective strategy than taxonomic and biogeographic prediction is probably careful screening of core collections. [ABSTRACT FROM AUTHOR]

DNA barcoding ("barcoding") has been proposed as a rapid and practical molecular method to identify species via diagnostic variation in short orthologous DNA sequences from one or a few universal genomic regions. It seeks to address in a rapid and simple way the "taxonomic impediment" of a greater need for taxonomic identifications than can be supplied by taxonomists. Using a complicated plant group, Solanum sect. Petota (wild potatoes), I tested barcoding with the most variable and frequently suggested plant barcoding regions: the internal nontranscribed spacer of nuclear ribosomal DNA (ITS) and the plastid markers trnH-psbA intergenic spacer and matK. These DNA regions fail to provide species-specific markers in sect. Petota because the ITS has too much intraspecific variation and the plastid markers lack sufficient polymorphism. The complications seen in wild potatoes are common in many plant groups, but they have not been assessed with barcoding. Barcoding is a retroactive procedure that relies on well-defined species to function, is based solely on a limited number of DNA sequences that are often inappropriate at the species level, has been poorly tested with geographically well-dispersed replicate samples from difficult taxonomic groups, and discounts substantial practical and theoretical problems in defining species. [ABSTRACT FROM AUTHOR]

The article presents a study on the nitrate reductase phylogeny of potato genomes. The study focused on the phylogeny of potato based on the origin of the polyploidy species. It staes that the species boundaries and affiliation of species has been an argument. The study analysis the relationships among the potato diploids and polyploids using nitrate reductase sequence data. Moreover, the data gathered are put to observations and are compared to prior plastid phylogenies.

The article focuses on the revision of the Solanum medians Complex (Solanum section Petota) which are widely distributed along the coastal lomas and up the western slopes of the Andes Mountains from central Peru and northern Chile. Research shows that its fertile diploid and sterile triploid cytotypes are common and believed to be associated with morphological variants. It was found that so much overlap of their taxonomy is impractical to use morphology for reliable identifications.

Chromosome pairing relationships within cultivated potato (Solonum tuberosum) and its wild tuber-bearing relatives (Solanum sect. Petota) hove been interpreted by genome formulas, developed in the early 1900s, through techniques of classic meiotic analysis of interspecific hybrids. Here we reexamine potato genome hypotheses with the first phylogenetic analysis of all major genomes of sect. Petota using cloned DNA sequences of the single-copy nuclear gene GBSSI (waxy). Our results provide the first molecular confirmation of allopolyploidy in wild potato. They both support prior hypotheses and identify novel genome origins never before proposed. The data will be useful to help design crossing strategies to incorporate wild species germplasm into cultivated potato. [ABSTRACT FROM AUTHOR]

Landrace potato cultivars are native to two areas in South America: the high Andes from eastern Venezuela to northern Argentina and the lowlands of south-central Chile. Potato first appeared outside of South America in Europe in 1567 and rapidly diffused worldwide. Two competing hypotheses suggested the origin of the "European" potato from the Andes or from lowland Chile, but the Andean origin has been widely accepted over the last 60 years. All modern potato cultivars predominantly have Chilean germplasm, explained as originating from breeding with Chilean landraces subsequent to the late blight epidemics beginning in 1845 in the UK. The Andean origin has been questioned recently through examination of landraces in India and the Canary Islands, but this evidence is inferential. Through a plastid DNA deletion marker from historical herbarium specimens, we report that the Andean potato predominated in the 1700s, but the Chilean potato was introduced into Europe as early as 1811 and became predominant long before the late blight epidemics in the UK. Our results provide the first direct evidence of these events and change the history of introduction of the European potato. They shed new light on the value of past breeding efforts to recreate the European potato from Andean forms and highlight the value of herbarium specimens in investigating origins of crop plants. [ABSTRACT FROM AUTHOR]

Contrasting taxonomic treatments of potato landraces have continued over the last century, with the recognition of anywhere from 1 to 21 distinct Linnean species, or of Cultivar Groups within the single species Solanum tuberosum. We provide one of the largest molecular marker studies of any crop landraces to date, to include an extensive study of 742 landraces of all cultivated species (or Cultivar Groups) and 8 closely related wild species progenitors, with 50 nuclear simple sequence repeat (SSR) (also known as microsatellite) primer pairs and a plastid DNA deletion marker that distinguishes most lowland Chilean from upland Andean landraces. Neighbor-joining results highlight a tendency to separate three groups: (i) putative diploids, (ii) putative tetraploids, and (iii) the hybrid cultivated species S. ajanhuiri (diploid), S. juzepczukii (triploid), and S. curtiobum (pentaploid). However, there are many exceptions to grouping by ploidy. Strong statistical support occurs only for S. ajanhuiri, S. juzepczukii, and S. curtilobum. In combination with recent morphological analyses and an examination of the identification history of these collections, we support the reclassification of the cultivated potatoes into four species: (i) S. tuberosum, with two Cultivar Groups (Andigenum Group of upland Andean genotypes containing diploids, triploids, and tetraploids, and the Chilotanum Group of lowland tetraploid Chilean landraces); (ii) S. ajanhuiri (diploid); (iii) S. juzepczukii (triploid); and (iv) S. curtilobum (pentaploid). For other classifications, consistent and stable identifications are impossible, and their classification as species is artificial and only maintains the confusion of users of the gene banks and literature. [ABSTRACT FROM AUTHOR]

The cultivated potato, Solanum tuberosum, ultimately traces its origin to Andean and Chilean landraces developed by pre-Colombian cultivators. These Andean landraces exhibit tremendous morphological and genetic diversity, and are distributed throughout the Andes, from western Venezuela to northern Argentina, and in southern Chile. The wild species progenitors of these landraces have long been in dispute, but all hypotheses center on a group of ≈20 morphologically very similar tuber-bearing (Solanum section Petota) wild taxa referred to as the S. brevicaule complex, distributed from central Peru to northern Argentina. We present phylogenetic analyses based on the representative cladistic diversity of 362 individual wild (261) and landrace (98) members of potato (all tuber-bearing) and three outgroup non-tuber-bearing members of Solanum section Etuberosum, genotyped with 438 robust amplified fragment length polymorphisms. Our analyses are consistent with a hypothesis of a "northern" (Peru) and "southern" (Bolivia and Argentina) cladistic split for members of the S. brevicaule complex, and with the need for considerable reduction of species in the complex. In contrast to all prior hypotheses, our data support a monophyletic origin of the landrace cultivars from the northern component of this complex in Peru, rather than from multiple independent origins from various northern and southern members. [ABSTRACT FROM AUTHOR]

Morphological data and single- to low-copy nuclear DNA restriction enzyme site data were used to test subspecies circumscriptions of Solanum bulbocastanum and S. cardiophyllum. A prior chloroplast DNA analysis showed these species to be part of two main clades: 1. S. bulbocastanum subsp. bulbocastanum, S. bulbocastanum subsp. dolichophyllum, S. bulbocastanum subsp. partitum, S. cardiophyllum subsp. cardiophyllum and S. cardiophyllum subsp. lanceolatum, and 2. S. cardiophyllum subsp. ehrenbergii and other Mexican diploid species. The nuclear DNA and morphological data showed S. cardiophyllum subsp. ehrenbergii to be slightly distinguishable from the other subspecies of S. cardiophyllum, and do not support the distinction of subspecies within either species. These data add to a growing body of evidence that there are too many wild potato taxa recognized. [ABSTRACT FROM AUTHOR]

This study tests the genetic difference between landrace populations of Solanum tuberosum L. subsp, tuberosum and subsp, andigenum (Juz. & Bukasov) Hawkes using nuclear DNA microsatellites. Microsatellitc loci were amplified in subsp, andigenum (35 accessions), subsp, tuberosum (35 accessions), and other cultivated and wild species (22 accessions). A total of 208 alleles were scored from 18 microsatellite loci spread throughout all 12 chromosomes of potato. Using an infinite allele model and a least squares method of analysis, microsatellite loci separated subsp, tuberosum from subsp, andigenum, and cultivated and wild species. These results support the genetic difference of these two populations and their recognition at some classification level. [ABSTRACT FROM AUTHOR]

Presents a study that examined morphological support for the classification of landrace populations of cultivated potatoes. Information on the cultivated potato species used in the study; Methodology used; Results and discussion.

Presents a study which explored the use of geographic information systems to describe the geographic distribution of wild potatoes. Materials and methods; Results; Discussion.

Deals with a study that examined the phylogenetic relationships of nine wild tomato species and closely related outgroups using DNA sequences of the structural gene granule-bound starch synthase. Information on wild tomatoes in South America; Methodology; Results and discussion.

Presents information on a study which assessed the species boundaries of wild potatoes by phenetic analyses of morphological data. Morphological criteria and species boundaries; Character state variation; Species distinction within series Longipedicellata.

Database management systems (DBMS's) today are usually built as subsystems on top of an operating system (OS). This design approach can lead to problems of unreliability and inefficient performance as well as forcing a duplication of functions between the DBMS and OS. A new design approach is proposed which eliminates much of this duplication by integrating the duplicated functions into independent subsystems used by both the DBMS and OS. Specifically, an I/O and file support subsystem and a security subsystem are defined. Both subsystems make use of a logical information model which models the stored information in secondary storage. The new database operating system organization and the logical information model are presented in detail. Design of the security subsystem is based on the access control model, and is extended with Boolean predicates to produce an access control model capable of enforcing content- dependent security policies. The access matrix is implemented using a combination of access lists and capabilities. Authorization models and multiple user processes are discussed in relation to the new system organization. The outline of a formal specification and proof of correctness of the security subsystem is also discussed. [ABSTRACT FROM AUTHOR]

Presents a paper on engineering computing environments, while describing a way to solve problems associated with engineering data exchange. Information on data exchange standards; What an engineering computing environment which applies data exchange standards to share technical data can benefit from; Details on normalized data structures.

Discusses the use of a chloroplast deoxyribonucleic acid (cpDNA) restriction enzyme, to test the hypotheses of wild potatoes in South America. Observations from tests carried out; What results strongly suggests; Hybridization in potatoes.

The article focuses on the genomic diversity of potato crops from identification of single nucleotide polymorphisms (SNP) through resequencing. It discusses the data analysis on diploid germplasm, phenotype variation and genotypes during potato breeding programs and wild germplasm in order to increase genome-wide diversity.

Oestrogen receptor (ER)-positive breast cancer (BC) is generally well responsive to endocrine therapy. Neoadjuvant endocrine therapy (NAET) is increasingly being used for downstaging ER-positive tumours. This study aims to analyse the effect of NAET on a well-characterised cohort of ER-positive BC with particular emphasis on receptor expression. This is a retrospective United Kingdom (UK) multicentre study of 391 patients who received NAET between October 2012 and October 2020. Detailed analyses of the paired pre- and post-NAET morphological changes and hormone receptor (HR) and human epidermal growth factor receptor 2 (HER2) expression were performed. The median duration of NAET was 86 days, with median survival and overall survival rates of 380 days and 93.4%, respectively. A total of 90.3% of cases achieved a pathological partial response, with a significantly higher rate of response in the HER2-low cancers. Following NAET, BC displayed some pathological changes involving the tumour stroma including central scarring and an increase in tumour infiltrating lymphocytes (TILs) and tumour cell morphology. Significant changes associated with the duration of NAET were observed in tumour grade (30.6% of cases), with downgrading identified in 19.3% of tumours (p < 0.001). The conversion of ER status from positive to low or negative was insignificant. The conversion of progesterone receptor (PR) and HER2 status to negative status was observed in 31.3% and 38.1% of cases, respectively (p < 0.001). HER2-low breast cancer decreased from 63% to 37% following NAET in the paired samples. Significant morphological and biomarker changes involving PR and HER2 expression occurred following NAET. The findings support biomarker testing on pre-treatment core biopsies and post-treatment residual carcinoma. [ABSTRACT FROM AUTHOR]

The article announces that Dr. Sandra Dianne Knapp has received the 2009 Peter Raven Award from the American Society of Plant Taxonomists.

The article announces that W. Hardy Eshbaugh has received the 2008 Peter Raven Award.

Talks about the widespread use of data engineering techniques. Detailed information on the research articles on the subject of data engineering techniques; Problems in building working systems.

Presents an obituary of Richard Frederic Stevens.

We report a case of alpelisib-induced uveitis. A 68-year-old female who had recently been given alpelisib for metastatic breast cancer presented with a 2-week history of bilateral worsening vision with a corresponding acute hypermetropic shift. Her unaided visual acuity was 6/60 in both eyes, with bilateral anterior uveitis, non-granulomatous keratic precipitates, posterior synechiae, and limited fundal view. There was also a mild iris bombe configuration, although the intraocular pressures were normal. Ocular ultrasound revealed bilateral uveal effusion, ciliary body congestion, dense vitreous cells, and exudative retinal detachments. These findings were also confirmed on multimodal imaging with widefield fundus photography (Optos) and optical coherence tomography. Based on the clinical features above, a diagnosis of alpelisib-induced panuveitis was diagnosed. She was then admitted and treated with a 3-day course of intravenous methylprednisolone and intensive topical steroids. Her clinical signs and symptoms started to improve, and she was discharged 4 days later. At 1 week of follow-up, her best-corrected visual acuity was 6/12 in both eyes, with broken posterior synechiae and resolution of exudative retinal detachments. This case highlights the importance of early ophthalmology involvement by the oncology team as oncology therapy can have potential unexpected ocular manifestations. [ABSTRACT FROM AUTHOR]

The last several years have seen revolutionary advances in DNA sequencing technologies with the advent of next-generation sequencing (NGS) techniques. NGS methods now allow millions of bases to be sequenced in one round, at a fraction of the cost relative to traditional Sanger sequencing. As costs and capabilities of these technologies continue to improve, we are only beginning to see the possibilities of NGS platforms, which are developing in parallel with online availability of a wide range of biological data sets and scientific publications and allowing us to address a variety of questions not possible before. As techniques and data sets continue to improve and grow, we are rapidly moving to the point where every organism, not just select "model organisms", is open to the power of NGS. This volume presents a brief synopsis of NGS technologies and the development of exemplary applications of such methods in the fields of molecular marker development, hybridization and introgression, transcriptome investigations, phylogenetic and ecological studies, polyploid genetics, and applications like large gene bank collections. [ABSTRACT FROM AUTHOR]

The article presents a study that deals with a disjunct population of solanum morelliforme or an epiphytic wild potato in Bolivia. It highlights the importance of the discovery as the first record of this species in South America, and the first species in the section growing in both North and Central America and in South America. It conducted a maxium entropy analysis of 19 climatic variables which matched the occurrence of the South American locality with precision.

The concept that traits should be associated with related organisms and that nearby populations of the same species are likely to be more similar to each other than to populations spread far apart has long been accepted. Consequently, taxonomic relationships and biogeographical data are commonly believed to have the power to predict the distribution of disease resistance genes among plant species. In this study, we test claims of such predictivity in a group of widely distributed wild potato species. There was no clear association between resistance to soft rot and taxonomic relationships. However, we have found some associations between resistance to soft rot and environmental data such as annual precipitation and annual mean temperature. In addition, we have noted that high levels of resistance are mostly found in species with high levels of phenotypic plasticity. The three most resistant species were Sohmum paucijugum, S. brevicaule, and S. connnersonii. [ABSTRACT FROM AUTHOR]

Comparative genetic linkage mapping using a common set of DNA markers in related species is an important methodology in plant genome research. Here, we demonstrate a comparative fluorescence in situ hybridization (FISH) mapping strategy in plants. A set of 13 bacterial artificial chromosome clones spanning the entire length of potato chromosome 6 was used for pachytene chromosome-based FISH mapping in seven distantly related Solanum species including potato, tomato, and eggplant. We discovered one paracentric inversion and one pericentric inversion within specific lineages of these species. The comparative FISH mapping data revealed the ancestral structure of this chromosome. We demonstrate that comparative FISH mapping is an efficient and powerful methodology to study chromosomal evolution among plant species diverged for up to 12 million years. [ABSTRACT FROM AUTHOR]

The article presents the morphometric study of species boundaries of the wild potato Solanum series Piurana (Solanaceae) and putatively related species from seven other series in Solanum section Petota in Peru. The morphological similarity of its constituent species has led to conflicting taxonomic treatments. Solanum series Piurana's limits and validity of constituent species are unresolved. Among its other series are Conicibaccata, Cuneoalata, Ingifolia, Megistacroloba and Simplicissima.

Thomas Beatson’s celebrated description in 1896 of bilateral oophorectomy as effective therapy for premenopausal breast cancer could be considered as the first demonstration of response of any cancer to a ‘targeted therapy.’ At that time, however, the understanding of the mechanism of the intervention was minimal. In recent years a host of new rationally designed, molecularly targeted cancer therapies have been introduced from both large pharmaceutic and small biotechnology companies, and the portfolio of new targeted treatments in the pipeline appears to be unending. The existence of this array of potential new therapies is the result of a prodigious effort in the researching and defining of the molecular components of the cancer phenotype, and the subsequent rational design of agents to target candidate pathways. Experience with endocrine therapy has shown that targeted therapies require the target to be not merely expressed in the cancer phenotype, but important in regulating growth of cancer cells. We may well look back at many of the current targeted therapy trials as unrealistically simplistic in failing to adequately and define the target phenotype. This approach risks rejecting highly active treatments for a small subgroup of a study population where minimal activity is present for the majority. The future for breast cancer therapy is promising, but it is important to be prepared for disappointment, as early success in animal models cannot guarantee a successful human therapy. Stunning results such as the adjuvant trastuzumab trials are likely to remain the exceptions rather that the rule, and most gains will be modest advances.A better understanding of the molecular biology of cancer may also aid in guiding the most appropriate use of existing therapies such as conventional chemotherapy. This knowledge will facilitate the rational selection of drug combinations and/or sequencing based on their mechanisms of action at a molecular level.The aim of this paper is to review the current state-of-the-art in novel targeted therapies for breast cancer based on an understanding of this disease at the molecular level, with particular reference to those agents entering the clinic. [ABSTRACT FROM AUTHOR]

A major justification for taxonomic research is its assumed ability to predict the presence of traits in a group for which the trait has been observed in a representative subset of the group. Taxonomy is regularly used by breeders interested in choosing potential sources of disease-resistant germplasm for cultivar improvement. We designed this study as an empirical test of prediction by associating resistance to white mold [caused by the fungal pathogen Sclerotinia sclerotiorum (Lib.) de Bary] to diverse potato (Solanum spp.) taxonomies and biogeography, using 144 accessions of 34 wild relatives of potato in Solanum sections Petota and Etuberosum. Tremendous variation for resistance to white mold occurs both within and among species. No consistent association was observed between white mold resistance and taxonomic series (based on a phenetic concept), clades (based on a cladistic concept), ploidy, breeding system, geographic distance, or climate parameters. Species and individual accessions with high proportions of white-mold-resistant plants have been identified in this study, but both often exhibit extensive variation and designation of either as resistant or susceptible must take this variation into account. Therefore, taxonomic relationships and ecogeographic data cannot be reliably used to predict where additional sources of white mold resistance genes will be found. [ABSTRACT FROM AUTHOR]

Describes the Solanum arcanum and Solanum huaylasense, two wild tomato species segregated from Solanum peruvianum sensu lato found in Northern Peru. Characteristics of the species; Morphological features of the wild tomatoes.

In 1993 we became aware of a worrying increase in apparent errors in the histopathological diagnosis of musculoskeletal tumours in our Unit. As a result all cases seen over the past 8 years were reviewed by an independent panel. Of the 1996 cases reviewed there was an error in 87. In 54 cases (2.7%) this had led to some significant change in the active management of the patient. The main areas where errors arose were in those very cases where clinical and radiological features were not helpful in confirming or refuting the diagnosis. The incidence of errors rose with the passage of time, possibly related to a deterioration in the pathologist's health. The error rate in diagnosing bone tumours in previously published series ranges from 9 to 40%. To ensure as accurate a rate of diagnosis as possible multidisciplinary working and regular audit are essential. [ABSTRACT FROM AUTHOR]