Miracle-dz/UniFAR-FTUs huggingface dataset:
The Impact of Radiotherapy on Patient-reported Outcomes of Immediate Implant-based Breast Reconstruction With and Without Mesh

Objective: To explore the impact of PMRT on PROs of IBBR performed with and without mesh. Summary of Background Data: PMRT is increasingly given to improve breast cancer outcomes but can adversely impact complications after IBBR. Little; however, is known about the impact of PMRT on the PROs of IBBR, especially when mesh is used. Methods: The implant Breast Reconstruction evAluation prospective cohort study recruited consecutive women undergoing immediate IBBR from 81 UK breast and plastic surgical units. Demographic, operative, oncological, and 3-month complication data were collected, and patients consented to receive validated PRO questionnaires at 18-months. The association between IBBR, PMRT, and PROs were investigated using mixed-effects regression models adjusted for clinically-relevant confounders and including a random-effect to account for potential clustering by center Results: A total of 1163 women consented to receive 18-month questionnaires of whom 730 (63%) completed it. Patients undergoing PMRT (214 patients) reported worse PROs in 3 BREAST-Q domains: satisfaction with breasts [–6.27 points, P = 0.008, 95% confidence interval (CI) (–10.91, –1.63)], satisfaction with outcome [–7.53 points, P = 0.002, CI (–12.20, –2.85)] and physical well-being [–6.55 points, P < 0.001, CI (–9.43, –3.67)]. Overall satisfaction was worse in the PMRT group [OR 0.497, P = 0.002, CI (0.32, 0.77)]. These effects were not ameliorated by mesh use. Conclusions: PMRT may adversely affect PROs after IBBR irrespective of whether mesh is used. These findings should be discussed with all patients considering IBBR and when indications for PMRT are borderline to enable informed decision-making regarding oncological and reconstructive treatment options. Trial registration: ISRCTN37664281.
Population abundance and early spring conditions determine variation in body mass of juvenile chamois

Abstract For species living in seasonal environments the understanding of demographic processes requires identifying the environmental factors during spring and summer that shape phenotypic variation. We assessed the effects of plant phenology and population abundance during spring–summer on variation in autumn body mass among cohorts (1995–2006) of juvenile alpine chamois (Rupicapra rupicapra). We computed several metrics based on the normalized difference vegetation index (NDVI) to assess interannual variation in plant phenology and productivity. Body mass of both sexes decreased similarly during years with late springs (−20%) and with increasing population abundance (−15%), with no interactive effect. Our results also suggested that forage quality more than forage quantity influenced body mass of juveniles. Variation in body mass of juveniles thus can be used as an indicator of the relationship between chamois populations and their environment. This study also demonstrates the utility of satellite-based data in increasing our understanding of the consequences of spring–summer conditions on life-history traits.
Cannibalism in Dolichophis jugularis (Serpentes: Colubridae): More than Random?

ABSTRACT Four cases of cannibalism among Dolichophis jugularis (Serpentes: Colubridae) are reported from Cyprus and Turkey. The number of cannibalism records for this species thus rises to at least six. Due to its opportunistic euryphagy, D. jugularis is potentially cannibalistic. Although pure opportunism cannot be ruled out, cannibalistic behaviour may be enhanced in this species by conditions such as starvation.
Symbiotic relationships between sponges and other organisms from the Sea of Cortes (Mexican Pacific coast): same problems, same solutions

This study provides a morphological description of three symbiotic associations between sponges (Haplosclerida) and other macroorganisms from the Sea of Cortes (Mexican Pacific Ocean). These associations include: (1) a two-sponge association (Haliclona sonorensis/Geodia media), (2) a sponge-red macroalga association (Haliclona caerulea/Jania adherens) and (3), a sponge-coral association (Chalinula nematifera/Pocillopora spp.). So far these interactions seem to be obligatory for the sponges (Haliclona spp. and C. nematifera), since we have never found them living in isolation. Interestingly, similar associations have been described from other places around the world. Associations quite similar to (1) have been described from the Caribbean, and associations (2) and (3) are comparable to others described from the Western Pacific. Instead of comparing these associations with their "sibling" associations worldwide, we discussed the ability of haplosclerid sponges to form symbiotic associations with other organisms, since these sponges pertain to the group of which the most associations have been described.
Propionibacteria in Italian hard cheeses

Summary - Economie losses for Parmigiano Reggiano and Grana Padano, for which production is about 200 000 tons per year, can result from "Iate blowing" caused by propionic acid bacteria (PAB). PAB contents of 306 milk samples for Grana cheese were analyzed. The mean value was 726 du/ml; however, when the 8 samples with the highest PAB content (>5 000 du/ml) are not included, this mean decreases to 377 du/ml. Sixty strains of PAB were isolated, identified (65% P freudenreichii, 25% P jensenii, 5% P thoenii and 5% P acidipropionici) and tested under different incubation temperatures (30, 22, 15°C), pH of the substrates (6.0, 5.5, 5.0) and concentrations of NaCI (0.5, 1.0, 1.5, 2.0, 2.5, 3.0%). The "optimal" condition was 30°C, with considerable slowing of the growth at lower temperature. ln the presence of NaCl, as the incubation temperature decreased, the number of the totally inhibited strains increased, while the total of those insensitive and those only partially inhibited remained the sa me up to 1.5% of NaCI and increased at higher concentrations. The strains resulted partially or strongly inhibited only at pH 5.0, while the total number of insensitive strains and those only partially inhibited increased as the temperature was lowered. An extreme adaptability of PAB even to very drastic conditions was noted: anywhere combinations such as low temperature « 22°C), high salt concentrations (> 2%) and low pH values «5.5) could effectively delay their development during the ripening of Grana cheese without total inhibition.
Glibenclamide as a neuroprotective antidementia drug

Abstract In the view of progressively aging human population and increased occurrence of dysmetabolic disorders, such as diabetes mellitus, cognitive impairment becomes a major threat to the national health. To date, the molecular mechanisms of cognitive dysfunction are partially described for diabetes and diseases of different nature, such as Alzheimer disease or Parkinson disease. The emergence of data pointing towards pleotropic effects of hypoglycaemic medicines indicates involvement of their targets in pathogenesis of cognitive impairment. We are aiming here to review available data on the most widely used hypoglycaemic drug, glibenclamide and find possible relationship of its targets to the pathogenesis of cognitive impairment.
Relation between Stipe Length, Environment, and the Taxonomic Characters of Laminaria

The characters normally used to separate Laminaria longicruris from L. agardhii are unsatisfactory because they change with the stipe length of the plants (presumably related to age) and the degree of wave exposure, and because forms with characters intermediate between the two species are common. At four stations with differing degree of exposure, young plants all had solid stipes and some of the older plants had hollow stipes, but the length at which a cavity first appeared increased with increasing wave action, while the proportion of the stipe that was hollow decreased. The shape of the base of the blade did not correlate with the condition of the stipe.
The importance of linking periods of the annual cycle for understanding life-history tradeoffs in a migratory songbird

Conditions experienced during development can have long-term consequences for individual success. In migratory songbirds, brood size and fledging date can influence mass at fledging which in turn has been shown to influence first year survival. However, tracking individuals across stages of the annual cycle is challenging, and as a result, the ways in which early life events affect survival in the longer term are not well understood. In this paper, we first used a brood manipulation experiment to demonstrate that migratory Savannah sparrows (Passerculus sandwichensis) fledging from reduced broods had higher mass at fledging relative to birds from control broods. We then used a dataset spanning 13 years to show a positive relationship between first year apparent survival and mass at fledging. Having established these relationships, we then used three years of field data involving multiple captures of individuals throughout the pre-migratory period and a multilevel path model to examine the hypothesis that conditions during development affect survival during migration by affecting an individual’s ability to accumulate sufficient lean tissue and fat mass prior to migration. We found a negative relationship between fledging mass with brood size and fledging date, and a positive relationship between pre-migratory fat mass with fledging mass. Our results provide the first evidence that conditions during development affect survival during migration through their effect on fat stores. These results are particularly important given recent evidence showing that body condition of songbirds at fledging is affected by climate change and anthropogenic changes to landscape structure. INTRODUCTION Conditions experienced during early development, such as poor nutrition, can have longterm consequences for an individual’s phenotype, subsequent performance, and fitness (Lindström 1999, Metcalfe and Monaghan 2001, Monaghan 2008). Many of these longterm effects may occur over varying time scales and under specific ecological contexts (Monaghan 2008). In migratory animals, the annual cycle is comprised of a series of life
Stomatal density, anatomy and nutrient concentrations of Scots pine needles are affected by elevated CO2 and temperature

Stomatal density, anatomy and nutrient concentrations of Scots pine ( Pinus sylvestris L.) needles were studied during 3 years of growth at elevated CO 2 (693 ± 30 m mol mol - 1 ), at elevated temperature (ambient + 2·8-6·2 ∞ C depending on the time of the year) and in a combination of elevated CO 2 and temperature in closed-top chambers. The treatments were started in August 1996. At elevated temperature, the needles that were grown in the first year (i.e. the 1997 cohort) were thinner, had thinner mesophyll in the abaxial side, thinner vascular cylinder and lower stomatal density than those grown at ambient temperature. The proportion of mesophyll area occupied by vascular cylinder or inter- cellular spaces were not changed. Lower stomatal density apparently did not lead to decreased use of water, as these needles had higher concentrations of less mobile nutrients (Ca, Mg, B, Zn and Mn), which could indicate increased total transpiration. In the 1997 and 1998 cohorts, elevation of temperature decreased concentrations of N, P, K, S and Cu. In the 1999 cohort, contradictory, higher concentrations of N and S at elevated temperature may be related to increased nutrient mineralization in the soil. Elevation of CO 2 did not affect stomatal density, needle thickness, thick- ness of epidermis or hypodermis, vascular cylinder or inter- cellular spaces. Concentrations of N, P, S and Cu decreased at elevated CO 2 . Reductions were transient and most dis- tinct in the 1997 cohort. The effects of CO 2 and temperature were in some cases interactive, which meant that in the combined treatment stomatal density decreased less than at elevated temperature, and concentrations of nutrients decreased less than expected on the basis of separate treat- ments, whereas the thickness of the epidermis and hypo- dermis decreased more than in the separate treatments. In conclusion, alterations in the anatomy and stomatal density of Scots pine needles were more distinct at elevated tem- perature than at elevated CO 2 . Both elevated CO 2 and tem- perature-induced changes in nutrient concentrations that partly corresponded to the biochemical and photosynthetic alterations in the same cohorts (Luomala et al. Plant, Cell and Environment 26, 645-660, 2003) Reductions in nutri- ent concentrations and alterations in the anatomy were transient and more evident in the needle cohort that was grown in the first treatment year.
MICROSATELLITE DNA ANALYSIS OF POPULATION STRUCTURE IN ALLEGHENY WOODRATS (NEOTOMA MAGISTER)

Abstract Eleven polymorphic microsatellite DNA markers were screened to investigate patterns and processes of genetic variation in Allegheny woodrats at 2 spatial scales, geographically distinct populations and subpopulations within populations. The microsatellite markers detected considerable genetic variation and diversity, with an average heterozygosity of 62.0% (range 25.7–75.0%) and an average of 10.4 alleles per locus (range 5–19). Subpopulations conformed to Hardy–Weinberg expectations in 98.9% of comparisons, and allele frequency differed among subpopulations in 99.3% of comparisons. All statistical tests indicated significant genetic subdivision at the population and subpopulation levels. Theoretical estimates of gene flow were low among subpopulations, suggesting that effective dispersal is limited among subpopulations separated by as little as 3 km. A significant range-wide relationship between geographic and genetic distance at both scales suggests isolation by distance as a mechanism for the observed differentiation. The relationship between genetic distance and geographic distance among the 19 subpopulations within the central Appalachians was significant but weak. Results suggest that Allegheny woodrats associated with clusters of geographically proximate rock outcrops may function as population units. We recommend that individual rock outcrops or groups of geographically proximate outcrops be considered as population units for management.
Population genetic structure of the short-beaked common dolphin from the Black Sea and the Turkish Straits System

Abstract Our study aims to assess the population connectivity, evolutionary history, and conservation status of the short-beaked common dolphin in the Black Sea and Turkish Straits System (TSS). We also include DNA sequences from the Atlantic Ocean and the Mediterranean Sea to provide a regional perspective to our localized study. Analysis of 366 base pairs of mitochondrial DNA D-loop fragments from 37 samples collected from short-beaked common dolphins in the Black Sea, TSS, and Aegean Sea revealed 13 haplotypes, eight of which have not been previously reported. While analysis of samples archived on GenBank revealed 89 different haplotypes across the region. The haplotype network contains two main peripheral groups that include individuals from all locations. Haplotypes from the Atlantic Ocean are scattered across the network and no obvious population separation was detected. Some shared haplotypes potentially indicate multi-directional colonization events of the Mediterranean Sea from the eastern Atlantic Ocean. Moreover, some less widely distributed haplotypes suggest some level of more recent genetic connectivity through the Strait of Gibraltar and the TSS and point out the importance of these straits in the dispersal of short-beaked common dolphins. The haplotype and nucleotide diversity values were lower in the Black Sea, TSS, and western Mediterranean Sea when compared to the Atlantic Ocean, supporting the expansion of Atlantic populations into the Mediterranean and the Black Seas. Differentiation was observed between the Atlantic Ocean, and the Mediterranean Sea, TSS and the Black Sea based on Фst but not between Mediterranean and the Black Seas. For common dolphins, which have high dispersal potential, the protection of open seas and narrow seaways to enhance connectivity may be crucial.
The value of proactive goal-setting and choice in 3- to 7-year-olds' use of working memory gating strategies in a naturalistic task.

Rule-guided behavior depends on the ability to strategically update and act on content held in working memory. Proactive and reactive control strategies were contrasted across two experiments using an adapted input/output gating paradigm (Chatham et al., 2014). Behavioral accuracies of 3-, 5-, and 7-year-olds were higher when a contextual cue appeared at the beginning of the task (input gating) rather than at the end (output gating). This finding supports prior work in older children, suggesting that children are better when input gating but rely on the more effortful output gating strategy for goal-oriented action selection (Unger et al., 2016). A manipulation was added to investigate whether children's use of WM strategies becomes more flexible when task goals are specified internally rather than externally provided by the experimenter. A shift toward more proactive control was observed when children chose the task goal amongst two alternatives. Scan path analyses of saccadic eye movement indicated that giving children agency and choice over the task goal resulted in less use of a reactive strategy than when the goal was determined by the experimenter.
Comparative morphology and phylogeny of Nicotiana section Suaveolentes (Solanaceae) in Australia and the South Pacific

Molecular phylogenies alone have failed to resolve evolutionary relationships of Nicotiana L. section Suaveolentes Goodsp. (Solanaceae), a section largely comprising Australian endemics. Comparative morphology of Suaveolentes is illustrated and characters, together with the chromosome number, coded for phylogenetic analysis. Morphological characters included discrete characters of seeds and trichomes studied by scanning electron and light microscopy, and gap-coded quantitative measurements of flowers and vegetative organs. These data were analysed using both maximum parsimony and splits network, and compared to and combined with molecular analyses based on published nuclear and chloroplast-DNA sequences. Among morphological characters, there was a high level of homoplasy, possibly attributable to convergent evolution, hybridisation and introgression, and the underlying polyploid origin of the group. There was some conflict between the morphological and molecular datasets; however, overall there was a level of concordance that identified a phylogenetic sequence of taxa that reflected a reduction in the chromosome number. With N. africana as the functional outgroup, analyses showed N. fragrans (New Caledonia and Tongatapu) and N. fatuhivensis (Marquesas islands, formerly N. fragrans var. fatuhivensis) to be a basal lineage in the Australian and South Pacific clade of Suaveolentes. N. forsteri (eastern mainland Australia, Lord Howe Island and New Caledonia) is the sister taxon to all other Australian species of Suaveolentes, which form a well supported monophyletic group. Within this Australian endemic group, species with a chromosome count of n = 24 or 23 are early lineages. Two clades with a reduced chromosome number are the ‘N. simulans clade’ (all taxa with n = 20) and the ‘N. suaveolens clade’ (n = 19, 18, 16, or 15). The position of N. cavicola (n = 20 or 23) is equivocal, and it and several other species require further study. Some widespread taxa require greater sampling of populations to test for variation in morphology, DNA sequences and chromosome number for further elucidation of the evolutionary history of Suaveolentes.
A morphological, geographical and karyological study of East Asian Bupleurum longiradiatum Turcz. and B. sachalinense Fr. Schmidt

Die ostasiatischen Arten Bupleurum longiradiatum Turcz. und B. sachalinense Fr. Schmidt, die der Sektion Bupleurum der Subsektion Archaeopleurum Lincz. angehoren, unterscheiden sich durch den Bau von Blutenstanden und die Areale, haben aber den gleichen Bau von Fruchten und unterscheiden sich durch Karyotypen nicht signifikant. Im Artikel werden Charakteristika von Karyotypen, Idiogramme, Synonyme, zitierte Literatur fur beide untersuchte Arten angefuhrt. The East Asian species Bupleurum longiradiatum Turcz. and B. sachalinense Fr. Schmidt which belong to the section Bupleurum, subsection Archaeopleurum Lincz. , differ in floscule structure and ranges, but have similar fruit structures and insignificantly differing karyotypes. The paper cites their karyotype characteristics, idiograms, synonyms, bibliography and features.
Measuring community structure of a forest using the wandering quarter method

A plant community can be sampled using a "wandering quarter" survey, a plotless survey method that requires no set-up and minimal equipment. Participants zig-zag from tree to tree, always heading in the same general compass direction. Data collected can be used to calculate several common measures of plant community structure, including species richness, species diversity, relative basal area, stems per hectare, relative dominance, and importance value. Hypotheses about the effect of various abiotic parameters, such as altitude, or aspects, or the effect of various forest management techniques, can be tested by comparing the parameters of community structure.
Ecological specialization and niche overlap of subterranean rodents inferred from DNA metabarcoding diet analysis

Knowledge of how animal species use food resources available in the environment can increase our understanding of many ecological processes. However, obtaining this information using traditional methods is difficult for species feeding on a large variety of food items in highly diverse environments. We amplified the DNA of plants for 306 scat and 40 soil samples, and applied an environmental DNA metabarcoding approach to investigate food preferences, degree of diet specialization and diet overlap of seven herbivore rodent species of the genus Ctenomys distributed in southern and midwestern Brazil. The metabarcoding approach revealed that these species consume more than 60% of the plant families recovered in soil samples, indicating generalist feeding habits of ctenomyids. The family Poaceae was the most common food resource retrieved in scats of all species as well in soil samples. Niche overlap analysis indicated high overlap in the plant families and molecular operational taxonomic units consumed, mainly among the southern species. Interspecific differences in diet composition were influenced, among other factors, by the availability of resources in the environment. In addition, our results provide support for the hypothesis that the allopatric distributions of ctenomyids allow them to exploit the same range of resources when available, possibly because of the absence of interspecific competition.
PROBING THE LIPOPROTEIN SECRETION PATHWAY IN BORRELIA BURGDORFERI

iii Acknowledgements. v Table of Contents.vii List of Figures. ix Abbreviations . xii Chapter I: Introduction.1 Lyme Disease . 1 Borrelia burgdorferi . 3 Protein transport in diderm (Gram-­negative) bacteria. 16 Lipoprotein transport. 30 B. burgdorferi lipoprotein transport. 41 Chapter II: Materials and Methods . 45 Chapter III: Functional analysis of the B. burgdorferi . 60 Lol pathway homologs . 60 Abstract . 60 Introduction. 61 Discussion. 88 Chapter IV: Localization of IpLA7 in B. burgdorferi . 92 viii Abstract . 92 Introduction. 92 Results. 94 Discussion.102 Chapter V: Investigation of the B. burgdorferi outer membrane proteome . 104 Abstract . 104 Introduction.105 Results.106 Chapter VI: Discussion and future directions . 127 References . 136