cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1569428.v1
title: Prognostic effect of hENT1, dCK and HuR expression by morphological type in periampullary adenocarcinoma, including pancreatic cancer

description: <i>Background</i>: Putative biomarkers of gemcitabine response have been extensively studied in pancreatic cancer, but less so in other types of periampullary adenocarcinoma. The most studied biomarker is human equilibrative nucleoside transporter 1 (hENT1), and the activating enzyme deoxycytidine kinase (dCK) has also been linked to treatment response. The RNA-binding protein human antigen R (HuR) has been demonstrated to confer increased dCK levels in vitro and to predict gemcitabine response in vivo. Here, we investigated the prognostic impact of hENT1, dCK and HuR in pancreatobiliary (PB) and intestinal (I) type periampullary cancers, respectively. <i>Material and methods</i>: Immunohistochemical expression of hENT1, dCK and HuR was evaluated in tissue microarrays with all primary tumours and 103 paired lymph node metastases from a consecutive retrospective cohort of 175 patients with resected periampullary adenocarcinomas. <i>Results</i>: In patients with PB-type tumours, neither hENT1 nor dCK expression was prognostic. A high HuR cytoplasmic/nuclear ratio was associated with a significantly reduced five-year overall survival (OS) in patients receiving adjuvant gemcitabine (HR 2.07, 95% CI 1.03–4.17) but not in untreated patients (p<sub>interaction</sub> = 0.028). In patients with I-type tumours receiving adjuvant chemotherapy, high dCK expression was significantly associated with a prolonged recurrence-free survival (RFS) (HR 0.09, 95% CI 0.01–0.73, p<sub>interaction</sub> = 0.023). Furthermore, HuR expression was associated with a prolonged OS and RFS in unadjusted but not in adjusted analysis and hENT1 expression was an independent predictor of a prolonged RFS (HR 0.24, 95% CI 0.10–0.59), regardless of adjuvant treatment. <i>Conclusion</i>: hENT1 expression is a favourable prognostic factor in I-type, but not in PB-type tumours. High dCK expression is a favourable prognostic factor in patients with I-type tumours receiving adjuvant treatment and a high cytoplasmic/nuclear HuR ratio is a negative prognostic factor in gemcitabine-treated PB-type tumours. Morphological subtype should always be considered in biomarker studies on periampullary cancer.
DOI: 10.6084/m9.figshare.1569417
title: Role of lysine binding residues in the global folding of the <i>lysC</i> riboswitch

description: ABSTRACTRiboswitches regulate gene expression by rearranging their structure upon metabolite binding. The lysine-sensing <i>lysC</i> riboswitch is a rare example of an RNA aptamer organized around a five-way helical junction in which ligand binding is performed exclusively through nucleotides located at the junction core. We have probed whether the nucleotides involved in ligand binding play any role in the global folding of the riboswitch. As predicted, our findings indicate that ligand-binding residues are critical for the lysine-dependent gene regulation mechanism. We also find that these residues are not important for the establishment of key magnesium-dependent tertiary interactions, suggesting that folding and ligand recognition are uncoupled in this riboswitch for the formation of specific interactions. However, FRET assays show that lysine binding results in an additional conformational change, indicating that lysine binding may also participate in a specific folding transition. Thus, in contrast to helical junctions being primary determinants in ribozymes and rRNA folding, we speculate that the helical junction of the lysine-sensing <i>lysC</i> riboswitch is not employed as structural a scaffold to direct global folding, but rather has a different role in establishing RNA-ligand interactions required for riboswitch regulation. Our work suggests that helical junctions may adopt different functions such as the coordination of global architecture or the formation of specific ligand binding site.
DOI: 10.6084/m9.figshare.1569423
title: A covariance correction that accounts for correlation estimation to improve finite-sample inference with generalized estimating equations: a study on its applicability with structured correlation matrices

description: When generalized estimating equations (GEEs) incorporate an unstructured working correlation matrix, the variances of regression parameter estimates can inflate due to the estimation of the correlation parameters. In previous work, an approximation for this inflation that results in a corrected version of the sandwich formula for the covariance matrix of regression parameter estimates was derived. Use of this correction for correlation structure selection also reduces the over-selection of the unstructured working correlation matrix. In this manuscript, we conduct a simulation study to demonstrate that an increase in variances of regression parameter estimates can occur when GEE incorporates structured working correlation matrices as well. Correspondingly, we show the ability of the corrected version of the sandwich formula to improve the validity of inference and correlation structure selection. We also study the relative influences of two popular corrections to a different source of bias in the empirical sandwich covariance estimator.
DOI: 10.6084/m9.figshare.1569423.v1
title: A covariance correction that accounts for correlation estimation to improve finite-sample inference with generalized estimating equations: a study on its applicability with structured correlation matrices

description: When generalized estimating equations (GEEs) incorporate an unstructured working correlation matrix, the variances of regression parameter estimates can inflate due to the estimation of the correlation parameters. In previous work, an approximation for this inflation that results in a corrected version of the sandwich formula for the covariance matrix of regression parameter estimates was derived. Use of this correction for correlation structure selection also reduces the over-selection of the unstructured working correlation matrix. In this manuscript, we conduct a simulation study to demonstrate that an increase in variances of regression parameter estimates can occur when GEE incorporates structured working correlation matrices as well. Correspondingly, we show the ability of the corrected version of the sandwich formula to improve the validity of inference and correlation structure selection. We also study the relative influences of two popular corrections to a different source of bias in the empirical sandwich covariance estimator.
DOI: 10.6084/m9.figshare.1569452.v4
title: Phosphorylation and dephosphorylation regulate APC/C<sup>Cdh1</sup> substrate degradation

description: The Anaphase Promoting Complex/Cyclosome (APC/C) ubiquitin ligase activated by its G1 specific adaptor protein Cdh1 is a major regulator of the cell cycle. The APC/C<sup>Cdh1</sup> mediates degradation of dozens of proteins, however, the kinetics and requirements for their degradation are largely unknown. We demonstrate that overexpression of the constitutive active <i>CDH1</i><sup><i>m11</i></sup> mutant that is not inhibited by phosphorylation results in mitotic exit in the absence of the FEAR and MEN pathways, and DNA re-replication in the absence of Cdc7 activity. This mode of mitotic exit also reveals additional requirements for APC/C<sup>Cdh1</sup> substrate degradation, which for some substrates such as Pds1 or Clb5 is dephosphorylation, but for others such as Cdc5 is phosphorylation.
DOI: 10.6084/m9.figshare.1569419
title: Anatomy and relationships of †<i>Aipichthys pretiosus</i> and †‘<i>Aipichthys</i>’ <i>nuchalis</i> (Acanthomorpha: Lampridomorpha), with a review of Late Cretaceous relatives of oarfishes and their allies

description: The Cenomanian acanthomorph teleost †<i>Aipichthys</i> is best known from two species: †<i>Aipichthys minor</i> and †<i>Aipichthys velifer</i>. Two poorly studied species of †<i>Aipichthys</i>, †<i>Aipichthys pretiosus</i> from Slovenia and †<i>Aipichthys nuchalis</i> from the English Chalk, have been excluded from all recent studies of the genus. Previous accounts of †<i>A. pretiosus</i> – the type species of †<i>Aipichthys</i> – are inadequate, while †<i>A. nuchalis</i> has been described as too incomplete to interpret. Here we completely redescribe †<i>A. pretiosus</i> and utilize computed tomography to reveal previously hidden skeletal anatomy of †<i>A. nuchalis</i>. †<i>Aipichthys pretiosus</i> has a long sagittal crest, with the supraoccipital, frontal and mesethmoid bones contributing to this structure. Based on this and other features, we find that †<i>A. pretiosus</i> belongs to a clade that is more closely related to extant Lampridiformes than all other nominal species of †<i>Aipichthys</i>. As †<i>A. pretiosus</i> is the type species for the genus, we recommend all other species of the genus should be temporarily referred to as †‘<i>Aipichthys</i>’. †‘<i>Aipichthys</i>’ <i>nuchalis</i> possesses a concave posterior margin and a thickened anterior margin to the supraoccipital crest, and is placed in a polytomy alongside †‘<i>A.</i>’ <i>minor</i>, †‘<i>A.</i>’ <i>velifer</i>, †‘<i>Aipichthys</i>’ <i>oblongus</i> and †<i>Freigichthys</i>. Further investigation is needed to determine whether †‘<i>Aipichthys</i>’ is congeneric with and can be reassigned to †<i>Freigichthys</i>, or whether a new generic name is needed for these taxa. We also include two additional taxa in our analysis: †<i>Nardovelifer altipinnis</i>, the oldest fossil previously attributed to the lampridiform crown, and †<i>Gigapteryx tethyestris</i>, an <i>incertae sedis</i> acanthopterygian. We find that †<i>Nardovelifer</i> has a number of primitive characters not found in crown Lampridiformes, and resolve it as a stem lampridiform. We find that †<i>Gigapteryx</i> is closely related to †<i>Pycnosteroides</i>, together forming the sister clade to all other lampridomorphs. Finally, we examine the diversity of Cretaceous lampridomorphs and discuss their palaeobiogeography and palaeoecology.
DOI: 10.6084/m9.figshare.1569419.v1
title: Anatomy and relationships of †<i>Aipichthys pretiosus</i> and †‘<i>Aipichthys</i>’ <i>nuchalis</i> (Acanthomorpha: Lampridomorpha), with a review of Late Cretaceous relatives of oarfishes and their allies

description: The Cenomanian acanthomorph teleost †<i>Aipichthys</i> is best known from two species: †<i>Aipichthys minor</i> and †<i>Aipichthys velifer</i>. Two poorly studied species of †<i>Aipichthys</i>, †<i>Aipichthys pretiosus</i> from Slovenia and †<i>Aipichthys nuchalis</i> from the English Chalk, have been excluded from all recent studies of the genus. Previous accounts of †<i>A. pretiosus</i> – the type species of †<i>Aipichthys</i> – are inadequate, while †<i>A. nuchalis</i> has been described as too incomplete to interpret. Here we completely redescribe †<i>A. pretiosus</i> and utilize computed tomography to reveal previously hidden skeletal anatomy of †<i>A. nuchalis</i>. †<i>Aipichthys pretiosus</i> has a long sagittal crest, with the supraoccipital, frontal and mesethmoid bones contributing to this structure. Based on this and other features, we find that †<i>A. pretiosus</i> belongs to a clade that is more closely related to extant Lampridiformes than all other nominal species of †<i>Aipichthys</i>. As †<i>A. pretiosus</i> is the type species for the genus, we recommend all other species of the genus should be temporarily referred to as †‘<i>Aipichthys</i>’. †‘<i>Aipichthys</i>’ <i>nuchalis</i> possesses a concave posterior margin and a thickened anterior margin to the supraoccipital crest, and is placed in a polytomy alongside †‘<i>A.</i>’ <i>minor</i>, †‘<i>A.</i>’ <i>velifer</i>, †‘<i>Aipichthys</i>’ <i>oblongus</i> and †<i>Freigichthys</i>. Further investigation is needed to determine whether †‘<i>Aipichthys</i>’ is congeneric with and can be reassigned to †<i>Freigichthys</i>, or whether a new generic name is needed for these taxa. We also include two additional taxa in our analysis: †<i>Nardovelifer altipinnis</i>, the oldest fossil previously attributed to the lampridiform crown, and †<i>Gigapteryx tethyestris</i>, an <i>incertae sedis</i> acanthopterygian. We find that †<i>Nardovelifer</i> has a number of primitive characters not found in crown Lampridiformes, and resolve it as a stem lampridiform. We find that †<i>Gigapteryx</i> is closely related to †<i>Pycnosteroides</i>, together forming the sister clade to all other lampridomorphs. Finally, we examine the diversity of Cretaceous lampridomorphs and discuss their palaeobiogeography and palaeoecology.
DOI: 10.6084/m9.figshare.1569452.v3
title: Phosphorylation and dephosphorylation regulate APC/C<sup>Cdh1</sup> substrate degradation

description: The Anaphase Promoting Complex/Cyclosome (APC/C) ubiquitin ligase activated by its G1 specific adaptor protein Cdh1 is a major regulator of the cell cycle. The APC/C<sup>Cdh1</sup> mediates degradation of dozens of proteins, however, the kinetics and requirements for their degradation are largely unknown. We demonstrate that overexpression of the constitutive active <i>CDH1</i><sup><i>m11</i></sup> mutant that is not inhibited by phosphorylation results in mitotic exit in the absence of the FEAR and MEN pathways, and DNA re-replication in the absence of Cdc7 activity. This mode of mitotic exit also reveals additional requirements for APC/C<sup>Cdh1</sup> substrate degradation, which for some substrates such as Pds1 or Clb5 is dephosphorylation, but for others such as Cdc5 is phosphorylation.
DOI: 10.6084/m9.figshare.1569412
title: Ecology 2050- Field sample training with animals- sweep net

description: Group members: Katrin Chapkis, Ava Kamali, Simranjit Kang, Jennifer Mariatha This lab was conducted at grassland, located adjacent to Danby woodlot, on October 1st 2015, at York University. The weather was sunny with a temperature of 15 degree Celsius, which can be perceived as a cold temperature. The Beaufort wind number was 4, which indicates a moderate breeze, and the wind speed range was 13mph to 18 mph. The information regarding the wind speed was achieved according to the Beaufort Wind Force Scale, which was mentioned in the lab manual. The cold weather might have had a significant effect on the movement of insects, birds, and other organisms. The purpose of this experiment was to introduce the different techniques of sampling, which are used to estimate the abundance and recognizable taxonomic units of animals. The following methods were studied in this lab: pans, pitfall traps, sweep nets, and distance- based techniques. Each individual was responsible for submitting only one dataset but every group member helped each other in order to achieve results with higher accuracy. The sweep net technique was experimented for the dataset of this lab report. The procedure started with setting a constant distance for the transect tape and the time which each trial would take approximately. Distance of 20 meters was assigned to the length of the transect tape and it was estimated that each trial would take about 10-12 minutes. In each trial, the transect tape with 20 meters length was randomly placed in the grassland, and the sweep net was swung back and forth with a great force along the transect line for 10- 12 minutes. At the end of each trail, the net was carefully held to avoid any stings from the captured samples and critically observed to record the number of total abundance and the RTUs. After analysing the trapped organisms and materials, only living insects or animals were counted, and at the end of each trial all of them were returned back to their environment. The totals of 10 trials were repeated for this experiment. In addition, it was possible not to capture any organisms at all since the weather was cold and organisms had less movement compared to a moderate temperature and weather.
DOI: 10.6084/m9.figshare.1569417.v3
title: Role of lysine binding residues in the global folding of the <i>lysC</i> riboswitch

description: ABSTRACTRiboswitches regulate gene expression by rearranging their structure upon metabolite binding. The lysine-sensing <i>lysC</i> riboswitch is a rare example of an RNA aptamer organized around a five-way helical junction in which ligand binding is performed exclusively through nucleotides located at the junction core. We have probed whether the nucleotides involved in ligand binding play any role in the global folding of the riboswitch. As predicted, our findings indicate that ligand-binding residues are critical for the lysine-dependent gene regulation mechanism. We also find that these residues are not important for the establishment of key magnesium-dependent tertiary interactions, suggesting that folding and ligand recognition are uncoupled in this riboswitch for the formation of specific interactions. However, FRET assays show that lysine binding results in an additional conformational change, indicating that lysine binding may also participate in a specific folding transition. Thus, in contrast to helical junctions being primary determinants in ribozymes and rRNA folding, we speculate that the helical junction of the lysine-sensing <i>lysC</i> riboswitch is not employed as structural a scaffold to direct global folding, but rather has a different role in establishing RNA-ligand interactions required for riboswitch regulation. Our work suggests that helical junctions may adopt different functions such as the coordination of global architecture or the formation of specific ligand binding site.
DOI: 10.6084/m9.figshare.1569412.v1
title: Ecology 2050- Field sample training with animals- sweep net

description: Group members: Katrin Chapkis, Ava Kamali, Simranjit Kang, Jennifer Mariatha This lab was conducted at grassland, located adjacent to Danby woodlot, on October 1st 2015, at York University. The weather was sunny with a temperature of 15 degree Celsius, which can be perceived as a cold temperature. The Beaufort wind number was 4, which indicates a moderate breeze, and the wind speed range was 13mph to 18 mph. The information regarding the wind speed was achieved according to the Beaufort Wind Force Scale, which was mentioned in the lab manual. The cold weather might have had a significant effect on the movement of insects, birds, and other organisms. The purpose of this experiment was to introduce the different techniques of sampling, which are used to estimate the abundance and recognizable taxonomic units of animals. The following methods were studied in this lab: pans, pitfall traps, sweep nets, and distance- based techniques. Each individual was responsible for submitting only one dataset but every group member helped each other in order to achieve results with higher accuracy. The sweep net technique was experimented for the dataset of this lab report. The procedure started with setting a constant distance for the transect tape and the time which each trial would take approximately. Distance of 20 meters was assigned to the length of the transect tape and it was estimated that each trial would take about 10-12 minutes. In each trial, the transect tape with 20 meters length was randomly placed in the grassland, and the sweep net was swung back and forth with a great force along the transect line for 10- 12 minutes. At the end of each trail, the net was carefully held to avoid any stings from the captured samples and critically observed to record the number of total abundance and the RTUs. After analysing the trapped organisms and materials, only living insects or animals were counted, and at the end of each trial all of them were returned back to their environment. The totals of 10 trials were repeated for this experiment. In addition, it was possible not to capture any organisms at all since the weather was cold and organisms had less movement compared to a moderate temperature and weather.
DOI: 10.6084/m9.figshare.1569417.v2
title: Role of lysine binding residues in the global folding of the <i>lysC</i> riboswitch

description: ABSTRACTRiboswitches regulate gene expression by rearranging their structure upon metabolite binding. The lysine-sensing <i>lysC</i> riboswitch is a rare example of an RNA aptamer organized around a five-way helical junction in which ligand binding is performed exclusively through nucleotides located at the junction core. We have probed whether the nucleotides involved in ligand binding play any role in the global folding of the riboswitch. As predicted, our findings indicate that ligand-binding residues are critical for the lysine-dependent gene regulation mechanism. We also find that these residues are not important for the establishment of key magnesium-dependent tertiary interactions, suggesting that folding and ligand recognition are uncoupled in this riboswitch for the formation of specific interactions. However, FRET assays show that lysine binding results in an additional conformational change, indicating that lysine binding may also participate in a specific folding transition. Thus, in contrast to helical junctions being primary determinants in ribozymes and rRNA folding, we speculate that the helical junction of the lysine-sensing <i>lysC</i> riboswitch is not employed as structural a scaffold to direct global folding, but rather has a different role in establishing RNA-ligand interactions required for riboswitch regulation. Our work suggests that helical junctions may adopt different functions such as the coordination of global architecture or the formation of specific ligand binding site.
DOI: 10.6084/m9.figshare.1569405
title: Phylogeny, species diversity and biogeographic patterns of the genus <i>Tricleocarpa</i> (Galaxauraceae, Rhodophyta) from the Indo-Pacific region, including <i>T. confertus</i> sp. nov. from Taiwan

description: Among four different genera in Galaxauraceae, species diversity of the genus <i>Tricleocarpa</i> Huisman & Borowitzka is underestimated and requires further examination. In this study, we explored a molecular phylogeny of <i>Tricleocarpa</i> with an emphasis on Taiwan species and reassessed species diversity of the genus from the Indo-Pacific region based on analyses of <i>rbc</i>L and COI-5P sequences and morphological observations. The molecular analyses showed that species of <i>Tricleocarpa</i> examined are grouped into seven clades: six clades in the <i>T. cylindrica</i> group (the <i>T. cylindrica</i> complex, <i>T. confertus, T. jejuensis, T. natalensis</i> and two uncharacterized <i>T</i>. ‘<i>cylindrica</i>’ clades) and one clade as the <i>T. fragilis</i> group. Overall, at least 12 species in <i>Tricleocarpa</i> were detected from the Indo-Pacific region, including a new species, <i>T. confertus</i> S.-L. Liu & S.-M. Lin, from Taiwan. Among them, <i>T. confertus</i> can be separated from other species of <i>Tricleocarpa</i> by a thallus consisting of dichotomous or trichotomous, articulated and moniliform branches with smooth surfaces, constrictions at nodes and slightly anti-triangular in shape. The cystocarp morphology of <i>T. confertus</i> is similar to the <i>T. cylindrica</i> group by having paraphyses intermixing with gonimoblast filaments. Recognition of this new species from other species is also supported by the DNA-based, algorithmic species delimitation approaches. With the combination of molecular phylogeny and species diversity reassessment, our phylogeographic analysis supported a trend that species in the <i>T. fragilis</i> group are restricted in their distribution to subtropical and tropical areas whereas species in the <i>T. cylindrica</i> group have a wide distribution, ranging from temperate through to tropical areas.