title: Logistic regression and boosting for labeled bags of instances

authors: Xu, Xin

subjects: computer science

abstract: In this paper we upgrade linear logistic regression and boosting to multi-instance data, where each example consists of a labeled bag of instances. This is done by connecting predictions for individual instances to a bag-level probability estimate by simple averaging and maximizing the likelihood at the bag level—in other words, by assuming that all instances contribute equally and independently to a bags label. We present empirical results for artificial data generated according to the underlying generative model that we assume, and also show that the two algorithms produce competitive results on the Musk benchmark datasets.

text: Logistic regression and boosting for labeled bags of instances In this paper we upgrade linear logistic regression and boosting to multi-instance data, where each example consists of a labeled bag of instances. This is done by connecting predictions for individual instances to a bag-level probability estimate by simple averaging and maximizing the likelihood at the bag level—in other words, by assuming that all instances contribute equally and independently to a bags label. We present empirical results for artificial data generated according to the underlying generative model that we assume, and also show that the two algorithms produce competitive results on the Musk benchmark datasets.

year: 2004

title: Optimized vitrification, cell cycle compatibility and volume of cytoplasts for bovine embryonic cloning

authors: Randall, Shantaya

subjects: Cell transfer cloning

abstract: Cell transfer cloning is a promising method for multiplying elite alleles in a population. Together with gene editing, it can increase the genetic gain of livestock and support  the adaptation of cattle to climate change. Embryos with superior genetics, including edited genes, can be expanded in vitro, and each single embryonic donor cell can be used in cell transfer to produce new embryos with a copy of those genes. Enucleated oocytes in metaphase II (MII cytoplasts) serve as recipient cells for the embryonic donors, supporting their reprogramming and development. Currently, the rate of healthy calves that can be produced from cloning with somatic cell donors is about 5% and the technology is associated with placental, fetal and neonatal abnormalities, referred to as the cloning syndrome. This is largely due to incomplete epigenetic reprogramming in somatic cells. The genome of a pluripotent embryo-derived donor is postulated to require less reprogramming to reach an embryonic state than a somatic donor, which could lead to improved embryo formation, increased numbers of healthy offspring and reduced animal welfare problems. These donors are also hypothesised to be more amenable to DNA editing. While the conditions for cytoplasts that receive somatic donors are well-researched, cytoplast conditions for embryo-derived donors remain to be optimised. The primary aim of this research project was to further the knowledge on bovine cell transfer methodology by trialling different treatments of cytoplasts that receive embryo-derived donors. 

Blastocysts were produced through in vitro fertilization and plated to generate embryo-derived outgrowths as a source of donors for cloning. The zona pellucida was removed with assisted hatching techniques before plating. The rate of embryo-derived outgrowth formation after natural hatching without assistance was 80%. This was raised to 88% when mechanical zona pellucida dissection was performed on blastocysts before plating, while enzymatically removing the zona pellucida lowered the production of primary embryo outgrowthsto 36%. Donor outgrowths were arrested into mitosis by incubation in 500 nM nocodazole overnight before fusion with cytoplasts and activation with ionomycin and cycloheximide. Such chemically activated reconstructs had a 22% pseudo-polar body extrusion rate and blastocyst development was 7%. This was lower than blastocyst development in reconstructs without nocodazole-synchronization and with ionomycin and 6-dimethylaminopurine activation (13%). Non-synchronized donors were fused to cytoplasts that had received various treatments: aging and cooling, volume increases, and vitrification. Reconstructs were activated with ionomycin and 6-dimethylaminopurine. Embryos constructed with cytoplasts that had been aged and cooled to alter their MII state had lowered blastocyst development (4%) compared to embryos constructed with 
cytoplasts that were not aged and cooled (15%). Increasing the volume of a MII cytoplast with embryo-derived donors did not significantly affect total blastocyst development (6%) compared to in control cytoplasts without altered volume (11%). Vitrified oocytes had a high survival rate after thawing (97%). Artificially activated zona-free vitrified oocytes were able to support development to the blastocyst stage, although this was at a lower rate (3%) than artificially activated fresh oocytes (22%). Vitrified cytoplasts had a high survival rate after thawing (92%) and were able to produce a blastocyst after cell transfer with somatic donors (2%). However, this blastocyst development occurred at a lower rate than with fresh cytoplasts and somatic donors (8%). The ability of vitrified cytoplasts to support the development of the embryo-derived donors to the blastocyst stage after cell transfer could not be proven. 

Before proceeding to in vivo cloning trials, confirmation of blastocyst ploidy, and continued refinement of vitrification protocols, through trialling different reagents and concentrations, is required. Further data on the use of vitrified cytoplasts in double ECT is required to elucidate the role of reprogramming factors in cytoplasts on embryo-derived donors. Embryo transfer of the produced blastocysts will be the final measure of the effect of the cytoplast conditions trialled on overall cloning efficiency. Successful embryo transfer would accomplish the ultimate research aim of this project: to establish that bovine embryonic pluripotent stem cells can be successfully reprogrammed during cloning to produce blastocysts and then live offspring.

text: Optimized vitrification, cell cycle compatibility and volume of cytoplasts for bovine embryonic cloning Cell transfer cloning is a promising method for multiplying elite alleles in a population. Together with gene editing, it can increase the genetic gain of livestock and support  the adaptation of cattle to climate change. Embryos with superior genetics, including edited genes, can be expanded in vitro, and each single embryonic donor cell can be used in cell transfer to produce new embryos with a copy of those genes. Enucleated oocytes in metaphase II (MII cytoplasts) serve as recipient cells for the embryonic donors, supporting their reprogramming and development. Currently, the rate of healthy calves that can be produced from cloning with somatic cell donors is about 5% and the technology is associated with placental, fetal and neonatal abnormalities, referred to as the cloning syndrome. This is largely due to incomplete epigenetic reprogramming in somatic cells. The genome of a pluripotent embryo-derived donor is postulated to require less reprogramming to reach an embryonic state than a somatic donor, which could lead to improved embryo formation, increased numbers of healthy offspring and reduced animal welfare problems. These donors are also hypothesised to be more amenable to DNA editing. While the conditions for cytoplasts that receive somatic donors are well-researched, cytoplast conditions for embryo-derived donors remain to be optimised. The primary aim of this research project was to further the knowledge on bovine cell transfer methodology by trialling different treatments of cytoplasts that receive embryo-derived donors. 

Blastocysts were produced through in vitro fertilization and plated to generate embryo-derived outgrowths as a source of donors for cloning. The zona pellucida was removed with assisted hatching techniques before plating. The rate of embryo-derived outgrowth formation after natural hatching without assistance was 80%. This was raised to 88% when mechanical zona pellucida dissection was performed on blastocysts before plating, while enzymatically removing the zona pellucida lowered the production of primary embryo outgrowthsto 36%. Donor outgrowths were arrested into mitosis by incubation in 500 nM nocodazole overnight before fusion with cytoplasts and activation with ionomycin and cycloheximide. Such chemically activated reconstructs had a 22% pseudo-polar body extrusion rate and blastocyst development was 7%. This was lower than blastocyst development in reconstructs without nocodazole-synchronization and with ionomycin and 6-dimethylaminopurine activation (13%). Non-synchronized donors were fused to cytoplasts that had received various treatments: aging and cooling, volume increases, and vitrification. Reconstructs were activated with ionomycin and 6-dimethylaminopurine. Embryos constructed with cytoplasts that had been aged and cooled to alter their MII state had lowered blastocyst development (4%) compared to embryos constructed with 
cytoplasts that were not aged and cooled (15%). Increasing the volume of a MII cytoplast with embryo-derived donors did not significantly affect total blastocyst development (6%) compared to in control cytoplasts without altered volume (11%). Vitrified oocytes had a high survival rate after thawing (97%). Artificially activated zona-free vitrified oocytes were able to support development to the blastocyst stage, although this was at a lower rate (3%) than artificially activated fresh oocytes (22%). Vitrified cytoplasts had a high survival rate after thawing (92%) and were able to produce a blastocyst after cell transfer with somatic donors (2%). However, this blastocyst development occurred at a lower rate than with fresh cytoplasts and somatic donors (8%). The ability of vitrified cytoplasts to support the development of the embryo-derived donors to the blastocyst stage after cell transfer could not be proven. 

Before proceeding to in vivo cloning trials, confirmation of blastocyst ploidy, and continued refinement of vitrification protocols, through trialling different reagents and concentrations, is required. Further data on the use of vitrified cytoplasts in double ECT is required to elucidate the role of reprogramming factors in cytoplasts on embryo-derived donors. Embryo transfer of the produced blastocysts will be the final measure of the effect of the cytoplast conditions trialled on overall cloning efficiency. Successful embryo transfer would accomplish the ultimate research aim of this project: to establish that bovine embryonic pluripotent stem cells can be successfully reprogrammed during cloning to produce blastocysts and then live offspring.

year: 2022

title: An exploration of the role of semantic relations in the theory and practice of translation (with special reference to English/Māori and Māori/English translation)

authors: Roa, Tom

subjects: clause relations

abstract: It is over forty years since Beekman and Callow, working within the context of the tagmemic tradition, drew attention to the potential significance so far as the theory and practice of translation are concerned of inter-propositional relations (also referred to as ‘discourse relations’, 'semantic relations', ‘semantico-pragmatic relations’, 'rhetorical relations’ and ‘clause relations’).  Since then, the importance of these relations has been increasingly acknowledged within linguistics and a range of other disciplines, including artificial intelligence. In spite of this, inter-propositional relations remain largely unexplored by the vast majority of those involved in translation. My aim in this research project was to determine (a) what impact, if any, a short training course in inter-propositional relations and inter-propositional relational signalling had on novice Māori-English/ English-Māori translators, and (b)  what impact my own understanding of these relations has had on my own practice as a translator. In connection with this, I conducted two studies.  

In the first of these studies, two small groups of novice translators were asked to translate seven text segments - some from English into te reo Māori, others from te reo Māori into English. They were then given a two-day workshop on inter-propositional relations and inter-propositional relational signalling in English and te reo Māori. No translation exercises were included in the workshop. The novice translators were then asked to translate the same text segments again. Comparison of the two sets of translations revealed some interesting differences, the second set indicating a higher level of sensitivity to inter-propositional relations and their signalling in the original text segments. This resulted in, it is argued here, translations that more accurately reflect authorial intentions as indicated in the source texts (see Chapter 3). In connection with this, it is relevant to note that, as indicated in the introductory chapter (Chapter 1) and in parts of the literature review (Chapter 2), while some of those involved in the Western tradition of translation theory and practice have argued that authorial intention is largely irrelevant in relation to textual interpretation, this essentially post-structural positioning is not available to those involved in translating indigenous texts within the context of indigenous worldviews.

In the second study, I used self-reflective think-aloud protocols to record my thoughts during the process of translating, from English into te reo Māori, text segments from five very different texts, all of these translations having been commissioned by different commissioning agencies. I then, making reference to the think-aloud transcripts, compared the source texts with the translations to determine the ways in which my reflections on inter-propositional relations and their signalling had impacted on the translations (Chapter 4).

My overall conclusion is that an understanding of inter-propositional relations and inter-propositional relational signalling can make a positive contribution to the theory and practice of translation and should be included in translator training and in the teaching of additional languages more generally (Chapter 5).

text: An exploration of the role of semantic relations in the theory and practice of translation (with special reference to English/Māori and Māori/English translation) It is over forty years since Beekman and Callow, working within the context of the tagmemic tradition, drew attention to the potential significance so far as the theory and practice of translation are concerned of inter-propositional relations (also referred to as ‘discourse relations’, 'semantic relations', ‘semantico-pragmatic relations’, 'rhetorical relations’ and ‘clause relations’).  Since then, the importance of these relations has been increasingly acknowledged within linguistics and a range of other disciplines, including artificial intelligence. In spite of this, inter-propositional relations remain largely unexplored by the vast majority of those involved in translation. My aim in this research project was to determine (a) what impact, if any, a short training course in inter-propositional relations and inter-propositional relational signalling had on novice Māori-English/ English-Māori translators, and (b)  what impact my own understanding of these relations has had on my own practice as a translator. In connection with this, I conducted two studies.  

In the first of these studies, two small groups of novice translators were asked to translate seven text segments - some from English into te reo Māori, others from te reo Māori into English. They were then given a two-day workshop on inter-propositional relations and inter-propositional relational signalling in English and te reo Māori. No translation exercises were included in the workshop. The novice translators were then asked to translate the same text segments again. Comparison of the two sets of translations revealed some interesting differences, the second set indicating a higher level of sensitivity to inter-propositional relations and their signalling in the original text segments. This resulted in, it is argued here, translations that more accurately reflect authorial intentions as indicated in the source texts (see Chapter 3). In connection with this, it is relevant to note that, as indicated in the introductory chapter (Chapter 1) and in parts of the literature review (Chapter 2), while some of those involved in the Western tradition of translation theory and practice have argued that authorial intention is largely irrelevant in relation to textual interpretation, this essentially post-structural positioning is not available to those involved in translating indigenous texts within the context of indigenous worldviews.

In the second study, I used self-reflective think-aloud protocols to record my thoughts during the process of translating, from English into te reo Māori, text segments from five very different texts, all of these translations having been commissioned by different commissioning agencies. I then, making reference to the think-aloud transcripts, compared the source texts with the translations to determine the ways in which my reflections on inter-propositional relations and their signalling had impacted on the translations (Chapter 4).

My overall conclusion is that an understanding of inter-propositional relations and inter-propositional relational signalling can make a positive contribution to the theory and practice of translation and should be included in translator training and in the teaching of additional languages more generally (Chapter 5).

year: 2016