Applications of Machine Learning for Predicting Selection Outcomes in Antibody Phage Display

Antibodies form an essential component of the adaptive immune system, but they also have important scientific and clinical applications. These applications exploit the proven ability of antibodies to bind strongly and specifically to nearly any biomolecular target (e.g. protein) of interest. To produce antibodies for scientific and clinical applications, researchers can use a wet-lab technique called antibody phage display. Antibody phage display starts with a library of diverse antibody fragments and selects and amplifies those fragments that bind to the target. Antibody phage display combined with next-generation sequencing (NGS) technology has the potential to yield greater insight into the selection process. Machine learning is an area of artificial intelligence uniquely suited to recognizing patterns in large datasets, like those produced by NGS. The research goals of this thesis were to (1) train machine learning models to predict the selection of antibody fragments in antibody phage display using only the sequence of the fragment; (2) validate the ability of the trained models to generalize to different experiments; and (3) reverse engineer the trained models to gain greater insight into the learned patterns and the selection process. Antibody phage display data produced by the Geyer lab (University of Saskatchewan, SK) using two libraries called F and S was used to train a set of machine learning models: naive Bayes network (NB), linear model (LM), artificial neural network (ANN), support vector machine (SVM) with a radial basis function kernel (RBF-SVM), a SVM with a string kernel (SSK-SVM), and a random forest (RF). In addition, key parameters of the RBF- and SSK-SVM were tuned using a gridsearch. The trained models were then used to predict which antibody-displaying phage would be observed after the 5th round of panning, and their prediction accuracy on this data was used to help select models for subsequent analyses. The models selected were the RBF- and SSK-SVM. To achieve the second research goal, data originating from library F was used to train the two SVMs while library S data was used to test them. Finally, the two SVM models trained on library F were deconstructed to understand what features of the input correspond to negative predictions, and what features correspond to positive predictions. The ANN, SVMs, and RF models had the best average classification accuracy (81.5%), but of this group, there was not one classifier that performed significantly better than the others. These classifiers could be used to help non-experts select clones from either library F or S for further wet-lab analyses. The SVMs trained on library F and tested on library S achieved an average classification accuracy of 66.7%, significantly better than would be achieved by relying on chance. These two SVMs could be used to help non-experts select clones for further wet-lab analyses, provided the library being used is not too different from library S. Finally, deconstructing the SVMs trained on library F yielded insight into the basis for their predictions. The predictions of the RBF-SVM were found to be highly dependent on the molecular weight of the relevant binding region (i.e. CDRH3)

Annual report town of Whitefield, New Hampshire for year ending December 31, 2015.

This is an annual report containing vital statistics for a town/city in the state of New Hampshire

Health and wellbeing of under-five year olds in the South Island 2017

In this report the New Zealand Child and Youth Epidemiology Service (NZCYES) provides data and information to contribute to the effective planning and funding of services to improve, promote and protect the health and wellbeing of New Zealand children in their earliest years. The indicators of child health and wellbeing reported in this report begin in the prenatal period and extend to around five years of age. Indicator data for this report were extracted in 2017 from a range of routinely collected datasets. For each indicator the report provides an analysis of the most recent data available at the time of writing, followed by evidence for good practice derived from current policies, guidelines and the evidence-based literature. Where possible, the evidence for good practice includes discussion of equity issues relevant to each indicator, to inform service planning and delivery. The 2017 report begins with the very earliest days in a child’s development, the prenatal period. Early enrolment with a lead maternity carer or district health board (DHB) primary maternity service, maternal smoking and maternal weight are sentinel indicators of the health and wellbeing of women who are pregnant. The next section presents birth outcome data including gestation at birth and birthweight, as well as data about fetal deaths (also known as stillbirths). Birth outcome data can also be used to help quantify the need for care for babies born prematurely or with low birthweight. Birth outcomes are associated with a number of factors, including access to high quality antenatal care (which can help to reduce rates of preterm birth, low birthweight, and stillbirth and also to identify when a newborn baby may require additional services). The mortality rate for children aged under five years is a high-level indicator of child health and well-being within a population. The 2017 report presents data on all deaths of under-five-year-olds, on deaths of infants in the first year of life, including sudden unexpected death in infancy (SUDI), and deaths of 1–4 year olds. Immunisation and Well Child/Tamariki Ora (WCTO) services provide a foundation for child health and wellbeing. The next three sections of the report present data on breastfeeding, immunisation coverage, and child weight. Hospitalisations for ambulatory care-sensitive conditions (ACSH) may provide an indication, at a community level, of accessibility of primary care services. However, ACSH rates are also influenced by other factors at a local level, including overall social determinants of health, and must be interpreted in the light of each DHB’s specific circumstances. The final section of this report provides data from the community oral health service on oral health of five-year-olds in the community, with further data on hospitalisations of under-five-year-olds for dental conditions. Two review topics were selected by DHBs for inclusion in this report: Making health easier: Reducing inequalities in child health through addressing low health literacy (by Dr Judith Adams) and Factors that influence inequity of oral health in New Zealand and what we can we do about them (by Deanna M Beckett and Alison M Meldrum, from the University of Otago Dental School). These two sections of the report can inform strategies to promote health and wellbeing for all children. Health services can provide information in a way that supports parents to build their knowledge and skills to keep their children well and safe. Healthy public policy and supportive environments are key components to promote good oral health for all children from their earliest years

Modular and Parameter-efficient Fine-tuning of Language Models

Transfer learning has recently become the dominant paradigm of natural language processing. Models pre-trained on unlabeled data can be fine-tuned for downstream tasks based on only a handful of examples. A long-term goal is to develop models that acquire new information at scale without incurring negative transfer and that generalize systematically to new settings. Modular deep learning has emerged as a promising solution to these challenges, by updating parameter-efficient units of computation locally and asynchronously. These units are often implemented as modules that are interlaid between layers, interpolated with pre-trained parameters, or concatenated to the inputs. Conditioned on tasks or examples, information is routed to multiple modules through a fixed or learned function, followed by an aggregation of their outputs. This property enables compositional generalization, by disentangling knowledge and recombining it in new ways. In this thesis, we provide a unified view of modularity in natural language processing, spanning across four dimensions; specifically, we disentangle modularity into computation functions, routing functions, aggregation functions, and the training setting. Along those axes, we propose multiple contributions: a research framework which encompasses all dimensions; a novel attention-based aggregation function which combines the knowledge stored within different modules; routing mechanisms for out of distribution generalization in cross-lingual transfer scenarios; a dataset and modular training strategies for multimodal and multilingual transfer learning; a modular pre-training strategy to tackle catastrophic interference of heterogeneous data

Health and wellbeing of under-five year olds in Hutt Valley, Capital & Coast and Wairarapa 2017

In this report the New Zealand Child and Youth Epidemiology Service (NZCYES) provides data and information to contribute to the effective planning and funding of services to improve, promote and protect the health and wellbeing of New Zealand children in their earliest years. The indicators of child health and wellbeing reported in this report begin in the prenatal period and extend to around five years of age. Indicator data for this report were extracted in 2017 from a range of routinely collected datasets. For each indicator the report provides an analysis of the most recent data available at the time of writing, followed by evidence for good practice derived from current policies, guidelines and the evidence-based literature. Where possible, the evidence for good practice includes discussion of equity issues relevant to each indicator, to inform service planning and delivery. The 2017 report begins with the very earliest days in a child’s development, the prenatal period. Early enrolment with a lead maternity carer or district health board (DHB) primary maternity service, maternal smoking and maternal weight are sentinel indicators of the health and wellbeing of women who are pregnant. The next section presents birth outcome data including gestation at birth and birthweight, as well as data about fetal deaths (also known as stillbirths). Birth outcome data can also be used to help quantify the need for care for babies born prematurely or with low birthweight. Birth outcomes are associated with a number of factors, including access to high quality antenatal care (which can help to reduce rates of preterm birth, low birthweight, and stillbirth and also to identify when a newborn baby may require additional services). The mortality rate for children aged under five years is a high-level indicator of child health and well-being within a population. The 2017 report presents data on all deaths of under-five-year-olds, on deaths of infants in the first year of life, including sudden unexpected death in infancy (SUDI), and deaths of 1–4 year olds. Immunisation and Well Child/Tamariki Ora (WCTO) services provide a foundation for child health and wellbeing. The next three sections of the report present data on breastfeeding, immunisation coverage, and child weight. Hospitalisations for ambulatory care-sensitive conditions (ASCH) may provide an indication, at a community level, of accessibility of primary care services. However, ACSH rates are also influenced by other factors at a local level, including overall social determinants of health, and must be interpreted in the light of each DHB’s specific circumstances. The final section of this report provides data from the community oral health service on oral health of five-year-olds in the community, with further data on hospitalisations of under-five-year-olds for dental conditions. Two review topics were selected by DHBs for inclusion in this report: Making health easier: Reducing inequalities in child health through addressing low health literacy (by Dr Judith Adams) and Factors that influence inequity of oral health in New Zealand and what we can we do about them (by Deanna M Beckett and Alison M Meldrum, from the University of Otago Dental School). These two sections of the report can inform strategies to promote health and wellbeing for all children. Health services can provide information in a way that supports parents to build their knowledge and skills to keep their children well and safe. Healthy public policy and supportive environments are key components to promote good oral health for all children from their earliest years

Health and wellbeing of under-five year olds in Nelson Marlborough and South Canterbury 2017

In this report the New Zealand Child and Youth Epidemiology Service (NZCYES) provides data and information to contribute to the effective planning and funding of services to improve, promote and protect the health and wellbeing of New Zealand children in their earliest years. The indicators of child health and wellbeing reported in this report begin in the prenatal period and extend to around five years of age. Indicator data for this report were extracted in 2017 from a range of routinely collected datasets. For each indicator the report provides an analysis of the most recent data available at the time of writing, followed by evidence for good practice derived from current policies, guidelines and the evidence-based literature. Where possible, the evidence for good practice includes discussion of equity issues relevant to each indicator, to inform service planning and delivery. The 2017 report begins with the very earliest days in a child’s development, the prenatal period. Early enrolment with a lead maternity carer or district health board (DHB) primary maternity service, maternal smoking and maternal weight are sentinel indicators of the health and wellbeing of women who are pregnant. The next section presents birth outcome data including gestation at birth and birthweight, as well as data about fetal deaths (also known as stillbirths). Birth outcome data can also be used to help quantify the need for care for babies born prematurely or with low birthweight. Birth outcomes are associated with a number of factors, including access to high quality antenatal care (which can help to reduce rates of preterm birth, low birthweight, and stillbirth and also to identify when a newborn baby may require additional services). The mortality rate for children aged under five years is a high-level indicator of child health and well-being within a population. The 2017 report presents data on all deaths of under-five-year-olds, on deaths of infants in the first year of life, including sudden unexpected death in infancy (SUDI), and deaths of 1–4 year olds. Immunisation and Well Child/Tamariki Ora (WCTO) services provide a foundation for child health and wellbeing. The next three sections of the report present data on breastfeeding, immunisation coverage, and child weight. Hospitalisations for ambulatory care-sensitive conditions (ACSH) may provide an indication, at a community level, of accessibility of primary care services. However, ACSH rates are also influenced by other factors at a local level, including overall social determinants of health, and must be interpreted in the light of each DHB’s specific circumstances. The final section of this report provides data from the community oral health service on oral health of five-year-olds in the community, with further data on hospitalisations of under-five-year-olds for dental conditions. Two review topics were selected by DHBs for inclusion in this report: Making health easier: Reducing inequalities in child health through addressing low health literacy (by Dr Judith Adams) and Factors that influence inequity of oral health in New Zealand and what we can we do about them (by Deanna M Beckett and Alison M Meldrum, from the University of Otago Dental School). These two sections of the report can inform strategies to promote health and wellbeing for all children. Health services can provide information in a way that supports parents to build their knowledge and skills to keep their children well and safe. Healthy public policy and supportive environments are key components to promote good oral health for all children from their earliest years

Planeamiento, diseño y evaluación técnico económico del sistema de riego del Programa de Frutales - fundo en la Universidad Nacional Agraria La Molina

Universidad Nacional Agraria La Molina. Facultad de Ingeniería Agrícola. Departamento Académico de Recursos HídricosEl presente trabajo de investigación consistió en realizar el planeamiento, diseño del sistema de riego por goteo y evaluación económica en el Programa de Investigación y Proyección Social en Frutales y el Programa el Fundo, en lo cual se seleccionó cultivos rentables como palto, maíz, frejol castilla y algodón. El proyecto en estudio se encuentra ubicado en la provincia de Lima, distrito de La Molina, latitud Sur de 12° 04 ' 48.81 " a 12° 05' 15.84" y longitud Oeste de 76° 56 ' 13.90 .. a 76° 56 ' 39.90 '' sobre el Meridiano de Greenwich, con la altitud que varía de 245 msnm. La extensión del terreno en estudio fue de 26.44 has, donde 16.78 has corresponden al programa de Investigación y Proyección Social en Frutales y 9.66 has al Programa el Fundo. El planeamiento y diseño del sistema de riego por goteo comprendió:- El planeamiento consistió en recabar información básica, realizar el balance hídrico, el diseño agronómico, la zonificación de turnos de riego y el trazado de la red matriz de riego. - El diseño agronómico, consistió en determinar las características del agua y el suelo, de tal manera de determinar las necesidades de agua del cultivo y la programación del riego del mismo. El diseño hidráulico comprendió:- La red matriz, fue diseñada y simulada con el software GESTAR - PREMIUN 2014, como resultado se obtuvo el dimensionamiento optimo de la red de tubería, manteniendo una tolerancia de presiones en la subunidad y además se calculó el requerimiento total de presión. - La estación de bombeo se diseñó, para satisfacer los requerimientos de 47.5 metros de presión, caudal máximo 29.11 lis y potencia de 19.23Kw, para ello se seleccionó 2 bombas turbina de eje vertical ubicadas en paralelo. - El sistema de filtrado diseñado comprendió seis filtros de grava con una capacidad de diseño de 25 m3/h y cuatro filtros de anillas con una capacidad de 30 m3/h cada uno. La evaluación económica comprendió la determinación de la inversión total realizada, los costos de operación y mantenimiento, costos de producción, así como los ingresos generados considerando los precios del mercado de la zona, los cuales se consideraron al medir en términos económicos la rentabilidad del proyecto. Se calculó los indicadores de rentabilidad como es el VAN y TIR.Tesi

Health and wellbeing of under-five year olds in the Northern region 2017

In this report the New Zealand Child and Youth Epidemiology Service (NZCYES) provides data and information to contribute to the effective planning and funding of services to improve, promote and protect the health and wellbeing of New Zealand children in their earliest years. The indicators of child health and wellbeing reported in this report begin in the prenatal period and extend to around five years of age. Indicator data for this report were extracted in 2017 from a range of routinely collected datasets. For each indicator the report provides an analysis of the most recent data available at the time of writing, followed by evidence for good practice derived from current policies, guidelines and the evidence-based literature. Where possible, the evidence for good practice includes discussion of equity issues relevant to each indicator, to inform service planning and delivery. The 2017 report begins with the very earliest days in a child’s development, the prenatal period. Early enrolment with a lead maternity carer or district health board (DHB) primary maternity service, maternal smoking and maternal weight are sentinel indicators of the health and wellbeing of women who are pregnant. The next section presents birth outcome data including gestation at birth and birthweight, as well as data about fetal deaths (also known as stillbirths). Birth outcome data can also be used to help quantify the need for care for babies born prematurely or with low birthweight. Birth outcomes are associated with a number of factors, including access to high quality antenatal care (which can help to reduce rates of preterm birth, low birthweight, and stillbirth and also to identify when a newborn baby may require additional services). The mortality rate for children aged under five years is a high-level indicator of child health and well-being within a population. The 2017 report presents data on all deaths of under-five-year-olds, on deaths of infants in the first year of life, including sudden unexpected death in infancy (SUDI), and deaths of 1–4 year olds. Immunisation and Well Child/Tamariki Ora (WCTO) services provide a foundation for child health and wellbeing. The next three sections of the report present data on breastfeeding, immunisation coverage, and child weight. Hospitalisations for ambulatory care-sensitive conditions (ACSH) may provide an indication, at a community level, of accessibility of primary care services. However, ACSH rates are also influenced by other factors at a local level, including overall social determinants of health, and must be interpreted in the light of each DHB’s specific circumstances. The final section of this report provides data from the community oral health service on oral health of five-year-olds in the community, with further data on hospitalisations of under-five-year-olds for dental conditions. Two review topics were selected by DHBs for inclusion in this report: Making health easier: Reducing inequalities in child health through addressing low health literacy (by Dr Judith Adams) and Factors that influence inequity of oral health in New Zealand and what we can we do about them (by Deanna M Beckett and Alison M Meldrum, from the University of Otago Dental School). These two sections of the report can inform strategies to promote health and wellbeing for all children. Health services can provide information in a way that supports parents to build their knowledge and skills to keep their children well and safe. Healthy public policy and supportive environments are key components to promote good oral health for all children from their earliest years. The report appendices provide detail that may be helpful when interpreting information presented in the report. They include detailed descriptions of the methods used to develop evidence for good practice, and the statistical methods used in the data analyses, descriptions of the data sources used for various indicators reported, explanation about classification of ethnicity and social and material deprivation in the report, and a list of the clinical codes relevant to each indicator

An ecological study of barley growing under three contrasting regimens of farm management

Using barley (Hordeum vulgare L.) as a phytometer, comparisons were made of the three systems of farm management (Organic, Mixed and Stockless), maintained as a long-term experiment by the Soil Research Association (Pye Research Centre) at Haughley in Suffolk. Special attention being paid to the geochemicals of the crops/soil system. Significant differences were indicated between both 'total' and 'available' geochemicals of the three soil systems. The differences of available geochemicals are undoubtedly related to the differing long-term management, especially the continuous and predominant use of organic manures and mulches on both the Organic and Mixed systems. The unexpected differences in total geochemicals (significantly more Ca, Mg and K in the Organic soils) is tentatively explained on the basis of deterioration of soil structural characteristics in the Stockless system, leading to interruption of the supply of geochemicals by capillary water. The data collected allowed crude geochemical budgets for the farm systems to be attempted and the work was, therefore, supplemented by the lysimeter studies. The indications for this work are that the geochemicals in the Organic soil are more readily 'available' to leaching than those of the Stockless soil. Phytometry, using both the old "Rika' barley variety used in the long-term experiment, and the new varieties 'Julia' and 'Sultan', did not, in the main, back up the above findings. This was especially true of the field experiments when environmental factors other than geochemical supply, probably govern the performance of the barley. However, in the majority of cases where significant differences were shown, the Organic system always shows better performance of the plant or greater flux of geochemicals into the plants than the Stockless system. No indication of a developed dependence of the barley on the three farm systems was obtained. Nitrogen fixation by soil microorganisms appear to be unimportant on the Haughley systems

Health and wellbeing of under-five year olds in Hawke’s Bay 2017

In this report the New Zealand Child and Youth Epidemiology Service (NZCYES) provides data and information to contribute to the effective planning and funding of services to improve, promote and protect the health and wellbeing of New Zealand children in their earliest years. The indicators of child health and wellbeing reported in this report begin in the prenatal period and extend to around five years of age. Indicator data for this report were extracted in 2017 from a range of routinely collected datasets. For each indicator the report provides an analysis of the most recent data available at the time of writing, followed by evidence for good practice derived from current policies, guidelines and the evidence-based literature. Where possible, the evidence for good practice includes discussion of equity issues relevant to each indicator, to inform service planning and delivery. The 2017 report begins with the very earliest days in a child’s development, the prenatal period. Early enrolment with a lead maternity carer or district health board (DHB) primary maternity service, maternal smoking and maternal weight are sentinel indicators of the health and wellbeing of women who are pregnant. The next section presents birth outcome data including gestation at birth and birthweight, as well as data about fetal deaths (also known as stillbirths). Birth outcome data can also be used to help quantify the need for care for babies born prematurely or with low birthweight. Birth outcomes are associated with a number of factors, including access to high quality antenatal care (which can help to reduce rates of preterm birth, low birthweight, and stillbirth and also to identify when a newborn baby may require additional services). The mortality rate for children aged under five years is a high-level indicator of child health and well-being within a population. The 2017 report presents data on all deaths of under-five-year-olds, on deaths of infants in the first year of life, including sudden unexpected death in infancy (SUDI), and deaths of 1–4 year olds. Immunisation and Well Child/Tamariki Ora (WCTO) services provide a foundation for child health and wellbeing. The next three sections of the report present data on breastfeeding, immunisation coverage, and child weight. Hospitalisations for ambulatory care-sensitive conditions (ACSH) may provide an indication, at a community level, of accessibility of primary care services. However, ACSH rates are also influenced by other factors at a local level, including overall social determinants of health, and must be interpreted in the light of each DHB’s specific circumstances. The final section of this report provides data from the community oral health service on oral health of five-year-olds in the community, with further data on hospitalisations of under-five-year-olds for dental conditions. Two review topics were selected by DHBs for inclusion in this report: Making health easier: Reducing inequalities in child health through addressing low health literacy (by Dr Judith Adams) and Factors that influence inequity of oral health in New Zealand and what we can we do about them (by Deanna M Beckett and Alison M Meldrum, from the University of Otago Dental School). These two sections of the report can inform strategies to promote health and wellbeing for all children. Health services can provide information in a way that supports parents to build their knowledge and skills to keep their children well and safe. Healthy public policy and supportive environments are key components to promote good oral health for all children from their earliest years