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Full-Text Articles in Entire DC Network
Mapping A Functional Cancer Genome Atlas, Ryan Dz-Wei Chow
Mapping A Functional Cancer Genome Atlas, Ryan Dz-Wei Chow
Yale Graduate School of Arts and Sciences Dissertations
Over the past decade, tremendous resources have been devoted to sequencing the genomes of patient cancers. But while the molecular portraits of cancer are now in higher resolution than ever before, it has remained challenging to derive clinically actionable insights from these data. A central issue is that tumor genome sequencing often can only tell us what mutations are present, not which ones are functionally important. Towards this end, I sought to build an improved toolkit for functional cancer genomics, with the overarching goal of creating experimental platforms that are practical, scalable, and flexible. In collaboration with several colleagues, I …
Relational Morality, Brian D. Earp
Relational Morality, Brian D. Earp
Yale Graduate School of Arts and Sciences Dissertations
Contemporary work in moral psychology has focused on judgments concerning interactions between strangers. However, it increasingly is recognized that much of human moral judgment takes place in the context of -- and is shaped by -- multiple more familiar social relationships, such as parent-child, teacher-student, close friends, long-term romantic partners, neighbors, teammates, and so on. In this dissertation, I show how such relationships are associated with distinctive patterns of socially prescribed cooperative functions (such as care, hierarchy, or mating), which can be used to predict out-of-sample moral judgments of both blame and praise regarding various actions in relational context. I …
The Organismal And Evolutionary Determinants Of Siphonophore Predation, Alejandro Damian Serrano
The Organismal And Evolutionary Determinants Of Siphonophore Predation, Alejandro Damian Serrano
Yale Graduate School of Arts and Sciences Dissertations
The open-ocean midwater is the largest habitat for animal life on Earth, and one of the most homogeneous environments in space and time. However, these waters harbor complex food webs involving predatory animals from manifold phyla, presenting unique adaptations to capturing the scarce prey resources. These conditions create a natural laboratory, with minimal abiotic disturbances, where interspecific interactions such as predation play a major role in shaping community dynamics and the evolution of form and function. Siphonophores play a central role in midwater food webs feeding across multiple trophic levels on different prey phyla (i.e. jellyfish, crustaceans, worms, fishes). Like …
Statistical Methods For Identifying Genetic Risk Factors Of Lung Diseases, Ming Chen
Statistical Methods For Identifying Genetic Risk Factors Of Lung Diseases, Ming Chen
Yale Graduate School of Arts and Sciences Dissertations
Great efforts have been made to understand the mechanism of complex diseases. Besides studying environmental factors and lifestyles, it is imperative to find disease causal genes. With the development of sequencing technology and the rapid accumulation of diverse types of high-throughput biological data, a promising direction to identify disease genes is through data integration. Genes affect diseases through different biological activities. Integrating different biological data can improve the power of gene discovery and the understanding of pathogenic mechanisms. In recent years, a great number of omics databases have become available. Methods for multi-omics data integration have successfully improved the statistical …
Measurement Of The Reactor Antineutrino Spectrum Of U-235 By Prospect And Daya Bay, Jeremy Gaison
Measurement Of The Reactor Antineutrino Spectrum Of U-235 By Prospect And Daya Bay, Jeremy Gaison
Yale Graduate School of Arts and Sciences Dissertations
Since their experimental discovery over 60 years ago, neutrinos have proven to be a fascinating means of exploring the physical universe. Through a variety of both natural and man-made sources, physicists have discovered many unusual features about these par- ticles from their oscillation between their different flavor states to their particularly small mass. There are still many questions to answer regarding these fundamental particles, though. Among these questions is whether a possible fourth type of neutrino exists, a sterile neutrino, which could resolve a range of discrepancies between recent measure- ments and predictions at a variety of different energies and …
From Eyes To Minds: Perceiving Perception, And Attending To Attention, Clara Colombatto
From Eyes To Minds: Perceiving Perception, And Attending To Attention, Clara Colombatto
Yale Graduate School of Arts and Sciences Dissertations
The most important visual stimuli that we encounter in everyday life may be other people, and in particular their eyes. We constantly monitor (and follow) where others are looking, and hundreds of studies have stressed the importance of eyes as uniquely powerful visual stimuli. This dissertation argues otherwise: The eyes are special only insofar as they signal deeper properties about the minds behind them—namely the nature and direction of others’ attention and intentions. We empirically support this view in two ways: First, in studies of ‘minds without eyes’, we demonstrate how well-known gaze effects (such as prioritized processing of eye …
Expanding The Reliable Paleomagnetic Constraints On Configurations Of Pre-Pangean Supercontinents, Zheng Gong
Expanding The Reliable Paleomagnetic Constraints On Configurations Of Pre-Pangean Supercontinents, Zheng Gong
Yale Graduate School of Arts and Sciences Dissertations
Supercontinents embody perhaps the longest cyclic process on our planet, profoundly influencing the evolution of Earth’s biosphere, geosphere, and atmosphere on timescales of hundred-million years or more. Yet, the configurations of pre-Pangean supercontinents, Rodinia, Nuna, and/or Kenorland, as well as their transition processes remain the subjects of debate, hampering the understanding of the interactions between the global tectonics and Earth’s evolution in deep time. Compared to other approaches, paleomagnetism is the only quantitative method to reconstruct pre-Pangean supercontinents in an absolute paleogeographic framework. However, a recent summary of global paleomagnetic data of Precambrian age reveals two problems. First is that …
Algorithmic Advances For The Design And Analysis Of Randomized Experiments, Christopher Robert Harshaw
Algorithmic Advances For The Design And Analysis Of Randomized Experiments, Christopher Robert Harshaw
Yale Graduate School of Arts and Sciences Dissertations
Randomized experiments are the gold standard for investigating the causal effect of treatment on a population. In this dissertation, we present algorithmic advances for three different problems arising in the design and analysis of randomized experiments: covariate balancing, variance estimation, and bipartite experiments. In the first chapter, we describe an inherent trade-off between covariate balancing and robustness, which we formulate as a distributional discrepancy problem. In order to navigate this trade-off, we present the Gram–Schmidt Walk Design which is based on the recent discrepancy algorithm of Bansal, Dadush, Garg, and Lovett (2019). By tightening the algorithmic analysis, we derive bounds …
Statistical Properties Of Nuclei: Beyond The Mean-Field Approximation, Paul Edward Fanto
Statistical Properties Of Nuclei: Beyond The Mean-Field Approximation, Paul Edward Fanto
Yale Graduate School of Arts and Sciences Dissertations
The statistical model of compound-nucleus reactions has important applications in fundamental nuclear science, nuclear astrophysics, and nuclear technology. This model relies on two theoretical areas: (i) statistical reaction theory, which describes the compound nucleus with the Gaussian orthogonal ensemble (GOE) of random-matrix theory; and (ii) statistical properties of nuclei, i.e., nuclear structure observables that determine statistical-model predictions of reaction rates. The GOE statistical theory predicts that the partial widths of compound-nucleus resonances follow the Porter-Thomas distribution (PTD) and that total $\gamma$-decay widths have a narrow distribution. However, recent experiments measured width distributions that were broader than statistical-model predictions. We study …
New Roles For Small Noncoding Rnas In Germline Development: Maternal Piwi And Pirnas Specifically Protect The Fertility Of Female Progeny, Lauren Gonzalez
New Roles For Small Noncoding Rnas In Germline Development: Maternal Piwi And Pirnas Specifically Protect The Fertility Of Female Progeny, Lauren Gonzalez
Yale Graduate School of Arts and Sciences Dissertations
The long-term survival of a species depends on the integrity of its genetic material and the inheritance of that genetic material across generations. In sexually-reproducing organisms, these processes are carried out by the germline: the tissue that produces eggs in females or sperm in males. PIWI proteins and their associated small noncoding piRNAs have been well-characterized for their roles in protecting genome integrity in the germline and promoting the self-renewal of germline stem cells, which support the continual production of eggs or sperm. In Drosophila, maternally-expressed PIWI proteins and piRNAs are also enriched in the germ plasm, the posterior region …
Rise Of The Modern Mediatrix: The Feminization Of Media And Mediating Labor, 1865-1945, Leana Hirschfeld-Kroen
Rise Of The Modern Mediatrix: The Feminization Of Media And Mediating Labor, 1865-1945, Leana Hirschfeld-Kroen
Yale Graduate School of Arts and Sciences Dissertations
This dissertation uncovers a vast archive of fictional female telegraph, telephone, and typewriter girls, combining rigorous historical research with feminist, psychoanalytic readings of mass cultural texts to show how the global gendering of low-level communication work shaped modern media. It begins in the United States, where women first performed this work, and explores three further national contexts (France, Germany, and Britain) where female operators and typists circulated as media icons of techno-social connection in an increasingly atomized age. The title “modern mediatrix” describes the essential mediating role white-collar woman workers have played in modern media infrastructure, from switchboard to editing …
Pipelined Asynchronous High Level Synthesis For General Programs, Rui Li
Pipelined Asynchronous High Level Synthesis For General Programs, Rui Li
Yale Graduate School of Arts and Sciences Dissertations
High-level synthesis (HLS) translates algorithms from software programming language into hardware. We use the dataflow HLS methodology to translate programs into asynchronous circuits by implementing programs using asynchronous dataflow elements as hardware building blocks. We extend the prior work in dataflow synthesis in the following aspects:i) we propose Fluid to synthesize pipelined dataflow circuits for real-world programs with complex control flows, which are not supported in the previous work; ii) we propose PipeLink to permit pipelined access to shared resources in the dataflow circuit. Dataflow circuit results in distributed control and an implicitly pipelined implementation. However, resource sharing in the …
The Social Consequences Of Close Votes: The Narrow Decriminalization Of Sex Work In New Zealand, Dana Hayward
The Social Consequences Of Close Votes: The Narrow Decriminalization Of Sex Work In New Zealand, Dana Hayward
Yale Graduate School of Arts and Sciences Dissertations
New Zealand became the first country in the world to fully decriminalize sex work at the national level when it passed the Prostitution Reform Act (PRA) by a single vote in 2003. In this dissertation, I suggest that a close vote is a prism that illuminates the relationship between law and social change, both theoretically and methodologically. In a series of three articles, I explore the social and political consequences of New Zealand’s narrowly-passed sex work law, concentrating specifically on media representations of sex work, national repeal initiatives, and local bylaw-making processes. In the first empirical chapter, I focus on …
The Wordline Effective Field Theory Of Spinning Gravitational Sources, Jingping Li
The Wordline Effective Field Theory Of Spinning Gravitational Sources, Jingping Li
Yale Graduate School of Arts and Sciences Dissertations
The advent of gravitational wave physics has raised great interest in efficient calculations of gravitational dynamics. In particular, the worldline effective field theory (EFT) has proven to be powerful for describing the dynamics of compact binary inspirals. In this thesis, we report on progress in this method on including rotating gravitational sources. It has been shown that a connection exists between the radiative amplitudes from spinless classical sources in Yang-Mills theory and dilaton-gravity theory, inspired by the double copy construction in the scattering amplitude community. We generalize this result to spinning sources and find that an additional axion channel is …
Improving The Cosmic Statistics Of Neutral Hydrogen, Naim Goksel Karacayli
Improving The Cosmic Statistics Of Neutral Hydrogen, Naim Goksel Karacayli
Yale Graduate School of Arts and Sciences Dissertations
The study of the cosmological large-scale structure seeks to understand the makings and the evolution of the universe. In this subject, I worked on improving current techniques and their application to the existing large, high-precision cosmological data sets. Specifically, my dissertation explores boosting power spectrum measurements at large scales for 21-cm intensity maps through reconstruction, and at small scales for Ly α forest by developing and applying the optimal estimator to hundreds of high-resolution spectra.The cosmic tidal reconstruction is a novel technique for low redshift (z < 2) 21-cm intensity mapping surveys (e.g. CHIME and HIRAX) that recovers the lost large-scale line-of-sight signal from local small-scale anisotropies formed by tidal interactions. My thesis shows this algorithm is robust against redshift space distortions and can recover the signal with approximately 70% efficiency for k < 0.1 h Mpc−1 using N-body simulations. If angular modes are also lost (known as the foreground wedge), the efficiency drops down to 30–50% range. I further introduce an analytical framework based on perturbation theory, which correctly predicts the shape of the reconstructed field’s 2D power spectrum and reveals that the reconstruction mostly utilizes angular modes with k > 0.3 h Mpc−1. Through absorption lines in quasar spectra, the Ly α forest technique …
Transcompartmental Sodium Imaging In Brain Cancer, Muhammad Khan
Transcompartmental Sodium Imaging In Brain Cancer, Muhammad Khan
Yale Graduate School of Arts and Sciences Dissertations
According to the World Health Organization (WHO), cancers are the second-leading cause of death in the United States, next to cardiovascular disease. Although treatments of some solid tumors with high mortality are showing promise, there is one exception: glioblastoma multiforme (GBM). Even with advanced therapies, median survival rate for GBM patients is dismal because most are not diagnosed early enough. A hallmark of normal physiology is maintenance of large ion gradients across the cell membrane, mainly for sodium (Na + ) and potassium (K + ) ions. Under normal conditions, high and low Na + in extracellular (Na + ) …
Practicality Of Quantum Random Access Memory, Connor Hann
Practicality Of Quantum Random Access Memory, Connor Hann
Yale Graduate School of Arts and Sciences Dissertations
Quantum computers are expected to revolutionize the world of computing, but major challenges remain to be addressed before this potential can be realized. One such challenge is the so-called data-input bottleneck: Even though quantum computers can quickly solve certain problems by rapidly analyzing large data sets, it can be difficult to load this data into a quantum computer in the first place. In order to quickly load large data sets into quantum states, a highly-specialized device called a Quantum Random Access Memory (QRAM) is required. Building a large-scale QRAM is a daunting engineering challenge, however, and concerns about QRAM’s practicality …
Optimization Of Orthogonal Translation Systems Enhances Access To The Human Phosphoproteome, Jack Michael Moen
Optimization Of Orthogonal Translation Systems Enhances Access To The Human Phosphoproteome, Jack Michael Moen
Yale Graduate School of Arts and Sciences Dissertations
Protein phosphorylation is a ubiquitous post-translational modification that governs signaling cascades and protein-protein interactions. Orthogonal translation systems, in which an orthogonal aminoacyl-tRNA synthetase and tRNA pair have been repurposed for insertion of a non-standard amino acid, have been developed for co-translational insertion of phospho-amino acids. Here, we systematically developed variants of phosphoserine and phosphothreonine orthogonal translation systems to minimize cellular toxicity and maximize translational fidelity. We characterized novel tRNA constructs to enhance cellular fitness and change decoding functionality. Multiple genetic background strains were developed to enhance the incorporation of phospho-amino acids into recombinant proteins. Utilizing large-scale DNA synthesis, we were …
The Roles Of Polyploidy, Climate, And Genetic Architecture In The Evolution Of Leaf Form In Viburnum (Adoxaceae), Morgan Kirstin Moeglein
The Roles Of Polyploidy, Climate, And Genetic Architecture In The Evolution Of Leaf Form In Viburnum (Adoxaceae), Morgan Kirstin Moeglein
Yale Graduate School of Arts and Sciences Dissertations
Plants exhibit extensive variation in leaf form, but the evolutionary drivers of this variation are not well understood. This dissertation leverages the wide diversity of leaf form and instances of leaf syndrome convergence in Viburnum to investigate trends in leaf trait evolution across the group. First, I explore how changes in chromosome number and genome size influence leaf characters of ecophysiological importance. It appears that even with extensive variation in chromosome number and genome size across Viburnum, nucleotypic changes largely do not constrain leaf traits related to ecophysiological function. I then look into a case of convergent evolution for leaf …
Statistical Estimation And Inference Improvements For Exoplanet Discovery, Parker Hinckley Holzer
Statistical Estimation And Inference Improvements For Exoplanet Discovery, Parker Hinckley Holzer
Yale Graduate School of Arts and Sciences Dissertations
The radial velocity method has been widely used by astronomers since the 1990's for discovering extra-solar planets, often referred to as simply "exoplanets". This method involves estimating the radial velocity of a distant star over time using the stellar light, followed by modeling such radial velocity estimates as a function of time using Keplerian-orbital equations with parameters that describe the exoplanet. While a number of approaches exist for estimating the radial velocity from the stellar light, we introduce a new approach for this that uses Hermite-Gaussian functions to reduce the estimation to linear least-squares regression. Furthermore, we demonstrate that this …
Integrating Genomics With The Fossil Record To Explore The Evolutionary History Of Echinoidea, Nicolas Mongiardino Koch
Integrating Genomics With The Fossil Record To Explore The Evolutionary History Of Echinoidea, Nicolas Mongiardino Koch
Yale Graduate School of Arts and Sciences Dissertations
Echinoidea constitutes one of five major clades of living echinoderms, marine animals uniquely characterized by a pentaradial symmetry. Approximately 1,000 living and 10,000 extinct species have been described, including many commonly known as sea urchins, heart urchins and sand dollars. Today, echinoids are ubiquitous in benthic marine environments, where they strongly affect the functioning of biodiverse communities such as coral reefs and kelp forests. Given the quality of their fossil record, their remarkable morphological complexity and our thorough understanding of their development, echinoids provide unparalleled opportunities to explore evolutionary questions in deep-time, providing access to the developmental and morphological underpinnings …
Machine Learning Based Variational Approaches For Problems In Solid-State Physics, Bradley Magnetta
Machine Learning Based Variational Approaches For Problems In Solid-State Physics, Bradley Magnetta
Yale Graduate School of Arts and Sciences Dissertations
In this work we utilize principles from optimization and machine learning to solve variational problems in solid-state physics. First we extend the quantum variational method to include an additional objective function term that ensures ground state solutions will have localized character, obtaining the so called Wannier functions. Here the additional term relies on dictionary learning to extract localized Wannier features from a dataset of known Wannier functions. Our approach displays a systematically controllable energy-localization trade-off, has an objective function that allows for the use of fast numerical solvers, and is capable of being used in highly-efficient self-consistent algorithms. Next we …
Pairwise Hydrodynamic Interactions Of Permeable Particles And Flow-Induced Structuring In Dilute Suspensions, Rodrigo Bento Reboucas
Pairwise Hydrodynamic Interactions Of Permeable Particles And Flow-Induced Structuring In Dilute Suspensions, Rodrigo Bento Reboucas
Yale Graduate School of Arts and Sciences Dissertations
The study of particle-level interactions in suspension flows enables a better understanding and control of systems where suspensions play a key role. Examples include the physiology of blood flow microcirculation, flow-induced segregation of polydisperse suspensions, particle aggregation in marine environments, and filtration processes, to name a few. In these systems, a detailed description of the hydrodynamic interactions between the particles and between the particles and fluid boundaries characterize the evolution of the suspension microstructure. Typically, the characteristic size of the particles is small compared to the imposed flow length scale, and hence low-Reynolds-number conditions usually apply. In the dilute regime, …
Cost-Effectiveness Analyses Of Typhoid Interventions In Epidemic And Endemic Settings, Maile Thayer Phillips
Cost-Effectiveness Analyses Of Typhoid Interventions In Epidemic And Endemic Settings, Maile Thayer Phillips
Yale Graduate School of Arts and Sciences Dissertations
Background: Typhoid fever is a major source of morbidity and mortality in developing countries, accounting for approximately 12-21 million infections, 119,000-269,000 deaths, and 2-23 million disability-adjusted life years (DALYs) annually. Typhoid fever is caused by infection with the bacteria Salmonella enterica serovar Typhi, which is mainly transmitted through fecal contamination of food or water. Due to these modes of transmission, most cases occur in low- and middle-income countries (LMICs) where sanitary conditions are poor and access to clean water and sanitation is not common. However, the scale of disease incidence is uncertain. Studies suggest that facility-based laboratory-confirmed estimates, the numbers …
Development Of The Nuclear-Electronic Orbital Method For Applications To Molecular Electrocatalyst Systems, Patrick Schneider
Development Of The Nuclear-Electronic Orbital Method For Applications To Molecular Electrocatalyst Systems, Patrick Schneider
Yale Graduate School of Arts and Sciences Dissertations
Studies of molecular electrocatalysts often involve input from quantum chemical computations in the pursuit of catalyst design targeting several desirable features. To this end, conventional density functional theory (DFT) calculations have proven to be a good match with a reasonable balance between computational accuracy and cost. However, a multicomponent method that treats select nuclei on the same quantum mechanical level as electrons would be useful for a more proper treatment of nuclear quantum effects. Such a multicomponent DFT method has been developed in recent years within the nuclear-electronic orbital (NEO) framework. However, for the multicomponent method to be practically applied …
Computational Investigations Of The Oxygen-Evolving Complex And Its Water Network, Krystle M. Reiss
Computational Investigations Of The Oxygen-Evolving Complex And Its Water Network, Krystle M. Reiss
Yale Graduate School of Arts and Sciences Dissertations
To oxidize two waters into molecular oxygen, the OEC requires channels via which it can bring in new substrate waters and release protons through PCET as the manganese centers are oxidized. Three water channels surround the OEC: the narrow, broad, and large. Each channel possesses its own unique set of properties that make it ideal for a different purpose. Using network analysis and novel occupancy analysis, the stability of each channel's water positions and hydrogen bond network was quantified, showing the stark differences between the channels. The narrow channel is very sensitive to the oxidation of Mn4, appearing to prepare …
Minimizing Tracer Interference To Assess In Vivo Hepatic Metabolism With Glutamine-Generated Mass Isotopomers, Stephan Siebel
Minimizing Tracer Interference To Assess In Vivo Hepatic Metabolism With Glutamine-Generated Mass Isotopomers, Stephan Siebel
Yale Graduate School of Arts and Sciences Dissertations
Stable isotope tracers are widely used to study the in vivo kinetics of central carbon metabolism in diseases such as obesity, type 2 diabetes mellitus (T2DM) and non-alcoholic fatty liver disease (NAFLD). However, despite their common use, 13C-labeled acetate, lactate, and propionate have led to large incongruities and inconsistencies in their in vivo measurement of hepatic metabolism. To resolve major discrepancies and recent controversies of hepatic metabolism we developed and validated [1,2-13C2]-L-glutamine as a novel tracer strategy for measuring hepatic central carbon metabolism. In our rodent studies [1,2-13C2]-L-glutamine generated a straightforward labeling pattern of key metabolites suitable for the interpretation …
Synthetic Studies Towards The Total Synthesis Of (–)-Lomaiviticin A, John A. Rose
Synthetic Studies Towards The Total Synthesis Of (–)-Lomaiviticin A, John A. Rose
Yale Graduate School of Arts and Sciences Dissertations
(–)-Lomaiviticin A (1) is a complex C2-symmetric bacterial metabolite which was isolated from a fermentation broth of Salinispora DPJ-19 by He and co-workers in 2001. The structure of 1 was proposed through detailed analysis of NMR spectral data (Figure 1). Due to the presence of a diazotetrahydrobenzo[b]fluorene substructure, 1 belongs to a family of natural products often referred to as “diazofluorenes” among which the kinamycins (A, C, and F seen in Figure 1) are the earliest known members. (–)-Lomaiviticin A (1) is the most cytotoxic member of the diazofluorene family known with half maximal inhibitory potencies (IC50S) in the nanomolar …
Social Control And Incarceration In Lesotho: A History Of Strategies, 1850-1970, Samuel John Severson
Social Control And Incarceration In Lesotho: A History Of Strategies, 1850-1970, Samuel John Severson
Yale Graduate School of Arts and Sciences Dissertations
This dissertation explores how technologies and infrastructures for promoting control and cohesion have interfaced with the social and political history of Lesotho over the longue durée. This approach allows for tracing lines of historical continuity and change during a period spanning the coalescing of the nation from communities on the Southern African Highveld in the early-19th century, the onset and grinding realities of British colonial rule and the rise of a local economy dependent on labor migration to South Africa, and the unravelling of empire and the challenges of governance in the years following official national liberation in 1966. I …
Novel Signal Reconstruction Techniques In Cyclotron Radiation Emission Spectroscopy For Neutrino Mass Measurement, Luis Elias Saldana
Novel Signal Reconstruction Techniques In Cyclotron Radiation Emission Spectroscopy For Neutrino Mass Measurement, Luis Elias Saldana
Yale Graduate School of Arts and Sciences Dissertations
The Project 8 experiment is developing Cyclotron Radiation Emission Spectroscopy (CRES) on the beta-decay spectrum of tritium for the measurement of the absolute neutrino mass scale. CRES is a frequency-based technique which aims to probe the endpoint of the tritium energy spectrum with a final target sensitivity of 0.04 eV, pushing the limits beyond the inverted mass hierarchy. A phased-approach experiment, both Phase I and Phase II efforts use a combination of 83mKr and molecular tritium T_2 as source gases. The technique relies on an accurate, precise, and well-understood reconstructed beta-spectrum whose endpoint and spectral shape near the endpoint may …