cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
LED-based photo-CIDNP hyperpolarization enables 19F MR imaging and 19F NMR spectroscopy of 3-fluoro-DL-tyrosine at 0.6 T
Creators: name: Bernarding, Johannes
name: Bruns, Christian
name: Prediger, Isabell
name: Plaumann, Markus
Publisher: name: arXiv
Year: 2022
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: Although 19F has high potential to serve as a background-free molecular marker in bioimaging, the molar amount of marker substance is often too small to enable 19F MR imaging or 19F NMR spectroscopy with a sufficiently high signal-to-noise ratio (SNR). Hyperpolarization methods such as parahydrogen-based hyperpolarization or dynamic nuclear polarization (DNP) can significantly improve the SNR, but require expensive and complex sample preparation and the removal of toxic catalysts and solvents. Therefore, we used the biologically compatible model of the fluorinated amino acid 3-fluoro-DL-tyrosine with riboflavin 5'-monophosphate (FMN) as a chromophore dissolved in D2O with 3.4% H2Odest. allowing to transform light energy into hyperpolarization of the 19F nucleus via photo-chemically induced dynamic nuclear polarization (photo-CIDNP). We used a low-cost high-power blue LED to illuminate the sample replacing traditionally used laser excitation, which is both potentially harmful and costly. For the first time, we present results of hyperpolarized 19F MRI and 19F NMR performed with a low-cost 0.6 T benchtop MRI system. The device allowed simultaneous dual channel 1H/19F NMR. 19F imaging was performed with a (0.94 mm)2 in-plane resolution. This enabled the spatial resolution of different degrees of hyperpolarization within the sample. We estimated the photo-CIDNP-based 19F signal enhancement at 0.6 T to be approximately 465. FMN did not bleach out even after multiple excitations, so that the signal-to-noise ratio could be further improved by averaging hyperpolarized signals. The results show that the easy-to-use experimental setup has a high potential to serve as an efficient preclinical tool for hyperpolarization studies in bioimaging.
description: 16 pages, 5 figures, supplementary information (4pages, 4 figures)
Evaluación del impacto en la utilización del libro de curso en el rendimiento académico estudiantil de la materia de cálculo integral, carrera de Ingeniería Agronómica. Universidad Central del Ecuador
Creators: name: Chere, Diego
Publisher: name: unknown
Year: 2023

description: Evaluación del impacto en la utilización del libro de curso en el rendimiento académico estudiantil de la materia de cálculo integral, carrera de Ingeniería Agronómica. Universidad Central del Ecuador
Evaluación del impacto en la utilización del libro de curso en el rendimiento académico estudiantil de la materia de cálculo integral, carrera de Ingeniería Agronómica. Universidad Central del Ecuador
Creators: name: Chere, Diego
Publisher: name: Humanities Commons
Year: 2023

description: Evaluación del impacto en la utilización del libro de curso en el rendimiento académico estudiantil de la materia de cálculo integral, carrera de Ingeniería Agronómica. Universidad Central del Ecuador
Travel time reliability based bridge network maintenance optimization under budget constraint
Creators: name: Zhang, Weili
name: Cao, Miao
name: Wang, Naiyu
Publisher: name: The University of British Columbia
Year: 2015

description: This study develops a decision model to assist bridge authorities in determining a preferred maintenance prioritization schedule for a degraded bridge network in a community that optimizes the performance of transportation systems within budgetary constraints at a regional scale. The study utilizes network analysis methods, structural reliability principles and meta-heuristic optimization algorithms to integrate individual descriptive parameters such as bridge capacity rating, condition rating, traffic demand, and location of the bridge, into global objective functions that define the overall network performance and maintenance cost. The performance of the network is measured in terms of travel time reliability between all possible origin/destination (OD) pairs. In addition to the global budgetary constraint, the optimization is also conditioned on local constraints imposed on traffic flow by insufficient load carrying capacity of deficient bridges. Uncertainties in traffic demands, vehicle weights and maintenance costs are also considered in the problem formulation. This decision model is illustrated with a hypothetical bridge network.
Francisco Núñez Muley, Petition (Granada, 1566)
Creators: name: Lisette, Balabarca Fataccioli
name: Lisette, Balabarca Fataccioli
name: Miguel-Prendes, Sol
name: Wacks, David
Publisher: name: unknown
Year: 2023
Subjects: subject: Spain--Andalusia
subject: Moriscos--Sources
subject: Spain
subject: Spain--Granada (Reino)

description: The Edict of 1567, or Anti-Morisco Edict, was promulgated by Spanish King Philip II on January 1, after being approved in Madrid on November 17, 1566. Its purpose was to eliminate specific Morisco customs, such as their language, dress, and dances. Núñez Muley's Petition is an attempt to persuade Christian authorities to delay enforcing the 1567 Edict. The author lists each of the prohibitions and refutes their effectiveness. He compares Morisco customs to those of other Christian and Muslim communities in the Mediterranean and argues that the prohibitions will not eradicate any putative Islamic practices but instead erase Morisco cultural identity. Moriscos, he claims, are sincere Christians and loyal subjects who support the king's decisions.

This unit contains an English language introduction and notes by Lisette Balabarca Fataccioli, the original Spanish text with facing English translation, and a short suggested bibliography for further reading.
New standard resources for systems biology: BiGG Models database and the visual pathway editor Escher
Creators: name: Dräger, Andreas
name: King, Zachary A.
name: Lu, Justin S.
name: Ebrahim, Ali
name: Sonnenschein, Nikolaus
name: Miller, Philip C.
name: Lerman, Joshua A.
name: Palsson, Bernhard O.
name: Lewis, Nathan E.
Publisher: name: F1000Research
Year: 2016

description: Background: Genome-scale metabolic network reconstructions enable the simulation and analysis of complex biological networks, thus providing insights into how thousands of genes together influence cell phenotypes. Accuracy in systems biology research requires standards in model construction, a variety of specific software tools, and access to high-quality metabolic networks.

Results: To meet these needs, we present BiGG Models database and a collection of software solutions for model building, curation, visualization, and simulation. BiGG Models currently contains more than 75 high-quality manually-curated genome-scale metabolic network reconstructions, which can be easily searched and browsed and include interactive pathway map visualizations.
These visualizations have been generated with the web-based Escher pathway builder. Escher allows users to draw pathways in a semi-automated way and can visualize data related to genes or proteins that are associated to pathways. An export function facilitates storing Escher maps in the community formats SBML and SBGN-ML. These features make Escher an ideal interactive model development tool.
In order to make all models in BiGG MIRIAM compliant, BiGG Models itself has become part of the MIRIAM registry and provides links a plethora of external databases for each model component. This rich annotation enables rapid comparison across models. New Systems Biology Ontology terms have been defined that are used to better highlight the role of model components. A comprehensive web API for programmatically accessing the database content enables interfacing with diverse modeling and analysis tools.

Conclusions: With these features and tools, BiGG Models provides a valuable database, structured for easy access and to help improve the quality, standardization, and accessibility of all genome-scale models. The development of this resource has boosted the development of community standards for constraintbased
modeling.

Availability: http://bigg.ucsd.edu, https://escher.github.io
A comparison of unscented and extended Kalman filtering for nonlinear system identification
Creators: name: Al-Hussein, Abdullah
name: Haldar, Achintya
Publisher: name: The University of British Columbia
Year: 2015

description: A nonlinear system identification-based structural health assessment procedure is presented in this paper. The procedure uses the unscented Kalman filter (UKF) concept. The weighted global iteration with an objective function is incorporated with the UKF algorithm to obtain stable, convergent, and optimal solution. An iterative least squares technique is also integrated with the UKF algorithm. The procedure is capable of assessing health of any type of structures, represented by finite elements. It can identify the structure using limited noise-contaminated dynamic responses, measured at a small part of large structural systems and without using input excitation information. In order to demonstrate its effectiveness, the proposed procedure is compared with the extended Kalman filter (EKF)-based procedure. For numerical verification, a two-dimensional five-story two-bay steel frame is considered. Defect-free and two defective states with small and severe defects are considered. The study shows that the proposed UKF-based procedure can assess structural health more accurately and efficiently than the EKF-based procedures for nonlinear system identification.
The effect of the novel small molecule drug 54118 on the C-X-C chemokine receptor type 4 in the context of cancer cell metastasis
Creators: name: Ding, Tiffany
name: Susriya Gangireddy
name: Miller, Richard
name: Shum, Andrew
Publisher: name: F1000Research
Year: 2016

description: The activation of a cell’s C-X-C Chemokine Receptor Type 4 (CXCR4) receptor by the natural ligand stromal cell-derived factor 1 (SDF1) is known to help guide these cells throughout the body. These receptors when activated on cancer cells promote metastasis. Calcium imaging was used to determine the effect of the drug 54118, which was synthesized in a Northwestern Evanston lab with many molecular similarities to small molecule SDF1, on melanoma cell line C8161, transfected with the CXCR4 receptor.

Results and analysis suggest that small molecule 54118 stimulates robust responses from all cells at a concentration of 10 micromolar, slight responses from the majority of cells at 1 micromolar, and very slight responses from the majority of cells at 0.1 micromolar. These results were used to generate a dose response curve, showing the correlation between the concentration of the drug 54118 and the effectiveness of stimulating cancer cell response. The conclusion is that agonist 54118 is a strong stimulator of cancer cells and stimulates in a dose-dependent manner. 54118 is one of few small molecules that act as potential agonists to the CXCR4 receptor and can be researched further for its uses in medicine.
Supplementary document for Rapid Coherent Raman hyperspectral imaging based on delay-spectral focusing dual comb method and deep learning algorithm - 6215348.pdf
Creators: name: Zhang, Yujia
name: Lu, Minjian
name: Hu, Jiaqi
name: Li, Yan
name: Shum, Perry
name: Chen, Jinna
name: Wei, Haoyun
Publisher: name: Optica Publishing Group
Year: 2025
Subjects: Uncategorized

description: The Supporting Information for deep learning part
On Indefinite Summation using the Theory of Integral Transforms
Creators: name: Li, Thomas
Publisher: name: figshare
Year: 2025
Subjects: classificationCode: 499999
subject: Other mathematical sciences not elsewhere classified

description: We present a novel approach to indefinite summation through integral transform methods. We first establish the Laplace transform’s utility in solving complex summation problems, then develop a generalized frame work of integral transforms that provides a systematic approach to evalu ating nontrivial indefinite sums. Using the continuous binomial transform as a central example, we derive key identities that demonstrate the frame work’s effectiveness. We also introduce a novel technique in addressing varying step sizes as well as nonlinear variable transformations in discrete indefinite summations. Our results show that integral transforms—with their flexible choice of kernels—serve as powerful tools for solving and analyzing indefinite summations.
Elementary_Theory_Indefinite_Summation_Integral_Transforms.pdf
Creators: name: Li, Thomas
Publisher: name: figshare
Year: 2025
Subjects: classificationCode: 499999
subject: Other mathematical sciences not elsewhere classified

description: We present a novel approach to indefinite summation through integral transform methods. We first establish the Laplace transform’s utility in solving complex summation problems, then develop a generalized frame work of integral transforms that provides a systematic approach to evalu ating nontrivial indefinite sums. Using the continuous binomial transform as a central example, we derive key identities that demonstrate the frame work’s effectiveness. We also introduce a novel technique in addressing varying step sizes as well as nonlinear variable transformations in discrete indefinite summations. Our results show that integral transforms—with their flexible choice of kernels—serve as powerful tools for solving and analyzing indefinite summations.
Circular Polarimetry of Suspect Wind-accreting Magnetic pre-Polars
Creators: name: Hakala, Pasi
name: Parsons, Steven G.
name: Marsh, Thomas R.
name: Gänsicke, Boris T.
name: Ramsay, Gavin
name: Schwope, Axel
name: Hermes, J. J.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We present results from a circular polarimetric survey of candidate detached magnetic white dwarf - M dwarf binaries obtained using the Nordic Optical Telescope, La Palma. We obtained phase resolved spectropolarimetry and imaging polarimetry of seven systems, five of which show clearly variable circular polarisation. The data indicate that these targets have white dwarfs with magnetic field strengths > 80 MG. Our study reveals that cyclotron emission can dominate the optical luminosity at wavelengths corresponding to the cyclotron emission harmonics, even in systems where the white dwarfs are only wind-accreting. This implies that a very significant fraction of the the stellar wind of the companion star is captured by the magnetic white dwarf reducing the magnetic braking in pre-CVs. Furthermore, the polarimetric confirmation of several detached, wind-accreting magnetic systems provides observational constraints on the models of magnetic CV evolution and white dwarf magnetic field generation. We also find that the white dwarf magnetic field configuration in at least two of these systems appears to be very complex.
description: 13 pages, 10 figures, accepted for publication in MNRAS, Figure 10 was replaced by a corrected one
Francisco Núñez Muley, Memorial (Granada, 1566)
Creators: name: Balabarca Fataccioli, Lisette
name: Miguel-Prendes, Sol
name: Wacks, David
Publisher: name: unknown
Year: 2023
Subjects: subject: Moriscos--Sources
subject: Moriscos--Historiography
subject: Spain--Granada (Reino)
subject: Spain

description: Núñez-Muley abstract

The Edict of 1567, or Anti-Morisco Edict, was promulgated by Spanish King Philip II on January 1, after being approved in Madrid on November 17, 1566. Its purpose was to eliminate specific Morisco customs, such as their language, dress, and dances. Núñez Muley's Petition is an attempt to persuade Christian authorities to delay enforcing the 1567 Edict. The author lists each of the prohibitions and refutes their effectiveness. He compares Morisco customs to those of other Christian and Muslim communities in the Mediterranean and argues that the prohibitions will not eradicate any putative Islamic practices but instead erase Morisco cultural identity. Moriscos, he claims, are sincere Christians and loyal subjects who support the king's decisions.

This unit contains a Spanish-language introduction and notes by Lisette Balabarca Fataccioli, and the original Spanish text, followed by a short bibliography of suggested readings.
Scintillation Event Localization in Hemi-Ellipsoid Detector for SPECT, a simulation study using Geant4 Monte-Carlo
Creators: name: Soysal, Hanif R.
name: Dey, J.
name: Donahue, W. P.
name: Matthews, K. L.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: Medical Physics (physics.med-ph)
subject: FOS: Physical sciences

description: A high sensitivity Cardiac SPECT system using curved crystals with pinhole collimation was proposed previously (Dey, IEEE TNS 2012, Bhusal et al, Med. Phys. 2019). Here, we hypothesize that a high curvature hemi-ellipsoid detector results in measurable differences in light distribution from events at different depths in the crystal. This was tested by analyzing the scintillation light in hemi-ellipsoid detector using Monte-Carlo (Geant4) and evaluation of both the localization error at detector and the back-projected errors in object-space. We used Geant4 to simulate the propagation of scintillation light in a monolithic hemi-ellipsoidal CsI crystal. A look-up table (LUT) was created to map the points inside the crystal to the expected light pattern on the crystal surface using Geant4. In thirteen zones across the crystal, gamma-rays were simulated and the resulting scintillator light intensity on the surface was captured, serving as our experimental interactions. A Poisson-statistics-based algorithm was developed to limit the search of the gamma-ray event locations into small regions of the LUT and fine-tuned by interpolating between selected LUT points by comparing the light distribution of the gamma interactions and LUT light patterns. The localized events were individually back-projected to the object mid-plane, and the errors recorded. Excluding some outliers (up to 2%), the localized errors averaged over all the zones was 0.71 (+/-0.44) mm with a worse case of 1.36 (+/-0.67) mm at the apex. When back-projected to the midplane of the object for Cardiac SPECT, the errors were <1mm and average error was 0.4(+/-0.22) mm, due to the high system magnification afforded by the detector. Thus, for our high sensitivity system, we were also able to achieve high resolution, assuming perfect pinhole collimator resolution recovery for Cardiac SPECT application.
description: This work is Accepted (on April 2022) for publication by Journal of Instrumentation; Draft manuscript will be updated with the published version; the Abstract is shortened for arXiv, see full document for complete abstract
End-to-End Deep Lip-reading: A Preliminary Study
Creators: name: Thapa, Kamal
Publisher: name: London South Bank University
Year: 2023
Subjects: end-to-end lip-reading
deep lip-reading

description: Deep lip-reading is the use of deep neural networks to extract speech from silent videos. Most works in lip-reading use a multi staged training approach due to the complex nature of the task. A single stage, end-to-end, unified training approach, which is an ideal of machine learning, is also the goal in lip-reading. However, pure end-to-end systems have so far failed to perform as good as non-end-to-end systems. Some exceptions to this are the very recent Temporal Convolutional Network (TCN) based architectures (Martinez et al., 2020; Martinez et al., 2021). This work lays out preliminary study of deep lip-reading, with a special focus on various end-to-end approaches. The research aims to test whether a purely end-to-end approach is justifiable for a task as complex as deep lip-reading. To achieve this, the meaning of pure end-to-end is first defined and several lip-reading systems that follow the definition are analysed. The system that most closely matches the definition is then adapted for pure end-to-end experiments. We make four main contributions: i) An analysis of 9 different end-to-end deep lip-reading systems, ii) Creation and public release of a pipeline to adapt sentence level Lipreading Sentences in the Wild 3 (LRS3) dataset into word level, iii) Pure end-to-end training of a TCN based network and evaluation on LRS3 word-level dataset as a proof of concept, iv) a public online portal to analyse visemes and experiment live end-to-end lip-reading inference. The study is able to verify that pure end-to-end is a sensible approach and an achievable goal for deep machine lip-reading.
N-polar GaN p-n junction diodes with low ideality factors
Creators: name: Nomoto, Kazuki
name: Xing, Huili Grace
name: Jena, Debdeep
name: Cho, YongJin
Publisher: name: arXiv
Year: 2022
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Applied Physics (physics.app-ph)
subject: FOS: Physical sciences

description: High-quality N-polar GaN p-n diodes are realized on single-crystal N-polar GaN bulk substrate by plasma-assisted molecular beam epitaxy. The room-temperature current-voltage characteristics reveal a high on/off current ratio of 10^11 at 4 V and an ideality factor of 1.6. As the temperature increases to 200 C, the apparent ideality factor gradually approaches 2. At such high temperatures, Shockley-Read-Hall recombination times of 0.32-0.46 ns are estimated. The measured electroluminescence spectrum is dominated by a strong near-band edge emission, while deep level and acceptor-related luminescence is greatly suppressed. A relatively high reverse breakdown field of 2.4 MV/cm without field-plates is achieved. This work indicates that the quality of N-polar GaN diodes is now approaching to that of their state-of-the-art Ga-polar counterparts.
description: 11 pages, 3 figures
Where and What: Driver Attention-based Object Detection
Creators: name: Rong, Yao
name: Kassautzki, Naemi-Rebecca
name: Fuhl, Wolfgang
name: Kasneci, Enkelejda
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Human-Computer Interaction (cs.HC)
subject: FOS: Computer and information sciences

description: Human drivers use their attentional mechanisms to focus on critical objects and make decisions while driving. As human attention can be revealed from gaze data, capturing and analyzing gaze information has emerged in recent years to benefit autonomous driving technology. Previous works in this context have primarily aimed at predicting "where" human drivers look at and lack knowledge of "what" objects drivers focus on. Our work bridges the gap between pixel-level and object-level attention prediction. Specifically, we propose to integrate an attention prediction module into a pretrained object detection framework and predict the attention in a grid-based style. Furthermore, critical objects are recognized based on predicted attended-to areas. We evaluate our proposed method on two driver attention datasets, BDD-A and DR(eye)VE. Our framework achieves competitive state-of-the-art performance in the attention prediction on both pixel-level and object-level but is far more efficient (75.3 GFLOPs less) in computation.
description: 22 pages
Una relectura del método sociológico: Emile Durkheim y el estudio  científico de las formaciones sociales
Creators: name: Zúñiga, Camila
Publisher: name: Humanities Commons
Year: 2023

description: Revisión del las reglas del método sociológico propuestas por Durkheim esta relectura resume los aspectos más importantes de las reglas propuestas y la base de la ideología que sientan estas reglas
title: Navigating Misperceptions: How Intersectionality Shapes the Experiences of Black Women Executive Leaders in K-12 Education
Creators: name: Edwards, Dana
Publisher: name: Maryland Shared Open Access Repository
Year: 2025
Subjects: subject: Intersectionality
subject: Black women
subject: K12 education
subject: cabinet
subject: central office
subject: district office

description: In K-12 public education, Black women serve in a variety of leadership roles in schools and central offices. Research is available and discusses the experiences of Black women leaders, teachers, principals, and superintendents; however, there is a gap in the literature about Black women in executive leadership within the school district’s central office, even more specifically as members of the superintendent’s cabinet. Research on school district central offices has centered on transforming organizational structures to impact student outcomes (Honig, 2014). There is a paucity of research that provides a deeper look at intersectionality (Crenshaw, 2019) concerning Black women executive leaders who are cabinet members. This qualitative dissertation explored the lived experiences of Black women executive leaders in K-12 school districts in the United States to learn how the intersectionality of race and gender influences their approach to leadership and the performance of their leadership responsibilities. Data sources included a survey, individual interviews, and a researcher’s journal. Twenty survey responses were gathered from self-selection, convenience, and snowball sampling. Six in-depth interviews were conducted with dedicated leaders from five school districts in the Northeast, Southeast, and Midwest regions of the United States. All had extensive leadership experience, with four of the six having held previous executive leadership roles. Their positions spanned the school system, including human resources, principal supervision, student services, and equity. Data were analyzed using a multi-layered coding approach, descriptive, in vivo, and theming, capturing exact key words, phrases, and experiences (Miles & Huberman, 2020) to better identify themes and patterns (Saldana, 2016) to ascertain the intersectional experience of Black women leaders. Findings revealed that intersectionality influenced participants’ approaches to leadership and work performance. Participants were conscious of the misperceptions people had of them and how bias influenced their interactions, preparation for work, and daily duties. This dissertation provides a forum for the voices of a population of Black women who exist but whose experiences have yet to be shared. Recommendations are provided for policy and workplace cultures to better support and create organizational culture changes for Black women executives in K-12 school districts.
title: Serotonergic modulation of habituation and associative learning in mice
Creators: name: Thomas, Janasia
Publisher: name: Digital Repository at the University of Maryland
Year: 2025
Subjects: subject: Neuroscience
subject: Serotonergic modulation
subject: Auditory Cortex
subject: Hearing and Communication Science
subject: Acoustic Startle Response
subject: Prepulse Inhibition

description: Psychedelic drugs are frequently used in therapy-related scenarios where they can have a long-term effect on mood and psychiatric issues such as depression and anxiety. Psychedelics are also used in relation to hearing, because they can influence perception of auditory stimuli. 2,5-Dimethoxy-4-iodoamphetamine, also known as DOI, is a psychedelic drug with effects on associative learning. In this experiment, ketanserin and saline are used as well. Ketanserin specifically is an antagonist and it’s believed to block the effects of the agonist DOI. Saline is used as a control to compare results amongst the different drugs. To investigate, we studied the effects of the serotonergic psychedelic drug, DOI, to assess its effects on habituation and associative learning during pre-pulse inhibition (PPI) of the acoustic startle response (ASR) in mice. ASR is a phenomenon where mice jump when exposed to a sudden stimulus. PPI is when a ‘warning noise’ will be played to prime the mice for a sudden, loud noise. Effects of ketanserin and saline during PPI and ASR were studied as well. The data showed that the dosage of DOI did not contribute to differences in ASR or PPI. Additionally, DOI correlates with a lower startle response with higher ISI’s, indicating associative learning and habituation. Ketanserin temporarily blocked habituation during two sessions, but others remained the same. In the saline sessions, habituation was shown. From these results, we can conclude that DOI may improve associative learning indicated by the changes in PPI with long ISI’s. Additionally, in the future, this experiment can be redone with a larger batch of mice to ensure that the results are accurate.
Gene model annotation mapping with use of local sequence similarity and advance distance scoring metrics
Creators: name: Krachunov, Milko
name: Kulev, Ognyan
name: Vassilev, Dimitar
name: Paweł Łabaj
Publisher: name: F1000Research
Year: 2016

description: Genome-scale expression profiling has become a key tool of functional genomics, critically supporting progress in the post-genomic era. It improves our understanding of living systems at the molecular level. The fast development of sequencing technology has recently led to many updates of genome sequences as well as gene models and has revealed the complexity of the gene model annotation of many species. This fast pace, however, has resulted in difficulties in mapping between corresponding alternative transcripts for different gene model annotations. To deal with these challenges, we present a new approach for mapping between gene model annotations.

Instead of full sequence alignment based scoring, we perform matching on individual ‘pseudo-exons’. To mimic the functional sequence interpretation, in the final score the influence of insertions/deletions and possible frameshifts are also taken into account. A fast local alignment tool, such as BLAT, is used to rapidly identify the matching candidates. These are then aligned more accurately using Needleman-Wunsch algorithm. The match candidates are scored according to the quantity of matched pseudo-exons for the reference gene in the selected annotation.

The proposed features were compared on the number of cross–annotation name matches. Most lead to small (below 1%), but consistent increase in name matches across the conducted tests. However, frameshifts were found sensitive to insertion and deletion errors. Leading frameshifts had to be disregarded to account for UTRs, and changing the alignment disturbed their application, necessitating further work.

Our way of mapping transcripts from different annotation is a first use of such approach. Our results have shown that, despite the small number of ambiguous candidates, there's a visible advantage in applying a sensitive exon-aware and frameshift approach, intended to provide a valid functional and amino-acid level mapping.
Marianna Charitonidou, Urban Scale Digital Twins and City Branding: Commoning Practices and Carescapes,2023 Architectural Humanities Research Association conference, 25-27 October 2023, Portsmouth University, UK
Creators: name: Charitonidou, Marianna
Publisher: name: Humanities Commons
Year: 2023

description: The paper explores how the reflection on urban scale digitals twins and the debates about the role of commoning practices in architecture and urban planning could be combined in a way that would address climate justice and social justice simultaneously. At the core of the paper is the idea that sustainable environmental design and regenerative design necessarily involve an exploration of how one can re-conceive the redistribution of wealth, land, and power. The paper examines the role of digital twins in predicting the characteristics of ‘leisurescapes’ and ‘carescapes’. Particular emphasis is placed on the potential of the utilization of urban scale digital twins by policymakers while deciding the branding strategies concerning the creation of sites destined for recreation and care. The paper also explores the role of care and recreation in re-thinking city branding and the ways in which urban scale digital twins can contribute to such endeavors. One of the main objectives of the paper is to shed light on how urban scale digital twins can contribute to the combination of “city branding” and sustainable development. In parallel, it examines how “city branding” can serve in establishing urban regeneration strategies. Another issue that is investigated is the role of urban scale digital twins in the "calibration" or the balancing of the tension between the so-called "city branding" and the so-called "city commoning". A tension that is useful for better grasping the notion of commons is the interrogation regarding the understanding of commons as community or as public space.
การพัฒนาผลิตภัณฑ์มาการองจากกากมะพร้าวเหลือใช้
Creators: name: กรวิทย์ สักแกแก้ว
Publisher: name: คณะเทคโนโลยีการเกษตร มหาวิทยาลัยราชภัฏมหาสารคาม
Year: 2024
Subjects: มาการอง
เมอแร็งก์
กากมะพร้าวเหลือใช้

description: วารสารเกษตรพระวรุณ, 21, 1, 136-145
Mathematical encoding within multi-resonant planetary systems as SETI beacons
Creators: name: Clement, Matthew S.
name: Raymond, Sean N.
name: Veras, Dimitri
name: Kipping, David
Publisher: name: arXiv
Year: 2022
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Popular Physics (physics.pop-ph)
subject: FOS: Physical sciences

description: How might an advanced alien civilization manipulate the orbits within a planetary system to create a durable signpost that communicates its existence? While it is still debated whether such a purposeful advertisement would be prudent and wise, we propose that mean-motion resonances between neighboring planets -- with orbital periods that form integer ratios -- could in principle be used to encode simple sequences that one would not expect to form in nature. In this Letter we build four multi-resonant planetary systems and test their long-term orbital stability. The four systems each contain 6 or 7 planets and consist of: (i) consecutive integers from 1 to 6; (ii) prime numbers from 2 to 11; (iii) the Fibonacci sequence from 1 to 13; and (iv) the Lazy Caterer sequence from 1 to 16. We built each system using N-body simulations with artificial migration forces. We evaluated the stability of each system over the full 10 Gyr integration of the Sun's main sequence phase. We then tested the stability of these systems for an additional 10 Gyr, during and after post-main sequence evolution of the central stars (assumed to be Sun-like) to their final, white dwarf phase. The only system that was destabilized was the consecutive integer sequence (system i). The other three sequences therefore represent potential SETI beacons.
description: Updated acknowledgements. 6 pages, 2 figures, 1 table, accepted for publication in MRNAS
Knowledge towards exercise and foot care among individuals with uncontrolled type 2 diabetes mellitus in secondary care settings in northeastern Thailand: a cross-sectional study
Creators: name: Ponlapat Yonglitthipagon
Publisher: name: Faculty of Associated Medical Sciences, Khon Kaen University, Thailand
Year: 2024
Subjects: Non-communicable disease
Community healthcare service
Diabetic foot care
Out-patient diabetes knowledge
Physical activity

description: Archives of Allied Health Sciences, 36, 2, 1-13
Loss Function Entropy Regularization for Diverse Decision Boundaries
Creators: name: Chong, Sue Sin
Publisher: name: arXiv
Year: 2022
Subjects: subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Is it possible to train several classifiers to perform meaningful crowd-sourcing to produce a better prediction label set without ground-truth annotation? This paper will modify the contrastive learning objectives to automatically train a self-complementing ensemble to produce a state-of-the-art prediction on the CIFAR10 and CIFAR100-20 tasks. This paper will present a straightforward method to modify a single unsupervised classification pipeline to automatically generate an ensemble of neural networks with varied decision boundaries to learn a more extensive feature set of classes. Loss Function Entropy Regularization (LFER) are regularization terms to be added to the pre-training and contrastive learning loss functions. LFER is a gear to modify the entropy state of the output space of unsupervised learning, thereby diversifying the latent representation of decision boundaries of neural networks. Ensemble trained with LFER has higher successful prediction accuracy for samples near decision boundaries. LFER is an adequate gear to perturb decision boundaries and has produced classifiers that beat state-of-the-art at the contrastive learning stage. Experiments show that LFER can produce an ensemble with accuracy comparable to the state-of-the-art yet have varied latent decision boundaries. It allows us to perform meaningful verification for samples near decision boundaries, encouraging the correct classification of near-boundary samples. By compounding the probability of correct prediction of a single sample amongst an ensemble of neural network trained, our method can improve upon a single classifier by denoising and affirming correct feature mappings.
description: 7 pages
Disaggregating community resilience objectives to achieve building performance goals
Creators: name: Wang, Naiyu
name: Ellingwood, Bruce R.
Publisher: name: The University of British Columbia
Year: 2015

description: Resilience is often regarded as an attribute of communities rather than of individual buildings, bridges and other civil infrastructure facilities. Previous research to support resilient infrastructure has considered, for the most part, actions and policies to achieve resilience objectives at the community level. While it is clear that a community cannot be resilient without resilient individual facilities, few attempts have been made to relate the performance criteria for individual facilities to community resilience goals in a quantitative manner. This paper presents a method for relating risk-informed performance criteria for individual buildings exposed to extreme hazards to broader community resilience objectives and illustrates the application of the method to two residential building inventories. The paper demonstrates the feasibility of disaggregating broader community resilience goals to obtain performance objective of individual facilities.
Approximating Permutations with Neural Network Components for Travelling Photographer Problem
Creators: name: Chong, Sue Sin
Publisher: name: arXiv
Year: 2022
Subjects: subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Most of the current inference techniques rely upon Bayesian inference on Probabilistic Graphical Models of observations and do predictions and classification on observations. However, there is very little literature on the mining of relationships between observations and building models of the relationship between sets of observations or the generating context of the observations. Moreover, event understanding of machines with observation inputs needs to understand the relationship between observations. Thus there is a crucial need to build models and develop effective data structures to accumulate and organize relationships between observations. Given a PGM model, this paper attempts to fit a permutation of states to a sequence of observation tokens (The Travelling Photographer Problem). We have devised a machine learning inspired architecture for randomized approximation of state permutation, facilitating parallelization of heuristic search of permutations. As a result, our algorithm can solve The Travelling Photographer Problem with minimal error. Furthermore, we demonstrate that by mimicking machine learning components such as normalization, dropout, and lambda layer with a randomized algorithm, we can devise an architecture that solves TPP, a permutation NP-Hard problem. Other than TPP, we can also provide a 2-Local improvement heuristic for the Travelling Salesman Problem (TSP) with similar ideas.
description: 11 pages
title: Inferring the Early History of Northern South America through Mitochondrial DNA Analysis
Creators: name: Rojas, Mateo
Publisher: name: Digital Repository at the University of Maryland
Year: 2025
Subjects: subject: Anthropology
subject: FOS: Sociology
subject: mtDNA
subject: ANTH
subject: Haplogroup
subject: Colombia

description: Prior to the mass colonization of the Americas, early peopling consisted of Indigenous Americans who, over the course of tens of thousands of years, came to occupy the continents that would later be settled by the ambitious European powers of the time. Through the use of mitochondrial DNA (mtDNA) sequencing throughout numerous samples, as well as temporal analysis of genetic mutations within samples of the same haplogroup, the migrations of different early indigenous populations can be tracked across the geography of the continent, and the ethnographic composition of different regions can be reconstructed with respect to the time period. Given that haplogroups belonging to maternal Amerindian descent are identified by haplogroups A, B, C, and D, and that genetic variations in haplogroups can be tracked over time, it is possible to approximate a model of the early genetic composition of Colombia and other regions of northern South America through the use of samples from model haplogroups like A2al, B2d14, C1d2, and D4h3a. For this study, 94 samples across these haplogroups have been surveyed, and individual phylogenetic trees have been constructed, which each infer a genetic timeline for the mutations found under each haplogroup. With the construction of a phylogenetic tree for each of the four haplogroups, a larger, cumulative phylogenetic tree was also constructed, which in combination with the known presences of haplogroups across the geography of Colombia, can provide insight into the early migration and settling patterns of these early pre-columbian Indigenous Americans.
Marianna Charitonidou, Urban Scale Digital Twins and City Branding: Commoning Practices and Carescapes,2023 Architectural Humanities Research Association conference, 25-27 October 2023, Portsmouth University, UK
Creators: name: Charitonidou, Marianna
Publisher: name: unknown
Year: 2023

description: The paper explores how the reflection on urban scale digitals twins and the debates about the role of commoning practices in architecture and urban planning could be combined in a way that would address climate justice and social justice simultaneously. At the core of the paper is the idea that sustainable environmental design and regenerative design necessarily involve an exploration of how one can re-conceive the redistribution of wealth, land, and power. The paper examines the role of digital twins in predicting the characteristics of 'leisurescapes' and 'carescapes'. Particular emphasis is placed on the potential of the utilization of urban scale digital twins by policymakers while deciding the branding strategies concerning the creation of sites destined for recreation and care. The paper also explores the role of care and recreation in re-thinking city branding and the ways in which urban scale digital twins can contribute to such endeavors. One of the main objectives of the paper is to shed light on how urban scale digital twins can contribute to the combination of "city branding" and sustainable development. In parallel, it examines how "city branding" can serve in establishing urban regeneration strategies. Another issue that is investigated is the role of urban scale digital twins in the "calibration" or the balancing of the tension between the so-called "city branding" and the so-called "city commoning". A tension that is useful for better grasping the notion of commons is the interrogation regarding the understanding of commons as community or as public space.
Space-like Singularities of General Relativity: A Phantom menace?
Creators: name: Ashtekar, Abhay
name: del Río, Adrián
name: Schneider, Marc
Publisher: name: arXiv
Year: 2022
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: The big bang and the Schwarzschild singularities are space-like. They are generally regarded as the "final frontiers" at which space-time ends and general relativity breaks down. We review the status of such space-like singularities from three increasingly more general perspectives. They are provided by (i) A reformulation of classical general relativity motivated by the Belinskii, Khalatnikov, Lifshitz conjecture on the behavior of the gravitational field near space-like singularities; (ii) The use of test quantum fields to probe the nature of these singularities; and, (iii) An analysis of the fate of these singularities in loop quantum gravity due to quantum geometry effects. At all three levels singularities turn out to be less menacing than one might a priori expect from classical general relativity. Our goal is to present an overview of the emerging conceptual picture and suggest lines for further work. In line with the \emph{Introduction to Current Research} theme, we have made an attempt to make it easily accessible to all researchers in gravitational physics.
description: Invited article under "Introduction to Current Research", GRG (at press). Special issue in memory of Prof. T. Padmanabhan
Value of information in retrofitting of flood defenses
Creators: name: Schweckendiek, T. (Timo)
name: Vrouwenvelder, A. C. W. M. (Ton)
Publisher: name: The University of British Columbia
Year: 2015

description: Dikes and levees play a crucial role in flood protection. The main causes of levee failures are of geotechnical nature; geotechnical failure modes are also the main contributors to the probability of failure of flood defences due to the typically large uncertainties in ground conditions. Hence, information on ground conditions and soil properties is crucial in safety assessments and retrofitting designs of levees. The present paper demonstrates how we can reduce these uncertainties and how we can provide input for rational decision making on investments in monitoring and site investigation. If working in a framework with an explicit target reliability, the value of such information can be expressed in terms of the savings that can be achieved in retrofitting costs. The key ingredients of the approach are Bayesian posterior analysis for reliability updating by incorporating the information from various sources and Bayesian (pre-posterior) decision analysis for estimating the uncertainty and expected values of the consequences and costs of the considered decision options. The optimal strategy is the one with the least expected cost to meet the pre-set reliability target (e.g. by a safety standard). Several examples and case studies addressing different sources of information, such as field observations and piezometer monitoring during floods or site investigation by Cone Penetration Tests (CPT), illustrate the impact of reliability updating and suggest that investments in inspection and monitoring are often worthwhile, especially when the prior uncertainties are large.
Machine learning and density functional theory
Creators: name: Pederson, Ryan
name: Kalita, Bhupalee
name: Burke, Kieron
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computational Physics (physics.comp-ph)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: Over the past decade machine learning has made significant advances in approximating density functionals, but whether this signals the end of human-designed functionals remains to be seen. Ryan Pederson, Bhupalee Kalita and Kieron Burke discuss the rise of machine learning for functional design.