cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Preliminary outcomes of the co-creation process
Creators: name: CIC Consorzio Italiano dei Compostatori
Publisher: name: Zenodo
Year: 2024

description: FER-PLAY is working to protect ecosystems, decrease EU dependence on fertiliser imports, and improve resource efficiency through the promotion of circular fertilisers. The project maps and assesses circular fertilisers made from secondary raw materials and highlight their multiple benefits to foster their wide-scale production and application.

The project work plan foresees a dedicated Work Package to gather first-hand perspectives of key stakeholders regarding barriers and opportunities for circular fertilisers deployment following a co-creation approach. Relevant stakeholders representing mainly the three target groups (end-users, producers and local administrations) and describing a variety of EU countries perspectives, are involved into discussions with the main scope of feeding FER-PLAY with a wider range of viewpoints that cover real needs and that can be later reflected on the main outcomes of the project: the assessment of impacts and trade-offs of the selected value-chains (resulting from WP2 “Multi-assessment of impacts, trade-offs and framework conditions of selected alternative fertiliser value chains”), the tailor-made guidelines (resulting from WP3) and the awareness-rising activities (part of WP4 “Dissemination, exploitation and communication”).

This document collects the preliminary outcomes from these co-creation discussions carried out from March 2023 to February 2024. It is conceived as a living document to serve as a “database” of inputs received during the activities with external stakeholders and to provide evidence on the process and will be updated if required.
First experimental time-of-flight-based proton radiography using low gain avalanche diodes
Creators: name: Ulrich-Pur, Felix
name: Bergauer, Thomas
name: Galatyuk, Tetyana
name: Hirtl, Albert
name: Kausel, Matthias
name: Kedych, Vadym
name: Kis, Mladen
name: Kozymka, Yevhen
name: Krüger, Wilhelm
name: Linev, Sergey
name: Michel, Jan
name: Pietraszko, Jerzy
name: Rost, Adrian
name: Schmidt, Christian Joachim
name: Träger, Michael
name: Traxler, Michael
Publisher: name: arXiv
Year: 2023
Subjects: subject: Medical Physics (physics.med-ph)
subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences

description: Ion computed tomography (iCT) is an imaging modality for the direct determination of the relative stopping power (RSP) distribution within a patient's body. Usually, this is done by estimating the path and energy loss of ions traversing the scanned volume via a tracking system and a separate residual energy detector. This study, on the other hand, introduces the first experimental study of a novel iCT approach based on time-of-flight (TOF) measurements, the so-called Sandwich TOF-iCT concept, which in contrast to any other iCT system, does not require a residual energy detector for the RSP determination. A small TOF-iCT demonstrator was built based on low gain avalanche diodes (LGAD), which are 4D-tracking detectors that allow to simultaneously measure the particle position and time-of-arrival with a precision better than 100um and 100ps, respectively. Using this demonstrator, the material and energy-dependent TOF was measured for several homogeneous PMMA slabs in order to calibrate the acquired TOF against the corresponding water equivalent thickness (WET). With this calibration, two proton radiographs (pRad) of a small aluminium stair phantom were recorded at MedAustron using 83 and 100.4MeV protons. Due to the simplified WET calibration models used in this very first experimental study of this novel approach, the difference between the measured and theoretical WET ranged between 37.09 and 51.12%. Nevertheless, the first TOF-based pRad was successfully recorded showing that LGADs are suitable detector candidates for TOF-iCT. While the system parameters and WET estimation algorithms require further optimization, this work was an important first step to realize Sandwich TOF-iCT. Due to its compact and cost-efficient design, Sandwich TOF-iCT has the potential to make iCT more feasible and attractive for clinical application, which, eventually, could enhance the treatment planning quality.
description: Preprint submitted to Physics in Medicine and Biology. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it
title: Willard Hall, Fairfax, VA.
Creators: name: (:Unkn) Unknown
Publisher: name: George Mason University
Year: 2006
Subjects: subject: Fairfax (Va.)--Pictorial works
subject: Postcards--Virginia--Fairfax
subject: Town Hall (Fairfax, Va.)

description: Text on front: Willard Hall, Fairfax, VA
Anomalous superfluid density in a disordered charge density wave material: Pd-intercalated ErTe$_3$
Creators: name: Iguchi, Yusuke
name: Straquadine, Joshua A.
name: Murthy, Chaitanya
name: Kivelson, Steven A.
name: Singh, Anisha G.
name: Fisher, Ian R.
name: Moler, Kathryn A.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: We image local superfluid density in single crystals of Pd-intercalated ErTe$_3$ below the superconducting critical temperature, $T_c$, well below the onset temperature, $T_{CDW}$, of (disordered) charge-density-wave order. We find no detectable inhomogeneities. We observe a rapid increase of the superfluid density below $T_c$, deviating from the behavior expected in conventional Bardeen-Cooper-Schrieffer, and show that the temperature dependence is qualitatively consistent with a combination of quantum and thermal phase fluctuations.
description: 15 pages, 12 figures
A Conservative Approach for Few-Shot Transfer in Off-Dynamics Reinforcement Learning
Creators: name: Daoudi, Paul
name: Prieur, Christophe
name: Robu, Bogdan
name: Barlier, Merwan
name: Santos, Ludovic Dos
Publisher: name: arXiv
Year: 2023
Subjects: subject: Machine Learning (cs.LG)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences

description: Off-dynamics Reinforcement Learning (ODRL) seeks to transfer a policy from a source environment to a target environment characterized by distinct yet similar dynamics. In this context, traditional RL agents depend excessively on the dynamics of the source environment, resulting in the discovery of policies that excel in this environment but fail to provide reasonable performance in the target one. In the few-shot framework, a limited number of transitions from the target environment are introduced to facilitate a more effective transfer. Addressing this challenge, we propose an innovative approach inspired by recent advancements in Imitation Learning and conservative RL algorithms. The proposed method introduces a penalty to regulate the trajectories generated by the source-trained policy. We evaluate our method across various environments representing diverse off-dynamics conditions, where access to the target environment is extremely limited. These experiments include high-dimensional systems relevant to real-world applications. Across most tested scenarios, our proposed method demonstrates performance improvements compared to existing baselines.
title: Newspaper Column: Congestion Prices for Dulles Tolls
Creators: name: Nicoson, William J.
Publisher: name: The Connection
Year: 1999
Subjects: subject: Toll roads
subject: Traffic
subject: Dulles Toll Road
subject: Dulles Greenway
subject: Commuting
subject: High Occupancy Vehicle (HOV)

description: PDF file distilled from original WordPerfect document. Original size 11" x 8.5".
description: Last week I called on Virginia Transportation Secretary Shirley Ybarra to emulate on the Dulles Toll Road the Greenway’s lower toll for drivers with Smart Card, thus reducing congestion at toll plazas with gates dedicated to Smart Carders. For some reason, she hasn’t yet adopted my suggestion. So let’s up the ante. During commuting hours, congestion at toll gates is bad, but congestion the length of non-HOV lanes is worse. Why not permit solo drivers to buy their way onto Dulles HOV lanes by paying a higher toll? This would reduce congestion for solo drivers who shift left and those who don’t. Vehicles with 2 or more occupants might have more company in HOV lanes, but a variable toll policy based on monitored congestion would perpetuate free flow in HOV lanes.
Supplementary document for Visual Intertial odometry enabled 3D Ultrasound and Photoacoustic imaging. - 6397124.pdf
Creators: name: Sankepalle, Deeksha
name: Anthony, Brian
name: Mallidi, Srivalleesha
Publisher: name: Optica Publishing Group
Year: 2025
Subjects: Biomedical Engineering not elsewhere classified

description: Supplementary Data
title: COMPUTATIONAL ANALYSIS OF THE PHYLOGENOMIC RELATIONSHIPS OF HUMAN AND SIMIAN ADENOVIRUSES AND THE CROSS-SPECIES TRANSMISSIONS
Creators: name: (:Unkn) Unknown
Publisher: name: George Mason University
Year: 2021

description: The phylogenetic relationships of HAdV and SAdV are not formally well defined by the International Committee on Taxonomy of Viruses (ICTV). All archived genomes will be analyzed at high resolution using genomics and bioinformatics to provide a comprehensive reference. Given their evolutionary closeness, possible zoonotic and anthroponosis transfers between human and non-human simian hosts will be examined using HAdV-E4 and SAdV-21 as examples, based on their clustering in the phylogenomic trees.
Scalable Infrastructure for Workload Characterization of Cluster Traces
Creators: name: van Loo, Thomas
name: Jindal, Anshul
name: Benedict, Shajulin
name: Chadha, Mohak
name: Gerndt, Michael
Publisher: name: arXiv
Year: 2022
Subjects: subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: FOS: Computer and information sciences

description: In the recent past, characterizing workloads has been attempted to gain a foothold in the emerging serverless cloud market, especially in the large production cloud clusters of Google, AWS, and so forth. While analyzing and characterizing real workloads from a large production cloud cluster benefits cloud providers, researchers, and daily users, analyzing the workload traces of these clusters has been an arduous task due to the heterogeneous nature of data. This article proposes a scalable infrastructure based on Google's dataproc for analyzing the workload traces of cloud environments. We evaluated the functioning of the proposed infrastructure using the workload traces of Google cloud cluster-usage-traces-v3. We perform the workload characterization on this dataset, focusing on the heterogeneity of the workload, the variations in job durations, aspects of resources consumption, and the overall availability of resources provided by the cluster. The findings reported in the paper will be beneficial for cloud infrastructure providers and users while managing the cloud computing resources, especially serverless platforms.
description: 9 pages, CLOSER 2022
Teacher as bricoleur: A grounded phenomenological case study of creativity in secondary school science education
Creators: name: Zipf, Reyna Karen
Publisher: name: CQUniversity
Year: 2024
Subjects: classificationCode: 390306
subject: Secondary education
classificationCode: 399999
subject: Other education not elsewhere classified
classificationCode: 390113
subject: Science, technology and engineering curriculum and pedagogy

description: This research investigated creativity in secondary school science education and identified the essences of pedagogical strategies that promote opportunities for secondary school students to engage in creative thinking in science. Science policy documents linked secondary school science with the development of student creativity. Indeed, science education literature was laden with the expectation to develop creativity and it was a recurring theme in science curriculum documents for secondary schools in Australia.Whilst science is implicitly understood to be a creative endeavour, and touted as a creative enterprise, it is doubtful whether secondary school science nurtures creativity. Research suggests students are turned off science by transmissive teaching and focus on canonical abstract content. Contemporary science teachers face conflicting demands to teach established scientific knowledge whilst representing science as practised by scientists. How to nurture student creativity is not explicit in science education literature. The research objective was to make explicit pedagogies secondary science teachers use to engage students in thinking creatively.A qualitative methodological approach was designed amalgamating grounded theory, phenomenology and case study to form a blended strategy, 'grounded, phenomenological case study', with which to explore creativity in secondary school science. A researcher-as-bricoleur stance was adopted to take advantage of serendipitous opportunities to further the research goals.The study found that these secondary science teachers drew on their pedagogical creativity and a bricoleur stance to enact creativity -focused science lessons. The teacher emphasis on the creative process rather than the end creative product provided opportunities for students to engage in creative thinking. The creative thinking process was characterised by spontaneity, difference, and both individual and collaborate input, risk, failure, fun, high quality questioning and had a natural energy sustained by student interest, ownership, and talk. The study also found there was no one-way to nurture creativity in school science. The notion of teacher-as-bricoleur was central to the enactment of opportunities for student creativity in secondary school science. The ability to recognise and take advantage of serendipitous opportunities to further student creativity was a key element, and dependent on teacher experience and teacher pedagogical creativity.
The most symmetric smooth cubic surface over a finite field of characteristic $2$
Creators: name: Vikulova, Anastasia V.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14J50

description: In this paper we find the largest automorphism group of a smooth cubic surface over any finite field of characteristic $2.$ We prove that if the order of the field is a power of $4,$ then the automorphism group of maximal order of~a~smooth cubic surface over this field is $\mathrm{PSU}_4(\mathbb{F}_2).$ If the order of the field of characteristic $2$ is not a power of $4,$ then we prove that the automorphism group of maximal order of a smooth cubic surface over this field is the symmetric group of degree $6.$ Moreover, we prove that smooth cubic surfaces with such properties are unique up to isomorphism.
Quantum Liquid in Lower Dimensions: From the perspective of Surface Tension
Creators: name: Adusumalli, Sri Satwika
name: Senapati, Kathaa
name: Singh, Shivam
name: Khan, Ayan
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: We analyze the surface tension in ultra-cold atomic gases in a quasi one-dimensional and one-dimensional geometry. In recent years, experimental observations have confirmed the ``clustering of atoms" to form droplets in ultra-cold atomic gases and the emergence of this new phase is attributed to the beyond mean-field interaction. However, two decades earlier, liquid formation was predicted due to the competition of two-body and three-body interactions. Here, we review both propositions and comment on the role of beyond mean-field and three-body interaction in liquid formation by calculating the surface tension.
description: 11 pages, 9 figures; To be published in Physics Letters A
From the origin of life to pandemics: Emergent phenomena in complex systems
Creators: name: Artime, Oriol
name: De Domenico, Manlio
Publisher: name: arXiv
Year: 2022
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: When a large number of similar entities interact among each other and with their environment at a low scale, unexpected outcomes at higher spatio-temporal scales might spontaneously arise. This nontrivial phenomenon, known as emergence, characterizes a broad range of distinct complex systems -- from physical to biological and social ones -- and is often related to collective behavior. It is ubiquitous, from non-living entities such as oscillators that under specific conditions synchronize, to living ones, such as birds flocking or fish schooling. Despite the ample phenomenological evidence of the existence of systems' emergent properties, central theoretical questions to the study of emergence remain still unanswered, such as the lack of a widely accepted, rigorous definition of the phenomenon or the identification of the essential physical conditions that favour emergence. We offer here a general overview of the phenomenon of emergence and sketch current and future challenges on the topic. Our short review also serves as an introduction to the Theme Issue "Emergent phenomena in complex physical and socio-technical systems: from cells to societies", where we provide a synthesis of the contents tackled in the Issue and outline how they relate to these challenges, spanning from current advances in our understanding on the origin of life to the large-scale propagation of infectious diseases.
description: 20 pages, 1 figure
A Short Proof of Bose-Einstein Condensation in the Gross-Pitaevskii Regime and Beyond
Creators: name: Brennecke, Christian
name: Brooks, Morris
name: Caraci, Cristina
name: Oldenburg, Jakob
Publisher: name: arXiv
Year: 2024
Subjects: subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We consider dilute Bose gases on the three dimensional unit torus that interact through a pair potential with scattering length of order $ N^{κ-1}$, for some $κ>0$. For the range $ κ\in [0, \frac1{43})$, \cite{ABS} proves complete BEC of low energy states into the zero momentum mode based on a unitary renormalization through operator exponentials that are quartic in creation and annihilation operators. In this paper, we give a new and self-contained proof of BEC of the ground state for $ κ\in [0, \frac1{20})$ by combining some of the key ideas of \cite{ABS} with the novel diagonalization approach introduced recently in \cite{Br}, which is based on the Schur complement formula. In particular, our proof avoids the use of operator exponentials and is significantly simpler than \cite{ABS}.
description: 13 pages + one appendix; accepted journal version
Supplementary document for Visual Intertial odometry enabled 3D Ultrasound and Photoacoustic imaging. - 6397124.pdf
Creators: name: Sankepalle, Deeksha
name: Anthony, Brian
name: Mallidi, Srivalleesha
Publisher: name: Optica Publishing Group
Year: 2023
Subjects: Biomedical Engineering not elsewhere classified

description: Supplementary Data
A model approach for detecting wild animals through blood fed mosquitoes in India: scope in indirect wildlife sampling and wildlife forensics
Creators: name: Vipin Sharma
name: Sharma, Vinita
name: Kumar, Mukesh
Publisher: name: F1000Research
Year: 2016

description: In this study we detected the wild animals through blood fed female mosquitoes collected in a controlled environment i.e. a zoological park situated at Dehradun, India and explained its scope in indirect wild animal sampling in fields and in wildlife forensics. The eighteen blood-fed mosquitoes were collected from Malsi Deer Park, Dehradun on a single day and DNA was isolated from the individual blood filled midgut of the mosquitoes. The three mitochondrial genes (Cytochrome b, 16S rRNA and 12S rRNA) were amplified on the DNAs from the blood collected from each mosquito. After DNA sequencing the seven animal species were detected from eighteen blood samples representing mainly the mammals and birds. The two species detected were not present in the zoological park, hence, it validates this approach and proves that it can be applied in fields. The approach is novel in a way that it is non-invasive in nature and has implications in detecting the wild animals indirectly and in wildlife forensics.
ORNA: A set-multicover based in-silico read normalization for RNA-seq data
Creators: name: Durai, Dilip Ariyur
name: Schulz, Marcel H
Publisher: name: F1000Research
Year: 2016

description: Rapid development in the field of high throughput sequencing (HTS) has led to massive amount of data being generated. However assembling such a huge amounts of data requires a high amount of memory and runtime. Studies have shown that much of the high-coverage data is redundant and could be removed without affecting the quality of the final assembly. But, to determining which reads to eliminate without the presence of a reference genome is a major task. Here we pose this problem as a set multicover problem. We consider the reads as a set of k-mers and the set of all possible k-mers makes the universe. We propose an algorithm to find the minimum number of reads whose union equals the universe and each k-mer in the universe is present at least a certain number of times. We tested the algorithm on datasets which vary in read length and coverage and compute the efficiency using the reduced datasets in a de novo transcriptome assembler. We found that we are able to achieve a significant reduction without losing out on important read information as evident from the minimum loss of the assembly quality.
T- and B-cell receptor repertoire sequencing: quality control and clone identification
Creators: name: Schaik, Barbera DC Van
name: Klarenbeek, Paul L
name: Doorenspleet, Marieke E
name: Pollastro, Sabrina
name: Musters, Anne
name: Balzaretti, Giulia
name: Esveldt, Rebecca E
name: Baas, Frank
name: Vries, Niek De
name: Kampen, Antoine HC Van
Publisher: name: F1000Research
Year: 2016

description: Next-generation sequencing (NGS) of T- and B-cell receptor repertoires recently became available as a powerful new research tool in immunology research. Applications include infectious diseases, auto immunity and fundamental research. This technique requires both elaborate wet-lab protocols and bioinformatics pipelines to analyze data. In contrast to other NGS applications the field has not yet settled on uniform techniques, quality control, nomenclature and thresholds. Common standard might provide a great step forward. Description of current protocols might fuel exchange of ideas and aid in establishing consensus.

Here we describe our workflow which is tailored to process many clinical samples at once. We will discuss identification of clones from NGS data and propose methods for quality assessment and bias correction. We will demonstrate how a wrong gene assignment has an effect on the clone frequency and how this can be corrected. Furthermore we will discuss an alternative way for the detection of the complementary determining region 3. Additionally, we will propose repertoire specific quality measures that can be  integrated into a repertoire data analysis workflow. Finally, we will show a method for identification of sample contamination.
Observing the quantum Mpemba effect in quantum simulations
Creators: name: Joshi, Lata Kh
name: Franke, Johannes
name: Rath, Aniket
name: Ares, Filiberto
name: Murciano, Sara
name: Kranzl, Florian
name: Blatt, Rainer
name: Zoller, Peter
name: Vermersch, Benoît
name: Calabrese, Pasquale
name: Roos, Christian F.
name: Joshi, Manoj K.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Quantum Physics (quant-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: The non-equilibrium physics of many-body quantum systems harbors various unconventional phenomena. In this study, we experimentally investigate one of the most puzzling of these phenomena -- the quantum Mpemba effect, where a tilted ferromagnet restores its symmetry more rapidly when it is farther from the symmetric state compared to when it is closer. We present the first experimental evidence of the occurrence of this effect in a trapped-ion quantum simulator. The symmetry breaking and restoration are monitored through entanglement asymmetry, probed via randomized measurements, and postprocessed using the classical shadows technique. Our findings are further substantiated by measuring the Frobenius distance between the experimental state and the stationary thermal symmetric theoretical state, offering direct evidence of subsystem thermalization.
description: 11 pages, 7 figures. Published version
Using Docker compose for the simple deployment of an integrated high-throughput screening platform
Creators: name: List, Markus
Publisher: name: F1000Research
Year: 2016

description: Dealing with massive amounts of biological data is unthinkable without state-of-the-art tools. Over time, these applications have become increasingly complex and can often only be used when a long list of preconditions are met. There are serious issues with the installation and maintenance of tools due to version conflicts, outdated repositories and poor documentation. Moreover, complex tasks require integrating several tools into a workflow. Open platforms like Galaxy and Taverna have emerged to simplify building and operating such workflows. Nevertheless, ensuring the fulfillment of all preconditions remains a critical issue.

A solution to encapsulate a tool with its dependencies in container images is Docker. An extension, called Docker compose, further facilitates interaction of several containers in a coherent software configuration. Here, we demonstrate the power of this approach by creating and deploying an integrated high-throughput screening (HTS) platform through Docker compose, which comprises systems for laboratory information management, HTS sample and plate management, HTS data analysis, systems biology analysis, and reverse-phase-protein array data management/analysis, as well as service containers for relational database management, load balancing and for a key-value store.

Docker is a promising solution to fully address issues in deploying scientific software even in cases where several tools need to be integrated. In addition, Docker compose allows, for instance, to deploy a complex HTS platform in a single command. We expect that the use of Docker in cases like this will enable the more widespread use of scientific software and free up time spent on dealing with software dependencies.
SparseLNR: Accelerating Sparse Tensor Computations Using Loop Nest Restructuring
Creators: name: Dias, Adhitha
name: Sundararajah, Kirshanthan
name: Saumya, Charitha
name: Kulkarni, Milind
Publisher: name: arXiv
Year: 2022
Subjects: subject: Programming Languages (cs.PL)
subject: Performance (cs.PF)
subject: FOS: Computer and information sciences

description: Sparse tensor algebra computations have become important in many real-world applications like machine learning, scientific simulations, and data mining. Hence, automated code generation and performance optimizations for tensor algebra kernels are paramount. Recent advancements such as the Tensor Algebra Compiler (TACO) greatly generalize and automate the code generation for tensor algebra expressions. However, the code generated by TACO for many important tensor computations remains suboptimal due to the absence of a scheduling directive to support transformations such as distribution/fusion. This paper extends TACO's scheduling space to support kernel distribution/loop fusion in order to reduce asymptotic time complexity and improve locality of complex tensor algebra computations. We develop an intermediate representation (IR) for tensor operations called branched iteration graph which specifies breakdown of the computation into smaller ones (kernel distribution) and then fuse (loop fusion) outermost dimensions of the loop nests, while the innermost dimensions are distributed, to increase data locality. We describe exchanges of intermediate results between space iteration spaces, transformation in the IR, and its programmatic invocation. Finally, we show that the transformation can be used to optimize sparse tensor kernels. Our results show that this new transformation significantly improves the performance of several real-world tensor algebra computations compared to TACO-generated code.
description: Accepted at International Conference on Supercomputing (ICS) '22
Trans-Planckian Philosophy of Cosmology
Creators: name: Schneider, Mike D.
Publisher: name: arXiv
Year: 2022
Subjects: subject: History and Philosophy of Physics (physics.hist-ph)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: I provide some philosophical groundwork for the recently proposed 'trans-Planckian censorship' conjecture in theoretical physics. In particular, I argue that structure formation in early universe cosmology is, at least as we typically understand it, autonomous with regards to quantum gravity, the high energy physics that governs the Planck regime in our universe. Trans-Planckian censorship is then seen as a means of rendering this autonomy an empirical constraint within ongoing quantum gravity research.
Antimicrobial peptides mechanisms of membrane lysis and permeation by computer simulations
Creators: name: Balatti, Galo Ezequiel
name: Martini, María Florencia
name: Pickholz, Mónica Andrea
Publisher: name: F1000Research
Year: 2016

description: Antimicrobial peptides (AMPs) are part of the innate immune system, attaching and inserting to the lipidic membranes of external agents among bacteria, fungi, viruses and eukaryotic parasites and killing the cells through a membrane permeation effect. Nevertheles, their molecular mechanisms are not well-known and three different leakage pathways was proposed: the “barrel-stave”, the “carpet” or the “toroidal-pore” models. Among AMPs, two peptides obtained from Australian tree frogs, the Aurein 1.2 and the Maculatin 1.2 are proposed as AMPs with different leakage pathways. Here, we carried out extensive Molecular Dynamics (MD) simulations to study the peptide interactions with lipid structures in order to shed light into these mechanisms.. We have used a coarse grain (CG) model within the MARTINI force field. Three simulation replicates were performed, looking to the self-assembly of 1000 lipids (2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine, POPC) in the presence of the peptides were performed. Furthermore, we simulate both peptides in a presence of a pre-equilibrated bilayer from two different initial configurations: aqueous phase and inside the bilayer. The simulations results showed two different pathways on the membrane leakage, in good agreement with experimental observations. While Maculatin can form a pore maintaining the structure of the bilayer, Aurein causes the total membrane destabilization and disintegration. A better understanding of AMPs molecular behavior can aim the development of new antimicrobials drugs.
Formation of millisecond pulsars with wide orbits
Creators: name: Wang, Bo
name: Liu, Dongdong
name: Guo, Yunlang
name: Chen, Hailiang
name: Tang, Wenshi
name: Li, Luhan
name: Han, Zhanwen
Publisher: name: arXiv
Year: 2024
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Millisecond pulsars (MSPs) are a kind of radio pulsars with short spin periods, playing a key role in many aspects of stellar astrophysics. In recent years, some more MSPs with wide orbits ($>30\,\rm d$) have been discovered, but their origin is still highly unclear. In the present work, according to an adiabatic power-law assumption for the mass-transfer process, we carried out a large number of complete binary evolution computations for the formation of MSPs with wide orbits through the iron core-collapse supernova (CCSN) channel, in which a neutron star (NS) originating from a CCSN accretes matter from a red-giant (RG) star and spun up to millisecond periods. We found that this channel can form the observed MSPs with wide orbits in the range of $30-1200\,{\rm d}$, in which the WD companions have masses in the range of $0.28-0.55\,\rm M_{\odot}$. We also found that almost all the observed MSPs can be reproduced by this channel in the WD companion mass versus orbital period diagram. We estimate that the Galactic numbers of the resulting MSPs from the CCSN channel are in the range of $\sim 4.8-8.5\times10^{5}$. Compared with the accretion-induced collapse channel, the CCSN channel provides a main way to produce MSPs with wide orbits.
description: 19 pages, 8 figures, 3 tables. Accepted for publication in MNRAS
title: Plan: Woodlands Development Corporation, "Development Plan: Exhibit G," undated
Creators: name: Woodlands Development Corporation
Publisher: name: George Mason University
Year: 2007
Subjects: subject: New communities

description: Textual: Plan, copy; 11” x 8.5” (27.9 cm x 21.6 cm)
description: Development Plan from Woodlands Development Corporation entitled "Development Plan: Exhibit G" that is undated. This development plan details the development of Woodlands, Texas, a new community development outside Houston, Texas. This community was started in 1974 and was aided by the federal guarantees program created by the 1974 Housing and Urban Development Act. The first three pages of the plan are given here. Planned Community Archives Collection, 641.01
A Novel Prompt-tuning Method: Incorporating Scenario-specific Concepts into a Verbalizer
Creators: name: Ma, Yong
name: Luo, Senlin
name: Shang, Yu-Ming
name: Li, Zhengjun
name: Liu, Yong
Publisher: name: arXiv
Year: 2024
Subjects: subject: Computation and Language (cs.CL)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: The verbalizer, which serves to map label words to class labels, is an essential component of prompt-tuning. In this paper, we present a novel approach to constructing verbalizers. While existing methods for verbalizer construction mainly rely on augmenting and refining sets of synonyms or related words based on class names, this paradigm suffers from a narrow perspective and lack of abstraction, resulting in limited coverage and high bias in the label-word space. To address this issue, we propose a label-word construction process that incorporates scenario-specific concepts. Specifically, we extract rich concepts from task-specific scenarios as label-word candidates and then develop a novel cascade calibration module to refine the candidates into a set of label words for each class. We evaluate the effectiveness of our proposed approach through extensive experiments on {five} widely used datasets for zero-shot text classification. The results demonstrate that our method outperforms existing methods and achieves state-of-the-art results.
New in silico approach to assess RNA secondary structures with non-canonical base pairs
Creators: name: Szóstak, Natalia
name: Rybarczyk, Agnieszka
name: Antczak, Maciej
name: Żok, Tomasz
name: Popenda, Mariusz
name: Adamiak, Ryszard
name: Błażewicz, Jacek
name: Szachniuk, Marta
Publisher: name: F1000Research
Year: 2016

description: The remarkable RNA molecules properties and diversity allow them to play important roles in the cellular processes. They can act not only as carriers of genetic information but also participate in the regulation of gene expressions and serve as catalysts in many biological pathways. The function of RNA is strongly dependent on its structure, therefore an appropriate recognition of this structure, on every level of organization, is crucial. One particular concern is the assessment of base-base interactions, described as the secondary structure. It greatly facilitates an interpretation of RNA function and allows for structure analysis on the tertiary level. Computational approaches consider mostly Watson-Crick and wobble base pairs. Handling of non-canonical interactions, important for a full description of RNA structure, is still a challenge.

Here we present a novel two-step in silico approach to asses RNA secondary structures with non-canonical base pairs. The knowledge of extended secondary structure can accelerate an advancement of the 3D RNA module concept and improve the module identification and search within available structures. It can also be useful in supporting new solutions to RNA motif discovery problems. Its first application to our on-going analysis of the mechanism of spontaneous degradation of RNA molecules showed improvement in accuracy of prediction of RNA degradants.

We believe that our work concerning the recognition of non-canonical interactions in RNA structures will be influential not only for the scientific community but also for clinical and pharmaceutical industry that take into consideration the RNA molecules.
title: Newspaper Column: Thoburn's Martyrdom
Creators: name: Nicoson, William J.
Publisher: name: The Reston Times
Year: 2001
Subjects: subject: Reston (Va.)
subject: Thoburn, John
subject: Fairfax County (VA)

description: PDF file distilled from original WordPerfect document. Original size 11" x 8.5".
description: His fellow inmates call him “Shrub.” John Thoburn’s failure to plant shrubs and trees at his driving range in the number and locations specified by Fairfax County has landed him in jail for contempt of court
Inspecting Energy Realising Pathways by a combination of genomics data and mechanistic approach
Creators: name: Follia, Laura
name: Ferrero, Giulio
name: Totis, Niccolò
name: Riganti, Chiara
name: Novelli, Francesco
name: Balbo, Gianfranco
name: Beccuti, Marco
name: Cordero, Francesca
Publisher: name: F1000Research
Year: 2016

description: In systems biology a great effort is devoted to study the aberrant signalling pathways involved in cancer progression and in cancer metabolism. In Pancreatic Ductal AdenoCarcinoma (PDAC) the protein Alpha-Enolase plays a key role in its metabolism: it is generally overexpressed and it is associated with tumour progression through the Warburg effect.

We started from a functional characterization of Alpha-Enolase investigating its role in Energy Realising Pathways (ERP) in PDAC cells using the mechanistic version of the metabolic model. To perform kinetic simulations it is necessary to determine all the kinetic parameters. Unfortunately, because of economical and technical reasons only few of them are well characterized.

As next step we will enrich the ERP model with the integration of genomic data characterizing PDAC patients.
Optics-assisted enhanced sensing at radio-frequencies in an optoelectromechanical system
Creators: name: Eshaqi-Sani, Najmeh
name: Zippilli, Stefano
name: Vitali, David
Publisher: name: arXiv
Year: 2024
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We investigate a scheme to enhance the sensitivity in detecting weak variations in a parameter of an optoelectromechanical system by detecting the system response at radio frequencies. We consider a setup, where either one or two mechanical modes mediate the interaction between an optical cavity and an rf resonator. This system can be operated in a regime of impedance matching where thermal fluctuations are redistributed among the system elements, and, in particular, rf output noise can be reduced to the quantum vacuum noise level. We show that this effect can be used to boost the sensitivity in detecting parameter variations also in regimes of high thermal noise. We characterize the performance of this protocol in detecting variations in the capacitance of the rf resonator.
description: 15 pages, 11 figures
Detecting Dark Matter Substructures on Small Scales with Fast Radio Bursts
Creators: name: Xiao, Huangyu
name: Dai, Liang
name: McQuinn, Matthew
Publisher: name: arXiv
Year: 2024
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We propose measuring the arrival time difference of Fast Radio Bursts (FRBs) along two adjacent sightlines as a new probe to dark matter substructures on scales down to $\sim 1\,$AU. We discuss two observational scenarios in which it may be possible to place interesting constraints on such models through monitoring repeating FRB sources: 1) By sending radio receivers to space to form a baseline of tens of AU or more and measuring the temporal variation of the arrival time difference between receivers. 2) By measuring the temporal variation of the arrival time difference between two lensed images of one strongly lensed repeater. In both scenarios, obtaining interesting constraints requires correlating the voltage time series to measure the radio-signal arrival time to sub-nanosecond precision. We find that two radio dishes separated by $20\,$AU may be sensitive to the enhancement of small-scale structures at $\sim 10^{-8}M_\odot$ masses in the QCD axion dark matter scenario or from an early epoch of matter-domination with a reheating temperature up to 60 MeV. Other dark matter models such as those composed of $\sim 10^{-13}M_{\odot}$ primordial black holes produced during inflation would also be probed by this method. We further show that a strong lensing situation of multiple images provides an equivalent $\sim 2000\,$AU baseline, which can be much more sensitive but with the uncertainty that intervening ISM decoherence may degrade the timing precision and that spatial variation in the FRB emission spot may result in confounding signals. We show that the lensing magnifications of Type Ia supernovea constrain a similar quantity to such FRB timing, with present limits being equivalent to ruling out the same parameter space that would be probed by a $0.14~$AU baseline.
description: 26 pages, 7 figures; matches published version
FAIR: Functional Analysis at Isoform Resolution by using long read technologies
Creators: name: Fuente, Lorena De La
name: Tardaguila, Manuel
name: Risco, Hector Del
name: Martí, Cristina
name: Pereira, Cecile
name: Rodríguez-Navarro, Susana
name: Macchietto, Marisa
name: Mortazavi, Ali
name: Moreno, Victoria
name: Conesa, Ana
Publisher: name: F1000Research
Year: 2016

description: Based on the claimed role transcript variants in conferring functional meaning and the lack of methods to study the functional implications of alternative splicing (AS) and alternative polyadenylation (APA), we have developed a new methodology called FAIR. This methodology will let to address the functional profiling of transcript and protein isoforms at a genome-wide level by using long-reads technologies. Moreover, we have implemented it in a software called Transcript2GO.
Therefore, using PacBio and Illumina data, FAIR can generate functional hypothesis about the role of alternative isoforms in our system. First, FAIR allows the functional annotation of each PacBio-resolved isoform which involves the ORF prediction and the annotation of several functional layers: miRNA binding sites, PFAM domains, post-translational modifications, UTR motifs, NMD prediction, repetitive elements, etc. Finally, it applies different statistical methods which combine both expression data and functional annotation over each PacBio-resolved isoform. Among the several included statistical methods, we can highlight the Feature Differential Splicing which is able to point out functional elements affected by AS/APA.

Using our rich annotation pipeline over a neural differentiation system, we found that nearly all genes expressing several isoforms have them annotated with at least one differential functional label, suggesting that functional profiling at isoform resolution is meaningful. We identified several functions enriched in genes regulated by differential splicing, as well as specific features as miRNAs regulated by AS/APA across conditions. Other functional insights of the relationship between function and differential splicing are easily revealed by the tools implemented in Transcript2GO.
BETA: Binarized Energy-Efficient Transformer Accelerator at the Edge
Creators: name: Ji, Yuhao
name: Fang, Chao
name: Wang, Zhongfeng
Publisher: name: arXiv
Year: 2024
Subjects: subject: Hardware Architecture (cs.AR)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: Existing binary Transformers are promising in edge deployment due to their compact model size, low computational complexity, and considerable inference accuracy. However, deploying binary Transformers faces challenges on prior processors due to inefficient execution of quantized matrix multiplication (QMM) and the energy consumption overhead caused by multi-precision activations. To tackle the challenges above, we first develop a computation flow abstraction method for binary Transformers to improve QMM execution efficiency by optimizing the computation order. Furthermore, a binarized energy-efficient Transformer accelerator, namely BETA, is proposed to boost the efficient deployment at the edge. Notably, BETA features a configurable QMM engine, accommodating diverse activation precisions of binary Transformers and offering high-parallelism and high-speed for QMMs with impressive energy efficiency. Experimental results evaluated on ZCU102 FPGA show BETA achieves an average energy efficiency of 174 GOPS/W, which is 1.76~21.92x higher than prior FPGA-based accelerators, showing BETA's good potential for edge Transformer acceleration.
description: This paper is accepted by 2024 IEEE International Symposium on Circuits and Systems (ISCAS 2024)
Mutational signatures of DNA repair deficiencies and cytotoxin exposures in C. elegans
Creators: name: Volkova, Nadezda
name: Meier, Bettina
name: Huici, Victor Gonzalez
name: Bertonlini, Simone
name: Campbell, Peter
name: Gartner, Anton
name: Gerstung, Moritz
Publisher: name: F1000Research
Year: 2016

description: Cancer is caused by alterations in the genome. These alterations can be an effect of combination of environmental factors damaging DNA and deficiencies in DNA repair and replication leading to characteristic mutational spectra.

Mutational signatures (Alexandrov et al. 2013) became a very useful tool of cancer investigation in the last years. However, the signatures identified so far mostly represent complex conglomerates of the action of different mutational processes. For many signatures, the link with the underlying mutational processes is still unclear.

In this study we used C. elegans as a model organism to present a systematic screen with 9 types of genotoxins under 58 different genetic conditions including single and double knock-outs of DNA repair associated genes. Upon exposure over several generations we used whole-genome sequencing to study patterns of DNA damage.

We studied the mutational spectra by analysing different types of genetic lesions including point mutations, indels and structural variants using rigorous quality control procedure. This approach allows us to dissect the precise individual contributions of each factor using zero-inflated negative binomial additive models, and also identify significant genetic and gene-mutagen interactions such as 3-fold increase in mutational burden for pms-2/pole-4 double knock-out and mutational spectra expansion for DMS exposure in polk-1 mutants. In summary, this analysis presents the first systematic catalogue of mutational signatures caused by genotoxins and DNA repair deficiencies.