cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Manuscript for paper or report on theory advances/test on diagonalization of operator through coordinate transformation (release 2)
Creators: name: Grillo, Vincenzo
name: Troiani, Filippo
name: Rotunno, Enzo
name: Padgett, Miles
name: Stellinga, Daan
name: Karimi, Ebrahim
name: Selyem, Adam
name: Toninelli, Ermes
name: Frabboni, Stefano
name: Leuchs, Gerd
name: Banzer, Peter
Publisher: name: Zenodo
Year: 2020
Subjects: Q-sort

description: The present deliverable D3.2, “Manuscript for Paper or Report on Theory Advances/Test on
 Diagonalization of Operator through Coordinate Transformation (release 2)“ is used to conclude and
 refine the topics identified in the previous release of the same deliverable.
 It lays the appropriate theoretical basis for the definition of a generalized sorter that would allow for the
 recognition of the protein without making a full image it.
 We called this process diagonalization, since the image of the protein should result in an abstract set
 of pixels, like a diagonal matrix.
 The results described in this deliverable are of the utmost importance in view of the final experiments
 of reconstruction of the proteins as foreseen in WP5.Thisproblem is very difficult to tackle for proteins
 that typically produce a small phase change.
High Lifetime Pregnancy and Low Contraceptive Usage Among Sex Workers Who Use Drugs- An Unmet Reproductive Health Need
Creators: name: Duff, Putu
name: Shoveller, Jean
name: Zhang, Ruth
name: Alexson, Debbie
name: Montaner, Julio
name: Shannon, K.
Publisher: name: BioMed Central
Year: 2016

description: Background: The objective of this study was to describe levels of pregnancy and contraceptive usage among a cohort of street-based female sex workers (FSWs) in Vancouver. Methods: The study sample was obtained from a community-based prospective cohort study (2006-2008) of 211 women in street-based sex work who use drugs, 176 of whom had reported at least one prior pregnancy. Descriptive statistics were used to estimate lifetime pregnancy prevalence, pregnancy outcomes (miscarriage, abortion, adoption, child apprehension, child custody), and contraceptive usage. In secondary analyses, associations between contraceptive usage, individual and interpersonal risk factors and high number of lifetime pregnancies (defined as greater than the sample mean of 4) were examined. Results: Among our sample, 84% reported a prior pregnancy, with a mean of 4 lifetime pregnancies (median = 3; IQR: 2-5). The median age of women reporting 5+ pregnancies was 38 years old [interquartile range (IQR): 25.0-39.0] compared to 34 years [IQR: 25.0-39.0] among women reporting 4 or fewer prior pregnancies. 45% were Caucasian and 47% were of Aboriginal ancestry. We observed high rates of previous abortion (median = 1;IQR:1-3), apprehension (median = 2; IQR:1-4) and adoption (median = 1; IQR:1-2) among FSWs who reported prior pregnancy. The use of hormonal and insertive contraceptives was limited. In bivariate analysis, tubal ligation (OR = 2.49; [95%CI = 1.14-5.45]), and permanent contraceptives (e.g., tubal ligation and hysterectomy) (OR = 2.76; [95%CI = 1.36-5.59]) were both significantly associated with having five or more pregnancies. Conclusion: These findings demonstrate high levels of unwanted pregnancy in the context of low utilization of effective contraceptives and suggest a need to improve the accessibility and utilization of reproductive health services, including family planning, which are appropriately targeted and tailored for FSWs in Vancouver.
DISINFORMATION NARRATIVES OF HATE AS A TOOL OF ESCALATING RUSSIA’S WAR AGAINST UKRAINE (BASED ON STOPFAKE FACT-CHECKING PROJECT MATERIALS)
Creators: name: Romaniuk, Viktoriia
Publisher: name: The Estonian Journal of Military Studies
Year: 2024

description: Since 2014, Russian propaganda has been aggressively using narratives of
hate as a tool to deprive Ukrainians of their human qualities, denying their right
to self determination and sovereignty. Following the Soviet tradition of discrediting
Ukrainian culture and history, Russian propaganda is trying to create an image of
Ukraine as a global evil to justify the war and killings of Ukrainians.
Based on the archives of StopFake, a Ukrainian fact checking organization, this ar
ticle analyses Russian disinformation narratives intended to dehumanise Ukrainians.
The article illustrates this narrative framework analysis through cases spotted
and debunked by Ukrainian fact checkers during the period of 2014–2022. As well
as dehumanising Ukrainians, we also examined how Russian disinformation has
manipulated and distorted the concepts of fascism and genocide to form a negative
image of Ukrainians and justify a war of aggression as a ‘humanitarian inter vention’.
The report also examines the key arguments of Russian disinformation used to
intimidate the audience. Among the main theoretical concepts we refer to in this
research are dehumanisation and genocide.
description: The Estonian Journal of Military Studies, No. 23 (2023)
Mice lacking caspase-2 are protected from behavioral changes, but not pathology, in the YAC128 model of Huntington disease
Creators: name: Carroll, Jeffrey B.
name: Southwell, Amber L.
name: Graham, Rona K.
name: Lerch, Jason P.
name: Ehrnhoefer, Dagmar E.
name: Cao, Li-Ping
name: Zhang, Wei-Ning
name: Deng, Yu
name: Bissada, Nagat
name: Henkelman, R. Mark
name: Hayden, Michael R.
Publisher: name: BioMed Central
Year: 2015

description: Background: Huntington Disease (HD) is a neurodegenerative disorder in which caspase activation and cleavage of substrates, including the huntingtin protein, has been invoked as a pathological mechanism. Specific changes in caspase-2 (casp2) activity have been suggested to contribute to the pathogenesis of HD, however unique casp2 cleavage substrates have remained elusive. We thus utilized mice completely lacking casp2 (casp2-/-) to examine the role played by casp2 in the progression of HD. This 'substrate agnostic' approach allows us to query the effect of casp2 on HD progression without pre-defining proteolytic substrates of interest. Results YAC128 HD model mice lacking casp2 show protection from well-validated motor and cognitive features of HD, including performance on rotarod, swimming T-maze, pre-pulse inhibition, spontaneous alternation and locomotor tasks. However, the specific pathological features of the YAC128 mice including striatal volume loss and testicular degeneration are unaltered in mice lacking casp2. The application of high-resolution magnetic resonance imaging (MRI) techniques validates specific neuropathology in the YAC128 mice that is not altered by ablation of casp2. Conclusions The rescue of behavioral phenotypes in the absence of pathological improvement suggests that different pathways may be operative in the dysfunction of neural circuitry in HD leading to behavioral changes compared to the processes leading to cell death and volume loss. Inhibition of caspase-2 activity may be associated with symptomatic improvement in HD.
SparCAssist: A Model Risk Assessment Assistant Based on Sparse Generated Counterfactuals
Creators: name: Zhang, Zijian
name: Setty, Vinay
name: Anand, Avishek
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computation and Language (cs.CL)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences
subject: I.2.m

description: We introduce SparcAssist, a general-purpose risk assessment tool for the machine learning models trained for language tasks. It evaluates models' risk by inspecting their behavior on counterfactuals, namely out-of-distribution instances generated based on the given data instance. The counterfactuals are generated by replacing tokens in rational subsequences identified by ExPred, while the replacements are retrieved using HotFlip or Masked-Language-Model-based algorithms. The main purpose of our system is to help the human annotators to assess the model's risk on deployment. The counterfactual instances generated during the assessment are the by-product and can be used to train more robust NLP models in the future.
description: 5 pages, 2 figures, submitted and accepted as a demo paper in SIGIR2022
NATIONALIST SAKHA WARRIORS FOR THE KREMLIN THE CASE OF YS TYMSY
Creators: name: Ventsel, Aimar
Publisher: name: The Estonian Journal of Military Studies
Year: 2024

description: Since the start of the full scale war between Ukraine and Russia, both
commentators and people who follow the war have paradoxically increasingly
acknowledged the multicultural nature of Russian society. There are two non Russian
ethnic groups who are associated with the ongoing war more than others: Chechens
and Buryats. Nevertheless, with approximately 200 ethnic groups, members from
more or less each one are represented in the Russian armed forces. There is the
popular assumption that most non Russians in Russia oppose the war, oppose the
Kremlin and are potential separatists. This chapter demonstrates that nothing can
be further from the truth. This is a presentation of the analysis of Ys Tymsy, a Sakha
pro Kremlin nationalist popular male movement. The movement is anti immigrant,
conservative, anti Western and homophobic. This ideology helps to find common
ground in the Kremlin’s anti Western conservative world view. Moreover, the con
cept of masculinity in the movement is rooted in a perception of the mythical Sakha
warrior. This makes all members of Ys Tymsy supporters of Putin’s war to the extent
that young Sakha men join the Russian army voluntarily.
description: The Estonian Journal of Military Studies, No. 23 (2023)
TANKS IN THE RUSSO-UKRAINIAN WAR
Creators: name: Paier, Anton
Publisher: name: The Estonian Journal of Military Studies
Year: 2024

description: The Russo Ukrainian war, after the initial Russian advance following the
invasion in February 2022, has turned into a stalemate characterised by grinding
trench and urban warfare which in some instances has been compared to WWI.
Despite the relative absence of fluid operations by massed mechanised formations,
armoured vehicles and tanks in particular have been intensely employed by both
opponents, resulting in heavy losses. When properly used in combination with other
arms, tanks have been a key factor on the battlefield. During the first year of hostili
ties the Russian army often suffered from a tactical mishandling of their armoured
units, leading to disproportionate losses of tanks and other AFVs compared to their
opponent. The great majority of the tanks employed in Ukraine so far are upgraded
late Cold War models, even if deliveries by NATO countries have introduced modern
Western models into the Ukrainian arsenal. The aim of this article is to give a sum
mary of the key characteristics of the main MBTs employed in Ukraine and to pro
vide a brief analysis of their role and impact.
description: The Estonian Journal of Military Studies, No. 23 (2023)
Liver Regeneration Associated Protein (ALR) Exhibits Antimetastatic Potential in Hepatocellular Carcinoma
Creators: name: Dayoub, Rania
name: Wagner, Hannah
name: Bataille, Frauke
name: Stöltzing, Oliver
name: Spruss, Thilo
name: Buechler, Christa
name: Schlitt, Hans-Jürgen
name: Weiss, Thomas S.
Publisher: name: Universität Regensburg
Year: 2010
Subjects: subject: Liver Regeneration HepG2 Cells MMP-9 mRNA Expression Atypical Mitotic Figures Angioinvasion
subject: 610 Medizin

description: Abstract

Augmenter of liver regeneration (ALR), which is critically important in liver regeneration and hepatocyte proliferation, is highly expressed in cirrhotic livers and hepatocellular carcinomas (HCC). In the current study, the functional role of ALR in hepatocancerogenesis was analyzed in more detail. HepG2 cells, in which the cytosolic 15 kDa ALR isoform was reexpressed stably, (HepG2-ALR) were used in migration and invasion assays using modified Boyden chambers. Epithelial-mesenchymal transition (EMT) markers were determined in HepG2-ALR cells in vitro and in HepG2-ALR tumors grown in nude mice. ALR protein was quantified in HCC and nontumorous tissues by immunohistochemistry. HepG2-ALR, compared with HepG2 cells, demonstrated reduced cell motility and increased expression of the epithelial cell markers E-cadherin and Zona occludens-1 (ZO-1), whereas SNAIL, a negative regulator of E-cadherin, was diminished. Matrix metalloproteinase MMP1 and MMP3 mRNA expression and activity were reduced. HepG2-ALR cell-derived subcutaneously grown tumors displayed fewer necrotic areas, more epithelial-like cell growth and fewer polymorphisms and atypical mitotic figures than tumors derived from HepG2 cells. Analysis of tumor tissues of 53 patients with HCC demonstrated an inverse correlation of ALR protein with histological angioinvasion and grading. The 15 kDa ALR isoform was found mainly in HCC tissues without histological angioinvasion 0. In summary the present data indicate that cytosolic ALR reduces hepatoma cell migration, augments epithelial growth and, therefore, may act as an antimetastatic and EMT reversing protein.
Physical and Circuit Compatible Modeling of VLSI Interconnects and Their Circuit Implications
Creators: name: Chen, Xinkang
Publisher: name: Purdue University Graduate School
Year: 2024
Subjects: classificationCode: 400802
subject: Electrical circuits and systems

description: Interconnects pose severe performance bottlenecks in advanced technology nodes due to multiple scaling challenges. To understand such problems and explore potential solutions, it is important to develop advanced models. This is particularly relevant for modern interconnects (especially vias) with complex structures with non- trivial current paths. In this dissertation, we develop a comprehensive physics-based interconnect models to capture surface and grain boundary scattering. We further analyze the circuit implications of 2D transition metal dichalcogenide (TMD)-augmented interconnects, which show potential in mitigating some of the scalability concerns of state-of-the-art interconnects. First, we propose a 2D spatially resolved model for surface scattering in rectangular interconnects based on the Fuchs-Sondheimer (FS) theory. The proposed spatially resolved FS (SRFS) model offers both spatial dependence and explicit relation of conductivity to physical parameters. We also couple the SRFS model with grain boundary scattering based on the Mayadas−Shatzkes (MS) theory. The SRFS-MS model is exact for diffusive surface scattering and offers a good approximation for elastic surface scattering. Furthermore, we develop a circuit-compatible version of the SRFS-MS model and show a close match with the physical SRFS-MS model (error < 0.7%). Moreover, we integrate temperature dependency, confirming that surface scattering has a negligible temperature-dependence. Second, we analyze the circuit implications of 2D TMD augmented interconnects and show the effective clock frequency of an AES circuit is boosted by 2%-32%. We also establish that the vertical resistivity of the TMD material must be below 22 kΩ-nm to obtain performance benefits over state-of-the-art interconnects in the worst-case process-temperature corner.
Liquid interface shaping and transport phenomena induced by spatially inhomogeneous vibrations
Creators: name: Apffel, Benjamin
name: Wilkinson, Christian
name: Fort, Emmanuel
Publisher: name: arXiv
Year: 2022
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: Vibrations can dynamically stabilize otherwise unstable liquid interfaces and produce new dynamic equilibria, called vibro-equilibria. Typically, the vibrations are homogeneous in the liquid and the liquid interface remains approximately flat. Here, we produce controlled vertical vibration gradients by taking advantage of the resonant oscillations of sinking submerged bubbles. The locally increased amplitude of the vibrations induces a local elevation of the liquid interface that can be controlled and engineered. The mean elevation of the interface can be linked theoretically with the local vibration amplitude by a simple formula that is tested experimentally. In addition, the transport of a floating body at the interface can be induced by secondary flows triggered by the amplitude gradients of the liquid vibrations.
A general approach to deriving diagnosability results of interconnection networks
Creators: name: Cheng, Eddie
name: Mao, Yaping
name: Qiu, Ke
name: Shen, Zhizhang
Publisher: name: arXiv
Year: 2022
Subjects: subject: Networking and Internet Architecture (cs.NI)
subject: Combinatorics (math.CO)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: We generalize an approach to deriving diagnosability results of various interconnection networks in terms of the popular $g$-good-neighbor and $g$-extra fault-tolerant models, as well as mainstream diagnostic models such as the PMC and the MM* models. As demonstrative examples, we show how to follow this constructive, and effective, process to derive the $g$-extra diagnosabilities of the hypercube, the $(n, k)$-star, and the arrangement graph. These results agree with those achieved individually, without duplicating structure independent technical details. Some of them come with a larger applicable range than those already known, and the result for the arrangement graph in terms of the MM* model is new.
description: Preliminary versions of some results of this paper were announced (without proofs) at 2019 International Conference on Modeling, Simulation, Optimization and Algorithm (ICMSOA 2019), November 9-10, 2019, Sanya, China. J. Phys: Conf. Ser. 1409 (2019) 012024
title: 01_1705
Creators: name: Wesley Baldwin, John
name: Baldwin, John W.
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2018
Subjects: subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris

description: L'ensemble de ces notes ont été crée par John Baldwin lors d'une de ses premières périodes de résidence à Paris. Ces documents comprennent tous les magistri qu’il avait pu rencontrer dans ses sources. Aux XIIème et XIIIème siècles, les universités n'existant pas encore, le titre de magister s'il évoque certainement une compétence n'est pas rattaché de façon systématique au passage par les écoles. De surcroît, les magistris sont le plus souvent désignés par leur seul prénom. La lecture de ces données est donc difficile et suppose un long travail pour tenter d'identifier un individu auquel on pourrait rattacher plusieurs mentions. John Baldwin avait donc renoncé à utiliser ces données pour donner un prolongement à sa magnifique étude sur les gradués d'université et leur emploi par les Capétiens et les Plantagenêts. Néanmoins, il a conservé ces données et elles sont potentiellement très utile dans le cadre de Studium, comme le sont toutes les mentions dans les volumes des Fasti Ecclesiae Gallicanae de chanoines portant ce titre de magister sans autres précisions. L'ampleur des dépouillements rend ces données très utiles et nous devons une grande reconnaissance à John Baldwin pour avoir pris la peine de faire photocopier ses fiches et de nous les avoir transmises amicalement.
Les données ainsi que les images des fiches sont accessibles sur le site Internet à l'adresse suivante : http://studium-baldwin.lamop.fr/.
Les transcriptions des fiches ont été effectuées par des étudiants de Paris 1 Panthéon - Sorbonne mais elles n'ont pas été corrigées par la suite.
description: Relation: https://lamop.hypotheses.org/
In vitro cytotoxicity of two novel oral formulations of Amphotericin B (iCo-009 and iCo-010) against Candida albicans, human monocytic and kidney cell lines
Creators: name: Leon, Carlos G
name: Lee, Jinkyung
name: Bartlett, Karen H.
name: Gershkovich, Pavel
name: Wasan, Ellen K
name: Zhao, Jinying
name: Clement, John G
name: Wasan, Kishor M
Publisher: name: BioMed Central
Year: 2016

description: Background: Invasive fungal infections such as candidiasis constitute an increasingly important medical problem. Drugs currently used for the treatment of candidiasis include polyenes (such as Amphotericin B) and azoles. Amphotericin B (AmpB) presents several limitations such as its nephrotoxicity and limited solubility. We have developed two novel lipid-based AmpB formulations which in vivo show less nephrotoxicity and enhanced solubility compared to Fungizone™ a commercial AmpB formulation. The purpose of this study was to determine the cytotoxicity of Fungizone™, Ambisome™ and two novel AmpB formulations (iCo-009 and iCo-010) against Candida albicans, human kidney (293T) cells and monocytic (THP1) cells. Methods: Cell cytotoxicity to the AmpB formulations was evaluated by MTS and LDH assays. In vitro anti-Candida albicans activity was assessed after a 48 h drug incubation. Results: None of the AmpB formulations tested showed cytotoxicity against 293T cells. In the case of THP1 cells only Fungizone™ and Ambisome™ showed cytotoxicity at 500 μg/L (n = 4-10, p < 0.05). The calculated EC50 to Candida albicans for the different formulations was as follows: 26.8 ± 2.9 for iCo-010, 74.6 ± 8.9 for iCo-009, 109 ± 31 for Ambisome™ and 87.1 ± 22 for Fungizone™ (μg of AmpB/L, n = 6-12, p < 0.05). Conclusions: The AmpB formulations analyzed were not cytotoxic to 293T cells. Cytotoxicity in THP1 cells was observed for Fungizone™ and Ambisome™, but not with the novel AmpB formulations. iCo-010 had higher efficacy compared to other three AmpB formulations in the Candida albicans model. The absence of cytotoxicity as well as its higher efficacy for the Candida model compared to Fungizone™ and Ambisome™ suggest that iCo-010 has potential in treating candidiasis.
Adaptive Traffic Signal Control for Developing Countries Using Fused Parameters Derived from Crowd-Source Data
Creators: name: Mishra, Sumit
name: Singh, Vishal
name: Gupta, Ankit
name: Bhattacharya, Devanjan
name: Mudgal, Abhisek
Publisher: name: arXiv
Year: 2022
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Systems and Control (eess.SY)
subject: FOS: Physical sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: Advancement of mobile technologies has enabled economical collection, storage, processing, and sharing of traffic data. These data are made accessible to intended users through various application program interfaces (API) and can be used to recognize and mitigate congestion in real time. In this paper, quantitative (time of arrival) and qualitative (color-coded congestion levels) data were acquired from the Google traffic APIs. New parameters that reflect heterogeneous traffic conditions were defined and utilized for real-time control of traffic signals while maintaining the green-to-red time ratio. The proposed method utilizes a congestion-avoiding principle commonly used in computer networking. Adaptive congestion levels were observed on three different intersections of Delhi (India), in peak hours. It showed good variation, hence sensitive for the control algorithm to act efficiently. Also, simulation study establishes that proposed control algorithm decreases waiting time and congestion. The proposed method provides an inexpensive alternative for traffic sensing and tracking technologies.
description: 15 pages, 11 figures, 7 tables, Accepted by Transportation Letters: the International Journal of Transportation Research
title: 01_0838
Creators: name: Wesley Baldwin, John
name: Baldwin, John W.
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2018
Subjects: subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris

description: L'ensemble de ces notes ont été crée par John Baldwin lors d'une de ses premières périodes de résidence à Paris. Ces documents comprennent tous les magistri qu’il avait pu rencontrer dans ses sources. Aux XIIème et XIIIème siècles, les universités n'existant pas encore, le titre de magister s'il évoque certainement une compétence n'est pas rattaché de façon systématique au passage par les écoles. De surcroît, les magistris sont le plus souvent désignés par leur seul prénom. La lecture de ces données est donc difficile et suppose un long travail pour tenter d'identifier un individu auquel on pourrait rattacher plusieurs mentions. John Baldwin avait donc renoncé à utiliser ces données pour donner un prolongement à sa magnifique étude sur les gradués d'université et leur emploi par les Capétiens et les Plantagenêts. Néanmoins, il a conservé ces données et elles sont potentiellement très utile dans le cadre de Studium, comme le sont toutes les mentions dans les volumes des Fasti Ecclesiae Gallicanae de chanoines portant ce titre de magister sans autres précisions. L'ampleur des dépouillements rend ces données très utiles et nous devons une grande reconnaissance à John Baldwin pour avoir pris la peine de faire photocopier ses fiches et de nous les avoir transmises amicalement.
Les données ainsi que les images des fiches sont accessibles sur le site Internet à l'adresse suivante : http://studium-baldwin.lamop.fr/.
Les transcriptions des fiches ont été effectuées par des étudiants de Paris 1 Panthéon - Sorbonne mais elles n'ont pas été corrigées par la suite.
description: Relation: https://lamop.hypotheses.org/
Error Metrics for Partially Coherent Wavefields
Creators: name: Levitan, Abraham
name: Comin, Riccardo
Publisher: name: arXiv
Year: 2022
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Lensless imaging methods that account for partial coherence have become very common in the past decade. However, there are no metrics in use for comparing partially coherent light fields, despite the widespread use of such metrics to compare fully coherent objects and wavefields. Here, we show how reformulating the mean squared error and Fourier ring correlation in terms of quantum state fidelity naturally generalizes them to partially coherent wavefields. These results fill an important gap in the lensless imaging literature and will enable quantitative assessments of the reliability and resolution of reconstructed partially coherent wavefields.
description: 4 pages, 1 figure
Functional categorization of unique expressed sequence tags obtained from the yeast-like growth phase of the elm pathogen Ophiostoma novo-ulmi
Creators: name: Hintz, William
name: Pinchback, Michael
name: De La Bastide, Paul
name: Burgess, Steven
name: Jacobi, Volker
name: Hamelin, Richard C.
name: Breuil, Colette
name: Bernier, Louis
Publisher: name: BioMed Central
Year: 2016

description: Background: The highly aggressive pathogenic fungus Ophiostoma novo-ulmi continues to be a serious threat to the American elm (Ulmus americana) in North America. Extensive studies have been conducted in North America to understand the mechanisms of virulence of this introduced pathogen and its evolving population structure, with a view to identifying potential strategies for the control of Dutch elm disease. As part of a larger study to examine the genomes of economically important Ophiostoma spp. and the genetic basis of virulence, we have constructed an expressed sequence tag (EST) library using total RNA extracted from the yeast-like growth phase of O. novo-ulmi (isolate H327). Results: A total of 4,386 readable EST sequences were annotated by determining their closest matches to known or theoretical sequences in public databases by BLASTX analysis. Searches matched 2,093 sequences to entries found in Genbank, including 1,761 matches with known proteins and 332 matches with unknown (hypothetical/predicted) proteins. Known proteins included a collection of 880 unique transcripts which were categorized to obtain a functional profile of the transcriptome and to evaluate physiological function. These assignments yielded 20 primary functional categories (FunCat), the largest including Metabolism (FunCat 01, 20.28% of total), Sub-cellular localization (70, 10.23%), Protein synthesis (12, 10.14%), Transcription (11, 8.27%), Biogenesis of cellular components (42, 8.15%), Cellular transport, facilitation and routes (20, 6.08%), Classification unresolved (98, 5.80%), Cell rescue, defence and virulence (32, 5.31%) and the unclassified category, or known sequences of unknown metabolic function (99, 7.5%). A list of specific transcripts of interest was compiled to initiate an evaluation of their impact upon strain virulence in subsequent studies. Conclusions: This is the first large-scale study of the O. novo-ulmi transcriptome. The expression profile obtained from the yeast-like growth phase of this species will facilitate a multigenic approach to gene expression studies to assess their role in the determination of pathogenicity for this species. The identification and evaluation of gene targets in such studies will be a prerequisite to the development of biological control strategies for this pathogen.
Experience Implementing a Performant Category-Theory Library in Coq
Creators: name: Gross, Jason
name: Chlipala, Adam
name: Spivak, David I.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Category Theory (math.CT)
subject: Logic in Computer Science (cs.LO)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: We describe our experience implementing a broad category-theory library in Coq. Category theory and computational performance are not usually mentioned in the same breath, but we have needed substantial engineering effort to teach Coq to cope with large categorical constructions without slowing proof script processing unacceptably. In this paper, we share the lessons we have learned about how to represent very abstract mathematical objects and arguments in Coq and how future proof assistants might be designed to better support such reasoning. One particular encoding trick to which we draw attention allows category-theoretic arguments involving duality to be internalized in Coq's logic with definitional equality. Ours may be the largest Coq development to date that uses the relatively new Coq version developed by homotopy type theorists, and we reflect on which new features were especially helpful.
description: The final publication will be available at link.springer.com. This version includes a full bibliography which does not fit in the Springer version; other than the more complete references, this is the version submitted as a final copy to ITP 2014
Data driven weak universal consistency
Creators: name: Santhanam, N.
name: Anantharam, V.
name: Szpankowski, W.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Information Theory (cs.IT)
subject: FOS: Computer and information sciences
subject: I.2.6; G.3; E.4
subject: 68T05, 94A15, 94A29

description: Many current applications in data science need rich model classes to adequately represent the statistics that may be driving the observations. But rich model classes may be too complex to admit estimators that converge to the truth with convergence rates that can be uniformly bounded over the entire collection of probability distributions comprising the model class, i.e. it may be impossible to guarantee uniform consistency of such estimators as the sample size increases. In such cases, it is conventional to settle for estimators with guarantees on convergence rate where the performance can be bounded in a model-dependent way, i.e. pointwise consistent estimators. But this viewpoint has the serious drawback that estimator performance is a function of the unknown model within the model class that is being estimated, and is therefore unknown. Even if an estimator is consistent, how well it is doing at any given time may not be clear, no matter what the sample size of the observations. Departing from the classical uniform/pointwise consistency dichotomy that leads to this impasse, a new analysis framework is explored by studying rich model classes that may only admit pointwise consistency guarantees, yet all the information about the unknown model driving the observations that is needed to gauge estimator accuracy can be inferred from the sample at hand. We expect that this data-derived estimation framework will be broadly applicable to a wide range of estimation problems by providing a methodology to deal with much richer model classes. In this paper we analyze the lossless compression problem in detail in this novel data-derived framework.
description: Published in JMLR 2022
Surfaces containing two circles through each point
Creators: name: Skopenkov, Mikhail
name: Krasauskas, Rimvydas
Publisher: name: arXiv
Year: 2015
Subjects: subject: Differential Geometry (math.DG)
subject: Algebraic Geometry (math.AG)
subject: Rings and Algebras (math.RA)
subject: FOS: Mathematics
subject: 51B10, 13F15, 16H05

description: We find all analytic surfaces in space $\mathbb{R}^3$ such that through each point of the surface one can draw two transversal circular arcs fully contained in the surface. The problem of finding such surfaces traces back to the works of Darboux from XIXth century. We prove that such a surface is an image of a subset of one of the following sets under some composition of inversions: - the set $\{\,p+q:p\inα,q\inβ\,\}$, where $α,β$ are two circles in $\mathbb{R}^3$; - the set $\{\,2\frac{[p \times q]}{|p+q|^2}:p\inα,q\inβ,p+q\ne 0\,\}$, where $α,β$ are two circles in ${S}^2$; - the set $\{\,(x,y,z): Q(x,y,z,x^2+y^2+z^2)=0\,\}$, where $Q\in\mathbb{R}[x,y,z,t]$ has degree $2$ or $1$. The proof uses a new factorization technique for quaternionic polynomials.
description: 26 pages, 1 figure; this consolidates updates of arXiv:1512.09062 and arXiv:1503.06481, and incorporates a correction to the published version
Computing reconstructions from nonuniform Fourier samples: Universality of stability barriers and stable sampling rates
Creators: name: Adcock, Ben
name: Gataric, Milana
name: Romero, José Luis
Publisher: name: arXiv
Year: 2016
Subjects: subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics
subject: 94A20, 94A12, 94A08, 42B05, 42C15, 65T40

description: We study the problem of recovering an unknown compactly-supported multivariate function from samples of its Fourier transform that are acquired nonuniformly, i.e. not necessarily on a uniform Cartesian grid. Reconstruction problems of this kind arise in various imaging applications, where Fourier samples are taken along radial lines or spirals for example. Specifically, we consider finite-dimensional reconstructions, where a limited number of samples is available, and investigate the rate of convergence of such approximate solutions and their numerical stability. We show that the proportion of Fourier samples that allow for stable approximations of a given numerical accuracy is independent of the specific sampling geometry and is therefore universal for different sampling scenarios. This allows us to relate both sufficient and necessary conditions for different sampling setups and to exploit several results that were previously available only for very specific sampling geometries. The results are obtained by developing: (i) a transference argument for different measures of the concentration of the Fourier transform and Fourier samples; (ii) frame bounds valid up to the critical sampling density, which depend explicitly on the sampling set and the spectrum. As an application, we identify sufficient and necessary conditions for stable and accurate reconstruction of algebraic polynomials or wavelet coefficients from nonuniform Fourier data.
description: 24 pages
Strategic Breeding for Parasitic Resistance in Sheep
Creators: name: Pavithra P1, K. Devadharshini1, Prabhakaran T2
Publisher: name: The Science world a Monthly e magazine
Year: 2024

description: Gastrointestinal nematodes (GINs) present a major challenge to global sheep and small ruminant production, with infections from parasites such as Haemonchus contortus leading to considerable economic losses. Dependence on anthelmintics has led to drug-resistant nematodes, underscoring the need for sustainable alternatives. Breeding for genetic resistance is a promising strategy, leveraging natural variation in resistance across sheep breeds. An integrated approach combining selective breeding, improved grazing practices, nutrition, and targeted anthelmintic use is key. Selection focuses on traits such as growth rate under parasite challenge, faecal egg count (FEC), and anaemia indicators. Ultimately, breeding for resistance offers lasting resilience against nematodes, reducing reliance on anthelmintics and minimizing pasture contamination in affected areas.
Remarks on Neumann boundary problems involving Jacobians
Creators: name: Da Lio, Francesca
name: Palmurella, Francesco
Publisher: name: arXiv
Year: 2017
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: 35J25, 30C70, 35B65

description: In this short note we explore the validity of Wente-type estimates for Neumann boundary problems involving Jacobians. We show in particular that such estimates do not in general hold under the same hypotheses on the data for Dirichlet boundary problems.
Coordinated increase in inhibitory and excitatory synapses onto retinal ganglion cells during development
Creators: name: Soto, Florentina
name: Bleckert, Adam
name: Lewis, Renate
name: Kang, Yunhee
name: Kerschensteiner, Daniel
name: Craig, Ann M
name: Wong, Rachel O
Publisher: name: BioMed Central
Year: 2016

description: Background: Neuronal output is shaped by a balance of excitation and inhibition. How this balance is attained in the central nervous system during development is not well understood, and is complicated by the fact that, in vivo, GABAergic and glycinergic synaptogenesis precedes that of glutamatergic synapses. Here, we determined the distributions of inhibitory postsynaptic sites on the dendritic arbors of individual neurons, and compared their developmental patterns with that of excitatory postsynaptic sites. We focused on retinal ganglion cells (RGCs), the output neurons of the retina, which receive excitatory input from bipolar cells and inhibitory input from amacrine cells. To visualize and map inhibitory postsynaptic sites, we generated transgenic mice in which RGCs express fluorescently tagged Neuroligin 2 (YFP-NL2) under the control of the Thy1 promoter. By labeling RGC dendrites biolistically in YFP-NL2-expressing retinas, we were able to map the spatial distribution and thus densities of inhibitory postsynaptic sites on the dendritic arbors of individual large-field RGCs across ages. Results: We demonstrate that YFP-NL2 is present at inhibitory synapses in the inner plexiform layer by its co-localization with gephyrin, the γ2 subunit of the GABAA receptor and glycine receptors. YFP-NL2 puncta were apposed to the vesicular inhibitory transmitter transporter VGAT but not to CtBP2, a marker of presynaptic ribbons found at bipolar cell terminals. Similar patterns of co-localization with synaptic markers were observed for endogenous NL2. We also verified that expression of YFP-NL2 in the transgenic line did not significantly alter spontaneous inhibitory synaptic transmission onto RGCs. Using these mice, we found that, on average, the density of inhibitory synapses on individual arbors increased gradually until eye opening (postnatal day 15). A small centro-peripheral gradient in density found in mature arbors was apparent at the earliest age we examined (postnatal day 8). Unexpectedly, the adult ratio of inhibitory/excitatory postsynaptic sites was rapidly attained, shortly after glutamatergic synaptogenesis commenced (postnatal day 7). Conclusion: Our observations suggest that bipolar and amacrine cell synaptogenesis onto RGCs appear coordinated to rapidly attain a balanced ratio of excitatory and inhibitory synapse densities prior to the onset of visual experience.
Partially massless theory in three dimensions and self-dual massive gravity
Creators: name: Galviz, Daniel
name: Khoudeir, Adel
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: Partially massless theory in three dimensions is revisited and its relationship with the self-dual massive gravity is considered. The only mode of the partially massless theory is shown explicitly through an action for a scalar field on (A)dS background. This fact can be generalized to higher dimensions. This degree of freedom is altered when a triadic Chern-Simons is introduced, giving rise to the self-dual massive gravity on (A)dS background. We present another physical system with partially massless symmetry and its connection with topologically massive gravity is discussed.
description: 8 pages, no figures, misprints corrected, title corrected
Sharp results on sampling with derivatives in shift-invariant spaces and multi-window Gabor frames
Creators: name: Gröchenig, Karlheinz
name: Romero, José Luis
name: Stöckler, Joachim
Publisher: name: arXiv
Year: 2017
Subjects: subject: Classical Analysis and ODEs (math.CA)
subject: FOS: Mathematics

description: We study the problem of sampling with derivatives in shift-invariant spaces generated by totally-positive functions of Gaussian type or by the hyperbolic secant. We provide sharp conditions in terms of weighted Beurling densities. As a by-product we derive new results about multi-window Gabor frames with respect to vectors of Hermite functions or totally positive functions.
description: 22 pages
A Resolution of the Poisson Problem for Elastic Plates
Creators: name: Da Lio, Francesca
name: Palmurella, Francesco
name: Rivière, Tristan
Publisher: name: arXiv
Year: 2018
Subjects: subject: Differential Geometry (math.DG)
subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: 30C70, 35B65, 35J30, 35J35, 35J66, 49Q10, 53A05, 53C42, 58E15, 58E30, 53A30, 74B20, 74K20

description: The Poisson problem consists in finding an immersed surface $Σ\subset\mathbb{R}^m$ minimising Germain's elastic energy (known as Willmore energy in geometry) with prescribed boundary, boundary Gauss map and area which constitutes a non-linear model for the equilibrium state of thin, clamped elastic plates originating from the work of S. Germain and S.D. Poisson or the early XIX century. We present a solution to this problem consisting in the minimisation of the total curvature energy $E(Σ)=\int_Σ|\operatorname{I\!I}_Σ|^2_{g_Σ}\,\mathrm{d}vol_Σ$ ($\operatorname{I\!I}_Σ$ is the second fundamental form of $Σ$), which is variationally equivalent to the elastic energy, in the case of boundary data of class $C^{1,1}$ and when the boundary curve is simple and closed. The minimum is realised by an immersed disk, possibly with a finite number of branch points in its interior, which is of class $C^{1,α}$ up to the boundary for some $0
description: 65 pages, 3 figures
Creating a knowledge translation trainee collaborative: from conceptualization to lessons learned in the first year
Creators: name: Cornelissen, Evelyn
name: Urquhart, Robin
name: Chan, Vivian W.
name: DeForge, Ryan T.
name: Colquhoun, Heather L.
name: Sibbald, Shannon
name: Witteman, Holly
Publisher: name: BioMed Central
Year: 2016

description: Trainees (e.g., graduate students, residents, fellows) are increasingly identifying knowledge translation as their research discipline. In Canada, a group of trainees have created a trainee-initiated and trainee-led national collaborative to provide a vehicle for trainees to examine the diversity of knowledge translation research and practice, and to link trainees from diverse geographical areas and disciplines. The aim of this paper is to describe our experience and lessons learned in creating the Knowledge Translation Trainee Collaborative. In this meeting report, we outline the process, challenges, and opportunities in planning and experiencing the collaborative's inaugural meeting as participant organizers, and present outcomes and learnings to date.
title: D’r Hoflieferant
Creators: name: Stoskopf, Gustave
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2022

description: TEI version for play in Alsatian. Play subtitle: Elsassiche Komödie in 3 Aufzügen von G. Stoskopf
The Nyquist sampling rate for spiraling curves
Creators: name: Jaming, Philippe
name: Negreira, Felipe
name: Romero, José Luis
Publisher: name: arXiv
Year: 2018
Subjects: subject: Classical Analysis and ODEs (math.CA)
subject: FOS: Mathematics
subject: 42C15, 42C30, 65T60, 94A12, 94A20

description: We consider the problem of reconstructing a compactly supported function from samples of its Fourier transform taken along a spiral. We determine the Nyquist sampling rate in terms of the density of the spiral and show that below this rate spirals suffer from an approximate form of aliasing. This sets a limit to the amount of undersampling that compressible signals admit when sampled along spirals. More precisely, we derive a lower bound on the condition number for the reconstruction of functions of bounded variation, and for functions that are sparse in the Haar wavelet basis.
description: 30 pages, 8 figures
Higgs inflation in the Palatini formulation with kinetic terms for the metric
Creators: name: Rasanen, Syksy
Publisher: name: arXiv
Year: 2018
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We consider scalar field inflation in the Palatini formulation of general relativity. The covariant derivative of the metric is then non-zero. From the effective theory point of view it should couple to other fields. We write down the most general couplings between it and a scalar field that are quadratic in derivatives. We consider both the case when the torsion is determined by the field equations and the case when it is assumed to be zero a priori. We find the metric derivative terms can significantly modify inflationary predictions. We specialise to Higgs inflation and terms of only up to dimension 4. Transforming to the Einstein frame, we show that by tuning the coefficients of the new terms, we can generate various effective inflationary potentials, including quadratic, hilltop-type, $α$-attractor and inflection point. Some of these can give inflation in agreement with observations, including with a large tensor-to-scalar ratio, even if the non-minimal coupling is zero.
description: 12+3 pages, no figures. v2. Added references and clarifications. Published version. v3: Corrected propagating typos, no major change
Multitaper estimation on arbitrary domains
Creators: name: Andén, Joakim
name: Romero, José Luis
Publisher: name: arXiv
Year: 2018
Subjects: subject: Statistics Theory (math.ST)
subject: Information Theory (cs.IT)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: Multitaper estimators have enjoyed significant success in estimating spectral densities from finite samples using as tapers Slepian functions defined on the acquisition domain. Unfortunately, the numerical calculation of these Slepian tapers is only tractable for certain symmetric domains, such as rectangles or disks. In addition, no performance bounds are currently available for the mean squared error of the spectral density estimate. This situation is inadequate for applications such as cryo-electron microscopy, where noise models must be estimated from irregular domains with small sample sizes. We show that the multitaper estimator only depends on the linear space spanned by the tapers. As a result, Slepian tapers may be replaced by proxy tapers spanning the same subspace (validating the common practice of using partially converged solutions to the Slepian eigenproblem as tapers). These proxies may consequently be calculated using standard numerical algorithms for block diagonalization. We also prove a set of performance bounds for multitaper estimators on arbitrary domains. The method is demonstrated on synthetic and experimental datasets from cryo-electron microscopy, where it reduces mean squared error by a factor of two or more compared to traditional methods.
description: 28 pages, 11 figures