cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Determining the subcellular location of new proteins from microscope images using local features.
Creators: name: Coelho, Luis Pedro
name: Kangas, Joshua D.
name: Armaghan W. Naik
name: Osuna-Highley, Elvira
name: Glory-Afshar, Estelle
name: Fuhrman, Margaret H.
name: Ramanuja  Simha
name: Berget, Peter B.
name: Jarvik, Jonathan
name: Murphy, Robert
Publisher: name: Figshare
Year: 2018
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: MOTIVATION: Evaluation of previous systems for automated determination of subcellular location from microscope images has been done using datasets in which each location class consisted of multiple images of the same representative protein. Here, we frame a more challenging and useful problem where previously unseen proteins are to be classified.
RESULTS: Using CD-tagging, we generated two new image datasets for evaluation of this problem, which contain several different proteins for each location class. Evaluation of previous methods on these new datasets showed that it is much harder to train a classifier that generalizes across different proteins than one that simply recognizes a protein it was trained on. We therefore developed and evaluated additional approaches, incorporating novel modifications of local features techniques. These extended the notion of local features to exploit both the protein image and any reference markers that were imaged in parallel. With these, we obtained a large accuracy improvement in our new datasets over existing methods. Additionally, these features help achieve classification improvements for other previously studied datasets.
AVAILABILITY: The datasets are available for download at http://murphylab.web.cmu.edu/data/. The software was written in Python and C++ and is available under an open-source license at http://murphylab.web.cmu.edu/software/. The code is split into a library, which can be easily reused for other data and a small driver script for reproducing all results presented here. A step-by-step tutorial on applying the methods to new datasets is also available at that address.
CONTACT: murphy@cmu.edu
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Coordinate suppression of Sdpr and Fhl1 expression in tumors of the breast, kidney, and prostate.
Creators: name: Li, Xun
name: Zhenyu  Jia
name: Yongquan  Shen
name: Ichikawa, Hitoshi
name: Jarvik, Jonathan
name: Nagele, Robert G.
name: Goldberg, Gary S.
Publisher: name: Figshare
Year: 2018
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: The Src tyrosine kinase associates with the focal adhesion adaptor protein Cas (Crk-associated substrate) to suppress the expression of potential tumor suppressor genes. For example, Src utilizes Cas to suppress the expression of the LIM-only protein Fhl1 (four and a half LIM domains 1), in order to promote non-anchored tumor-cell growth and migration. Here, we report that the promoter region of the Fhl1 gene was methylated more in Src-transformed cells than non-transformed cells. In addition, global expression analysis indicates that Fhl1 induced expression of serum deprivation response factor (Sdpr) in Src-transformed cells. Moreover, Fhl1 and Sdpr was expressed in approximately 87% and 40% of samples obtained from non-transformed breast, 100% of samples obtained from non-transformed kidney, and over 60% of samples obtained from non-transformed prostate. In contrast, Fhl1 and Sdpr was detected in approximately 40% and 7% of matched samples from mammary carcinoma, less than 11% of matched samples from kidney carcinoma, and in less than 22% of matched samples from prostate carcinoma. These data indicate that Fhl1 and Sdpr expression was significantly reduced in tumors of the breast (P < 0.02 and P < 0.001), kidney (P < 0.01), and prostate (P < 0.05). In addition, although Src can activate mitogen-activated protein kinase (MAPK) to promote tumor-cell growth, our data indicate that Src did not rely on MAPK activity to suppress the expression of Fhl1 and Sdpr in transformed cells. Thus, Src induced methylation of the promoter region of the Fhl1 gene; Src suppressed Fhl1 and Sdpr expression independent of mitogen-activated protein kinase (MAPK) activity; Fhl1 induced the expression of Sdpr in Src-transformed cells; and Fhl1 and Sdpr expression was suppressed in tumors of the breast, kidney, and prostate.
title: Editorial
Creators: name: Connelly, Graham
Publisher: name: Strathprints - University of Strathclyde
Year: 2021

description: Welcome to the autumn/fall 2021 issue of SJRCC. This is the second issue of our new two issues per year (spring and autumn) format. Regular readers will have spotted that we have a new strapline - 'an international journal of group and family care experience' – to emphasise our international reach and a scope that encompasses all care experience.
The Cauchy-Lagrangian method for numerical analysis of Euler flow
Creators: name: Podvigina, O.
name: Zheligovsky, V.
name: Frisch, U.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Numerical Analysis (math.NA)
subject: Chaotic Dynamics (nlin.CD)
subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: A novel semi-Lagrangian method is introduced to solve numerically the Euler equation for ideal incompressible flow in arbitrary space dimension. It exploits the time-analyticity of fluid particle trajectories and requires, in principle, only limited spatial smoothness of the initial data. Efficient generation of high-order time-Taylor coefficients is made possible by a recurrence relation that follows from the Cauchy invariants formulation of the Euler equation (Zheligovsky & Frisch, J. Fluid Mech. 2014, 749, 404-430). Truncated time-Taylor series of very high order allow the use of time steps vastly exceeding the Courant-Friedrichs-Lewy limit, without compromising the accuracy of the solution. Tests performed on the two-dimensional Euler equation indicate that the Cauchy-Lagrangian method is more - and occasionally much more - efficient and less prone to instability than Eulerian Runge-Kutta methods, and less prone to rapid growth of rounding errors than the high-order Eulerian time-Taylor algorithm. We also develop tools of analysis adapted to the Cauchy-Lagrangian method, such as the monitoring of the radius of convergence of the time-Taylor series. Certain other fluid equations can be handled similarly.
description: 30 pp., 13 figures, 45 references. Minor revision. In press in Journal of Scientific Computing
Spin effects induced by thermal perturbation in a normal metal/magnetic insulator system
Creators: name: Lyapilin, I. I.
name: Okorokov, M. S.
name: Ustinov, V. V.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Using one of the methods of quantum nonequilibrium statistical physics we have investigated the spin transport transverse to the normal metal/ferromagnetic insulator interface in hybrid nanostructures. An approximation of the effective parameters, when each of the interacting subsystems (electron spin, magnon, and phonon) is characterized by its own effective temperature have been considered. The generalized Bloch equations which describe the spin-wave current propagation in the dielectric have been derived. Finally, two sides of the spin transport "coin" have been revealed: the diffusive nature of the magnon motion and magnon relaxation processes, responsible for the spin pumping and the spin-torque effect.
ИМОМ ДОРАҚУТНИЙНИНГ БИЗГАЧА ЕТИБ КЕЛГАН ҚЎЛЁЗМА АСАРЛАРИ
Creators: name: Саидов, Шахбоз
Publisher: name: Zenodo
Year: 2023

description: Бу китоб ҳақида Имом Балқийний ўзларининг "Маҳосин" китобларида гапирганлар лекин бу китобнинг васфи борасида ҳеч қандай сўз айтмаганлар.
Molecular subtyping and the construction of a predictive model of colorectal cancer based on ion channel genes
Creators: name: Liu, Ming
name: AI, lianjie
Publisher: name: figshare
Year: 2023
Subjects: classificationCode: 321109
subject: Predictive and prognostic markers
classificationCode: 321108
subject: Molecular targets

description: Colorectal cancer (CRC) is a highly heterogeneous malignancy with an unfavorable prognosis. This study aimed to address the heterogeneity of colorectal cancer (CRC) by classifying it into ion channel subtypes, and to develop predictive models on the basis of ion channel genes to forecast the survival and immunological state of CRC patients. These models will guide postoperative immunotherapy and drug treatment.
Atomic-Scale Modelling of Solid-state Precipitation in Aluminium Alloys
Creators: name: Su, Shenghan
Publisher: name: Monash University
Year: 2024
Subjects: classificationCode: 401607
subject: Metals and alloy materials

description: Aluminium is the second most used metal today, owing to its relatively low density, good corrosion resistance, as well as high electrical and thermal conductivities. While conventional aluminium alloys find application in cans, containers, and portable electronics, advanced high-strength aluminium alloys have been extensively used in aerospace industries. Generally, the high strength of such alloys is attributed to uniformly and densely distributed nano-scale plate-shaped precipitates in the aluminium matrix. This thesis explores a novel precipitation mechanism by combining computational and experimental techniques, constituting an initial step towards the development of high-performance aluminium alloys.
Colonization of a territory by a stochastic population under a strong Allee effect and a low immigration pressure
Creators: name: Be'er, Shay
name: Assaf, Michael
name: Meerson, Baruch
Publisher: name: arXiv
Year: 2015
Subjects: subject: Populations and Evolution (q-bio.PE)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Biological sciences
subject: FOS: Physical sciences

description: We study the dynamics of colonization of a territory by a stochastic population at low immigration pressure. We assume a sufficiently strong Allee effect that introduces, in deterministic theory, a large critical population size for colonization. At low immigration rates, the average pre-colonization population size is small thus invalidating the WKB approximation to the master equation. We circumvent this difficulty by deriving an exact zero-flux solution of the master equation and matching it with an approximate non-zero-flux solution of the pertinent Fokker-Planck equation in a small region around the critical population size. This procedure provides an accurate evaluation of the quasi-stationary probability distribution of population sizes in the pre-colonization state, and of the mean time to colonization, for a wide range of immigration rates. At sufficiently high immigration rates our results agree with WKB results obtained previously. At low immigration rates the results can be very different.
description: 8 pages, 4 figures
Molecular subtyping and the construction of a predictive model of colorectal cancer based on ion channel genes
Creators: name: Liu, Ming
name: Ai, Lianjie
Publisher: name: figshare
Year: 2023
Subjects: classificationCode: 321109
subject: Predictive and prognostic markers
classificationCode: 321108
subject: Molecular targets

description: Colorectal cancer (CRC) is a highly heterogeneous malignancy with an unfavorable prognosis. This study aimed to address the heterogeneity of colorectal cancer (CRC) by classifying it into ion channel subtypes, and to develop predictive models on the basis of ion channel genes to forecast the survival and immunological state of CRC patients. These models will guide postoperative immunotherapy and drug treatment.
NFFA-Europe Pilot - D16.1 - Design of the service platform
Creators: name: Aversa, Rossella
name: Jejkal, Thomas
name: Panighel, Mirco
name: Modolo, Irene
name: Osmenaj, Elda
name: Brandino, Giuseppe Piero
Publisher: name: Zenodo
Year: 2021

description: This deliverable presents the initial design of the infrastructure for the NFFA-Europe Pilot (NEP). The infrastructure is planned to consist of diverse elements for the Data and the Metadata Management, as well as different services (in the frontend, in the backend, and for Virtual Access) which will be gradually developed and integrated in a seamless way. We distinguish between the basic elements, which are essential parts of the infrastructure planned in the NEP proposal, and additional elements which were not initially planned but might improve the interconnections and facilitate the Research Users, in case they will be developed as output of the scouting activities of the Task 16.4 of the Joint Activity 6 (Work Package 16). The elements of the infrastructure will be connected to each other and will be accessed by users or by other services thanks to interfaces.
Drosophila APC2 and APC1 have overlapping roles in the larval brain despite their distinct intracellular localizations.
Creators: name: Akong, Kathryn
name: McCartney, Brooke M.
name: Peifer, Mark
Publisher: name: Figshare
Year: 2018
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: The tumor suppressor APC and its homologs, first identified for a role in colon cancer, negatively regulate Wnt signaling in both oncogenesis and normal development, and play Wnt-independent roles in cytoskeletal regulation. Both Drosophila and mammals have two APC family members. We further explored the functions of the Drosophila APCs using the larval brain as a model. We found that both proteins are expressed in the brain. APC2 has a highly dynamic, asymmetric localization through the larval neuroblast cell cycle relative to known mediators of embryonic neuroblast asymmetric divisions. Adherens junction proteins also are asymmetrically localized in neuroblasts. In addition they accumulate with APC2 and APC1 in nerves formed by axons of the progeny of each neuroblast-ganglion mother cell cluster. APC2 and APC1 localize to very different places when expressed in the larval brain: APC2 localizes to the cell cortex and APC1 to centrosomes and microtubules. Despite this, they play redundant roles in the brain; while each single mutant is normal, the zygotic double mutant has severely reduced numbers of larval neuroblasts. Our experiments suggest that this does not result from misregulation of Wg signaling, and thus may involve the cytoskeletal or adhesive roles of APC proteins.
Short intervals asymptotic formulae for binary problems with primes and powers, II: density $1$
Creators: name: Languasco, Alessandro
name: Zaccagnini, Alessandro
Publisher: name: arXiv
Year: 2015
Subjects: subject: Number Theory (math.NT)
subject: FOS: Mathematics

description: We prove that suitable asymptotic formulae in short intervals hold for the problems of representing an integer as a sum of a prime square and a square, or a prime square. Such results are obtained both assuming the Riemann Hypothesis and in the unconditional case.
description: revised version
title: Moving towards organisational resilience : a practical application of the 'whole system approach' in the secure care sector
Creators: name: Pollock, Kevin
name: Gillespie, James
Publisher: name: Strathprints - University of Strathclyde
Year: 2021

description: Kibble is a Scottish specialist child and youth care charity and social enterprise. It has been a successful organisation since 1841, adapting and changing to maintain its ability to deliver relevant, high-quality services, in a high-risk and high-value sector. Kibble's organisational resilience is founded on sound risk management and learning from experiences. Since 2014, Kibble has introduced several related initiatives, including business continuity and enterprise risk management, improving resilience, and learning across the organisation. Key to its development as a learning organisation is its cohesive vision, open systems thinking, updating heuristic and practice models, team learning and improving individual capabilities while avoiding a blame culture when things go wrong. With this approach enhancing crisis-preparedness, Kibble continues to learn, develop, and provide high-quality services to support young people. However, there is limited research on organisational resilience and learning at establishments such as Kibble. This paper seeks to increase the body of knowledge and provide practical guidance for improving resilience and learning practice in the care sector. The Benchmarking Resilience Tool (BRT-13b) is introduced as an effective method for organisations to assess their resilience capability and address any performance gaps.
Drosophila APC2 and APC1 play overlapping roles in wingless signaling in the embryo and imaginal discs.
Creators: name: Akong, Kathryn
name: Grevengoed, Elizabeth E.
name: Price, Meredith H.
name: McCartney, Brooke M.
name: Hayden, Melissa A.
name: DeNofrio, Jan C.
name: Peifer, Mark
Publisher: name: Figshare
Year: 2018
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: The regulation of signal transduction plays a key role in cell fate choices, and its disregulation contributes to oncogenesis. This duality is exemplified by the tumor suppressor APC. Originally identified for its role in colon tumors, APC family members were subsequently shown to negatively regulate Wnt signaling in both development and disease. The analysis of the normal roles of APC proteins is complicated by the presence of two APC family members in flies and mice. Previous work demonstrated that, in some tissues, single mutations in each gene have no effect, raising the question of whether there is functional overlap between the two APCs or whether APC-independent mechanisms of Wnt regulation exist. We addressed this by eliminating the function of both Drosophila APC genes simultaneously. We find that APC1 and APC2 play overlapping roles in regulating Wingless signaling in the embryonic epidermis and the imaginal discs. Surprisingly, APC1 function in embryos occurs at levels of expression nearly too low to detect. Further, the overlapping functions exist despite striking differences in the intracellular localization of the two APC family members.
On the Limit and Applicability of Dynamic Homogenization
Creators: name: Srivastava, Ankit
name: Nemat-Nasser, Sia
Publisher: name: arXiv
Year: 2014
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Recent years have seen considerable research success in the field of dynamic homogenization which seeks to define frequency dependent effective properties for heterogeneous composites for the purpose of studying wave propagation. There is an approximation involved in replacing a heterogeneous composite with its homogenized equivalent. In this paper we propose a quantification to this approximation. We study the problem of reflection at the interface of a layered periodic composite and its dynamic homogenized equivalent. It is shown that if the homogenized parameters are to appropriately represent the layered composite in a finite setting and at a given frequency, then reflection at this special interface must be close to zero at that frequency. We show that a comprehensive homogenization scheme proposed in an earlier paper results in negligible reflection in the low frequency regime, thereby suggesting its applicability in a finite composite setting. In this paper we explicitly study a 2-phase composite and a 3-phase composite which exhibits negative effective properties over its second branch. We show that based upon the reflected energy profile of the two cases, there exist good arguments for considering the second branch of a 3-phase composite a true negative branch with negative group velocity. The results open intriguing questions regarding the effects of replacing a semi-infinite periodic composite with its Bloch-wave (infinite domain) dynamic properties on such phenomenon as negative refraction.
Effect of inducible nitric oxide synthase on cerebral blood flow after experimental traumatic brain injury in mice.
Creators: name: Foley, Lesley
name: T. Kevin  Hitchens
name: Melick, John A.
name: Hulya  Bayir
name: Ho, Chien
name: Kochanek, Patrick M.
Publisher: name: Figshare
Year: 2018
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: Inducible nitric oxide synthase (iNOS) has been suggested to play a complex role in the response to central nervous system insults such as traumatic brain injury (TBI) and cerebral ischemia. In the current study, we quantified maps of regional cerebral blood flow (CBF) using an arterial spin-labeling magnetic resonance imaging (MRI) technique, at 24 and 72 h after experimental TBI in iNOS knockout (KO) and wild-type (WT) mice. Our hypothesis was that iNOS would contribute to the level of CBF at 72 h after experimental TBI in mice. Comparing anatomical brain regions of interest (ROIs) at 24-h post controlled cortical impact (CCI), there were significant reductions in CBF in the hemisphere, cortex, and contusion-rich area of the cortex of injured animals versus naive, regardless of genotype. Regional assessment of CBF at 72 h after injury demonstrated that recovery of CBF was reduced in the ipsilateral hippocampus, thalamus, and amygdala/piriform cortex in iNOS KO versus WT mice by 26%, 15%, and 21%, respectively; this attenuated recovery was restricted to structures outside the contusion. These regions with reduced CBF in iNOS KO mice represented ROIs where CBF in the WT was either numerically or statistically greater than that seen in respective WT naive, suggesting a contribution of iNOS to delayed posttraumatic hyperemia. However, pixel analysis denoted that the contribution of iNOS to CBF at 72 h was not limited to hyperemia flows. In conclusion, iNOS plays a role in the recovery of CBF after CCI in mice. Questions remain if this effect represents a homeostatic component of CBF recovery, pathologic vasodilatation linked to inflammation, or NO-mediated facilitation of angiogenesis.
TEMPUS, a Timepix4-based system for event-based X-rays detection
Creators: name: Correa Magdalena, Jonathan
name: Ignatenko, Alexandr
name: Pennicard, David
name: Lange, Sabine
name: Fridman, Sergei
name: Karl, Sebastian
name: Lohse, Leon
name: Senfftleen, Bjoern
name: Sergeev, Ilya
name: Velten, Sven
name: Prajapat, Deepak
name: Bocklage, Lars
name: Bromberger, Hubertus
name: Samartsev, Andrey
name: Chumakov, Aleksandr
name: Rueffer, Rudolf
name: von Zanthier, Joachim
name: Roehlsberger, Ralf
name: Graafsma, Heinz
Publisher: name: Deutsches Elektronen-Synchrotron, DESY, Hamburg
Year: 2024

description: A readout system based on the Timepix4 ASIC, is being developed for photon science. The TEMPUS detector can be operated in two distinct modes: a photon counting mode, which allows for conventional full-frame readout at rates up to 40 kfps; and an event-driven time-stamping mode, which allows excellent time resolution in the nanosecond regime in measurements with moderate X-ray flux. In this paper, we introduce the initial prototype, a single-chip system, and present the first results obtained at PETRA III and ESRF.
Factorization of a class of matrix-functions with stable partial indices
Creators: name: Mishuris, Gennady
name: Rogosin, Sergei
Publisher: name: arXiv
Year: 2015
Subjects: subject: Complex Variables (math.CV)
subject: Functional Analysis (math.FA)
subject: FOS: Mathematics
subject: 15A23, 15A54, 30E25, 45E10

description: A new effective method for factorization of a class of nonrational $n\times n$ matrix-functions with \emph{stable partial indices} is proposed. The method is a generalization of the one recently proposed by the authors which was valid for the canonical factorization only. The class of considered matrices is motivated by problems originated from applications. The properties and details of the asymptotic procedure are illustrated by examples. The efficiency of the procedure is highlighted by numerical results.
description: 22 pages, 7 figures. arXiv admin note: text overlap with arXiv:1402.2120
Detection and assignment of CYP21 mutations using peptide mass signature genotyping.
Creators: name: Xuemei  Zeng
name: Witchel, Selma F.
name: Dobrowolski, Steven F.
name: Moulder, Peter V
name: Jarvik, Jonathan
name: Telmer, Cheryl A.
Publisher: name: Figshare
Year: 2018
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: Congenital adrenal hyperplasia (CAH) is a common inborn error of steroidogenesis. The clinical spectrum of CAH ranges from the severe classical form, which can be fatal in the newborn, to simple virilizing forms or a milder non-classical form which is often not diagnosed until puberty. Recessive mutations in the autosomal gene encoding 21-hydroxylase (CYP21) are responsible for approximately 95% of CAH cases. Since CYP21 genotype is generally predictive of the presence and severity of the disorder, accurate CYP21 genotyping is of clear medical significance. Determining the CYP21 genotype of an individual, using standard methods, is difficult due to the presence of a nearly identical pseudogene (CYP21P) in close proximity to the functional gene. To address the need for a comprehensive test for mutations in the CYP21 gene, we developed a multiplexed peptide mass signature genotyping (PMSG) assay and applied the assay to 151 DNA samples. CAH patients had been previously characterized for the 10 most common mutations. The PMSG assay detected all common mutations; in addition it identified six known rare mutations and also discovered four new mutations (two frameshifts in the first half of the gene, P42fs and S171fs, and two point mutations, H365Y and R479L). This assay has the potential to provide high-throughput, cost-effective analysis of the CYP21 gene to detect known mutations and identify novel variants in samples obtained from patients with CAH, individuals suspected to have CAH, and heterozygous carriers.
Endosomal trafficking and proprotein convertase cleavage of cis Golgi protein GP73 produces marker for hepatocellular carcinoma.
Creators: name: Bachert, Collin
name: Fimmel, Claus
name: Linstedt, Adam
Publisher: name: Figshare
Year: 2018
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: Serum GP73 levels are significantly increased in patients with hepatocellular carcinoma (HCC), potentially providing a marker for early detection. However, GP73 is an integral membrane protein localized to the cis Golgi and is not known to be secreted. Based on its presence in sera, we sought to determine whether GP73 might normally be released from cells and to elucidate the mechanism of this release. Indeed, a soluble form of GP73 was released from cultured cells and compared with the Golgi-localized full-length protein, the molecular weight was slightly reduced, suggesting that cleavage releases the GP73 ectodomain. Sequence analysis revealed a proprotein convertase (PC) consensus site, and, indeed, the ubiquitous PC furin was capable of cleaving purified GP73. Further, alanine substitutions in the PC site blocked both the in vitro and the in vivo cleavage of GP73. Using a cleavage-specific antibody, cleaved GP73 was found in the trans Golgi network and endosomes, suggesting that GP73 cleavage occurs as GP73 cycles distal to the early Golgi. We conclude that the endosomal trafficking of GP73 allows for PC-mediated cleavage, resulting in GP73 secretion, and provides a molecular mechanism for its presence as a serum biomarker for HCC.
title: A critical analysis of the recent developments in alternative care space across South Asia amidst the Covid-19 crisis
Creators: name: Modi, Kiran
name: Kalra, Gurneet
name: Prasad, Leena
name: Narsimha, Rajeshwari
name: Singh, Jyoti
Publisher: name: Strathprints - University of Strathclyde
Year: 2021

description: In many situations of conflicts, natural disasters, or pandemics, it is always the children who are the most vulnerable. With the world shutting down due to the invisible threat to civilisation, the most affected are the children living in alternative care settings and the children who are on possible verge of family breakdown and ending up in institutions. Their limited knowledge and lack of independence often results in an increased exposure to several risk factors such as abuse, maltreatment, deprivations, and violations This paper aims at focusing on the recent developments in policies and arrangements in the alternative care space in the South Asian countries, namely Afghanistan, Bangladesh, Bhutan, India, Nepal, Pakistan, and Sri Lanka, amidst the COVID-19 pandemic. The purpose of the study is to understand the impact of COVID-19 on alternative care space in South Asian countries, its effect on the children living in alternative care, and to understand the measures taken by respective governments in these countries to support them during the pandemic. An assessment of the recent developments in the policies related to alternative care space in different countries is crucial for understanding the problems faced when dealing with children in institutional care as well as the impact on the de-institutionalisation process due to COVID-19. This paper is a secondary review of desk research on such developments to understand the possible post-COVID-19 impacts on functionary and regulatory changes in alternative care systems for 'Children without Parental Care' in the South Asian region.
Enhanced photostability of genetically encodable fluoromodules based on fluorogenic cyanine dyes and a promiscuous protein partner.
Creators: name: Shank, Nathaniel I.
name: Zanotti, Kimberly J.
name: Lanni, Frederick
name: Berget, Peter B.
name: Armitage, Bruce
Publisher: name: Figshare
Year: 2018
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: Fluoromodules are discrete complexes of biomolecules and fluorogenic dyes. Binding of the dyes to their cognate biomolecule partners results in enhanced dye fluorescence. We exploited a previously reported promiscuous binding interaction between a single-chain, variable fragment antibody protein and a family of cyanine dyes to create new protein-dye fluoromodules that exhibit enhanced photostability while retaining high affinity protein-dye binding. Modifications to the dye structure included electron-withdrawing groups that provide resistance to photo-oxidative damage. Low nanomolar equilibrium dissociation constants were found for the new dyes. Fluorescence microscopy illustrates how yeast can be surface-labeled with three different colors based on a single protein and appropriately chosen dyes.
Short intervals asymptotic formulae for binary problems with primes and powers, I: density $3/2$
Creators: name: Languasco, Alessandro
name: Zaccagnini, Alessandro
Publisher: name: arXiv
Year: 2015
Subjects: subject: Number Theory (math.NT)
subject: FOS: Mathematics

description: We prove that suitable asymptotic formulae in short intervals hold for the problems of representing an integer as a sum of a prime and a square, or a prime square. Such results are obtained both assuming the Riemann Hypothesis and in the unconditional case.
description: revised version
Primordial mass segregation in simulations of star formation?
Creators: name: Parker, Richard J.
name: Dale, James E.
name: Ercolano, Barbara
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We take the end result of smoothed particle hydrodynamics (SPH) simulations of star formation which include feedback from photoionisation and stellar winds and evolve them for a further 10Myr using $N$-body simulations. We compare the evolution of each simulation to a control run without feedback, and to a run with photoionisation feedback only. In common with previous work, we find that the presence of feedback prevents the runaway growth of massive stars, and the resulting star-forming regions are less dense, and preserve their initial substructure for longer. The addition of stellar winds to the feedback produces only marginal differences compared to the simulations with just photoionisation feedback. We search for mass segregation at different stages in the simulations; before feedback is switched on in the SPH runs, at the end of the SPH runs (before $N$-body integration) and during the $N$-body evolution. Whether a simulation is primordially mass segregated (i.e. before dynamical evolution) depends extensively on how mass segregation is defined, and different methods for measuring mass segregation give apparently contradictory results. Primordial mass segregation is also less common in the simulations when star formation occurs under the influence of feedback. Further dynamical mass segregation can also take place during the subsequent (gas-free) dynamical evolution. Taken together, our results suggest that extreme caution should be exercised when interpreting the spatial distribution of massive stars relative to low-mass stars in simulations.
description: 14 pages, 11 figures, accepted for publication in MNRAS
Vosoritide in achondroplasia: a profile of its use
Creators: name: Heo, Young-A
Publisher: name: Adis Journals
Year: 2022
Subjects: Medicine

description: Declarations Funding The preparation of this review was not supported by any external funding. Authorship and conflict of interest Young-A Heo, a salaried employee of Adis International Ltd/Springer Nature and an editor of Drugs & Therapy Perspectives, was not involved in any publishing decisions for the manuscript and declares no relevant conflicts of interest. All authors contributed to the review and are responsible for the article content Ethics approval, Consent to participate, Consent for publication, Availability of data and material, Code availability Not applicable
 Additional information about this Adis Drug Review can be found here
 Abstract Subcutaneous vosoritide (Voxzogo®), a modified recombinant human C-type natriuretic peptide (CNP) analogue, is the first precision therapy approved for the treatment of achondroplasia in the EU, USA and multiple other countries. It is indicated for patients aged ≥ 2 years with open epiphyses in the EU and those aged ≥ 5 years with open epiphyses in the USA. In a phase 3 trial (study 111-301), vosoritide 15 μg/kg/day significantly improved annualized growth velocity and height Z-score compared with placebo, without worsening upper-to-lower body segment ratio in children with achondroplasia. The growth-promoting effects of vosoritide persisted with continued treatment for up to 60 months. Vosoritide is generally well tolerated, with most adverse events being mild in severity. Longer-term safety data revealed no new safety signals.
Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.
Creators: name: Welkin H. Pope
name: Jacobs-Sera, Deborah
name: Russell, Daniel A.
name: Peebles, Craig L.
name: Alcoser, Turi A.
name: Alexander, Lisa M.
name: Bayles, Ian M.
name: Keshav  Budwal
name: Campbell, Ian W.
name: Cohen, Lianne B.
name: English, Belle E. V.
name: Filliger, Laura Z.
name: Fox, Tyler M.
name: Guerra, Stephanie L.
name: Siping  He
name: Healy, Kaitlin E.
name: Jarvik, Jonathan
name: Jasinto, Paul G.
name: Antonio-Javier Lopez
name: Medenbach, Andrew J.
name: Pferdehirt, Rachel E.
name: Resiss, Michael J.
name: Savitskaya, Judith
name: Sheldon, Kathryn E.
name: Madav K. Shroff
name: Thompson, Jasper V.
name: Wirtshafter, Hannah S.
Publisher: name: Figshare
Year: 2018
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists.
Divide and conquer is always best: sensitivity of methyl correlation experiments.
Creators: name: Kaustubh Sinha
name: Jen-Jacobson, Linda
name: Rule, Gordon
Publisher: name: Figshare
Year: 2018
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: The HMCM [CG]CBCA experiment (Tugarinov and Kay in J Am Chem Soc 125:13868-13878, 2003) correlates methyl carbon and proton shifts to Cγ, Cβ, and Cα resonances for the purpose of resonance assignments. The relative sensitivity of the HMCM[CG]CBCA sequence experiment is compared to a divide-and-conquer approach to assess whether it is best to collect all of the methyl correlations at once, or to perform separate experiments for each correlation. A straightforward analysis shows that the divide-and-conquer approach is intrinsically more sensitive, and should always be used to obtain methyl-Cγ, Cβ, and Cα correlations. The improvement in signal-to-noise associated with separate experiments is illustrated by the detection of methyl-aliphatic correlations in a 65 kDa protein-DNA complex.
The Connection Between Emotions and Attention
Creators: name: Dsouza, Daniella
name: Dainer-Best, Justin
name: Krslovic, Kristian
name: Derrell, Amanda
name: K. N’Kira Hailey
name: Mencarini, Lily
name: Traub, Gabriel
Publisher: name: Open Science Framework
Year: 2023
Subjects: subject: Social and Behavioral Sciences

description: A class project for PSY CL taught at Bard College in Fall 2022 and Spring 2023
Drosophila ventral furrow morphogenesis: a proteomic analysis.
Creators: name: Gong, Lei
name: Puri, Mamta
name: Unlu, Mustafa
name: Young, Margaret
name: Robertson, Katherine
name: Viswanathan, Surya
name: Krishnaswamy, Arun
name: Dowd, Susan R.
name: Minden, Jonathan
Publisher: name: Figshare
Year: 2018
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: Ventral furrow formation is a key morphogenetic event during Drosophila gastrulation that leads to the internalization of mesodermal precursors. While genetic analysis has revealed the genes involved in the specification of ventral furrow cells, few of the structural proteins that act as mediators of ventral cell behavior have been identified. A comparative proteomics approach employing difference gel electrophoresis was used to identify more than fifty proteins with altered abundance levels or isoform changes in ventralized versus lateralized embryos. Curiously, the majority of protein differences between these embryos appeared well before gastrulation, only a few protein changes coincided with gastrulation, suggesting that the ventral cells are primed for cell shape change. Three proteasome subunits were found to differ between ventralized and lateralized embryos. RNAi knockdown of these proteasome subunits and time-dependent difference-proteins caused ventral furrow defects, validating the role of these proteins in ventral furrow morphogenesis.
Choices and Contexts in India’s Constitutional Founding
Creators: name: Dann, Philipp
Publisher: name: Humboldt-Universität zu Berlin
Year: 2022
Subjects: subject: Constitutional ideas
subject: Contextual analysis
subject: Alternative modernities
subject: 340 Recht
subject: 320 Politikwissenschaft (Politik und Regierung)

description: ‘India’s founding moment’ a moment of breath-taking political imagination and it is one of the great achievements of Madhav Khosla. to unpack important parts of its pre-history and emergence. This article will look at two questions—one about alternatives and the other about contexts. Regarding alternatives, I am interested in the paths not taken and an understanding of possibilities. I try to get a sense of possible alternative futures or modernities that the founding generation pondered, in the best case allowing us to wonder what we can learn from the choices made as well as from the paths rejected. The other question I raise is the question of the intellectual contexts, in which the founding took place. Coming from a non-Indian perspective, I am interested in the entanglements, the contexts and potentially migrating ideas that emerge.
title: Developing philosophical discussions with children and young people in residential care homes
Creators: name: Halvorsen, Terje Jostein
Publisher: name: Strathprints - University of Strathclyde
Year: 2021

description: Philosophical discussion in small groups is a method already known in the field of residential child care, through Kohlberg's theory on how to promote young people's ability for moral reasoning. This paper offers a presentation of two philosophers, Matthew Lipman and Gareth Matthews, who advise approaches similar to the Kohlbergian approach but where the aim is to promote cognitive development in multiple domains. Their approaches may prove useful in the endeavours to improve the educational achievements of children and young people in residential care homes. Moreover, these approaches may also promote social competence and social functioning. According to the author, the philosophical knowledge needed to initiate and lead discussions, can yield an additional benefit in the form of a more stringent and in-depth professional reasoning.
Full model details from Gaps in modelling animal migration with evolutionary game theory: infection can favour the loss of migration
Creators: name: Shaw, Allison K.
name: Torstenson, Martha
name: Craft, Meggan E.
name: Binning, Sandra A.
Publisher: name: The Royal Society
Year: 2023
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: Health Care
subject: Diseases
subject: 111706 Epidemiology
subject: FOS: Health sciences
subject: 60801 Animal Behaviour
subject: 10202 Biological Mathematics
subject: FOS: Mathematics

description: Ongoing environmental changes alter how natural selection shapes animal migration. Understanding how these changes play out theoretically can be done using evolutionary game theoretic (EGT) approaches, such as looking for evolutionarily stable strategies. Here, we first describe historical patterns of how EGT models have explored different drivers of migration. We find that there are substantial gaps in both the taxa (mammals, amphibians, reptiles, insects) and mechanisms (mutualism, interspecific competition) included in past EGT models of migration. Although enemy interactions, including parasites, are increasingly considered in models of animal migration, they remain the least studied of factors for migration considered to date. Furthermore, few papers look at changes in migration in response to perturbations (e.g. climate change, new species interactions). To address this gap, we present a new EGT model to understand how infection with a novel parasite changes host migration. We find three possible outcomes when migrants encounter novel parasites: maintenance of migration (despite the added infection cost), loss of migration (evolutionary shift to residency) or population collapse, depending on the risk and cost of getting infected, and the cost currency. Our work demonstrates how emerging infection can alter animal behaviour such as migration.This article is part of the theme issue ‘Half a century of evolutionary games: a synthesis of theory, application and future directions’.
Literature search results and Literature search references from Gaps in modelling animal migration with evolutionary game theory: infection can favour the loss of migration
Creators: name: Shaw, Allison K.
name: Torstenson, Martha
name: Craft, Meggan E.
name: Binning, Sandra A.
Publisher: name: The Royal Society
Year: 2023
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: Health Care
subject: Diseases
subject: 111706 Epidemiology
subject: FOS: Health sciences
subject: 60801 Animal Behaviour
subject: 10202 Biological Mathematics
subject: FOS: Mathematics

description: Ongoing environmental changes alter how natural selection shapes animal migration. Understanding how these changes play out theoretically can be done using evolutionary game theoretic (EGT) approaches, such as looking for evolutionarily stable strategies. Here, we first describe historical patterns of how EGT models have explored different drivers of migration. We find that there are substantial gaps in both the taxa (mammals, amphibians, reptiles, insects) and mechanisms (mutualism, interspecific competition) included in past EGT models of migration. Although enemy interactions, including parasites, are increasingly considered in models of animal migration, they remain the least studied of factors for migration considered to date. Furthermore, few papers look at changes in migration in response to perturbations (e.g. climate change, new species interactions). To address this gap, we present a new EGT model to understand how infection with a novel parasite changes host migration. We find three possible outcomes when migrants encounter novel parasites: maintenance of migration (despite the added infection cost), loss of migration (evolutionary shift to residency) or population collapse, depending on the risk and cost of getting infected, and the cost currency. Our work demonstrates how emerging infection can alter animal behaviour such as migration.This article is part of the theme issue ‘Half a century of evolutionary games: a synthesis of theory, application and future directions’.
Searching for tidal tails around $ω$ Centauri using RR Lyrae Stars
Creators: name: Fernández-Trincado, J. G.
name: Vivas, A. K.
name: Mateu, C. E.
name: Zinn, R.
name: Robin, A. C.
name: Valenzuela, O.
name: Moreno, E.
name: Pichardo, B.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We present a survey for RR Lyrae stars in an area of 50 deg$^2$ around the globular cluster $ω$ Centauri, aimed to detect debris material from the alleged progenitor galaxy of the cluster. We detected 48 RR Lyrae stars of which only 11 have been previously reported. Ten among the eleven previously known stars were found inside the tidal radius of the cluster. The rest were located outside the tidal radius up to distances of $\sim 6$ degrees from the center of the cluster. Several of those stars are located at distances similar to that of $ω$ Centauri. We investigated the probability that those stars may have been stripped off the cluster by studying their properties (mean periods), calculating the expected halo/thick disk population of RR Lyrae stars in this part of the sky, analyzing the radial velocity of a sub-sample of the RR Lyrae stars, and finally, studying the probable orbits of this sub-sample around the Galaxy. None of these investigations support the scenario that there is significant tidal debris around $ω$ Centauri, confirming previous studies in the region. It is puzzling that tidal debris have been found elsewhere but not near the cluster itself.
description: 11 pages, 11 figures, Accepted