cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Pooled Analysis of a Self-Sampling HPV DNA Test as a Cervical Cancer Primary Screening Method
Creators: name: Qiao, Y.-L.
name: Belinson, J. L.
name: Hu, S.-Y.
name: Niyazi, M.
name: Chen, F.
name: Pan, Q.-J.
name: Li, C.-Q.
name: Castle, P. E.
name: Zhang, X.
name: Zhao, F.-H.
name: Lewkowitz, A. K.
name: Ma, J.-F.
name: Li, S.-M.
name: Lin, M. J.
name: Smith, J. S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: BackgroundWorldwide, one-seventh of cervical cancers occur in China, which lacks a national screening program. By evaluating the diagnostic accuracy of self-collected cervicovaginal specimens tested for human papillomavirus (HPV) DNA (Self-HPV testing) in China, we sought to determine whether Self-HPV testing may serve as a primary cervical cancer screening method in low-resource settings.MethodsWe compiled individual patient data from five population-based cervical cancer–screening studies in China. Participants (n = 13 140) received Self-HPV testing, physician-collected cervical specimens for HPV testing (Physician-HPV testing), liquid-based cytology (LBC), and visual inspection with acetic acid (VIA). Screen-positive women underwent colposcopy and confirmatory biopsy. We analyzed the accuracies of pooled Self-HPV testing, Physician-HPV testing, VIA, and LBC to detect biopsy-confirmed cervical intraepithelial neoplasia grade 2 or more severe (CIN2+) and CIN3+. All statistical tests were two-sided.ResultsOf 13 004 women included in the analysis, 507 (3.9%) were diagnosed as CIN2+, 273 (2.1%) as CIN3+, and 37 (0.3%) with cervical cancer. Self-HPV testing had 86.2% sensitivity and 80.7% specificity for detecting CIN2+ and 86.1% sensitivity and 79.5% specificity for detecting CIN3+. VIA had statistically significantly lower sensitivity for detecting CIN2+ (50.3%) and CIN3+ (55.7%) and higher specificity for detecting CIN2+ (87.4%) and CIN3+ (86.9%) (all P values < .001) than Self-HPV testing, LBC had lower sensitivity for detecting CIN2+ (80.7%, P = .015), similar sensitivity for detecting CIN3+ (89.0%, P = .341), and higher specificity for detecting CIN2+ (94.0%, P < .001) and CIN3+ (92.8%, P < .001) than Self-HPV testing. Physician-HPV testing was more sensitive for detecting CIN2+ (97.0%) and CIN3+ (97.8%) but similarly specific for detecting CIN2+ (82.7%) and CIN3+ (81.3%) (all P values <.001) than Self-HPV testing.ConclusionsThe sensitivity of Self-HPV testing compared favorably with that of LBC and was superior to the sensitivity of VIA. Self-HPV testing may complement current screening programs by increasing population coverage in settings that do not have easy access to comprehensive cytology-based screening.
Risk of Non-Melanoma Cancers in First-Degree Relatives of CDKN2A Mutation Carriers
Creators: name: Mukherjee, Bhramar
name: Millikan, Robert C.
name: Orlow, Irene
name: From, Lynn
name: Kricker, Anne
name: Everett, Jessica
name: Gruber, Stephen B.
name: Rosso, Stefano
name: Zanetti, Roberto
name: Berwick, Marianne
name: Jeter, Joanne
name: Armstrong, Bruce K.
name: Begg, Colin B.
name: Raskin, Leon
name: Marrett, Loraine D.
name: Kanetsky, Peter A.
name: DeLancey, John Oliver
name: Culver, Hoda Anton
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: The purpose of this study was to quantify the risk of cancers other than melanoma among family members of CDKN2A mutation carriers using data from the Genes, Environment and Melanoma study. Relative risks (RRs) of all non-melanoma cancers among first-degree relatives (FDRs) of melanoma patients with CDKN2A mutations (n = 65) and FDRs of melanoma patients without mutations (n = 3537) were calculated as the ratio of estimated event rates (number of cancers/total person-years) in FDRs of carriers vs noncarriers with exact Clopper–Pearson-type tests and 95% confidence intervals (CIs). All statistical tests were two-sided. There were 56 (13.1%) non-melanoma cancers reported among 429 FDRs of mutation carriers and 2199 (9.4%) non-melanoma cancers in 23 452 FDRs of noncarriers. The FDRs of carriers had an increased risk of any cancer other than melanoma (56 cancers among 429 FDRs of carrier probands vs 2199 cancers among 23 452 FDRs of noncarrier probands; RR = 1.5, 95% CI = 1.2 to 2.0, P = .005), gastrointestinal cancer (20 cancers among 429 FDRs of carrier probands vs 506 cancers among 23 452 FDRs of noncarrier probands; RR = 2.4, 95% CI = 1.4 to 3.7, P = .001), and pancreatic cancer (five cancers among 429 FDRs of carrier probands vs 41 cancers among 23 452 FDRs of noncarrier probands; RR = 7.4, 95% CI = 2.3 to 18.7, P = .002). Wilms tumor was reported in two FDRs of carrier probands and three FDRs of noncarrier probands (RR = 40.4, 95% CI = 3.4 to 352.7, P = .005). The lifetime risk of any cancer other than melanoma among CDKN2A mutation carriers was estimated as 59.0% by age 85 years (95% CI = 39.0% to 75.4%) by the kin-cohort method, under the standard assumptions of Mendelian genetics on the genotype distribution of FDRs conditional on proband genotype.
Gene therapy of PDE6B-retinopathy as the phototransduction cycle molecule: relevance and the most promising treatment methods
Creators: name: Safonova, Varvara
name: Kopylova, Vera
Publisher: name: IIOABJ
Year: 2023
Subjects: Retinitis pigmentosa
PDE6B
transcriptome analysis
phosphodiesterase
small molecule
treatment

description: Retinitis pigmentosa (RP) is a group of inherited retinal disorders characterized by the progressive photoreceptors and pigment epithelial cells dysfunction. It is the most common genetic retinal degeneration, responsible for loss of vision of most young people worldwide. Symptoms of RP include deterioration of vision in the dark, a decrease in peripheral vision ending up in tunnel vision. More than 50 different genes are involved in the development of RP. The products of these genes are involved in various processes of the visual and phototransduction cycles or are structural elements of the retina. In this paper we focused on one clinical example PDE6B-associated retinitis pigmentosa and analysis of the vision loss pathogenesis, gene network regulation and possible treatment approaches.
Euwallacea destruens
Creators: name: Rabaglia, Robert J.
name: Beaver, Roger A.
name: Johnson, Andrew J.
name: Schmaedick, Mark A.
name: Smith, Sarah M.
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Curculionidae
Euwallacea
Euwallacea destruens

description: * Euwallacea destruens (Blandford) Xyleborus destruens Blandford, 1896: 221. Euwallacea destruens (Blandford): Wood 1989: 173. Beeson (1929) reported this species from Savai‘i and Upolu, Samoa. It is widely distributed in Asia, Australia and the Pacific Islands. Beaver (1976) reported it from rain forests above 600 m in Samoa; in this survey, only one specimen was collected in an ethanol-baited funnel trap at about 34 m on Tutuila Island; the species may be more common in higher elevation rain forests on the Island. Current survey records: American Samoa: Tutuila Isl., Auto, 26 iv–4 v 2017, UHR Ethanol-baited multifunnel trap in 2° scrub, -14.2734 -170.6316, M. Meredith coll. (1, NMNH).
description: Published as part of Rabaglia, Robert J., Beaver, Roger A., Johnson, Andrew J., Schmaedick, Mark A. & Smith, Sarah M., 2020, The bark and ambrosia beetles (Coleoptera: Curculionidae: Scolytinae and Platypodinae) of American Samoa, pp. 171-195 in Zootaxa 4808 (1) on page 180, DOI: 10.11646/zootaxa.4808.1.11, http://zenodo.org/record/3927891
description: {"references": ["Blandford, W. F. H. (1896) Descriptions of new Scolytidae from the Indo-Malayan and Austro-Malayan regions. Transactions of the Entomological Society of London, 1896, 191 - 228. https: // doi. org / 10.1111 / j. 1365 - 2311.1896. tb 00962. x", "Wood, S. L. (1989) Nomenclatural changes and new species of Scolytidae (Coleoptera). Part IV. The Great Basin Naturalist, 49, 167 - 185. https: // doi. org / 10.5962 / bhl. part. 22642", "Beeson, C. F. C. (1929) Platypodidae and Scolytidae. In: Insects of Samoa and the Samoan terrestrial Arthropoda. Part IV. Coleoptera (4) [1927 - 1935]. Trustees of the British Museum, London, pp. 217 - 248.", "Beaver, R. A. (1976) The biology of Samoan bark and ambrosia beetles (Coleoptera, Scolytidae and Platypodidae). Bulletin of Entomological Research, 65, 531 - 548. https: // doi. org / 10.1017 / S 0007485300006210"]}
Every $3$-dimensional convex body can be covered by $14$ smaller homothetic copies
Creators: name: Prymak, A.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Metric Geometry (math.MG)
subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: Primary 52A15, Secondary 52A37, 52A40, 52C17, 90C05

description: We show that every $3$-dimensional convex body can be covered by $14$ smaller homothetic copies. The previous result was $16$ copies established by Papadoperakis in 1999, while a conjecture by Hadwiger is $8$. We modify Papadoperakis's approach and develop a discretization technique that reduces the problem to verification of feasibility of a number of linear programs with rational coefficients, which is done with computer assistance using exact arithmetic.
Germline Genetic Contributions to Risk for Esophageal Adenocarcinoma, Barrett's Esophagus, and Gastroesophageal Reflux
Creators: name: Romero, Y.
name: Reid, B. J.
name: Bernstein, L.
name: Shaheen, N. J.
name: Ye, W.
name: Nordenstedt, H.
name: Risch, H. A.
name: D'Amato, M.
name: Liu, G.
name: Zucchelli, M.
name: Murray, L. J.
name: MacGregor, S.
name: Bird, N. C.
name: Vaughan, T. L.
name: Tornblom, H.
name: Chow, W.-H.
name: Schmidt, P. T.
name: Whiteman, D. C.
name: Wu, A. H.
name: Hardie, L. J.
name: Pedersen, N. L.
name: Gammon, M. D.
name: Onstad, L. E.
name: Hysi, P.
name: Casson, A. G.
name: Spector, T. D.
name: Magnusson, P. K. E.
name: Bresso, F.
name: Corley, D. A.
name: Ek, W. E.
name: Levine, D. M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Esophageal adenocarcinoma (EA) is an increasingly common cancer with poor survival. Barrett’s esophagus (BE) is the main precursor to EA, and every year 0.12% to 0.5% of BE patients progress to EA. BE typically arises on a background of chronic gastroesophageal reflux (GERD), one of the risk factors for EA.
Additional file 2 of The renal pelvis urobiome in the unilateral kidney stone patients revealed by 2bRAD-M
Creators: name: Hong, Sen-Yuan
name: Yang, Yuan-Yuan
name: Xu, Jin-Zhou
name: Xia, Qi-Dong
name: Wang, Shao-Gang
name: Xun, Yang
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Marine Biology

description: Additional file 2: Table S2. Sequencing information summary: number of raw reads, enzyme reads, and clean reads and percentage of enzyme reads and clean reads
Quantum Rabi dynamics of trapped atoms far in the deep strong coupling regime
Creators: name: Koch, Johannes
name: Hunanyan, Geram R.
name: Ockenfels, Till
name: Rico, Enrique
name: Solano, Enrique
name: Weitz, Martin
Publisher: name: arXiv
Year: 2021
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The coupling of a two-level system with an electromagnetic field, whose fully quantized version is the quantum Rabi model, is among the central topics of quantum physics. When the coupling strength becomes large enough that the field mode frequency is reached, the deep strong coupling regime is approached, and excitations can be created from the vacuum. Here we demonstrate a periodic variant of the quantum Rabi model in which the two-level system is encoded in the Bloch band structure of cold rubidium atoms in optical potentials. With this method we achieve a Rabi coupling strength of 6.5 times the field mode frequency, which is far in the deep strong coupling regime, and observe a subcycle timescale raise in bosonic field mode excitations. In a measurement recorded in the basis of the coupling term of the quantum Rabi Hamiltonian, a freezing of dynamics is revealed for small frequency splittings of the two-level system, as expected when the coupling term dominates over all other energy scales, and a revival for larger splittings. Our work demonstrates a route to realize quantum-engineering applications in yet unexplored parameter regimes.
description: 26 pages, 6 figures
Pleiotropic Effects of the Trichloroethylene-Associated P81S VHL Mutation on Metabolism, Apoptosis, and ATM-Mediated DNA Damage Response
Creators: name: DeSimone, M. C.
name: Rathmell, W. K.
name: Threadgill, D. W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: BackgroundThe risk relevance of the P81S von Hippel-Lindau (VHL) gene hotspot mutation identified in clear cell renal cell carcinoma from individuals exposed occupationally to trichloroethylene (TCE) is not known. VHL mutations in hereditary VHL syndrome strongly correlate with phenotypic associations, but specific sporadic mutations in VHL that uniquely alter its protein function may provide a selective growth advantage for somatic cells harboring these mutations.MethodsVHL deficient (Vhl -/-) mouse embryonic stem cells were generated that stably express wild-type, P81S, or R167Q human VHL protein. Under hypoxic conditions, cell lines were examined for hypoxia-inducible transcription factor family (HIF) stabilization and E3-ubiquitin ligase complex interactions. In vivo, teratomas were examined for tumor size, proliferation, apoptosis, and immunohistochemistry and subjected to gene expression analysis. Wild-type, R167Q, and P81S VHL-expressing teratomas were also exposed to 5 Gy ionizing radiation to quantify apoptotic response. Proliferation and apoptosis and teratoma growth were analyzed by either Student t test or analysis of variance with Bonferroni correction. All statistical tests were two-sided.ResultsThe P81S VHL mutation produces deregulation of HIF factors in cell culture but exhibits a growth advantage in the tumor microenvironment, in part because of suppression of apoptosis (P81S mean = 0.9%, 95% confidence interval = 0.6 to 1.2%; WT mean = 7.6%; 95% confidence interval = 6.4 to 8.8%; P < .001) coupled with sustained proliferation. Transcriptional analysis of P81S teratomas revealed the induction of metabolic pathways, antiapoptotic genes, and global suppression of key DNA damage response genes not observed in VHL wild-type or R167Q mutants. In vivo irradiation exposure showed that P81S mutant is resistant to ionizing radiation–induced apoptosis.ConclusionsThe TCE-associated P81S VHL mutation can initiate a unique adaptive response required for selective tumor growth through pleiotropic effects on metabolic diversification, apoptosis suppression, and alteration of the DNA damage response.
Why adiabatic quantum annealing is unlikely to yield speed-up
Creators: name: Villanueva, Aarón
name: Najafi, Peyman
name: Kappen, Hilbert J.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We study quantum annealing for combinatorial optimization with Hamiltonian $H = z H_f + H_0$ where $H_f$ is diagonal, $H_0=-|ϕ\rangle \langle ϕ|$ is the equal superposition state projector and $z$ the annealing parameter. We analytically compute the minimal spectral gap as $\mathcal{O}(1/\sqrt{N})$ with $N$ the total number of states and its location $z_*$. We show that quantum speed-up requires an annealing schedule which demands a precise knowledge of $z_*$, which can be computed only if the density of states of the optimization problem is known. However, in general the density of states is intractable to compute, making quadratic speed-up unfeasible for any practical combinatoric optimization problems. We conjecture that it is likely that this negative result also applies for any other instance independent transverse Hamiltonians such as $H_0 = -\sum_{i=1}^n σ_i^x$.
description: 23 pages, 6 figures, updated to published version
Fredholm Pfaffian $τ$-functions for orthogonal isospectral and isomonodromic systems
Creators: name: Bertola, M.
name: Del Monte, F.
name: Harnad, J.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Mathematical Physics (math-ph)
subject: Combinatorics (math.CO)
subject: Exactly Solvable and Integrable Systems (nlin.SI)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We extend the approach to $τ$-functions as Widom constants developed by Cafasso, Gavrylenko and Lisovyy to orthogonal loop group Drinfeld-Sokolov hierarchies and isomonodromic deformations systems. The combinatorial expansion of the $τ$-function as a sum of correlators, each expressed as products of finite determinants, follows from using multicomponent fermionic vacuum expectation values of certain dressing operators encoding the initial conditions and the dependence on the flow (or deformation) parameters. When reduced to the orthogonal case, these correlators become finite Pfaffians and the determinantal $τ$-functions, both in the Drinfeld-Sokolov and isomonodromic case, become squares of $τ$-functions of Pfaffian type. The results are illustrated by several examples, consisting of polynomial $τ$-functions of orthogonal Drinfeld-Sokolov type and of isomonodromic ones with four regular singular points.
Recycled entanglement detection by arbitrarily many sequential and independent pairs of observers
Creators: name: Pandit, Mahasweta
name: Srivastava, Chirag
name: Sen, Ujjwal
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We investigate the witnessing of two-qubit entangled states by sequential and independent pairs of observers, with both observers of each pair acting independently on their part of the shared state from spatially separated laboratories, and subsequently passing their qubits to the next pair in the sequence. It has previously been conjectured that not more than one pair of observers can detect Clauser-Horne-Shimony-Holt "Bell-nonlocal" correlations in a similar set-up. This is intriguing since it is possible to have an arbitrarily long sequence of Bell-nonlocal correlations when only a single observer is allowed to share a bipartite state with multiple observers at the other end. It is therefore interesting to ask whether such restrictions are also present when entangled correlations are considered in the scenario of multiple pairs of observers. We find that a two-qubit entangled state can be used to witness entanglement arbitrarily many times, by pairs of observers, acting sequentially and independently. We prove the statement to be true when the initial pair of observers in the sequence share any pure entangled state or when they share a state from a class of mixed entangled states. We demonstrate that the phenomenon can also be observed for a certain class of entangled states in which an arbitrarily long sequence of observer pairs witnessing entanglement is reached in the limit of the initial entanglement content tending to a vanishing amount.
description: 6 pages, 1 figure
Prediction of Late Disease Recurrence and Extended Adjuvant Letrozole Benefit by the HOXB13/IL17BR Biomarker
Creators: name: Bhan, Atul K.
name: Zarrella, Elizabeth
name: Ingle, James N.
name: Zhang, Yi
name: Schnabel, Catherine A.
name: Porter, Peggy
name: Muss, Hyman B.
name: Binns, Shemeica N.
name: Sgroi, Dennis C.
name: Goss, Paul E.
name: Steffel, Lauren
name: Erlander, Mark G.
name: Pritchard, Katherine I.
name: Szymonifka, Jackie
name: Finkelstein, Dianne M.
name: Shepherd, Lois E.
name: Rimm, David L.
name: Tu, Dongsheng
name: Carney, Erin
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: BackgroundBiomarkers to optimize extended adjuvant endocrine therapy for women with estrogen receptor (ER)–positive breast cancer are limited. The HOXB13/IL17BR (H/I) biomarker predicts recurrence risk in ER-positive, lymph node–negative breast cancer patients. H/I was evaluated in MA.17 trial for prognostic performance for late recurrence and treatment benefit from extended adjuvant letrozole.MethodsA prospective–retrospective, nested case-control design of 83 recurrences matched to 166 nonrecurrences from letrozole- and placebo-treated patients within MA.17 was conducted. Expression of H/I within primary tumors was determined by reverse-transcription polymerase chain reaction with a prespecified cutpoint. The predictive ability of H/I for ascertaining benefit from letrozole was determined using multivariable conditional logistic regression including standard clinicopathological factors as covariates. All statistical tests were two-sided.ResultsHigh H/I was statistically significantly associated with a decrease in late recurrence in patients receiving extended letrozole therapy (odds ratio [OR] = 0.35; 95% confidence interval [CI] = 0.16 to 0.75; P = .007). In an adjusted model with standard clinicopathological factors, high H/I remained statistically significantly associated with patient benefit from letrozole (OR = 0.33; 95% CI = 0.15 to 0.73; P = .006). Reduction in the absolute risk of recurrence at 5 years was 16.5% for patients with high H/I (P = .007). The interaction between H/I and letrozole treatment was statistically significant (P = .03).ConclusionsIn the absence of extended letrozole therapy, high H/I identifies a subgroup of ER-positive patients disease-free after 5 years of tamoxifen who are at risk for late recurrence. When extended endocrine therapy with letrozole is prescribed, high H/I predicts benefit from therapy and a decreased probability of late disease recurrence.
Quantum metrology with boundary time crystals
Creators: name: Montenegro, V.
name: Genoni, M. G.
name: Bayat, A.
name: Paris, M. G. A.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantum sensing is one of the arenas that exemplifies the superiority of quantum technologies over their classical counterparts. Such superiority, however, can be diminished due to unavoidable noise and decoherence of the probe. Thus, metrological strategies to fight against or profit from decoherence are highly desirable. This is the case of certain types of decoherence-driven many-body systems supporting dissipative phase transitions, which might be helpful for sensing. Boundary time crystals are exotic dissipative phases of matter in which the time-translational symmetry is broken, and long-lasting oscillations emerge in open quantum systems at the thermodynamic limit. We show that the transition from a symmetry unbroken into a boundary time crystal phase, described by a second-order transition, reveals quantum-enhanced sensitivity quantified through quantum Fisher information. We also determine the critical exponents of the system and establish their relationship. Our scheme is indeed a demonstration of harnessing decoherence for achieving quantum-enhanced sensitivity. From a practical perspective, it has the advantage of being independent of initialization and can be captured by a simple measurement.
description: 7 pages main text, 5 figures
Additional file 1 of Drivers of respiratory health care demand in Acre state, Brazilian Amazon: a cross-sectional study
Creators: name: Morello, Thiago
name: Lima, Aldo Santos
name: da Silva, Rubicleis Gomes
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1.
Quantum Metric Unveils Defect Freezing in Non-Hermitian Systems
Creators: name: Sim, Karin
name: Defenu, Nicolò
name: Molignini, Paolo
name: Chitra, R.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Non-Hermiticity in quantum Hamiltonians leads to nonunitary time evolution and possibly complex energy eigenvalues, which can lead to a rich phenomenology with no Hermitian counterpart. In this work, we study the dynamics of an exactly solvable non-Hermitian system, hosting both $\mathcal{PT}$-symmetric and $\mathcal{PT}$-broken modes subject to a linear quench. Employing a fully consistent framework, in which the Hilbert space is endowed with a nontrivial dynamical metric, we analyze the dynamics of the generated defects. In contrast to Hermitian systems, our study reveals that PT -broken time evolution leads to defect freezing and hence the violation of adiabaticity. This physics necessitates the so-called metric framework, as it is missed by the oft used approach of normalizing quantities by the time-dependent norm of the state. Our results are relevant for a wide class of experimental systems.
description: Main text: 7 pages and 3 figures
Local ferromagnetic resonance measurements of mesoscopically patterned ferromagnets using deterministically placed nanodiamonds
Creators: name: Rable, Jeffrey
name: Piazza, Benjamin
name: Dwivedi, Jyotirmay
name: Samarth, Nitin
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Nitrogen-vacancy centers in diamond have recently been established as effective sensors of the magnetization dynamics in vicinal ferromagnetic materials. We demonstrate sub-100 nm placement accuracy of nitrogen-vacancy-containing nanodiamonds and use these as local sensors that probe optically detected ferromagnetic resonance in mesoscopically patterned Permalloy islands. These measurements reveal variations in the ferromagnetic resonance signal at different sites on these structures with distinct behavior in the edge and the bulk of patterned features. These test measurements establish an easily implemented approach for spatially targeted measurements of spin dynamics in mesoscale ferromagnets. In principle, the methodology can also be extended to local studies of nanoscale ferromagnets such as single magnetic nanowires and nanoparticles.
Compactified N=1 supersymmetric Yang-Mills theory on the lattice: Continuity and the disappearance of the deconfinement transition
Creators: name: Bergner, G.
name: Piemonte, S.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: Fermion boundary conditions play a relevant role in revealing the confinement mechanism of N=1 supersymmetric Yang-Mills theory with one compactified space-time dimension. A deconfinement phase transition occurs for a sufficiently small compactification radius, equivalent to a high temperature in the thermal theory where antiperiodic fermion boundary conditions are applied. Periodic fermion boundary conditions, on the other hand, are related to the Witten index and confinement is expected to persist independently of the length of the compactified dimension. We study this aspect with lattice Monte Carlo simulations for different values of the fermion mass parameter that breaks supersymmetry softly. We find a deconfined region that shrinks when the fermion mass is lowered. Deconfinement takes place between two confined regions at large and small compactification radii, that would correspond to low and high temperatures in the thermal theory. At the smallest fermion masses we find no indication of a deconfinement transition. These results are a first signal for the predicted continuity in the compactification of supersymmetric Yang-Mills theory.
description: 17 pages, 9 Figures
Risks of Colorectal and Other Cancers After Endometrial  Cancer for Women With Lynch Syndrome
Creators: name: Gallinger, Steven
name: Kalady, Matthew F.
name: Rosty, Christophe
name: Giles, Graham G.
name: Marchand, Loic Le
name: Tucker, Katherine M.
name: Goldblatt, Jack
name: Parry, Susan
name: Young, Joanne P.
name: Macrae, Finlay A.
name: Jenkins, Mark A.
name: Baron, John A.
name: Buchanan, Daniel D.
name: Haile, Robert W.
name: Lindor, Noralane M.
name: Leggett, Barbara
name: Ahnen, Dennis J.
name: Winship, Ingrid
name: Hopper, John L.
name: Newcomb, Polly A.
name: Win, Aung Ko
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Lynch syndrome is an autosomal dominantly inherited disorder caused by germline mutations in DNA mismatch repair (MMR) genes. Previous studies have shown that MMR gene mutation carriers are at increased risk of colorectal, endometrial, and several other cancers following an initial diagnosis of colorectal cancer. We estimated cancer risks following an endometrial cancer diagnosis for women carrying MMR gene mutations.
Overcoming Exploration: Deep Reinforcement Learning for Continuous Control in Cluttered Environments from Temporal Logic Specifications
Creators: name: Cai, Mingyu
name: Aasi, Erfan
name: Belta, Calin
name: Vasile, Cristian-Ioan
Publisher: name: arXiv
Year: 2022
Subjects: subject: Robotics (cs.RO)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Model-free continuous control for robot navigation tasks using Deep Reinforcement Learning (DRL) that relies on noisy policies for exploration is sensitive to the density of rewards. In practice, robots are usually deployed in cluttered environments, containing many obstacles and narrow passageways. Designing dense effective rewards is challenging, resulting in exploration issues during training. Such a problem becomes even more serious when tasks are described using temporal logic specifications. This work presents a deep policy gradient algorithm for controlling a robot with unknown dynamics operating in a cluttered environment when the task is specified as a Linear Temporal Logic (LTL) formula. To overcome the environmental challenge of exploration during training, we propose a novel path planning-guided reward scheme by integrating sampling-based methods to effectively complete goal-reaching missions. To facilitate LTL satisfaction, our approach decomposes the LTL mission into sub-goal-reaching tasks that are solved in a distributed manner. Our framework is shown to significantly improve performance (effectiveness, efficiency) and exploration of robots tasked with complex missions in large-scale cluttered environments. A video demonstration can be found on YouTube Channel: https://youtu.be/yMh_NUNWxho.
description: IEEE Robotics and Automation Letters
Time-optimal universal quantum gates on superconducting circuits
Creators: name: Li, Ze
name: Liang, Ming-Jie
name: Xue, Zheng-Yuan
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Decoherence is inevitable when manipulating quantum systems. It decreases the quality of quantum manipulations and thus is one of the main obstacles for large-scale quantum computation, where high-fidelity quantum gates are needed. Generally, the longer a gate operation is, the more decoherence-induced gate infidelity will be. Therefore, how to shorten the gate time becomes an urgent problem to be solved. To this end, time-optimal control based on solving the quantum brachistochrone equation is a straightforward solution. Here, based on time-optimal control, we propose a scheme to realize universal quantum gates on superconducting qubits in a two-dimensional square lattice configuration, and the two-qubit gate fidelity approaches 99.9\%. Meanwhile, we can further accelerate the Z-axis gate considerably by adjusting the detuning of the external driving. Finally, in order to reduce the influence of the dephasing error, decoherence-free subspace encoding is also incorporated in our physical implementation. Therefore, we present a fast quantum scheme which is promising for large-scale quantum computation.
description: v2 accepted
Additional file 4 of The renal pelvis urobiome in the unilateral kidney stone patients revealed by 2bRAD-M
Creators: name: Hong, Sen-Yuan
name: Yang, Yuan-Yuan
name: Xu, Jin-Zhou
name: Xia, Qi-Dong
name: Wang, Shao-Gang
name: Xun, Yang
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Marine Biology

description: Additional file 4: Table S3. List of the 20 species in the optimal marker set
Editorial: Advances in brain imaging and stimulation methods for cognitive function investigation
Creators: name: Yuan, Zhen
name: Palm, Ulrich
name: Boettiger, Charlotte A.
name: Assenza, Giovanni
Publisher: name: Frontiers Media SA
Year: 2023

description: The Research Topic “Advances in brain imaging and stimulation methods for cognitive function investigation” gathers basic research and clinical results of experimental brain imaging and stimulation techniques which are used to investigate mechanisms of cognitive function and dysfunction.
Temporal Trends in Presentation and Survival for HIV-Associated Lymphoma in the Antiretroviral Therapy Era
Creators: name: Burkholder, G. A.
name: Napravnik, S.
name: Deeks, S. G.
name: Patel, M. R.
name: Gopal, S.
name: Reid, E. G.
name: Yanik, E. L.
name: Rodriguez, B.
name: Richards, K. L.
name: Achenbach, C. J.
name: Moore, R. D.
name: Cole, S. R.
name: Mayer, K. H.
name: Eron, J. J.
name: Kitahata, M. M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Lymphoma is the leading cause of cancer-related death among HIV-infected patients in the antiretroviral therapy (ART) era.
Giant spin torque efficiency in naturally oxidized polycrystalline TaAs thin films
Creators: name: Yanez, Wilson
name: Ou, Yongxi
name: Xiao, Run
name: Ghosh, Supriya
name: Dwivedi, Jyotirmay
name: Steinebronn, Emma
name: Richardella, Anthony
name: Mkhoyan, K. Andre
name: Samarth, Nitin
Publisher: name: arXiv
Year: 2022
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We report the measurement of efficient charge-to-spin conversion at room temperature in Weyl semimetal/ferromagnet heterostructures with both oxidized and pristine interfaces. Polycrystalline films of the Weyl semimetal, TaAs, are grown by molecular beam epitaxy on (001) GaAs and interfaced with a metallic ferromagnet (Ni$_{0.8}$Fe$_{0.2}$). Spin torque ferromagnetic resonance (ST-FMR) measurements in samples with an oxidized interface yield a spin torque efficiency as large as $ξ_{\mathrm{FMR}}=0.45\pm 0.25$ for a 8 nm Ni$_{0.8}$Fe$_{0.2}$ layer thickness. By studying ST-FMR in these samples with varying Ni$_{0.8}$Fe$_{0.2}$ layer thickness, we extract a damping-like torque efficiency as high as $ξ_{\mathrm{DL}}=1.36\pm 0.66$. In samples with a pristine (unoxidized) interface, the spin torque efficiency has opposite sign to that observed in oxidized samples ($ξ_{\mathrm{FMR}}=-0.27\pm 0.14$ for a 5 nm Ni$_{0.8}$Fe$_{0.2}$ layer thickness). We also find a lower bound on the spin Hall conductivity ($424 \pm 110 \frac{\hbar}{e}$ S/cm) which is surprisingly consistent with theoretical predictions for the single crystal Weyl semimetal state of TaAs.
Xylosandrus compactus
Creators: name: Rabaglia, Robert J.
name: Beaver, Roger A.
name: Johnson, Andrew J.
name: Schmaedick, Mark A.
name: Smith, Sarah M.
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Curculionidae
Xylosandrus
Xylosandrus compactus

description: * Xylosandrus compactus (Eichhoff) Xyleborus compactus Eichhoff, 1876: 201. Xylosandrus compactus (Eichhoff): Nunberg 1959: 434. Beaver (1976) recorded this species for the first time in Samoa (Upolu), and stated that it was presumably a fairly recent introduction, but had spread to the edge of the rain forest. It is widely distributed in tropical and subtropical areas on most continents, and in some areas is a serious pest of cultivated trees and natural forests. It was commonly found in most locations trapped during this survey. Current survey records: American Samoa: Tutuila Isl.: Mapusaga, 20 viii 2000, Galleries in tree seedlings in screenhouse, M. Schmaedick coll. (2, RABC; 5, ASCC); Other locations Tutuila Isl.: Aoa, Asili, Fagaalu, Fagaitua, Masausi, Pago Pago; Aunu‘u Isl., 12 i -1 ii 2017, Ethanol-baited multifunnel trap in mangrove swamp, -14.2879 -170.5571, M. Meredith coll (1, ASCC); Ofu Isl., Ofu, 16 v–6 vi 2018, Quercivorol-baited multifunnel trap in Rhus 2° forest, -14.1674 -169.6761, M. Schmaedick coll. (1, ASCC); Ta‘ū Isl.: Faleasao, 6–10 iv 2015, Yellow pan trap in 2° scrub, -14.2186 -169.4812, M. Schmaedick (1, ASCC), Other locations Ta‘ū Isl.: Ta‘ū.
description: Published as part of Rabaglia, Robert J., Beaver, Roger A., Johnson, Andrew J., Schmaedick, Mark A. & Smith, Sarah M., 2020, The bark and ambrosia beetles (Coleoptera: Curculionidae: Scolytinae and Platypodinae) of American Samoa, pp. 171-195 in Zootaxa 4808 (1) on page 184, DOI: 10.11646/zootaxa.4808.1.11, http://zenodo.org/record/3927891
description: {"references": ["Eichhoff, W. J. (1876) Tomicides. In: Chapuis F & Eichhoff WJ, Scolytides recueillis au Japon par M. G. Lewis. Annales de la Societe Entomologique de Belgique, 18, 195 - 204.", "Nunberg, M. (1959) Die Gattung Xyleborus Eichhoff (Coleoptera: Scolytidae). Erganzungen Berichtigungen und Erweiterung der Diagnosen. Beitrage zur Entomologie, 9, 413 - 466.", "Beaver, R. A. (1976) The biology of Samoan bark and ambrosia beetles (Coleoptera, Scolytidae and Platypodidae). Bulletin of Entomological Research, 65, 531 - 548. https: // doi. org / 10.1017 / S 0007485300006210"]}
Lanthanide molecular nanomagnets as probabilistic bits
Creators: name: Gutiérrez-Finol, Gerliz M.
name: Giménez-Santamarina, Silvia
name: Hu, Ziqi
name: Rosaleny, Lorena E.
name: Cardona-Serra, Salvador
name: Gaita-Ariño, Alejandro
Publisher: name: arXiv
Year: 2023
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Over the decades, the spin dynamics of a large set of lanthanide complexes have been explored. Lanthanide-based molecular nanomagnets are bistable spin systems, generally conceptualized as classical bits, but many lanthanide complexes have also been presented as candidate quantum bits (qubits). Here we offer a third alternative and model them as probabilistic bits (p-bits), where their stochastic behavior constitutes a computational resource instead of a limitation. We present a modelling tool for molecular spin p-bits, we demonstrate its capability to simulate bulk magnetic relaxation data and ac experiments and to simulate a minimal p-bit network under realistic conditions. Finally, we go back to a recent systematic data gathering and screen the best lanthanide complexes for p-bit behavior, lay out the performance of the different lanthanide ions and chemical families and offer some chemical design considerations.
25-Hydroxyvitamin D Levels and Survival in Advanced Pancreatic Cancer: Findings From CALGB 80303 (Alliance)
Creators: name: Venook, Alan P.
name: Niedzwiecki, Donna
name: Jiang, Chen
name: O’Reilly, Eileen M.
name: Owzar, Kouros
name: Kindler, Hedy L.
name: Mulcahy, Mary F.
name: Fuchs, Charles
name: Van Loon, Katherine
name: Innocenti, Federico
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Data from animal and cell-line models suggest that vitamin D metabolism plays an important role in pancreatic tumor behavior. Although vitamin D deficiency has been implicated in numerous cancers, the vitamin D status of patients with advanced pancreatic cancer and the effect of baseline vitamin D levels on survival are unknown.
Nearest neighbor ratio imputation with incomplete multi-nomial outcome in survey sampling
Creators: name: Gao, Chenyin
name: Thompson, Katherine Jenny
name: Yang, Shu
name: Kim, Jae Kwang
Publisher: name: arXiv
Year: 2022
Subjects: subject: Methodology (stat.ME)
subject: Applications (stat.AP)
subject: FOS: Computer and information sciences

description: Nonresponse is a common problem in survey sampling. Appropriate treatment can be challenging, especially when dealing with detailed breakdowns of totals. Often, the nearest neighbor imputation method is used to handle such incomplete multinomial data. In this article, we investigate the nearest neighbor ratio imputation estimator, in which auxiliary variables are used to identify the closest donor and the vector of proportions from the donor is applied to the total of the recipient to implement ratio imputation. To estimate the asymptotic variance, we first treat the nearest neighbor ratio imputation as a special case of predictive matching imputation and apply the linearization method of \cite{yang2020asymptotic}. To account for the non-negligible sampling fractions, parametric and generalized additive models are employed to incorporate the smoothness of the imputation estimator, which results in a valid variance estimator. We apply the proposed method to estimate expenditures detail items based on empirical data from the 2018 collection of the Service Annual Survey, conducted by the United States Census Bureau. Our simulation results demonstrate the validity of our proposed estimators and also confirm that the derived variance estimators have good performance even when the sampling fraction is non-negligible.
description: Accepted for publication in JRSS(A)
Tuning quantum fluctuations with an external magnetic field: Casimir-Polder interaction between an atom and a graphene sheet
Creators: name: Cysne, T.
name: Kort-Kamp, W. J. M.
name: Oliver, D.
name: Pinheiro, F. A.
name: Rosa, F. S. S.
name: Farina, C.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We investigate the dispersive Casimir-Polder interaction between a Rubidium atom and a suspended graphene sheet subjected to an external magnetic field B. We demonstrate that this concrete physical system allows for an unprecedented control of dispersive interactions at micro and nanoscales. Indeed, we show that the application of an external magnetic field can induce a 80% reduction of the Casimir-Polder energy relative to its value without the field. We also show that sharp discontinuities emerge in the Casimir-Polder interaction energy for certain values of the applied magnetic field at low temperatures. Moreover, for sufficiently large distances these discontinuities show up as a plateau-like pattern with a quantized Casimir-Polder interaction energy, in a phenomenon that can be explained in terms of the quantum Hall effect. In addition, we point out the importance of thermal effects in the Casimir-Polder interaction, which we show that must be taken into account even for considerably short distances. In this case, the discontinuities in the atom-graphene dispersive interaction do not occur, which by no means prevents the tuning of the interaction in ~50% by the application of the external magnetic field.
description: The first two authors listed contributed equally to this work and are joint first authors. 5 pages, 4 figures
Temperature Dependence of Spin and Charge Orders in the Doped Two-Dimensional Hubbard Model
Creators: name: Xiao, Bo
name: He, Yuan-Yao
name: Georges, Antoine
name: Zhang, Shiwei
Publisher: name: arXiv
Year: 2022
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Competing and intertwined orders including inhomogeneous patterns of spin and charge are observed in many correlated electron materials, such as high-temperature superconductors. Introducing a new development of the constrained-path auxiliary-field quantum Monte Carlo (AFQMC) method, we study the interplay between thermal and quantum fluctuations in the two-dimensional Hubbard model. We obtain an accurate and systematic characterization of the evolution of the spin and charge correlations as a function of temperature $T$ and how it connects to the ground state, at three representative doping levels $δ= 1/5$, $1/8$, and $1/10$. We find increasing short-range commensurate antiferromagnetic correlations as $T$ is lowered. As the correlation length grows sufficiently large, a modulated spin-density-wave (SDW) appears. At $δ= 1/5$, the SDW saturates and remains short-ranged as $T \rightarrow 0$. In contrast, at $δ= 1/8$ and $1/10$ this evolves into a ground-state stripe phase. We study the relation between spin and charge orders and find that formation of charge order appears to be driven by that of the spin order. We identify a finite-temperature phase transition below which charge ordering sets in and discuss the implications of our results for the nature of this transition.
description: 21 pages, 15 figures
Effect of Cytotoxic Chemotherapy on Markers of Molecular Age in Patients With Breast Cancer
Creators: name: Muss, Hyman B.
name: Gordon, Brittaney-Belle
name: Sanoff, Hanna K.
name: Torrice, Chad
name: Rudolph, K. Lenhard
name: Drobish, Amy
name: Alston, Shani
name: Williams, Grant
name: Jolly, Trevor A.
name: Deal, Allison M.
name: Ibrahim, Joseph G.
name: Kleinhans, Karin
name: Carey, Lisa A.
name: Hurria, Arti
name: Sorrentino, Jessica
name: Krishnamurthy, Janakiraman
name: Sharpless, Norman E.
name: Dillon, Patrick
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Senescent cells, which express p16 INK4a, accumulate with aging and contribute to age-related pathology. To understand whether cytotoxic agents promote molecular aging, we measured expression of p16 INK4a and other senescence markers in breast cancer patients treated with adjuvant chemotherapy.