bluuebunny/crossref_metadata_2025 huggingface dataset:
Face and Content Validity of Tympanostomy Tube Simulator With Variable Canal Size
Authors: Monk Aurelia S. , Larabee Landon , Bacon Daniel R. , Woodard Andrew , Kimple Adam J. , DeMason Christine E.
Published: January 2025

Simulators allow junior otolaryngology residents to practice the delicate procedure of pressure equalization tube (PET) insertion. However, most simulators lack the ability to mimic the differing anatomic complexities between patients, such as variable external auditory canal (EAC) size. We developed a novel low‐cost, medium‐fidelity 3‐dimensional‐printed PET simulator with different EAC sizes to better reflect procedure complexity. Additionally, a variety of materials were tested to mimic the elastic modulus of the tympanic membrane, with “Press'n Seal” cling film being chosen for its cost‐effectiveness and tactile similarity. Ten otolaryngologists performed PET insertion on both EAC sizes followed by a survey to assess face and content validity. Results indicated both high face and content validity, with most participants agreeing the simulator provided a realistic experience and would be useful for training. While our study has a small sample size, our PET simulator adds a unique and valuable addition to PET training.
Applying the Singapore Model in Cambodia and Thailand? Implications for Transnational Policy Transfer
Authors: Lee Celia , Liu Hong , Van Cao Thi
Published: January 2025

The dominant narrative has traditionally framed the Global North as the source of effective political and economic development, with knowledge and expertise flowing unidirectionally to the Global South. However, the rise of the Global South has fostered institutionalized South‒South exchanges, enabling nations to move beyond aid‐recipient roles and engage in mutual learning. This article expands the discourse on policy transfer by examining Singapore's executive development programmes for Cambodian and Thai public officials (2014–2023). Unlike North‒South transfers, typically characterized by donor dominance, South‒South exchanges highlight the active participation of multiple stakeholders and the critical importance of local contexts in shaping outcomes. The findings reveal that successful South‒South policy transfer is contingent upon both structural adaptation and a fundamental shift in mindset. By emphasizing these complexities, this study provides fresh insights into the evolving dynamics of global development and the agency of the Global South.
Proposal: Bold New Indications for Transcatheter Pulmonary Flow Restrictors
Authors: Schranz Dietmar
Published: January 2025

This proposal presents a proof of concept for the use of pulmonary flow restrictors (PFRs) based on MVP™-devices, drawing from clinical experience, and explores their potential role in the management of newborns with hypoplastic left heart syndrome (HLHS), other complex left heart lesions, and infants with end-stage dilated cardiomyopathy (DCM). At this early stage of age, manually adjusted PFRs can be tailored to patient’s size and hemodynamic needs. Although currently used off-label, PFRs have substantial potential to improve outcomes in these vulnerable patient populations. When integrated into a holistic treatment strategy, they represent a promising advancement in care. There is significant potential to reduce mortality and improve the quality of life for neonates with HLHS and variants, as well as to support age-dependent functional regeneration in DCM, all while avoiding the need for advanced surgical procedures, including general anesthesia. The main barrier to broader adoption is the limited availability of appropriately sized MVP devices. However, with ongoing patient-centered knowledge sharing and refinement of transcatheter techniques, there is reason for optimism that PFRs, tailored for individual patients, could provide significant benefits to thousands of infants with congenital heart disease and DCM worldwide.
Complexity Framework for Forbidden Subgraphs I: The Framework
Authors: Johnson Matthew , Martin Barnaby , Oostveen Jelle J. , Pandey Sukanya , Paulusma Daniël , Smith Siani , van Leeuwen Erik Jan
Published: January 2025

For a set of graphs

$${\mathcal {H}}$$

H

, a graph G is

$${\mathcal {H}}$$

H

-subgraph-free if G does not contain any graph from 

$${{{\mathcal {H}}}}$$

H

as a subgraph. We propose general and easy-to-state conditions on graph problems that explain a large set of results for

$${\mathcal {H}}$$

H

-subgraph-free graphs. Namely, a graph problem must be efficiently solvable on graphs of bounded treewidth, computationally hard on subcubic graphs, and computational hardness must be preserved under edge subdivision of subcubic graphs. Our meta-classification says that if a graph problem 

$$\Pi $$

Π

satisfies all three conditions, then for every finite set

$${{{\mathcal {H}}}}$$

H

, it is “efficiently solvable” on

$${{{\mathcal {H}}}}$$

H

-subgraph-free graphs if

$${\mathcal {H}}$$

H

contains a disjoint union of one or more paths and subdivided claws, and

$$\Pi $$

Π

is “computationally hard” otherwise. We apply our meta-classification on many well-known partitioning, covering and packing problems, network design problems and width parameter problems to obtain a dichotomy between polynomial-time solvability and -completeness. For distance-metric problems, we obtain a dichotomy between almost-linear-time solvability and having no subquadratic-time algorithm (conditioned on some hardness hypotheses). Apart from capturing a large number of explicitly and implicitly known results in the literature, we also prove a number of new results. Moreover, we perform an extensive comparison between the subgraph framework and the existing frameworks for the minor and topological minor relations, and pose several new open problems and research directions.
Genome sizes of grasses (Poaceae), chromosomal evolution, paleogenomics and the ancestral grass karyotype (AGK)
Authors: Tkach Natalia , Winterfeld Grit , Röser Martin
Published: January 2025

Grasses are one of the largest angiosperm families, widespread and economically important. Variation in genome size has functional consequences and is an essential parameter for understanding evolutionary patterns. In this study, we report the nuclear genome sizes (2C values) of 32 species and subspecies from 27 genera of Poaceae, including most of its subfamilies, examined by flow cytometry. Obtained genome sizes were analyzed together with the chromosome numbers to give information on the size of monoploid chromosome sets with the chromosome base number x and the mean chromosome size and then supplemented with the previously published data to obtain a deeper insight into the genome size evolution in grasses. Monoploid genomes of < 0.6 pg/1Cx and chromosomes of < 0.1 pg are presumably characteristic of the subfamilies Arundinoideae, Chloridoideae, Micrairoideae and the Oryzoideae. The larger 1Cx values (1.2–1.8 pg) of the evolutionarily ‘early diverging’ subfamilies Anomochlooideae and Pharoideae are discussed in context with the origin of grasses and the pan-grass whole-genome duplication. The data indicate that the ancestral grass had a monoploid genome of this size, which is less than half the size previously assumed. Genome size data and available chromosome numbers support the concept of the ancestral grass karyotype (AGK) with x = 12. The AGK seems to have been conserved in some grass subfamilies (Bambusoideae, Oryzoideae, Pharoideae, parts of the Pooideae), while the major genome rearrangements are lineage-specific and occurred after the separation of the BOP and the PACMAD clades, i.e. when the diversification of their subfamilies had begun.
Demographic and clinical trends of young breast cancer patients from the national cancer database: disproportionate effect on minority populations
Authors: Mark Cynthia , Pujara Vivek , Boyle Marissa K. , Yuan Yuan , Lee Jin Sun
Published: January 2025

Purpose

There is an increasing incidence of young breast cancer (YBC) patients with uncertainty surrounding the factors and patterns that are contributing.

Methods

We obtained characteristics and survival data from 206,156 YBC patients (≤ 40 years of age) diagnosed between 2005 and 2019 from the National Cancer Database (NCDB). Patients were subdivided into two comparison groups based on year of diagnosis (2005–2009, Old vs. 2015–2019, New group). A Chi-square test of independence was employed to measure the changes. Cox proportional hazards model was used to explore the variables influencing overall survival (OS).

Results

Comparison between Old (55,397 patients) and New groups (67,930 patients) showed an increase in the proportion of Hispanic (8.4% vs 10.0%), Black (16.0% vs 16.6%), and Asian (4.8% vs 6.7%) populations. In the New group, black patients had a significantly worse OS, p < 0.001. Additionally, there was a reduction in the proportion of patients with private insurance (43,940 (81.7%) vs 51,104 (76.4%)) and an increase in patients with Medicaid (5,893 (11.0%) vs 10,694 (16.0%)). Finally, there was a significant increase in hormone positive disease (35,142 (70.0%) vs 49,409 (75.8%), p = < 0.001).

Conclusions

Within YBC patients, the proportion of underrepresented and underserved population is increasing, with an impact on OS. We also see an increase in hormone positive disease. Awareness of these at-risk populations is important for early identification of breast cancer and mitigation of poorer outcomes. Also, there are increasing rates of hormone positive disease which can cause substantial personal and societal implications, such as impacts on family planning and early menopause.
Loneliness Among Parents in Sweden Who Regret Having Children
Authors: Bodin Maja , Fängström Karin
Published: January 2025

Loneliness is a common feeling often framed in negative terms. It can take several forms, including social, emotional, and existential loneliness, or through the concept of solitude, which is the desire to be alone. This qualitative study explores these types of loneliness among Swedish parents who regret having children. Our analysis of 29 interviews shows that loneliness is intertwined with regretting parenthood. Participants perceived that parental regret was unconventional, socially taboo, and unspeakable, which resulted in feelings of loneliness, shame, and guilt. They also reported that healthcare professionals, friends, and family rarely acknowledge parental feelings of regret and loneliness. Since loneliness is associated with the potential for mental health issues, it is important to build support structures for parents. In Sweden, the welfare state relies on healthcare professionals (such as nurses, midwives, and psychologists) to support parents. There is hence a need to create better support structures for parents dealing with regret and loneliness, including specialized training for healthcare professionals who work with these vulnerable groups.
Quantifying VMAT2 target occupancy at effective valbenazine doses and comparing to a novel VMAT2 inhibitor: a translational PET study
Authors: Terry-Lorenzo Ryan , Albrecht Daniel , Crouch Sabrinia , Wong Richard , Loewen Gordon , Giri Nagdeep , Skor Heather , Lin Kelly , Sandiego Christine M. , Pajonas Meghan , Rabiner Eugenii A. , Gunn Roger N. , Russell David S. , Haubenberger Dietrich
Published: January 2025

Positron emission tomography (PET) is frequently used to obtain target occupancy (%TO) of central nervous system (CNS) drug candidates during clinical development. Obtaining %TO with PET can be particularly powerful when the %TO associated with efficacy is known for a protein target. Using the radiotracer [18F]AV-133, the relationship between plasma concentration (PK) and %TO of NBI-750142, an experimental inhibitor of the vesicular monoamine transporter type 2 (VMAT2) was obtained in both nonhuman primate (NHP) and human. This work established [18F]AV-133 PET as capable of providing a VMAT2 inhibitor PK-%TO relationship that translated from NHP to human. To establish the VMAT2%TO benchmark, PET was performed in NHP with NBI-98782, the main active metabolite of valbenazine, and this PK-%TO relationship was used to estimate VMAT2%TO at NBI-98782 exposures associated with valbenazine therapeutic effects in the treatment of tardive dyskinesia (TD). This work defined 85–90% as the VMAT2%TO achieved by exposures associated with daily dosing with 80 mg valbenazine, a dosing regimen known to exhibit a large effect size in the treatment of TD and in the treatment of chorea associated with Huntington’s Disease. NBI-750142 was estimated to achieve 36–78% VMAT2 target occupancy at acceptable doses, indicating potential inferiority in conferring clinical benefit compared to valbenazine. It is recommended that the %TO benchmark of valbenazine derived from [18F]AV-133 PET serve as a gold standard biomarker to evaluate novel VMAT2 inhibitors undergoing clinical development.
Characterisation of heritable TP53-related cancer syndrome in Sweden—a nationwide study of genotype-phenotype correlations in 90 families
Authors: Omran Meis , Liu Yaxuan , Sun Zhang Alexander , Poluha Anna , Stenmark-Askmalm Marie , Persson Fredrik , Hallbeck Anna-Lotta , Rosén Anna , Helgadottir Hafdis T. , Tham Emma , Bajalica-Lagercrantz Svetlana
Published: January 2025

We aimed to describe the clinical characteristics of families with heritable TP53-related cancer (hTP53rc) syndrome in Sweden with class 4 and 5 germline TP53 variants (gTP53), and to evaluate the genotype-phenotype correlation. These results were also used to evaluate our previously published phenotype prediction model based on TP53 missense variants and their impact on protein conformation. 90 families with hTP53rc were initially identified in Sweden. After variant reclassification using the TP53-specific ACMG criteria, 83 families remained (176 carriers) to harbour a pathogenic (class 5) or likely pathogenic (class 4) variant in TP53. Of these, 112 carriers (64%) had a previous history of cancer, and 35 (31%) had developed more than one primary tumour. 16% of the families met the stricter criteria for Classic Li-Fraumeni syndrome, 45% the updated Chompret criteria, 35% for hereditary breast cancer (HBC), and the remaining 5% were classified as “Others”. We identified 42 different gTP53 variants of which 22 were missense. The most frequently observed variant was the missense c.542 G > A, p.R181H identified in 14/29 (48%) of HBC families. Fifteen of the 20 informative missense variants (75%) were phenotypically predicted correctly using our previously published in silico prediction model. The TP53 p.R181H was identified as a common Swedish variant predominantly associated with an HBC phenotype. Apart from this variant, there were no significant genotype-phenotype correlations. Therefore, due to phenotypic overlap it is still too early to stratify surveillance programme for different TP53-carriers.
ATG8 delipidation is not universally critical for autophagy in plants
Authors: Zou Yong , Ohlsson Jonas A. , Holla Sanjana , Sabljić Igor , Leong Jia Xuan , Ballhaus Florentine , Krebs Melanie , Schumacher Karin , Moschou Panagiotis N. , Stael Simon , Üstün Suayib , Dagdas Yasin , Bozhkov Peter V. , Minina Elena A.
Published: January 2025

Intracellular recycling via autophagy is governed by post-translational modifications of the autophagy-related (ATG) proteins. One notable example is ATG4-dependent delipidation of ATG8, a process that plays critical but distinct roles in autophagosome formation in yeast and mammals. Here, we aim to elucidate the specific contribution of this process to autophagosome formation in species representative of evolutionarily distant green plant lineages: unicellular green alga Chlamydomonas reinhardtii, with a relatively simple set of ATG genes, and a vascular plant Arabidopsis thaliana, harboring expanded ATG gene families. Remarkably, the more complex autophagy machinery of Arabidopsis renders ATG8 delipidation entirely dispensable for the maturation of autophagosomes, autophagic flux, and related stress tolerance; whereas autophagy in Chlamydomonas strictly depends on the ATG4-mediated delipidation of ATG8. Importantly, we also demonstrate the distinct impact of different Arabidopsis ATG8 orthologs on autophagosome formation, especially prevalent under nitrogen depletion, providing new insight into potential drivers behind the expansion of the ATG8 family in higher plants. Our findings underscore the evolutionary diversification of the molecular mechanism governing the maturation of autophagosomes in eukaryotic lineages and highlight how this conserved pathway is tailored to diverse organisms.
Assessment of energy management and power quality improvement of hydrogen based microgrid system through novel PSO-MWWO technique
Authors: Murtza Qamar Hafiz Ghulam , Guo Xiaoqiang , Seif Ghith Ehab , Tlija Mehdi , Siddique Abubakar
Published: January 2025

A hybrid microgrid powered by hydrogen is an energy infrastructure that depends on hydrogen as its primary energy carrier within a localized network. This study proposed a novel bi-level optimization approach to enhance power quality and cost efficiency of the system. In the quest to improve energy management systems (EMS) and enhance power quality, a bi-level optimization approach named Particle swarm optimization-Modified water wave optimization (PSO-MWWO) has been proposed. This method integrates adaptive population size and an adaptive wavelength coefficient to boost its overall effectiveness. It is attractive with specialists in energy management systems (EMS), control systems, and hydrogen technologies can significantly augment the efficiency of coordination endeavours. PSO-MWWO can incorporate environmental considerations, such as minimizing emissions or exploiting the use of renewable energy resources (RESs) in hydrogen production and consumption. This paper thoroughly examines its implementation, operation, and unique features, with a particular emphasis on the power quality of a hydrogen based microgrid. The achieved results and numerical analysis affirm the superiority of the proposed technique compared to other traditional methods like mixed integer linear programming (MILP), HOMER, Variable mesh optimization (VMO), and Cataclysmic genetic algorithm in optimizing component sizing, renewable production, hydrogen production, reliability, cost effective, and overall efficacy. This substantiates its practical utility in real-time applications. The efficacy of this method is empirically demonstrated through the implementation in MATLAB software.
Marine carbon burial enhanced by microbial carbonate formation at hydrocarbon seeps
Authors: Smrzka Daniel , Tseng Yiting , Zwicker Jennifer , Schröder-Ritzrau Andrea , Frank Norbert , Schmitt Anne-Désirée , Pape Thomas , Birgel Daniel , Peckmann Jörn , Lin Saulwood , Bohrmann Gerhard
Published: January 2025

Some of the carbon removed from Earth’s surface is stored within authigenic carbonate in marine sediments. Methane seeps are crucial sites of global marine carbon cycling sustaining microbial activity, enabling carbonate formation and the transfer of methane-derived carbon to the geosphere. Carbon sequestration rates depend on carbonate precipitation rates, which can be accelerated by mat-forming microorganisms that are ubiquitous at methane seeps and other Earth surface environments today. We investigate a 5-m-long drill core from an active methane seep at 1350 m water depth in the South China Sea with an exceptional abundance of pink and clear aragonite cement derived from the sulfate-driven anaerobic oxidation of methane, yet both cements precipitated under different conditions. Phase-specific 230Th/U-based ages, lipid biomarker compositions, and calcium isotope data suggest that pink aragonite is a product of in situ biofilm mineralization. First estimated precipitation rates of these individual cements in the seep carbonates range from 0.04 cm/ka for clear aragonite to 1.0 cm/ka for pink aragonite, suggesting an up to 25-fold increase in precipitation rates associated with biofilm mineralization. These results provide first kinetic constraints for future quantitative carbon cycle models, emphasizing the role of biofilms in accelerating carbon sequestration in marine authigenic carbonates.
Short- and long-term impact of governance on firm performance in emerging and developed economies: a comparative analysis
Authors: Natto Dinah , Mokoaleli-Mokoteli Thabang
Published: January 2025

This study examines the short- and long-term effects of internal and external governance on firm performance in both emerging and developed markets. The complex interplay between governance mechanisms and their impact on firms' financial outcomes requires further investigation, especially in the distinct and evolving economic contexts of these markets. Using the generalized method of moments, we assess the influence of internal and external corporate governance on firm performance while controlling for factors such as economic growth. Countries in the sample were selected based on their prominent roles within their respective economic blocs and unique economic and firm characteristics. We found that the internal governance mechanisms support firm performance in both emerging and developed markets in the short run. However, other factors play a more significant role in the long run. The results suggest that managers should strive to balance short-term gains with long-term sustainable growth view of company. For policymakers in emerging and developed markets, this study highlights the importance of designing governance frameworks that support firm performance across varying time horizons. This research offers a novel contribution by exploring the distinct short- and long-run interactions between governance machanisms and firm performance, comparing this dynamics across emerging and developed markets.
Low-temperature domain-wall dynamics in weak ferromagnets
Authors: Kuz’menko A. P.
Published: July 2002

The nonlinear and multidimensional supersonic dynamics of domain walls in weak ferromagnets—orthoferrites and iron borate—are investigated experimentally at low temperatures in magnetic fields much less than the spin-flop field. A qualitative physical model of the observed effects is presented, and an elastically induced spin-reorientation mechanism of magnetization reversal is observed and investigated. This mechanism is accompanied by the unsteady motion of the domain walls, the velocity of which is considerably higher than the limiting velocity for their steady-state motion.
A nonlinear regularization method for the analysis of photon correlation spectroscopy data
Authors: Honerkamp J. , Maier D. , Weese J.
Published: July 2002

In photon correlation spectroscopy, a time correlation function of the scattered light intensity is measured. Among other parameters, the relaxation time spectrum can be calculated from such measurement. This is usually done in two steps. First, the scattered field time correlation function is determined. In the second step, the relaxation time spectrum is calculated by solving a linear integral equation with Tikhonov regularization. With an adequate error model and a nonlinear regularization method, the analysis of photon correlation spectroscopy data can be improved considerably. We give a description of the improved method and illustrate its advantages.
BRST quantization of gauge theories like SL(2,R) on inner product spaces
Authors: Marnelius Robert , Quaade Ulrich
Published: July 2002

Some general formulas are derived for the solutions of a BRST quantization on inner product spaces of finite dimensional bosonic gauge theories invariant under arbitrary Lie groups. A detailed analysis is then performed of SL(2,R) invariant models and some possible geometries of the Lagrange multipliers are derived together with explicit results for a class of SL(2,R) models. Gauge models invariant under a nonunimodular gauge group are also studied in some detail.
The effect of low-frequency turbulence on flux, particle, and energy confinement in a field-reversed configuration
Authors: Krall N. A.
Published: July 2002

A recent stability calculation solved the dispersion matrix to find three distinct unstable modes in three distinct regions of the field-reversed configuration (FRC). In the present work the transport produced by these three low-frequency modes is calculated, and both global transport scaling estimates and local transport coefficients are obtained. The result is that low-frequency drift wave transport agrees with most present experimental measurements of particle, flux, and energy loss both in terms of magnitude and scaling, becoming less dominant as the collision frequency decreases.
Ionization behind strong normal shock waves in argon
Authors: Kaniel A. , Igra O. , Ben-Dor G. , Mond M.
Published: July 2002

The ionization of argon by strong normal shock waves is studied. The conservation equations are solved to yield the plasma behavior behind the shock wave front. Very good agreement is obtained between experimental findings and the present numerical results for the electron number density, plasma density, and degree of ionization, especially at the electron avalanche region of the relaxation zone. The high accuracy of the present numerical solutions in reproducing the electron avalanche is attributed to the use of accurate threshold collision cross sections for excitation of argon by electron collisions. To support this claim it is demonstrated that if different assumptions were used to describe the ionization process, then the computed results would be different only upstream of the electron avalanche region, i.e., it is shown that the proposed model for ionizing shock waves enables a highly accurate reproduction of the electron avalanche but is less accurate in predicting its exact location.
Aneurisms in laser-driven blast waves
Authors: Stamper J. A. , Ripin B. H. , Peterkin R. E. , Stellingwerf R. F.
Published: July 2002

When a short-pulse laser beam is focused onto a solid target in a few torr ambient gas, the expanding target plasma couples to the resulting ambient plasma. Dark-field shadowgrams show that a thin, nearly spherical blast front is produced. These shadowgrams also show that certain regions of the blast front (called aneurisms) may project well ahead of the neighboring, spherical part. Several mechanisms for aneurisms are discussed. One class of aneurisms is consistently produced along the laser axis when the laser energy is greater than about 10 J. Two-dimensional, hydrodynamic computer simulations of these on-axis aneurisms show that they can be accounted for by the laser heating of an on-axis channel.
Sensor-independent stimulus representations
Authors: Levin David N.
Published: July 2002

This paper shows how time-dependent sensory data from an evolving stimulus can be blindly rescaled in a nonlinear time-dependent fashion to create a time series of stimulus representations that are invariant under any unknown invertible transformation of the sensory data. These representations are invariant, because they encode “inner” properties of the time series of stimulus configurations themselves. This means that any two devices, possibly equipped with significantly different sensors, will create the same rescaled representation of an evolving stimulus, as long as they are sensitive to the same internal degrees of freedom of the stimulus. Such sensor-independent stimulus representations will also be unaffected by a wide variety of processes that invertibly remap sensor states, including: (
i
) altered performance of a device's detector; (
ii
) changes in the observational environment external to the sensory device and the stimulus; and (
iii
) certain modifications of the presentation of the stimuli themselves. In an intelligent sensory device, this kind of representation “engine” could function as a “front end” that passes rescaled sensor state representations to the device's pattern analysis module. Because the effects of many extraneous observational conditions have been “filtered out” of these representations, it would not be necessary to recalibrate the device's detectors or to retrain its pattern analysis module in order to account for these factors.
Structural variation of the pseudoautosomal region between and within inbred mouse strains.
Authors: Kipling D , Wilson H E , Thomson E J , Lee M , Perry J , Palmer S , Ashworth A , Cooke H J
Published: July 2002

The pseudoautosomal region (PAR) is a segment of shared homology between the sex chromosomes. Here we report additional probes for this region of the mouse genome. Genetic and fluorescence in situ hybridization analyses indicate that one probe, PAR-4, hybridizes to the pseudoautosomal telomere and a minor locus at the telomere of chromosome 9 and that a PCR assay based on the PAR-4 sequence amplifies only the pseudoautosomal locus (DXYHgu1). The region detected by PAR-4 is structurally unstable; it shows polymorphism both between mouse strains and between animals of the same inbred strain, which implies an unusually high mutation rate. Variation occurs in the region adjacent to a (TTAGGG)n array. Two pseudoautosomal probes can also hybridize to the distal telomeres of chromosomes 9 and 13, and all three telomeres contain DXYMov15. The similarity between these telomeres may reflect ancestral telomere-telomere exchange.
Molecular cloning of a protein kinase whose phosphorylation is regulated by genetic adhesion during Chlamydomonas fertilization.
Authors: Kurvari V , Zhang Y , Luo Y , Snell W J
Published: July 2002

Fertilization in Chlamydomonas is initiated by adhesive interactions between gametes of opposite mating types through flagellar glycoproteins called agglutinins. Interactions between these cell adhesion molecules signal for the activation of adenylyl cyclase through an interplay of protein kinases and ultimately result in formation of a diploid zygote. One of the early events during adhesion-induced signal transduction is the rapid inactivation of a flagellar protein kinase that phosphorylates a 48-kDa protein in the flagella. We report the biochemical and molecular characterization of the 48-kDa protein. Experiments using a bacterially expressed fusion protein show that the 48-kDa protein is capable of autophosphorylation on serine and tyrosine and phosphorylation of bovine beta-casein on serine, confirming that the 48-kDa protein itself has protein kinase activity. This protein kinase exhibits limited homology to members of the eukaryotic protein kinase superfamily and may be an important element in a signaling pathway in fertilization.
A modified gambler's ruin model of polyethylene chains in the amorphous region.
Authors: Duan Z H , Howard L N
Published: July 2002

Polyethylene chains in the amorphous region between two crystalline lamellae M unit apart are modeled as random walks with one-step memory on a cubic lattice between two absorbing boundaries. These walks avoid the two preceding steps, though they are not true self-avoiding walks. Systems of difference equations are introduced to calculate the statistics of the restricted random walks. They yield that the fraction of loops is (2M - 2)/(2M + 1), the fraction of ties 3/(2M + 1), the average length of loops 2M - 0.5, the average length of ties 2/3M2 + 2/3M - 4/3, the average length of walks equals 3M - 3, the variance of the loop length 16/15M3 + O(M2), the variance of the tie length 28/45M4 + O(M3), and the variance of the walk length 2M3 + O(M2).
The Ku-like protein from Saccharomyces cerevisiae is required in vitro for the assembly of a stable multiprotein complex at a eukaryotic origin of replication.
Authors: Shakibai N , Kumar V , Eisenberg S
Published: July 2002

We have previously shown that three distinct DNA-binding activities, in crude form, are necessary for the ATP-dependent assembly of a specific and stable multiprotein complex at a yeast origin of replication. Here we show the purification of one of these DNA binding activities, referred to as origin binding factor 2 (OBF2). The purified protein is a heterodimer composed of two polypeptides with molecular mass values of 65 and 80 kDa as determined by SDS/PAGE. Purified OBF2 not only binds DNA but also supports the formation of a protein complex at essential sequences within the ARS121 origin of replication. Interestingly, OBF2 binds tightly and nonspecifically to both duplex DNA and single-stranded DNA. The interaction with duplex DNA occurs at the termini. N-terminal sequencing of the 65-kDa subunit has revealed that this polypeptide is identical to the previously identified HDF1 peptide, a yeast homolog of the small subunit of the mammalian Ku autoantigen. Although the potential involvement of Ku in DNA metabolic events has been proposed, this is the first requirement for a Ku-like protein in the assembly of a protein complex at essential sequences within a eukaryotic origin of replication.
A brief survey of symmetry in mathematics
Authors: Mostow G. D.
Published: July 2002

This paper presents a brief survey of the idea of symmetry in
mathematics, as exemplified by some particular developments in algebra,
differential equations, topology, and number theory.
The newt ribozyme is part of a riboprotein complex
Authors: Luzi Ettore , Eckstein Fritz , Barsacchi Giuseppina
Published: July 2002

Strand-specific transcripts of a satellite DNA of the newts,
Notophthalmus
and
Triturus
, are present in cells in monomeric and multimeric sizes. These transcripts undergo self-catalyzed, site-specific cleavage
in vitro
: the reaction requires Mg
2+
and is mediated by a “hammerhead” domain. Transcription of the newt ribozyme appears to be performed by RNA polymerase II under the control of a proximal sequence element and a distal sequence element.
In vitro
, the newt ribozyme can cleave in
trans
an RNA substrate, suggesting that
in vivo
it might be involved in RNA processing events, perhaps as a riboprotein complex. Here we show that the newt ribozyme is in fact present as a riboprotein particle of about 12 S in the oocytes of
Triturus.
In addition, reconstitution experiments and gel-shift analyses show that a complex is assembled
in vitro
on the monomeric ribozyme molecules. UV cross-linking studies identify a few polypeptide species, ranging from 31 to 65 kDa, associated to the newt ribozyme with different affinities. Finally, we find that an appropriate oligoribonucleotide substrate is specifically cleaved by the riboproteic activity in S-100 ovary extracts.
On degree 2 Galois representations over 𝔽
4
Authors: Shepherd-Barron Nicholas , Taylor Richard
Published: July 2002

We discuss proofs of some new special cases of Serre’s conjecture
on odd, degree 2 representations of
G
ℚ
.
Filamentary microstructure and linear temperature dependence of normal state transport in optimized high temperature superconductors
Authors: Phillips J. C.
Published: July 2002

A filamentary model of “metallic” conduction in layered high temperature superconductive cuprates explains the concurrence of normal state resistivities (Hall mobilities) linear in
T
(
T
−2
) with optimized superconductivity. The model predicts the lowest temperature
T
0
for which linearity holds and it also predicts the maximum superconductive transition temperature
T
c
. The theory abandons the effective medium approximation that includes Fermi liquid as well as all other nonpercolative models in favor of countable smart basis states.
Single-particle selection and alignment with heavy atom cluster-antibody conjugates
Authors: Jensen Grant J. , Kornberg Roger D.
Published: July 2002

A method is proposed for selecting and aligning images of single biological particles to obtain high-resolution structural information by cryoelectron microscopy. The particles will be labeled with multiple heavy atom clusters to permit the precise determination of particle locations and relative orientations even when imaged close to focus with a low electron dose, conditions optimal for recording high-resolution detail. Heavy atom clusters should also allow selection of images free from many kinds of defects, including specimen movement and particle inhomogeneity. Heavy atom clusters may be introduced in a general way by the construction of “adaptor” molecules based on single-chain Fv antibody fragments, consisting of a constant framework region engineered for optimal cluster binding and a variable antigen binding region selected for a specific target. The success of the method depends on the mobility of the heavy atom cluster on the particle, on the precision to which clusters can be located in an image, and on the sufficiency of cluster projections alone to orient and select particles for averaging. The necessary computational algorithms were developed and implemented in simulations that address the feasibility of the method.
Molecular mechanisms of sound amplification in the mammalian cochlea
Authors: Ashmore Jonathan F. , Géléoc Gwénaëlle S. G. , Harbott Lene
Published: July 2002

Mammalian hearing depends on the enhanced mechanical properties of
the basilar membrane within the cochlear duct. The enhancement arises
through the action of outer hair cells that act like force generators
within the organ of Corti. Simple considerations show that underlying
mechanism of somatic motility depends on local area changes within the
lateral membrane of the cell. The molecular basis for this phenomenon
is a dense array of particles that are inserted into the basolateral
membrane and that are capable of sensing membrane potential field. We
show here that outer hair cells selectively take up fructose, at rates
high enough to suggest that a sugar transporter may be part of the
motor complex. The relation of these findings to a recent candidate for
the molecular motor is also discussed.
Extension of transverse relaxation-optimized spectroscopy techniques to allosteric proteins: CO- and paramagnetic fluoromet-hemoglobin [β(
15
N-valine)]
Authors: Nocek Judith M. , Huang Kai , Hoffman Brian M.
Published: July 2002

We present the first steps in applying transverse relaxation-optimized spectroscopy (TROSY) techniques to the study of allosterism. Each β-chain of the hemoglobin (Hb) tetramer has 17 valine residues. We have
15
N-labeled the β-chain Val residues and detected 16 of the 17
1
H-
15
N correlation peaks for β-chain Val of the R state CO-Hb structure by using the TROSY technique. Sequence-specific assignments are suggested, based mainly on analysis of the
1
H pseudocontact-shift increments produced by oxidizing the diamagnetic R state HbCO to the paramagnetic R state fluoromet form. When possible, we support these assignments with sequential nuclear Overhauser effect (NOE) information obtained from a two-dimensional [
1
H,
1
H]-NOESY-TROSY experiment (NOESY, NOE spectroscopy). We have induced further the R-T conformational change by adding the allosteric effector, inositol hexaphosphate, to the fluoromet-Hb sample. This change induces substantial increments in the
1
H and
15
N chemical shifts, and we discuss the implication of these findings in the context of the tentative sequence assignments. These preliminary results suggest that amide nitrogen and amide proton chemical shifts in a selectively labeled sample are site-specific probes for monitoring the allosteric response of the ensemble-averaged solution structure of Hb. More important, the chemical-shift dispersion obtained is adequate to permit a complete assignment of the backbone
15
N/
13
C resonances upon nonselective labeling.
Which circulant preconditioner is better?
Authors: Strela V. , Tyrtyshnikov E.
Published: July 2002

The eigenvalue clustering of matrices

S
n

−
1

A
n

S_n^{-1}A_n

and

C
n

−
1

A
n

C_n^{-1}A_n

is experimentally studied, where

A
n

A_n

,

S
n

S_n

and

C
n

C_n

respectively are Toeplitz matrices, Strang, and optimal circulant preconditioners generated by the Fourier expansion of a function

f
(
x
)

f(x)

. Some illustrations are given to show how the clustering depends on the smoothness of

f
(
x
)

f(x)

and which preconditioner is preferable. An original technique for experimental exploration of the clustering rate is presented. This technique is based on the bisection idea and on the Toeplitz decomposition of a three-matrix product

C
A
C

CAC

, where

A
A

is a Toeplitz matrix and

C
C

is a circulant. In particular, it is proved that the Toeplitz (displacement) rank of

C
A
C

CAC

is not greater than 4, provided that

C
C

and

A
A

are symmetric.
Computation of ℤ₃-invariants of real quadratic fields
Authors: Taya Hisao
Published: July 2002

Let

k
k

be a real quadratic field and

p
p

an odd prime number which splits in

k
k

. In a previous work, the author gave a sufficient condition for the Iwasawa invariant

λ
p

(
k
)

\lambda _p(k)

of the cyclotomic

Z

p

\mathbb {Z}_p

-extension of

k
k

to be zero. The purpose of this paper is to study the case

p
=
3

p=3

of this result and give new examples of

k
k

with

λ
3

(
k
)
=
0

\lambda _3(k)=0

, by using information on the initial layer of the cyclotomic

Z

3

\mathbb {Z}_3

-extension of

k
k

.
The number of polyhedral (3-connected planar) graphs
Authors: Duijvestijn A.
Published: July 2002

Data is presented on the number of 3-connected planar graphs, isomorphic to the graphs of convex polyhedra, with up to 26 edges. Results have been checked with the the number of rooted c-nets of R.C. Mullin and P.J. Schellenberg and Liu Yanpei.
Computation of relative class numbers of CM-fields
Authors: Louboutin Stéphane
Published: July 2002

It was well known that it is easy to compute relative class numbers of abelian CM-fields by using generalized Bernoulli numbers (see Theorem 4.17 in Introduction to cyclotomic fields by L. C. Washington, Grad. Texts in Math., vol. 83, Springer-Verlag, 1982). Here, we provide a technique for computing the relative class number of any CM-field.
Seven consecutive primes in arithmetic progression
Authors: Dubner Harvey , Nelson Harry
Published: July 2002

It is conjectured that there exist arbitrarily long sequences of consecutive primes in arithmetic progression. In 1967, the first such sequence of 6 consecutive primes in arithmetic progression was found. Searching for 7 consecutive primes in arithmetic progression is difficult because it is necessary that a prescribed set of at least 1254 numbers between the first and last prime all be composite. This article describes the search theory and methods, and lists the only known example of 7 consecutive primes in arithmetic progression.
Factors of generalized Fermat numbers
Authors: Björn Anders , Riesel Hans
Published: July 2002

A search for prime factors of the generalized Fermat numbers

F
n

(
a
,
b
)
=

a

2
n

+

b

2
n

F_n(a,b)=a^{2^n}+b^{2^n}

has been carried out for all pairs

(
a
,
b
)

(a,b)

with

a
,
b
≤
12

a,b\leq 12

and GCD

(
a
,
b
)
=
1

(a,b)=1

. The search limit

k
k

on the factors, which all have the form

p
=
k
⋅

2
m

+
1

p=k\cdot 2^m+1

, was

k
=

10
9

k=10^9

for

m
≤
100

m\leq 100

and

k
=
3
⋅

10
6

k=3\cdot 10^6

for

101
≤
m
≤
1000

101\leq m\leq 1000

. Many larger primes of this form have also been tried as factors of

F
n

(
a
,
b
)

F_n(a,b)

. Several thousand new factors were found, which are given in our tables.—For the smaller of the numbers, i.e. for

n
≤
15

n\leq 15

, or, if

a
,
b
≤
8

a,b\leq 8

, for

n
≤
16

n\leq 16

, the cofactors, after removal of the factors found, were subjected to primality tests, and if composite with

n
≤
11

n\leq 11

, searched for larger factors by using the ECM, and in some cases the MPQS, PPMPQS, or SNFS. As a result all numbers with

n
≤
7

n\leq 7

are now completely factored.
Factoring elementary groups of prime cube order into subsets
Authors: Szabó Sándor , Ward Coburn
Published: July 2002

Let

p
p

be a prime and let

G
G

be the

3
3

-fold direct product of the cyclic group of order

p
p

. Rédei conjectured if

G
G

is the direct product of subsets

A
A

and

B
B

, each of which contains the identity element of

G
G

, then either

A
A

or

B
B

does not generate all of

G
G

. The paper verifies Rédei’s conjecture for

p
≤
11

p\leq 11

.
A convergence theorem for the fast multipole method for 2 dimensional scattering problems
Authors: Labreuche Christophe
Published: July 2002

The Fast Multipole Method (FMM) designed by V. Rokhlin rapidly computes the field scattered from an obstacle. This computation consists of solving an integral equation on the boundary of the obstacle. The main result of this paper shows the convergence of the FMM for the two dimensional Helmholtz equation. Before giving the theorem, we give an overview of the main ideas of the FMM. This is done following the papers of V. Rokhlin. Nevertheless, the way we present the FMM is slightly different. The FMM is finally applied to an acoustic problem with an impedance boundary condition. The moment method is used to discretize this continuous problem.
Numerical conformal mapping based on the generalised conjugation operator
Authors: Li Bao , Syngellakis Stavros
Published: July 2002

An iterative procedure for numerical conformal mapping is presented which imposes no restriction on the boundary complexity. The formulation involves two analytically equivalent boundary integral equations established by applying the conjugation operator to the real and the imaginary parts of an analytical function. The conventional approach is to use only one and ignore the other equation. However, the discrete version of the operator using the boundary element method (BEM) leads to two non-equivalent sets of linear equations forming an over-determined system. The generalised conjugation operator is introduced so that both sets of equations can be utilised and their least-square solution determined without any additional computational cost, a strategy largely responsible for the stability and efficiency of the proposed method. Numerical tests on various samples including problems with cracked domains suggest global convergence, although this cannot be proved theoretically. The computational efficiency appears significantly higher than that reported earlier by other investigators.
A negative-norm least squares method for Reissner-Mindlin plates
Authors: Bramble James , Sun Tong
Published: July 2002

In this paper a least squares method, using the minus one norm developed by Bramble, Lazarov, and Pasciak, is introduced to approximate the solution of the Reissner-Mindlin plate problem with small parameter

t
t

, the thickness of the plate. The reformulation of Brezzi and Fortin is employed to prevent locking. Taking advantage of the least squares approach, we use only continuous finite elements for all the unknowns. In particular, we may use continuous linear finite elements. The difficulty of satisfying the inf-sup condition is overcome by the introduction of a stabilization term into the least squares bilinear form, which is very cheap computationally. It is proved that the error of the discrete solution is optimal with respect to regularity and uniform with respect to the parameter

t
t

. Apart from the simplicity of the elements, the stability theorem gives a natural block diagonal preconditioner of the resulting least squares system. For each diagonal block, one only needs a preconditioner for a second order elliptic problem.
Euclid’s algorithm and the Lanczos method over finite fields
Authors: Teitelbaum Jeremy
Published: July 2002

This paper shows that there is a close relationship between the Euclidean algorithm for polynomials and the Lanczos method for solving sparse linear systems, especially when working over finite fields. It uses this relationship to account rigorously for the appearance of self-orthogonal vectors arising in the course of the Lanczos algorithm. It presents an improved Lanczos method which overcomes problems with self-orthogonality and compares this improved algorithm with the Euclidean algorithm.
Normal bases via general Gauss periods
Authors: Feisel Sandra , von zur Gathen Joachim , Shokrollahi M.
Published: July 2002

Gauss periods have been used successfully as a tool for constructing normal bases in finite fields. Starting from a primitive

r
r

th root of unity, one obtains under certain conditions a normal basis for

F

q
n

\mathbb {F}_{q^n}

over

F

q

\mathbb {F}_q

, where

r
r

is a prime and

n
k
=
r
−
1

nk=r-1

for some integer

k
k

. We generalize this construction by allowing arbitrary integers

r
r

with

n
k
=
φ
(
r
)

nk=\varphi (r)

, and find in many cases smaller values of

k
k

than is possible with the previously known approach.