bluuebunny/crossref_metadata_2025_split huggingface dataset:
Equitemporal optics: a method to generate subpicosecond x-ray pulses (abstract)
Authors: Csonka P. L. 
Published: July 2002

Certain classes of experiments would benefit from the availability of x-ray pulses of shorter time duration than what can be achieved today. These include accurate measurements of frequency and those of time resolution. One way to generate short x-ray pulses, is to utilize only part of an originally longer train of photons, and discard the rest. This approach is of little help if the phenomenon under study (such as synchrotron radiation pumped x-ray lasers) requires not only short pulses, but also high instantaneous photon intensity. When the time averaged photon intensity cannot be increased, the required threshold for the instantaneous intensity could nevertheless be reached (and the time resolution improved), if the time duration of individual photon pulses could be reduced without losing significant numbers of photons in the process. The term ‘‘equitemporal optics’’ denotes a collection of optical elements which can bring about a photon pulse length compression of this type. We demonstrate in general that practical equitemporal optics for x rays requires at least one optical element which is nonstationary. It is also shown that an equitemporal optics can be constructed for x rays by making use of only a single rotating mirror, while all other elements are stationary, provided that at least one of the stationary elements is a reflector. Furthermore, that reflector cannot be a single continuous mirror, but must contain more than one appropriately positioned discontinuous section. The number of sections must not be less than the time compression factor, ft, by which the original pulse length is to be reduced. Examples of appropriate reflectors are given. An equitemporal design of this type is presented which utilizes such a reflector together with a mirror rotating with a constant angular velocity. The time compression factor of this device is calculated.
It depends, among other things, on the emittance of the photon beam and the mirror speed of rotation. Limiting parameters and conditions will be discussed. Assuming the photon beam emittances produced by the PEP ring in Stanford, in conjunction with mirror speeds which can be achieved in practice, one can show that subpicosecond x-ray photon pulses can be generated in this manner. Alternatively, assuming the projected lower PEP emittances, one expects pulses of only a few femtoseconds duration. Concurrently, the same device will increase the instantaneous x-ray intensity by a factor in the range 102–104. The device may also be utilized to sharpen the leading (or trailing) edge of a photon pulse, without significantly altering the total pulse length.
Properties and applications of fast rotors in dynamical optics (abstract)
Authors: Csonka P. L. 
Published: July 2002

The term ‘‘dynamical optics’’ is defined as a set of optical elements at least one of which is nonstationary as seen from the laboratory. Present technology allows the construction of fast rotating mirrors as components in dynamical optical systems. Calculations show that such systems can be used to achieve subpicosecond x-ray pulses and extremely high instantaneous intensities, and, alternatively they can be utilized to saturate the transverse coherence of x-ray beams thereby making possible to perform certain interference experiments. Some properties and additional applications of fast rotating mirrors are discussed: (1) The focusing properties of rotating mirrors can differ significantly from those of stationary reflectors, even though the mirrors are, of course, nonrelativistic. A small (diameter &lt;1 mm) plane mirror when rotating can have a focal length fm down to a few meters. By changing the speed of rotation, the focal length can be altered continuously from its minimum value, fm, through infinity (when the mirror is at rest) to −fm (when it’s rotation is reversed). Thus, mirrors can be constructed which can be made to both focus and defocus with continuously and accurately variable focal length. (2) Rotating mirrors will induce a frequency change Δω in the reflected beam, allowing one in principle to tune across resonance lines, and also ‘‘active monochromatization’’ of x-rays, i.e., increasing the spectral intensity in a selected range, while decreasing it outside that range, all this without any change in the total photon beam intensity. This option is of interest when the total photon intensity cannot be increased beyond a certain limit, high resolution monochromatization is available, and large spectral density is called for in a chosen frequency range.
(3) The maximum speed whch a rotor can tolerate is determined by its shape as well as its mechanical properties, such as density, elasticity, and tensile strength. Because of their high intrinsic symmetry, spherical rotors are of interest both theoretically and experimentally, but higher speeds can be achieved by rotors specifically shaped for that purpose. A variety of examples will be given to illustrate the relationship between rotor speed and selected parameters.
SR instrumentation for optimized anomalous scattering and high resolution structure studies of proteins and nucleic acids (invited)
Authors: Deacon A. , Habash J. , Harrop S. J. , Helliwell J. R. , Hunter W. N. , Leonard G. A. , Peterson M. , Hadener A. , Kalb (Gilboa) A. J. , Allinson N. M. , Castelli C. , Moon K. , McSweeney S. , Gonzalez A. , Thompson A. W. , Ealick S. , Szebenyi D. M. , Walter R. 
Published: July 2002

Crystal structure solution by anomalous dispersion methods has been greatly facilitated using the rapidly tunable station 9.5 at the Daresbury SRS. Both SIROAS and MAD techniques, with IP data, have been used in the phasing of a brominated nucleotide and a seleno deaminase, respectively. The electron density maps in each case are interpretable. Throughput of projects could be improved upon with a better duty cycle detector. Another category of data collection is that at very high resolution. Detailed structure refinement pushes the limits of resolution and data quality. Station 9.5 has been used to collect high resolution (1.4 Å) native data for the protein concanavalin A. This utilized very short wavelengths (0.7 Å), the image plate, and crystal freezing. A total of 155 407 measurements from two crystals benefited from the on-line nature of the IP detector device, but a slow and quick pass are required to capture the full dynamic range of the data. There are data seen to 1.2 Å and beyond for a pure Mn substituted form of the protein, but a higher intensity still is required to actually record these data. By comparison, trials at CHESS, on a multipole wiggler (station A1) with a CCD (without image intensifier) system, yield native concanavalin A data to 0.98 Å and beyond. This demonstrates that the combination of yet higher intensity and the ease of use of a CCD offers worthwhile improvements; in this case an increase in the data by a factor of (1.4/0.98)3, thus at least doubling the data to parameter ratio for protein structure model refinement and potentially opening up direct structure determination of proteins of the size of concanavalin A (25 kDa).
Finally, possibilities at ESRF and further detector developments, such as mosaic CCDs and scintillator coatings, offer further impetus for the field. These include more intense rapidly tunable beams for anomalous dispersion-based structure solution and ‘‘ideal’’ higher resolution data collection and reactivity studies. ESRF BL19 is described; facilities on BL19 will include a system for freezing and storing crystals at cryogenic temperatures, so that data can be recorded from the same crystal on different runs. Overall, there have been tremendous strides made in this field in the last 15 years, and yet further improvements are to come.
Rotationally invariant linear magnetoelastic theory (abstract)
Authors: Rinaldi S. 
Published: July 2002

The magnetoelastic effects are usually described on the basis of an expression for the magnetoelastic energy which is a function of the symmetric strain εij and of the magnetization direction cosines αi and which has the form Eme=Bijkeεijαkαl, the number of different Bijkl being limited by symmetry. This expression, however, does not satisfy the principle of rotational invariance, i.e., the coupling energy varies when the reference system is rotated; this is equivalent to saying that it does not properly describe the effects of an applied strain containing an antisymmetric component ωij. This problem was previously recognized, studied for special cases, and related effects were observed. However, to our best knowledge, no explicit calculation of rotationally invariant magnetoelastic energy has been previously reported for the general cases of cubic and uniaxial symmetry. We will simply derive these expressions starting from an expansion of the energy of a magnetoelastic system in terms of the particles displacement gradients uij, using the definitions of the symmetric and antisymmetric strain tensors (εij=uij+uji; wij=uij−uji) and
imposing the rotational invariance. It results that, at the lowest order, the rotational invariant expression for the magnetoelastic energy has the form: Eme=Bijklεijαkαl +Pijklwijαkαl +Qijkl(αm)wijεkl +Rijkl(αm)wijwkl; explicit expressions for Pijkl, Qijkl(αm), and Rijkl(αm) will be given for the cases of uniaxial and cubic symmetry. Finally it will be shown how, using a simple transformation, the known theory on the elastic properties of magnetoelastic materials can be used for applied strains having antisymmetric components.
Amplification of the MYC Gene in Osteosarcoma Secondary to Paget′s Disease of Bone
Authors: Ueda Takafumi , Healey John H. , Huvos Andrew G. , Ladanyi Marc 
Published: July 2002

Purpose. In a previous series of 25 human osteosarcoma samples studied for MYC gene amplification, we found
amplification in two cases (8%), including one arising in association with Paget′s disease (pagetic osteosarcoma). Based
on this observation, we further investigated the prevalence of MYC gene amplification in pagetic osteosarcomas.Methods. MYC gene amplification was assessed by Southern blot analysis using frozen tissue samples in five cases of
pagetic osteosarcoma and 53 cases of primary (non‐pagetic) osteosarcoma. Amplification was considered present if the
MYC copy number was six or greater.Results. Three out of five patients (60%) with pagetic osteosarcoma showed MYC gene amplification, whereas it was
present in only 5/53 patients (9.4%) with primary osteosarcoma. The incidence of MYC amplification in pagetic
osteosarcoma was thus significantly higher than that in primary osteosarcoma (p = 0.016).Discussion. The finding that MYC gene amplification may be more common in pagetic than primary osteosarcoma
warrants further study and suggests pathogenetic differences between primary osteosarcomas and those arising in the
setting of Paget′s disease. Three of the four pagetic osteosarcomas from the present study were previously shown to be
immunoreactive for p53, suggesting that p53 mutation may also be a frequent genetic lesion in these tumors.
Detection of EWS/FLI‐1 by Immunostaining. An Adjunctive Tool in Diagnosis of Ewing′s Sarcoma and Primitive Neuroectodermal Tumour on Cytological Samples and Paraffin‐Embedded Archival Material
Authors: Nilsson Gunnar , Wang Min , Wejde Johan , Kreicbergs Andris , Larsson Olle 
Published: July 2002

Purpose. Recently we showed that the 68‐kDa fusion protein derived
from the EWS/FLI1 hybrid gene can be specifically detected by Western blotting using
a polyclonal antibody to the C‐terminal of FLI1 on biopsy material from Ewing′s
sarcoma. The aim of this study was to investigate whether this antibody also could be
used for immunocytochemistry and immunohistochemistry in diagnosis of
Ewing′s sarcoma.Methods. Immunostaining on paraffin‐embedded archival material,
fine‐needle aspirates and tumour touch imprints from Ewing′s sarcomas and primitive
neuroectodermal tumours (PNET) for detection of the fusion protein was performed.
Most cases were also analysed by Western blotting.Tumours of differential
diagnostic importance were also included.Results. Eighty per cent (12/15 cases) of the Ewing tumours exhibited a positive
immunoreactivity for the FLI1 antibody. The signal was mainly localised in the nuclei
of the tumour cells, which seems reasonable since EWS/FLI1 is a transcription factor.
The signal was found to be specific since it did not appear when the blocking peptide
was added to the antibody solution.Moreover, two other types of small‐round cell tumours
(i.e. neuroblastoma and alveolar rhabdomyosarcoma) were negative as well as most
normal tissues.Discussion. Immunostaining of histological and cytological specimens
with the FLI1 antibody can be of diagnostic relevance in Ewing tumours carrying
t(11;22).The absence of immunoreactivity in non‐Ewing cells is most likely due to a
low expression of the wild‐type FLI1 protein.
Using imperfect secondary structure predictions to improve molecular structure computations.
Authors: Chen C C , Singh J P , Altman R B 
Published: July 2002

Abstract
MOTIVATION: Until ab initio structure prediction methods are perfected, the estimation of structure for protein molecules will depend on combining multiple sources of experimental and theoretical data. Secondary structure predictions are a particularly useful source of structural information, but are currently only approximately 70% correct, on average. Structure computation algorithms which incorporate secondary structure information must therefore have methods for dealing with predictions that are imperfect. EXPERIMENTS PERFORMED: We have modified our algorithm for probabilistic least squares structural computations to accept 'disjunctive' constraints, in which a constraint is provided as a set of possible values, each weighted with a probability. Thus, when a helix is predicted, the distances associated with a helix are given most of the weight, but some weights can be allocated to the other possibilities (strand and coil). We have tested a variety of strategies for this weighting scheme in conjunction with a baseline synthetic set of sparse distance data, and compared it with strategies which do not use disjunctive constraints. RESULTS: Naive interpretations in which predictions were taken as 100% correct led to poor-quality structures. Interpretations that allow disjunctive constraints are quite robust, and even relatively poor predictions (58% correct) can significantly increase the quality of computed structures (almost halving the RMS error from the known structure). CONCLUSIONS: Secondary structure predictions can be used to improve the quality of three-dimensional structural computations. In fact, when interpreted appropriately, imperfect predictions can provide almost as much improvement as perfect predictions in three-dimensional structure calculations.
Application of distance geometry to 3D visualization of sequence relationships.
Authors: Forster M , Heath A , Afzal M 
Published: July 2002

Abstract
SUMMARY: We describe the application of distance geometry methods to the three-dimensional visualization of sequence relationships, with examples for mumps virus SH gene cDNA and prion protein sequences. Sequence-sequence distance measures may be obtained from either a multiple sequence alignment or from sets of pairwise alignments. AVAILABILITY: C/Perl code and HTML/VRML files from http://www.nibsc.ac.uk/dg3dseq/
Estimated Travel Time and Spatial Access to Abortion Facilities in the US Before and After the Dobbs v Jackson Women’s Health Decision
Authors: Rader Benjamin , Upadhyay Ushma D. , Sehgal Neil K. R. , Reis Ben Y. , Brownstein John S. , Hswen Yulin 
Published: November 2022

ImportanceAbortion facility closures resulted in a substantial decrease in access to abortion care in the US.ObjectivesTo investigate the changes in travel time to the nearest abortion facility after the Dobbs v Jackson Women’s Health Organization (referred to hereafter as Dobbs) US Supreme Court decision.Design, Setting, and ParticipantsRepeated cross-sectional spatial analysis of travel time from each census tract in the contiguous US (n = 82 993) to the nearest abortion facility (n = 1134) listed in the Advancing New Standards in Reproductive Health database. Census tract boundaries and demographics were defined by the 2020 American Community Survey. The spatial analysis compared access during the pre-Dobbs period (January-December 2021) with the post-Dobbs period (September 2022) for the estimated 63 718 431 females aged 15 to 44 years (reproductive age for this analysis) in the US (excluding Alaska and Hawaii).ExposuresThe Dobbs ruling and subsequent state laws restricting abortion procedures. The pre-Dobbs period measured abortion access to all facilities providing abortions in 2021. Post-Dobbs abortion access was measured by simulating the closure of all facilities in the 15 states with existing total or 6-week abortion bans in effect as of September 30, 2022.Main Outcomes and MeasuresMedian and mean changes in surface travel time (eg, car, public transportation) to an abortion facility in the post-Dobbs period compared with the pre-Dobbs period and the total percentage of females of reproductive age living more than 60 minutes from abortion facilities during the pre- and post-Dobbs periods.ResultsOf 1134 abortion facilities in the US (at least 1 in every state; 8 in Alaska and Hawaii excluded), 749 were considered active during the pre-Dobbs period and 671 were considered active during a simulated post-Dobbs period. Median (IQR) and mean (SD) travel times to pre-Dobbs abortion facilities were estimated to be 10.9 (4.3-32.4) and 27.8 (42.0) minutes. Travel time to abortion facilities in the post-Dobbs period significantly increased (paired sample t test P &amp;lt;.001) to an estimated median (IQR) of 17.0 (4.9-124.5) minutes and a mean (SD) of and 100.4 (161.5) minutes. In the post-Dobbs period, an estimated 33.3% (sensitivity interval, 32.3%-34.8%) of females of reproductive age lived in a census tract more than 60 minutes from an abortion facility compared with 14.6.% (sensitivity interval, 13.0%-16.9%) of females of reproductive age in the pre-Dobbs period.Conclusions and RelevanceIn this repeated cross-sectional spatial analysis, estimated travel time to abortion facilities in the US was significantly greater in the post-Dobbs period after accounting for the closure of abortion facilities in states with total or 6-week abortion bans compared with the pre-Dobbs period, during which all facilities providing abortions in 2021 were considered active.
An Instrument for Measuring Critical Appraisal Self‐Efficacy in Rheumatology Trainees
Authors: Aizer Juliet , Abramson Erika L. , Berman Jessica R. , Paget Stephen A. , Frey Marianna B. , Cooley Victoria , Li Ying , Hoffman Katherine L. , Schell Julie A. , Tiongson Michael D. , Lin Myriam A. , Mandl Lisa A. 
Published: November 2022

ObjectiveSelf‐efficacy, the internal belief that one can perform a specific task successfully, influences behavior. To promote critical appraisal of medical literature, rheumatology training programs should foster both competence and self‐efficacy for critical appraisal. This study aimed to investigate whether select items from the Clinical Research Appraisal Inventory (CRAI), an instrument measuring clinical research self‐efficacy, could be used to measure critical appraisal self‐efficacy (CASE).MethodsOne hundred twenty‐five trainees from 33 rheumatology programs were sent a questionnaire that included two sections of the CRAI. Six CRAI items relevant to CASE were identified a priori; responses generated a CASE score (total score range 0‐10; higher = greater confidence in one's ability to perform a specific task successfully). CASE scores' internal structure and relation to domain‐concordant variables were analyzed.ResultsQuestionnaires were completed by 112 of 125 (89.6%) trainees. CASE scores ranged from 0.5 to 8.2. The six CRAI items contributing to the CASE score demonstrated high internal consistency (Cronbach's α = 0.95) and unidimensionality. Criterion validity was supported by the findings that participants with higher CASE scores rated their epidemiology and biostatistics understanding higher than that of peers (P < 0.0001) and were more likely to report referring to studies to answer clinical questions (odds ratio 2.47, 95% confidence interval 1.41‐4.33; P = 0.002). The correlation of CASE scores with percentage of questions answered correctly was only moderate, supporting discriminant validity.ConclusionThe six‐item CASE instrument demonstrated content validity, internal consistency, discriminative capability, and criterion validity, including correlation with self‐reported behavior, supporting its potential as a useful measure of critical appraisal self‐efficacy.
Controlled Nitrogen Doping in Crumpled Graphene for Improved Alkali Metal‐Ion Storage under Low‐Temperature Conditions
Authors: Lee Kyungbin , Lee Michael J. , Lim Jeonghoon , Ryu Kun , Li Mochen , Noda Suguru , Kwon Seok Joon , Lee Seung Woo 
Published: November 2022

AbstractThe significant performance decay in conventional graphite anodes under low‐temperature conditions is attributed to the slow diffusion of alkali metal ions, requiring new strategies to enhance the charge storage kinetics at low temperatures. Here, nitrogen (N)‐doped defective crumpled graphene (NCG) is employed as a promising anode to enable stable low‐temperature operation of alkali metal‐ion storage by exploiting the surface‐controlled charge storage mechanisms. At a low temperature of −40 °C, the NCG anodes maintain high capacities of ≈172 mAh g−1 for lithium (Li)‐ion, ≈107 mAh g−1 for sodium (Na)‐ion, and ≈118 mAh g−1 for potassium (K)‐ion at 0.01 A g−1 with outstanding rate‐capability and cycling stability. A combination of density functional theory (DFT) and electrochemical analysis further reveals the role of the N‐functional groups and defect sites in improving the utilization of the surface‐controlled charge storage mechanisms. In addition, the full cell with the NCG anode and a LiFePO4 cathode shows a high capacity of ≈73 mAh g−1 at 0.5 °C even at −40 °C. The results highlight the importance of utilizing the surface‐controlled charge storage mechanisms with controlled defect structures and functional groups on the carbon surface to improve the charge storage performance of alkali metal‐ion under low‐temperature conditions.
Regulation and Reconstruction of Cell Phenotype Gradients Along the Tendon‐Bone Interface
Authors: Dang Gao‐Peng , Qin Wen , Wan Qian‐Qian , Gu Jun‐Ting , Wang Kai‐Yan , Mu Zhao , Gao Bo , Jiao Kai , Tay Franklin R. , Niu Li‐Na 
Published: November 2022

AbstractTendon–bone interface is prevalent in the human body. It is divided into four zones: tendon (soft tissue), unmineralized fibrocartilage, mineralized fibrocartilage, and bone (hard tissue). Tendon–bone interface is characterized by a cell phenotype gradient that appears in the different zones. The cell phenotype gradients at the tendon–bone interface are orchestrated by specific intracellular molecular mechanisms, extracellular factors, immune signals, and neurovascular factors. These features have inspired scientists to design systems that mimic natural cell phenotype gradients. These biomimetic systems include the construction of cell sheets, regulation of cellular microenvironments, and the design of gradient functional scaffolds. Exploration of methods to mimic cell phenotype gradients is instructional for future clinical applications in reconstituting the tendon–bone interface. The present review elucidates the gradient composition of the tendon–bone interface. The associated regulatory mechanisms and applications are discussed, with the anticipation of creating a mise en scène for future research in interface tissue engineering.