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At least 973 records · Page 54

Opportunities and challenges for assigning cofactors in cryo-EM density maps of chlorophyll-containing proteins

Abstract The accurate assignment of cofactors in cryo-electron microscopy maps is crucial in determining protein function. This is particularly true for chlorophylls (Chls), for which small structural differences lead to important functional differences. Recent cryo-electron microscopy structures of Chl-containing protein complexes exemplify the difficulties in distinguishing Chl b and Chl f from Chl a . We use these structures as examples to discuss general issues arising from local resolution differences, properties of electrostatic potential maps, and the chemical environment which must be considered to make accurate assignments. We offer suggestions for how to improve the reliability of such assignments.

59 BASIC BIOLOGICAL SCIENCES↗

Use of differential plasma rotation to prevent disruptive tearing mode onset from 3-wave coupling

Abstract Plasma differential rotation is found to be capable of preventing disruptive neoclassical tearing modes (NTMs) seeded by nonlinear three-wave coupling. As tearing modes degrade confinement and can lead to disruptions, stabilization strategies are crucial to the successful operation of future devices. In ITER-relevant scenarios on DIII-D, rotationally coupled m / n = 1/1 and 3/2 modes have been observed to drive 2/1 islands through three-wave coupling. The frequency of the driven 2/1 mode is set by matching conditions and the frequencies of the driving modes. When the driven mode frequency matches the local plasma rotation frequency, e.g. at low differential rotation, the driven 2/1 island can grow into a disruptive NTM. Using neutral beam torque as an actuator to scan the differential rotation, these experiments demonstrate that a sufficiently large frequency mismatch prevents destabilization of disruptive 2/1 NTMs by three-wave coupling. This work indicates that differential rotation can be used as an actuator to prevent NTMs seeded by three-wave coupling.

Richner, N. J. (ORCID:0000000155443915)↗

Sources of Intermodel Spread in the Lapse Rate and Water Vapor Feedbacks

Abstract Sources of intermodel differences in the global lapse rate (LR) and water vapor (WV) feedbacks are assessed using CO2 forcing simulations from 28 general circulation models. Tropical surface warming leads to significant warming and moistening in the tropical and extratropical upper troposphere, signifying a nonlocal, tropical influence on extratropical radiation and feedbacks. Model spread in the locally defined LR and WV feedbacks is pronounced in the Southern Ocean because of large-scale ocean upwelling, which reduces surface warming and decouples the surface from the tropospheric response. The magnitude of local extratropical feedbacks across models and over time is well characterized using the ratio of tropical to extratropical surface warming. It is shown that model differences in locally defined LR and WV feedbacks, particularly over the southern extratropics, drive model variability in the global feedbacks. The cross-model correlation between the global LR and WV feedbacks therefore does not arise from their covariation in the tropics, but rather from the pattern of warming exerting a common control on extratropical feedback responses. Because local feedbacks over the Southern Hemisphere are an important contributor to the global feedback, the partitioning of surface warming between the tropics and the southern extratropics is a key determinant of the spread in the global LR and WV feedbacks. It is also shown that model Antarctic sea ice climatology influences sea ice area changes and southern extratropical surface warming. As a result, model discrepancies in climatological Antarctic sea ice area have a significant impact on the intermodel spread of the global LR and WV feedbacks.

54 ENVIRONMENTAL SCIENCES↗

Methodology for object-oriented real-time systems analysis and design: Software engineering

Successful application of software engineering methodologies requires an integrated analysis and design life-cycle in which the various phases flow smoothly 'seamlessly' from analysis through design to implementation. Furthermore, different analysis methodologies often lead to different structuring of the system so that the transition from analysis to design may be awkward depending on the design methodology to be used. This is especially important when object-oriented programming is to be used for implementation when the original specification and perhaps high-level design is non-object oriented. Two approaches to real-time systems analysis which can lead to an object-oriented design are contrasted: (1) modeling the system using structured analysis with real-time extensions which emphasizes data and control flows followed by the abstraction of objects where the operations or methods of the objects correspond to processes in the data flow diagrams and then design in terms of these objects; and (2) modeling the system from the beginning as a set of naturally occurring concurrent entities (objects) each having its own time-behavior defined by a set of states and state-transition rules and seamlessly transforming the analysis models into high-level design models. A new concept of a 'real-time systems-analysis object' is introduced and becomes the basic building block of a series of seamlessly-connected models which progress from the object-oriented real-time systems analysis and design system analysis logical models through the physical architectural models and the high-level design stages. The methodology is appropriate to the overall specification including hardware and software modules. In software modules, the systems analysis objects are transformed into software objects.

Schoeffler, James D.↗

(abstract)Electron Impact Emission Cross Sections for Modeling UV Auroral and Dayglow Observations of the Upper Atmospheres of Planets

In the upper atmospheres of the Jovian and Terrestrial planets a dominant mechanism for energy transfer occurs through electron collisional processes with neutral species leading to UV radiation. In response to the need for accurate collision cross sections to model spectroscopic observations of planetary systems, JPL has measured in the laboratory emission cross sections and medium resolution spectra of H, H(sub 2), N(sub 2), SO(sub 2), and other important planetary gases.Voyager and International Ultraviolet Explorer (IUE) spacecraft have established that band systems of H(sub 2) and N(sub 2) are the dominant UV molecular emissions in the solar system produced by electron impact. Applications of our data to models of Voyager, IUE, Galileo, and Hubble Space Telescope observations of the planets will be described.

molecular emissions↗

Repeated exposure to eucalyptus wood smoke alters pulmonary gene and metabolic profiles in male Long-Evans rats

Abstract Exposure to wildfire smoke is associated with both acute and chronic cardiopulmonary illnesses, which are of special concern for wildland firefighters who experience repeated exposure to wood smoke. It is necessary to better understand the underlying pathophysiology by which wood smoke exposure increases pulmonary disease burdens in this population. We hypothesize that wood smoke exposure produces pulmonary dysfunction, lung inflammation, and gene expression profiles associated with future pulmonary complications. Male Long-Evans rats were intermittently exposed to smoldering eucalyptus wood smoke at 2 concentrations, low (11.0 ± 1.89 mg/m3) and high (23.7 ± 0.077 mg/m3), over a 2-week period. Whole-body plethysmography was measured intermittently throughout. Lung tissue and lavage fluid were collected 24 h after the final exposure for transcriptomics and metabolomics. Increasing smoke exposure upregulated neutrophils and select cytokines in the bronchoalveolar lavage fluid. In total, 3446 genes were differentially expressed in the lungs of rats in the high smoke exposure and only 1 gene in the low smoke exposure (Cd151). Genes altered in the high smoke group reflected changes to the Eukaryotic Initiation Factor 2 stress and oxidative stress responses, which mirrored metabolomics analyses. xMWAS-integrated analysis revealed that smoke exposure significantly altered pathways associated with oxidative stress, lung morphogenesis, and tumor proliferation pathways. These results indicate that intermittent, 2-week exposure to eucalyptus wood smoke leads to transcriptomic and metabolic changes in the lung that may predict future lung disease development. Collectively, these findings provide insight into cellular signaling pathways that may contribute to the chronic pulmonary conditions observed in wildland firefighters.

Toxicology↗

Repair of a mirror coating on a large optic for high laser damage applications using ion milling and over-coating methods

Here, when an optical coating is damaged, deposited incorrectly, or is otherwise unsuitable, the conventional method to restore the optic often entails repolishing the optic surface, which can incur a large cost and long lead time. We propose three alternative options to repolishing, including (i) burying the unsuitable coating under another optical coating, (ii) using ion milling to etch the unsuitable coating completely from the optic surface and then recoating the optic, and (iii) using ion milling to etch through a number of unsuitable layers, leaving the rest of the coating intact, and then recoating the layers that were etched. Repairs were made on test optics with dielectric mirror coatings according to the above three options. The mirror coatings to be repaired were quarter wave stacks of HfO 2 and SiO 2 layers for high reflection at 1054 nm at 45 deg incidence in P-polarization. One of the coating layers was purposely deposited incorrectly as Hf metal instead of HfO2 to evaluate the ability of each repair method to restore the coating’s high laser-induced damage threshold (LIDT) of 64.0 J/cm 2 . The repaired coating with the highest resistance to laser-induced damage was achieved using repair method (ii) with an LIDT of 49.0 to 61.0 J/cm 2 .

36 MATERIALS SCIENCE↗

HACA's Heritage: A Free-Radical Pathway to Phenanthrene in Circumstellar Envelopes of Asymptotic Giant Branch Stars

The hydrogen-abstraction/acetylene-addition (HACA) mechanism has been central for the last decades in attempting to rationalize the formation of polycyclic aromatic hydrocarbons (PAHs) as detected in carbonaceous meteorites such as in Murchison. Nevertheless, the basic reaction mechanisms leading to the formation of even the simplest tricyclic PAHs like anthracene and phenanthrene are still elusive. By exploring the previously unknown chemistry of the ortho -biphenylyl radical with acetylene, we deliver compelling evidence on the efficient synthesis of phenanthrene in carbon-rich circumstellar environments. However, the lack of formation of the anthracene isomer implies that HACA alone cannot be responsible for the formation of PAHs in extreme environments. Considering the overall picture, alternative pathways such as vinylacetylene-mediated reactions are required to play a crucial role in the synthesis of complex PAHs in circumstellar envelopes of dying carbon-rich stars.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Carbon Dioxide Capture at Nucleophilic Hydroxide Sites in Oxidation‐Resistant Cyclodextrin‐Based Metal–Organic Frameworks**

Abstract Carbon capture and sequestration (CCS) from industrial point sources and direct air capture are necessary to combat global climate change. A particular challenge faced by amine‐based sorbents—the current leading technology—is poor stability towards O 2 . Here, we demonstrate that CO 2 chemisorption in γ‐cylodextrin‐based metal–organic frameworks (CD‐MOFs) occurs via HCO 3 − formation at nucleophilic OH − sites within the framework pores, rather than via previously proposed pathways. The new framework KHCO 3 CD‐MOF possesses rapid and high‐capacity CO 2 uptake, good thermal, oxidative, and cycling stabilities, and selective CO 2 capture under mixed gas conditions. Because of its low cost and performance under realistic conditions, KHCO 3 CD‐MOF is a promising new platform for CCS. More broadly, our work demonstrates that the encapsulation of reactive OH − sites within a porous framework represents a potentially general strategy for the design of oxidation‐resistant adsorbents for CO 2 capture.

Zick, Mary E.↗

Exact sum rules for quantum billiards of arbitrary shape

Highlights: Sum rules of order one for domains of arbitrary shape are considered. The sum rules are proved to be finite. Exact expressions for number of examples are obtained. These expressions are verified with accurate numerical tests. -- Abstract: We have derived explicit expressions for the sum rules of order one of the eigenvalues of the negative Laplacian on two dimensional domains of arbitrary shape. Taking into account the leading asymptotic behavior of these eigenvalues, as given from Weyl’s law, we show that it is possible to define sum rules that are finite, using different prescriptions. We provide the explicit expressions and test them on a number of non trivial examples, comparing the exact results with precise numerical results.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Cancer cachexia decreases specific force and accelerates fatigue in limb muscle

Highlights: •C-26 cancer cachexia causes a significant decrease in limb muscle absolute force. •C-26 cancer cachexia causes a significant decrease in limb muscle specific force. •C-26 cancer cachexia decreases fatigue resistance in the soleus muscle. •C-26 cancer cachexia prolongs time to peak twitch tension in limb muscle. •C-26 cancer cachexia prolongs one half twitch relaxation time in limb muscle. -- Abstract: Cancer cachexia is a complex metabolic syndrome that is characterized by the loss of skeletal muscle mass and weakness, which compromises physical function, reduces quality of life, and ultimately can lead to mortality. Experimental models of cancer cachexia have recapitulated this skeletal muscle atrophy and consequent decline in muscle force generating capacity. However, more recently, we provided evidence that during severe cancer cachexia muscle weakness in the diaphragm muscle cannot be entirely accounted for by the muscle atrophy. This indicates that muscle weakness is not just a consequence of muscle atrophy but that there is also significant contractile dysfunction. The current study aimed to determine whether contractile dysfunction is also present in limb muscles during severe Colon-26 (C26) carcinoma cachexia by studying the glycolytic extensor digitorum longus (EDL) muscle and the oxidative soleus muscle, which has an activity pattern that more closely resembles the diaphragm. Severe C-26 cancer cachexia caused significant muscle fiber atrophy and a reduction in maximum absolute force in both the EDL and soleus muscles. However, normalization to muscle cross sectional area further demonstrated a 13% decrease in maximum isometric specific force in the EDL and an even greater decrease (17%) in maximum isometric specific force in the soleus. Time to peak tension and half relaxation time were also significantly slowed in both the EDL and the solei from C-26 mice compared to controls. Since, in addition to postural control, the oxidative soleus is also important for normal locomotion, we further performed a fatigue trial in the soleus and found that the decrease in relative force was greater and more rapid in solei from C-26 mice compared to controls. These data demonstrate that severe cancer cachexia causes profound muscle weakness that is not entirely explained by the muscle atrophy. In addition, cancer cachexia decreases the fatigue resistance of the soleus muscle, a postural muscle typically resistant to fatigue. Thus, specifically targeting contractile dysfunction represents an additional means to counter muscle weakness in cancer cachexia, in addition to targeting the prevention of muscle atrophy.

60 APPLIED LIFE SCIENCES↗

RADAMS: Resilient and adaptive alert and attention management strategy against Informational Denial-of-Service (IDoS) attacks

Attacks exploiting human attentional vulnerability have posed severe threats to cybersecurity. In this work, we identify and formally define a new type of proactive attentional attacks called Informational Denial-of-Service (IDoS) attacks that generate a large volume of feint attacks to overload human operators and hide real attacks among feints. Here, we incorporate human factors (e.g., levels of expertise, stress, and efficiency) and empirical psychological results (e.g., the Yerkes-Dodson law and the sunk cost fallacy) to model the operators’ attention dynamics and their decision-making processes along with the real-time alert monitoring and inspection. To assist human operators in dismissing the feints and escalating the real attacks timely and accurately, we develop a Resilient and Adaptive Data-driven alert and Attention Management Strategy (RADAMS) that de-emphasizes alerts selectively based on the abstracted category labels of the alerts. RADAMS uses reinforcement learning to achieve a customized and transferable design for various human operators and evolving IDoS attacks. The integrated modeling and theoretical analysis lead to the Product Principle of Attention (PPoA), fundamental limits, and the tradeoff among crucial human and economic factors. Experimental results corroborate that the proposed strategy outperforms the default strategy and can reduce the IDoS risk by as much as 20%. Besides, the strategy is resilient to large variations of costs, attack frequencies, and human attention capacities. We have recognized interesting phenomena such as attentional risk equivalency, attacker’s dilemma, and the half-truth optimal attack strategy.

97 MATHEMATICS AND COMPUTING↗

Spectroscopic studies of Dy3+ doped borate glasses for cool white light generation

Highlights: • BAZN glasses with Dy{sup 3+} ions were prepared using melt quench technique. • Under n-UV excitation the BAZN glasses show white light emission. • Energy transfer through cross-relaxation leads to concentration quenching. • Calculated CIE coordinates are close to the commercial w-LED. • 0.5 mol% of Dy{sup 3+} in these glasses are apt for cool white light generation. - Abstract: The Dy{sup 3+} ions doped Na{sub 2}O-ZnO-Al{sub 2}O{sub 3}-B{sub 2}O{sub 3} (BAZN) glasses with variable doping concentrations were synthesized by melt-quenching technique. The XRD pattern reveals amorphous nature of the as-synthesized glass. The FT-IR spectrum reveals various stretching and bending vibration of aluminates, borate and some other groups. The emission spectra exhibit two intense bands at around 482 nm (blue) and 575 nm (yellow) corresponding to the {sup 4}F{sub 9/2} → {sup 6}H{sub 15/2} and F{sub 9/2} → {sup 6}H{sub 13/2} transitions respectively. The CIE chromaticity coordinates of the as-synthesized glasses are lying in white region and in proximity to the coordinates for white light specified by National Television Standard Committee and commercial phosphor converted white light emitting devices. The decay profile of BAZN glasses showed bi-exponential behavior due to the energy transfer mechanism from excited donor ion to unexcited acceptor ion. The above-mentioned studies show potential of the as-synthesized Dy{sup 3+} doped BAZN glasses in solid state lighting applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Origin of relaxor behavior in 0.78(Na0.5Bi0.5)TiO3-0.2SrTiO3-0.02BaTiO3 ceramic: An electrical modulus study

Highlights: • Implementation of IS technique to study thermal evolution of polar nano regions. • Indirect evidence of the existence of polar nano regions well above T{sub B} and below T{sub f}. • Visualization of relaxation dynamics of PNRs on cooling by a schematic diagram. - Abstract: The relaxation dynamics of the polar nano-regions (PNRs) in the 0.78Na{sub 0.5}Bi{sub 0.5}TiO{sub 3}-0.2SrTiO{sub 3}-0.02BaTiO{sub 3} lead free ternary system over a wide temperature range (50–650 °C) is investigated using complex electric modulus formalism. The modulus spectra are analyzed across three characteristic temperatures T{sub B}, T{sub m}, and T{sub f} with a special focus on the evolution of dynamics of PNRs. Portraying high capacitance of shoulder response as compared to the bulk response in M{sup (}f) spectra shows indirectly the presence of highly polarisable entities that persist even above T{sub B} and below T{sub f}. The activation energies extracted from an Arrhenius fit to the relaxation time of both bulk and shoulder response signify different relaxation mechanisms. Further, the value of the stretched exponent β and the scaling behavior study of the M{sup (}f) spectra envisage temperature sensitive dipolar relaxation.

36 MATERIALS SCIENCE↗

Future Intensity‐Duration‐Frequency Curves of Extreme Precipitation in the Midwest United States From Convection‐Permitting Modeling

Abstract During the last four decades, global warming has statistically significant intensified extreme precipitation events in the Midwestern United States (defined here as the region covering Illinois, Indiana, Ohio, and Kentucky), leading to increased risks to human life, property, and infrastructure. To enable climate change adaptation and resilience across various economic and social sectors in this region, updated information about future climate changes, specifically at finer spatial scales, is essential. Leveraging a new 150‐year dynamical downscaling data set at convection‐permitting resolution, this study introduces a framework to construct the projected future intensity‐duration‐frequency (IDF) curves of heavy precipitation, which are prominent tools for infrastructure design and water resources management. This framework generates IDF curves at both sub‐daily and multi‐day duration utilizing hourly in situ observations as well as quantile‐based statistical techniques in bias‐correction and return levels selection. The assumption of non‐stationarity in the distribution parameter fitting process is also implemented in this workflow. Compared to historical IDF curves for 1980–2022, future projected IDF curves for 2058–2100 under Representative Concentration Pathway (RCP) 4.5 and RCP 8.5 scenarios indicate an average intensity increase of approximately 15% and 25%, respectively, across 74 stations, considering both annual and seasonal timescales. Future projections suggest that extreme precipitation events may become more severe across six investigated return periods, with longer return periods showing a greater increase. The frequency of future extreme precipitation events in the Midwest region is also projected to double. Furthermore, current results reveal spatial heterogeneity of future trends across stations owing to the high‐resolution input data set. Plain Language Summary This study investigates the evolving nature of extreme precipitation events in the Midwestern United States under a changing climate. By leveraging a high‐resolution dynamical downscaling data set, we construct projected intensity‐duration‐frequency (IDF) curves for future extreme rainfall events. These curves serve as vital tools for infrastructure planning and water resource management. Our analysis reveals a significant increase in both the intensity and frequency of extreme precipitation events in the region. Future projected IDF curves for the late century indicate an average intensity increase of approximately 15%–25% compared to historical values. Moreover, the frequency of such events is expected to double. Spatial heterogeneity in future trends is observed across different stations within the Midwest, highlighting the importance of high‐resolution modeling in capturing localized climate variability. These findings underscore the urgent need for climate adaptation strategies to mitigate the increasing risks associated with extreme precipitation events in the region. Key Points This study introduces a workflow to construct future intensity‐duration‐frequency (IDF) curves over the Midwest United States using a new convection‐permitting modeling data set The current IDF construction workflow reproduces well the historical observed IDF 30 curves in summer months with median relative errors of 2.4% among 74 stations and 6 investigated durations The projected IDF curves show diverse future trends of extreme precipitation across stations, with intensity increases of approximately 15% and 25% under RCP4.5 and RCP8.5 climate scenarios, respectively, and a doubling of frequency on average

Nguyen, Trung↗