bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamic changes to the plant cuticle include the production of volatile cuticular wax–derived compounds
Authors: Chen Jeff Y. , Kuruparan Aswini , Zamani-Babgohari Mahbobeh , Gonzales-Vigil Eliana
Published: November 2023

The cuticle is a hydrophobic structure that seals plant aerial surfaces from the surrounding environment. To better understand how cuticular wax composition changes over development, we conducted an untargeted screen of leaf surface lipids from black cottonwood (
Populus trichocarpa
). We observed major shifts to the lipid profile across development, from a phenolic and terpene-dominated profile in young leaves to an aliphatic wax-dominated profile in mature leaves. Contrary to the general pattern, levels of aliphatic
cis
-9-alkenes decreased in older leaves following their accumulation. A thorough examination revealed that the decrease in
cis
-9-alkenes was accompanied by a concomitant increase in aldehydes, one of them being the volatile compound nonanal. By applying exogenous alkenes to
P. trichocarpa
leaves, we show that unsaturated waxes in the cuticle undergo spontaneous oxidative cleavage to generate aldehydes and that this process occurs similarly in other alkene-accumulating systems such as balsam poplar (
Populus balsamifera
) leaves and corn (
Zea mays
) silk. Moreover, we show that the production of cuticular wax–derived compounds can be extended to other wax components. In bread wheat (
Triticum aestivum
), 9-hydroxy-14,16-hentriacontanedione likely decomposes to generate 2-heptadecanone and 7-octyloxepan-2-one (a caprolactone). These findings highlight an unusual route to the production of plant volatiles that are structurally encoded within cuticular wax precursors. These processes could play a role in modulating ecological interactions and open the possibility for engineering bioactive volatile compounds into plant waxes.
Low- and high-frequency vibrations synergistically enhance singlet exciton fission through robust vibronic resonances
Authors: Bhattacharyya Atandrita , Sahu Amitav , Patra Sanjoy , Tiwari Vivek
Published: November 2023

Singlet exciton fission (SEF) is initiated by ultrafast internal conversion of a singlet exciton into a correlated triplet pair

(
T
T
)

1

. The “reaction coordinates” for ultrafast SEF even in archetypal systems such as pentacene thin film remain unclear. Couplings between fast electrons and slow nuclei are ubiquitous across a range of phenomena in chemistry. Accordingly, spectroscopic detection of vibrational coherences in the

(
T
T
)

1

photoproduct motivated investigations into a possible role of vibronic coupling, akin to that reported in several photosynthetic proteins. However, acenes are very different from chlorophylls with 10× larger vibrational displacements upon photoexcitation and low-frequency vibrations modulating intermolecular orbital overlaps. Whether (and if so how) these unique features carry any mechanistic significance for SEF remains a poorly understood question. Accordingly, synthetic design of new molecules aiming to mimic this process across the solar spectrum has broadly relied on tuning electronic couplings. We address this gap and identify previously unrecognized synergistic interplay of vibrations, which in striking contrast to photosynthesis, vitally enhances SEF across a broad, nonselective and, therefore, unavoidable range of vibrational frequencies. We argue that attaching mechanistic significance to spectroscopically observed prominent quantum beats is misleading. Instead, we show that vibronic mixing leads to anisotropic quantum beats and propose readily implementable polarization-based two-dimensional electronic spectroscopy experiments which uniquely distinguish vibrations which drive vibronic mixing and promote SEF, against spectator vibrations simply accompanying ultrafast internal conversion. Our findings introduce crucial ingredients in synthetic design of SEF materials and spectroscopy experiments aiming to decipher mechanistic details from quantum beats.
Tuning electrical and optical properties of InAs/GaAs1−x
Sb
x
quantum dots
Authors: Bao Yidi , Liu Wen , Liu Qing , Chen Xiaoling , Yang Fuhua , Wang Xiaodong
Published: November 2023

Understanding the electrical and optical properties of InAs/GaAs(Sb) quantum dots (QDs) is essential for designing and improving the performance of related semiconductor QD devices. In this paper, the effects of In segregation, QD size, capping layer thickness and Sb composition on the electrical and optical properties of type I and type II InAs/GaAs1−x
Sb
x
(

0

⩽
x
⩽

1

) QDs are systematically investigated and general regularities are summarized. The comparisons of electron distribution probabilities, interband and intraband transition energies and absorption coefficients show that In segregation and QD size have a strong influence on the electron energy level positions of InAs QDs and that the trade-offs between absorption peak energy, absorption intensity and radiative lifetime of InAs/GaAs1−x
Sb
x
QDs can be optimized by adjusting the thickness and Sb composition of the GaAs1−x
Sb
x
capping layer. The results obtained are promising for the applications in the pre-design and performance feedback of the QD devices such as QD lasers, QD infrared detectors and intermediate band solar cells.
Efficient DFT prediction of chemical and structural stability using van der Waals correction: application for A3B2Ga3O12 garnets (A = Lu, Y and B = Al, Sc)
Authors: Pramchu Sittichain , Supatutkul Chumpol , Srisakonsub Phatthranit
Published: November 2023

Several seamless van der Waals (vdW) correction methods available for a wide range of systems could be expected to enhance stability predictions by accounting for the vdW effect. The stability of material can be evaluated using chemical potential phase diagram (CPD) which reveals the elemental chemical potential conditions for a successful synthesis. In this work, viability of various vdW correction approaches in improving the accuracy of stability prediction for A3B2Ga3O12 garnets (A = Lu, Y and B = Al, Sc) has been studied. From the results, we have found that vdW-df-cx, Grimme-D3, vdW-df-c09, and vdW-df2-c09 significantly improve ΔH prediction with MAPE of >5.0% lower than PBE, which exhibit their potential for stability prediction based on the CPD analysis. For CPD construction whose reliability is based on ΔH prediction, vdW-df-cx which can minimize the MAPE in ΔH, relative to experimental data, is selected as the best method among all studied vdW approaches. A more accurate description of total energy of O2 molecule and the competing compounds with layered structure can be also acquired by incorporating vdW interaction. However, the MAPE in lattice constant reveals that there is no significant improvement of lattice constant prediction for the studied garnets and their competing compounds. The vdW method which gives the MAPE in lattice constant slightly lower than that of PBE is vdW-df2-b86r. Although we found that the vdW corrections can improve material stability prediction, there is still room for the development of a novel DFT-based vdW method capable of accurately predicting both the lattice constant and ΔH of solids, including complex materials like garnets.
Quantum systems in silicon carbide for sensing applications
Authors: Castelletto S , Lew C T-K , Lin Wu-Xi , Xu Jin-Shi
Published: November 2023

This paper summarizes recent studies identifying key qubit systems in silicon carbide (SiC) for quantum sensing of magnetic, electric fields, and temperature at the nano and microscale. The properties of colour centres in SiC, that can be used for quantum sensing, are reviewed with a focus on paramagnetic colour centres and their spin Hamiltonians describing Zeeman splitting, Stark effect, and hyperfine interactions. These properties are then mapped onto various methods for their initialization, control, and read-out. We then summarised methods used for a spin and charge state control in various colour centres in SiC. These properties and methods are then described in the context of quantum sensing applications in magnetometry, thermometry, and electrometry. Current state-of-the art sensitivities are compiled and approaches to enhance the sensitivity are proposed. The large variety of methods for control and read-out, combined with the ability to scale this material in integrated photonics chips operating in harsh environments, places SiC at the forefront of future quantum sensing technology based on semiconductors.
Interference effect on Goos–Hänchen shifts of anisotropic medium interface
Authors: Li Zihan , Chen Ze , Li Yong , Zhang Zhihai , Zhuang Guoce , Liu Jianli , Meng Yang
Published: November 2023

We present a comprehensive analysis of the anomalous Goos–Hänchen (GH) displacement that occurs during the reflection of light beams at an interface between air and an anisotropic medium. This analysis also applies to the Imbert–Fedorov effect. Our study suggests that the anomalous GH displacement is primarily caused by polarization-dependent abnormal interference effects between the direct and cross-reflected light fields. Using the interface between air and a type II Weyl semimetal as an example, we provide a clear physical explanation for the relationship between spin-dependent abnormal interference effects and anomalous GH displacement. We demonstrate that spin-dependent constructive interference leads to a reduction in the GH displacement of the total reflected light field, while spin-dependent destructive interference results in an increase in the GH displacement of the total reflected light field.
Large-field Astronomical Image Restoration and Superresolution Reconstruction using Deep Learning
Authors: Long Ma , Jiangbin Du , Jiayao Zhao , Xuhao Wang , Yangfan Peng
Published: November 2023

The existing astronomical image restoration and superresolution reconstruction methods have problems such as low efficiency and poor results when dealing with images possessing large fields of view. Furthermore, these methods typically only handle fixed-size images and require step-by-step processing, which is inconvenient. In this paper, a neural network called Res&RecNet is proposed for the restoration and superresolution reconstruction of astronomical images with large fields of view for direct imaging instruments. This network performs feature extraction, feature correction, and progressive generation to achieve image restoration and superresolution reconstruction. The network is constructed using fully convolutional layers, allowing it to handle images of any size. The network can be trained using small samples and can perform image restoration and superresolution reconstruction in an end-to-end manner, resulting in high efficiency. Experimental results show that the network is highly effective in terms of processing astronomical images with complex scenes, generating image restoration results that improve the peak signal-to-noise ratio (PSNR) and structural similarity index measure (SSIM) by 4.69 (dB)/0.073 and superresolution reconstruction results that improve the PSNR and SSIM by 1.97 (dB)/0.077 over those of the best existing algorithms, respectively.
Planar matrices and arrays of Feynman diagrams: poles for higher k
Authors: Guevara Alfredo , Zhang Yong
Published: November 2023

Planar arrays of tree diagrams were introduced as a generalization of Feynman diagrams that enable the computation of biadjoint amplitudes

m

n

(
k
)

for k > 2. In this follow-up work, we investigate the poles of

m

n

(
k
)

from the perspective of such arrays. For general k, we characterize the underlying polytope as a Flag Complex and propose a computation of the amplitude-based solely on the knowledge of the poles, whose number is drastically less than the number of the full arrays. As an example, we first provide all the poles for the cases (k, n) = (3, 7), (3, 8), (3, 9), (3, 10), (4, 8) and (4, 9) in terms of their planar arrays of degenerate Feynman diagrams. We then implement simple compatibility criteria together with an addition operation between arrays and recover the full collections/arrays for such cases. Along the way, we implement hard and soft kinematical limits, which provide a map between the poles in kinematic space and their combinatoric arrays. We use the operation to give a proof of a previously conjectured combinatorial duality for arrays in (k, n) and (n − k, n). We also outline the relation to boundary maps of the hypersimplex Δ
k,n
and rays in the tropical Grassmannian

Tr
(
k
,
n
)

.
Study of the influence of virtual guard ring width on the performance of SPAD detectors in 180 nm standard CMOS technology
Authors: Liu Danlu , Li Ming , Xu Tang , Dong Jie , Fang Yuming , Xu Yue
Published: November 2023

The influence of the virtual guard ring width (GRW) on the performance of the p-well/deep n-well single-photon avalanche diode (SPAD) in a 180 nm standard CMOS process was investigated. TCAD simulation demonstrates that the electric field strength and current density in the guard ring are obviously enhanced when GRW is decreased to 1 μm. It is experimentally found that, compared with an SPAD with GRW = 2 μm, the dark count rate (DCR) and afterpulsing probability (AP) of the SPAD with GRW = 1 μm is significantly increased by 2.7 times and twofold, respectively, meanwhile, its photon detection probability (PDP) is saturated and hard to be promoted at over 2 V excess bias voltage. Although the fill factor (FF) can be enlarged by reducing GRW, the dark noise of devices is negatively affected due to the enhanced trap-assisted tunneling (TAT) effect in the 1 μm guard ring region. By comparison, the SPAD with GRW = 2 μm can achieve a better trade-off between the FF and noise performance. Our study provides a design guideline for guard rings to realize a low-noise SPAD for large-array applications.
Helical sample-stepping for faster speckle-based multi-modal tomography with the Unified Modulated Pattern Analysis (UMPA) model
Authors: Savatović Sara , De Marco Fabio , Riedel Mirko , Di Trapani Vittorio , Margini Marco , Lautizi Ginevra , Hammel Jörg U. , Herzen Julia , Thibault Pierre
Published: November 2023

Speckle-based imaging (SBI) is a multi-modal X-ray imaging technique that gives access to absorption, phase-contrast, and dark-field signals from a single dataset.
However, it is often difficult to disentangle the different signals from a single measurement.
Having complementary data obtained by repeating the scan under slightly varied conditions (multiframe approach) can significantly enhance the accuracy of signal extraction and, consequently, improve the overall quality of the final reconstruction.
In order to retrieve the different channels, SBI relies on a reference pattern, generated by the addition of a wavefront marker in the beam (i.e., a sandpaper or gratings).
Here, we show how a continuous helical acquisition can extend the field of view (FOV) and speed up the acquisition while maintaining a multiframe approach for the signal retrieval of a test object.
Climatic effects on landscape multifunctionality in urban parks: a view for integrating ecological supply and human benefits
Authors: Yan Ming , Chen Liding , Sun Ranhao
Published: November 2023

The rapid and relentless development of urban areas highlights the importance of landscape multifunctionality. However, there is limited research on the temporal dynamics and climatic effects of urban landscape multifunctionality. This study aimed to address this gap by analyzing the features of multiple landscape functions triggered by seasonal climate change in different urban park types. In this study, we investigated five typical urban landscape functions (alleviating urban heat islands, vegetation growth, biodiversity promotion, alleviation of waterlogging, and provision of recreational activities) by establishing a set of indices: ecological supply capability (SP
), proportion of ecological supply (SPP
), capability of human benefits (BP
), and human benefits efficiency (BEP
) of urban parks. The average SP
of the landscape functions was 58% in summer and 46% in winter. During the transition from summer to winter, urban parks witnessed a significant decrease in SPP
for alleviating the urban heat island, dropping from 34% to 5%. The primary landscape functions shifted from alleviating the urban heat island (34%) and providing recreation (29%) to providing recreation (38%) and biodiversity promotion (29%). Concerning park types, nature parks provided the highest SP
, whereas community parks provided the highest BEP
. This study has useful implications for landscape management in urban parks, particularly regarding timely adjustments across seasonal climates. It is possible to promote sustainable and effective human well-being by maximizing landscape functions.
Significant relationships between drought indicators and impacts for the 2018–2019 drought in Germany
Authors: Shyrokaya Anastasiya , Messori Gabriele , Pechlivanidis Ilias , Pappenberger Florian , Cloke Hannah L , Di Baldassarre Giuliano
Published: November 2023

Despite the scientific progress in drought detection and forecasting, it remains challenging to accurately predict the corresponding impact of a drought event. This is due to the complex relationships between (multiple) drought indicators and adverse impacts across different places/hydroclimatic conditions, sectors, and spatiotemporal scales. In this study, we explored these relationships by analyzing the impacts of the severe 2018–2019 central European drought event in Germany. We first computed the standardized precipitation index (SPI), the standardized precipitation evaporation index (SPEI), the standardized soil moisture index (SSMI) and the standardized streamflow index (SSFI) over various accumulation periods, and then related these indicators to sectorial losses from the European drought impact report inventory (EDII) and media sources. To cope with the uncertainty associated with both drought indicators and impact data, we developed a fuzzy method to categorize them. Lastly, we applied the method at the region level (EU NUTS1) by correlating monthly time series. Our findings revealed strong and significant relationships between drought indicators and impacts over different accumulation periods, albeit in some cases region-specific and time-variant. Furthermore, our analysis established the interconnectedness between various sectors, which displayed systematically co-occurring impacts. As such, our work provides a new framework to explore drought indicators-impacts dependencies across space, time, sectors, and scales. In addition, it emphasizes the need to leverage available impact data to better forecast drought impacts.
Asymptotic analysis of the narrow escape problem in general shaped domain with several absorbing necks
Authors: Li Xiaofei , Lin Shengqi
Published: November 2023

This paper considers the two-dimensional narrow escape problem in a domain which is composed of a relatively big head and several absorbing narrow necks. The narrow escape problem is to compute the mean first passage time (MFPT) of a Brownian particle traveling from inside the head to the end of the necks. The original model for MFPT is to solve a mixed Dirichlet–Neumann boundary value problem for the Poisson equation in the composite domain, and is computationally challenging. In this paper, we compute the MFPT by solving an equivalent Neumann–Robin type boundary value problem. By solving the new model, we obtain the three-term asymptotic expansion of the MFPT. We also conduct numerical experiments to show the accuracy of the high order expansion. As far as we know, this is the first result on high order asymptotic solution for narrow escape problem (NEP) in a general shaped domain with several absorbing neck windows. This work is motivated by Li (2014 J. Phys. A: Math. Theor.
47 505202), where the Neumann–Robin model was proposed to solve the NEP in a domain with a single absorbing neck.
On two possible ways to recover ordinary thermodynamics from extended thermodynamics of polyatomic gases
Authors: Demontis F , Pennisi S
Published: November 2023

We consider two possible ways, i.e. the Maxwellian iteration (MI) and the Chapman–Enskog method (CEM), to recover relativistic ordinary thermodynamics from relativistic extended thermodynamics of Polyatomic gases with N moments. Both of these methods give the Eckart equations which are the relativistic version of the Navier–Stokes and Fourier laws as a first iteration. However, these methods do not lead to the same expressions of the heat conductivity χ, the shear viscosity µ, and the bulk viscosity ν which appear as coefficients in the Eckart equations. In particular, we prove that the expressions of χ, µ, and ν obtained via the CEM do not depend on N, while those obtained through the MI depend on N. Moreover, we also prove that these two methods lead to the same results in the nonrelativistic limit.
High temperature tribological properties of Fe-Mo-Ni-Cu-Graphite self-lubricating guide sliding plates
Authors: Yan Xiaoni , Yang Wei , Zhao Yingxiang , Deng Wen , Shi Junwen , Guo Junde
Published: November 2023

High-temperature self-lubricating Fe-Mo-Ni-Cu-graphite materials with varying copper contents were prepared by powder metallurgy technology. The microstructure and wear surface of the sintered alloy were observed and analyzed using optical microscopy and scanning electron microscopy. The focus was on discussion of the influence of copper content on the tribological properties of the iron-based material. The results indicate that the friction coefficient and wear rate of the sintered material against a 40Cr steel disc show a decreasing trend after friction with an increase in copper content. Particularly, at a copper content of 15%, the friction coefficient is lowest at both room temperature and 500 °C, exhibiting the best wear resistance. The wear rate is in the order of 10–7 cm3/N•m, indicating mild wear. The predominant wear mechanism for both the material and the counterpart disc is adhesive wear. During friction, the formation of a black-brown lubricating composite film composed of Fe2O3, graphite, Fe2O3 • Fe3O4, CuO, and Fe3O4 on the material’s surface plays a crucial role in providing excellent high-temperature anti-friction properties.
Off-the-shelf optical systems design enabled by an evolution strategy: front stop case
Authors: Madrid-Sánchez Alejandro , Ortiz-Ocampo José , Trujillo Carlos , Ottevaere Heidi
Published: November 2023

Commercial off-the-shelf optics enable economic and rapid solutions in the photonics industry and academia. However, the design of optical systems with off-the-shelf optics is a time-consuming task for experienced optical designers and hopeless for novice designers. In this paper, we propose an automatic optical design tool to generate optical systems using only off-the-shelf optical components without human assistance. Our solution is based on an evolution strategy (ES) that performs a discrete combinatorial optimization following optical design-based methodologies that satisfy user-defined specifications. Unlike the conventional methods, the algorithm decreases the design process time and provides optical designers with several optical solutions from where to choose and adapt for targeted applications. In this work, the ES is described and tested with front stop optical configurations. We demonstrate the broad solution domain of the algorithm through the generation of optical systems with F-numbers within a range F/1 to F/90 and field of views up to 300 mm at the image plane. To analyze the solution domain and the characteristics of the solution, we used the design specifications of 29 commercially available scan lenses and compared the performance of different ES parameters. The compatibility of our algorithm with (standard) commercially available optical design software unlocks automatic design tools for off-the-shelf optical systems.
Bioprinted in vitro tissue models: an emerging platform for developing therapeutic interventions and disease modelling
Authors: Bhardwaj Nandana , Dey Souradeep , Bhar Bibrita , Mandal Biman B
Published: November 2023

In the past decade, the use of three-dimensional (3D) bioprinting technology for the development of in vitro tissue models has attracted a great deal of attention. This is due to its remarkable precision in constructing different functional tissues and organs, enabling studies of their biology. In addition, this high-throughput technology has been extended to therapeutics, as it provides an alternative functional platform for rapid drug screening and disease modelling. Functional tissue models fabricated using 3D bioprinting mimic native tissues and help in the development of platforms for personalized drug screening and disease modelling due to their high throughput and ease of customization. Moreover, bioprinted 3D tissue models mimic native tissues more closely and provide added advantages over earlier conventional tissue models, such as monoculture, co-culture, explants, etc. In this context, this review article provides an overview of different bioprinted in vitro tissue models of skin, bone, neural tissue, vascular tissue, cartilage, liver and cardiac tissue. This article explores advancements and innovations in these models in terms of developing improved therapeutic interventions. Herein, we provide an insight into the development of different bioprinted tissue models for applications in drug screening and disease modelling. The needs and advantages of bioprinted tissue models as compared with conventional in vitro models are discussed. Furthermore, the different biomaterials, cell sources and bioprinting techniques used to develop tissue models are briefly reviewed. Thereafter, different bioprinted tissue models, namely skin, liver, vascular, cardiac, cartilage, bone and neural tissue, are discussed in detail with a special emphasis on drug screening and disease modelling. Finally, challenges and future prospects are highlighted and discussed. Taken together, this review highlights the different approaches and strategies used for the development of different 3D bioprinted in vitro tissue models for improved therapeutic interventions.
Research on electromagnetic electroosmotic flow of Jeffrey fluid through semicircular microchannel
Authors: Dong Jiayin , Li Dongsheng , Yu Mengqi , Li Kun
Published: November 2023

This work extends the previous research on electroosmotic flow in semicircular microchannels, further investigating the electromagnetic electroosmotic flow of Jeffrey fluid under the combined action of the electric field force and electromagnetic force. The analytic solution of velocity is derived using the variable separation method. The influences of oscillation Reynolds number

R
e
,

Hartmann number

H
a
,

electric width

K
,

relaxation time

D
e

and retardation time

λ

2

ω

on velocity are examined through graphical analysis. The results show that an increase in Reynolds number

R
e

leads to stronger oscillations in the velocity profile at any Hartmann number

H
a
,

and the change in velocity oscillations becomes more pronounced with increasing Hartmann number

H
a
.

Specifically, at lower Hartmann numbers

H
a
,

the velocity increases with an increase in electric width

K

and relaxation time

D
e
,

but decreases with an increase in retardation time

λ

2

ω
.

An interesting finding is that, at higher Hartmann numbers

H
a
,

the velocity of the Jeffrey fluid still decreases under the influence of obstruction in the channel. Furthermore, the results of this study are compared with those of previous scholars to validate their accuracy.
Development of a roof-mounted stand-alone wind turbine system for house-hold power generation
Authors: Surve Minendra L , Deshmukh Prashant D , Kale Bharatbhushan S , Ghadge Akshay R , Patil Manish V
Published: November 2023

In recent years, the development of sustainable energy sources has attracted increasing interest due to worries about the environmental effects of greenhouse gas emissions. Renewable energy and technology may provide a solution to the persistent environmental issues that developing nations are currently experiencing. In this work, it has been demonstrated that the design, analysis, and implementation of the newly developed small roof-mounted stand-alone wind turbine systems for household energy production. It is specially designed for sites with low altitudes (12 m above ground) and low wind speeds (range of 1–12 m s−1). The wind turbine system involves the mechanical design of the 3-blade rotor and its installation on a micro-capacity and self-contained 325 W wind turbine. The experimental analysis reveals that the peak power coefficient (CP) is quite good, about 0.13, and the output power is 43.75 W. The comparative analysis is also done to validate that the results are consistent with micro-capacity systems that have been tested under similar conditions. This work provides insight into the development of roof-mounted stand-alone wind turbine systems, which have a lot of potential for green applications and to make up for people who don’t have access to electricity.
Rescuing off-equilibrium simulation data through dynamic experimental data with dynAMMo
Authors: Kolloff Christopher , Olsson Simon
Published: November 2023

Long-timescale behavior of proteins is fundamental to many biological processes. Molecular dynamics (MD) simulations and biophysical experiments are often used to study protein dynamics. However, high computational demands of MD limit what timescales are feasible to study, often missing rare events, which are critical to explain experiments. On the other hand, experiments are limited by low resolution. We present dynamic augmented Markov models (dynAMMo) to bridge the gap between these data and overcome their respective limitations. For the first time, dynAMMo enables the construction of mechanistic models of slow exchange processes that have been not observed in MD data by integrating dynamic experimental observables. As a consequence, dynAMMo allows us to bypass costly and extensive simulations, yet providing mechanistic insights of the system. Validated with controlled model systems and a well-studied protein, dynAMMo offers a new approach to quantitatively model protein dynamics on long timescales in an unprecedented manner.
Real fundamental Chevalley involutions and conjugacy classes
Authors: Han Gang , Sun Binyong
Published: November 2023

Let

G

\mathsf G

be a connected reductive linear algebraic group defined over

R

\mathbb R

, and let

C
:

G

→

G

C: \mathsf G\rightarrow \mathsf G

be a fundamental Chevalley involution. We show that for every

g
∈

G

(

R

)

g\in \mathsf G(\mathbb R)

,

C
(
g
)

C(g)

is conjugate to

g

−
1

g^{-1}

in the group

G

(

R

)

\mathsf G(\mathbb R)

. Similar result on the Lie algebras is also obtained.
A note on extreme points of the unit ball of Hardy-Lorentz spaces
Authors: Carrillo-Alanís Javier , Curbera Guillermo
Published: November 2023

We show that inner functions are extreme points of the unit ball of the Hardy-Lorentz space

H
(
Λ
(
φ
)
)

H(\Lambda (\varphi ))

, for

Λ
(
φ
)

\Lambda (\varphi )

a Lorentz space with

φ
\varphi

strictly increasing and strictly concave.
Mechanisms underlying Myosin 10′s contribution to the maintenance of mitotic spindle bipolarity
Authors: Yim Yang-In , Pedrosa Antonio , Wu Xufeng , Chinthalapudi Krishna , Cheney Richard E. , Hammer John A.
Published: November 2023

Myosin 10 (Myo10) couples microtubules and integrin-based adhesions to movement along actin filaments via its microtubule-binding MyTH4 domain and integrin-binding FERM domain, respectively. Here we show that Myo10-depleted HeLa cells and mouse embryo fibroblasts (MEFs) both exhibit a pronounced increase in the frequency of multipolar spindles. Staining of unsynchronized metaphase cells showed that the primary driver of spindle multipolarity in Myo10-depleted MEFs and in Myo10-depleted HeLa cells lacking supernumerary centrosomes is pericentriolar material (PCM) fragmentation, which creates y-tubulin-positive acentriolar foci that serve as extra spindle poles. For HeLa cells possessing supernumerary centrosomes, Myo10 depletion further accentuates spindle multipolarity by impairing the clustering of the extra spindle poles. Complementation experiments show that Myo10 must interact with both microtubules and integrins to promote PCM/pole integrity. Conversely, Myo10 only needs interact with integrins to promote supernumerary centrosome clustering. Importantly, images of metaphase Halo–Myo10 knockin cells show that the myosin localizes exclusively to the spindle and the tips of adhesive retraction fibers. We conclude that Myo10 promotes PCM/pole integrity in part by interacting with spindle microtubules, and that it promotes supernumerary centrosome clustering by supporting retraction fiber-based cell adhesion, which likely serves to anchor the microtubule-based forces driving pole focusing.
Deposition of Sevelamer crystals in gastrointestinal tract and lung parenchyma: A rare autopsy finding
Authors: Liu J , Zaidi A , Sonawane S S , Guzman G , Qazi O
Published: November 2023

Introduction/Objective

Sevelamer carbonate is a non-calcium-based phosphate binder used for the management of hyperphosphatemia in patients with end stage renal disease. The well-known side effects of sevelamer include nausea, vomiting and abdominal pain. However, there are few case reports which described the deposition of sevelamer crystals in the gastrointestinal tract causing mucosal injury, pseudotumor or obstruction.

Methods/Case Report

We hereby present a case of a 43-year-old decedent female with past medical history of seizures, hypertension, cocaine use, type B aortic dissection status post thoracic endovascular aortic repair, total arch replacement, reconstruction of innominate, carotid, and subclavian artery who presented with hematochezia concerning for possible aorto-esophageal fistula on 10/06/2022 and acute kidney injury. Imaging showed a thrombus in mid-esophagus, blood in trachea and narrowing of the left main stem bronchus. Labs revealed worsening of BUN and creatinine and up trending hyperphosphatemia and therefore sevelamer carbonate via nasogastric route was started on 10/13/22.

Unfortunately, the patient’s hospital course was complicated, and she passed away on 11/14/2022. At autopsy, the deceased had gross evidence of acute lung injury with diffuse alveolar hemorrhage, aorta-bronchial ruptured aneurysm defect and aorto-esophageal fistulas. On histopathological examination, the stomach, small and large bowel showed autolysis, necrosis, and numerous rectangular shaped, non-polarizable crystals. The crystals with characteristic morphology of “fish scale” with hues of pink in the center and yellow to orange in the periphery were identified as sevelamer crystals. Interestingly, crystal deposition was also identified in lung parenchyma and rarely in aortic wall and the fistula.

Results (if a Case Study enter NA)

NA

Conclusion

As one of the more commonly used resins in end stage kidney disease, gastrointestinal adverse effect of sevelamer carbonate is often underrecognized. Our case report heightens the awareness of the characteristic morphology of this biologically inert agent, sevelamer to those who are unaware of their morphology. This case also highlights the adverse effect of sevelamer in all patients presenting with gastrointestinal symptoms, such as gastrointestinal bleeding and abdominal pain with the use of sevelamer.
HER2 amplification in cases with low HER2 expression by immunohistochemistry (IHC): A Single Institutional Experience
Authors: Podany P , Golastani R , Zhan H , Liang Y , Harigopal M , Krishnamurti U
Published: November 2023

Introduction/Objective

HER2 testing in invasive breast carcinoma (IBC) is the standard of care to determine patient eligibility for HER2 directed therapy with trasuzumab. Initial testing of tissue by HER2 immunohistochemistry (IHC) can be positive, negative, or equivocal. In equivocal cases as well as negative cases in our institution HER2 FISH is also performed. According to ASCO/CAP guidelines a subset of equivocal and negative IHC cases are considered HER2 positive if they meet criteria for increased HER2/CEP17 ratio and HER2 copy number by FISH, allowing more patients to be treated with HER2 directed therapies. HER2 grouping per ASCO is as follows; Group 1: HER2 copy number ≥4 signals/cell, Group 2: <4.0 signals/cell, Group 3: ≥6 signals/cell, Group 4: HER2 copy number ≥4 and <6 signals/cell, Group 5: HER2 copy number <4 signals/cell

Methods/Case Report

All cases of IBC resection with HER2 IHC and FISH results from Jan 2018-Dec 2021 were included in this study. All cases positive for HER2 by IHC alone (3+ staining) were excluded. The ASCO/CAP 2018 guidelines for HER2 testing in breast cancer were used to evaluate HER2 positivity by FISH and the relation to IHC scores

Results (if a Case Study enter NA)

A total of 2630 IBC cases with both HER2 IHC and FISH testing were included. Of these, 131 (5.0%) were in FISH group 1, 17 (0.7%) in group 2, 11 (0.4%) in group 3, 161 (6.1%) in group 4, and 2310 (87.8%) in group 5. A total of 142 (5.4%) cases that were HER2 equivocal or negative by IHC were HER2 positive by FISH. Specifically, 0.3% of cases with an IHC score of 0, 1.4% with a score of 1+, and 14.6% of cases with a score of 2+ were positive by FISH. Of the 14.6% IHC 2+ cases that were FISH positive 13.3% were in FISH group 1 (115 cases) and 1.3% (11 cases) in FISH group 3. Of FISH positive cases 1.4% had an IHC score of 0, 9.9% had an IHC score of 1 and 88.7% had a score of 2

Conclusion

At our institution 14.6% of IBC with equivocal HER2 staining on IHC, 1.4% of cases with negative (1+) staining and 0.3% of cases with negative (0) were HER2 FISH positive. Since HER2 FISH is not reflexively performed on cases HER2 negative by IHC, this additional 1.7% will qualify for HER2 targeted therapy

Interpretation of low HER2 expression by IHC by traditional IHC assay may miss a small percentage of cases eligible for HER2 directed therapy. Accurate interpretation of HER2 low by IHC is critical as recent clinical trials have shown that low HER2 expression with IHC scores of 1+ or 2+ without gene amplification by FISH could benefit from Trastuzumab Deruxtecan
Comparison of FDA-Approved vs. Mayo Clinic’s Ki-67 Immunostaining Protocols for Breast Cancer Specimens: A Quantitative Analysis Using Artificial Intelligence (AI) Based Image Analysis Algorithms
Authors: Stoy L , del Rosario K , Plagge A , Lewis K , Yasir S , Chen Z
Published: November 2023

Introduction/Objective

Ki-67, a nuclear protein present during the active phases of the cell cycle, is an important prognostic and predictive marker for many tumor types, including breast cancer. This study compared the results of breast cancer specimens immunohistochemically (IHC) stained with the FDA-approved vs. Mayo Clinic’s (MC) validated Ki-67 protocol using AI-based image analysis algorithms for quantitative examination at an individual cell level.

Methods/Case Report

Sixty-two breast cancer specimens were selected with a rough equal representation of Ki-67 percentage in low (<10%), intermediate (10-20%) and high (>20%) categories. Two adjacent sections of each specimen were stained with the FDA and MC protocols, respectively, and scanned to obtain whole slide digital images. Two AI algorithms, one with tumor cell identification and the other without, were used to quantify positive and negative cells and calculate Ki-67 percentages.

Results (if a Case Study enter NA)

Both algorithms show high concordance between the two staining protocols, with r-squared scores of 0.989 and 0.992, respectively, analyzing with or without tumor identification. AI identified tumor better on MC stained slides vs. FDA stained slides. The results demonstrate a high-performance concordance between the MC and the FDA IHC staining protocols.

Conclusion

The data also illustrates the accuracy of using AI image analysis algorithms to compare different IHC protocols at an individual cell level. The AI tumor identification difference in slides stained with two IHC protocols reflects the importance of training an algorithm with a specific staining protocol to achieve optimal tumor recognition.
Invasive Paget disease of the breast: two unique cases with diagnostic conundrum
Authors: Shirai S , Saluja K , Zhang S , Guo T
Published: November 2023

Introduction/Objective

Invasive Paget disease of the breast is a rare entity with diagnostic challenges. It has been reported in 4-8% of cases of mammary Paget disease, while Paget disease itself represents only 1-4% of all breast carcinomas. The pigmented variant of this entity brings even greater diagnostic challenge. Herein, we present two patients with Paget disease of the breast with dermal invasion, one case with associated ulceration and another with pigmentation.

Methods/Case Report

Patient 1 is a 47-year-old female with a 9 mm right breast mass with a lobulated margins and calcifications. Simple mastectomy was grossly notable for nipple ulceration. Patient 2 is a 54-year-old female with a cm irregular mass in the right breast. Grossly, the nipple appeared blackened and mildly everted.

Results (if a Case Study enter NA)

Histopathologic evaluation of the nipple sections from patient 1 show invasive Paget disease with associated ulceration, with a depth of invasion of 4.5 mm. The breast biomarkers on the nipple section show tumor cells are negative for ER (0%) and PR (0%), and positive for HER2/neu (3+). Additionally, there was a separate 1.5 cm invasive ductal carcinoma, combined Nottingham histologic grade 3, pathologic stage of pT1c. The nipple sections from patient 2 show pigmented, invasive Paget disease, with a 1.5 mm depth of invasion. The tumor cells are positive for CK7 (weak), ER and PR, and negative for HER2/neu (1+). HMB45 and MART1 show increased reactivity in melanocytes. She also had a separate 2.5 cm invasive ductal carcinoma, combined Nottingham histologic grade 3, pathologic stage of pT2.

Conclusion

We present two unique cases of breast invasive Paget disease: one with associated ulceration, which brings challenges with tumor staging; and another one with pigmentation, which can be mistaken as melanoma.

Invasive Paget disease must be distinguished from locally advanced breast cancer presenting as satellite skin nodules or skin ulceration, as it can lead to erroneous tumor over-staging as pT4b. It is important to recognize these two variations of invasive Paget disease so as to avoid over-staging or misdiagnosis, respectively, and to be cognizant of the fact that the treatment and prognosis differ.
Assessment of potential biomarkers for early detection and management of Glomerulonephritis patients with diabetic diseases
Authors: Addissouky T A , Khalil A A , El Agroudy A E
Published: November 2023

Introduction/Objective

Glomerulonephritis is a serious kidney disease that can lead to kidney failure if not detected and treated early. Several potential biomarkers have been identified to aid in early detection of this condition. it is important to investigate and validate these novel biomarkers to improve patient outcomes in the management of glomerulonephritis.

Methods/Case Report

The various biomarkers such as Creatinine, urinary exosomes, Cystatin-C, interleukin-6, tumor necrosis factor-alpha (TNF-α), Fasting blood glucose, Albumin, MicroRNAs, and complement activation factors (C3, C4d) were measured and calculated in 98 infected cases with diabetic patients who had acute kidney diseases. The same biomarkers had been implemented for 87 cases with chronic renal disease on dialysis. Also, the same parameters were determined in 82 healthy persons as controls. Alternative markers' levels were determined by using Microscopic, Biochemical, ELISA, and RT-PCR techniques. The biopsy had been applied only to infected patients.

Imaging diagnostic tools have been applied to all cases.

Results (if a Case Study enter NA)

The studied biomarkers have high sensitivity from 81.35% to 94.72% and accuracy from 88.76% to 96.83% as well as their cut off which approved the aim of this study. Thereafter, the studied markers' reports assisted in detecting glomerulonephritis diseases at early stages.

Conclusion

Alternative biomarkers (Cystatin-C, interleukin-6, tumor necrosis factor-alpha (TNF-α), urinary exosomes, MicroRNAs, and complement activation factors (C3, C4d)) are considered as prospective markers to differentiate healthy individuals from chronic kidney disease by their significant results. Hence, if the studied biomarker has been measured regularly for outpatients who complain of renal diseases, that can be assisted in the early detection of kidney diseases, including glomerulonephritis, and then it can be well managed.
Unusual pattern of microsatellite instability in gastric neuroendocrine tumor
Authors: Lack M , Abdo M E , Hamza A
Published: November 2023

Introduction/Objective

Evaluation of microsatellite instability (MSI) is routinely performed in gastrointestinal tract adenocarcinomas including gastric adenocarcinoma. It confers a good prognosis and is predictive of response to immunotherapy. However, the role of MSI in prognosis and treatment of well differentiated neuroendocrine tumors is controversial. Accordingly, MSI status is not extensively evaluated in neuroendocrine tumors. Limited available literature reports the usual paired losses and loss of MSH6 only in gastric well differentiated neuroendocrine tumor is unheard of. The purpose of this case is to report loss of MSH6 only in a patient with gastric well differentiated neuroendocrine tumor, grade 2.

Methods/Case Report

A 64-year-old female presented with abdominal pain and nausea. Endoscopy revealed erythematous nodules in the stomach which were removed by endoscopic mucosal resection. Microscopically, the tumor had vague nested appearance with areas more infiltrative appearance. However, cytologically tumor cells were bland and monotonous. Immunohistochemical stains showed the tumor cells to be positive for synaptophysin, chromogranin, pancytokeratin, and Cam 5.2, and negative for CK 7, CK 20 and CDX2. Ki-67 proliferation index was 3.7%. Therefore, diagnosis of well differentiated neuroendocrine tumor, grade 2 was rendered. Additionally, MSI by immunohistochemistry was ordered which showed intact nuclear expression of MSH2, MLH1 and PMS2 but loss of nuclear expression for MSH6.

Results (if a Case Study enter NA)

NA

Conclusion

This case highlights the fact that MSI in gastric neuroendocrine tumors can manifest as only MSH6 loss. Whether or not, it is of clinical and prognostic utility, is still up for debate.