bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of displacing the separation plate on the heat exchange effectiveness of unglazed double skin transpired solar collector
Authors: Talha Muhammad , Talha Tariq , Mazhar Abdur Rehman , Afzal Ahtasham , Moiz Muhammad
Published: June 2024

Achieving zero-carbon or low-carbon buildings is possible by implementing innovative approaches and incorporating renewable energy sources into the building infrastructure. Thermal energy collection has become critical amid challenges such as climate change, global warming, and environmental pollution. One such thermal energy collection system is Transpired Solar Collector (TSC). TSCs are a well-proven and readily available technology and are a green energy alternative for large space heating. The utilization of Computational Fluid Dynamics (CFD) analysis for the optimization of TSC is a robust and cost-effective approach. A recent variant of TSC, the Double Skin Transpired Solar Collector (DTSC), has been studied for optimisation. The numerical simulations targeted one single parameter: distance of separation plate from the main absorber plate.
Development and analysis of a smart cold storage system for fruit warehouses
Authors: Sher Ahsan , Khan Umais , Rafique Mouhammad Nouman , Ikram Muhammad Asjad , Mazhar Abdur Rehman
Published: June 2024

This research explores the innovative integration of traditional refrigeration systems with Object Detection via Artificial Intelligence. It leverages the use of an AI algorithm to optimize the temperature and enhance the overall efficiency of the system. This research presents a smart, eco-friendly cold storage system for fruits and vegetables to remain fresh for a longer period. Following the incorporation of Object Detection for intelligent temperature control for this system which will further improve the energy efficiency. The Object Detection component of the project uses computer vision to recognize objects within the cold storage and dynamically change the temperature to ensure optimal preservation based on the kind and number of contents. It will also provide information related to the state of the product (for example, if an apple is stale or fresh). The whole information will be accessible via the internet so we can access the data of the cold storage any time anywhere. The temperature and state of the fruits will also be displayed on the lcd. The practical application of this project is to be used in the agricultural and transport industry for long-term efficient storage of different objects in any compartment.
Durability Assessment of Recycled Aggregate Geopolymer Concrete Mixed with Wastewater
Authors: Aasim Muhammad Tayyab , Tariq Muhammad Shaheer , Danish Muhammad , Abbasi Iqra , Raza Ali , Haider Hammad
Published: June 2024

The advancement of an environmentally friendly setting is complex due to the significant carbon footprint of cement, substantial construction and demolition waste, and large quantities of industrial waste wastewater. This study aims to increase building sustainability by analyzing the long-term durability of recycled aggregate geopolymer concrete (RGC) manufactured using four different wastewaters. To evaluate each wastewater’s effect on sulfuric acid resistance and chloride ion migration (CIM) at various curing times, RGC was used in place of fresh water in the tests. The results revealed that, when it came to acid attack, RGC made with fertilizer industry wastewater had the highest mass loss (41% higher compared to control concrete) and CIM (29% higher compared to control concrete). According to statistical studies, using wastewater from textile, fertilizer, and sugar firms did not substantially alter mass loss from acid attack or CIM.
Tensile and Flexural Properties of Recycled HDPE for Application in Building Products
Authors: Ahmed Shehryar , Ali Majid
Published: June 2024

Plastic waste generation is a major environmental threat with farreaching consequences that needs to be dealt with. High density polyethylene (HDPE) is a common plastic waste coming out of daily household products. Recycling of HDPE plastic waste has been a viable alternate to disposal. To the best of author’s knowledge, no work has been reported on the material properties of recycled HDPE in perspective of building products. This study investigates the tensile and flexural properties of mechanically recycled HDPE for potential application in building products. The specimen’s behaviour under loading has also been reported. Based on the findings, 2.5% elongation at fracture was observed having 14.25 MPa strength against tension. Whereas, 32.6 MPa modulus of rupture was obtained with toughness index of 1.45 against flexure. In addition, potential application of recycled HDPE for manufacturing building products has been discussed keeping in line the material properties of recycled plastic. The adoption of recycled waste material instead of conventional materials can significantly influence the construction industry positively.
Hommage à Étienne Guyon
Authors: Hulin Jean-Pierre , Pieranski Pawel , Fermigier Marc , Bico José , Reyssat Étienne , Roman Benoît , Fadel Kamil , Bénard Christine , Leduc Michèle , Counillon Christian
Published: June 2024

Étienne Guyon nous a quittés en juillet dernier. Au cours de sa carrière, il a eu une diversité impressionnante d’activités liées aux sciences comme aux lettres, à la recherche comme à l’enseignement et à la diffusion scientifique.

Les articles du présent dossier abordent quelques facettes de cette diversité : chercheur à Orsay puis à l’ESPCI, auteur de 200 articles dans des revues internationales et de nombreux livres, directeur du Palais de la découverte puis de l’École normale supérieure, membre et président particulièrement actif de la Société Française de Physique.
On graph-based network parameters and component factors in networks
Authors: Jin Ting , Hu Tongtong , Dai Guowei , Su Kunqi , Xiao Shijun
Published: June 2024

Many physical structures can conveniently be simulated by networks. To study the properties of the network, we use a graph to simulate the network. A graph H is called an F-factor of a graph G, if H is a spanning subgraph of G and every connected component of H is isomorphic to a graph from the graph set F. An F-factor is also referred as a component factor. The graph-based network parameter degree sum of G is defined by

$ \sigma_k{(G)}=\underset{X\subseteq V(G)}\min\,{\{\underset{x\in X}{\mathrm\Sigma}\,d_G{(x)}:X\text{is an independent set of}k\text{vertices}\}.}$

In this article, we give the precise degree sum condition for a graph to have {P2, C3, P5, T (3)}-factor and {K1,1, K1,2, …, K1,k, T (2k + 1)}-factor. We also obtain similar results for {P2, C3, P5, T (3)}-factor avoidable graph and {K1,1, K1,2, …, K1,k, T (2k + 1)}-factor avoidable graph, respectively.
Kontinuierliche Nierenersatztherapie
Authors: Bethke Nicole , Khadzhynov Dmytro
Published: June 2024

Zusammenfassend stellt die kontinuierliche Nierenersatztherapie (CKRT: „continuous kidney replacement therapy“) eine sichere Option der Nierenersatztherapie (KRT) dar. Durch die lokale Wirksamkeit der zitratbasierten Antikoagulation wird eine systemische Antikoagulation vermieden und das Blutungsrisiko reduziert. Ebenso ermöglicht die Verwendung der regionalen Antikoagulation eine unkomplizierte Anpassung an spezifische klinische Gegebenheiten. Dennoch ist es wichtig, den Elektrolythaushalt während der CKRT sorgfältig zu überwachen, um potenzielle Überdosierungen und mögliche Komplikationen zu minimieren sowie die Effektivität des Verfahrens zu gewährleisten. In diesem Artikel geben wir einen Überblick über die am häufigsten auftretenden Komplikationen während der CKRT-Anwendung, wobei der Fokus auf der Optimierung und Fehlerbehebung von Antikoagulation und Elektrolytstörungen liegt – letztlich Faktoren, die die Sicherheit und Effektivität des Verfahrens maßgeblich definieren.
Remission of refractory esophageal lichen planus induced by tofacitinib
Authors: Bieneck Valentina , Decker Annegrit , Schmitt-Graeff Annette , Kreisel Wolfgang , Schauer Franziska
Published: June 2024

As of now, there exists no established therapy for ELP. Retinoids, which are standard in treating cutaneous LP, do not exhibit positive effects in ELP. While topical glucocorticosteroids often yield favorable responses in esophageal inflammation, some cases prove recalcitrant or refractory. In such instances, various immunosuppressive therapies have been attempted with variable success.

This report details a severe case of ELP that showed resistance to prednisolone, acitretin, alitretinoin, adalimumab, tacrolimus, hydroxychloroquine plus mycophenolate mofetil, and cyclophosphamide. The initiation of the JAK inhibitor tofacitinib induced an impressive clinical, endoscopic, and histological remission. This positive response to a JAK inhibitor is discussed in the context of our evolving understanding of the immune-mediated pathogenesis of this disease.
Integrative Genetic Variation, DNA Methylation, and Gene Expression
Analysis of Escitalopram and Aripiprazole Treatment Outcomes in Depression: A
CAN-BIND-1 Study
Authors: Islam Farhana , Lisoway Amanda , Oh Edward S. , Fiori Laura M. , Magarbeh Leen , Elsheikh Samar S. M. , Kim Helena K. , Kloiber Stefan , Kennedy James L. , Frey Benicio N. , Milev Roumen , Soares Claudio N. , Parikh Sagar V. , Placenza Franca , Hassel Stefanie , Taylor Valerie H. , Leri Francesco , Blier Pierre , Uher Rudolf , Farzan Faranak , Lam Raymond W. , Turecki Gustavo , Foster Jane A. , Rotzinger Susan , Kennedy Sidney H. , Müller Daniel J.
Published: June 2024

Introduction Little is known about the interplay between genetics and
epigenetics on antidepressant treatment (1) response and remission, (2) side
effects, and (3) serum levels. This study explored the relationship among single
nucleotide polymorphisms (SNPs), DNA methylation (DNAm), and mRNA levels of four
pharmacokinetic genes, CYP2C19, CYP2D6, CYP3A4, and
ABCB1, and its effect on these outcomes.

Methods The Canadian Biomarker Integration Network for Depression-1
dataset consisted of 177 individuals with major depressive disorder treated for
8 weeks with escitalopram (ESC) followed by 8 weeks with ESC monotherapy or
augmentation with aripiprazole. DNAm quantitative trait loci (mQTL), identified
by SNP-CpG associations between 20 SNPs and 60 CpG sites in whole blood, were
tested for associations with our outcomes, followed by causal inference tests
(CITs) to identify methylation-mediated genetic effects.

Results Eleven cis-SNP-CpG pairs (q<0.05) constituting four
unique SNPs were identified. Although no significant associations were observed
between mQTLs and response/remission, CYP2C19 rs4244285 was associated
with treatment-related weight gain (q=0.027) and serum concentrations of
ESCadj (q<0.001). Between weeks 2-4, 6.7% and 14.9% of
those with *1/*1 (normal metabolizers) and *1/*2 (intermediate metabolizers)
genotypes, respectively, reported ≥2 lbs of weight gain. In contrast, the *2/*2
genotype (poor metabolizers) did not report weight gain during this period and
demonstrated the highest ESCadj concentrations. CITs did not indicate
that these effects were epigenetically mediated.

Discussion These results elucidate functional mechanisms underlying the
established associations between CYP2C19 rs4244285 and ESC
pharmacokinetics. This mQTL SNP as a marker for antidepressant-related weight
gain needs to be further explored.
Achieving Digestive Autonomy and Gastrointestinal Continuity in a Patient with Short Bowel Syndrome Secondary to Concomitant Jejunal Atresia and Small Intestinal Hirschsprung's Disease
Authors: Velasquez Alejandro R. , Xu Thomas O. , Liu Yu-Ting , Kidwai Sulaiman , Russell Teresa L. , Tiusaba Laura , Artis Krystal , Sandler Anthony , Badillo Andrea , Levitt Marc A.
Published: June 2024

Concomitant presentation of jejunal atresia and Hirschsprung's disease is rare and places children at high risk for developing short bowel syndrome and parenteral nutrition dependence, which can affect the feasibility/timing of pull-through. A patient was born with jejunal atresia with a delayed diagnosis of Hirschsprung's disease. After several procedures and bowel resections, the patient was ultimately left with an end jejunostomy and long Hartman's pouch with short bowel syndrome, dependent on parenteral nutrition. The patient initially presented to our institution at age 2 with failure to thrive secondary to an obstructed/dilated jejunostomy and mild enterocolitis of their defunctionalized segment. The patient subsequently underwent completion of subtotal colectomy and revision of jejunostomy utilizing a serial transverse enteroplasty to manage the dilated bowel and gain length. The patient was able to wean off parenteral nutrition and achieve nutritional autonomy by age 5. Following this, the patient was able to undergo an ileoanal pull-through. After the pull-through, the patient was able to pass stool independently and suffered no major complications to date. Serial transverse enteroplasty can be successfully utilized in patients with a history of Hirschsprung's disease and jejunal atresia to achieve nutritional autonomy and ultimately reestablish gastrointestinal continuity with pull-through.
The Addition of α-Hydroxy-benzylphosphonates to Dialkyl Acetyl­enedicarboxylates; Catalytic Hydrogenation of the Adducts
Authors: Milen Mátyás , Keglevich György , Bese Cintia , Kovács Csenge , Dancsó András
Published: June 2024

α-Hydroxy-benzylphosphonates obtained by the Pudovik reaction of substituted benzaldehydes and dialkyl phosphites were added to the triple bond of dialkyl acetylenedicarboxylates. Optimum conditions involved a 24 hours stirring in the presence of 10% diazabicycloundecene in dichloromethane to afford the adducts as a mixture of predominant E- and a minor Z-isomers in 75–90% yields after flash chromatography. The structures of the geometrical isomers were confirmed by NOE- and ROE-measurements. Catalytic hydrogenation of the olefinic moiety of the adducts led to the diastereoisomers of corresponding saturated derivatives.
Systemic Therapy for Metastatic Colon Cancer: New Frontiers
Authors: Pumpalova Yoanna S.
Published: June 2024

We have made steady gains in improving overall survival in patients with metastatic, unresectable, colon cancer in the last 5 to 10 years. The backbone of systemic treatment for most patients remains combination chemotherapy, but the field is becoming increasingly biomarker driven, with exciting new targeted therapies on the horizon. This review is organized in sections corresponding to currently relevant biomarkers in colon cancer and will summarize first-, second-, and third-line standard of care for metastatic, unresectable, colon cancer. The last section is intended to introduce the reader to promising agents and novel therapeutic strategies currently under investigation.
A Perspective on the state-of-the-art functionalized 2D materials
Authors: Duran T. A. , Yayak Y. O. , Aydin H. , Peeters F. M. , Yagmurcukardes M.
Published: June 2024

Two-dimensional (2D) ultra-thin materials are more crucial than their bulk counterparts for the covalent functionalization of their surface owing to atomic thinness, large surface-to-volume ratio, and high reactivity of surface atoms having unoccupied orbitals. Since the surface of a 2D material is composed of atoms having unoccupied orbitals, covalent functionalization enables one to improve or precisely modify the properties of the ultra-thin materials. Chemical functionalization of 2D materials not only modifies their intrinsic properties but also makes them adapted for nanotechnology applications. Such engineered materials have been used in many different applications with their improved properties. In the present Perspective, we begin with a brief history of functionalization followed by the introduction of functionalized 2D materials. Our Perspective is composed of the following sections: the applications areas of 2D graphene and graphene oxide crystals, transition metal dichalcogenides, and in-plane anisotropic black phosphorus, all of which have been widely used in different nanotechnology applications. Finally, our Perspectives on the future directions of applications of functionalized 2D materials are given. The present Perspective sheds light on the current progress in nanotechnological applications of engineered 2D materials through surface functionalization.
Flexible automated system for laser modified layer by layer assembly
Authors: Leake Kaelyn , Eberbach Tristan , Stensland Alexander , Watts Lauren , Yochum Hank
Published: June 2024

An open-source automated system for laser modified layer by layer assembly is described. This flexible system, the first designed to be used with this process, can be used to fabricate a range of laser patterned, layer by layer thin films. The Arduino microcontroller-based system features a stepper motor-controlled turntable that holds solutions and water rinses for dipping. The substrate can be moved vertically to be dipped into each of the solutions throughout the process. A semiconductor laser is used to modify the thickness of the thin film during the chosen dipping cycles. Several aspects of the robotic system are easily controlled via software, including the average laser power, irradiation time, horizontal laser position, and vertical substrate position. The system is fully automated and, once started, does not require any user interaction. To demonstrate the capability of the automated system for patterning, electrochromic thin film devices using 50-bilayer laser patterned films using the polymers poly(allylamine hydrochloride) and sodium poly[2-(3-thienyl)-ethoxy-4-butylsulfonate] are presented. One device is patterned with the shape of a large “C,” created by irradiating the sample (55 mW average power, 405 nm) while the substrate was moved vertically up and down or the laser was moved horizontally. The laser irradiates the sample during only the dipping in the polycation polymer solution. A second electrochromic thin film device is based on a sample with five parallel laser patterned lines, where each line is fabricated with different average laser powers and, hence, different thicknesses. The thicknesses of the lines vary by about 30 nm.
Broadening access to small-molecule parameterization with the force field toolkit
Authors: Zeng Yunlin , Pavlova Anna , Nelson Philip M. , Glick Zachary L. , Yang Lan , Pang Yui Tik , Spivak Mariano , Licari Giuseppe , Tajkhorshid Emad , Sherrill C. David , Gumbart James C.
Published: June 2024

Access to accurate force-field parameters for small molecules is crucial for computational studies of their interactions with proteins. Although a number of general force fields for small molecules exist, e.g., CGenFF, GAFF, and OPLS, they do not cover all common chemical groups and their combinations. The Force Field Toolkit (ffTK) provides a comprehensive graphical interface that streamlines the development of classical parameters for small molecules directly from quantum mechanical (QM) calculations, allowing for force-field generation for almost any chemical group and validation of the fit relative to the target data. ffTK relies on supported external software for the QM calculations, but it can generate the necessary QM input files and parse and analyze the QM output. In previous ffTK versions, support for Gaussian and ORCA QM packages was implemented. Here, we add support for Psi4, an open-source QM package free for all users, thereby broadening user access to ffTK. We also compare the parameter sets obtained with the new ffTK version using Gaussian, ORCA, and Psi4 for three molecules: pyrrolidine, n-propylammonium cation, and chlorobenzene. Despite minor differences between the resulting parameter sets for each compound, most prominently in the dihedral and improper terms, we show that conformational distributions sampled in molecular dynamics simulations using these parameter sets are quite comparable.
Studies on the compositional dependent structural and electrical properties of CaTiO3-modified K0.5Na0.5NbO3 piezoelectric system
Authors: Sahoo Satyaranjan , Pradhan Dhiren K. , Kumari Shalini , Sahu Abhisikta , Samantaray Koyal Suman , Singh Charanjeet , Mishra Anupam , Rahaman Md. Mijanur , Kumar Ashok , Thomas Reji , Rack Philip D. , Pradhan Dillip K.
Published: June 2024

Lead-free piezoelectric ceramics of (1 − x)K0.5Na0.5NbO3-xCaTiO3 were fabricated, and their crystal structure, microstructure, and electrical properties were systematically studied. Rietveld refinement of the x-ray diffraction data and Raman spectroscopic analyses revealed a composition-dependent structural phase transition: three phase transitions, namely, from a pure orthorhombic phase for x ≤ 0.02 to a mixed phase of orthorhombic and tetragonal phases (0.03 ≤ x ≤ 0.08) and finally another mixed phase of tetragonal + cubic for x = 0.10 and 0.15 at room temperature (RT). The morphological study reveals a decrease in grain size along with a more uniform distribution of grains as the concentration of CaTiO3 (CT) increases; notably, a homogeneous distribution of grains is observed for x = 0.05. The temperature-dependent dielectric properties show two phase transitions, from orthorhombic to tetragonal (TO-T) and tetragonal to cubic (TC), for unmodified K0.5Na0.5NbO3 (KNN). However, both the phase transition temperatures (TO-T and TC) decrease, and the transition peaks broaden with an increase in CT substitution, and for x > 0.06, the TO-T shifted below RT. The broadening of the transition peak at TO-T may be due to the relaxation behavior. Among the prepared samples, the 5 mol. % CT-modified KNN shows the optimum electrical properties (d33 = 114 pC/N, ɛr = 412, and 2Pr = 15.25 μC/cm2) at RT. The enhanced electrical properties for x = 0.05 are due to the coexistence of orthorhombic and tetragonal phases, facilitating easy polarization rotation and flattening of the free energy profile. A phase diagram has been constructed based on the information gathered from the temperature-dependent dielectric measurements, RT x-ray diffraction, and Raman spectroscopy data and is discussed in detail.
Adsorption of monoclonal antibody fragments at the water–oil interface: A coarse-grained molecular dynamics study
Authors: Saurabh Suman , Lei Li , Li Zongyi , Seddon John M. , Lu Jian R. , Kalonia Cavan , Bresme Fernando
Published: June 2024

Monoclonal antibodies (mAbs) can undergo structural changes due to interaction with oil–water interfaces during storage. Such changes can lead to aggregation, resulting in a loss of therapeutic efficacy. Therefore, understanding the microscopic mechanism controlling mAb adsorption is crucial to developing strategies that can minimize the impact of interfaces on the therapeutic properties of mAbs. In this study, we used MARTINI coarse-grained molecular dynamics simulations to investigate the adsorption of the Fab and Fc domains of the monoclonal antibody COE3 at the oil–water interface. Our aim was to determine the regions on the protein surface that drive mAb adsorption. We also investigate the role of protein concentration on protein orientation and protrusion to the oil phase. While our structural analyses compare favorably with recent neutron reflectivity measurements, we observe some differences. Unlike the monolayer at the interface predicted by neutron reflectivity experiments, our simulations indicate the presence of a secondary diffused layer near the interface. We also find that under certain conditions, protein–oil interaction can lead to a considerable distortion in the protein structure, resulting in enhanced adsorption behavior.
Modeling and experiment of femtosecond laser processing of micro-holes arrays in quartz
Authors: Shangguan Duansen , Liu Yuhui , Chen Liping , Su Chang , Liu Jing
Published: June 2024

Quartz material irradiated by femtosecond laser has increasingly attracted widespread attention for the micro-fabrication of photonic devices. Mechanism exploration is beneficial for accelerating the digital progress of laser processing. However, the mechanism between femtosecond laser and quartz is complicated and needs further theoretical investigation. This paper established the theoretical model based on the ionization model with the Drude equation to study the space–time evolution of free electron density and its influence on the absorption coefficient, reflectivity, and ablation depth. In addition, we achieved a 10 × 10 micro-holes array with a pore size less than 10 μm, cone angle less than 2° in a 0.25 mm thick quartz on the condition of a laser pulse energy Ep = 3 μJ, scanning velocity v = 0.1 mm/s, and defocusing distance Δf = −0.3 mm via the bottom-up femtosecond laser processing. The work gives a new insight into further understanding the ablation mechanism of transparent materials etching by the femtosecond laser. It provides a practical technical scheme for preparing commercial quartz photonic devices.
Distributed Nash equilibrium seeking in noncooperative game with partial decision information of neighbors
Authors: Jin Xin , Lu Kaihong , Wang Zhengxin , Chen Xiaojie
Published: June 2024

In the real world, individuals may conceal some of their real decision information to their neighbors due to competition. It is a challenge to explore the distributed Nash equilibrium when individuals play the noncooperative game with partial decision information in complex networks. In this paper, we investigate the distributed Nash equilibrium seeking problem with partial decision information of neighbors. Specifically, we construct a two-layer network model, where players in the first layer engage in game interactions and players in the second layer exchange estimations of real actions with each other. We also consider the case where the actions of some players remain unchanged due to the cost of updating or personal reluctance. By means of the Lyapunov function method and LaSalle’s invariance principle, we obtain the sufficient conditions in which the consensus of individual actions and estimations can be achieved and the population actions can converge to the Nash equilibrium point. Furthermore, we investigate the case with switched topologies and derive the sufficient conditions for the convergence of individual actions to Nash equilibrium by the average dwell time method. Finally, we give numerical examples for cases of fixed and switched topologies to verify our theoretical results.
Unveiling a common phase transition pathway of high-density amorphous ices through time-resolved x-ray scattering
Authors: Yang Cheolhee , Ladd-Parada Marjorie , Nam Kyeongmin , Jeong Sangmin , You Seonju , Eklund Tobias , Späh Alexander , Pathak Harshad , Lee Jae Hyuk , Eom Intae , Kim Minseok , Perakis Fivos , Nilsson Anders , Kim Kyung Hwan , Amann-Winkel Katrin
Published: June 2024

Here, we investigate the hypothesis that despite the existence of at least two high-density amorphous ices, only one high-density liquid state exists in water. We prepared a very-high-density amorphous ice (VHDA) sample and rapidly increased its temperature to around 205 ± 10 K using laser-induced isochoric heating. This temperature falls within the so-called “no-man’s land” well above the glass-liquid transition, wherein the IR laser pulse creates a metastable liquid state. Subsequently, this high-density liquid (HDL) state of water decompresses over time, and we examined the time-dependent structural changes using short x-ray pulses from a free electron laser. We observed a liquid–liquid transition to low-density liquid water (LDL) over time scales ranging from 20 ns to 3 μs, consistent with previous experimental results using expanded high-density amorphous ice (eHDA) as the initial state. In addition, the resulting LDL derived both from VHDA and eHDA displays similar density and degree of inhomogeneity. Our observation supports the idea that regardless of the initial annealing states of the high-density amorphous ices, the same HDL and final LDL states are reached at temperatures around 205 K.
A non-hierarchical multi-layer multi-configurational time-dependent Hartree approach for quantum dynamics on general potential energy surfaces
Authors: Ellerbrock Roman , Hoppe Hannes , Manthe Uwe
Published: June 2024

The correlation discrete variable representation (CDVR) enables multi-layer multi-configurational time-dependent Hartree (MCTDH) quantum dynamics simulations on general potential energy surfaces. In a recent study [R. Ellerbrock and U. Manthe, J. Chem. Phys. 156, 134107 (2022)], an improved CDVR that can account for the symmetry properties of a tree-shaped wavefunction representation has been introduced. This non-hierarchical CDVR drastically reduces the number of grid points required in the time-dependent quadrature used to evaluate all potential energy matrix elements. While the first studies on the non-hierarchical CDVR approach have been restricted to single-layer calculations, here the complete theory required for the implementation of the non-hierarchical CDVR approach in the multi-layer MCTDH context will be presented. Detailed equations facilitating the efficient recursive computation of all matrix elements are derived, and a new notation adapted to the symmetry properties of the tree-shaped representation is introduced. Calculations studying the non-adiabatic quantum dynamics of photoexcited pyrazine in 24 dimensions illustrate the properties of the non-hierarchical multi-layer CDVR.
An all-atom protein generative model
Authors: Chu Alexander E. , Kim Jinho , Cheng Lucy , El Nesr Gina , Xu Minkai , Shuai Richard W. , Huang Po-Ssu
Published: June 2024

Proteins mediate their functions through chemical interactions; modeling these interactions, which are typically through sidechains, is an important need in protein design. However, constructing an all-atom generative model requires an appropriate scheme for managing the jointly continuous and discrete nature of proteins encoded in the structure and sequence. We describe an all-atom diffusion model of protein structure, Protpardelle, which represents all sidechain states at once as a “superposition” state; superpositions defining a protein are collapsed into individual residue types and conformations during sample generation. When combined with sequence design methods, our model is able to codesign all-atom protein structure and sequence. Generated proteins are of good quality under the typical quality, diversity, and novelty metrics, and sidechains reproduce the chemical features and behavior of natural proteins. Finally, we explore the potential of our model to conduct all-atom protein design and scaffold functional motifs in a backbone- and rotamer-free way.
Eliminating malaria vectors with precision-guided sterile males
Authors: Apte Reema A. , Smidler Andrea L. , Pai James J. , Chow Martha L. , Chen Sanle , Mondal Agastya , Sánchez C. Héctor M. , Antoshechkin Igor , Marshall John M. , Akbari Omar S.
Published: June 2024

Controlling the principal African malaria vector, the mosquito
Anopheles gambiae
, is considered essential to curtail malaria transmission. However, existing vector control technologies rely on insecticides, which are becoming increasingly ineffective. Sterile insect technique (SIT) is a powerful suppression approach that has successfully eradicated a number of insect pests, yet the
A. gambiae
toolkit lacks the requisite technologies for its implementation. SIT relies on iterative mass releases of nonbiting, nondriving, sterile males which seek out and mate with monandrous wild females. Once mated, females are permanently sterilized due to mating-induced refractoriness, which results in population suppression of the subsequent generation. However, sterilization by traditional methods renders males unfit, making the creation of precise genetic sterilization methods imperative. Here, we introduce a vector control technology termed precision-guided sterile insect technique (pgSIT), in
A. gambiae
for inducible, programmed male sterilization and female elimination for wide-scale use in SIT campaigns. Using a binary CRISPR strategy, we cross separate engineered Cas9 and gRNA strains to disrupt male-fertility and female-essential genes, yielding >99.5% male sterility and >99.9% female lethality in hybrid progeny. We demonstrate that these genetically sterilized males have good longevity, are able to induce sustained population suppression in cage trials, and are predicted to eliminate wild
A. gambiae
populations using mathematical models, making them ideal candidates for release. This work provides a valuable addition to the malaria genetic biocontrol toolkit, enabling scalable SIT-like confinable, species-specific, and safe suppression in the species.
A metabolic inhibitor blocks cellular fucosylation and enables production of afucosylated antibodies
Authors: Gilormini Pierre-André , Thota V. Narasimharao , Fers-Lidou Anthony , Ashmus Roger A. , Nodwell Matthew , Brockerman Jacob , Kuo Chu-Wei , Wang Yang , Gray Taylor E. , Nitin  , McDonagh Anthony W. , Guu Shih-Yun , Ertunc Nursah , Yeo Dominick , Zandberg Wesley F. , Khoo Kay-Hooi , Britton Robert , Vocadlo David J.
Published: June 2024

The fucosylation of glycoproteins regulates diverse physiological processes. Inhibitors that can control cellular levels of protein fucosylation have consequently emerged as being of high interest. One area where inhibitors of fucosylation have gained significant attention is in the production of afucosylated antibodies, which exhibit superior antibody-dependent cell cytotoxicity as compared to their fucosylated counterparts. Here, we describe β-carbafucose, a fucose derivative in which the endocyclic ring oxygen is replaced by a methylene group, and show that it acts as a potent metabolic inhibitor within cells to antagonize protein fucosylation. β-carbafucose is assimilated by the fucose salvage pathway to form GDP-carbafucose which, due to its being unable to form the oxocarbenium ion-like transition states used by fucosyltransferases, is an incompetent substrate for these enzymes. β-carbafucose treatment of a CHO cell line used for high-level production of the therapeutic antibody Herceptin leads to dose-dependent reductions in core fucosylation without affecting cell growth or antibody production. Mass spectrometry analyses of the intact antibody and
N
-glycans show that β-carbafucose is not incorporated into the antibody
N
-glycans at detectable levels. We expect that β-carbafucose will serve as a useful research tool for the community and may find immediate application for the rapid production of afucosylated antibodies for therapeutic purposes.
Pathogenic variants in autism gene
KATNAL2
cause hydrocephalus and disrupt neuronal connectivity by impairing ciliary microtubule dynamics
Authors: DeSpenza Tyrone , Singh Amrita , Allington Garrett , Zhao Shujuan , Lee Junghoon , Kiziltug Emre , Prina Mackenzi L. , Desmet Nicole , Dang Huy Q. , Fields Jennifer , Nelson-Williams Carol , Zhang Junhui , Mekbib Kedous Y. , Dennis Evan , Mehta Neel H. , Duy Phan Q. , Shimelis Hermela , Walsh Lauren K. , Marlier Arnaud , Deniz Engin , Lake Evelyn M. R. , Constable R. Todd , Hoffman Ellen J. , Lifton Richard P. , Gulledge Allan , Fiering Steven , Moreno-De-Luca Andres , Haider Shozeb , Alper Seth L. , Jin Sheng Chih , Kahle Kristopher T. , Luikart Bryan W.
Published: June 2024

Enlargement of the cerebrospinal fluid (CSF)–filled brain ventricles (cerebral ventriculomegaly), the cardinal feature of congenital hydrocephalus (CH), is increasingly recognized among patients with autism spectrum disorders (ASD).
KATNAL2,
a member of Katanin family microtubule-severing ATPases, is a known ASD risk gene, but its roles in human brain development remain unclear. Here, we show that nonsense truncation of
Katnal2
(
Katnal2Δ
17
) in mice results in classic ciliopathy phenotypes, including impaired spermatogenesis and cerebral ventriculomegaly. In both humans and mice,
KATNAL2
is highly expressed in ciliated radial glia of the fetal ventricular–subventricular zone as well as in their postnatal ependymal and neuronal progeny. The ventriculomegaly observed in
Katnal2
Δ17
mice is associated with disrupted primary cilia and ependymal planar cell polarity that results in impaired cilia-generated CSF flow. Further, prefrontal pyramidal neurons in ventriculomegalic
Katnal2
Δ
17
mice exhibit decreased excitatory drive and reduced high-frequency firing. Consistent with these findings in mice, we identified rare, damaging heterozygous germline variants in
KATNAL2
in five unrelated patients with neurosurgically treated CH and comorbid ASD or other neurodevelopmental disorders. Mice engineered with the orthologous ASD-associated KATNAL2 F244L missense variant recapitulated the ventriculomegaly found in human patients. Together, these data suggest
KATNAL2
pathogenic variants alter intraventricular CSF homeostasis and parenchymal neuronal connectivity by disrupting microtubule dynamics in fetal radial glia and their postnatal ependymal and neuronal descendants. The results identify a molecular mechanism underlying the development of ventriculomegaly in a genetic subset of patients with ASD and may explain persistence of neurodevelopmental phenotypes in some patients with CH despite neurosurgical CSF shunting.
On the role of seamounts in upwelling deep-ocean waters through turbulent mixing
Authors: Mashayek Ali , Gula Jonathan , Baker Lois E. , Naveira Garabato Alberto C. , Cimoli Laura , Riley James J. , de Lavergne Casimir
Published: June 2024

Turbulent mixing in the ocean exerts an important control on the rate and structure of the overturning circulation. However, the balance of processes underpinning this mixing is subject to significant uncertainties, limiting our understanding of the overturning’s deep upwelling limb. Here, we investigate the hitherto primarily neglected role of tens of thousands of seamounts in sustaining deep-ocean upwelling. Dynamical theory indicates that seamounts may stir and mix deep waters by generating lee waves and topographic wake vortices. At low latitudes, stirring and mixing are predicted to be enhanced by a layered vortex regime in the wakes. Using three realistic regional simulations spanning equatorial to middle latitudes, we show that layered wake vortices and elevated mixing are widespread around seamounts. We identify scalings that relate mixing rate within seamount wakes to topographic and hydrographic parameters. We then apply such scalings to a global seamount dataset and an ocean climatology to show that seamount-generated mixing makes an important contribution to the upwelling of deep waters. Our work thus brings seamounts to the fore of the deep-ocean mixing problem and urges observational, theoretical, and modeling efforts toward incorporating the seamounts’ mixing effects in conceptual and numerical ocean circulation models.
Parvalbumin gates chronic pain through the modulation of firing patterns in inhibitory neurons
Authors: Qiu Haoyi , Miraucourt Loïs S. , Petitjean Hugues , Xu Mengyi , Theriault Catherine , Davidova Albena , Soubeyre Vanessa , Poulen Gaetan , Lonjon Nicolas , Vachiery-Lahaye Florence , Bauchet Luc , Levesque-Damphousse Philipa , Estall Jennifer L. , Bourinet Emmanuel , Sharif-Naeini Reza
Published: June 2024

Spinal cord dorsal horn inhibition is critical to the processing of sensory inputs, and its impairment leads to mechanical allodynia. How this decreased inhibition occurs and whether its restoration alleviates allodynic pain are poorly understood. Here, we show that a critical step in the loss of inhibitory tone is the change in the firing pattern of inhibitory parvalbumin (PV)-expressing neurons (PVNs). Our results show that PV, a calcium-binding protein, controls the firing activity of PVNs by enabling them to sustain high-frequency tonic firing patterns. Upon nerve injury, PVNs transition to adaptive firing and decrease their PV expression. Interestingly, decreased PV is necessary and sufficient for the development of mechanical allodynia and the transition of PVNs to adaptive firing. This transition of the firing pattern is due to the recruitment of calcium-activated potassium (SK) channels, and blocking them during chronic pain restores normal tonic firing and alleviates chronic pain. Our findings indicate that PV is essential for controlling the firing pattern of PVNs and for preventing allodynia. Developing approaches to manipulate these mechanisms may lead to different strategies for chronic pain relief.
High sugar diet–induced fatty acid oxidation potentiates cytokine-dependent cardiac ECM remodeling
Authors: Gera Jayati , Kumar Dheeraj , Chauhan Gunjan , Choudhary Adarsh , Rani Lavi , Mandal Lolitika , Mandal Sudip
Published: June 2024

Context-dependent physiological remodeling of the extracellular matrix (ECM) is essential for development and organ homeostasis. On the other hand, consumption of high-caloric diet leverages ECM remodeling to create pathological conditions that impede the functionality of different organs, including the heart. However, the mechanistic basis of high caloric diet–induced ECM remodeling has yet to be elucidated. Employing in vivo molecular genetic analyses in Drosophila, we demonstrate that high dietary sugar triggers ROS-independent activation of JNK signaling to promote fatty acid oxidation (FAO) in the pericardial cells (nephrocytes). An elevated level of FAO, in turn, induces histone acetylation–dependent transcriptional upregulation of the cytokine Unpaired 3 (Upd3). Release of pericardial Upd3 augments fat body-specific expression of the cardiac ECM protein Pericardin, leading to progressive cardiac fibrosis. Importantly, this pathway is quite distinct from the ROS-Ask1-JNK/p38 axis that regulates Upd3 expression under normal physiological conditions. Our results unravel an unknown physiological role of FAO in cytokine-dependent ECM remodeling, bearing implications in diabetic fibrosis.
Kodama-like vector fields in axisymmetric spacetimes
Authors: Dorau Philipp , Verch Rainer
Published: June 2024

We extend the concept of the Kodama symmetry, a quasi-local time translation symmetry for dynamical spherically symmetric spacetimes, to a specific class of dynamical axisymmetric spacetimes, namely the families of Kerr–Vaidya and Kerr–Vaidya–de Sitter spacetimes. We study some geometrical properties of the asymptotically flat Kerr–Vaidya metric, such as the Brown–York mass and the Einstein tensor. Furthermore, we propose a generalization of the Kerr–Vaidya metric to an asymptotic de Sitter background. We show that for these classes of dynamical axisymmetric black hole spacetimes, there exists a timelike vector field that exhibits similar properties to the Kodama vector field in spherical symmetry. This includes the construction of a covariantly conserved current and a corresponding locally conserved charge, which in the Kerr–Vaidya case converges to the Brown–York mass in the asymptotically flat region.
Uniqueness and numerical method for phaseless inverse diffraction grating problem with known superposition of incident point sources
Authors: Niu Tian , Lv Junliang , Gao Jiahui
Published: June 2024

In this paper, we establish the uniqueness of identifying a smooth grating profile with a mixed boundary condition (MBC) or transmission boundary conditions (TBCs) from phaseless data. The existing uniqueness result requires the measured data to be in a bounded domain. To break this restriction, we design an incident system consisting of the superposition of point sources to reduce the measurement data from a bounded domain to a line above the grating profile. We derive reciprocity relations for point sources, diffracted fields, and total fields, respectively. Based on Rayleigh’s expansion and reciprocity relation of the total field, a grating profile with a MBC or TBCs can be uniquely determined from the phaseless total field data. An iterative algorithm is proposed to recover the Fourier modes of grating profiles at a fixed wavenumber. To implement this algorithm, we derive the Fréchet derivative of the total field operator and its adjoint operator. Some numerical examples are presented to verify the correctness of theoretical results and to show the effectiveness of our numerical algorithm.
Neutron-absorption gratings fabricated by ultrasound-assisted filling method based on gadolinium particles
Authors: Lei Yaohu , Li Xiqi , Wei Chi , Li Zhuozhao , Xu Guiwen , Liu Xin , Huang Jianheng , Wang Shengxiang , Li Ji
Published: June 2024

Neutron differential phase-contrast imaging (DPCI) plays a pivotal role in analyzing magnetic domain structures and field gradients in materials, necessitating high-quality neutron absorption gratings for enhanced fringe contrast. Traditional fabrication techniques, typically filling gadolinium (Gd) or Gd-containing materials into the corresponding grating structures, face challenges in achieving optimal Gd filling ratios and thickness, limiting the neutron DPCI system’s performance. This paper introduces an approach utilizing ultrasound-assisted filling method to introduce Gd particles into grating trenches with dense deposition, achieving an absorption grating period of 42 μm. This method achieves an equivalent Gd thickness of 80.3 μm, corresponding to the filling ratio of 53.53%, as confirmed by scanning electron microscopy and x-ray micro-imaging. The utilization of an ultrasound not only improves the Gd filling ratio, but also suggests potential scalability for large-area grating production, marking a significant advancement in neutron DPCI technology by providing high-quality components.
Manufacturing fused silica hemispherical resonators using polymer glass suspension and replication molding
Authors: Atwa Yahya , Shakeel Hamza
Published: June 2024

This work introduces a new method for manufacturing fused silica (FS)-based hemispherical resonators (HSRs) using a printable polymer glass mixture and replication molding. This process involves 3D printing to create the mold, followed by the casting of a photo-reactive pre-polymer glass mixture. This technique allows us to produce complex 3D geometries and offers faster production of resonators compared to other traditional methods. In this study, we manufactured three devices and successfully identified resonance modes with two (N = 2), three (N = 3) and four (N = 4) nodes/antinodes in all three HSRs, demonstrating the repeatability of our new manufacturing method. The highest quality factor of 482 k was achieved for the N = 3 resonance mode using the ring-down method. Some of the key advantages of our method include producing multiple devices efficiently with relatively good surface quality, making it a viable option for producing high-precision devices in the future. Our new fabrication technique results in a device surface roughness of ∼100 nm (measured over an area of 250 μm × 250 μm) and manufacturing yield of over 90%. Moreover, all the steps involved in this method can be completed outside of a specialized cleanroom environment.
Advanced defect spectroscopy in wide-bandgap semiconductors: review and recent results
Authors: Fregolent Manuel , Piva Francesco , Buffolo Matteo , Santi Carlo De , Cester Andrea , Higashiwaki Masataka , Meneghesso Gaudenzio , Zanoni Enrico , Meneghini Matteo
Published: June 2024

The study of deep-level defects in semiconductors has always played a strategic role in the development of electronic and optoelectronic devices. Deep levels have a strong impact on many of the device properties, including efficiency, stability, and reliability, because they can drive several physical processes. Despite the advancements in crystal growth, wide- and ultrawide-bandgap semiconductors (such as gallium nitride and gallium oxide) are still strongly affected by the formation of defects that, in general, can act as carrier traps or generation-recombination centers (G-R). Conventional techniques used for deep-level analysis in silicon need to be adapted for identifying and characterizing defects in wide-bandgap materials. This topical review paper presents an overview of reviews of the theory of deep levels in semiconductors; in addition, we present a review and original results on the application, limits, and perspectives of two widely adopted common deep-level detection techniques, namely capacitance deep-level transient spectroscopy and deep-level optical spectroscopy, with specific focus on wide-bandgap semiconductors. Finally, the most common traps of GaN and β-Ga2O3 are reviewed.