bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast reconstruction of programmable interferometers with intensity-only measurements
Authors: Bantysh B I , Chernyavskiy A Yu , Fldzhyan S A , Bogdanov Yu I 
Published: December 2023

Abstract
Programmable linear optical interferometers are promising for classical and quantum applications. Their integrated design makes it possible to create more scalable and stable devices. To use them in practice, one has to reconstruct the whole device model taking the manufacturing errors into account. The inability to address individual interferometer elements complicates the reconstruction problem. A naive approach is to train the model via some complex optimization procedure. A faster optimization-free algorithm has been recently proposed (Bantysh et al 2023 Opt. Express
31 16729–42). However, it requires the full transfer matrix tomography while a more practical setup measures only the fields intensities at the interferometer output. In this paper, we propose the modification of the fast algorithm, which uses additional set of interferometer configurations in order to reconstruct the model in the case of intensity-only measurements. We show that it performs slightly worse than the original fast algorithm but it is more practical and still does not require intensive numerical optimization.
Measurement of yields and angular distributions of γ-quanta from the interaction of 14.1 MeV neutrons with oxygen, phosphorus, and sulfur*
Authors: Grozdanov D. N. , Fedorov N. A. , Dabylova S. B. , Kopatch Yu. N. , Ruskov I. N. , Skoy V. R. , Tretyakova T. Yu. , Hramco C. , Kharlamov P. I. , Pampushik G. V. , Filonchik P. G. , Andreev A. V. 
Published: December 2023

Abstract
A study of the inelastic scattering of neutrons with an energy of

MeV on the nuclei of oxygen, phosphorus, and sulfur was performed at the TANGRA facility at JINR (Dubna). The experiment aimed to refine existing data and obtain new data on the yields and angular distributions of γ-quanta emitted by the studied nuclei due to neutron-induced nuclear reactions using the tagged neutron method. Two types of detector systems were used to register γ-quanta. The γ-ray yields were measured using a high-purity germanium (HPGe) detector. The angular distributions of γ-rays were obtained using a system of 18 scintillation detectors based on bismuth germanite Bi

Ge

O

(BGO) located around the sample. The performed experiments measured the yields of two transitions for the reaction of tagged neutrons with

O, nine transitions for the reaction with

P, and nine transitions for the reaction with

S for the first time. The angular anisotropy of the γ-radiation accompanying the inelastic scattering of neutrons with an energy of

MeV on

P nuclei was also measured for the first time.
The treatment of wastewater from pangasius catfish ponds using peat-derived adsorbent materials
Authors: Thang Ho Sy , Thao Nguyen Minh , Nguyen Vo Thang , Man Nguyen Quang , Khieu Dinh Quang 
Published: December 2023

Abstract
Peat (Mekong River Delta, Vietnam) was naturally dried, and then mixed with coal slag in the ratio of 70:30 by weight to use as adsorbent to treat wastewater from Pangasius catfish ponds in batches. The adsorbent was used in a specific designed system to treat Pangasius pond wastewater in a continuous flow model at a speed of 0.3 m3.h−1. The treatment system has operated for 9 consecutive hours in each experiment batch. The results show that the system can treat a large amount of wastewater (64.8 m3) with the efficiency (%) of BOD5 of 95.78%, COD of 95.3%, total phosphorous of 73% and total nitrogen of 89.79%. After treatment, the quality of wastewater has met the standards to be discharged into the environment.
Untangling free carrier and exciton dynamics in layered hybrid perovskites using ultrafast optical and terahertz spectroscopy
Authors: Balogun Folusho Helen , Gallop Nathaniel P , Sirbu Dumitru , Hutchinson Jake D , Hill Nathan , Woolley Jack M , Walker David , York Stephen , Docampo Pablo , Milot Rebecca L 
Published: December 2023

Abstract
Layered hybrid perovskites (LPKs) are promising as alternatives or additives to 3D metal halide perovskites for optoelectronic applications including photovoltaic cells, LEDs and lasers due to their increased stability. However, high exciton binding energies in these materials mean that excitons are the majority species under the operating conditions of many devices. Although the efficiency of devices that incorporate LPKs has been increasing, much is still unknown about the interplay of excitons and free charge-carriers in these materials, which is vital information for understanding how optoelectronic properties dictate device efficiency. In this work, we employ optical pump/THz probe spectroscopy (OPTP) and visible transient absorption spectroscopy (TAS) to analyse the optoelectronic properties and charge-carrier dynamics of phenylethylammonium lead iodide (PEA)2PbI4. By combining these techniques, we are able to disentangle the contributions from excitons and free charge-carriers. We observe fast cooling of free charge-carriers and exciton formation on a timescale of ∼400 fs followed by slower bimolecular recombination of residual free charge-carriers with a rate constant k
2 ∼ 109 cm3s−1. Excitons recombine via two monomolecular processes with lifetimes t
1 ∼ 11 ps and t2 ∼ 83 ps. Furthermore, we detect signatures of exciton–phonon coupling in the transient absorption kinetic traces. These findings provide new insight into the interplay between free charge-carriers and excitons as well as a possible mechanism to further understand the charge-carrier dynamics in LPKs.
Electrochemical sensor based on PVP coated cobalt ferrite/graphite/PANI nanocomposite for the detection of hydrazine
Authors: Desai Nakul , Sudhakar Y N , Patil Rutuja Rajendra , Chandran Achania , M Nidhin , Agnihotri Ananya S 
Published: December 2023

Abstract
In this study, we developed a multi-layered electrode as an efficient nanocomposite electrochemical sensor for detecting carcinogenic hydrazine in water. Nano-cobalt ferrite (CoFe2O4) was prepared using poly (vinylpyrrolidone) (PVP), mixed with an optimum quantity of graphite and pasted on a stainless-steel current collector. The nanocomposite was further hybridised by electrodepositing with polyaniline (PANI). The obtained composite was characterized using XRD, FTIR, SEM, and electrochemical techniques. XRD analysis shows the successful formation of composite from individual precursors. According to SEM, wrinkled and layered morphology for graphite and aggregate clusters for cobalt with spike or tubular structure for polyaniline were observed. When subjected to amperometry current, the prepared electrode showed different peaks for different concentrations of hydrazine, such as 1 μM to 100 μM. Cyclic voltammetry studies showed an increase in oxidation and reduction peaks. These studies will lead to a new platform for their potential applications in detecting toxic materials in real samples such as water, plastic bottle, water etc.,
ACE2-Fc and DPP4-Fc decoy receptors against SARS-CoV-2 and MERS-CoV variants: a quick therapeutic option for current and future coronaviruses outbreaks
Authors: Alfaleh Mohamed A , Alsulaiman Reem M , Almahboub Sarah A , Nezamuldeen Leena , Zawawi Ayat , Aljehani Najwa D , Yasir Muhammad , Abdulal Rwaa H , Alkhaldi Rami , Helal Assala , Alamri Sawsan S , Malki Jana , Alhabbab Rowa Y , Abujamel Turki S , Alhakamy Nabil A , Alnami Aisha , Algaissi Abdullah , Hassanain Mazen , Hashem Anwar M 
Published: December 2023

Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and the Middle East respiratory syndrome coronavirus (MERS-CoV) are highly pathogenic human coronaviruses (CoVs). Anti-CoVs mAbs and vaccines may be effective, but the emergence of neutralization escape variants is inevitable. Angiotensin-converting enzyme 2 and dipeptidyl peptidase 4 enzyme are the getaway receptors for SARS-CoV-2 and MERS-CoV, respectively. Thus, we reformatted these receptors as Fc-fusion decoy receptors. Then, we tested them in parallel with anti-SARS-CoV (ab1-IgG) and anti-MERS-CoV (M336-IgG) mAbs against several variants using pseudovirus neutralization assay. The generated Fc-based decoy receptors exhibited a strong inhibitory effect against all pseudotyped CoVs. Results showed that although mAbs can be effective antiviral drugs, they might rapidly lose their efficacy against highly mutated viruses. We suggest that receptor traps can be engineered as Fc-fusion proteins for highly mutating viruses with known entry receptors, for a faster and effective therapeutic response even against virus harboring antibodies escape mutations.
Understanding change in benthic marine systems
Authors: Johnson Craig R , Dudgeon Steve 
Published: December 2023

Abstract

Background
The unprecedented influence of human activities on natural ecosystems in the 21st century has resulted in increasingly frequent large-scale changes in ecological communities. This has heightened interest in understanding such changes and effective means to manage them. Accurate interpretation of state changes is challenging because of difficulties translating theory to empirical study, and most theory emphasizes systems near equilibrium, which may not be relevant in rapidly changing environments.

Scope
We review concepts of long-transient stages and phase shifts between stable community states, both smooth, continuous and discontinuous shifts, and the relationships among them. Three principal challenges emerge when applying these concepts. The first is how to interpret observed change in communities – distinguishing multiple stable states from long transients, or reversible shifts in the phase portrait of single attractor systems. The second is how to quantify the magnitudes of three sources of variability that cause switches between community states: (1) ‘noise’ in species’ abundances, (2) ‘wiggle’ in system parameters and (3) trends in parameters that affect the topography of the basin of attraction. The third challenge is how variability of the system shapes evidence used to interpret community changes. We outline a novel approach using critical length scales to potentially address these challenges. These concepts are highlighted by a review of recent examples involving macroalgae as key players in marine benthic ecosystems.

Conclusions
Real-world examples show three or more stable configurations of ecological communities may exist for a given set of parameters, and transient stages may persist for long periods necessitating their respective consideration. The characteristic length scale (CLS) is a useful metric that uniquely identifies a community ‘basin of attraction’, enabling phase shifts to be distinguished from long transients. Variabilities of CLSs and time series data may likewise provide proactive management measures to mitigate phase shifts and loss of ecosystem services. Continued challenges remain in distinguishing continuous from discontinuous phase shifts because their respective dynamics lack unique signatures.
Plant–microbe interactions through a lens: tales from the mycorrhizosphere
Authors: Williams Alex , Sinanaj Besiana , Hoysted Grace A 
Published: December 2023

Abstract

Background
The soil microbiome plays a pivotal role in maintaining ecological balance, supporting food production, preserving water quality and safeguarding human health. Understanding the intricate dynamics within the soil microbiome necessitates unravelling complex bacterial–fungal interactions (BFIs). BFIs occur in diverse habitats, such as the phyllosphere, rhizosphere and bulk soil, where they exert substantial influence on plant–microbe associations, nutrient cycling and overall ecosystem functions. In various symbiotic associations, fungi form mycorrhizal connections with plant roots, enhancing nutrient uptake through the root and mycorrhizal pathways. Concurrently, specific soil bacteria, including mycorrhiza helper bacteria, play a pivotal role in nutrient acquisition and promoting plant growth. Chemical communication and biofilm formation further shape plant–microbial interactions, affecting plant growth, disease resistance and nutrient acquisition processes.

Scope
Promoting synergistic interactions between mycorrhizal fungi and soil microbes holds immense potential for advancing ecological knowledge and conservation. However, despite the significant progress, gaps remain in our understanding of the evolutionary significance, perception, functional traits and ecological relevance of BFIs. Here we review recent findings obtained with respect to complex microbial communities – particularly in the mycorrhizosphere – and include the latest advances in the field, outlining their profound impacts on our understanding of ecosystem dynamics and plant physiology and function.

Conclusions
Deepening our understanding of plant BFIs can help assess their capabilities with regard to ecological and agricultural safe-guarding, in particular buffering soil stresses, and ensuring sustainable land management practices. Preserving and enhancing soil biodiversity emerge as critical imperatives in sustaining life on Earth amidst pressures of anthropogenic climate change. A holistic approach integrates scientific knowledge on bacteria and fungi, which includes their potential to foster resilient soil ecosystems for present and future generations.
Practice Patterns and Perspectives of the Off-Label Use of GLP-1 Agonists for Cosmetic Weight Loss
Authors: Han Sabrina H , Ockerman Kyle , Furnas Heather , Mars Patricia , Klenke Audrey , Ching Jessica , Momeni Arash , Sorice-Virk Sarah 
Published: December 2023

Abstract

Background
The off-label use of glucagon-like peptide 1 (GLP-1) agonists for cosmetic weight loss has captured the interest of the public. However, there is a paucity of published data on their utilization, implications, and management, particularly in the plastic surgery community.

Objectives
This study aims to explore the current practice patterns of aesthetic plastic surgeons regarding the off-label implementation of GLP-1 agonists.

Methods
A 35-question survey was sent to the 2600 members of The Aesthetic Society in July 2023. The survey collected physician demographics, practice settings, patient population demographics, and the use and management of GLP-1 agonists in their practice. No identifying variables were collected; all responses were anonymous.

Results
A total of 368 respondents were included. A quarter of respondents (25.3%) prescribed or utilized GLP-1 agonists in their practice. Nearly a third (29.9%) reported personal use of the medication, of which 71 (70.3%) indicated it was for cosmetic weight loss. Many aspects of the current treatment, counseling, and follow-up practices were similar among prescribing plastic surgeons. However, there were discrepancies in screening, nutrition counseling, and perioperative management. The majority believed that GLP-1 agonists were effective for weight loss (68.9%), profitable for business (57.8%), and would recommend its implementation to other plastic surgeons (68.5%).

Conclusions
As leaders in the aesthetic field, it behooves plastic surgeons to take charge of shaping public opinion surrounding the growing off-label use of GLP-1 agonists for cosmetic weight loss. Plastic surgeons' leadership is imperative in establishing safe and ethical guidelines and protocols for proper screening, management, and patient care.

Level of Evidence: 4
Levator Extension Method for Correcting Double Eyelids in Elderly Asian Patients: A Reliable and Flexible Blepharoplasty Technique
Authors: Han Dong Wan , Choi Jaeik , Lee Seokui , Song Seung Han 
Published: December 2023

Abstract

Background
Conventional tarsal fixation techniques for creating a static double-eyelid fold frequently result in a nonmobile overdepression of the fold, which is particularly pronounced in elderly patients.

Objectives
We propose a novel surgical approach aimed at achieving better results with fewer complications. This approach involves imitating the natural double-fold physiology by employing a turn-over flap of the orbital outer septum and carefully managing the pretarsal soft tissue to create a double fold.

Methods
A total of 503 patients underwent double-eyelid surgery, involving a turn-over flap of the outer orbital septum and pretarsal soft-tissue management. The orbital septum was exposed and transversely opened superior to the incision margin and the pretarsal soft issue was removed as necessary. Turn-over flaps were trimmed and attached to the dermis and orbicularis oculi muscle of the lower flap. Patient follow-up occurred for 2 to 7 years (mean, 3.8 years).

Results
This surgical method achieves a double fold with shallow or moderate depth, creating a natural-appearing fold line. Of the 503 patients, 94% of respondents provided a satisfaction score of 4 and 5 points; 20 people provided a score of 3 points; 10 were dissatisfied. A review of the patient chart showed that there were no specific complications in &gt;94% (473) of patients.

Conclusions
We proposed a double-eyelid surgery technique using the outer septum to control the depth and pretarsal soft-tissue management to minimize resistance in the creation of the double eyelid. Our method showed a high patient satisfaction rate and fewer complications in elderly Asians.
PDBImages: a command-line tool for automated macromolecular structure visualization
Authors: Midlik Adam , Nair Sreenath , Anyango Stephen , Deshpande Mandar , Sehnal David , Varadi Mihaly , Velankar Sameer 
Published: December 2023

Abstract

Summary
PDBImages is an innovative, open-source Node.js package that harnesses the power of the popular macromolecule structure visualization software Mol*. Designed for use by the scientific community, PDBImages provides a means to generate high-quality images for PDB and AlphaFold DB models. Its unique ability to render and save images directly to files in a browserless mode sets it apart, offering users a streamlined, automated process for macromolecular structure visualization. Here, we detail the implementation of PDBImages, enumerating its diverse image types, and elaborating on its user-friendly setup. This powerful tool opens a new gateway for researchers to visualize, analyse, and share their work, fostering a deeper understanding of bioinformatics.

Availability and implementation
PDBImages is available as an npm package from https://www.npmjs.com/package/pdb-images. The source code is available from https://github.com/PDBeurope/pdb-images.
GDmicro: classifying host disease status with GCN and deep adaptation network based on the human gut microbiome data
Authors: Liao Herui , Shang Jiayu , Sun Yanni 
Published: December 2023

Abstract

Motivation
With advances in metagenomic sequencing technologies, there are accumulating studies revealing the associations between the human gut microbiome and some human diseases. These associations shed light on using gut microbiome data to distinguish case and control samples of a specific disease, which is also called host disease status classification. Importantly, using learning-based models to distinguish the disease and control samples is expected to identify important biomarkers more accurately than abundance-based statistical analysis. However, available tools have not fully addressed two challenges associated with this task: limited labeled microbiome data and decreased accuracy in cross-studies. The confounding factors, such as the diet, technical biases in sample collection/sequencing across different studies/cohorts often jeopardize the generalization of the learning model.

Results
To address these challenges, we develop a new tool GDmicro, which combines semi-supervised learning and domain adaptation to achieve a more generalized model using limited labeled samples. We evaluated GDmicro on human gut microbiome data from 11 cohorts covering 5 different diseases. The results show that GDmicro has better performance and robustness than state-of-the-art tools. In particular, it improves the AUC from 0.783 to 0.949 in identifying inflammatory bowel disease. Furthermore, GDmicro can identify potential biomarkers with greater accuracy than abundance-based statistical analysis methods. It also reveals the contribution of these biomarkers to the host’s disease status.

Availability and implementation
https://github.com/liaoherui/GDmicro.
tANCHOR fast and cost-effective cell-based immunization approach with focus on the receptor-binding domain of SARS-CoV-2
Authors: Bernauer Hubert , Schlör Anja , Maier Josef , Bannert Norbert , Hanack Katja , Ivanusic Daniel 
Published: December 2023

Abstract
Successful induction of antibodies in model organisms like mice depends strongly on antigen design and delivery. New antigen designs for immunization are helpful for developing future therapeutic monoclonal antibodies (mAbs). One of the gold standards to induce antibodies in mice is to express and purify the antigen for vaccination. This is especially time-consuming when mAbs are needed rapidly. We closed this gap and used the display technology tetraspanin anchor to develop a reliable immunization technique without the need to purify the antigen. This technique is able to speed up the immunization step enormously and we have demonstrated that we were able to induce antibodies against different proteins with a focus on the receptor-binding domain of SARS-CoV-2 and the extracellular loop of canine cluster of differentiation 20 displayed on the surface of human cells.
Novel variants in ABCA12 cause erythrokeratodermia variabilis
Authors: Liu Yihe , Mo Ran , Chen Zhiming , Yang Yong 
Published: December 2023

We present a patient clinically diagnosed with erythrokeratodermia variabilis harbored compound heterozygous variants in the ABCA12 gene, including an unreported c.3653A&gt;G variant and c.7247C&gt;T, both of which were predicted to be pathogenic.
This finding provide evidence that ABCA12 pathogenic variants were associated with recessive erythrokeratodermia variabilis, an otherwise dominant disorder.
This case highlighted the clinical diversity of ABCA12 variants and the genetic heterogeneity underlying the erythrokeratodermia variabilis, which is significant for genetic counseling and prenatal diagnosis.
The immunobiology of herpes simplex virus encephalitis and post-viral autoimmunity
Authors: Cleaver Jonathan , Jeffery Katie , Klenerman Paul , Lim Ming , Handunnetthi Lahiru , Irani Sarosh R , Handel Adam 
Published: December 2023

Abstract
Herpes simplex virus encephalitis (HSE) is the leading cause of non-epidemic encephalitis in the developed world and, despite antiviral therapy, mortality and morbidity is high. The emergence of post-HSE autoimmune encephalitis reveals a new immunological paradigm in autoantibody-mediated disease. A reductionist evaluation of the immunobiological mechanisms in HSE is crucial to dissect the origins of post-viral autoimmunity and supply rational approaches to the selection of immunotherapeutics.
Herein, we review the latest evidence behind the phenotypic progression and underlying immunobiology of HSE including the cytokine/chemokine environment, the role of pathogen-recognition receptors, T- and B-cell immunity and relevant inborn errors of immunity. Second, we provide a contemporary review of published patients with post-HSE autoimmune encephalitis from a combined cohort of 110 patients. Third, we integrate novel mechanisms of autoimmunization in deep cervical lymph nodes to explore hypotheses around post-HSE autoimmune encephalitis and challenge these against mechanisms of molecular mimicry and others. Finally, we explore translational concepts where neuroglial surface autoantibodies have been observed with other neuroinfectious diseases and those that generate brain damage including traumatic brain injury, ischaemic stroke and neurodegenerative disease.
Overall, the clinical and immunological landscape of HSE is an important and evolving field, from which precision immunotherapeutics could soon emerge.