bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new Bayesian factor analysis method improves detection of genes and biological processes affected by perturbations in single-cell CRISPR screening
Authors: Zhou Yifan , Luo Kaixuan , Liang Lifan , Chen Mengjie , He Xin 
Published: September 2023

AbstractClustered regularly interspaced short palindromic repeats (CRISPR) screening coupled with single-cell RNA sequencing has emerged as a powerful tool to characterize the effects of genetic perturbations on the whole transcriptome at a single-cell level. However, due to its sparsity and complex structure, analysis of single-cell CRISPR screening data is challenging. In particular, standard differential expression analysis methods are often underpowered to detect genes affected by CRISPR perturbations. We developed a statistical method for such data, called guided sparse factor analysis (GSFA). GSFA infers latent factors that represent coregulated genes or gene modules; by borrowing information from these factors, it infers the effects of genetic perturbations on individual genes. We demonstrated through extensive simulation studies that GSFA detects perturbation effects with much higher power than state-of-the-art methods. Using single-cell CRISPR data from human CD8+ T cells and neural progenitor cells, we showed that GSFA identified biologically relevant gene modules and specific genes affected by CRISPR perturbations, many of which were missed by existing methods, providing new insights into the functions of genes involved in T cell activation and neurodevelopment.
Selective reduction of visceral adipose tissue with injectable ice slurry
Authors: Moradi Tuchayi Sara , Khachatryan Yeva , Wang Ying , Rox Anderson R. , Wang Jialiang S. , Wein Marc N. , Garibyan Lilit 
Published: September 2023

AbstractReduction in visceral adipose tissue (VAT) mass reduces body weight and metabolic disease risk in obese patients. However surgical removal of VAT is highly invasive and thus not clinically feasible. We developed an injectable ice slurry for selective reduction of adipose tissue through cryolipolysis. The aim of this study was to investigate safety, feasibility and mechanism of ice slurry-induced cryolipolysis of VAT. Perigonadal VAT in diet-induced obese mice and rats was subjected to slurry or sham treatment. Body weight and blood chemistry were monitored for 56 days post-treatment. Histological analysis and molecular studies were performed to elucidate mechanisms of fat reduction. Treatment of VAT was well tolerated in all animals. Slurry induced adipocyte cell death via selective cryolipolysis; significant weight loss was noted at day 21 post-treatment. RNA sequencing from treated VAT samples showed increased expression of genes involved in inflammation, immune response, collagen biosynthesis and wound healing, and decreased expression of adipokines. This study demonstrates that slurry treatment is safe and effective in inducing cryolipolysis of VAT and subsequent weight loss in mice. Ice slurry is promising as a minimally-invasive treatment to reduce visceral adipose tissue.
Validation of airway porcine epithelial cells as an alternative to human in vitro preclinical studies
Authors: Genna Vincenzo Giuseppe , Adamo Davide , Galaverni Giulia , Lepore Fabio , Boraldi Federica , Quaglino Daniela , Lococo Filippo , Pellegrini Graziella 
Published: September 2023

AbstractAnimal models are currently used in several fields of biomedical research as useful alternatives to human-based studies. However, the obtained results do not always effectively translate into clinical applications, due to interspecies anatomical and physiological differences. Detailed comparability studies are therefore required to verify whether the selected animal species could be a representative model for the disease or for cellular process under investigation. This has proven to be fundamental to obtaining reliable data from preclinical studies. Among the different species, swine is deemed an excellent animal model in many fields of biological research, and has been largely used in respiratory medicine, considering the high homology between human and swine airways. In the context of in vitro studies, the validation of porcine airway epithelial cells as an alternative to human epithelial cells is crucial. In this paper, porcine and human tracheal and bronchial epithelial cells are compared in terms of in vivo tissue architecture and in vitro cell behaviour under standard and airlifted conditions, analyzing the regenerative, proliferative and differentiative potentials of these cells. We report multiple analogies between the two species, validating the employment of porcine airway epithelial cells for most in vitro preclinical studies, although with some limitations due to species-related divergences.
Multistage entanglement swapping using superconducting qubits in the absence and presence of dissipative environment without Bell state measurement
Authors: Salimian S. , Tavassoly M. K. , Ghasemi M. 
Published: September 2023

AbstractIn recent decades the entangled state generation is of great importance in the quantum information processing and technologies. In this paper, producing the distributed entangled state of superconducting (SC) qubits is considered using an entanglement swapping protocol in three successive stages. The SC qubit pairs $$(i,\,i+1$$

(
i
,

i
+
1

with $$i=1,\,3,\,5,\,7)$$

i
=
1
,

3
,

5
,

7
)

, where each pair of the qubits has been placed on a separate chip, are initially prepared in maximally entangled states. The external magnetic fields on capacitively coupled pairs $$(2,\,3)$$

(
2
,

3
)

and $$(6,\,7)$$

(
6
,

7
)

are implemented for modulating the frequency of qubits. Then, the SC qubits $$(1,\,4)$$

(
1
,

4
)

and $$(5,\,8)$$

(
5
,

8
)

are converted into entangled states via operating proper measurements instead of Bell state measurement (which is generally a hard task). Finally, the distributed entangled state of target SC qubits $$(1,\,8)$$

(
1
,

8
)

can be obtained by applying external magnetic fields on qubits $$(4,\,5)$$

(
4
,

5
)

and via operating suitable measurements. This process is studied in the absence and presence of thermal decoherence effects. The concurrence, as a measure of entanglement between two target qubits, success probability of the distributed entangled states and the corresponding fidelities are evaluated, by which we find that the state of target SC qubits $$(1,\,8)$$

(
1
,

8
)

is converted to Bell state with maximum entanglement at some moments of time. Under appropriate conditions the maximum of success probability of the obtained states in each stage approaches 1. However, the maxima of concurrence and success probability gradually decrease due to the thermal noise as time goes on. Moreover, compelling amounts of fidelity, success probability and entanglement can be obtained for the achieved entangled states.
Bifunctional thiourea-based organocatalyst promoted kinetic resolution polymerization of racemic lactide to isotactic polylactide
Authors: Dai Jiang , Xiong Wei , Li Dong-Yu , Cai Zhongzheng , Zhu Jian-Bo 
Published: September 2023

We designed a series of bifunctional thiourea-based organocatalysts by combining two stereogenic elements, which promoted kinetic resolution polymerization of racemic lactide to produce isotactic polylactide with Pm up to 0.96.
Incidence of Anxiety and Depression after Achievement of
Inactive/low Disease Activity in
Axial/Spondyloarthropathy
Authors: Bayrak Esra Dilşat , Aktas Ilknur 
Published: September 2023

Abstract
Objectives Axial spondyloarthropathy (axSpA) is a common rheumatic disease
in young people and has important physiosocial implications. The purpose of this
study is to examine the frequency of anxiety and depression in axSpA patients
and to check whether achieving inactive/low disease activity or taking
TNF inhibitors has a positive effect on anxiety/depression and quality
of life (QOL).
Methods 149 axSpA patients were examined cross-sectionally over a period
of two years. Baseline characteristics were recorded. Disease activity is
measured using the ASDAS-CRP index. The patients were evaluated in 2 groups
according to their disease activity, as inactive-low disease activity or
moderate-high disease activity. The treatments they received were analysed into
two groups as NSAIDs and TNF inhibitors. Anxiety and depression were assessed
using the Hospital Anxiety and Depression Scale (HADS). Quality of life was
measured with the EuroQOL (EQ5D).
Results 33.6% of all axSpA patients were diagnosed with probable
anxiety disorder and 47% with probable depression. These rates were
similar in inactive-low disease activity patients, with 38% for anxiety
and 32% for depression. While the incidence of anxiety and depression
did not change between patients with inactive- low disease activity and
moderate-high disease activity (for anxiety p=0.173 and for depression
p=0.375), there was also no difference between patients receiving TNF
inhibitor treatment and NSAIDs (p=0.149 and p=0.235).
Radiographic form of axSpA was predictive of probable anxiety and depression.
Peripheral arthritis is also predictive of probable depression.
Conclusion Although axSpA patients had inactive-low disease activity and
received TNF inhibitors, there was no significant reduction in the incidence of
anxiety and depression. In addition to controlling disease activity and
inflammation, regular psychosocial assessment should be part of the management
of axSpA patients.
Discovery of Divergent, Light-Controlled Catalysis Triggered by Ligand Photodissociation from Cobalt Complexes
Authors: Vystavkin Nikita , Barday Manuel , Teskey Christopher J. 
Published: September 2023

AbstractPhotochemistry has become a key area of research in synthetic chemistry over the last few decades. More recently, interest has grown in merging this area with transition metal catalysis to develop new reactivity. One key photoinduced step in this context is ligand dissociation from transition metal complexes. This has been used to develop light-gated catalysis, allowing for on/off control over a reaction. However, this concept can only result in a single product outcome. Our group has focused on the development of cobalt-catalyzed reactivity switches, enabled by a simple photodissociation step, which promotes one mechanistic path or another. As such, we can use a single catalytic platform to yield two different outcomes depending on whether the reaction is irradiated with light or not. This short review will focus on works in this area by our group and others.1	Introduction2	Photocontrolled Hydroboration3	Hydrogenation and Hydroformylation4	Conclusion
Impact of Size for Gestational Age on Multivariate Analysis of Factors Associated with Necrotizing Enterocolitis in Preterm Infants: Retrospective Cohort Study
Authors: Sánchez-Rosado Mariela , Reis Jordan D. , Jaleel Mambarambath A. , Clipp Kimberly , Mangona Kate L.M. , Brown L Steven , Nelson David B. , Wyckoff Myra H. , Verma Diksha , Kiefaber Isabelle , Lair Cheryl S. , Nayak Sujir P. , Burchfield Patti J. , Thomas Anita , Brion Luc P. 
Published: September 2023

Objective Necrotizing enterocolitis (NEC) primarily affects preterm, especially small for gestational age (SGA), infants. This study was designed to (1) describe frequency and timing of NEC in SGA versus non-SGA infants and (2) assess whether NEC is independently associated with the severity of intrauterine growth failure.
Study Design Retrospective cohort study of infants without severe congenital malformations born <33 weeks' gestational age (GA) carried out from 2009 to 2021. The frequency and time of NEC were compared between SGA and non-SGA infants. Multivariate logistic regression was used to assess whether NEC was independently associated with intrauterine growth restriction. Severe growth restriction was defined as birth weight Z-score <  −2.
Results Among 2,940 infants, the frequency of NEC was higher in SGA than in non-SGA infants (25/268 [9.3%] vs. 110/2,672 [4.1%], respectively, p < 0.001). NEC developed 2 weeks later in SGA than non-SGA infants. In multivariate analysis, the adjusted odds of NEC increased with extreme prematurity (<28 weeks' GA) and with severe but not moderate growth restriction. The adjusted odds of NEC increased with urinary tract infection or sepsis within a week prior to NEC, were lower in infants fed their mother's own milk until discharge, and did not change over five epochs. NEC was independently associated with antenatal steroid (ANS) exposure in infants with birth weight (BW) Z-score < 0.
Conclusion NEC was more frequent in SGA than in non-SGA infants and developed 2 weeks later in SGA infants. NEC was independently associated with severe intrauterine growth failure and with ANS exposure in infants with BW Z-score < 0.
Key Points
Timing of Endoscopic Transmural Drainage for Pancreatic Necrosis: Expanding the Horizon!
Authors: Rana Surinder Singh 
Published: September 2023

AbstractEndoscopic transluminal drainage (ETD) has been traditionally performed on collections that have a well-formed enclosing wall and therefore it was advocated for walled-off necrosis. However, recently, retrospective studies have reported that ETD can be safely performed in patients with collections without a well-formed wall also and reported outcomes better than those patients who were treated with percutaneous drainage. The evidence for safety and efficacy of early ETD for infected pancreatic necrosis is scanty and therefore, in this news and views, I will be discussing a recently published systematic review and meta-analysis comparing outcomes after early (<4 weeks) and standard (≥4 weeks) drainage of pancreatic necrosis.
wfl Python toolkit for creating machine learning interatomic potentials and related atomistic simulation workflows
Authors: Gelžinytė Elena , Wengert Simon , Stenczel Tamás K. , Heenen Hendrik H. , Reuter Karsten , Csányi Gábor , Bernstein Noam 
Published: September 2023

Predictive atomistic simulations are increasingly employed for data intensive high throughput studies that take advantage of constantly growing computational resources. To handle the sheer number of individual calculations that are needed in such studies, workflow management packages for atomistic simulations have been developed for a rapidly growing user base. These packages are predominantly designed to handle computationally heavy ab initio calculations, usually with a focus on data provenance and reproducibility. However, in related simulation communities, e.g., the developers of machine learning interatomic potentials (MLIPs), the computational requirements are somewhat different: the types, sizes, and numbers of computational tasks are more diverse and, therefore, require additional ways of parallelization and local or remote execution for optimal efficiency. In this work, we present the atomistic simulation and MLIP fitting workflow management package wfl and Python remote execution package ExPyRe to meet these requirements. With wfl and ExPyRe, versatile atomic simulation environment based workflows that perform diverse procedures can be written. This capability is based on a low-level developer-oriented framework, which can be utilized to construct high level functionality for user-friendly programs. Such high level capabilities to automate machine learning interatomic potential fitting procedures are already incorporated in wfl, which we use to showcase its capabilities in this work. We believe that wfl fills an important niche in several growing simulation communities and will aid the development of efficient custom computational tasks.
Companion Rabbits: A Case Study Concerning Sudden-Onset Inappropriate Urination
Authors: Fry BSc (Hons) MSc CCAB Deborah 
Published: September 2023

Abstract
Despite their domestication some 1500 years ago, the behavioural repertoire of companion rabbits barely differs from that of wild rabbits. When presented with a companion rabbit behaviour issue, it is, therefore, necessary to consider their management in relation to the habitat, biology and behaviour of wild rabbits. Health factors may also be implicated; although as a prey species, rabbits naturally hide signs of disease or injury. This can complicate a health diagnosis.
This case study concerns an elderly spayed female indoor rabbit, Meg, who shared a positive relationship with her caregiver. Meg had experienced degenerative musculoskeletal changes for which treatment was on-going, and had previously had treatment for dental spurs and pododermatitis. Prior to Meg’s behaviour assessment, her caregiver sought advice from their Veterinary Surgeon due to Meg’s recent-onset urination outside her litter-trays overnight and occasionally during the day. The Veterinary Surgeon referred Meg to a Certificated Clinical Animal Behaviourist (CCAB) for a behaviour assessment which was conducted remotely using a questionnaire, home-layout diagram, photographs, video-footage and video-conference software. A behaviour diagnosis was made regarding Meg’s emotional and motivational state, and additional stressors were identified. Due to likely health and behaviour overlap, the CCAB further liaised with the referring Veterinary Surgeon. A treatment plan was devised, which Meg’s caregiver diligently implemented. Meg responded well to her treatment plan and over the course of 3 weeks, inappropriate urination ceased. In turn, the welfare of Meg and her caregiver significantly improved.

Information
© The Author 2023
Banks of templates for directed and all-sky narrow-band searches of continuous gravitational waves from spinning neutron stars with several spindowns
Authors: Pisarski Andrzej , Jaranowski Piotr 
Published: September 2023

Abstract
We construct efficient banks of templates suitable for searches of continuous gravitational waves from isolated spinning neutron stars. We assume that the search algorithm is based on the time-domain maximum-likelihood

F

-statistic and we consider narrow-band searches with several spindown parameters included. Our template banks are suitable for both all-sky and directed searches and they enable the usage of the fast Fourier transform in the computation of the

F

-statistic as well as, in the case of all-sky searches, efficient resampling of data to barycentric time.
Compact wideband filter with wide stopband using transition-free spoof surface plasmon polaritons
Authors: Ren Baoping , Qin Chunhua , Guan Xuehui , Xu Kai-Da 
Published: September 2023

Abstract
In this article, a newly spoof surface plasmon polaritons (SSPPs) is proposed and used to design a compact wideband bandpass filter (BPF). Different from the traditional SSPP unit cell with one-shaped structure, the unit cell of the proposed SSPPs consists of an H-shaped slotline and a bilateral T-shaped slotline. Benefiting from the hybrid structure, no transition portion is needed for impedance matching in the design of the microwave filter, which highly reduces the horizontal size of the SSPPs-based filter. The transition structure of microstrip to slotline provides a capacitance with a highpass frequency response, which enables the realization of a passband by cooperating with the natural lowpass property of SSPPs. Also, the upper and lower cutoff frequencies of the proposed filter can be adjusted independently by the key parameters. Besides, a wide upper stopband can be obtained by properly designing the SSPPs unit cell and the microstrip to slotline structure. Finally, a well-designed BPF operated at 1.3–6.2 GHz and its upper stopband rejection reaching 20 GHz is fabricated and measured. The test results are in good agreement with the simulations, which verifies the feasibility of the proposed structure and design method.
Bare W-based MXenes (WCrC and MoWC) anode with high specific capacity for Li and Mg-ion batteries
Authors: Zhou Min , Shen Yanqing , Lv LingLing , Zhang Yu , Meng Xianghui , Yang Xin , He Qirui , Zhang Bing , Zhou Zhongxiang 
Published: September 2023

Abstract
The emergence of double transition metal MXenes (DTMs) has addressed the challenges associated with the high molar weight and non-metallic characteristics of early transition metal MXenes. In this study, we investigate the performance of WCrC and MoWC, DTMs, as anodes in Li/Mg-ion batteries (LIBs/MIBs) using first-principles calculations. The synergistic effect between the dual metal terminals is analyzed. Our findings reveal that the W terminal provides good electronic conductivity, while the Mo/Cr terminal reduces the molar mass, leading to enhanced energy density. The theoretical capacitance values are 648.81 mAh g−1 (WCrC anode) and 551.82 mAh g−1 (MoWC anode) in LIB, and 432.54 mAh g−1 (WCrC anode) and 367.88 mAh g−1 (MoWC anode) in MIBs. Both anodes exhibit low diffusion barriers with 0.045 eV for Li and 0.079 eV for Mg. They also maintain structural rigidity throughout the battery cycle. This study highlights the crucial role of the dual metal transition terminal synergistic effect in MXenes, influencing adatom adsorption behavior, reducing molar mass, and lowering diffusion barriers. These results contribute to the advancement of MXene surface engineering and offer valuable insights for battery research.
GNSS-INS-dynamic fusion with robustness to outliers based on external force state estimation
Authors: Ye Xiaoyu , Song Fujun , Tang Meng , Guo Yunwei , Zeng Qinghua 
Published: September 2023

Abstract
Multi-source information fusion state estimation algorithms are an important means for drones to perceive ego-state, and accurate and robust estimation of external forces is crucial for precise control of quadrotors. This paper proposes a method that integrates a dynamic model into a multi-rate extended Kalman filter (EKF) framework on manifold. By estimating the magnitude of the external force acting on vehicle, meanwhile, a dynamic constraint on velocity loop is established to reduce the discrepancy between the model-predicted motion and the actual motion. Moreover, the estimated external force is integrated into the zero velocity update criterion for zero speed judgment, effectively reducing false detections while improving the accuracy of zero speed state recognition. However, multi-source measurements significantly increase the probability of data signal errors. To address this issue, we use a robust estimation algorithm to improve EKF’s sensitivity to abnormal measurements, flexibly adjusting measurement weights while rejecting unreasonable measurements. Validation with open-source indoor and outdoor datasets shows that our algorithm improves pose estimation performance while maintaining accurate positioning accuracy compared to non-dynamic fusion under the same filtering parameters, particularly in global navigation satellite system short time denied. It provides accurate external force estimation, offering multi-source data support in areas such as human–machine interaction and carrying variable mass payloads.