bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating surrogates, utility graphs and indicator sets for soil capacity and security assessments using legacy data
Authors: Ng Wartini , Evangelista Sandra J. , Padarian José , Pachon Julio , O’Donoghue Tom , Xue Peipei , Francos Nicolas , McBratney Alex B. 
Published: February 2024

Context Legacy data from prior studies enable preliminary analysis for soil security assessment which will inform future research questions. Aims This study aims to utilise the soil security assessment framework (SSAF) to evaluate the capacity of soil in fulfilling various roles and understand the underlying drivers. Methods The framework entails: (1) defining a combination of role(s) × dimension(s) and identifying a target indicator (a soil property that can be used to evaluate a particular role × dimension combination) or a surrogate indicator (an alternative indicator when there is not a clear target indicator); (2) transforming the indicator into a unitless score (ranging from 0 to 1) using a utility graph based on expert knowledge; (3) fitting the remaining soil properties (potential indicators) into utility graphs and weighing them using (a) ordination and (b) regression method. The application of this framework is demonstrated in evaluating two soil roles: nutrient storage and habitat for biodiversity (with pH and microbial DNA Shannon’s diversity index as surrogates, respectively) for an area in the lower Hunter Valley region, New South Wales, Australia. Key results The regression model provides utility estimates that were similar to those obtained from surrogates, in comparison to the utility derived from the ordination model. Conclusions This study provides a methodological pathway to examine the capacity and drivers of fulfilling different soil roles. The standardisation of this method opens the door to a complete quantification under the SSAF. Implications Indicators derived from a legacy dataset can be used for soil security assessment.
Density functional theory for doped TiO2: current research strategies and advancements
Authors: Zavatski Siarhei , Neilande Elina , Bandarenka Hanna , Popov Anatoli , Piskunov Sergei , Bocharov Dmitry 
Published: February 2024

Abstract
Since the inception of the density functional theory (DFT) by Hohenberg and Kohn in 1964, it rapidly became an indispensable theoretical tool across various disciplines, such as chemistry, biology, and materials science, among others. This theory has ushered in a new era of computational research, paving the way for substantial advancements in fundamental understanding. Today, DFT is routinely employed for a diverse range of applications, such as probing new material properties and providing a profound understanding of the mechanisms underlying physical, chemical, and biological processes. Even after decades of active utilization, the improvement of DFT principles has never been slowed down, meaning that more accurate theoretical results are continuously generated with time. This work highlights the latest achievements acquired by DFT in the specific research field, namely the theoretical investigations of doped TiO2 systems, which have not been comprehensively reviewed and summarized yet. Successful progress in this niche is currently hard to imagine without the support by DFT. It can accurately reveal new TiO2 properties after introducing the desired dopant and help to find the optimal system design for a specific application prior to proceeding to more time-consuming and expensive experimental research. Hence, by evaluating a selection of the most recent research studies, we aim to highlight the pertinent aspects of DFT as they relate to the study of doped TiO2 systems. We also aim to shed light on the strengths and weaknesses of DFT and present the primary strategies employed thus far to predict the properties of various doped TiO2 systems reliably.
Voxel-wise dose rate calculation in clinical pencil beam scanning proton therapy
Authors: Daartz Juliane , Madden Thomas M , Lalonde Arthur , Cascio Ethan , Verburg Joost , Shih Helen , MacDonald Shannon , Hachadorian Rachael , Schuemann Jan 
Published: February 2024

Abstract

Objective. Clinical outcomes after proton therapy have shown some variability that is not fully understood. Different approaches have been suggested to explain the biological outcome, but none has yet provided a comprehensive and satisfactory rationale for observed toxicities. The relatively recent transition from passive scattering (PS) to pencil beam scanning (PBS) treatments has significantly increased the voxel-wise dose rate in proton therapy. In addition, the dose rate distribution is no longer uniform along the cross section of the target but rather highly heterogeneous, following the spot placement. We suggest investigating dose rate as potential contributor to a more complex proton RBE model. Approach. Due to the time structure of the PBS beam delivery the instantaneous dose rate is highly variable voxel by voxel. Several possible parameters to represent voxel-wise dose rate for a given clinical PBS treatment plan are detailed. These quantities were implemented in the scripting environment of our treatment planning system, and computations experimentally verified. Sample applications to treated patient plans are shown. Main results. Computed dose rates we experimentally confirmed. Dose rate maps vary depending on which method is used to represent them. Mainly, the underlying time and dose intervals chosen determine the topography of the resultant distributions. The maximum dose rates experienced by any target voxel in a given PBS treatment plan in our system range from ∼100 to ∼450 Gy(RBE)/min, a factor of 10–100 increase compared to PS. These dose rate distributions are very heterogeneous, with distinct hot spots. Significance. Voxel-wise dose rates for current clinical PBS treatment plans vary greatly from clinically established practice with PS. The exploration of different dose rate measures to evaluate potential correlations with observed clinical outcomes is suggested, potentially adding a missing component in the understanding of proton relative biological effectiveness (RBE).
Impact of MRI RF coil design on the RF-induced heating of medical implants: fixed B
1
+
rms exposure versus normal operating mode
Authors: Yao Aiping , Li Zihan , Ma Mingjuan 
Published: February 2024

Abstract
A direct comparison of the impact of RF coil design under specific absorption rate and

B
1
+

rms

limitations are investigated and quantified using RF coils of different geometries and topologies at 64 MHz and 128 MHz. The RF-induced in vivo electric field and power deposition of a 50 cm long pacemaker and 55 cm long deep brain stimulator (DBS) are evaluated within two anatomical models exposed with these RF coils. The associated uncertainty is quantified and analyzed under a fixed

B
1
+

rms

incident and normal operating mode. For a fixed

B
1
+

rms

incident, the in vivo incident field shows a much higher uncertainty (>5.6 dB) to the RF coil diameter compared to other design parameters (e.g. <2.2 dB for coil length and topology), while the associated uncertainty reduced greatly (e.g. <1.5 dB) under normal operating mode exposure. Similar uncertainties are observed in the power deposition near the pacemaker and DBS electrode. Compared to the normal operating mode, applying a fixed

B
1
+

rms

field to the untested implant will lead to a large variation in the induced incident and power deposition of the implant, as a result, a larger safe margin when different coil designs (e.g. coil diameter) are considered.
MDT: semi-supervised medical image segmentation with mixup-decoupling training
Authors: Long Jianwu , Ren Yan , Yang Chengxin , Ren Pengcheng , Zeng Ziqin 
Published: February 2024

Abstract

Objective. In the field of medicine, semi-supervised segmentation algorithms hold crucial research significance while also facing substantial challenges, primarily due to the extreme scarcity of expert-level annotated medical image data. However, many existing semi-supervised methods still process labeled and unlabeled data in inconsistent ways, which can lead to knowledge learned from labeled data being discarded to some extent. This not only lacks a variety of perturbations to explore potential robust information in unlabeled data but also ignores the confirmation bias and class imbalance issues in pseudo-labeling methods. Approach. To solve these problems, this paper proposes a semi-supervised medical image segmentation method ‘mixup-decoupling training (MDT)’ that combines the idea of consistency and pseudo-labeling. Firstly, MDT introduces a new perturbation strategy ‘mixup-decoupling’ to fully regularize training data. It not only mixes labeled and unlabeled data at the data level but also performs decoupling operations between the output predictions of mixed target data and labeled data at the feature level to obtain strong version predictions of unlabeled data. Then it establishes a dual learning paradigm based on consistency and pseudo-labeling. Secondly, MDT employs a novel categorical entropy filtering approach to pick high-confidence pseudo-labels for unlabeled data, facilitating more refined supervision. Main results. This paper compares MDT with other advanced semi-supervised methods on 2D and 3D datasets separately. A large number of experimental results show that MDT achieves competitive segmentation performance and outperforms other state-of-the-art semi-supervised segmentation methods. Significance. This paper proposes a semi-supervised medical image segmentation method MDT, which greatly reduces the demand for manually labeled data and eases the difficulty of data annotation to a great extent. In addition, MDT not only outperforms many advanced semi-supervised image segmentation methods in quantitative and qualitative experimental results, but also provides a new and developable idea for semi-supervised learning and computer-aided diagnosis technology research.
Early bolt looseness monitoring using the leading waves energy in piezoelectric active sensing
Authors: Wang Tao , Wang Hu , Yang Dan , Tan Bohai , Deng Shaohua , Lu Guangtao 
Published: February 2024

Abstract
Bolt monitoring plays a vital role in ensuring the safe operation of engineering structures. The utilization of piezoelectric (PZT) active sensing and analysis of ultrasonic energy transmitted through the interface of bolted connections has demonstrated high feasibility for monitoring bolt looseness. However, the ultrasonic energy saturation effect (i.e. the response signal energy changes slightly as the bolt preload variation) near the rated bolt preload restricts its applicability in early detection of bolt loosening. In this paper, for the energy saturation in the PZT active sensing method, a new bolt looseness indicator with the energy of leading waves (i.e. the first several wave packets) in the response signal is proposed for bolt loosening monitoring, especially for the early bolt loosening monitoring since the energy of the leading wave packets has the linear relationship with bolt preload. The experimental results show that the energy of the first several wave packets in the response signals can be as a looseness indicator of bolt preload. Within the entire range of bolt preload, the indicator exhibits a linear relationship with the bolt preload. Moreover, this method successfully resolves the challenge of energy saturation, providing an effective approach for monitoring bolt preload.
Searching for the light leptophilic gauge boson Z

x
via four-lepton final states at the CEPC*
Authors: Yue 岳 Chong-Xing 崇兴 , Li 李 Yan-Yu 妍钰 , Wang 王 Mei-Shu-Yu 美舒羽 , Zhang 张 Xin-Meng 欣蒙 
Published: February 2024

Abstract
We investigate the possibility of detecting the leptophilic gauge boson

predicted by the

model via the processes

and

at the Circular Electron Positron Collider (CEPC) with a center of mass energy

GeV and luminosity

. We provide the expected sensitivities of the CEPC to the parameter space at the

,

,

, and

levels.
Plasma density enhancement in radio-frequency hollow electrode discharge
Authors: HE 贺 Liuliang 柳良 , (何锋) Feng HE , (欧阳吉庭) Jiting OUYANG 
Published: February 2024

Abstract
The plasma density enhancement outside hollow electrodes in capacitively coupled radio-frequency (RF) discharges is investigated by a two-dimensional (2D) particle-in-cell/Monte-Carlo collision (PIC/MCC) model. Results show that plasma exists inside the cavity when the sheath inside the hollow electrode hole is fully collapsed, which is an essential condition for the plasma density enhancement outside hollow electrodes. In addition, the existence of the electron density peak at the orifice is generated via the hollow cathode effect (HCE), which plays an important role in the density enhancement. It is also found that the radial width of bulk plasma at the orifice affects the magnitude of the density enhancement, and narrow radial plasma bulk width at the orifice is not beneficial to obtain high-density plasma outside hollow electrodes. Higher electron density at the orifice, combined with larger radial plasma bulk width at the orifice, causes higher electron density outside hollow electrodes. The results also imply that the HCE strength inside the cavity cannot be determined by the magnitude of the electron density outside hollow electrodes.
No Increase in Masked Hypertension Prevalence in Children With Sickle Cell Disease in France
Authors: Bokov Plamen , Koehl Berengere , Benzouid Chérine , Verlhac Suzanne , Missud Florence , Benkerrou Malika , Delclaux Christophe 
Published: February 2024

Abstract

BACKGROUND
An important prevalence (32%–45%) of masked hypertension has been reported in children with sickle cell disease (SCD). Stroke screening is well established using transcranial Doppler (TCD) ultrasound. The objectives of our proof-of-concept study in childhood SCD were to evaluate the prevalence of hypertension and its relationships with cerebral vasculopathy (TCD velocity) and to further evaluate in a subgroup of children the correlations of cardiovascular autonomic nervous system indices with TCD velocity.

METHODS
Ambulatory blood pressure measurement (ABPM) and TCD velocity were obtained in children with SCD and in a restricted sample, cardiac sympathovagal balance using heart rate variability analyses, baroreflex sensitivity, and pulse wave velocity were measured.

RESULTS
In 41 children with SCD (median age 14.0 years, 19 girls, SS/Sβ + thalassemia/SC: 33/2/6), ABPM results showed masked hypertension in 2/41 (5%, 95% confidence interval, 0–11) children, consistent with the prevalence in the general pediatric population, elevated blood pressure (BP) in 4/41 (10%) children, and a lack of a normal nocturnal dip in 19/41 children (46%). Children with increased TCD velocity had lower nocturnal dipping of systolic BP. In the 10 participants with extensive cardiovascular assessment, increased TCD velocity was associated with parasympathetic withdrawal and baroreflex failure. Exaggerated orthostatic pressor response or orthostatic hypertension was observed in 7/10 children that was linked to parasympathetic withdrawal.

CONCLUSIONS
Autonomic nervous system dysfunction, namely loss of parasympathetic modulation, of SCD contributes to increase TCD velocity but is not associated with an increased prevalence of masked hypertension.

CLINICAL TRIALS REGISTRATION
NCT04911049.
Highly efficient clustering of long-read transcriptomic data with GeLuster
Authors: Ma Junchi , Zhao Xiaoyu , Qi Enfeng , Han Renmin , Yu Ting , Li Guojun 
Published: February 2024

Abstract

Motivation
The advancement of long-read RNA sequencing technologies leads to a bright future for transcriptome analysis, in which clustering long reads according to their gene family of origin is of great importance. However, existing de novo clustering algorithms require plenty of computing resources.

Results
We developed a new algorithm GeLuster for clustering long RNA-seq reads. Based on our tests on one simulated dataset and nine real datasets, GeLuster exhibited superior performance. On the tested Nanopore datasets it ran 2.9–17.5 times as fast as the second-fastest method with less than one-seventh of memory consumption, while achieving higher clustering accuracy. And on the PacBio data, GeLuster also had a similar performance. It sets the stage for large-scale transcriptome study in future.

Availability and implementation
GeLuster is freely available at https://github.com/yutingsdu/GeLuster.
Protein language models meet reduced amino acid alphabets
Authors: Ieremie Ioan , Ewing Rob M , Niranjan Mahesan 
Published: February 2024

Abstract

Motivation
Protein language models (PLMs), which borrowed ideas for modelling and inference from natural language processing, have demonstrated the ability to extract meaningful representations in an unsupervised way. This led to significant performance improvement in several downstream tasks. Clustering amino acids based on their physical–chemical properties to achieve reduced alphabets has been of interest in past research, but their application to PLMs or folding models is unexplored.

Results
Here, we investigate the efficacy of PLMs trained on reduced amino acid alphabets in capturing evolutionary information, and we explore how the loss of protein sequence information impacts learned representations and downstream task performance. Our empirical work shows that PLMs trained on the full alphabet and a large number of sequences capture fine details that are lost in alphabet reduction methods. We further show the ability of a structure prediction model(ESMFold) to fold CASP14 protein sequences translated using a reduced alphabet. For 10 proteins out of the 50 targets, reduced alphabets improve structural predictions with LDDT-Cα differences of up to 19%.

Availability and implementation
Trained models and code are available at github.com/Ieremie/reduced-alph-PLM.
531 - Physician-assessed effectiveness and patient-reported outcomes in adult and adolescent patients with atopic dermatitis treated with dupilumab: real-world insights 1 year into the GLOBOSTAD multinational prospective observational study
Authors: Ferrucci Silvia M , Calzavara-Pinton Piergiacomo , Murrell Dédée F , Fougerousse Anne-Claire , Karlova Iva , Lapeere Hilde , Holzer Gregor , Al-Ahmad Mona , Chu Chia-Yu , Foti Caterina , Pérez-García Bibiana , Wu Jiangming , Ardeleanu Marius , Bosman Kwinten 
Published: February 2024

Abstract

Introduction
The GLOBOSTAD study aims to assess the extended real-world effectiveness of dupilumab in patients with atopic dermatitis (AD) receiving dupilumab as part of their normal care.

Objectives
To report patient-reported outcomes and physician-­assessed AD clinical measures for evaluating disease characteristics, severity, and treatment effectiveness 1 year after initiating dupilumab treatment.

Methods
This 5-year, multinational, prospective, observational study (NCT03992417) enrolled patients aged ≥12 years with moderate-to-severe AD. Patients received dupilumab based on country-specific prescribing information. Assessments were performed at baseline, 3 months (± 1 month), 6 months (± 2 months), and 12 months (± 2 months). Data are reported as observed for enrollment/safety (N = 955; data cutoff: March 2023) and follow-up (N = 903) populations including 13 adolescent patients with AD (≥12 and &lt;18 years old).

Results
In this study, 758/863/705 patients completed ≥1 follow-up assessment at 3 months/6 months/12 months, respectively. During the study the mean (standard deviation [SD]) Eczema Area and Severity Index (EASI; &gt;21 = severe; ≤7 = mild/no disease) scores decreased from 25.1 (12.8) at baseline to 6.1 (8.0) at 3 months, 4.6 (6.4) at 6 months and sustaining throughout the observation period [12 months; 4.2 (8.4)]. Mean Patient-Oriented Eczema Measure (SD) improved from 19.7 (6.4) at baseline descending to 8.7 (6.6) at 3 months, 7.7 (6.0) at 6 months and 7.1 (5.8) at 12 months. A significant improvement was also observed in Dermatology Life Quality Index (DLQI) from 13.7 (7.1) to 5.3 (5.1) to 4.4 (4.4) to 3.9 (4.2); and children’s DLQI from 12.2 (6.2) to 2.7 (2.9) to 2.9 (3.0) to 4.8 (4.8) by the end of the 3, 6 and 12-months observational period respectively. Dupilumab-related adverse events were reported in 187 (20.8%) patients.

Conclusions
In a real-world scenario, the initiation of dupilumab treatment led to early and sustained improvements in AD outcome measures throughout the 1-year observational period. Safety data remained consistent with findings from previous studies.
553 - Tralokinumab real-world patient-reported outcomes in moderate-to-severe atopic dermatitis adult patients in the United States: 6-month interim analysis
Authors: Lio Peter , Kim Yestle , Balu Sanjeev , Costantino Halley , Bates Dawn , Rene Cassandra , Lopez Amanda , Soung Jennifer 
Published: February 2024

Abstract

Introduction/Background
Tralokinumab, an IL-13 targeted biologic approved in the United States (US) for adult patients with moderate-to-severe atopic dermatitis (AD), improved patient-reported outcomes (PROs) in clinical trials and after 4 weeks of use in the real-world setting.

Objectives
This 6-month interim analysis evaluated the real-world impact of tralokinumab on PROs in adult patients.

Methods
This is an interim analysis of an ongoing 52-week patient survey study enrolling US AD patients from the AdbryTM AdvocateTM Program. Patients completed the baseline survey close to tralokinumab initiation. Data on demographics and PROs including weekly itch numeric rating scale (NRS), eczema-related weekly sleep NRS, Dermatology Life Quality Index (DLQI), and Treatment Satisfaction Questionnaire for Medication (TSQM-9) were collected. Percent and absolute changes from baseline to 6 months of treatment were calculated. Outcomes are stratified by previous dupilumab use. The percentage of patients experiencing minimal clinically important difference (MCID) was also calculated for itch NRS (3-point reduction) and DLQI (4-point reduction).

Results
As of May 2023, 102 patients completed baseline, 1-month, and 6-month surveys. Of these, 59.8% were female, mean age was 44.2 years (SD=15.7), 82.4% were white, and 85.3% had private insurance. 84.3% were previously treated with topical corticosteroids (TCS) and 52.9% were dupilumab-experienced patients. Over 6 months, there was an improvement in the mean sleep interference NRS (40%), average weekly itch NRS (39%), worst weekly itch NRS (33%), PO-SCORAD (37%), and DLQI (52%). There were improvements in mean TSQM-9 global satisfaction (11.06 points), TSQM-9 convenience (3.92 points), and TSQM-9 effectiveness (14.60 points) scores. Median MCIDs were met by 57.1% on the sleep interference NRS, 51.7% of patients on the average weekly itch NRS, 50.0% on the worst weekly itch NRS, and 68.7% on the DLQI. Relative to the dupilumab-experienced cohort, the dupilumab-naïve patients showed markedly improved outcomes [median MCIDs of 65.6% v 48.4% on sleep NRS; 59.5% v 44.4% on average weekly itch NRS; 61.4% v 39.6% on worst weekly itch NRS; 61.4% v 35.3% on PO-SCORAD; and 75.6% v 61.9% on DLQI].

Conclusions
This 6-month interim analysis shows that tralokinumab improved quality of life outcomes related to itch, sleep, and treatment satisfaction when used either in dupilumab-naïve or in dupilumab-experienced patients. These patients will continue to be followed for up to 52 weeks of treatment with tralokinumab.