bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrating plan complexity and dosiomics features with deep learning in patient-specific quality assurance for volumetric modulated arc therapy
Authors: Han Ce , Zhang Ji , Yu Bing , Zheng Haoze , Wu Yibo , Lin Zhixi , Ning Boda , Yi Jinling , Xie Congying , Jin Xiance 
Published: July 2023

Abstract
Purpose
To investigate the feasibility and performance of deep learning (DL) models combined with plan complexity (PC) and dosiomics features in the patient-specific quality assurance (PSQA) for patients underwent volumetric modulated arc therapy (VMAT).

Methods
Total of 201 VMAT plans with measured PSQA results were retrospectively enrolled and divided into training and testing sets randomly at 7:3. PC metrics were calculated using house-built algorithm based on Matlab. Dosiomics features were extracted and selected using Random Forest (RF) from planning target volume (PTV) and overlap regions with 3D dose distributions. The top 50 dosiomics and 5 PC features were selected based on feature importance screening. A DL DenseNet was adapted and trained for the PSQA prediction.

Results
The measured average gamma passing rate (GPR) of these VMAT plans was 97.94% ± 1.87%, 94.33% ± 3.22%, and 87.27% ± 4.81% at the criteria of 3%/3 mm, 3%/2 mm, and 2%/2 mm, respectively. Models with PC features alone demonstrated the lowest area under curve (AUC). The AUC and sensitivity of PC and dosiomics (D) combined model at 2%/2 mm were 0.915 and 0.833, respectively. The AUCs of DL models were improved from 0.943, 0.849, 0.841 to 0.948, 0.890, 0.942 in the combined models (PC + D + DL) at 3%/3 mm, 3%/2 mm and 2%/2 mm, respectively. A best AUC of 0.942 with a sensitivity, specificity and accuracy of 100%, 81.8%, and 83.6% was achieved with combined model (PC + D + DL) at 2%/2 mm.

Conclusions
Integrating DL with dosiomics and PC metrics is promising in the prediction of GPRs in PSQA for patients underwent VMAT.
Dermatophytosis caused by Trichophyton mentagrophytes complex in organic pigs
Authors: Sylvén Kaisa Ryytty , Bergefur Ann-Louise , Jacobson Magdalena , Wallgren Per , Selling Lena Eliasson 
Published: July 2023

Abstract
Background
Dermatophytosis (ringworm) caused by members of the Trichophyton mentagrophytes complex is rarely diagnosed in pigs but has been recognized as an increasingly common infection in humans. Further, resistance to antifungal drugs have been reported both in Asia and in Europe. This is the first scientific report of infection by the T. mentagrophytes complex in pigs in the Nordic countries.

Case presentation
Skin lesions developed in grower pigs in an organic fattening pig farm with outdoor production and following laboratory analyses, dermatophytosis caused by members of the T. mentagrophytes complex was diagnosed. Infection was linked to poor hygiene, high humidity, and moderate outdoor temperatures, in combination with high pig density. A farm worker developed a skin lesion after close contact with affected pigs, which highlighted the zoonotic potential of porcine dermatophytosis. The dermatophytes may have originated from the herd supplying the growers where similar lesions occurred in pigs. Further, pigs from another organic fattening herd that received growers from the same supplier herd also developed dermatophytosis. The lesions healed without treatment as the housing conditions were improved. Isolation of affected pigs prevented spread to other pigs

Conclusion
Members of the T. mentagrophytes complex can cause ringworm in pigs. The fungi probably persist in the haircoat and may cause overt disease when environmental conditions promote growth of mycelia.
Overlapping filter bank convolutional neural network for multisubject multicategory motor imagery brain-computer interface
Authors: Luo Jing , Li Jundong , Mao Qi , Shi Zhenghao , Liu Haiqin , Ren Xiaoyong , Hei Xinhong 
Published: July 2023

Abstract
Background
Motor imagery brain-computer interfaces (BCIs) is a classic and potential BCI technology achieving brain computer integration. In motor imagery BCI, the operational frequency band of the EEG greatly affects the performance of motor imagery EEG recognition model. However, as most algorithms used a broad frequency band, the discrimination from multiple sub-bands were not fully utilized. Thus, using convolutional neural network (CNNs) to extract discriminative features from EEG signals of different frequency components is a promising method in multisubject EEG recognition.

Methods
This paper presents a novel overlapping filter bank CNN to incorporate discriminative information from multiple frequency components in multisubject motor imagery recognition. Specifically, two overlapping filter banks with fixed low-cut frequency or sliding low-cut frequency are employed to obtain multiple frequency component representations of EEG signals. Then, multiple CNN models are trained separately. Finally, the output probabilities of multiple CNN models are integrated to determine the predicted EEG label.

Results
Experiments were conducted based on four popular CNN backbone models and three public datasets. And the results showed that the overlapping filter bank CNN was efficient and universal in improving multisubject motor imagery BCI performance. Specifically, compared with the original backbone model, the proposed method can improve the average accuracy by 3.69 percentage points, F1 score by 0.04, and AUC by 0.03. In addition, the proposed method performed best among the comparison with the state-of-the-art methods.

Conclusion
The proposed overlapping filter bank CNN framework with fixed low-cut frequency is an efficient and universal method to improve the performance of multisubject motor imagery BCI.
GreenHill: a de novo chromosome-level scaffolding and phasing tool using Hi-C
Authors: Ouchi Shun , Kajitani Rei , Itoh Takehiko 
Published: July 2023

AbstractChromosome-level haplotype-resolved genome assembly is an important resource in molecular biology. However, current de novo haplotype assemblers require parental data or reference genomes and often fail to provide chromosome-level results. We present GreenHill, a novel scaffolding and phasing tool that considers various assemblers’ contigs as input to reconstruct chromosome-level haplotypes using Hi-C without parental or reference data. Its unique functions include new error correction based on Hi-C contacts and the simultaneous use of Hi-C and long reads. Benchmarks reveal that GreenHill outperforms other approaches in contiguity and phasing accuracy, and the majority of chromosome arms are entirely phased.
Sex differences in the effects of prematurity and/or low birthweight on neurodevelopmental outcomes: systematic review and meta-analyses
Authors: Christians Julian K. , Ahmadzadeh-Seddeighi Saboura , Bilal Alishba , Bogdanovic Anastasia , Ho Rebecca , Leung Estee V. , MacGregor Megan A. , Nadasdy Nolan M. , Principe Gabriella M. 
Published: July 2023

Abstract
Background
Premature birth and/or low birthweight have long-lasting effects on cognition. The purpose of the present systematic review is to examine whether the effects of prematurity and/or low birth weight on neurodevelopmental outcomes differ between males and females.

Methods
Web of Science, Scopus, and Ovid MEDLINE were searched for studies of humans born premature and/or of low birthweight, where neurodevelopmental phenotypes were measured at 1 year of age or older. Studies must have reported outcomes in such a way that it was possible to assess whether effects were greater in one sex than the other. Risk of bias was assessed using both the Newcastle–Ottawa scale and the National Institutes of Health Quality assessment tool for observational cohort and cross-sectional studies.

Results
Seventy-five studies were included for descriptive synthesis, although only 24 presented data in a way that could be extracted for meta-analyses. Meta-analyses found that severe and moderate prematurity/low birthweight impaired cognitive function, and severe prematurity/low birthweight also increased internalizing problem scores. Moderate, but not severe, prematurity/low birthweight significantly increased externalizing problem scores. In no case did effects of prematurity/low birthweight differ between males and females. Heterogeneity among studies was generally high and significant, although age at assessment was not a significant moderator of effect. Descriptive synthesis did not identify an obvious excess or deficiency of male-biased or female-biased effects for any trait category. Individual study quality was generally good, and we found no evidence of publication bias.

Conclusions
We found no evidence that the sexes differ in their susceptibility to the effects of severe or moderate prematurity/low birthweight on cognitive function, internalizing traits or externalizing traits. Result heterogeneity tended to be high, but this reflects that one sex is not consistently more affected than the other. Frequently stated generalizations that one sex is more susceptible to prenatal adversity should be re-evaluated.
Non-overdose acute care hospitalizations for opioid use disorder among commercially-insured adults: a retrospective cohort study
Authors: Raman Sudha R. , Ford Cassie B. , Hammill Bradley G. , Clark Amy G. , Clifton Dana C. , Jackson George L. 
Published: July 2023

Abstract
Background
Acute care inpatient admissions outside of psychiatric facilities have been increasingly identified as a critical touchpoint for opioid use disorder (OUD) treatment. We sought to describe non-opioid overdose hospitalizations with documented OUD and examine receipt of post-discharge outpatient buprenorphine.

Methods
We examined acute care hospitalizations with an OUD diagnosis in any position within US commercially-insured adults age 18–64 years (IBM MarketScan claims, 2013–2017), excluding opioid overdose diagnoses. We included individuals with ≥ 6 months of continuous enrollment prior to the index hospitalization and ≥ 10 days following discharge. We described demographic and hospitalization characteristics, including outpatient buprenorphine receipt within 10 days of discharge.

Results
Most (87%) hospitalizations with documented OUD did not include opioid overdose. Of 56,717 hospitalizations (49,959 individuals), 56.8% had a primary diagnosis other than OUD, 37.0% had documentation of an alcohol-related diagnosis code, and 5.8% end in a self-directed discharge. Where opioid use disorder was not the primary diagnosis, 36.5% were due to other substance use disorders, and 23.1% were due to psychiatric disorders. Of all non-overdose hospitalizations who had prescription medication insurance coverage and who were discharged to an outpatient setting (n = 49, 237), 8.8% filled an outpatient buprenorphine prescription within 10 days of discharge.

Conclusions
Non-overdose OUD hospitalizations often occur with substance use disorders and psychiatric disorders, and very few are followed by timely outpatient buprenorphine. Addressing the OUD treatment gap during hospitalization may include implementing medication for OUD for inpatients with a broad range of diagnoses.
Practices and challenges related to antibiotic use in paediatric treatment in hospitals and health centres in Niger and Uganda: a mixed methods study
Authors: Mambula Grace , Nanjebe Deborah , Munene Aurelia , Guindo Ousmane , Salifou Aichatou , Mamaty Abdoul-Aziz , Rattigan Susan , Ellis Sally , Khavessian Nathalie , van der Pluijm Rob W , Marquer Caroline , Adehossi Irene Aicha , Langendorf Céline 
Published: July 2023

Abstract
Background
Antibiotic resistance is a significant public health problem and is responsible for high mortality in children and new-borns. Strengthening the rational use of antibiotics and improving the quality and access to existing antibiotics are important factors in the fight against antibiotic resistance. This study aims to provide knowledge on the use of antibiotics in children in resource-limited countries in order to identify problems and possible avenues for improvement of antibiotics use.

Methods
We conducted a retrospective study in July 2020 and collected quantitative clinical and therapeutic data on antibiotic prescriptions between January and December 2019 in 4 hospitals or health centres in both Uganda and Niger, respectively from January to December 2019. Semi-structured interviews and focus groups were conducted among healthcare personnel and carers for children under 17 years of age, respectively.

Results
A total of 1,622 children in Uganda and 660 children in Niger (mean age of 3.9 years (SD 4.43)) who received at least one antibiotic were included in the study. In hospital settings, 98.4 to 100% of children prescribed at least one antibiotic received at least one injectable antibiotic. Most hospitalized children received more than one antibiotic in both Uganda (52.1%) and Niger (71.1%). According to the WHO-AWaRe index, the proportion of prescriptions of antibiotics belonging to the Watch category was 21.8% (432/1982) in Uganda and 32.0% (371/1158) in Niger. No antibiotics from the Reserve category were prescribed. Health care provider’s prescribing practices are rarely guided by microbiological analyses. Prescribers are faced with numerous constraints, such as lack of standard national guidelines, unavailability of essential antibiotics at the level of hospital pharmacies, the limited financial means of the families, and pressure to prescribe antibiotics from caregivers as well as from drug company representatives. The quality of some antibiotics provided by the National Medical Stores to the public and private hospitals has been questioned by some health professionals. Self-medication is a widespread practice for the antibiotic treatment of children for economic and access reasons.

Conclusion
The study findings indicate that an intersection of policy, institutional norms and practices including individual caregiver or health provider factors, influence antibiotic prescription, administration and dispensing practices.
Targeting the glycine-rich domain of TDP-43 with antibodies prevents its aggregation in vitro and reduces neurofilament levels in vivo
Authors: Riemenschneider Henrick , Simonetti Francesca , Sheth Udit , Katona Eszter , Roth Stefan , Hutten Saskia , Farny Daniel , Michaelsen Meike , Nuscher Brigitte , Schmidt Michael K. , Flatley Andrew , Schepers Aloys , Gruijs da Silva Lara A. , Zhou Qihui , Klopstock Thomas , Liesz Arthur , Arzberger Thomas , Herms Jochen , Feederle Regina , Gendron Tania F. , Dormann Dorothee , Edbauer Dieter 
Published: July 2023

Abstract
Cytoplasmic aggregation and concomitant nuclear clearance of the RNA-binding protein TDP-43 are found in ~ 90% of cases of amyotrophic lateral sclerosis and ~ 45% of patients living with frontotemporal lobar degeneration, but no disease-modifying therapy is available. Antibody therapy targeting other aggregating proteins associated with neurodegenerative disorders has shown beneficial effects in animal models and clinical trials. The most effective epitopes for safe antibody therapy targeting TDP-43 are unknown. Here, we identified safe and effective epitopes in TDP-43 for active and potential future passive immunotherapy. We prescreened 15 peptide antigens covering all regions of TDP-43 to identify the most immunogenic epitopes and to raise novel monoclonal antibodies in wild-type mice. Most peptides induced a considerable antibody response and no antigen triggered obvious side effects. Thus, we immunized mice with rapidly progressing TDP-43 proteinopathy (“rNLS8” model) with the nine most immunogenic peptides in five pools prior to TDP-43ΔNLS transgene induction. Strikingly, combined administration of two N-terminal peptides induced genetic background-specific sudden lethality in several mice and was therefore discontinued. Despite a strong antibody response, no TDP-43 peptide prevented the rapid body weight loss or reduced phospho-TDP-43 levels as well as the profound astrogliosis and microgliosis in rNLS8 mice. However, immunization with a C-terminal peptide containing the disease-associated phospho-serines 409/410 significantly lowered serum neurofilament light chain levels, indicative of reduced neuroaxonal damage. Transcriptomic profiling showed a pronounced neuroinflammatory signature (IL-1β, TNF-α, NfκB) in rNLS8 mice and suggested modest benefits of immunization targeting the glycine-rich region. Several novel monoclonal antibodies targeting the glycine-rich domain potently reduced phase separation and aggregation of TDP-43 in vitro and prevented cellular uptake of preformed aggregates. Our unbiased screen suggests that targeting the RRM2 domain and the C-terminal region of TDP-43 by active or passive immunization may be beneficial in TDP-43 proteinopathies by inhibiting cardinal processes of disease progression.

Graphical Abstract
Phosphorus leaching risk from black soil increased due to conversion of arid agricultural land to paddy land in northeast China
Authors: Xie Zi-jian , Zhu Dong , Wei Wei-wei , Ye Chun , Wang Hao , Li Chun-hua 
Published: July 2023

Abstract
Background
Land-use change from arid agricultural land to paddy land may increase soil phosphorus (P) leaching in the black soil region. However, little information is available for soil P leaching risk assessment from soil profiles due to the land-use conversion in the black soil region of northeast China.

Results
This study explored the effect of land-use change from arid agricultural land to paddy land on soil P leaching change point, P leaching risk and P fractions. Conversion from arid agricultural land to paddy land decrease soil P leaching change point (0–20 cm: 59.63 mg kg−1 vs. 35.35 mg kg−1; 20–40 cm: 24.31 mg kg−1 vs. 17.20 mg kg−1; 40–60 cm: 32.91 mg kg−1 vs. 10.45 mg kg−1); 30.9% of arid agricultural soils were at risk of P leaching into the shallow groundwater, compared to 87.5% of paddy soils, implying a high risk of P leaching after land-use conversion. P fraction analysis using the Hedley sequential extraction method showed that moderately active P, including NaOH-Pi, NaOH-Po, and HCl-Pi, were the dominant fractions in the tested soils. HCl-Pi and NaOH-Pi were the major P fraction of moderately active P in arid agricultural land and paddy land, respectively, indicating that land-use change leads to the conversion from Ca-bound P to P associated with Fe and Al.

Conclusions
The soil P leaching change point decreased due to land-use conversion from arid agricultural soils to paddy soils, which may lead to higher P leaching risk. Therefore, it is necessary to strengthen the management and control of soil P loss in areas with large-scaled conversion from arid agricultural land to paddy fields.

Graphical Abstract
Heritage and the COVID-19 pandemic: the meaning of visitation
Authors: Dewi Cut , Rofe Matthew , Nichols Julie , Izziah Izziah 
Published: July 2023

AbstractThe onset of the COVID-19 pandemic has impacted global mobility. ‘Lockdowns’ and travel bans have been used as control measures by international governments. Consequently, the ways that we use buildings have also been impacted by these actions. Thus, this paper explores the roles of heritage sites in a post-COVID-19 pandemic society. This research is part of the Urban Heritage and Community Resilience: Conservation, Tourism, and Pandemic project, and it employs methods such as semistructured interviews, participant observations, archival research, and focus group discussions (FGDs). This paper is based on semistructured interviews conducted with one hundred eighteen participants across ten popular heritage sites in Banda Aceh and Aceh Besar, Indonesia. The findings confirm the debated claim in postdisaster studies asserting that some of these Acehnese heritage sites, especially those imbued with religious values, have become places of resilience. Specifically, during the pandemic, these sites have facilitated community resilience by helping people feel closer to God. For practising Acehnese Muslims, prayer at home is culturally acceptable, but praying at the mosque, which is one of the essential heritages of the Acehnese, has contributed to and strengthened the sense of community resilience. Therefore, visitation and participation in heritage sites that include experiencing the sense of place and conducting religious and cultural activities is integral to community resilience.
Identification of parameters and indicators for implementing circularity in the construction industry
Authors: Kazmi Rizwan , Chakraborty Manjari 
Published: July 2023

AbstractThe increase in population, rapid urbanization, the required infrastructure development, the linear development model adopted by the construction stakeholders, and the unaccountability of construction waste have put tremendous stress on existing natural resources. The world has witnessed a situation where resource optimization through mitigation strategies has become significant for sustainable construction. A circular economy keeps the resources in the loop for the longest possible, eliminating waste from the system. This paper attempts to identify the parameters and relevant indicators for bringing circularity to the construction industry. During the research, 144 indicators were identified through a literature review which was followed by a three-round Delphi survey to attain consensus from 30 experts. Finally, after three rounds, 78 indicators were shortlisted, which received maximum consensus among the experts (W = 0.75). Construction stakeholders and decision-makers can use the identified list of indicators to bring circularity to the construction industry.
Using Music as a Tool for Distress Reduction During Cancer Chemotherapy Treatment
Authors: Harper Felicity W.K. , Heath Allison S. , Moore Tanina Foster , Kim Seongho , Heath Elisabeth I. 
Published: July 2023

PURPOSE Music may be an effective therapeutic tool during cancer treatment to improve patient psychological and physical well-being. Current research shows a positive effect of music on psychological outcomes; however, many of these studies lacked significant sample size and rigor in monitoring type of music used and duration of music use during treatment. METHODS Participants (N = 750) in this open-label, multisite, day-based permuted block randomization study were adult patients receiving outpatient chemotherapy infusion. Patients were randomly assigned to either music (listen to music for up to 60 minutes) or control (no music) conditions. Music patients were allowed to self-select an iPod shuffle programmed with up to 500 minutes of music from a single genre (eg, Motown, 60s, 70s, 80s, classical, and country). Outcomes were self-reported change in pain, positive and negative mood, and distress. RESULTS Patients who listened to self-selected music during infusion showed significant benefit in improved positive mood and reduced negative mood and distress (but not pain) from pre- to post-intervention (all two-sample t-tests P < .05). LASSO penalized linear regression models showed a selective benefit for some patients on the basis of relationship ( P = .032) and employment ( P = .029) status with those who were married or widowed and those on disability showing better outcomes. CONCLUSION Music medicine is a low-touch, low-risk, and cost-effective way to manage patients' psychological well-being in the often stressful context of a cancer infusion clinic. Future research should be directed to understanding what other factors may mitigate negative mood states and pain for certain groups during treatment.