bluuebunny/crossref_metadata_2025_split huggingface dataset:
Weak coupling of neurons enables very high-frequency and ultra-fast oscillations through the interplay of synchronized phase shifts
Authors: Přibylová Lenka , Ševčík Jan , Eclerová Veronika , Klimeš Petr , Brázdil Milan , Meijer Hil G. E. 
Published: December 2023

Abstract
Recently, in the past decade, high-frequency oscillations (HFOs), very high-frequency oscillations (VHFOs), and ultra-fast oscillations (UFOs) were reported in epileptic patients with drug-resistant epilepsy. However, to this day, the physiological origin of these events has yet to be understood. Our study establishes a mathematical framework based on bifurcation theory for investigating the occurrence of VHFOs and UFOs in depth EEG signals of patients with focal epilepsy, focusing on the potential role of reduced connection strength between neurons in an epileptic focus. We demonstrate that synchronization of a weakly coupled network can generate very and ultra high-frequency signals detectable by nearby microelectrodes. In particular, we show that a bistability region enables the persistence of phase-shift synchronized clusters of neurons. This phenomenon is observed for different hippocampal neuron models, including Morris–Lecar, Destexhe–Paré, and an interneuron model. The mechanism seems to be robust for small coupling, and it also persists with random noise affecting the external current. Our findings suggest that weakened neuronal connections could contribute to the production of oscillations with frequencies above 1000 Hz, which could advance our understanding of epilepsy pathology and potentially improve treatment strategies. However, further exploration of various coupling types and complex network models is needed.
Improving Medium-Range Ensemble Weather Forecasts with Hierarchical Ensemble Transformers
Authors: Bouallègue Zied Ben , Weyn Jonathan A. , Clare Mariana C. A. , Dramsch Jesper , Dueben Peter , Chantry Matthew 
Published: December 2023

Abstract
Statistical postprocessing of global ensemble weather forecasts is revisited by leveraging recent developments in machine learning. Verification of past forecasts is exploited to learn systematic deficiencies of numerical weather predictions in order to boost postprocessed forecast performance. Here, we introduce postprocessing of ensembles with transformers (PoET), a postprocessing approach based on hierarchical transformers. PoET has two major characteristics: 1) the postprocessing is applied directly to the ensemble members rather than to a predictive distribution or a functional of it, and 2) the method is ensemble-size agnostic in the sense that the number of ensemble members in training and inference mode can differ. The PoET output is a set of calibrated members that has the same size as the original ensemble but with improved reliability. Performance assessments show that PoET can bring up to 20% improvement in skill globally for 2-m temperature and 2% for precipitation forecasts and outperforms the simpler statistical member-by-member method, used here as a competitive benchmark. PoET is also applied to the ENS-10 benchmark dataset for ensemble postprocessing and provides better results when compared to other deep learning solutions that are evaluated for most parameters. Furthermore, because each ensemble member is calibrated separately, downstream applications should directly benefit from the improvement made on the ensemble forecast with postprocessing.
Exploring the Differences in Kinetic Energy Spectra between the NCEP FNL and ERA5 Datasets
Authors: Li Zongheng , Peng Jun , Zhang Lifeng , Guan Jiping 
Published: December 2023

Abstract
Two global atmospheric circulation datasets (ERA5 and NCEP FNL) with horizontal resolutions of 0.25° × 0.25° are investigated in terms of kinetic energy (KE) spectra at 200 hPa (roughly between 11 and 12 km). The horizontal KE (HKE) in NCEP FNL is larger and flatter than that in ERA5 at subsynoptic scales and mesoscales. Restoring the energy of this wavenumber range to the physical space shows that the HKE in NCEP FNL is larger than that in ERA5 over most areas but smaller mainly in the Indo-Pacific warm pool. The spectral budgets show that at these scales, the positive contribution from net vertical flux in ERA5 is stronger than that in NCEP FNL, while the negative contribution from available potential energy (APE) conversion is smaller; assuming that the atmosphere is in a quasi-stationary state, more dissipation is found in ERA5 than in NCEP FNL, which should be responsible for the HKE spectrum in ERA5 to be steeper and weaker than that in NCEP FNL. Our formulation shows that the APE conversion and net vertical flux are related to the pressure vertical velocity (PVV). The APE conversion and net vertical flux differences between the two datasets, like the PVV difference, are mainly from the tropical region. At large scales, the vertical motion in ERA5 is larger than that in NCEP FNL. The amplitude differences of the PVV spectra between two datasets are consistent with those of the large-scale precipitation spectra associated with microphysics parameterizations. These results support that vertical motion is a key dynamical factor explaining energy discrepancies at mesoscales.

Significance Statement
The atmospheric kinetic energy spectrum reflects energy distribution characteristics in atmospheric motion at different scales. According to the Helmholtz decomposition, the horizontal wind field can be decomposed into two parts: rotational wind field and divergent wind field. We explore the dynamical causes of the atmospheric energy spectra differences among different datasets from the perspective of rotational and divergent components of motion. Our results reveal that the differences in energy spectra and their energy budget at scales below a few hundred kilometers are relatively significant in tropical regions and are closely related to vertical motion. A better understanding of the differences in kinetic energy spectra will contribute to the improvement of atmospheric models.
Discovery of a non-canonical GRHL1 binding site using deep convolutional and recurrent neural networks
Authors: Proft Sebastian , Leiz Janna , Heinemann Udo , Seelow Dominik , Schmidt-Ott Kai M. , Rutkiewicz Maria 
Published: December 2023

Abstract
Background
Transcription factors regulate gene expression by binding to transcription factor binding sites (TFBSs). Most models for predicting TFBSs are based on position weight matrices (PWMs), which require a specific motif to be present in the DNA sequence and do not consider interdependencies of nucleotides. Novel approaches such as Transcription Factor Flexible Models or recurrent neural networks consequently provide higher accuracies. However, it is unclear whether such approaches can uncover novel non-canonical, hitherto unexpected TFBSs relevant to human transcriptional regulation.

Results
In this study, we trained a convolutional recurrent neural network with HT-SELEX data for GRHL1 binding and applied it to a set of GRHL1 binding sites obtained from ChIP-Seq experiments from human cells. We identified 46 non-canonical GRHL1 binding sites, which were not found by a conventional PWM approach. Unexpectedly, some of the newly predicted binding sequences lacked the CNNG core motif, so far considered obligatory for GRHL1 binding. Using isothermal titration calorimetry, we experimentally confirmed binding between the GRHL1-DNA binding domain and predicted GRHL1 binding sites, including a non-canonical GRHL1 binding site. Mutagenesis of individual nucleotides revealed a correlation between predicted binding strength and experimentally validated binding affinity across representative sequences. This correlation was neither observed with a PWM-based nor another deep learning approach.

Conclusions
Our results show that convolutional recurrent neural networks may uncover unanticipated binding sites and facilitate quantitative transcription factor binding predictions.
Exploring the challenges to using telecardiology as perceived by pre-hospital emergency care personnel: a qualitative study
Authors: Bijani Mostafa , Abedi Saeed , Zare Azam , Tavacol Ziba , Abadi Fozieh , Alkamel Abdulhakim 
Published: December 2023

AbstractBackgroundToday, using the medical technology of telecardiology, as part of advanced medical services, plays an essential role in providing care to cardiac patients in life-threatening conditions who need emergency care. However, pre-hospital emergency care personnel are faced with certain challenges in using telecardiology, with adverse effects on their performance. Therefore, the present study aimed to investigate the challenges to using telecardiology as viewed by pre-hospital emergency care personnel in Southern Iran.MethodsThe present study is a qualitative work of research with a content analysis approach. Selected using purposeful sampling, 19 pre-hospital emergency care personnel were interviewed on a semi-structured, personal, in-depth basis. The qualitative data obtained were analyzed using the Graneheim and Lundman’s conventional content analysis approach (2004).ResultsBased on the qualitative data analysis, 3 themes and 8 subthemes were obtained. The three main themes included professional barriers (lack of clinical knowledge of telecardiology, lack of clinical skill in telecardiology, violation of patients’ privacy, lack of clinical guidelines on telecardiology), medical equipment and telecommunication barriers (poor reception and ineffective means of communication, low charge on the battery of tele-electrocardiogram machines), and organizational management barriers (serious lack of cardiologists available for medical counseling and lack of continual personal development of the telecardiology personnel).ConclusionSenior managers in pre-hospital emergency care services are recommended to use the results of this study to identify the influential factors in using telecardiology and take the necessary measures to eliminate the existing barriers toward making optimal use of telemedicine, thereby improving the quality of care provided for cardiac patients.
Prevalence of frailty and associated factors in older adults seeking care at Swedish emergency departments
Authors: Källberg Ann-Sofie , Berg Lena M , Skogli Sara , Bjurbo Charlotte , Muntlin Åsa , Ehrenberg Anna 
Published: December 2023

Abstract
Background
Internationally, prolonged length of stay for older adults in the emergency department (ED) is associated with increased risk of in-hospital adverse events. In Sweden patients 65 years and older account for 35% of emergency visits, and according to consensus from an international expert group, all persons over 70 should be screened for frailty. This is not routinely done in Swedish EDs, and therefore, knowledge about prevalence, characteristics and clinical outcomes associated with frailty is limited.

Aim
To describe the prevalence of frailty and associated factors in older adults seeking care at Swedish EDs.

Methods
The study has a cross-sectional design. Data was collected at three hospital-based EDs, varying in level and size of setting, for one month. Patients age 70 and older presenting at the EDs and agreed to participate were screened for frailty using the FRail Elderly Support researcH group (FRESH) instrument. Data were analysed using descriptive statistics to assess the distribution of patient characteristics and clinical outcomes. Multivariate logistic regression was used to model the association between frailty and demographic characteristics, and Cox regression was used to model the association between frailty and clinical outcomes.

Results
A total of 3101 patients were eligible for inclusion; of these, 984 (32%) were included and screened for frailty. Of the final sample, 57.3% were assessed as frail. Characteristics significantly associated with frailty were living in a residential care facility, age (> 80 years), being a woman and arriving with emergency medical service (EMS). There was a significant association between frailty and admittance to in-hospital care.

Conclusion
Our study shows a high prevalence of frailty in older people. Factors associated with frailty were living in a residential care facility, age ≥ 80 years, being a woman and arriving with EMS to the ED and being admitted to in-hospital care. Frailty screening should be incorporated in the triage system to identify frail patients who need tailored interventions. More studies using the FRESH instrument are needed to further confirm our findings and to develop the methods for screening for frailty in the ED.
Threshold growth has a limited role in differentiating hepatocellular carcinoma from other focal hepatic lesions
Authors: Lyu Rong , Wang Di , Hu Weijuan , Gao Zhongsong , Yu Changlu , Wang Jiao , Li Mingge , Jia Kefeng 
Published: December 2023

Abstract
Background and Objective
The role of threshold growth, as one of the major features (MFs) of hepatocellular carcinoma (HCC) in the Liver Imaging Reporting and Data System (LI-RADS) is inconsistent. This study evaluated the LI-RADS diagnostic performance for HCC when threshold growth was removed or replaced by independently significant ancillary features (AFs).

Materials and Methods
This retrospective institutional review board-approved study included patients with a high HCC risk who underwent gadoxetic acid-enhanced MRIs. The MRI findings were consistent with pathologically proven focal hepatic observations. The pathological results were used as the gold standard reference. The sizes of the lesions with and without threshold growth were compared. Univariate and multivariate logistic regression analyses were used to confirm the independently significant AFs of HCC. In addition to the classification criteria of LI-RADS version 2018 (LI-RADS v2018), the lesions were also reclassified according to the following two schemes: scheme A, using all MFs except threshold growth, with threshold growth feature treated as an AF favouring malignancy; and scheme B, replacing the threshold growth feature with independently significant AFs and treated them as new MFs. The diagnostic performance of the above two LI-RADS schemes for HCC was calculated and compared with that of LI-RADS v2018.

Results
A total of 379 patients and 426 observations were included. Threshold growth was not an independent significant MF for HCC diagnosis [odds ratio (OR), 1.0; 95% confidence interval (CI), 0.6–1.8; p = 0.927]. For all three groups of observations (HCCs, non-HCC malignancies, and benign lesions), the mean size with threshold growth was smaller than that without threshold growth (all p < 0.05). The nodule-in-nodule feature was an independent significant AF (OR, 9.8; 95% CI, 1.2–79.3; p = 0.032) and was used to replace threshold growth as a new MF in scheme B. The sensitivities of schemes A and B were 74.0% and 75.6%, respectively. The specificities of schemes A and B were the same (88.6%). None of the diagnostic performance metrics for HCC (sensitivity, specificity, accuracy) of either scheme A or B was significantly different from those of LI-RADS v2018 (all p > 0.05).

Conclusion
Threshold growth is not an independently significant MF for HCC diagnosis. The diagnostic performance of LI-RADS for HCC is not affected regardless of whether threshold growth is removed from the list of MFs or replaced with an independently significant and more HCC-specific AF, which is the nodule-in-nodule feature.
Trends in amount of use to upper limb function in patients with subacute stroke: a cross-sectional study using segmental regression analysis
Authors: Hirayama Koichiro , Matsuda Marina , Teruya Moe , Fuchigami Takeshi , Morioka Shu 
Published: December 2023

Abstract
Background
Hemiparesis affects approximately 33–80% of patients with stroke, and a quarter of these individuals experience difficulty with the voluntary use of their paretic upper limb for performing activities of daily living within five years of stroke onset. Therefore, assessing upper limb functionality and use after a stroke is crucial. The Fugl-Meyer Assessment (FMA) and the Motor Activity Log (MAL) are the two most widely used methods for assessing post-stroke paretic upper limb. While previous research has shown a strong correlation between the FMA of Upper Extremity (FMA-UE) and the MAL scores, to date, no study has investigated the differences in the characteristics and trends of upper extremity usage frequency in the FMA-UE. This study aimed to statistically categorize the FMA-UE scores using segmental regression analysis and identify disparities in the trends of paretic upper extremity utilization frequency in MAL.

Methods
Patients with first-episode subacute stroke were chosen for the cohort study. The primary assessments used were FMA-UE and MAL Amount of Use (MAL-A); age, gender, and time since onset served as secondary assessments. Segmental regression analysis was used, with FMA-UE as the independent variable and MAL-A as the dependent variable. R2 values were calculated using linear and polynomial regression on binary values, and the coefficients of determination were compared using segmental regression analysis.

Results
The study included 203 participants with a mean age of 70.1 ± 13.1 years; 113 were male and 90 female. The mean time since onset was 29.2 ± 14.8 days, the mean FMA-UE score was 43.6 ± 22.3 points, and the mean MAL-A score was 2.3 ± 2.0 points. The segmental regression analysis revealed that the inflection point for FMA-UE was 45.3 points, and the slope of the regression line underwent a transformation before and after the inflection point.

Conclusions
This study indicates that the trend in the amount of use of paretic upper limb utilization changes around inflection point 45 in the FMA-UE. These findings could be useful for designing rehabilitation strategies to improve paretic upper limb utilization by increasing exercise duration in patients with subacute stroke.
Abnormal alterations of regional spontaneous neuronal activity and functional connectivity in insomnia patients with difficulty falling asleep: a resting-state fMRI study
Authors: Jiang Tongfei , Yin Xuejiao , Zhu Liying , Jia Weilin , Tan Zhongjian , Li Bin , Guo Jing 
Published: December 2023

Abstract
Background
Insomnia disorder (ID) seriously affects people’s daily life. Difficulty falling asleep is the most commonly reported complaint in patients with ID. However, the mechanism of prolonged sleep latency (SL) is still obscure. The aim of our present study was to investigate the relationship between prolonged SL and alterations in spontaneous neural activity and brain functional connectivity (FC) in ID patients using functional magnetic resonance imaging (fMRI).

Methods
A total of 52 insomniacs with difficulty falling asleep and 30 matched healthy controls (HCs) underwent resting-state fMRI. The amplitude of low-frequency fluctuation (ALFF) was measured and group differences were compared. The peak areas with significantly different ALFF values were identified as the seed regions to calculate FC to the whole brain. SL was assessed by a wrist actigraphy device in ID patients. The Pittsburgh Sleep Quality Index (PSQI), Hamilton Anxiety Rating Scale (HAMA), and Hyperarousal Scale (HAS) were evaluated in both ID patients and HCs. Finally, correlation analyses were performed between the clinical features and FC/ALFF values.

Results
ID patients showed higher PSQI, HAMA, HAS scores than HCs. The functional MRI results indicated increased ALFF value in the left insula and right amygdala and decreased ALFF value in the right superior parietal lobe (SPL) in ID patients. The seed-based FC analysis demonstrated increased FC between the left insula and the bilateral precentral gyrus and FC between the right amygdala and the left posterior cingulate cortex (PCC) in patients with ID. Correlation analysis indicated that the increased FC value of the right amygdala-left PCC was positively correlated with SL measured by actigraphy.

Conclusion
This study revealed abnormal regional spontaneous fluctuations in the right amygdala, left insula, and right SPL, as well as increased FC in the left insula-precentral and right amygdala-left PCC. Moreover, the prolonged SL was positively correlated with the abnormal FC in the right amygdala-left PCC in ID patients. The current study showed the correlation between prolonged SL and the abnormal function of emotion-related brain regions in ID patients, which may contribute to a better understanding of the neural mechanisms underlying difficulty falling asleep in patients with ID.

Clinical Trial Registration
http://www.chictr.org.cn., ChiCTR1800015282. Registered on 20th March 2018.
Congenital herpes simplex with ophthalmic and multisystem features: a case report
Authors: Pereira Samuel Montenegro , Lima Rian Vilar , Muniz Maria Carolina Rocha , Araújo Marcus Breno Farias , de Moraes Ferreira Júnior Luiz , de Queiroz Sales Martins Juliana Tiburtino , Luz Cláudia Faustino Coelho , Cid David Antônio Camelo , da Rocha Lucena Daniel 
Published: December 2023

Abstract
Background
Neonatal herpes simplex virus (HSV) infection is rare and has significant morbimortality rates. Approximately 85% of newborns are infected intrapartum, and risk factors for mother-to-child transmission include vaginal delivery, primary maternal infection, and prolonged rupture of membranes. Neonatal HSV can manifest with isolated mucocutaneous lesions, neurological involvement, or disseminated disease. In general, herpetic infection can cause blepharoconjunctivitis or keratitis. We report a rare case of congenital herpes with ophthalmologic manifestations and multisystemic involvement.

Case presentation
A preterm infant, born at 32 weeks and 2 days, with presumed neonatal infection developed intestinal and respiratory complications, as well as hyperemic lesions on the left nostril and oral mucosa. An ophthalmological assessment was requested and brought up the suspicion of HSV infection, indicating empirical treatment with endovenous acyclovir. Later, a new ocular examination was suggestive of panuveitis. Afterward, serum IgM antibodies to HSV-1 and HSV-2 were positive. Proper antiviral therapy led to an improvement in the condition.

Discussion
Neonatal herpes is associated with a high risk of persistent skin lesions, long-term neurological disability and other lasting sequelae. It is essential to consider HSV infection in cases of neonatal conjunctivitis, especially in patients with an epithelial defect and no improvement after initial treatment with topical or systemic antibiotics.

Conclusions
In the management of neonatal HSV, early diagnosis is essential for the timely initiation of antiviral therapy. Our report highlights that ocular assessment can be crucial in the correct diagnostic investigation of this condition.