bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utilizing 2D-region-based CNNs for automatic dendritic spine detection in 3D live cell imaging
Authors: Vogel Fabian W. , Alipek Sercan , Eppler Jens-Bastian , Osuna-Vargas Pamela , Triesch Jochen , Bissen Diane , Acker-Palmer Amparo , Rumpel Simon , Kaschube Matthias 
Published: November 2023

AbstractDendritic spines are considered a morphological proxy for excitatory synapses, rendering them a target of many different lines of research. Over recent years, it has become possible to simultaneously image large numbers of dendritic spines in 3D volumes of neural tissue. In contrast, currently no automated method for 3D spine detection exists that comes close to the detection performance reached by human experts. However, exploiting such datasets requires new tools for the fully automated detection and analysis of large numbers of spines. Here, we developed an efficient analysis pipeline to detect large numbers of dendritic spines in volumetric fluorescence imaging data acquired by two-photon imaging in vivo. The core of our pipeline is a deep convolutional neural network that was pretrained on a general-purpose image library and then optimized on the spine detection task. This transfer learning approach is data efficient while achieving a high detection precision. To train and validate the model we generated a labeled dataset using five human expert annotators to account for the variability in human spine detection. The pipeline enables fully automated dendritic spine detection reaching a performance slightly below that of the human experts. Our method for spine detection is fast, accurate and robust, and thus well suited for large-scale datasets with thousands of spines. The code is easily applicable to new datasets, achieving high detection performance, even without any retraining or adjustment of model parameters.
Insights on microstructural evolution and capacity fade on diatom $$\hbox {SiO}_2$$ anodes for lithium-ion batteries
Authors: Hua Weicheng , Nylund Inger-Emma , Cova Federico , Svensson Ann Mari , Blanco Maria Valeria 
Published: November 2023

Abstract$$\hbox {SiO}_2$$

SiO
2

is a promising material for developing high-capacity anodes for lithium-ion batteries (LIBs). However, microstructural changes of $$\hbox {SiO}_2$$

SiO
2

anodes at the particle and electrode level upon prolonged cycling remains unclear. In this work, the causes leading to capacity fade on $$\hbox {SiO}_2$$

SiO
2

anodes were investigated and simple strategies to attenuate anode degradation were explored. Nanostructured $$\hbox {SiO}_2$$

SiO
2

from diatomaceous earth was integrated into anodes containing different quantities of conductive carbon in the form of either a conductive additive or a nanometric coating layer. Galvanostatic cycling was conducted for 200 cycles and distinctive trends on capacity fade were identified. A thorough analysis of the anodes at selected cycle numbers was performed using a toolset of characterization techniques, including electrochemical impedance spectroscopy, FIB-SEM cross-sectional analysis and TEM inspections. Significant fragmentation of $$\hbox {SiO}_2$$

SiO
2

particles surface and formation of filigree structures upon cycling are reported for the first time. Morphological changes are accompanied by an increase in impedance and a loss of electroactive surface area. Carbon-coating is found to restrict particle fracture and to increase capacity retention to 66%, compared to 47% for uncoated samples after 200 cycles. Results provide valuable insights to improve cycling stability of $$\hbox {SiO}_2$$

SiO
2

anodes for next-generation LIBs.
Value of radiomics-based two-dimensional ultrasound for diagnosing early diabetic nephropathy
Authors: Su Xuee , Lin Shu , Huang Yinqiong 
Published: November 2023

AbstractDespite efforts to diagnose diabetic nephropathy (DN) using biochemical data or ultrasound imaging separately, a significant gap exists regarding the development of integrated models combining both modalities for enhanced early DN diagnosis. Therefore, we aimed to assess the ability of machine learning models containing two-dimensional ultrasound imaging and biochemical data to diagnose early DN in patients with type 2 diabetes mellitus (T2DM). This retrospective study included 219 patients, divided into a training or test group at an 8:2 ratio. Features were selected using minimum redundancy maximum relevance and random forest-recursive feature elimination. The predictive performance of the models was evaluated using the area under the receiver operating characteristic curve (AUC) for sensitivity, specificity, Matthews Correlation Coefficient, F1 score, and accuracy. K-nearest neighbor, support vector machine, and logistic regression models could diagnose early DN, with AUC values of 0.94, 0.85, and 0.85 in the training cohort and 0.91, 0.84, and 0.84 in the test cohort, respectively. Early DN diagnosing using two-dimensional ultrasound-based radiomics models can potentially revolutionize T2DM patient care by enabling proactive interventions, ultimately improving patient outcomes. Our integrated approach showcases the power of artificial intelligence in medical imaging, enhancing early disease detection strategies with far-reaching applications across medical disciplines.
Thrombocytopenia and venous thromboembolic events after BNT162b2, CoronaVac, ChAdOx1 vaccines and SARS-CoV-2 infection: a self-controlled case series study
Authors: Ab Rahman Norazida , Lim Ming Tsuey , Lee Fei Yee , Wo Wee Kee , Yeoh Hee Sheong , Peariasamy Kalaiarasu M. , Sivasampu Sheamini ,   the SAFECOVAC Study Group, Ramli Azuana , Lee Sing Chet , Choo Sim Mei , Appanan Maheshwara Rao , King Teck Long , Yen Chia How , Anak Jam Emelyne Bani , Mahmud Fatihah , Mohamad Nor Fariz Safhan , Badrul Hisham Muhammad Hazrul , Saharudin Siti Nurhafizah , Ayub Nor Aliya , Sevalingam Raj Kumar , Bahari Rashidah , Ibrahim Nor Nadziroh , Mohd Noor Nurain , Mohamed Nor Lisa , Zainal Abidin Nurul Huda , Wong Hin Seng , Ghazali Siti Nur Akmal , Rozkhaidi Nurul Afifah , Shaduqi Norzubaidatulhikmah , Hossain Hanisah , Lay Jeannette Jieni , Mohamad Nazri Nor Azizah 
Published: November 2023

AbstractThis study assessed the association between COVID-19 vaccines, SARS-CoV-2 infection and the risk of thrombocytopenia and venous thromboembolism (VTE). This self-controlled case series study used hospital records between 1st February 2021 and 28th February 2022 linked to the national immunisation registry and COVID-19 surveillance data in Malaysia. Conditional Poisson regression was used to estimate incidence rate ratios (IRR) of events in the risk period (day 1–21 post-exposure) relative to control period with the corresponding 95% confidence interval (CI) adjusted for calendar period. We found no significant increased risk of thrombocytopenia in 1–21 days following BNT162b2, CoronaVac and ChAdOx1 vaccines while the risk was increased following SARS-CoV-2 infection (IRR 15.52, 95% CI 13.38–18.00). Similarly, vaccination with BNT162b2, CoronaVac, or ChAdOx1 was not associated with an increased risk of VTE during the 1–21 days risk period. SARS-CoV-2 infection was associated with increased risk of VTE (IRR 39.84, 95% CI 27.45–32.44). Our findings showed low event rates of thrombocytopenia and VTE following booster vaccination with comparable safety profiles between those who received homologous and heterologous booster combinations. Our findings showed the risk of thrombocytopenia and VTE was not increased after COVID-19 vaccination while the risks were substantially higher after SARS-CoV-2 infection.
Diagnostic role and immune correlates of programmed cell death-related genes in hepatocellular carcinoma
Authors: He Zhanao , Zhang Jie , Huang Wukui 
Published: November 2023

AbstractProgrammed cell death (PCD) is thought to have multiple roles in tumors. Here, the roles of PCD-related genes were comprehensively analyzed to evaluate their values in hepatocellular carcinoma (HCC) diagnosis and prognosis. Gene expression and single-cell data of HCC patients, and PCD-related genes were collected from public databases. The diagnostic and prognostic roles of differentially expressed PCD-related genes in HCC were explored by univariate and multivariate Cox regression analyses. Single-cell data were further analyzed for the immune cells and expression of feature genes. Finally, we evaluated the expression of genes by quantitative real-time polymerase chain reaction and Western blot, and the proportion of immune cells was detected by flow cytometry in HCC samples. We obtained 52 differentially expressed PCD-related genes in HCC, based on which the consensus clustering analysis cluster 2 was found to have a worse prognosis than cluster 1. Then 10 feature genes were identified using LASSO analysis, and programmed cell death index (PCDI) was calculated to divided HCC patients into high-PCDI and low-PCDI groups. Worse prognosis was observed in high-PCDI group. Cox regression analysis showed that PCDI is an independent prognostic risk factor for HCC patients. Additionally, SERPINE1 and G6PD of feature genes significantly affect patient survival. Macrophages and Tregs were significantly positively correlated with PCDI. G6PD mainly expressed in macrophages, SERPINE1 mainly expressed in fibroblast. The experimental results confirmed the high expression of SERPINE1 and G6PD in HCC compared with the control, and the infiltration level of macrophages and Treg in HCC was also obviously elevated. PCDI may be a new predictor for the diagnosis of patients with HCC. The association of SERPINE1 and G6PD with the immune environment will provide new clues for HCC therapy.
Housing conditions affect enterocyte death mode and turnover rate in mouse small intestine
Authors: Matsuoka Yosuke , Tsujimoto Yoshihide 
Published: November 2023

AbstractSmall intestinal enterocytes are continuously renewed. Shedding/death of enterocytes involves receptor-interacting protein kinase 1 (RIPK1)-dependent (but RIPK3-independent) necrotic death, but the regulatory mechanism of the processes is not fully understood. Here, we show that mouse housing conditions, such as the type of bedding material and the presence or absence of a Shepherd Shack, affect enterocyte turnover rate and determine whether enterocyte shedding/death is RIPK1-independent or -dependent. Mice housed with ALPHA-dri (αDri, hard paper chip) bedding material without a Shepherd Shack had a higher, largely RIPK1-dependent enterocyte turnover rate and higher blood corticosterone levels, suggesting the involvement of minor stress, whereas mice housed with αDri plus a Shepherd Shack or with Soft Chip had a lower, RIPK1-independent turnover rate and lower blood corticosterone levels. Corticosterone administration to a small intestine culture derived from mice housed with αDri plus a Shepherd Shack or with Soft Chip increased enterocyte shedding/death and turnover. By using kinase inhibitors and knockout mice, we showed that the switch from RIPK1-independent to RIPK1-dependent enterocyte shedding/death and turnover involves suppression of TANK-binding kinase 1. Our results demonstrate that housing conditions may cause minor stress, which alters the mode of enterocyte shedding/death and enterocyte turnover rate in mice.
Sexual dysfunction in women with breast cancer of Northeast Brazil: a retrospective longitudinal study
Authors: Sousa Rodrigues Guedes Thais , Barbosa Otoni Gonçalves Guedes Marcello , Mikael Lopes Johnnatas , de Castro Santana Rebeca , Borba de Vasconcelos Jamily , Regina de Medeiros Eva , Leandro da Cunha Vitor , Almeida Gomes Dantas Amanda , Jerez-Roig Javier , Bezerra de Souza Dyego Leandro 
Published: November 2023

AbstractBreast cancer treatment leads to physical and psychological changes. The aim of this study was to analyze the incidence of sexual dysfunction and its risk factors in women diagnosed with breast cancer. This retrospective cohort study included women diagnosed and treated for breast cancer (exposed group, n = 90) and healthy women (non-exposed group, n = 93). Data were collected from February 2019 to October 2021 in the state of Rio Grande do Norte (Northeast Brazil), from medical records and using the Female Sexual Function Index (FSFI) questionnaire. Data were collected from medical records and using the Female Sexual Function Index (FSFI) questionnaire. Primary outcomes were analyzed using binary logistic regression. The Mann–Whitney test was used to analyze FSFI domains between groups. The exposed group had a 74% incidence of sexual dysfunction and 3.9 times increased chances of having sexual dysfunction compared with the non-exposed group (OR 3.9, CI 1.8 to 8.2, p < 0.001). Presence of comorbidities increased the chances of sexual dysfunction by 2.5 times (OR 2.5, CI 1.2 to 4.9, p = 0.009). Women diagnosed and treated for breast cancer had a higher incidence of sexual dysfunction than healthy women. Furthermore, comorbidities also increased the chances of sexual dysfunction regardless of exposure to breast cancer.
Prevalence and factors associated with possible cases of familial hypercholesterolemia in Brazilian adults: a cross-sectional study
Authors: de Sá Ana Carolina Micheletti Gomide Nogu , Gomes Crizian Saar , Prates Elton Junio Sady , Brant Luisa Campos Caldeira , Malta Deborah Carvalho 
Published: November 2023

AbstractThis study aimed to estimate the prevalence of possible cases of FH and analyze associated factors in the adult Brazilian population. Cross-sectional study with laboratory data from the Brazilian National Health Survey, with 8521 participants. Possible cases of FH were defined according to the Dutch Lipid Clinic Network criteria. The prevalence and 95% confidence intervals (95% CI) of possible cases of FH were estimated according to sociodemographic variables, lifestyle, diabetes, hypertension, altered tests, treatment and self-rated health. Logistic regression was used to analyze the associations. The prevalence of possible cases of FH was 0.96%, higher in women, between 45 and 59 years, white race/skin color and others, less education, people with diabetes, hypertension and total cholesterol ≥ 310 mg/dL. The presence of FH was positively associated with regular self-rated health (OR 1.96; 95% CI 0.99–3.84), poor/very poor (OR 3.02; 95% CI 1.30–7.03) and negatively with black race/skin color (OR 0.10; 95% CI 0.02–0.46) and complete elementary school, incomplete high school (OR 0.47; 95% CI 0.23–0.98) and complete high school and more (OR 0.45; 95% CI 0.21–0.95). FH affects 1:104 Brazilian adults, these findings contribute to understanding the burden of disease in Brazil. Due to the scarcity of studies on FH in low- and middle-income countries, further studies are desirable.
The effect of speech pathology on automatic speaker verification: a large-scale study
Authors: Tayebi Arasteh Soroosh , Weise Tobias , Schuster Maria , Noeth Elmar , Maier Andreas , Yang Seung Hee 
Published: November 2023

AbstractNavigating the challenges of data-driven speech processing, one of the primary hurdles is accessing reliable pathological speech data. While public datasets appear to offer solutions, they come with inherent risks of potential unintended exposure of patient health information via re-identification attacks. Using a comprehensive real-world pathological speech corpus, with over n$$=$$
=
3800 test subjects spanning various age groups and speech disorders, we employed a deep-learning-driven automatic speaker verification (ASV) approach. This resulted in a notable mean equal error rate (EER) of $$0.89 \pm 0.06 \%$$

0.89
±
0.06
%

, outstripping traditional benchmarks. Our comprehensive assessments demonstrate that pathological speech overall faces heightened privacy breach risks compared to healthy speech. Specifically, adults with dysphonia are at heightened re-identification risks, whereas conditions like dysarthria yield results comparable to those of healthy speakers. Crucially, speech intelligibility does not influence the ASV system’s performance metrics. In pediatric cases, particularly those with cleft lip and palate, the recording environment plays a decisive role in re-identification. Merging data across pathological types led to a marked EER decrease, suggesting the potential benefits of pathological diversity in ASV, accompanied by a logarithmic boost in ASV effectiveness. In essence, this research sheds light on the dynamics between pathological speech and speaker verification, emphasizing its crucial role in safeguarding patient confidentiality in our increasingly digitized healthcare era.
Prevalence of peripheral retinal findings in retinal patients using ultra-widefield pseudocolor fundus imaging
Authors: Sharma Paripoorna , Shareef Ihab , Kalaw Fritz Gerald P. , Kako Rasha Nabil , Lin Andrew , Alex Varsha , Nudleman Eric , Walker Evan H. , Borooah Shyamanga 
Published: November 2023

AbstractUltra-widefield retinal imaging is increasingly used in ophthalmology and optometry practices to image patients identifying peripheral abnormalities. However, the clinical relevance of these peripheral retinal abnormalities is unclear. This cross-sectional study aims to firstly validate a new grading system, secondly, assess the prevalence of peripheral retinal abnormalities in retinal patients, and finally understand how peripheral findings may associate with retinal disease. Ultra-widefield pseudocolor fundus images were taken from the eyes of clinic patients. Demographic data and clinical diagnosis for each patient was noted. The grading system was validated using masked retinal specialists. Logistic regression identified associations between retinal disease and peripheral retinal findings. Using the grading system, inter-observer agreement was 76.1% with Cohen’s Kappa coefficient 0.542 (p < 0.0001) and the test–retest agreement was 95.1% with Kappa 0.677(p < 0.0001). 971 images were included, with 625 eyes (64.4%) having peripheral abnormalities. Peripheral drusen was the most common abnormality (n = 221, 22.76%) and correlated with age-related macular degeneration (p < 0.001). Novel correlations were also identified between diabetic retinopathy and retinal pigmentation as well as pigmentary degeneration. This study provides a validated system for identifying peripheral abnormalities and adds to literature highlighting peripheral retinal associations with retinal disease which would benefit from further study.
A new technique for the analysis of metabolic pathways of cytidine analogues and cytidine deaminase activities in cells
Authors: Ligasová Anna , Piskláková Barbora , Friedecký David , Koberna Karel 
Published: November 2023

AbstractDeoxycytidine analogues (dCas) are widely used for the treatment of malignant diseases. They are commonly inactivated by cytidine deaminase (CDD), or by deoxycytidine monophosphate deaminase (dCMP deaminase). Additional metabolic pathways, such as phosphorylation, can substantially contribute to their (in)activation. Here, a new technique for the analysis of these pathways in cells is described. It is based on the use of 5-ethynyl 2′-deoxycytidine (EdC) and its conversion to 5-ethynyl 2′-deoxyuridine (EdU). Its use was tested for the estimation of the role of CDD and dCMP deaminase in five cancer and four non-cancer cell lines. The technique provides the possibility to address the aggregated impact of cytidine transporters, CDD, dCMP deaminase, and deoxycytidine kinase on EdC metabolism. Using this technique, we developed a quick and cheap method for the identification of cell lines exhibiting a lack of CDD activity. The data showed that in contrast to the cancer cells, all the non-cancer cells used in the study exhibited low, if any, CDD content and their cytidine deaminase activity can be exclusively attributed to dCMP deaminase. The technique also confirmed the importance of deoxycytidine kinase for dCas metabolism and indicated that dCMP deaminase can be fundamental in dCas deamination as well as CDD. Moreover, the described technique provides the possibility to perform the simultaneous testing of cytotoxicity and DNA replication activity.
Sugar responsiveness could determine foraging patterns in yellowjackets
Authors: Masciocchi Maité , Mattiacci Analía , Villacide José M. , Buteler Micaela , Porrino Agustina P. , Martínez Andrés S. 
Published: November 2023

AbstractSympatric-related species often exhibit resource partitioning. This can occur through different mechanisms, such as behavioral, morphological, and sensory variations, leading to qualitative, temporal, or spatial differences in resource exploitation, such as consuming different types of food. Sensory-based niche partitioning could be the underlying mechanism through which closely related species effectively reduce niche overlap. Here we ask whether variations in sensory responses to carbohydrates could reflect differences in the foraging patterns of two Vespula species present in Patagonia. For this, we established (i) the response thresholds toward carbohydrate solutions of foraging V. germanica and V. vulgaris in the laboratory, (ii) the sugar concentration of foraged carbohydrates in the field, and (iii) possible effects of incoming sugar concentration and performance at individual and colony levels. Results indicate a higher sucrose response threshold in V. germanica than V. vulgaris. Field results indicate that higher carbohydrate concentrations foraged by V. germanica, with 57% of V. germanica foragers returning with concentrations above 50% w/w, while only 23% of V. vulgaris foragers did so. These differences in sucrose sensitivity and foraging patterns positively correlate with colony size, irrespective of the species. Our results suggest that competition could be reduced in these closely related invasive social wasp species through sensory differences in their sugar perception levels, which would lead to them foraging different carbohydrate sources. This study suggests that sensory niche partitioning could promote species coexistence in these social wasps.
Generation and influence of eccentric ideas on social networks
Authors: Pandey Sriniwas , Cao Yiding , Dong Yingjun , Kim Minjun , MacLaren Neil G. , Dionne Shelley D. , Yammarino Francis J. , Sayama Hiroki 
Published: November 2023

AbstractStudying extreme ideas in routine choices and discussions is of utmost importance to understand the increasing polarization in society. In this study, we focus on understanding the generation and influence of extreme ideas in routine conversations which we label “eccentric” ideas. The eccentricity of any idea is defined as the deviation of that idea from the norm of the social neighborhood. We collected and analyzed data from two sources of different nature: public social media and online experiments in a controlled environment. We compared the popularity of ideas against their eccentricity to understand individuals’ fascination towards eccentricity. We found that more eccentric ideas have a higher probability of getting a greater number of “likes”. Additionally, we demonstrate that the social neighborhood of an individual conceals eccentricity changes in one’s own opinions and facilitates generation of eccentric ideas at a collective level.