bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine-learning predicts time-series prognosis factors in metastatic prostate cancer patients treated with androgen deprivation therapy
Authors: Saito Shinpei , Sakamoto Shinichi , Higuchi Kosuke , Sato Kodai , Zhao Xue , Wakai Ken , Kanesaka Manato , Kamada Shuhei , Takeuchi Nobuyoshi , Sazuka Tomokazu , Imamura Yusuke , Anzai Naohiko , Ichikawa Tomohiko , Kawakami Eiryo 
Published: April 2023

AbstractMachine learning technology is expected to support diagnosis and prognosis prediction in medicine. We used machine learning to construct a new prognostic prediction model for prostate cancer patients based on longitudinal data obtained from age at diagnosis, peripheral blood and urine tests of 340 prostate cancer patients. Random survival forest (RSF) and survival tree were used for machine learning. In the time-series prognostic prediction model for metastatic prostate cancer patients, the RSF model showed better prediction accuracy than the conventional Cox proportional hazards model for almost all time periods of progression-free survival (PFS), overall survival (OS) and cancer-specific survival (CSS). Based on the RSF model, we created a clinically applicable prognostic prediction model using survival trees for OS and CSS by combining the values of lactate dehydrogenase (LDH) before starting treatment and alkaline phosphatase (ALP) at 120 days after treatment. Machine learning provides useful information for predicting the prognosis of metastatic prostate cancer prior to treatment intervention by considering the nonlinear and combined impacts of multiple features. The addition of data after the start of treatment would allow for more precise prognostic risk assessment of patients and would be beneficial for subsequent treatment selection.
Resting-state functional connectivity disruption between the left and right pallidum as a biomarker for subthreshold depression
Authors: Sato Yosuke , Okada Go , Yokoyama Satoshi , Ichikawa Naho , Takamura Masahiro , Mitsuyama Yuki , Shimizu Ayaka , Itai Eri , Shinzato Hotaka , Kawato Mitsuo , Yahata Noriaki , Okamoto Yasumasa 
Published: April 2023

AbstractAlthough the identification of late adolescents with subthreshold depression (StD) may provide a basis for developing effective interventions that could lead to a reduction in the prevalence of StD and prevent the development of major depressive disorder, knowledge about the neural basis of StD remains limited. The purpose of this study was to develop a generalizable classifier for StD and to shed light on the underlying neural mechanisms of StD in late adolescents. Resting-state functional magnetic resonance imaging data of 91 individuals (30 StD subjects, 61 healthy controls) were included to build an StD classifier, and eight functional connections were selected by using the combination of two machine learning algorithms. We applied this biomarker to an independent cohort (n = 43) and confirmed that it showed generalization performance (area under the curve = 0.84/0.75 for the training/test datasets). Moreover, the most important functional connection was between the left and right pallidum, which may be related to clinically important dysfunctions in subjects with StD such as anhedonia and hyposensitivity to rewards. Investigation of whether modulation of the identified functional connections can be an effective treatment for StD may be an important topic of future research.
Predicting work disability among people with chronic conditions: a prospective cohort study
Authors: Nyberg Solja T. , Airaksinen Jaakko , Pentti Jaana , Ervasti Jenni , Jokela Markus , Vahtera Jussi , Virtanen Marianna , Elovainio Marko , Batty G. David , Kivimäki Mika 
Published: April 2023

AbstractFew risk prediction scores are available to identify people at increased risk of work disability, particularly for those with an existing morbidity. We examined the predictive performance of disability risk scores for employees with chronic disease. We used prospective data from 88,521 employed participants (mean age 43.1) in the Finnish Public Sector Study including people with chronic disorders: musculoskeletal disorder, depression, migraine, respiratory disease, hypertension, cancer, coronary heart disease, diabetes, comorbid depression and cardiometabolic disease. A total of 105 predictors were assessed at baseline. During a mean follow-up of 8.6 years, 6836 (7.7%) participants were granted a disability pension. C-statistics for the 8-item Finnish Institute of Occupational Health (FIOH) risk score, comprising age, self-rated health, number of sickness absences, socioeconomic position, number of chronic illnesses, sleep problems, BMI, and smoking at baseline, exceeded 0.72 for all disease groups and was 0.80 (95% CI 0.80–0.81) for participants with musculoskeletal disorders, 0.83 (0.82–0.84) for those with migraine, and 0.82 (0.81–0.83) for individuals with respiratory disease. Predictive performance was not significantly improved in models with re-estimated coefficients or a new set of predictors. These findings suggest that the 8-item FIOH work disability risk score may serve as a scalable screening tool in identifying individuals with increased risk for work disability.
Insights into nanoparticle shape transformation by energetic ions
Authors: Leino Aleksi A. , Jantunen Ville E. , Mota-Santiago Pablo , Kluth Patrick , Djurabekova Flyura 
Published: April 2023

AbstractShape modification of embedded nanoparticles can be achieved by means of swift heavy ion irradiation. During irradiation, the particles elongate and align with the direction of the ion beam, presumably due to nanometer-scale phase transitions induced by individual ion impacts. However, the details of this transformation are not fully understood. The shape of metal nanoparticles embedded in dielectric matrices defines the non-linear optical properties of the composite material. Therefore, understanding the transformation process better is beneficial for producing materials with the desired optical properties. We study the elongation mechanism of gold nanoparticles using atomistic simulations. Here we focus on long-timescale processes and adhesion between the nanoparticle and the matrix. Without the necessity of ad-hoc assumptions used earlier, our simulations show that, due to adhesion with the oxide, the nanoparticles can grow in aspect ratio while in the molten state even after silicon dioxide solidifies. Moreover, they demonstrate the active role of the matrix: Only explicit simulations of ion impacts around the embedded nanoparticle provide the mechanism for continuous elongation up to experimental values of aspect ratio. Experimental transmission electron microscopy micrographs of nanoparticles after high-fluence irradiation support the simulations. The elongated nanoparticles in experiments and their interface structures with silica, as characterized by the micrographs, are consistent with the simulations. These findings bring ion beam technology forward as a precise tool for shaping embedded nanostructures for various optical applications.
Molecular dynamics study of low molecular weight gel forming salt-triggered dipeptide
Authors: Jia Xiangfeng , Chen Jingfei , Xu Wen , Wang Qi , Wei Xiaofeng , Ma Yongshan , Chen Feiyong , Zhang Guiqin 
Published: April 2023

AbstractMolecular dynamics simulation method was used to study the aggregation of Na and Ca salts in different concentrations of Naphthalene-dipeptide (2NapFF) solutions. The results show that high-valence Ca2+ triggers the formation of a gel at a certain dipeptide concentration, and the low-valence Na+ system follows the aggregation law of general surfactants. The results also show that hydrophobic and electrostatic forces are the main driving forces for the formation of dipeptide aggregates, and that hydrogen bonds do not play a major role in the formation of dipeptide solution aggregates. Hydrophobic and electrostatic effects are the main driving forces for the formation of gels in dipeptide solutions triggered by Ca2+. Electrostatic attraction drives Ca2+ to form a weak coordination with four oxygen atoms on two carboxyl groups, which causes the dipeptide molecules to form a gel with a branched network structure.
Left ventricular function changes and echocardiographic predictors in adult survivors of fulminant myocarditis treated with the Chinese protocol
Authors: Jiang Luying , Zhang Kaiyue , Zhang Chunran , Liu Yujian , Jiang Jiangang , Wang Daowen , Zuo Houjuan , Wang Hong 
Published: April 2023

AbstractDisagreement exists regarding the long-term prognosis and recovery of left ventricular (LV) function in patients with fulminant myocarditis (FM). This study reported the outcome and LV ejection fraction (EF) changes in FM treated with Chinese protocol, and assessed whether global longitudinal strain (GLS) by two-dimensional speckle tracking echocardiography (2-D STE) could provide additional information. This retrospective study included 46 FM adult patients who applied timely circulatory support and immunomodulatory therapy with adequate doses of both glucocorticoids and immunoglobulins as core approaches and survived after acute phase. They all presented with acute onset of cardiac symptoms < 2 weeks. LV end-diastolic dimensions, LVEF and GLS at discharge and 2-year were obtained and compared. We then performed linear regression and ROC analysis to determine independent factors to predict normalization of GLS at 2-year. At 2 years, the survival was 100% in our cohort. And the GLS improved modestly (15.40 ± 3.89% vs 17.24 ± 2.89%, P = 0.002). At two years, a proportion of patients whose LV function remained abnormal, being 22% evaluated by EF (< 55%) and higher to 37% by GLS (< 17%). Moreover, GLS at discharge but not at presentation correlated with GLS at 2-year (r = 0.402, P = 0.007). The FM adult treated with Chinese protocol have good survival and modest improvement of LV function during 2-year.
Adaptation to the shallow sea floor environment of a species of marine worms, Oligobrachia mashikoi, generally inhabiting deep-sea water
Authors: Ogiso Shouzo , Watanabe Kazuki , Maruyama Yusuke , Miyake Hiroshi , Hatano Kaito , Hirayama Jun , Hattori Atsuhiko , Watabe Yukina , Sekiguchi Toshio , Kitani Yoichiro , Furusawa Yukihiro , Tabuchi Yoshiaki , Matsubara Hajime , Nakagiri Mana , Toyota Kenji , Sasayama Yuichi , Suzuki Nobuo 
Published: April 2023

AbstractBeard worms from the family Siboglinidae, are peculiar animals and are known for their symbiotic relationships with sulfur bacteria. Most Siboglinids inhabit the deep-sea floor, thus making difficult to make any observations in situ. One species, Oligobrachia mashikoi, occurs in the shallow depths (24.5 m) of the Sea of Japan. Taking advantage of its shallow-water habitat, the first ecological survey of O. mashikoi was performed over a course of 7 years, which revealed that its tentacle-expanding behavior was dependent on the temperature and illuminance of the sea water. Furthermore, there were significantly more O. mashikoi with expanding tentacles during the nighttime than during the daytime, and the prevention of light eliminated these differences in the number of expending tentacles. These results confirmed that the tentacle-expanding behavior is controlled by environmental light signals. Consistent with this, we identified a gene encoding a photoreceptor molecule, neuropsin, in O. mashikoi, and the expression thereof is dependent on the time of day. We assume that the described behavioral response of O. mashikoi to light signals represent an adaptation to a shallow-water environment within the predominantly deep-sea taxon.
The impact of pandemic-related stress on attentional bias and anxiety in alexithymia during the COVID-19 pandemic
Authors: Lee Shu-Hui , Lee Kuan-Te 
Published: April 2023

AbstractThe COVID-19 pandemic had negative consequences for mental health, yet it is unknown how and to what extent the psychological outcomes of this stressful event are moderated by individual traits. Alexithymia is a risk factor for psychopathology, and thus likely predicted individual differences in resilience or vulnerability to stressful events during the pandemic. This study explored the moderating role of alexithymia in the relationships of pandemic-related stress with anxiety levels and attentional bias. The participants were 103 Taiwanese individuals who completed a survey during the outbreak of the Omicron wave. Additionally, an emotional Stroop task including pandemic-related or neutral stimuli was used to measure attentional bias. Our results demonstrate that pandemic-related stress had a lesser impact on anxiety in individuals with a higher level of alexithymia. Moreover, we found that in individuals with higher exposure to pandemic-related stressors, a higher level of alexithymia indicated less attentional bias toward COVID-19-related information. Thus, it is plausible that individuals with alexithymia tended to avoid pandemic-related information, which could temporarily relieve stressors during the pandemic.
Statistical control of structural networks with limited interventions to minimize cellular phenotypic diversity represented by point attractors
Authors: Kim Jongwan , Hopper Corbin , Cho Kwang-Hyun 
Published: April 2023

AbstractThe underlying genetic networks of cells give rise to diverse behaviors known as phenotypes. Control of this cellular phenotypic diversity (CPD) may reveal key targets that govern differentiation during development or drug resistance in cancer. This work establishes an approach to control CPD that encompasses practical constraints, including model limitations, the number of simultaneous control targets, which targets are viable for control, and the granularity of control. Cellular networks are often limited to the structure of interactions, due to the practical difficulty of modeling interaction dynamics. However, these dynamics are essential to CPD. In response, our statistical control approach infers the CPD directly from the structure of a network, by considering an ensemble average function over all possible Boolean dynamics for each node in the network. These ensemble average functions are combined with an acyclic form of the network to infer the number of point attractors. Our approach is applied to several known biological models and shown to outperform existing approaches. Statistical control of CPD offers a new avenue to contend with systemic processes such as differentiation and cancer, despite practical limitations in the field.
Correlation between electroencephalographic markers in the healthy brain
Authors: Päeske Laura , Uudeberg Tuuli , Hinrikus Hiie , Lass Jaanus , Bachmann Maie 
Published: April 2023

AbstractMental disorders have an increasing tendency and represent the main burden of disease to society today. A wide variety of electroencephalographic (EEG) markers have been successfully used to assess different symptoms of mental disorders. Different EEG markers have demonstrated similar classification accuracy, raising a question of their independence. The current study is aimed to investigate the hypotheses that different EEG markers reveal partly the same EEG features reflecting brain functioning and therefore provide overlapping information. The assessment of the correlations between EEG signal frequency band power, dynamics, and functional connectivity markers demonstrates that a statistically significant correlation is evident in 37 of 66 (56%) comparisons performed between 12 markers of different natures. A significant correlation between the majority of the markers supports the similarity of information in the markers. The results of the performed study confirm the hypotheses that different EEG markers reflect partly the same features in brain functioning. Higuchi’s fractal dimension has demonstrated a significant correlation with the 82% of other markers and is suggested to reveal a wide spectrum of various brain disorders. This marker is preferable in the early detection of symptoms of mental disorders.
The ephemeral fumarolic mineralization of the 2021 Tajogaite volcanic eruption (La Palma, Canary Islands, Spain)
Authors: Campeny Marc , Menéndez Inmaculada , Ibáñez-Insa Jordi , Rivera-Martínez Jesús , Yepes Jorge , Álvarez-Pousa Soledad , Méndez-Ramos Jorge , Mangas José 
Published: April 2023

AbstractThe present work aims to characterize the ephemeral mineral assemblage related to the fumarolic fields of the Tajogaite volcano, formed in 2021 in La Palma Island (Canary Islands, Spain). A set of 73 samples was obtained after two sampling campaigns in different fumarole sectors of the studied area. Mineralization related to these fumaroles formed efflorescent patches located at variable distance from the main volcanic craters. Distal patches are predominantly whitish, while in the vicinities they typically show yellowish to orange colours. Field observations also revealed that fumaroles usually occur in elevated topographic areas as well as over fractured and porous volcanic pyroclastic materials. The mineralogical and textural characterisation of the Tajogaite fumaroles unfolds a complex mineral assemblage, comprising cryptocrystalline phases related to low (< 200 °C) and medium temperature (200–400 °C) conditions. In Tajogaite, we propose a classification of three different fumarolic mineralization types: (1) fluorides and chlorides located in proximal fumarolic areas (~ 300–180 °C); (2) native sulphur associated with gypsum, mascagnite and salammoniac (~ 120–100 °C) and (3) sulphates and alkaline carbonates typically occurred in distal fumarolic areas (< 100 °C). Finally, we present a schematic model of the formation of Tajogaite fumarolic mineralization and their compositional evolution developed during the cooling of the volcanic system.
Co-evolution of large inverted repeats and G-quadruplex DNA in fungal mitochondria may facilitate mitogenome stability: the case of Malassezia
Authors: Christinaki Anastasia C. , Theelen Bart , Zania Alkmini , Coutinho Selene Dall’ Acqua , Cabañes Javier F. , Boekhout Teun , Kouvelis Vassili N. 
Published: April 2023

AbstractMitogenomes are essential due to their contribution to cell respiration. Recently they have also been implicated in fungal pathogenicity mechanisms. Members of the basidiomycetous yeast genus Malassezia are an important fungal component of the human skin microbiome, linked to various skin diseases, bloodstream infections, and they are increasingly implicated in gut diseases and certain cancers. In this study, the comparative analysis of Malassezia mitogenomes contributed to phylogenetic tree construction for all species. The mitogenomes presented significant size and gene order diversity which correlates to their phylogeny. Most importantly, they showed the inclusion of large inverted repeats (LIRs) and G-quadruplex (G4) DNA elements, rendering Malassezia mitogenomes a valuable test case for elucidating the evolutionary mechanisms responsible for this genome diversity. Both LIRs and G4s coexist and convergently evolved to provide genome stability through recombination. This mechanism is common in chloroplasts but, hitherto, rarely found in mitogenomes.
An improved SIFT algorithm for registration between SAR and optical images
Authors: Zhang Wannan , Zhao Yuqian 
Published: April 2023

AbstractAiming at improving the performance of scale invariant feature transform (SIFT) algorithm during the registration of optical and synthetic aperture radar (SAR) images, a new SIFT algorithm is proposed. Firstly, the nonlinear diffusion scale space of optical and SAR images is constructed by using nonlinear diffusion filtering, the uniform gradient information is calculated by using multi-scale Sobel operator and multi-scale exponential weighted mean ratio operator respectively. Then, after removing the first layer of the scale space with the image blocking strategy, the scale space is partitioned, and Harris feature points are extracted on the basis of consistent gradient information to obtain stable and uniform point features. Descriptors are constructed based on gradient position and direction histogram templates and normalized to overcome nonlinear radiation differences between images. Finally, the correct matching point pairs are obtained by using bilateral fast approximate nearest neighbor (FLANN) search matching method and random sampling consistent (RANSAC) method, and the affine transformation model parameters are obtained. Compared with the other two algorithms, the CMR of this algorithm is improved by 80.53%, 75.61% and 81.74% respectively in the three groups of images, and the RMSE is reduced by 0.6491, 1.0287 and 0.6306 respectively.
A cuproptosis-related lncRNA signature to predict prognosis and immune microenvironment of colon adenocarcinoma
Authors: Li Dongming , Qu Guangzhen , Ling Shen , Sun Yuanlin , Cui Yingnan , Yang Yingchi , Cao Xueyuan 
Published: April 2023

AbstractCuproptosis is a novel cell death modality but its regulatory role in the colon cancer remains obscure. This study is committed to establishing a cuproptosis-related lncRNA (CRL) signature to forecast the prognosis for colon adenocarcinoma (COAD). The Cancer Genome Atlas (TCGA) samples were randomly divided into training and validation cohorts. LASSO-COX analysis was performed to construct a prognostic signature consisting of five CRLs (AC015712.2, ZEB1-AS1, SNHG26, AP001619.1, and ZKSCAN2-DT). We found the patients with high-risk scores suffered from poor prognosis in training cohort (p < 0.001) and validation cohort (p = 0.004). Nomogram was created based on the 5-CRL signature. Calibration curves, receiver operating characteristic (ROC) curves, and decision curve analysis (DCA) demonstrated the nomogram performed well in 1‑, 3‑, and 5‑year overall survival (OS). Subsequently, we observed increased infiltration of multiple immune cells and upregulated expression of immune checkpoints and RNA methylation modification genes in high-risk patients. Additionally, gene set enrichment analysis (GSEA) revealed two tumor-related pathways, including MAPK and Wnt signaling pathways. Finally, we found AKT inhibitors, all-trans retinoic acid (ATRA), camptothecin, and thapsigargin had more sensitivity to antitumor therapy in high-risk patients. Collectively, this CRL signature is promising for the prognostic prediction and precise therapy of COAD.
A moonlighting role for LysM peptidoglycan binding domains underpins Enterococcus faecalis daughter cell separation
Authors: Salamaga Bartłomiej , Turner Robert D. , Elsarmane Fathe , Galley Nicola F. , Kulakauskas Saulius , Mesnage Stéphane 
Published: April 2023

AbstractControl of cell size and morphology is of paramount importance for bacterial fitness. In the opportunistic pathogen Enterococcus faecalis, the formation of diplococci and short cell chains facilitates innate immune evasion and dissemination in the host. Minimisation of cell chain size relies on the activity of a peptidoglycan hydrolase called AtlA, dedicated to septum cleavage. To prevent autolysis, AtlA activity is tightly controlled, both temporally and spatially. Here, we show that the restricted localization of AtlA at the septum occurs via an unexpected mechanism. We demonstrate that the C-terminal LysM domain that allows the enzyme to bind peptidoglycan is essential to target this enzyme to the septum inside the cell before its translocation across the membrane. We identify a membrane-bound cytoplasmic protein partner (called AdmA) involved in the recruitment of AtlA via its LysM domains. This work reveals a moonlighting role for LysM domains, and a mechanism evolved to restrict the subcellular localization of a potentially lethal autolysin to its site of action.