bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene fusions are frequent in ACTH-secreting neuroendocrine neoplasms of the pancreas, but not in their non-pancreatic counterparts
Authors: Agaimy Abbas , Kasajima Atsuko , Stoehr Robert , Haller Florian , Schubart Christoph , Tögel Lars , Pfarr Nicole , von Werder Alexander , Pavel Marianne E. , Sessa Fausto , Uccella Silvia , La Rosa Stefano , Klöppel Günter 
Published: January 2023

Abstract
Ectopic Cushing syndrome is a rare clinical disorder resulting from excessive adrenocorticotrophic hormone (ACTH) produced by non-pituitary neoplasms, mainly neuroendocrine neoplasms (NENs) of the lung, pancreas, and gastrointestinal tract, and other less common sites. The genetic background of ACTH-producing NENs has not been well studied. Inspired by an index case of ACTH-producing pancreatic NEN carrying a gene fusion, we postulated that ACTH-producing NENs might be enriched for gene fusions. We herein examined 21 ACTH-secreting NENs of the pancreas (10), lung (9), thymus (1), and kidney (1) using targeted RNA sequencing. The tumors were classified according to the most recent WHO classification as NET-G1/typical carcinoid (n = 4), NETG-2/atypical carcinoid (n = 14), and NET-G3 (n = 3). Overall, targeted RNA sequencing was successful in 11 cases (4 of 10 pancreatic tumors, 5 of 9 pulmonary tumors, and in the one renal and one thymic tumor). All four successfully tested pancreatic tumors revealed a gene fusion: two had a EWSR1::BEND2 and one case each had a KMT2A::BCOR and a TFG::ADGRG7 fusion, respectively. EWSR1 rearrangements were confirmed in both tumors with a EWSR1::BEND2 by FISH. Gene fusions were mutually exclusive with ATRX, DAXX, and MEN1 mutations (the most frequently mutated genes in NETs) in all four cases. Using RNA-based variant assessment (n = 16) or via the TSO500 panel (n = 5), no pathogenic BCOR mutations were detected in any of the cases. Taken together, gene fusions were detected in 4/4 (100%) pancreatic versus 0/7 (0%) non-pancreatic tumors, respectively. These results suggest a potential role for gene fusions in triggering the ACTH production in pancreatic NENs presenting with ectopic Cushing syndrome. While the exact mechanisms responsible for the ectopic ACTH secretion are beyond the scope of this study, overexpressed fusion proteins might be involved in promoter-mediated overexpression of pre-ACTH precursors in analogy to the mechanisms postulated for EWSR1::CREB1-mediated paraneoplastic phenomena in certain mesenchymal neoplasms. The genetic background of the ACTH-producing non-pancreatic NENs remains to be further studied.
HER2/neu-based vaccination with li-Key hybrid, GM-CSF immunoadjuvant and trastuzumab as a potent triple-negative breast cancer treatment
Authors: Zhou Yihan 
Published: January 2023

Abstract
Purpose
Constituting 15 to 20% of breast cancer cases, the triple-negative subtype lacks effective treatments as being less responsive to hormone-associated therapies. Alternatively, a more powerful immunotherapeutic vaccination can trigger immune recognition and destruction against breast cancer by incorporating oncological antigens such as human epidermal growth factor receptor 2 (HER2/neu). Currently, HER2/neu-based vaccines have finished three phases with breast cancer patients, in conjunction with granulocyte-macrophage colony-stimulating factor (GM-CSF) that was proven to be a promising vaccine adjuvant in other cancer trials previously.

Methods
Completed HER2/neu-based vaccine trials with GM-CSF immunoadjuvants for breast cancer were summarised, and additionally, the article discussed prominent findings of vaccine effectiveness in triple-negative breast cancer, regarding li-Key hybrid in vaccine design and co-administration of anti-HER2/neu trastuzumab.

Results
Nine clinical trials of three HER2/neu epitopes, one with li-Key hybrid, were analysed with or without the presence of trastuzumab. Immunological responses and minimal toxicities were observed in these epitopes, and disease-free survival was especially improved in the triple-negative population.

Conclusion
HER2/neu-based peptide vaccine is a safe and effective approach against breast cancer, and its benefits can be potentially furthered by combining the li-Key hybrid vaccine with targeted drugs and adjuvants selected to enhance cross-presentation for exogenous vaccine antigens.

Graphical abstract
Native and exotic plants play different roles in urban pollination networks across seasons
Authors: Zaninotto Vincent , Thebault Elisa , Dajoz Isabelle 
Published: January 2023

AbstractUrban areas often host exotic plant species, whether managed or spontaneous. These plants are suspected of affecting pollinator diversity and the structure of pollination networks. However, in dense cityscapes, exotic plants also provide additional flower resources during periods of scarcity, and the consequences for the seasonal dynamics of networks still need to be investigated. For two consecutive years, we monitored monthly plant–pollinator networks in 12 green spaces in Paris, France. We focused on seasonal variations in the availability and attractiveness of flower resources, comparing native and exotic plants at both the species and community levels. We also considered their respective contributions to network properties over time (specialization and nestedness). Exotic plants provided more abundant and diverse flower resources than native plants, especially from late summer on. However, native plants received more visits and attracted more pollinator species at the community level; and during certain times of the year at the species level as well. Exotic plants were involved in more generalist interactions, increasingly so over the seasons. In addition, they contributed more to network nestedness than native plants. These results show that exotic plants are major components of plant–pollinator interactions in a dense urban landscape, even though they are less attractive than natives. They constitute a core of generalist interactions that increase nestedness and can participate in the overall stability of the network. However, most exotic species were seldom visited by insects. Pollinator communities may benefit from including more native species when managing urban green spaces.
Consistent responses to moisture stress despite diverse growth forms within mountain fynbos communities
Authors: Skelton Robert P. , West Adam G. , Buttner Daniel , Dawson Todd E. 
Published: January 2023

AbstractUnderstanding climate change impacts on the Cape Floristic Region requires improved knowledge of plant physiological responses to the environment. Studies examining physiological responses of mountain fynbos have consisted of campaign-based measurements, capturing snapshots of plant water relations and photosynthesis. We examine conclusions drawn from prior studies by tracking in situ physiological responses of three species, representing dominant growth forms (proteoid, ericoid, restioid), over 2 years using miniature continuous sap flow technology, long-term observations of leaf/culm water potential and gas exchange, and xylem vulnerability to embolism. We observed considerable inter-specific variation in the timing and extent of seasonal declines in productivity. Shallow-rooted Erica monsoniana exhibited steep within-season declines in sap flow and water potentials, and pronounced inter-annual variability in total daily sap flux (Js). Protea repens showed steady reductions in Js across both years, despite deeper roots and less negative water potentials. Cannomois congesta—a shallow-rooted restioid—was least negatively impacted. Following rehydrating rain at the end of summer, gas exchange recovery was lower in the drier year compared with the normal year, but did not differ between species. Loss of function in the drier year was partially accounted for by loss of xylem transport capacity in Erica and Cannomois, but not Protea. Hitherto unseen water use patterns, including inter-annual variability of gas exchange associated with contrasting water uptake properties, reveal that species use different mechanisms to cope with summer dry periods. Revealing physiological responses of key growth forms enhances predictions of plant function within mountain fynbos under future conditions.
Quantifying terminal white bands in Salix from the Yenisei river, Siberia and their relationship to late-season flooding
Authors: Thaxton Richard D. , Panyushkina Irina P. , Meko David M. , von Arx Georg , Agafonov Leonid I. 
Published: January 2023

Abstract
Key Message
Wood fiber cell wall thickness best characterizes white bands found at the end of certain growth rings in Salix alba. Evidence suggests these features are related to late-season hydrology.

Abstract
Recent, record-breaking discharge in the Yenisei River, Siberia, is part of a larger trend of increasing river flow in the Arctic driven by Arctic Amplification. These changes in magnitude and timing of discharge can lead to increased risk of extreme flood events, with implications for infrastructure, ecosystems, and climate. To better understand the effect of these changes on riparian tree growth along the lower reaches of the Yenisei River, we collected white willow (Salix alba) cross sections from a fluvial fill flat terrace that occasionally floods when water levels are extremely high. These samples displayed bands of lighter colored wood at the end of certain annual growth rings that we hypothesized were related to flood events. To identify the characteristics and causes of these features, we use an approach known as quantitative wood anatomy (QWA) to measure variation in fiber cell dimensions across tree rings, particularly fiber lumen area (LA) and cell wall thickness (CWT). We investigate (1) which cell parameters and method to extract intra-annual data from annual tree rings best capture terminal white bands identified in Salix, and (2) if these patterns are related to flood magnitude and/or duration. We find that fiber CWT best captures terminal white bands found in Salix rings. Time series derived from CWT measurements correlate with July water-level durations, but at levels too low to be labeled flooding. Although both terminal white bands and July flooding have reduced since 1980, questions remain as to the cause of terminal white bands. Understanding how riparian vegetation responds to changes in hydrology can help us better manage riparian ecosystems and understand the impacts of a changing Arctic hydrological regime.
Long-term effects of exercise interventions on physical activity in breast cancer patients: a systematic review and meta-analysis of randomized controlled trials
Authors: Goldschmidt Siri , Schmidt Martina E. , Steindorf Karen 
Published: January 2023

Abstract
Background
Benefits of exercise interventions for cancer patients are well established. This systematic review aimed to investigate the sustainability of exercise interventions with respect to physical activity behaviour of breast cancer patients in the longer term.

Methods
The databases Pubmed, Cochrane, Embase, and Web of Science were systematically searched for randomized controlled trials (RCTs) investigating aerobic exercise, resistance exercise, or combined exercise interventions in breast cancer patients and assessing physical activity at least 2 months after the intervention. Random-effect models were used to calculate standardized mean differences (SMD).

Results
A total of 27 RCTs with 4120 participants were included in the review, of which 11 RCTs with 1545 participants had appropriate data for the meta-analyses. Physical activity was mainly self-reported, and most exercise interventions were supervised. Exercise interventions tended to show a moderate significant effect up to 6 months for moderate to vigorous physical activity (SMD [95% CI] = 0.39 [0.07, 0.70]) and small, non-significant effects on total physical activity at 6 months (SMD [95% CI] = 0.14 [− 0.00, 0.28]) and up to 60 months after the intervention (SMD = 0.29 [-0.31, 0.90]). Differences between intervention characteristics, such as supervised versus unsupervised, were inconclusive due to the small number of RCTs.

Conclusions
The physical activity behaviour in breast cancer patients remained improved for several months beyond the end of exercise interventions, but effects were small to moderate and diminished over time. Future studies should clarify how to maintain a healthy level of physical activity after completion of an exercise intervention.
Learning ensembles of deep neural networks for extreme rainfall event detection
Authors: Folino Gianluigi , Guarascio Massimo , Chiaravalloti Francesco 
Published: January 2023

AbstractAccurate rainfall estimation is crucial to adequately assess the risk associated with extreme events capable of triggering floods and landslides. Data gathered from Rain Gauges (RGs), sensors devoted to measuring the intensity of the rain at individual points, are commonly used to feed interpolation methods (e.g., the Kriging geostatistical approach) and estimate the precipitation field over an area of interest. However, the information provided by RGs could be insufficient to model complex phenomena, and computationally expensive interpolation methods could not be used in real-time environments. Integrating additional data sources (e.g., radar and geostationary satellites) is an effective solution for improving the quality of the estimate, but it needs to cope with Big Data issues. To overcome all these issues, we propose a Rainfall Estimation Model (REM) based on an Ensemble of Deep Neural Networks (DeepEns-REM) that can automatically fuse heterogeneous data sources. The usage of Residual Blocks in the base models and the adoption of a Snapshot procedure to build the ensemble guarantees a fast convergence and scalability. Experimental results, conducted on a real dataset concerning a southern region in Italy, demonstrate the quality of the proposal in comparison with the Kriging interpolation technique and other machine learning techniques, especially in the case of exceptional rainfall events.
Meta-transfer learning for emotion recognition
Authors: Nguyen Dung , Nguyen Duc Thanh , Sridharan Sridha , Denman Simon , Nguyen Thanh Thi , Dean David , Fookes Clinton 
Published: January 2023

AbstractDeep learning has been widely adopted in automatic emotion recognition and has lead to significant progress in the field. However, due to insufficient training data, pre-trained models are limited in their generalisation ability, leading to poor performance on novel test sets. To mitigate this challenge, transfer learning performed by fine-tuning pr-etrained models on novel domains has been applied. However, the fine-tuned knowledge may overwrite and/or discard important knowledge learnt in pre-trained models. In this paper, we address this issue by proposing a PathNet-based meta-transfer learning method that is able to (i) transfer emotional knowledge learnt from one visual/audio emotion domain to another domain and (ii) transfer emotional knowledge learnt from multiple audio emotion domains to one another to improve overall emotion recognition accuracy. To show the robustness of our proposed method, extensive experiments on facial expression-based emotion recognition and speech emotion recognition are carried out on three bench-marking data sets: SAVEE, EMODB, and eNTERFACE. Experimental results show that our proposed method achieves superior performance compared with existing transfer learning methods.
High-resolution monitoring of groundwater quality in unconsolidated aquifers using UV-Vis spectrometry
Authors: Haas Johannes , Retter Alice , Kornfeind Lukas , Wagner Christoph , Griebler Christian , Birk Steffen 
Published: January 2023

AbstractIn many countries, groundwater quality is routinely monitored in yearly or quarterly intervals. Such frequencies, however, may not be sufficient for investigations into the temporal dynamics of water quality, due to seasonal variability or responses to extreme events. One approach to overcome this limitation is the use of in-situ sensors, such as UV-Vis spectrometers. With a focus on nitrate as an abundant groundwater contaminant, we explored the suitability of these sensors for high-resolution groundwater monitoring in shallow unconsolidated oxic aquifers. In-situ nitrate measurements in four selected wells compared well with values from lab analyses determined in pumped groundwater samples. Most importantly, our results revealed distinct seasonal patterns and, at two sites, pronounced short-term fluctuations in nitrate concentrations concomitant to patterns observed in precipitation, hydraulic head and groundwater temperature. Such dynamics in water quality, and thus the causal relationship with hydrological events and land use, will unfortunately be overlooked when following conventional sampling schemes with the risk of non-representative time series if routine sampling is timed unfavorably. Finally, we provide practical advice for deployment of the sensor.
Analyzing spatio-temporal mechanisms of land subsidence in the Parowan Valley, Utah, USA
Authors: Li Jiawei , Smith Ryan , Grote Katherine 
Published: January 2023

AbstractParowan Valley, Utah (USA), is an agricultural region experiencing rapid subsidence due to extensive groundwater extraction from aquifers with a significant portion of fine-grained sediments. To analyze the subsidence spatio-temporally, time-series Interferometric Synthetic Aperture Radar (InSAR) of 155 Sentinel-1 C-band scenes were processed. These data showed approximately 30 cm of ground subsidence in Parowan Valley from 2014 to 2020. Because of the high temporal sampling rate of the Sentinel-1 satellite (12-day cycle), it is possible to determine the seasonal changes of ground deformation and relate this to groundwater extraction. To better understand the relationship between ground deformation and groundwater extraction in the Parowan Valley, temporal changes in hydraulic head data from US Geological Survey observation wells were monitored. Additionally, well logs were analyzed and used to construct a map that showed the percentage of fine-grained material in the subsurface. The investigation of hydraulic head and geology, together with InSAR-derived ground displacement data, indicates that the most subsidence occurs where there is a co-occurrence of high groundwater demand and a high percentage of fine-grained sediments, but recharge likely plays a role in mitigating subsidence in some areas. The subsidence developed in Parowan Valley shows a long-term trend as well as seasonal variation and appears to be influenced by both agricultural activity and annual precipitation.
Artificial intelligence-guided discovery of gastric cancer continuum
Authors: Vo Daniella , Ghosh Pradipta , Sahoo Debashis 
Published: January 2023

Abstract
Background
Detailed understanding of pre-, early and late neoplastic states in gastric cancer helps develop better models of risk of progression to gastric cancers (GCs) and medical treatment to intercept such progression.

Methods
We built a Boolean implication network of gastric cancer and deployed machine learning algorithms to develop predictive models of known pre-neoplastic states, e.g., atrophic gastritis, intestinal metaplasia (IM) and low- to high-grade intestinal neoplasia (L/HGIN), and GC. Our approach exploits the presence of asymmetric Boolean implication relationships that are likely to be invariant across almost all gastric cancer datasets. Invariant asymmetric Boolean implication relationships can decipher fundamental time-series underlying the biological data. Pursuing this method, we developed a healthy mucosa → GC continuum model based on this approach.

Results
Our model performed better against publicly available models for distinguishing healthy versus GC samples. Although not trained on IM and L/HGIN datasets, the model could identify the risk of progression to GC via the metaplasia → dysplasia → neoplasia cascade in patient samples. The model could rank all publicly available mouse models for their ability to best recapitulate the gene expression patterns during human GC initiation and progression.

Conclusions
A Boolean implication network enabled the identification of hitherto undefined continuum states during GC initiation. The developed model could now serve as a starting point for rationalizing candidate therapeutic targets to intercept GC progression.
Developing future heat-resilient vegetable crops
Authors: Saeed Faisal , Chaudhry Usman Khalid , Raza Ali , Charagh Sidra , Bakhsh Allah , Bohra Abhishek , Ali Sumbul , Chitikineni Annapurna , Saeed Yasir , Visser Richard G. F. , Siddique Kadambot H. M. , Varshney Rajeev K. 
Published: January 2023

AbstractClimate change seriously impacts global agriculture, with rising temperatures directly affecting the yield. Vegetables are an essential part of daily human consumption and thus have importance among all agricultural crops. The human population is increasing daily, so there is a need for alternative ways which can be helpful in maximizing the harvestable yield of vegetables. The increase in temperature directly affects the plants’ biochemical and molecular processes; having a significant impact on quality and yield. Breeding for climate-resilient crops with good yields takes a long time and lots of breeding efforts. However, with the advent of new omics technologies, such as genomics, transcriptomics, proteomics, and metabolomics, the efficiency and efficacy of unearthing information on pathways associated with high-temperature stress resilience has improved in many of the vegetable crops. Besides omics, the use of genomics-assisted breeding and new breeding approaches such as gene editing and speed breeding allow creation of modern vegetable cultivars that are more resilient to high temperatures. Collectively, these approaches will shorten the time to create and release novel vegetable varieties to meet growing demands for productivity and quality. This review discusses the effects of heat stress on vegetables and highlights recent research with a focus on how omics and genome editing can produce temperature-resilient vegetables more efficiently and faster.
Masticaticatory muscles characteristics in relation to adiposity and general muscular fitness: a population-based study
Authors: Meisel Peter , Daboul Amro , Bülow Robin , Eremenko Michael , Völzke Henry , Biffar Rainer , Kocher Thomas 
Published: January 2023

AbstractThere is still considerable controversy surrounding the impact of mastication on obesity. The aim of this study was to identify the interplay between the masticatory muscles, teeth, and general muscular fitness and how they contribute to body adiposity in a general German population. This cross-sectional study included 616 participants (300 male, 316 female, age 31–93 years) from the population-based Study of Health in Pomerania. The cross-sectional areas of the masseter, medial and lateral pterygoid muscles were measured using magnetic resonance imaging (MRI), muscular fitness assessed by hand grip strength (HGS) and body fat distribution was measured by bioelectrical impedance analysis (BIA) and MRI. The overall prevalence of obesity was high in our cohort. The cross-sectional area of the masseter muscles was positively associated with the number of teeth, body mass index (BMI) and HGS, and negatively associated with the BIA-assessed body fat when adjusted for age, sex, teeth, and BMI. Especially the correlation was strong (p < 0.001). Analogous relationships were observed between the masseter, HGS and MRI-assessed subcutaneous fat. These associations were most pronounced with masseter, but also significant with both pterygoid muscles. Though the masticatory muscles were affected by the number of teeth, teeth had no impact on the relations between masseter muscle and adiposity. Physical fitness and masticatory performance are associated with body shape, controlled and directed by the relevant muscles.