bluuebunny/crossref_metadata_2025_split huggingface dataset:
Movements and behaviour of blue whales satellite tagged in an Australian upwelling system
Authors: Mӧller Luciana M. , Attard Catherine R. M. , Bilgmann Kerstin , Andrews-Goff Virginia , Jonsen Ian , Paton David , Double Michael C. 
Published: December 2020

AbstractKnowledge about the movement ecology of endangered species is needed to identify biologically important areas and the spatio-temporal scale of potential human impacts on species. Blue whales (Balaenoptera musculus) are endangered due to twentieth century whaling and currently threatened by human activities. In Australia, they feed in the Great Southern Australian Coastal Upwelling System (GSACUS) during the austral summer. We investigate their movements, occupancy, behaviour, and environmental drivers to inform conservation management. Thirteen whales were satellite tagged, biopsy sampled and photo-identified in 2015. All were genetically confirmed to be of the pygmy subspecies (B. m. brevicauda). In the GSACUS, whales spent most of their time over the continental shelf and likely foraging in association with several seascape variables (sea surface temperature variability, depth, wind speed, sea surface height anomaly, and chlorophylla). When whales left the region, they migrated west and then north along the Australian coast until they reached West Timor and Indonesia, where their movements indicated breeding or foraging behaviour. These results highlight the importance of the GSACUS as a foraging ground for pygmy blue whales inhabiting the eastern Indian Ocean and indicate the whales’ migratory route to proposed breeding grounds off Indonesia. Information about the spatio-temporal scale of potential human impacts can now be used to protect this little-known subspecies of blue whale.
ALK variants, PD-L1 expression, and their association with outcomes in ALK-positive NSCLC patients
Authors: Chang Gee-Chen , Yang Tsung-Ying , Chen Kun-Chieh , Hsu Kuo-Hsuan , Huang Yen-Hsiang , Su Kang-Yi , Yu Sung-Liang , Tseng Jeng-Sen 
Published: December 2020

AbstractIt remains unclear how programmed death-ligand 1 (PD-L1) expression interacts with anaplastic lymphoma kinase (ALK) mutation, its variants, and the outcome of treatment. One hundred and twenty four out of 1255 patients (9.9%) were deemed ALK-positive by the Ventana IHC assay. PD-L1 status and ALK variants were available in 100 and 59 patients, respectively. PD-L1 positive (TPS ≥ 1%) and strong positive (TPS ≥ 50%) rate was 50% and 16%, respectively. A total of 64 variant types were detected in 59 patients. V1 (32.8%) and V3a/b (28.1%) were the most common variants. There was no significant association between ALK variants and the PD-L1 expression. The presence of V3a/b subtype independently predicted a worse overall survival in patients receiving ALK inhibitor(s) (aHR 5.10 [95% CI 1.22–21.25], P = 0.025) and platinum plus pemetrexed (aHR 9.62 [95% CI 1.90–48.80], P = 0.006). While incorporating ALK variants and PD-L1 expression together, patients with non-V3a/b/positive PD-L1 showed a trend towards longer OS. In conclusion, ALK-positive NSCLC patients possess a high PD-L1 expression rate. Although there was no significant association between PD-L1 expression and ALK variants, the outcome of ALK-positive patients could be sorted by these two biomarkers.
Non-invasive measurement of leaf water content and pressure–volume curves using terahertz radiation
Authors: Li Ran , Lu Yaojie , Peters Jennifer M. R. , Choat Brendan , Lee Andrew J. 
Published: December 2020

AbstractIn this paper we describe a non-invasive method of measuring leaf water content using THz radiation and combine this with psychrometry for determination of leaf pressure–volume relationships. In contrast to prior investigations using THz radiation to measure plant water status, the reported method exploits the differential absorption characteristic of THz radiation at multiple frequencies within plant leaves to determine absolute water content in real-time. By combining the THz system with a psychrometer, pressure–volume curves were generated in a completely automated fashion for the determination of leaf tissue water relations parameters including water potential at turgor loss, osmotic potential at full turgor and the relative water content at the turgor loss point. This novel methodology provides for repeated, non-destructive measurement of leaf water content and greatly increased efficiency in generation of leaf PV curves by reducing user handling time.
Layer-wise relevance propagation of InteractionNet explains protein–ligand interactions at the atom level
Authors: Cho Hyeoncheol , Lee Eok Kyun , Choi Insung S. 
Published: December 2020

AbstractDevelopment of deep-learning models for intermolecular noncovalent (NC) interactions between proteins and ligands has great potential in the chemical and pharmaceutical tasks, including structure–activity relationship and drug design. It still remains an open question how to convert the three-dimensional, structural information of a protein–ligand complex into a graph representation in the graph neural networks (GNNs). It is also difficult to know whether a trained GNN model learns the NC interactions properly. Herein, we propose a GNN architecture that learns two distinct graphs—one for the intramolecular covalent bonds in a protein and a ligand, and the other for the intermolecular NC interactions between the protein and the ligand—separately by the corresponding covalent and NC convolutional layers. The graph separation has some advantages, such as independent evaluation on the contribution of each convolutional step to the prediction of dissociation constants, and facile analysis of graph-building strategies for the NC interactions. In addition to its prediction performance that is comparable to that of a state-of-the art model, the analysis with an explainability strategy of layer-wise relevance propagation shows that our model successfully predicts the important characteristics of the NC interactions, especially in the aspect of hydrogen bonding, in the chemical interpretation of protein–ligand binding.
The effect of the papillary renal cell carcinoma subtype on oncological outcomes
Authors: Pan Honghong , Ye Liefu , Zhu Qingguo , Yang Zesong , Hu Minxiong 
Published: December 2020

AbstractThe study aimed to compare the clinicopathological features and prognosis between type I and type II papillary renal cell carcinoma (PRCC) and to investigate whether the subtypes of PRCC would affect oncological outcomes. A total of 102 patients with PRCC were recruited, of which 42 were type I PRCC and 60 type II. The clinicopathological features and oncologic outcomes of the patients were evaluated. The type II cases had a higher WHO/ISUP grading (P < 0.001), T (P = 0.003), N (P = 0.010) stage and stage grouping (P = 0.011) than the type I. During a median follow-up period of 61.4 months, 1-year cancer specific survival (CSS) of the type I was 100%, 5-year CSS was 95.2%, the 1-year CSS of the type II was 96.2%, and 5-year CSS was 75.7%. The univariate analysis showed that subtype, symptoms, TNM, stage grouping, WHO/ISUP grading and surgical methods appeared to affect prognosis of the patients with PRCC. However, multivariate analysis revealed that only stage grouping was the independent risk factor. After the stage grouping factor was adjusted for the analysis, there were no statistically significant differences in CSS (P = 0.214) and PFS (P = 0.190) between the localized type I and type II PRCC groups. Compared with type I PRCC, type II had higher pathological T, N stage and WHO/ISUP grading. However, it was the Stage grouping that made a great difference to oncological outcomes, rather than the subtype of PRCC.
Early evidence of a shift in juvenile fish communities in response to conditions in nursery areas
Authors: Matić-Skoko Sanja , Vrdoljak Dario , Uvanović Hana , Pavičić Mišo , Tutman Pero , Bojanić Varezić Dubravka 
Published: December 2020

AbstractA multivariate analysis of juvenile fish community data, sampled at two nursery sites at an interval of 17 years (2000—early, and 2017—late), was conducted to elucidate the trends of change in littoral juvenile fish communities along the eastern Adriatic coast. Fishing, trophic and taxonomic composition to the community data were analysed for possible causality. The ichthyofaunal composition differed significantly for Site, Period and all interactions. According to the mMDS ordination plot, four groups of communities were defined, with clear cyclicity. No patterns were found in species composition between sites in the early period, while the observed community changes were governed by the same pattern at both sites in the late period. The species that contributed most to the observed changes were non-commercial, small, benthic resident fishes, such as gobiids and blennids, or those associated with canopy alga for shelter and feeding. The analysis correctly allocated samples based on community information to Sites and Periods. The data obtained provided an invaluable opportunity to test for the generality of potential patterns of change in littoral fish communities, suggesting that significantly modified juvenile fish communities may be the result of constant human embankment and marine infrastructure construction along the coast in recent decades, rather than climate change or fishing pressure, as generally considered.
Control of Mooij correlations at the nanoscale in the disordered metallic Ta–nanoisland FeNi multilayers
Authors: Kovaleva N. N. , Kusmartsev F. V. , Mekhiya A. B. , Trunkin I. N. , Chvostova D. , Davydov A. B. , Oveshnikov L. N. , Pacherova O. , Sherstnev I. A. , Kusmartseva A. , Kugel K. I. , Dejneka A. , Pudonin F. A. , Luo Y. , Aronzon B. A. 
Published: December 2020

AbstractLocalisation phenomena in highly disordered metals close to the extreme conditions determined by the Mott-Ioffe-Regel (MIR) limit when the electron mean free path is approximately equal to the interatomic distance is a challenging problem. Here, to shed light on these localisation phenomena, we studied the dc transport and optical conductivity properties of nanoscaled multilayered films composed of disordered metallic Ta and magnetic FeNi nanoisland layers, where ferromagnetic FeNi nanoislands have giant magnetic moments of 10$$^3$$

3

–10$$^5$$

5

Bohr magnetons ($$\mu _{\mathrm{B}}$$

μ
B

). In these multilayered structures, FeNi nanoisland giant magnetic moments are interacting due to the indirect exchange forces acting via the Ta electron subsystem. We discovered that the localisation phenomena in the disordered Ta layer lead to a decrease in the Drude contribution of free charge carriers and the appearance of the low-energy electronic excitations in the 1–2 eV spectral range characteristic of electronic correlations, which may accompany the formation of electronic inhomogeneities. From the consistent results of the dc transport and optical studies we found that with an increase in the FeNi layer thickness across the percolation threshold evolution from the superferromagnetic to ferromagnetic behaviour within the FeNi layer leads to the delocalisation of Ta electrons from the associated localised electronic states. On the contrary, we discovered that when the FeNi layer is discontinuous and represented by randomly distributed superparamagnetic FeNi nanoislands, the Ta layer normalized dc conductivity falls down below the MIR limit by about 60%. The discovered effect leading to the dc conductivity fall below the MIR limit can be associated with non-ergodicity and purely quantum (many-body) localisation phenomena, which need to be challenged further.
Biosorption of Pb (II) and Zn (II) from aqueous solution by Oceanobacillus profundus isolated from an abandoned mine
Authors: Mwandira Wilson , Nakashima Kazunori , Kawasaki Satoru , Arabelo Allison , Banda Kawawa , Nyambe Imasiku , Chirwa Meki , Ito Mayumi , Sato Tsutomu , Igarashi Toshifumi , Nakata Hokuto , Nakayama Shouta , Ishizuka Mayumi 
Published: December 2020

AbstractThe present study investigated biosorption of Pb (II) and Zn (II) using a heavy metal tolerant bacterium Oceanobacillus profundus KBZ 3-2 isolated from a contaminated site. The effects of process parameters such as effect on bacterial growth, pH and initial lead ion concentration were studied. The results showed that the maximum removal percentage for Pb (II) was 97% at an initial concentration of 50 mg/L whereas maximum removal percentage for Zn (II) was at 54% at an initial concentration of 2 mg/L obtained at pH 6 and 30 °C. The isolated bacteria were found to sequester both Pb (II) and Zn (II) in the extracellular polymeric substance (EPS). The EPS facilitates ion exchange and metal chelation-complexation by virtue of the existence of ionizable functional groups such as carboxyl, sulfate, and phosphate present in the protein and polysaccharides. Therefore, the use of indigenous bacteria in the remediation of contaminated water is an eco-friendly way of solving anthropogenic contamination.
SIRT3, a metabolic target linked to ataxia-telangiectasia mutated (ATM) gene deficiency in diffuse large B-cell lymphoma
Authors: Bhalla Kavita , Jaber Sausan , Reagan Kayla , Hamburg Arielle , Underwood Karen F. , Jhajharia Aditya , Singh Maninder , Bhandary Binny , Bhat Shambhu , Nanaji Nahid M. , Hisa Ruching , McCracken Carrie , Creasy Heather Huot , Lapidus Rena G. , Kingsbury Tami , Mayer Dirk , Polster Brian , Gartenhaus Ronald B. 
Published: December 2020

AbstractInactivation of Ataxia-telangiectasia mutated (ATM) gene results in an increased risk to develop cancer. We show that ATM deficiency in diffuse large B-cell lymphoma (DLBCL) significantly induce mitochondrial deacetylase sirtuin-3 (SIRT3) activity, disrupted mitochondrial structure, decreased mitochondrial respiration, and compromised TCA flux compared with DLBCL cells expressing wild type (WT)-ATM. This corresponded to enrichment of glutamate receptor and glutamine pathways in ATM deficient background compared to WT-ATM DLBCL cells. ATM−/− DLBCL cells have decreased apoptosis in contrast to radiosensitive non-cancerous A-T cells. In vivo studies using gain and loss of SIRT3 expression showed that SIRT3 promotes growth of ATM CRISPR knockout DLBCL xenografts compared to wild-type ATM control xenografts. Importantly, screening of DLBCL patient samples identified SIRT3 as a putative therapeutic target, and validated an inverse relationship between ATM and SIRT3 expression. Our data predicts SIRT3 as an important therapeutic target for DLBCL patients with ATM null phenotype.
Effects of cow dung and wood biochars and green manure on soil fertility and tiger nut (Cyperus esculentus L.) performance on a savanna Alfisol
Authors: Adekiya Aruna Olasekan , Olaniran Abiola Folakemi , Adenusi Titilayo Tolulope , Aremu Charity , Ejue Wutem Sunny , Iranloye Yetunde Mary , Gbadamosi Abiodun , Olayanju Adeniyi 
Published: December 2020

AbstractTwo field experiments were conducted concurrently in 2019. The study investigated the effects of single and combined application of wood biochar (WB) and cow dung biochar (CDB) with green manure (GM) on soil properties, performance, and tuber qualities of tiger nut. The treatments consisted of: CDB at 10 t ha−1, WB at 10 t ha−1, GM—Tithonia diversifolia at 10 t ha−1, CDB + GM, WB + GM, control. The six treatments were arranged in RCBD with three replications. CDB, WB, and GM either sole or combined increased moisture content, SOC, nutrient contents, culturable microorganisms, performance, moisture, ash, fiber, and protein contents of the tiger nut compared with the control. CDB has a higher N, C: N ratio, P, K, Ca, Mg, CEC, and pH relative to. CDB alone and CDB + GM increased growth and yield compared with WB alone and WB + GM. CDB + GM has the highest value of growth and yield of tiger nut. GM alone improved growth and yield of tiger nut compared with the two sole biochar treatments. CDB + GM and WB + GM increased growth and yield of tiger nut compared with their sole forms. This was adduced to biochar allowing the retention of nutrients from rapidly decomposing Tithonia within the rooting zone, thereby promoting better effectiveness of nutrient uptake and increase in yield. Therefore, for good soil fertility and tiger nut yield, it is important that the addition of a fast releasing nutrient source to biochar be sought.
Proton pump inhibitors and the risk of Alzheimer’s disease and non-Alzheimer’s dementias
Authors: Torres-Bondia Francisco , Dakterzada Farida , Galván Leonardo , Buti Miquel , Besanson Gaston , Gill Eric , Buil Roman , de Batlle Jordi , Piñol-Ripoll Gerard 
Published: December 2020

AbstractProton pump inhibitors (PPIs) are among the most prescribed medications. Previous epidemiological studies have presented contradictory results about PPIs and the risk of dementia. Our objective was to investigate the association between the use of PPIs and an increasing risk of incident AD or non-AD dementias. A community-based retrospective cohort study was conducted based on the data available from 1st January 2002 to 31st December 2015 in the Catalan health service (CatSalut) system. This cohort included all PPI users (N = 36,360) and non-users (N = 99,362). A lag window of 5 years was considered between the beginning of the PPI treatment and the diagnosis of dementia. PPI use was not associated with the risk of AD (adjusted odds ratio (OR) 1.06) (95% CI 0.93–1.21; p = 0.408). A weakly but significantly increased risk of non-AD dementias was observed among PPI users (adjusted OR 1.20, 95% CI 1.05–1.37; p = 0.007). A higher dose of PPIs was not associated with an increased risk of either AD or non-AD dementias (OR 1.20; 95% CI 0.91–1.61 and OR 0.95; 95% CI 0.74–1.22, respectively). Regarding the number of PPIs used, we observed an increased risk of AD (OR 1.47; 95% CI 1.18–1.83) and non-AD dementias (OR 1.38; 95% CI 1.12–1.70) in users of two types of PPIs compared with those who used only one type. We did not find a higher incidence of AD among PPI users, but a weak increase in the risk of non-AD dementias among PPI users was observed.
Anti-IL-17A treatment reduces serum inflammatory, angiogenic and tissue remodeling biomarkers accompanied by less synovial high endothelial venules in peripheral spondyloarthritis
Authors: Kaaij Merlijn H. , Helder Boy , van Mens Leonieke J. J. , van de Sande Marleen G. H. , Baeten Dominique L. P. , Tas Sander W. 
Published: December 2020

AbstractSpondyloarthritis (SpA) is characterized by inflammation and new bone formation. The exact pathophysiology underlying these processes remains elusive. We propose that the extensive neoangiogenesis in SpA could play a role both in sustaining/enhancing inflammation and in new bone formation. While ample data is available on effects of anti-TNF on angiogenesis, effects of IL-17A blockade on serum markers are largely unknown. We aimed to assess the impact of secukinumab (anti-IL-17A) on synovial neoangiogenesis in peripheral SpA, and how this related to changes in inflammatory and tissue remodeling biomarkers. Serum samples from 20 active peripheral SpA patients included in a 12 week open-label trial with secukinumab were analyzed for several markers of angiogenesis and tissue remodeling. Synovial biopsies taken before and after treatment were stained for vascular markers. Serum levels of MMP-3, osteopontin, IL-6 (all P < 0.001), IL-31, S100A8, S100A9, Vascular Endothelial Growth Factor A (VEGF-A), IL-33, TNF-α (all P < 0.05) decreased significantly upon anti-IL17A treatment. Secukinumab treatment resulted in a decrease in the number of synovial high endothelial venules and lymphoid aggregate score. These results indicate that anti-IL-17A not only diminishes inflammation, but also impacts angiogenesis and tissue remodeling/new bone formation. This may have important implications for disease progression and/or structural damage.
Prediction of disease progression and outcomes in multiple sclerosis with machine learning
Authors: Pinto Mauro F. , Oliveira Hugo , Batista Sónia , Cruz Luís , Pinto Mafalda , Correia Inês , Martins Pedro , Teixeira César 
Published: December 2020

AbstractMultiple Sclerosis is a chronic inflammatory disease, affecting the Central Nervous System and leading to irreversible neurological damage, such as long term functional impairment and disability. It has no cure and the symptoms vary widely, depending on the affected regions, amount of damage, and the ability to activate compensatory mechanisms, which constitutes a challenge to evaluate and predict its course. Additionally, relapsing-remitting patients can evolve its course into a secondary progressive, characterized by a slow progression of disability independent of relapses. With clinical information from Multiple Sclerosis patients, we developed a machine learning exploration framework concerning this disease evolution, more specifically to obtain three predictions: one on conversion to secondary progressive course and two on disease severity with rapid accumulation of disability, concerning the 6th and 10th years of progression. For the first case, the best results were obtained within two years: AUC=$$0.86\pm 0.07$$0.86±0.07, sensitivity=$$0.76\pm 0.14$$0.76±0.14and specificity=$$0.77\pm 0.05$$0.77±0.05; and for the second, the best results were obtained for the 6th year of progression, also within two years: AUC=$$0.89\pm 0.03$$0.89±0.03, sensitivity=$$0.84\pm 0.11$$0.84±0.11, and specificity=$$0.81\pm 0.05$$0.81±0.05. The Expanded Disability Status Scale value, the majority of functional systems, affected functions during relapses, and age at onset were described as the most predictive features. These results demonstrate the possibility of predicting Multiple Sclerosis progression by using machine learning, which may help to understand this disease’s dynamics and thus, advise physicians on medication intake.
Mathematical formulation and parametric analysis of in vitro cell models in microfluidic devices: application to different stages of glioblastoma evolution
Authors: Ayensa-Jiménez Jacobo , Pérez-Aliacar Marina , Randelovic Teodora , Oliván Sara , Fernández Luis , Sanz-Herrera José Antonio , Ochoa Ignacio , Doweidar Mohamed H. , Doblaré Manuel 
Published: December 2020

AbstractIn silico models and computer simulation are invaluable tools to better understand complex biological processes such as cancer evolution. However, the complexity of the biological environment, with many cell mechanisms in response to changing physical and chemical external stimuli, makes the associated mathematical models highly non-linear and multiparametric. One of the main problems of these models is the determination of the parameters’ values, which are usually fitted for specific conditions, making the conclusions drawn difficult to generalise. We analyse here an important biological problem: the evolution of hypoxia-driven migratory structures in Glioblastoma Multiforme (GBM), the most aggressive and lethal primary brain tumour. We establish a mathematical model considering the interaction of the tumour cells with oxygen concentration in what is called the go or grow paradigm. We reproduce in this work three different experiments, showing the main GBM structures (pseudopalisade and necrotic core formation), only changing the initial and boundary conditions. We prove that it is possible to obtain versatile mathematical tools which, together with a sound parametric analysis, allow to explain complex biological phenomena. We show the utility of this hybrid “biomimetic in vitro-in silico” platform to help to elucidate the mechanisms involved in cancer processes, to better understand the role of the different phenomena, to test new scientific hypotheses and to design new data-driven experiments.