bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of the Human Protein Atlas Image Classification competition
Authors: Ouyang Wei , Winsnes Casper F. , Hjelmare Martin , Cesnik Anthony J. , Åkesson Lovisa , Xu Hao , Sullivan Devin P. , Dai Shubin , Lan Jun , Jinmo Park , Galib Shaikat M. , Henkel Christof , Hwang Kevin , Poplavskiy Dmytro , Tunguz Bojan , Wolfinger Russel D. , Gu Yinzheng , Li Chuanpeng , Xie Jinbin , Buslov Dmitry , Fironov Sergei , Kiselev Alexander , Panchenko Dmytro , Cao Xuan , Wei Runmin , Wu Yuanhao , Zhu Xun , Tseng Kuan-Lun , Gao Zhifeng , Ju Cheng , Yi Xiaohan , Zheng Hongdong , Kappel Constantin , Lundberg Emma 
Published: November 2019

AbstractPinpointing subcellular protein localizations from microscopy images is easy to the trained eye, but challenging to automate. Based on the Human Protein Atlas image collection, we held a competition to identify deep learning solutions to solve this task. Challenges included training on highly imbalanced classes and predicting multiple labels per image. Over 3 months, 2,172 teams participated. Despite convergence on popular networks and training techniques, there was considerable variety among the solutions. Participants applied strategies for modifying neural networks and loss functions, augmenting data and using pretrained networks. The winning models far outperformed our previous effort at multi-label classification of protein localization patterns by ~20%. These models can be used as classifiers to annotate new images, feature extractors to measure pattern similarity or pretrained networks for a wide range of biological applications.
Impact of molecular testing on thyroid nodule neoplastic diagnosis, stratified by 4-cm size, in a surgical series
Authors: Shrestha Rupendra T. , Kizilgul Muhammed , Shahi Maryam , Amin Khalid , Evasovich Maria R. , Burmeister Lynn A. 
Published: November 2019

AbstractWhether molecular testing adds diagnostic value to the evaluation of thyroid nodules 4-cm or larger is unknown. The impact of molecular testing on cytopathologic-histopathologic diagnosis of neoplasm (adenoma or malignant), stratified by nodule size <or≥ 4-cm, was analyzed from a surgical series. Of 490 index nodules, molecular testing was performed on 18% of 353 nodules <4-cm and 8.8% of 137 nodules ≥4-cm (p = 0.0118). Adenoma was higher (30% vs 14%) and malignancy lower in nodules ≥4-cm vs <4-cm (p < 0.0001). Molecular testing impacted the finding of malignancy in the <4-cm group. Molecular testing of the ≥4-cm AUS and FN cytology subcategory impacted neoplasm discovery (combining adenoma and malignancy), with mutation positive 100% (3/3), mutation negative 38% (3/8), no mutation testing 88% (21/24), p = 0.0122. In conclusion, more adenoma was found in nodules ≥4-cm, including those with benign cytology, which was not explained by available molecular testing results. Molecular testing impacted the finding of malignancy in thyroid nodules <4-cm. The overall number of ≥4-cm nodules with molecular testing in this study was too low to exclude its diagnostic value in this setting. Further study is recommended to include molecular testing in nodules ≥4-cm, including those with benign cytology, to identify follicular adenoma.
Computational screening of nanoparticles coupling to Aβ40 peptides and fibrils
Authors: Sen Soumyo , Vuković Lela , Král Petr 
Published: November 2019

AbstractBlocking the formation, growth, and breaking of amyloid fibrils by synthetic nanosystems could provide a treatment of neurodegenerative diseases. With this in mind, here atomistic molecular dynamics simulations are used to screen for nanoparticles (NPs), covered with different mixtures of ligands, including positively and negatively charged ligands, Aβ40-cut-peptide, and synthetic inhibitor ligands, in their selective coupling to Aβ40 peptides and their fibrils. The simulations reveal that only Aβ40-cut-peptide-covered NPs have strong and selective coupling to Aβ40 monomers. On the other hand, positive, positive-neutral, Janus, and peptide NPs couple to the beta sheet surfaces of Aβ40 fibrils and only the negative-neutral NPs couple to the fibril tips.
Amazonian Biomass Burning Enhances Tropical Andean Glaciers Melting
Authors: Magalhães Newton de , Evangelista Heitor , Condom Thomas , Rabatel Antoine , Ginot Patrick 
Published: November 2019

AbstractThe melting of tropical glaciers provides water resources to millions of people, involving social, ecological and economic demands. At present, these water reservoirs are threatened by the accelerating rates of mass loss associated with modern climate changes related to greenhouse gas emissions and ultimately land use/cover change. Until now, the effects of land use/cover change on the tropical Andean glaciers of South America through biomass burning activities have not been investigated. In this study, we quantitatively examine the hypothesis that regional land use/cover change is a contributor to the observed glacier mass loss, taking into account the role of Amazonian biomass burning. We demonstrated here, for the first time, that for tropical Andean glaciers, a massive contribution of black carbon emitted from biomass burning in the Amazon Basin does exist. This is favorable due to its positioning with respect to Amazon Basin fire hot spots and the predominant wind direction during the transition from the dry to wet seasons (Aug-Sep-Oct), when most fire events occur. We investigated changes in Bolivian Zongo Glacier albedo due to impurities on snow, including black carbon surface deposition and its potential for increasing annual glacier melting. We showed that the magnitude of the impact of Amazonian biomass burning depends on the dust content in snow. When high concentration of dust is present (e.g. 100 ppm of dust), the dust absorbs most of the radiation that otherwise would be absorbed by the BC. Our estimations point to a melting factor of 3.3 ± 0.8% for black carbon, and 5.0 ± 1.0% for black carbon in the presence of low dust content (e.g. 10 ppm of dust). For the 2010 hydrological year, we reported an increase in runoff corresponding to 4.5% of the annual discharge during the seasonal peak fire season, which is consistent with our predictions.
A real-time spatio-temporal syndromic surveillance system with application to small companion animals
Authors: Hale Alison C. , Sánchez-Vizcaíno Fernando , Rowlingson Barry , Radford Alan D. , Giorgi Emanuele , O’Brien Sarah J. , Diggle Peter J. 
Published: November 2019

AbstractLack of disease surveillance in small companion animals worldwide has contributed to a deficit in our ability to detect and respond to outbreaks. In this paper we describe the first real-time syndromic surveillance system that conducts integrated spatio-temporal analysis of data from a national network of veterinary premises for the early detection of disease outbreaks in small animals. We illustrate the system’s performance using data relating to gastrointestinal disease in dogs and cats. The data consist of approximately one million electronic health records for dogs and cats, collected from 458 UK veterinary premises between March 2014 and 2016. For this illustration, the system predicts the relative reporting rate of gastrointestinal disease amongst all presentations, and updates its predictions as new data accrue. The system was able to detect simulated outbreaks of varying spatial geometry, extent and severity. The system is flexible: it generates outcomes that are easily interpretable; the user can set their own outbreak detection thresholds. The system provides the foundation for prompt detection and control of health threats in companion animals.
Prognostic and therapeutic potential of Adenylate kinase 2 in lung adenocarcinoma
Authors: Liu Huibin , Pu Yan , Amina Quhai , Wang Qiang , Zhang Mengmeng , Song Jianzhong , Guo Jun , Mardan Mahmut 
Published: November 2019

AbstractAdenylate kinase 2 (AK2), an isoenzyme of the AK family, may have momentous extra-mitochondrial functions, especially in tumourigenesis in addition to the well-known control of energy metabolism. In this study, we provided the first evidence that AK2 is overexpressed in lung adenocarcinoma. The positive expression of AK2 is associated with tumor progression, and poor survival in patients with pulmonary adenocarcinoma. Knockdown of AK2 could suppress proliferation, migration, and invasion as well as induce apoptosis and autophagy in human lung adenocarcinoma cells. Remarkably, silencing AK2 exerted the greater tumor suppression roles when combined with hydroxychloroquine, an effective autophagy inhibitor, in vitro and in xenografts mouse models. Our data have probably provided preclinical proof that systematic inhibition of AK2 and autophagy could be therapeutically effective on lung cancer.
Sand mining in the Mekong Delta revisited - current scales of local sediment deficits
Authors: Jordan Christian , Tiede Jan , Lojek Oliver , Visscher Jan , Apel Heiko , Nguyen Hong Quan , Quang Chau Nguyen Xuan , Schlurmann Torsten 
Published: November 2019

AbstractThe delta of the Mekong River in Vietnam has been heavily impacted by anthropogenic stresses in recent years, such as upstream dam construction and sand mining within the main and distributary channels, leading to riverbank and coastal erosion. Intensive bathymetric surveys, conducted within the Tien River branch during the dry and wet season 2018, reveal a high magnitude of sand mining activities. For the year 2018, an analysis of bathymetric maps and the local refilling processes leads to an estimated sand extraction volume of 4.64 $$\pm $$± 0.31 Mm$${}^{3}$$3/yr in the study area, which covered around 20 km. Reported statistics of sand mining for all of the Mekong’s channels within the delta, which have a cumulative length of several hundred kilometres, are 17.77 Mm$${}^{3}$$3/yr for this period. Results from this study highlight that these statistics are likely too conservative. It is also shown that natural sediment supplies from upper reaches of the Mekong are insufficient to compensate for the loss of extracted bed aggregates, illustrating the non-sustainable nature of the local sand mining practices.
Population genetics of Liriomyza trifolii (Diptera: Agromyzidae) and comparison with four Liriomyza species in China based on COI, EF-1a and microsatellites loci
Authors: Chen Jing-Yun , Chang Ya-Wen , Tang Xiao-Tian , Zheng Si-Zhu , Du Yu-Zhou 
Published: November 2019

AbstractLiriomyza is a large genus that includes polyphagous and invasive species (L. trifolii, L. sativae, and L. huidobrensis), and oligophagous species such as L. Chinensis in China. Effective control of these invasive and oligophagous species is not easy due to the fast invasion rate, interspecific competition, and pesticide resistance. In this study, we investigated population genetics of five Liriomyza species L. trifolii, L. sativae, L. huidobrensis, L. bryoniae, and L. chinensis based on COI and EF-1a genes, and microsatellite DNA. These five Liriomyza species revealed highly conservative characteristics in the COI gene among populations collected from different geographical regions and host plants. By contrast, the mutation rate of the EF-1a gene was higher than COI, and phylogenetic tree based on EF-1a showed that haplotypes of L. trifolii and L. sativae were not distinguished well. Genetic differentiation in microsatellite loci was obvious among the five species. Our results also indicated that geographic isolation had a greater impact on genetic differentiation in L. trifolii than the host plant. Populations of L. trifolii in China showed a high to moderate level of genetic differentiation and they had divided into two groups representing the coastal areas of southern China and northern regions. The genetic diversity of the southern group was higher than the northern group. We speculated that the invasion of L. trifolii likely occurred in southern regions of China and then spread northward. Bottleneck analyses revealed that the L. trifolii population in China was in a steady growth period.
Highly divergent lineage of narrow-headed vole from the Late Pleistocene Europe
Authors: Baca Mateusz , Popović Danijela , Lemanik Anna , Baca Katarzyna , Horáček Ivan , Nadachowski Adam 
Published: November 2019

AbstractDuring the Late Pleistocene, narrow-headed voles (Lasiopodomys gregalis) inhabited Eurasia’s vast territories, frequently becoming the dominant small mammal species among steppe-tundra communities. We investigated the relationship between this species’ European and Asiatic populations by sequencing the mtDNA genomes of two extant specimens from Russia and 10 individuals from five Central European sites, dated to the post-LGM period. Phylogenetic analyses based on a large portion of mtDNA genomes highly supported the positioning ofL. gregaliswithinArvicolinae. The phylogeny based on mtDNA cytochromebsequences revealed a deep divergence of European narrow-headed voles from Asiatic ones and their sister position against the extantL. gregalisandL. raddei. The divergence of the European lineage was estimated to a minimum 230 thousand years ago. This suggest, contrary to the current biogeographic hypotheses, that during the interglacial periods narrow-headed vole did not retreat from Europe but survived the unfavourable conditions within the refugial areas. Based on this result, we propose to establish a cryptic species status for the Late Pleistocene European narrow-headed vole and to name this taxonLasiopodomys anglicus.
Real-time prediction of patient immune cell modulation during irreversible electroporation therapy
Authors: Beitel-White N. , Martin R. C. G. , Li Y. , Brock R. M. , Allen I. C. , Davalos R. V. 
Published: November 2019

AbstractImmunotherapies have demonstrated limited efficacy in pancreatic ductal adenocarcinoma (PDAC) patients despite their success in treating other tumor types. This limitation is largely due to the relatively immunosuppressive environment surrounding the tumor. A focal ablative technique called irreversible electroporation (IRE) has been shown to modulate this environment, enhancing the efficacy of immunotherapy. One enhancing factor related to improved prognosis is a decrease in regulatory T cells (Treg). This decrease has been previously unpredictable for clinicians using IRE, who currently have limited real-time metrics for determining the activation of the patient’s immune response. Here, we report that larger overall changes in output current are correlated with larger decreases in T cell populations 24 hours post-treatment. This result suggests that clinicians can make real-time decisions regarding optimal follow-up therapy based on the range of output current delivered during treatment. This capability could maximize the immunomodulating effect of IRE in synergy with follow-up immunotherapy. Additionally, these results suggest that feedback from a preliminary IRE treatment of the local tumor may help inform clinicians regarding the timing and choice of subsequent therapies, such as resection, immunotherapy, chemotherapy, or follow-up thermal or non-thermal ablation.
Self-harm behaviour and externally-directed aggression in psychiatric outpatients: a multicentre, prospective study (viormed-2 study)
Authors: Scocco Paolo , Macis Ambra , Ferrari Clarissa , Bava Mattia , Bianconi Giorgio , Bulgari Viola , Candini Valentina , Carrà Giuseppe , Cavalera Cesare , Clerici Massimo , Conte Giovanni , Cricelli Marta , Teresa Ferla Maria , Iozzino Laura , Stefana Alberto , de Girolamo Giovanni 
Published: November 2019

AbstractThe aim of the project was to investigate differences between outpatients with Severe Mental Disorders (SMDs) with and without a history of Self-Harm behaviour (SHb) and/or Violent behaviour against other people (Vb) in relation to: (a) socio-demographic and clinical characteristics, (b) violent behaviour during a 1-year FU, (c) predictors of SHb and Vb during the FU. Outpatients with SMDs, with and without a history of Vb were enrolled. They were divided in four groups: patients with lifetime Vb (V), patients with both Vb and SHb (V-SH), patients with only SHb (SH) and patients with no history of SHb and Vb (control group, CONT). The frequency and severity of SHb and Vb during the FU were assessed every two weeks by the MOAS. Overall 246 patients were enrolled. BPRS-E Depression item, the SLOF Social acceptability, the BDHI Indirect Aggression, the BIS Motor Impulsiveness and the STAXI-2 Control-Out showed significant correlations with all the four groups (p < 0.030). V and V-SH patient groups reached higher scores in all MOAS sub-scales. Age among the SH group and BPRS-E affect-anxiety subscale among the V group significantly predicted aggression against people. In people with SMDs a history of SHb or Vb is associated with different medium-term outcomes.
Covalent Epitope Decoration of Carbon Electrodes using Solid Phase Peptide Synthesis
Authors: Candelaria Lindsay , Kalugin Peter N. , Kowalski Brian M. , Kalugin Nikolai G. 
Published: November 2019

AbstractLong-term, minimally perturbative brain electrophysiology requires electrodes to seamlessly integrate into surrounding tissue. In this work, we demonstrate electrodes composed of covalently functionalized graphite, decorated with various functional affinity and epitope tags, and use them to detect changes in electrical potential on the surfaces of illuminated quantum dots and near fluorescing molecules. Affinity and epitope tagging of carbon was achieved using direct attachment of biotin and solid phase peptide synthesis (SPPS) of histidine (His)- and human influenza hemagglutinin (HA)-tags. Surface modification was confirmed with Auger, Energy-Dispersive X-ray (EDX), Raman, and fluorescence spectroscopy. Photoresponse was detected with compatible binding protein-surface tag combinations, confirming desired tag and electrode functionality. These results provide a path to organic, biofunctionalized, fully molecularly-defined electrodes for neuronal applications, and to a wide range of other secondary reactions and modifications of carbon; potential uses include affinity chromatography, DNA sequencing technologies, biomolecular sensors, and surfaces and scaffolds for targeted interfaces with biological tissues.
Development of a diagnostic compatible BCG vaccine against Bovine tuberculosis
Authors: Chandran Aneesh , Williams Kerstin , Mendum Tom , Stewart Graham , Clark Simon , Zadi Sirine , Lanni Faye , McLeod Neil , Williams Ann , Villarreal-Ramos Bernardo , Vordermeier Martin , Maroudam Veerasamy , Prasad Aravind , Bharti Neeraj , Banerjee Ruma , Manjari Kasibhatla Sunitha , McFadden Johnjoe 
Published: November 2019

AbstractBovine tuberculosis (BTB) caused by Mycobacterium bovis remains a major problem in both the developed and developing countries. Control of BTB in the UK is carried out by test and slaughter of infected animals, based primarily on the tuberculin skin test (PPD). Vaccination with the attenuated strain of the M. bovis pathogen, BCG, is not used to control bovine tuberculosis in cattle at present, due to its variable efficacy and because it interferes with the PPD test. Diagnostic tests capable of Differentiating Infected from Vaccinated Animals (DIVA) have been developed that detect immune responses to M. bovis antigens absent in BCG; but these are too expensive and insufficiently sensitive to be used for BTB control worldwide. To address these problems we aimed to generate a synergistic vaccine and diagnostic approach that would permit the vaccination of cattle without interfering with the conventional PPD-based surveillance. The approach was to widen the pool of M. bovis antigens that could be used as DIVA targets, by identifying antigenic proteins that could be deleted from BCG without affecting the persistence and protective efficacy of the vaccine in cattle. Using transposon mutagenesis we identified genes that were essential and those that were non-essential for persistence in bovine lymph nodes. We then inactivated selected immunogenic, but non-essential genes in BCG Danish to create a diagnostic-compatible triple knock-out ΔBCG TK strain. The protective efficacy of the ΔBCG TK was tested in guinea pigs experimentally infected with M. bovis by aerosol and found to be equivalent to wild-type BCG. A complementary diagnostic skin test was developed with the antigenic proteins encoded by the deleted genes which did not cross-react in vaccinated or in uninfected guinea pigs. This study demonstrates the functionality of a new and improved BCG strain which retains its protective efficacy but is diagnostically compatible with a novel DIVA skin test that could be implemented in control programmes.
The circadian clock uses different environmental time cues to synchronize emergence and locomotion of the solitary bee Osmia bicornis
Authors: Beer Katharina , Schenk Mariela , Helfrich-Förster Charlotte , Holzschuh Andrea 
Published: November 2019

AbstractLife on earth adapted to the daily reoccurring changes in environment by evolving an endogenous circadian clock. Although the circadian clock has a crucial impact on survival and behavior of solitary bees, many aspects of solitary bee clock mechanisms remain unknown. Our study is the first to show that the circadian clock governs emergence in Osmia bicornis, a bee species which overwinters as adult inside its cocoon. Therefore, its eclosion from the pupal case is separated by an interjacent diapause from its emergence in spring. We show that this bee species synchronizes its emergence to the morning. The daily rhythms of emergence are triggered by temperature cycles but not by light cycles. In contrast to this, the bee’s daily rhythms in locomotion are synchronized by light cycles. Thus, we show that the circadian clock of O. bicornis is set by either temperature or light, depending on what activity is timed. Light is a valuable cue for setting the circadian clock when bees have left the nest. However, for pre-emerged bees, temperature is the most important cue, which may represent an evolutionary adaptation of the circadian system to the cavity-nesting life style of O. bicornis.
NV center based nano-NMR enhanced by deep learning
Authors: Aharon Nati , Rotem Amit , McGuinness Liam P. , Jelezko Fedor , Retzker Alex , Ringel Zohar 
Published: November 2019

AbstractThe growing field of nano nuclear magnetic resonance (nano-NMR) seeks to estimate spectra or discriminate between spectra of minuscule amounts of complex molecules. While this field holds great promise, nano-NMR experiments suffer from detrimental inherent noise. This strong noise masks to the weak signal and results in a very low signal-to-noise ratio. Moreover, the noise model is usually complex and unknown, which renders the data processing of the measurement results very complicated. Hence, spectra discrimination is hard to achieve and in particular, it is difficult to reach the optimal discrimination. In this work we present strong indications that this difficulty can be overcome by deep learning (DL) algorithms. The DL algorithms can mitigate the adversarial effects of the noise efficiently by effectively learning the noise model. We show that in the case of frequency discrimination DL algorithms reach the optimal discrimination without having any pre-knowledge of the physical model. Moreover, the DL discrimination scheme outperform Bayesian methods when verified on noisy experimental data obtained by a single Nitrogen-Vacancy (NV) center. In the case of frequency resolution we show that this approach outperforms Bayesian methods even when the latter have full pre-knowledge of the noise model and the former has none. These DL algorithms also emerge as much more efficient in terms of computational resources and run times. Since in many real-world scenarios the noise is complex and difficult to model, we argue that DL is likely to become a dominant tool in the field.