bluuebunny/crossref_metadata_2025_split huggingface dataset:
A dataset of road-killed vertebrates collected via citizen science from 2014–2020
Authors: Heigl Florian , Teufelbauer Norbert , Resch Stefan , Schweiger Silke , Stückler Susanne , Dörler Daniel 
Published: August 2022

AbstractData on road-killed animals is essential for assessing the impact of roads on biodiversity. In most European countries data on road-killed huntable wildlife exists, but data on other vertebrate species (e.g. amphibians, reptiles, small mammals) is scarce. Therefore, we conducted a citizen science project on road-killed vertebrates as a useful supplement to data on huntable wildlife collected by public authorities. The dataset contains 15198 reports with 17163 individual road-killed vertebrates collected by 912 participants. The reports were made in 44 countries, but the majority of data was reported in Austria. We implemented a data validation routine which led to three quality levels. Reports in quality level 1 are published via GBIF, reports in quality level 2 via Zenodo and reports in quality level 3 were deleted. The dataset is relevant for the scientific community studying impacts of roads on fauna as well as for those who are responsible for road planning and implementing mitigation measures.
An Electroencephalography-based Database for studying the Effects of Acoustic Therapies for Tinnitus Treatment
Authors: Cuevas-Romero Alma Rosa , Alonso-Valerdi Luz María , Intriago-Campos Luis Alejandro , Ibarra-Zárate David Isaac 
Published: August 2022

AbstractThe present database provides demographic (age and sex), clinical (hearing loss and acoustic properties of tinnitus), psychometric (based on Tinnitus Handicapped Inventory and Hospital Anxiety and Depression Scale) and electroencephalographic information of 89 tinnitus sufferers who were semi-randomly treated for eight weeks with one of five acoustic therapies. These were (1) placebo (relaxing music), (2) tinnitus retraining therapy, (3) auditory discrimination therapy, (4) enriched acoustic environment, and (5) binaural beats therapy. Fourteen healthy volunteers who were exposed to relaxing music and followed the same experimental procedure as tinnitus sufferers were additionally included in the study (control group). The database is available at https://doi.org/10.17632/kj443jc4yc.1. Acoustic therapies were monitored one week after, three weeks after, five weeks after, and eight weeks after the acoustic therapy. This study was previously approved by the local Ethical Committee (CONBIOETICA19CEI00820130520), it was registered as a clinical trial (ISRCTN14553550) in BioMed Central (Springer Nature), the protocol was published in 2016, it attracted L’Oréal-UNESCO Organization as a sponsor, and six journal publications have resulted from the analysis of this database.
Nitrogen use aggravates bacterial diversity and network complexity responses to temperature
Authors: Xing Xiaoyi , Xu Huifang , Wang Dou , Yang Xianjun , Qin Hongling , Zhu Baoli 
Published: August 2022

AbstractRising temperature affects microbial composition and function in agriculture field, especially under nitrogen fertilization. In this study, we investigated the bacterial community of paddy soil incubated at controlled temperatures (5 °C, 15 °C, 25 °C, and 35 °C). Results showed that the response of bacterial communities to temperature was not uniform. Temperature elevation from 15 to 25 °C abruptly shifted the soil bacterial community, whereas elevation from 5 to 15 °C and from 25 to 35 °C had a marginal effect. The bacterial α-diversity was higher at 5 °C and 15 °C, owing to the massively distributed taxa with low abundance. However, as the temperature increased to 25 °C and 35 °C, these taxa were diminished, whereas Firmicutes significantly increased, resulting in a strong decline in α-diversity. Simultaneously, bacterial network complexity significantly increased at 25 °C and 35 °C, indicating the bacteria had closer interactions. Nitrogen application aggravated the variation in bacterial diversity and network complexity among temperatures. Interestingly, most complex network was observed under higher temperatures in fertilized soils. Collectively, these results indicate that nitrogen exacerbates the response of the soil bacterial community to temperature, and association between diversity and network complexity may be present.
Structural characterization of aspartate-semialdehyde dehydrogenase from Pseudomonas aeruginosa and Neisseria gonorrhoeae
Authors: Teakel S. L. , Fairman J. W. , Muruthi M. M. , Abendroth J. , Dranow D. M. , Lorimer D. D. , Myler P. J. , Edwards T. E. , Forwood J. K. 
Published: August 2022

AbstractGonorrhoea infection rates and the risk of infection from opportunistic pathogens including P. aeruginosa have both risen globally, in part due to increasing broad-spectrum antibiotic resistance. Development of new antimicrobial drugs is necessary and urgent to counter infections from drug resistant bacteria. Aspartate-semialdehyde dehydrogenase (ASADH) is a key enzyme in the aspartate biosynthetic pathway, which is critical for amino acid and metabolite biosynthesis in most microorganisms including important human pathogens. Here we present the first structures of two ASADH proteins from N. gonorrhoeae and P. aeruginosa solved by X-ray crystallography. These high-resolution structures present an ideal platform for in silico drug design, offering potential targets for antimicrobial drug development as emerging multidrug resistant strains of bacteria become more prevalent.
Genetic structure and trait variation within a maple hybrid zone underscore North China as an overlooked diversity hotspot
Authors: Yang Rui , Deng Ya-Wen , Liu Yan , Zhao Jing , Bao Lei , Ge Jian-Ping , Wang Hong-Fang 
Published: August 2022

AbstractTertiary relict flora in East Asia can be divided into northern and southern regions. North China is a diversity hotspot because it can be the secondary contact zone of ancient lineages from the two regions. To test the extent of ancient lineages hybridization and distinguish between the putative species pair Acer pictum subsp. mono and Acer truncatum, we conducted genetic and ecological studies within a maple hybrid zone in North China. Our results suggest that the two lineages of Acer coexist in the hybrid zone and that adult and offspring populations show typical bimodal genetic patterns. Hybrid individuals are established at intermediate altitudes between the two parental lineages. Flowering phenology is divergent between lineages, whereas the complex sexual system of Acer may ensure pollination among lineages. Leaf and fruit morphologies are different between the northern and southern origin lineages, corresponding to A. pictum subsp. mono and A. truncatum, respectively. Reduced gene flow between lineages suggests that they should be considered as two species. However, large morphological variations within each species and the existence of hybrids offer low reliability of species identification based solely on morphological traits. Our study underscores North China as an overlooked diversity hotspot that requires further study in the future.
Low pH structure of heliorhodopsin reveals chloride binding site and intramolecular signaling pathway
Authors: Besaw Jessica E. , Reichenwallner Jörg , De Guzman Paolo , Tucs Andrejs , Kuo Anling , Morizumi Takefumi , Tsuda Koji , Sljoka Adnan , Miller R. J. Dwayne , Ernst Oliver P. 
Published: August 2022

AbstractWithin the microbial rhodopsin family, heliorhodopsins (HeRs) form a phylogenetically distinct group of light-harvesting retinal proteins with largely unknown functions. We have determined the 1.97 Å resolution X-ray crystal structure of Thermoplasmatales archaeon SG8-52-1 heliorhodopsin (TaHeR) in the presence of NaCl under acidic conditions (pH 4.5), which complements the known 2.4 Å TaHeR structure acquired at pH 8.0. The low pH structure revealed that the hydrophilic Schiff base cavity (SBC) accommodates a chloride anion to stabilize the protonated retinal Schiff base when its primary counterion (Glu-108) is neutralized. Comparison of the two structures at different pH revealed conformational changes connecting the SBC and the extracellular loop linking helices A–B. We corroborated this intramolecular signaling transduction pathway with computational studies, which revealed allosteric network changes propagating from the perturbed SBC to the intracellular and extracellular space, suggesting TaHeR may function as a sensory rhodopsin. This intramolecular signaling mechanism may be conserved among HeRs, as similar changes were observed for HeR 48C12 between its pH 8.8 and pH 4.3 structures. We additionally performed DEER experiments, which suggests that TaHeR forms possible dimer-of-dimer associations which may be integral to its putative functionality as a light sensor in binding a transducer protein.
Predicting social anxiety in young adults with machine learning of resting-state brain functional radiomic features
Authors: Kim Byung-Hoon , Kim Min-Kyeong , Jo Hye-Jeong , Kim Jae-Jin 
Published: August 2022

AbstractSocial anxiety is a symptom widely prevalent among young adults, and when present in excess, can lead to maladaptive patterns of social behavior. Recent approaches that incorporate brain functional radiomic features and machine learning have shown potential for predicting certain phenotypes or disorders from functional magnetic resonance images. In this study, we aimed to predict the level of social anxiety in young adult participants by training machine learning models with resting-state brain functional radiomic features including the regional homogeneity, fractional amplitude of low-frequency fluctuation, fractional resting-state physiological fluctuation amplitude, and degree centrality. Among the machine learning models, the XGBoost model achieved the best performance with balanced accuracy of 77.7% and F1 score of 0.815. Analysis of input feature importance demonstrated that the orbitofrontal cortex and the degree centrality were most relevant to predicting the level of social anxiety among the input brain regions and the input type of radiomic features, respectively. These results suggest potential validity for predicting social anxiety with machine learning of the resting-state brain functional radiomic features and provide further understanding of the neural basis of the symptom.
An image based application in Matlab for automated modelling and morphological analysis of insect wings
Authors: Eshghi Shahab , Nabati Fatemeh , Shafaghi Shaghayegh , Nooraeefar Vahid , Darvizeh Abolfazl , Gorb Stanislav N. , Rajabi Hamed 
Published: August 2022

AbstractDespite extensive research on the biomechanics of insect wings over the past years, direct mechanical measurements on sensitive wing specimens remain very challenging. This is especially true for examining delicate museum specimens. This has made the finite element method popular in studies of wing biomechanics. Considering the complexities of insect wings, developing a wing model is usually error-prone and time-consuming. Hence, numerical studies in this area have often accompanied oversimplified models. Here we address this challenge by developing a new tool for fast, precise modelling of insect wings. This application, calledWingGram, uses computer vision to detect the boundaries of wings and wing cells from a 2D image. The app can be used to develop wing models that include complex venations, corrugations and camber.WingGramcan extract geometric features of the wings, including dimensions of the wing domain and subdomains and the location of vein junctions. Allowing researchers to simply model wings with a variety of forms, shapes and sizes, our application can facilitate studies of insect wing morphology and biomechanics. Being an open-access resource,WingGramhas a unique application to expand how scientists, educators, and industry professionals analyse insect wings and similar shell structures in other fields, such as aerospace.
Application of XGBoost model for in-situ water saturation determination in Canadian oil-sands by LF-NMR and density data
Authors: Markovic Strahinja , Bryan Jonathan L. , Rezaee Reza , Turakhanov Aman , Cheremisin Alexey , Kantzas Apostolos , Koroteev Dmitry 
Published: August 2022

AbstractWater saturation determination is among the most challenging tasks in petrophysical well-logging, which directly impacts the decision-making process in hydrocarbon exploration and production. Low-field nuclear magnetic resonance (LF-NMR) measurements can provide reliable evaluation. However, quantification of oil and water volumes is problematic when their NMR signals are not distinct. To overcome this, we developed two machine learning frameworks for predicting relative water content in oil-sand samples using LF-NMR spin–spin (T2) relaxation and bulk density data to derive a model based on Extreme Gradient Boosting. The first one facilitates feature engineering based on empirical knowledge from the T2 relaxation distribution analysis domain and mutual information feature extraction technique, while the second model considers whole samples’ NMR T2-relaxation distribution. The NMR T2 distributions were obtained for 82 Canadian oil-sands samples at ambient and reservoir temperatures (164 data points). The true water content was determined by Dean-Stark extraction. The statistical scores confirm the strong generalization ability of the feature engineering LF-NMR model in predicting relative water content by Dean-Stark—root-mean-square error of 0.67% and mean-absolute error of 0.53% (R2 = 0.90). Results indicate that this approach can be extended for the improved in-situ water saturation evaluation by LF-NMR and bulk density measurements.
CX-5461 causes nucleolar compaction, alteration of peri- and intranucleolar chromatin arrangement, an increase in both heterochromatin and DNA damage response
Authors: Snyers Luc , Laffer Sylvia , Löhnert Renate , Weipoltshammer Klara , Schöfer Christian 
Published: August 2022

AbstractIn this study, we characterize the changes in nucleolar morphology and its dynamics induced by the recently introduced compound CX-5461, an inhibitor of ribosome synthesis. Time-lapse imaging, immunofluorescence and ultrastructural analysis revealed that exposure of cells to CX-5461 has a profound impact on their nucleolar morphology and function: nucleoli acquired a compact, spherical shape and display enlarged, ring-like masses of perinucleolar condensed chromatin. Tunnels consisting of chromatin developed as transient structures running through nucleoli. Nucleolar components involved in rRNA transcription, fibrillar centres and dense fibrillar component with their major constituents ribosomal DNA, RNA polymerase I and fibrillarin maintain their topological arrangement but become reduced in number and move towards the nucleolar periphery. Nucleolar changes are paralleled by an increased amount of the DNA damage response indicator γH2AX and DNA unwinding enzyme topoisomerase I in nucleoli and the perinucleolar area suggesting that CX-5461 induces torsional stress and DNA damage in rDNA. This is corroborated by the irreversibility of the observed altered nucleolar phenotypes. We demonstrate that incubation with CX-5461, apart from leading to specific morphological alterations, increases senescence and decreases cell replication. We discuss that these alterations differ from those observed with other drugs interfering with nucleolar functions.
Diabetic retinopathy screening and treatment through the Brazilian National Health Insurance
Authors: Fernandes Arthur Gustavo , Ferraz Aline Nunes , Brant Rodrigo , Malerbi Fernando Korn 
Published: August 2022

AbstractThe current study aimed to investigate diabetic retinopathy (DR) screening and treatment coverages among diabetic patients evaluated through the Brazilian National Health Insurance from 2014 to 2019. The Brazilian Public Health System Information Database was used as the primary data source. DR screening coverage was calculated as the rate of procedures of clinical dilated fundus exam and color fundus photograph over the number of diabetic patients. DR treatment coverage was calculated as the rate of procedures of intravitreal injection, photocoagulation, and panretinal photocoagulation over the number of diabetic patients presumably in need of DR treatment. The overall screening coverage increased from 12.1% in 2014 to 21.2% in 2019 (p < 0.001) with substantial regional discrepancies so that North region was the only one with no changes along the period. The overall treatment coverage increased from 27.7% in 2014 to 44.1% in 2019, with Southeast and Midwest absorbing the demand for service from the North, Northeast and South. Despite an improvement along the past years, both screening and treatment coverages for DR in diabetes patients are ineffective in Brazil. Public health policies should address resources disparities throughout the country aiming to offer same healthcare conditions to patients regardless their geographic location.
Topology optimization of a heat-assisted magnetic recording write head to reduce transition curvature using a binary optimization algorithm utilizing the adjoint method
Authors: Wautischer Gregor , Abert Claas , Bruckner Florian , Slanovc Florian , Suess Dieter 
Published: August 2022

AbstractIn this work, the possibility to reduce transition curvature in heat-assisted magnetic recording, using a conventional write head design, by shaping the recording field to counteract the circular profile of the heat pulse is investigated. Topology optimization of the head tip is performed in order to create the desired cross-track field profile for increasing distances from the write head tip. For the topology optimization, the adjoint method is utilized to calculate the necessary gradients and a binary optimization scheme is proposed. The optimizations are performed considering linearized material parameters reducing the computational complexity and the results are compared to optimizations incorporating the full non-linear material behavior. The optimized field profiles are evaluated for their influence on the read-back process. To do so, switching probability phase diagrams are calculated and the curvature parameter, the signal to noise ratio and the channel bit density are extracted. The presented results show that while transition curvature can be reduced by shaping the cross-track profile of the write field, this alone does not consequently lead to an improvement of the read back process. Therefore, completely new head designs, considering additional parameters have to be investigated.
Verteporfin ameliorates fibrotic aspects of Dupuytren’s disease nodular fibroblasts irrespective the activation state of the cells
Authors: Puerta Cavanzo Nataly , Riesmeijer Sophie A. , Holt-Kedde Iris L. , Werker Paul M. N. , Piersma Bram , Olinga Peter , Bank Ruud A. 
Published: August 2022

AbstractDupuytren’s disease is a chronic, progressive fibroproliferative condition of the hand fascia which results in digital contraction. So far, treatments do not directly interfere with the (myo)fibroblasts that are responsible for the formation of the collagen-rich cords and its contraction. Here we investigated whether verteporfin (VP) is able to inhibit the activation and subsequent differentiation of DD nodular fibroblasts into myofibroblasts. Fibroblasts were isolated from nodules of 7 Dupuytren patients. Cells are treated (1) for 48 h with 5 ng/ml transforming growth factor β1 (TGF-β1) followed by 48 h with/without 250 nM VP in the absence of TGF-β1, or treated (2) for 48 h with TGF-β1 followed by 48 h with/without VP in the presence of TGF-β1. mRNA levels were measured by means of Real-Time PCR, and proteins were visualized by means of Western blotting and/or immunofluorescence. Quantitative data were statistically analyzed with GraphPad Prism using the paired t-test. We found that fibroblasts activated for 48 h with TGF-β1 show a decrease in mRNA levels of COL1A1, COL3A1, COL4A1, PLOD2, FN1EDA, CCN2 and SERPINE1 when exposed for another 48 h with VP, whereas no decrease is seen for ACTA2, YAP1, SMAD2 and SMAD3 mRNA levels. Cells exposed for an additional 48 h with TGF-β1, but now in the presence of VP, are not further activated anymore, whereas in the absence of VP the cells continue to differentiate into myofibroblasts. Collagen type I, fibronectin-extra domain A, α-smooth muscle actin, YAP1, Smad2 and Smad3 protein levels were attenuated by both VP treatments. We conclude that VP has strong anti-fibrotic properties: it is able to halt the differentiation of fibroblasts into myofibroblasts, and is also able to reverse the activation status of fibroblasts. The decreased protein levels of YAP1, Smad2 and Smad3 in the presence of VP explain in part the strong anti-fibrotic properties of VP. Verteporfin is clinically used as a photosensitizer for photodynamic therapy to eliminate abnormal blood vessels in the eye to attenuate macular degeneration. The antifibrotic properties of VP do not rely on photo-activation, as we used the molecule in its non-photoinduced state.
A delay deviation tolerance IP geolocation method with error estimation
Authors: Zu Shuodi , Luo Xiangyang , Du Shaoyong , Wang Liang 
Published: August 2022

AbstractIP geolocation is an important basis of location-based network services, while error estimation is an important basis for judging the reliability of results. Most of the existing IP geolocation algorithms cannot estimate the geolocation error. A few can achieve error estimation through high-precision delay measurement, but their performance is also affected by the common delay inflation in the actual network. A new IP target location estimation method is proposed in this manuscript to achieve geolocation with reliable error estimation of IP targets in actual network. Firstly, after the landmark set divided into training set and verification set for path detection, the metropolitan area network (MAN) topology is extracted through train path set. Secondly, the governed landmarks are searched level by level through the MAN, and the minimum covering circles are calculated through the geographical distribution of the landmarks to infer the routers’ area center. Then, geolocation errors are counted after simulated geolocation through the verification path set, and the minimum mean square error radius of the error mean and the minimum covering circle radius is calculated as the router area radius. Finally, the path to the IP target is measured and compared with the MAN to get the location estimation result. The experimental results based on 12 cities in China show that compared with the existing typical algorithms, the proposed method not only improves the error estimation accuracy, but also has finer geolocation granularity and lower median error.