bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping protein interactions in the active TOM-TIM23 supercomplex
Authors: Gomkale Ridhima , Linden Andreas , Neumann Piotr , Schendzielorz Alexander Benjamin , Stoldt Stefan , Dybkov Olexandr , Kilisch Markus , Schulz Christian , Cruz-Zaragoza Luis Daniel , Schwappach Blanche , Ficner Ralf , Jakobs Stefan , Urlaub Henning , Rehling Peter 
Published: September 2021

AbstractNuclear-encoded mitochondrial proteins destined for the matrix have to be transported across two membranes. The TOM and TIM23 complexes facilitate the transport of precursor proteins with N-terminal targeting signals into the matrix. During transport, precursors are recognized by the TIM23 complex in the inner membrane for handover from the TOM complex. However, we have little knowledge on the organization of the TOM-TIM23 transition zone and on how precursor transfer between the translocases occurs. Here, we have designed a precursor protein that is stalled during matrix transport in a TOM-TIM23-spanning manner and enables purification of the translocation intermediate. Combining chemical cross-linking with mass spectrometric analyses and structural modeling allows us to map the molecular environment of the intermembrane space interface of TOM and TIM23 as well as the import motor interactions with amino acid resolution. Our analyses provide a framework for understanding presequence handover and translocation during matrix protein transport.
Approaching disorder-tolerant semiconducting polymers
Authors: Yan Xinwen , Xiong Miao , Deng Xin-Yu , Liu Kai-Kai , Li Jia-Tong , Wang Xue-Qing , Zhang Song , Prine Nathaniel , Zhang Zhuoqiong , Huang Wanying , Wang Yishan , Wang Jie-Yu , Gu Xiaodan , So Shu Kong , Zhu Jia , Lei Ting 
Published: September 2021

AbstractDoping has been widely used to control the charge carrier concentration in organic semiconductors. However, in conjugated polymers, n-doping is often limited by the tradeoff between doping efficiency and charge carrier mobilities, since dopants often randomly distribute within polymers, leading to significant structural and energetic disorder. Here, we screen a large number of polymer building block combinations and explore the possibility of designing n-type conjugated polymers with good tolerance to dopant-induced disorder. We show that a carefully designed conjugated polymer with a single dominant planar backbone conformation, high torsional barrier at each dihedral angle, and zigzag backbone curvature is highly dopable and can tolerate dopant-induced disorder. With these features, the designed diketopyrrolopyrrole (DPP)-based polymer can be efficiently n-doped and exhibit high n-type electrical conductivities over 120 S cm−1, much higher than the reference polymers with similar chemical structures. This work provides a polymer design concept for highly dopable and highly conductive polymeric semiconductors.
Dataset for predicting single-spot proton ranges in proton therapy of prostate cancer
Authors: Freitas Hugo , Magalhaes Martins Paulo , Tessonnier Thomas , Ackermann Benjamin , Brons Stephan , Seco Joao 
Published: September 2021

AbstractThe number of radiotherapy patients treated with protons has increased from less than 60,000 in 2007 to more than 220,000 in 2019. However, the considerable uncertainty in the positioning of the Bragg peak deeper in the patient raised new challenges in the proton therapy of prostate cancer (PCPT). Here, we describe and share a dataset where 43 single-spot anterior beams with defined proton energies were delivered to a prostate phantom with an inserted endorectal balloon (ERB) filled either with water only or with a silicon-water mixture. The nuclear reactions between the protons and the silicon yield a distinct prompt gamma energy line of 1.78 MeV. Such energy peak could be identified by means of prompt gamma spectroscopy (PGS) for the protons hitting the ERB with a three-sigma threshold. The application of a background-suppression technique showed an increased rejection capability for protons hitting the prostate and the ERB with water only. We describe each dataset, document the full processing chain, and provide the scripts for the statistical analysis.
Dihydroergotamine and triptan use to treat migraine during pregnancy and the risk of adverse pregnancy outcomes
Authors: Bérard Anick , Strom Shannon , Zhao Jin-Ping , Kori Shashi , Albrecht Detlef 
Published: September 2021

AbstractMigraine is prevalent during pregnancy. Antimigraine medications such as dihydroergotamine (DHE) and triptans have been associated with adverse pregnancy outcomes in individual studies but lack of consensus remains. We compared the risk of prematurity, low birth weight (LBW), major congenital malformations (MCM), and spontaneous abortions (SA) associated with gestational use of DHE or triptans. Three cohort and one nested-case–control analyses were conducted within the Quebec Pregnancy Cohort to assess the risk of prematurity, LBW, MCM, and SA. Exposure was defined dichotomously as use of DHE or triptan during pregnancy. Generalized estimation equations were built to quantify the associations, adjusting for potential confounders. 233,900 eligible pregnancies were included in the analyses on prematurity, LBW, and MCM; 29,104 cases of SA were identified. Seventy-eight subjects (0.03%) were exposed to DHE and 526 (0.22%) to triptans. Adjusting for potential confounders, DHE and triptans were associated with increased risks of prematurity, LBW, MCM, and SA but not all estimates were statistically significant. DHE was associated with the risk of prematurity (aRR: 4.12, 95% CI 1.21–13.99); triptans were associated with the risk of SA (aOR: 1.63, 95% CI 1.34–1.98). After considering maternal migraine, all antimigraine specific medications increased the risk of some adverse pregnancy outcomes, but estimates were unstable.
Intravenous injection of cyclophilin A realizes the transient and reversible opening of barrier of neural vasculature through basigin in endothelial cells
Authors: Nakada-Honda Narumi , Cui Dan , Matsuda Satoshi , Ikeda Eiji 
Published: September 2021

AbstractNeural vasculature forms the blood–brain barrier against the delivery of systemically administered therapeutic drugs into parenchyma of neural tissues. Therefore, procedures to open the blood–brain barrier with minimal damage to tissues would lead to the great progress in therapeutic strategy for intractable neural diseases. In this study, through analyses with mouse in vitro brain microvascular endothelial cells and in vivo neural vasculature, we demonstrate that the administration of cyclophilin A (CypA), a ligand of basigin which is expressed in barrier-forming endothelial cells, realizes the artificial opening of blood–brain barrier. Monolayers of endothelial cells lost their barrier properties through the disappearance of claudin-5, an integral tight junction molecule, from cell membranes in a transient and reversible manner. Furthermore, the intravenous injection of a single dose of CypA into mice resulted in the opening of blood–brain barrier for a certain period which enabled the enhanced delivery of systemically administered doxorubicin into the parenchyma of neural tissues. These findings that the pre-injection of a single dose of CypA realizes an artificial, transient as well as reversible opening of blood–brain barrier are considered to be a great step toward the establishment of therapeutic protocols to overcome the intractability of neural diseases.
Proteomic and molecular dynamic investigations of PTM-induced structural fluctuations in breast and ovarian cancer
Authors: Tikhonov Dmitry , Kulikova Liudmila , Kopylov Arthur T. , Rudnev Vladimir , Stepanov Alexander , Malsagova Kristina , Izotov Alexander , Kulikov Dmitry , Zulkarnaev Alexey , Enikeev Dmitry , Potoldykova Natalia , Kaysheva Anna L. 
Published: September 2021

AbstractPost-translational processing leads to conformational changes in protein structure that modulate molecular functions and change the signature of metabolic transformations and immune responses. Some post-translational modifications (PTMs), such as phosphorylation and acetylation, are strongly related to oncogenic processes and malignancy. This study investigated a PTM pattern in patients with gender-specific ovarian or breast cancer. Proteomic profiling and analysis of cancer-specific PTM patterns were performed using high-resolution UPLC-MS/MS. Structural analysis, topology, and stability of PTMs associated with sex-specific cancers were analyzed using molecular dynamics modeling. We identified highly specific PTMs, of which 12 modified peptides from eight distinct proteins derived from patients with ovarian cancer and 6 peptides of three proteins favored patients from the group with breast cancer. We found that all defined PTMs were localized in the compact and stable structural motifs exposed outside the solvent environment. PTMs increase the solvent-accessible surface area of the modified moiety and its active environment. The observed conformational fluctuations are still inadequate to activate the structural degradation and enhance protein elimination/clearance; however, it is sufficient for the significant modulation of protein activity.
Profiles of microRNA in aqueous humor of normal tension glaucoma patients using RNA sequencing
Authors: Seong Hyemin , Cho Hyun-kyung , Kee Changwon , Song Dae Hyun , Cho Min-Chul , Kang Sang Soo 
Published: September 2021

AbstractWe aimed to identify and compare microRNAs (miRNAs) from individual aqueous humor samples between normal-tension glaucoma (NTG) patients and normal controls. Aqueous humor (80 to 120 µl) was collected before cataract surgery. Six stable NTG patients and seven age-matched controls were included in the final analysis. RNA sequencing was conducted for RNA samples extracted from the 13 aqueous humor samples, and bioinformatics analysis was employed for the miRNA targets and related pathways. Two hundred and twenty-eight discrete miRNAs were detected in the aqueous humor and consistently expressed in all samples. Eight significantly upregulated miRNAs were found in the NTG patients compared to the controls (fold-change > 2, p < 0.05). They were hsa-let-7a-5p, hsa-let-7c-5p, hsa-let-7f-5p, hsa-miR-192-5p, hsa-miR-10a-5p, hsa-miR-10b-5p, hsa-miR-375, and hsa-miR-143-3p. These miRNAs were predicted to be associated with the biological processes of apoptosis, autophagy, neurogenesis, and aging in the gene ontology categories. The related Kyoto encyclopedia of genes and genomes pathways were extracellular matrix-receptor interaction, mucin-type O-glycan biosynthesis, biotin metabolism, and signaling pathways regulating the pluripotency of stem cells. The differentially expressed miRNA in the NTG samples compared to the controls suggest the possible roles of miRNA in the pathogenesis of NTG. The underlying miRNA-associated pathways further imply novel targets for the pathogenesis of NTG.
Artificial intelligence-based detection of epimacular membrane from color fundus photographs
Authors: Shao Enhua , Liu Congxin , Wang Lei , Song Dan , Guo Libin , Yao Xuan , Xiong Jianhao , Wang Bin , Hu Yuntao 
Published: September 2021

AbstractEpiretinal membrane (ERM) is a common ophthalmological disorder of high prevalence. Its symptoms include metamorphopsia, blurred vision, and decreased visual acuity. Early diagnosis and timely treatment of ERM is crucial to preventing vision loss. Although optical coherence tomography (OCT) is regarded as a de facto standard for ERM diagnosis due to its intuitiveness and high sensitivity, ophthalmoscopic examination or fundus photographs still have the advantages of price and accessibility. Artificial intelligence (AI) has been widely applied in the health care industry for its robust and significant performance in detecting various diseases. In this study, we validated the use of a previously trained deep neural network based-AI model in ERM detection based on color fundus photographs. An independent test set of fundus photographs was labeled by a group of ophthalmologists according to their corresponding OCT images as the gold standard. Then the test set was interpreted by other ophthalmologists and AI model without knowing their OCT results. Compared with manual diagnosis based on fundus photographs alone, the AI model had comparable accuracy (AI model 77.08% vs. integrated manual diagnosis 75.69%, χ2 = 0.038, P = 0.845, McNemar’s test), higher sensitivity (75.90% vs. 63.86%, χ2 = 4.500, P = 0.034, McNemar’s test), under the cost of lower but reasonable specificity (78.69% vs. 91.80%, χ2 = 6.125, P = 0.013, McNemar’s test). Thus our AI model can serve as a possible alternative for manual diagnosis in ERM screening.
Capturing spike train temporal pattern with wavelet average coefficient for brain machine interface
Authors: Wen Shixian , Yin Allen , Tseng Po-He , Itti Laurent , Lebedev Mikhail A. , Nicolelis Miguel 
Published: September 2021

AbstractMotor brain machine interfaces (BMIs) directly link the brain to artificial actuators and have the potential to mitigate severe body paralysis caused by neurological injury or disease. Most BMI systems involve a decoder that analyzes neural spike counts to infer movement intent. However, many classical BMI decoders (1) fail to take advantage of temporal patterns of spike trains, possibly over long time horizons; (2) are insufficient to achieve good BMI performance at high temporal resolution, as the underlying Gaussian assumption of decoders based on spike counts is violated. Here, we propose a new statistical feature that represents temporal patterns or temporal codes of spike events with richer description—wavelet average coefficients (WAC)—to be used as decoder input instead of spike counts. We constructed a wavelet decoder framework by using WAC features with a sliding-window approach, and compared the resulting decoder against classical decoders (Wiener and Kalman family) and new deep learning based decoders ( Long Short-Term Memory) using spike count features. We found that the sliding-window approach boosts decoding temporal resolution, and using WAC features significantly improves decoding performance over using spike count features.
Cross-cultural validation of the stroke riskometer using generalizability theory
Authors: Medvedev Oleg , Truong Quoc Cuong , Merkin Alexander , Borotkanics Robert , Krishnamurthi Rita , Feigin Valery 
Published: September 2021

AbstractThe Stroke Riskometer mobile application is a novel, validated way to provide personalized stroke risk assessment for individuals and motivate them to reduce their risks. Although this app is being used worldwide, its reliability across different countries has not yet been rigorously investigated using appropriate methodology. The Generalizability Theory (G-Theory) is an advanced statistical method suitable for examining reliability and generalizability of assessment scores across different samples, cultural and other contexts and for evaluating sources of measurement errors. G-Theory was applied to the Stroke Riskometer data sampled from 1300 participants in 13 countries using two-facet nested observational design (person by item nested in the country). The Stroke Riskometer demonstrated strong reliability in measuring stroke risks across the countries with coefficients G relative and absolute of 0.84, 95%CI [0.79; 0.89] and 0.82, 95%CI [0.76; 0.88] respectively. D-study analyses revealed that the Stroke Riskometer has optimal reliability in its current form in measuring stroke risk for each country and no modifications are required. These results suggest that the Stroke Riskometer’s scores are generalizable across sample population and countries permitting cross-cultural comparisons. Further studies investigating reliability of the Stroke Riskometer over time in longitudinal study design are warranted.
New early phenotypic markers for cucumber green mottle mosaic virus disease in cucumbers exposed to fluctuating extreme temperatures
Authors: Molad Ori , Smith Elisheva , Luria Neta , Sela Noa , Lachman Oded , Bakelman Elena , Leibman Diana , Dombrovsky Aviv 
Published: September 2021

AbstractStudies of early stages of cucumber green mottle mosaic virus (CGMMV) disease have been recently focused on plant molecular responses. However, extreme diurnal environmental temperatures, characteristic of global climate changes, could affect plant susceptibility and disease phenotype progression. Our studies of CGMMV disease progression, under simulated extreme temperature waves, have revealed two new disease initiation phenotypes that developed gradually, preceding severe symptom manifestations of post-recovery CGMMV systemic infections. 'Early post-recovery stage' bright yellow islands (BYIs) with defined boundaries amid asymptomatic leaf blades were first emerging followed by 'late post-recovery stage' BYIs with diffused boundaries. A deduced CGMMV disease progression scheme, postulating BYI symptom occurrence time-windows, revealed BYIs in field grown cucumber plants exposed to extreme diurnal temperatures. Profiling ontology of cucumber differentially expressed genes in BYIs vs the associated dark-green surrounding tissues disclosed activation of jasmonic acid (JA) pathway in 'early post-recovery stage' BYIs. JA signaling was inactivated in 'late post-recovery stage' BYIs concomitant with increasing expressions of JA signaling inhibitors and downregulation of JA responsive phenylpropanoid pathway. Our results disclosed a new phenotypic description of CGMMV disease initiation, characteristic of cucumbers grown under extreme environmental temperature fluctuations. The BYI phenotypes could define a time-window for CGMMV disease management applications.
Usefulness of computed tomography-measured psoas muscle thickness per height for predicting mortality in patients undergoing hemodialysis
Authors: Yajima Takahiro , Arao Maiko , Yajima Kumiko , Takahashi Hiroshi 
Published: September 2021

AbstractComputed tomography (CT)-measured psoas muscle thickness standardized for height (PMTH) has emerged as a promising predictor of mortality. The study aimed to investigate whether PMTH could accurately predict mortality in patients undergoing hemodialysis. We examined 207 patients (mean age: 63.1 years; men: 66.2%) undergoing hemodialysis for more than 6 months in hospital affiliated clinic. PMTH was calculated at the L3 vertebra level using CT. Patients were divided according to the PMTH cut-off points: 8.44 mm/m in women and 8.85 mm/m in men; thereafter, they were combined into low and high PMTH groups. PMTH was independently correlated with the simplified creatinine index (β = 0.213, P = 0.021) and geriatric nutritional risk index (β = 0.295, P < 0.0001) in multivariate regression analysis. During a median follow-up of 3.7 (1.8–6.4) years, 76 patients died, including 41 from cardiovascular causes. In the multivariate Cox regression analysis, low PMTH (adjusted hazard ratio, 2.48; 95% confidence interval, 1.36–4.70) was independently associated with an increased risk of all-cause mortality. The addition of binary PMTH groups to the baseline risk model tended to improve net reclassification improvement (0.460, p = 0.060). In conclusion, PMTH may be an indicator of protein energy wasting and a useful tool for predicting mortality in patients undergoing hemodialysis.
Intraocular lens power calculations in eyes with pseudoexfoliation syndrome
Authors: Wlaź Aleksandra , Kustra Agnieszka , Rozegnał-Madej Agnieszka , Żarnowski Tomasz 
Published: September 2021

AbstractTo compare refractive outcomes after cataract surgery in pseudoexfoliation syndrome (PEX) and control eyes and to investigate the accuracy of 3 intraocular lens (IOL) calculation formulas in these eyes. In this prospective comparative study 42 eyes (PEX group) and 38 eyes (control group) of 80 patients were included. The follow-up was 3 months. The refractive prediction error (RPE), mean absolute error (MAE), median absolute error (MedAE) and the percentages of eyes within ± 0.25 D, ± 0.5 D, ± 1.0 D and ± 2.0 D of prediction error were calculated. Three IOL calculation formulas (SRK/T, Barrett Universal II and Hill-RBF) were evaluated. PEX produced statistically significantly higher mean absolute errors and lower percentages of eyes within ± 0.5 D than control eyes in all investigated IOL calculation formulas. There were no statistically significant differences in the median absolute errors between the 3 formulas in either PEX or control eyes. Refractive outcomes after cataract surgery are statistically significantly worse in PEX than in control eyes. All three IOL calculation formulas produced similar results in both PEX and control eyes.Trial registration: ClinicalTrials.gov registration number NCT04783909.
Tectonostratigraphy of the Jurassic accretionary prisms in the Sikhote-Alin region of Russian Far East
Authors: Golozubov Vladimir V. , Simanenko Ludmila F. 
Published: September 2021

AbstractWe propose a scheme to subdivide the Samarka terrane, a Jurassic accretionary prism fragment, into tectonostratigraphic complexes. This subdivision provides a basis to study these formations and map them on a medium- to large-scale. Each complex corresponds to a certain stage in the accretionary prism formation. Thus, the complexes composed of subduction mélange and olistostromes (in our case, Ust-Zhuravlevka and Sebuchar complexes), can be correlated to episodes when the underthrusting of seamounts hampered subduction, as evidenced by seamount fragments contained in the complexes. Episodes of relatively quiet subduction have also been identified, resulting in complexes composed mainly of normally bedded terrigenous and biogenic formations (Tudovaka and Udeka and, partially, Ariadnoe complexes). Particularly considered is the Okrainka-Sergeevka allochthonous complex – a fragment of continental plate overhanging a subduction zone. It was included in the accretionary prism during gravitational sliding on the internal slope of the paleotrench. All volcanic rocks in the accretionary prism are allochthonous fragments of the accreted oceanic crust. The absence of the Jurassic-Berriasian volcanic belt related to this prism, as well as synchronous autochthonous volcanism, indicates that the Samarka terrane accretionary prism formed under conditions of flat-slab subduction, similar to modern examples along the Andean margin.
Effect of single tube sections on the structural safety of Chinese solar greenhouse skeletons
Authors: Liu Xingan , Li Zhenkun , Zhang Lei , Liu Yu , Li Yiming , Li Tianlai 
Published: September 2021

AbstractIn recent years, the use of single-tube skeletons for the construction of Chinese solar greenhouses has increased. As a consequence, during the selection of the construction materials, the safety of these structures has become an important issue. The single tube section has various forms, but there is no scientific theory to guide the selection process. To the best of our knowledge, the scientific analysis of the impact of single pipe cross section on the safety of greenhouse skeleton has not been addressed so far. In this context, the finite element analysis software was used to calculate and analyze the stress elements, displacement of round tube, Ω tube, elliptic tube and square tube under the same load conditions. We used the Chinese Standard values as a reference and analyzed structural features of different sizes and thicknesses of the greenhouse steel skeleton sections under non-uniform snow load. The results showed that, under the same load condition, the maximum stress in the four skeleton materials was all located at the connection of the transverse tension bar and the front roof. In addition, under same load condition, the greenhouse skeleton with elliptic tube presented the smallest cross-sectional displacement between the different materials tested. The effect of increasing the size of the greenhouse frame was better than that of increasing the greenhouse material thickness. All this work will provide theoretical guidance to the material selection of this structure.