bluuebunny/crossref_metadata_2025_split huggingface dataset:
Critical assessment of protein intrinsic disorder prediction
Authors: Necci Marco , Piovesan Damiano ,   CAID Predictors, Hoque Md Tamjidul , Walsh Ian , Iqbal Sumaiya , Vendruscolo Michele , Sormanni Pietro , Wang Chen , Raimondi Daniele , Sharma Ronesh , Zhou Yaoqi , Litfin Thomas , Galzitskaya Oxana Valerianovna , Lobanov Michail Yu. , Vranken Wim , Wallner Björn , Mirabello Claudio , Malhis Nawar , Dosztányi Zsuzsanna , Erdős Gábor , Mészáros Bálint , Gao Jianzhao , Wang Kui , Hu Gang , Wu Zhonghua , Sharma Alok , Hanson Jack , Paliwal Kuldip , Callebaut Isabelle , Bitard-Feildel Tristan , Orlando Gabriele , Peng Zhenling , Xu Jinbo , Wang Sheng , Jones David T. , Cozzetto Domenico , Meng Fanchi , Yan Jing , Gsponer Jörg , Cheng Jianlin , Wu Tianqi , Kurgan Lukasz ,   DisProt Curators, Promponas Vasilis J. , Tamana Stella , Marino-Buslje Cristina , Martínez-Pérez Elizabeth , Chasapi Anastasia , Ouzounis Christos , Dunker A. Keith , Kajava Andrey V. , Leclercq Jeremy Y. , Aykac-Fas Burcu , Lambrughi Matteo , Maiani Emiliano , Papaleo Elena , Chemes Lucia Beatriz , Álvarez Lucía , González-Foutel Nicolás S. , Iglesias Valentin , Pujols Jordi , Ventura Salvador , Palopoli Nicolás , Benítez Guillermo Ignacio , Parisi Gustavo , Bassot Claudio , Elofsson Arne , Govindarajan Sudha , Lamb John , Salvatore Marco , Hatos András , Monzon Alexander Miguel , Bevilacqua Martina , Mičetić Ivan , Minervini Giovanni , Paladin Lisanna , Quaglia Federica , Leonardi Emanuela , Davey Norman , Horvath Tamas , Kovacs Orsolya Panna , Murvai Nikoletta , Pancsa Rita , Schad Eva , Szabo Beata , Tantos Agnes , Macedo-Ribeiro Sandra , Manso Jose Antonio , Pereira Pedro José Barbosa , Davidović Radoslav , Veljkovic Nevena , Hajdu-Soltész Borbála , Pajkos Mátyás , Szaniszló Tamás , Guharoy Mainak , Lazar Tamas , Macossay-Castillo Mauricio , Tompa Peter , Tosatto Silvio C. E. 
Published: April 2021

AbstractIntrinsically disordered proteins, defying the traditional protein structure–function paradigm, are a challenge to study experimentally. Because a large part of our knowledge rests on computational predictions, it is crucial that their accuracy is high. The Critical Assessment of protein Intrinsic Disorder prediction (CAID) experiment was established as a community-based blind test to determine the state of the art in prediction of intrinsically disordered regions and the subset of residues involved in binding. A total of 43 methods were evaluated on a dataset of 646 proteins from DisProt. The best methods use deep learning techniques and notably outperform physicochemical methods. The top disorder predictor has Fmax = 0.483 on the full dataset and Fmax = 0.792 following filtering out of bona fide structured regions. Disordered binding regions remain hard to predict, with Fmax = 0.231. Interestingly, computing times among methods can vary by up to four orders of magnitude.
Biallelic variants in the SORD gene are one of the most common causes of hereditary neuropathy among Czech patients
Authors: Laššuthová P. , Mazanec R. , Staněk D. , Sedláčková L. , Plevová B. , Haberlová J. , Seeman P. 
Published: April 2021

AbstractRecently, biallelic variants in the SORD gene were identified as causal for axonal hereditary neuropathy (HN). We ascertained the spectrum and frequency of SORD variants among a large cohort of Czech patients with unknown cause of HN. Exome sequencing data were analysed for SORD (58 patients). The prevalent c.757del variant was tested with fragment analysis (931 patients). Sanger sequencing in additional 70 patients was done. PCR primers were designed to amplify the SORD gene with the exclusion of the pseudogene SORD2P. Sequence differences between gene and pseudogene were identified and frequencies of SNPs were calculated. Eighteen patients from 16 unrelated families with biallelic variants in the SORD gene were found and the c.757del was present in all patients on at least one allele. Three novel, probably pathogenic, variants were detected, always in a heterozygous state in combination with the c.757del on the second allele. Patients presented with a slowly progressive axonal HN. Almost all patients had moderate pes cavus deformity. SORD neuropathy is frequent in Czech patients and the third most common cause of autosomal recessive HN. The c.757del is highly prevalent. Specific amplification of the SORD gene with the exclusion of the pseudogene is essential for a precise molecular diagnostics.
Semianalytical solution for the transient temperature in a scattering and absorbing slab consisting of three layers heated by a light source
Authors: Reitzle Dominik , Geiger Simeon , Liemert André , Kienle Alwin 
Published: April 2021

AbstractWe derived a semianalytical solution for the time-dependent temperature distribution in a three-layered laterally infinite scattering and absorbing slab illuminated by an obliquely incident collimated beam of light. The light propagation was modeled by the low-order $$P_1$$

P
1

and $$P_3$$

P
3

approximations to the radiative transfer equation with closed form expressions for eigenvalues and eigenvectors, yielding a quickly computable solution, while the heat conduction was modeled by the Fourier equation. The solution was compared to a numerical solution using a Monte Carlo simulation for the light propagation and an FEM method for the heat conduction. The results showed that using the $$P_3$$

P
3

solution for the light propagation offers a large advantage in accuracy with only a moderate increase in calculation time compared to the $$P_1$$

P
1

solution. Also, while the $$P_3$$

P
3

solution is not a very good approximation for the spatially resolved absorbance itself, its application as a source term for the heat conduction equation does yield a very good approximation for the time-dependent temperature.
Size segregation of irregular granular materials captured by time-resolved 3D imaging
Authors: Gajjar Parmesh , Johnson Chris G. , Carr James , Chrispeels Kevin , Gray J. M. N. T. , Withers Philip J. 
Published: April 2021

AbstractWhen opening a box of mixed nuts, a common experience is to find the largest nuts at the top. This well-known effect is the result of size-segregation where differently sized ‘particles’ sort themselves into distinct layers when shaken, vibrated or sheared. Colloquially this is known as the ‘Brazil-nut effect’. While there have been many studies into the phenomena, difficulties observing granular materials mean that we still know relatively little about the process by which irregular larger particles (the Brazil nuts) reach the top. Here, for the first time, we capture the complex dynamics of Brazil nut motion within a sheared nut mixture through time-lapse X-ray Computed Tomography (CT). We have found that the Brazil nuts do not start to rise until they have first rotated sufficiently towards the vertical axis and then ultimately return to a flat orientation when they reach the surface. We also consider why certain Brazil nuts do not rise through the pack. This study highlights the important role of particle shape and orientation in segregation. Further, this ability to track the motion in 3D will pave the way for new experimental studies of segregating mixtures and will open the door to even more realistic simulations and powerful predictive models. Understanding the effect of size and shape on segregation has implications far beyond food products including various anti-mixing behaviors critical to many industries such as pharmaceuticals and mining.
The tumor suppressor archipelago E3 ligase is required for spermatid differentiation in Drosophila testis
Authors: Vedelek Viktor , Kovács Attila L. , Juhász Gábor , Alzyoud Elham , Sinka Rita 
Published: April 2021

AbstractThe human orthologue of the tumor suppressor protein FBW7 is encoded by the Drosophila archipelago (ago) gene. Ago is an F-box protein that gives substrate specificity to its SCF ubiquitin ligase complex. It has a central role in multiple biological processes in a tissue-specific manner such as cell proliferation, cellular differentiation, hypoxia-induced gene expression. Here we present a previously unknown tissue-specific role of Ago in spermatid differentiation. We identified a classical mutant of ago which is semi-lethal and male-sterile. During the characterization of ago function in testis, we found that ago plays role in spermatid development, following meiosis. We confirmed spermatogenesis defects by silencing ago by RNAi in testes. The ago mutants show multiple abnormalities in elongating and elongated spermatids, including aberration of the cyst morphology, malformed mitochondrial structures, and individualization defects. Additionally, we determined the subcellular localization of Ago protein with mCherry-Ago transgene in spermatids. Our findings highlight the potential roles of Ago in different cellular processes of spermatogenesis, like spermatid individualization, and regulation of mitochondrial morphology.
Physician-guided, hybrid genetic testing exerts promising effects on health-related behavior without compromising quality of life
Authors: Schricker Severin , Monje David Callau , Dippon Juergen , Kimmel Martin , Alscher Mark Dominik , Schanz Moritz 
Published: April 2021

AbstractGenetic risk analysis is increasingly in demand by participants. Hybrid genetic testing has the advantage over direct to consumer testing by involving a physician who guides the process and offers counseling after receiving the results. The objective of this study was to determine whether a structured physician moderated primary preventive, hybrid genetic risk assessment enhanced counseling program leads to improvement in lifestyle and does not impair quality of life. Risk genes for malignant, cardiovascular, coagulation, storage diseases and pharmacogenetics (> 100 genes) were tested. Screening, consultation and genetic counseling embedded in a primary/secondary prevention check-up program for executives of surrounding companies took place in a single center in Germany. Follow-up included established questionnaires for quality of life, nutrition and physical activity. Analysis included n = 244 participants. Median age at baseline was 49 years (interquartile range: 44–55), 93% were male, 3% (n = 7 of 136 responses) were smoker. Mean body mass index was 25.2 kg/m2. Follow-up response rate was 74% (n = 180), mean follow-up time was 6.8 months (standard deviation = 2.1). In 91 participants (37.8%, 91/241) at least one pathogenic variant was found, 60 thereof were clinically relevant (24.9%, 60/241). 238 participants (98%, 238/241) had > 1 pharmacogenetic variant, only 2 (0.8%, 2/241) took a correspondingly affected drug (56 participants took ≥ 1 drug/day). The energy expenditure significantly increased by ≈ 35% [median multiple of energy expenditure of 1.34 (confidence interval = 1.15–1.57, p < 0.001)] metabolic equivalents of task (MET)-min/week; participants spent on average 41 min (p < 0.001) less in sedentary activities per day and spent more time for lunch (≈ 2 additional minutes/day; p = 0.031). Indicators of the consumption of red meat and sweet pastries significantly decreased (both adjusted p = 0.049). Neither quality of life in general nor subgroup analysis of participants with at least one conspicuous genetic risk differed significantly over follow-up. Hybrid genetic testing and counseling exerted positive effects on health-related behavior and was not associated with major psychological adverse effects in the short-term follow-up. The approach seems to be feasible for use in preventive health care.
The other-race effect and holistic processing across racial groups
Authors: Wong Hoo Keat , Estudillo Alejandro J. , Stephen Ian D. , Keeble David R. T. 
Published: April 2021

AbstractIt is widely accepted that holistic processing is important for face perception. However, it remains unclear whether the other-race effect (ORE) (i.e. superior recognition for own-race faces) arises from reduced holistic processing of other-race faces. To address this issue, we adopted a cross-cultural design where Malaysian Chinese, African, European Caucasian and Australian Caucasian participants performed four different tasks: (1) yes–no face recognition, (2) composite, (3) whole-part and (4) global–local tasks. Each face task was completed with unfamiliar own- and other-race faces. Results showed a pronounced ORE in the face recognition task. Both composite-face and whole-part effects were found; however, these holistic effects did not appear to be stronger for other-race faces than for own-race faces. In the global–local task, Malaysian Chinese and African participants demonstrated a stronger global processing bias compared to both European- and Australian-Caucasian participants. Importantly, we found little or no cross-task correlation between any of the holistic processing measures and face recognition ability. Overall, our findings cast doubt on the prevailing account that the ORE in face recognition is due to reduced holistic processing in other-race faces. Further studies should adopt an interactionist approach taking into account cultural, motivational, and socio-cognitive factors.
Usefulness of semi-automatic harmonization strategy of standardized uptake values for multicenter PET studies
Authors: Daisaki Hiromitsu , Kitajima Kazuhiro , Nakajo Masatoyo , Watabe Tadashi , Ito Kimiteru , Sakamoto Fumi , Nakahara Tadaki , Ishibashi Mana , Toriihara Akira 
Published: April 2021

AbstractThis study assessed the possibility of semi-automatic harmonization of standardized uptake values (SUVs) in multicenter studies. Phantom data were acquired using 16 PET/CT scanners (including 3 PET/CT scanners with a silicon photomultiplier detector). PET images obtained using 30-min/bed scans for optimum harmonization filter calculations and using 90–180-s/bed scans for SUV validation under clinical conditions were obtained. Time of flight and a reconstruction method with point-spread function correction were allowed. The optimal full width at half maximum of the 3D-Gaussian filter that minimizes the root mean square error with the median value of the JSNM harmonization range was calculated semi-automatically. The SUVmax and the SUVpeak of the hot spheres were measured, and the inter-scanner coefficient of variation (COV) was calculated before and after harmonization. The harmonization filter was applied to 11 of the 15 PET/CT scanners in which the SUV calibration accuracy had been verified, but not in the remaining 4 scanners. Under noiseless conditions before harmonization, the inter-scanner COVs of the SUVmax and the SUVpeak were as high as 21.57% and 12.20%, respectively, decreasing to 8.79% and 5.73% after harmonization, respectively. Harmonization brought the SUVmax of all the hot spheres to within the harmonization range. Even under clinical conditions affected by image noise, the inter-scanner COVs for the SUVmax and SUVpeak were as high as 8.83% and 5.18% after harmonization, respectively. By applying an optimal harmonization filter that is calculated semi-automatically, the harmonization of SUVs according to the JSNM strategy is possible in multicenter studies, thereby reducing inter-scanner COVs.
Characterization of bacterial communities associated with blood-fed and starved tropical bed bugs, Cimex hemipterus (F.) (Hemiptera): a high throughput metabarcoding analysis
Authors: Lim Li , Ab Majid Abdul Hafiz 
Published: April 2021

AbstractWith the development of new metagenomic techniques, the microbial community structure of common bed bugs, Cimex lectularius, is well-studied, while information regarding the constituents of the bacterial communities associated with tropical bed bugs, Cimex hemipterus, is lacking. In this study, the bacteria communities in the blood-fed and starved tropical bed bugs were analysed and characterized by amplifying the v3-v4 hypervariable region of the 16S rRNA gene region, followed by MiSeq Illumina sequencing. Across all samples, Proteobacteria made up more than 99% of the microbial community. An alpha-proteobacterium Wolbachia and gamma-proteobacterium, including Dickeya chrysanthemi and Pseudomonas, were the dominant OTUs at the genus level. Although the dominant OTUs of bacterial communities of blood-fed and starved bed bugs were the same, bacterial genera present in lower numbers were varied. The bacteria load in starved bed bugs was also higher than blood-fed bed bugs.
The effects of antibiotic exposure on asthma in children with atopic dermatitis
Authors: Chen I-Lun , Tsai Ming-Kai , Chung Hao-Wei , Hsieh Hui-Min , Huang Yu-Ting , Lin Yi-Ching , Hung Chih-Hsing 
Published: April 2021

AbstractEarly-life antibiotic use is associated with allergic diseases. The risk factors for the progression from atopic dermatitis (AD) to asthma or allergic rhinitis are still unknown. We aimed to investigate the association between exposure to different antibiotics and the risk of new-onset asthma in children with AD. By using the Longitudinal Health Insurance Database 2005, we selected AD patients less than 6 years old identified by ICD-9-CM code 691.8. The case group was defined as those having new-onset asthma, and the control group was defined as those without an asthma history. Information on antibiotic exposure in the 5 years prior to the index date was collected from drug prescription records. We estimated the adjusted odds ratio by using conditional logistic regression, adjusted for age, sex, index year, other potential risk factors and antibiotics. Antibiotic exposure was associated with the development of asthma in patients with AD (aOR = 3.68, 95% CI 2.13–6.36), particularly for patients less than 5 years old (aOR = 4.14, 95% CI 2.24–7.64) (p for trend < 0.001), even though lower cumulative antibiotic defined daily doses (DDDs) were associated with new-onset asthma occurrence. Antibiotic exposure, especially macrolide exposure, is associated with an increased risk of asthma in patients with AD.
Severe allo-immune antibody-associated peripheral and central nervous system diseases after allogeneic hematopoietic stem cell transplantation
Authors: Hümmert Martin W. , Stadler Michael , Hambach Lothar , Gingele Stefan , Bredt Martin , Wattjes Mike P. , Göhring Gudrun , Venturini Letizia , Möhn Nora , Stangel Martin , Trebst Corinna , Ganser Arnold , Wegner Florian , Skripuletz Thomas 
Published: April 2021

AbstractAllogeneic hematopoietic stem cell transplantation (alloHSCT) is a curative treatment for hematologic malignancies. Acute and chronic graft-versus-host disease (GvHD) are the major immune-mediated complications after alloHSCT. However, there is controversy whether neurologic complications after alloHSCT might represent manifestations of GvHD. We report three patients who acquired distinct, severe immune-mediated peripheral or central nervous system diseases after alloHSCT without other, concomitant GvHD manifestations. One patient had been diagnosed with B-cell chronic lymphocytic leukemia and two patients with high risk myelodysplastic syndrome. Patient #1 presented as LGI1- and GAD-IgG positive immune-mediated encephalitis, patient #2 was diagnosed with MOG-IgG positive encephalomyelitis, and patient #3 had chronic inflammatory polyneuropathy associated with SSA(Ro)-IgG positive Sjögren’s syndrome. 100% donor chimerism was detectable in the peripheral blood in all three. The specific antibodies were undetectable in donors’ and patients’ blood before alloHSCT suggesting that the antibodies had arisen from the transplanted donor immune system. Early intensive immunotherapy led to improvement of clinical symptoms and stability of the neurological disease, however, at the cost of losing the graft-versus-malignancy effect in one patient. In conclusion, we provide evidence of isolated, severe allo-immune diseases of the peripheral and central nervous system as complications of alloHSCT (“neuro-GvHD”). Interdisciplinary surveillance and thorough diagnostic work-up are needed for early diagnosis and treatment of neuro-immunologic complications after alloHSCT to improve the otherwise poor outcome.
Rare-earth metal catalysts for high-pressure synthesis of rare diamonds
Authors: Palyanov Yuri N. , Borzdov Yuri M. , Kupriyanov Igor N. , Khohkhryakov Alexander F. , Nechaev Denis V. 
Published: April 2021

AbstractThe combination of the unique properties of diamond and the prospects for its high-technology applications urges the search for new solvents–catalysts for the synthesis of diamonds with rare and unusual properties. Here we report the synthesis of diamond from melts of 15 rare-earth metals (REM) at 7.8 GPa and 1800–2100 °C. The boundary conditions for diamond crystallization and the optimal parameters for single crystal diamond synthesis are determined. Depending on the REM catalyst, diamond crystallizes in the form of cube–octahedrons, octahedrons and specific crystals bound by tetragon–trioctahedron and trigon–trioctahedron faces. The synthesized diamonds are nitrogen-free and belong to the rare type II, indicating that the rare-earth metals act as both solvent–catalysts and nitrogen getters. It is found that the REM catalysts enable synthesis of diamond doped with group IV elements with formation of impurity–vacancy color centers, promising for the emerging quantum technologies. Our study demonstrates a new field of application of rare-earth metals.
Ruxolitinib early administration reduces acute GVHD after alternative donor hematopoietic stem cell transplantation in acute leukemia
Authors: Zhang Binglei , Chen Lingyun , Zhou Jian , Zu Yingling , Gui Ruirui , Li Zhen , Wang Juan , Yu Fengkuan , Zhang Yanli , Zhao Huifang , Ji Zhenyu , Song Yongping 
Published: April 2021

AbstractThis study aimed to observe the safety and clinical efficacy of early application of ruxolitinib to prevent acute graft-versus-host disease (aGVHD) after alternative donor transplantation in acute leukemia. There were 57 patients undergoing allo-HSCT at the Affiliated Cancer Hospital of Zhengzhou University from July 2017 to October 2019. They were divided into control(16 patients) and ruxolitinib (41 patients) groups. For aGVHD prophylaxis, the control group received post-transplantation cyclophosphamide, antithymocyte globulin-Fresenius, cyclosporine A, and mycophenolate mofetil, while in the ruxolitinib group, ruxolitinib 5 mg/d in adults or 0.07–0.1 mg/(kg d) in children was administered from the day of neutrophil engraftment to 100 days post-transplantation based on control group. We found 55 patients had successful reconstitution of hematopoiesis; No significant difference was found in cGVHD, hemorrhagic cystitis, pulmonary infection, intestinal infection, Epstein-Barr virus infection, cytomegalovirus infection, relapse, death, and nonrelapse mortality. The incidences of aGVHD (50 vs. 22%, P = 0.046) and grade II–IV aGVHD (42.9 vs. 12.2%, P = 0.013) were significantly higher in the control group than in the ruxolitinib group. No significant differences were observed in overall survival (P = 0.514), disease-free survival (P = 0.691), and cumulative platelet transfusion within 100 days post-transplantation between two groups. This suggests early application of ruxolitinib can reduce the incidence and severity of aGVHD and patients are well tolerated.