bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative genome, transcriptome, microRNA, and degradome analysis of water dropwort (Oenanthe javanica) in response to water stress
Authors: Liu Jie-Xia , Jiang Qian , Tao Jian-Ping , Feng Kai , Li Tong , Duan Ao-Qi , Wang Hao , Xu Zhi-Sheng , Liu Hui , Xiong Ai-Sheng 
Published: December 2021

AbstractWater dropwort (Liyang Baiqin,Oenanthe javanica(BI.) DC.) is an aquatic perennial plant from the Apiaceae family with abundant protein, dietary fiber, vitamins, and minerals. It usually grows in wet soils and can even grow in water. Here, whole-genome sequencing ofO. javanicavia HiSeq 2000 sequencing technology was reported for the first time. The genome size was 1.28 Gb, including 42,270 genes, of which 93.92% could be functionally annotated. An online database of the whole-genome sequences of water dropwort, Water dropwortDB, was established to share the results and facilitate further research onO. javanica(database homepage:http://apiaceae.njau.edu.cn/waterdropwortdb). Water dropwortDB offers whole-genome and transcriptome sequences and a Basic Local Alignment Search Tool. Comparative analysis with other species showed that the evolutionary relationship betweenO. javanicaandDaucus carotawas the closest. Twenty-five gene families ofO. javanicawere found to be expanded, and some genetic factors (such as genes and miRNAs) related to phenotypic and anatomic differentiation inO. javanicaunder different water conditions were further investigated. Two miRNA and target gene pairs (miR408 andOja15472, miR171 andOja47040) were remarkably regulated by water stress. The obtained reference genome ofO. javanicaprovides important information for future work, thus making in-depth genetic breeding and gene editing possible. The present study also provides a foundation for the understanding of theO. javanicaresponse to water stress, including morphological, anatomical, and genetic differentiation.
Histone variant H2A.Z regulates zygotic genome activation
Authors: Ibarra-Morales Dafne , Rauer Michael , Quarato Piergiuseppe , Rabbani Leily , Zenk Fides , Schulte-Sasse Mariana , Cardamone Francesco , Gomez-Auli Alejandro , Cecere Germano , Iovino Nicola 
Published: December 2021

AbstractDuring embryogenesis, the genome shifts from transcriptionally quiescent to extensively active in a process known as Zygotic Genome Activation (ZGA). In Drosophila, the pioneer factor Zelda is known to be essential for the progression of development; still, it regulates the activation of only a small subset of genes at ZGA. However, thousands of genes do not require Zelda, suggesting that other mechanisms exist. By conducting GRO-seq, HiC and ChIP-seq in Drosophila embryos, we demonstrate that up to 65% of zygotically activated genes are enriched for the histone variant H2A.Z. H2A.Z enrichment precedes ZGA and RNA Polymerase II loading onto chromatin. In vivo knockdown of maternally contributed Domino, a histone chaperone and ATPase, reduces H2A.Z deposition at transcription start sites, causes global downregulation of housekeeping genes at ZGA, and compromises the establishment of the 3D chromatin structure. We infer that H2A.Z is essential for the de novo establishment of transcriptional programs during ZGA via chromatin reorganization.
Cross-species analysis of viral nucleic acid interacting proteins identifies TAOKs as innate immune regulators
Authors: Pennemann Friederike L. , Mussabekova Assel , Urban Christian , Stukalov Alexey , Andersen Line Lykke , Grass Vincent , Lavacca Teresa Maria , Holze Cathleen , Oubraham Lila , Benamrouche Yasmine , Girardi Enrico , Boulos Rasha E. , Hartmann Rune , Superti-Furga Giulio , Habjan Matthias , Imler Jean-Luc , Meignin Carine , Pichlmair Andreas 
Published: December 2021

AbstractThe cell intrinsic antiviral response of multicellular organisms developed over millions of years and critically relies on the ability to sense and eliminate viral nucleic acids. Here we use an affinity proteomics approach in evolutionary distant species (human, mouse and fly) to identify proteins that are conserved in their ability to associate with diverse viral nucleic acids. This approach shows a core of orthologous proteins targeting viral genetic material and species-specific interactions. Functional characterization of the influence of 181 candidates on replication of 6 distinct viruses in human cells and flies identifies 128 nucleic acid binding proteins with an impact on virus growth. We identify the family of TAO kinases (TAOK1, −2 and −3) as dsRNA-interacting antiviral proteins and show their requirement for type-I interferon induction. Depletion of TAO kinases in mammals or flies leads to an impaired response to virus infection characterized by a reduced induction of interferon stimulated genes in mammals and impaired expression of srg1 and diedel in flies. Overall, our study shows a larger set of proteins able to mediate the interaction between viral genetic material and host factors than anticipated so far, attesting to the ancestral roots of innate immunity and to the lineage-specific pressures exerted by viruses.
Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment
Authors: Remple Kristina L. , Silbiger Nyssa J. , Quinlan Zachary A. , Fox Michael D. , Kelly Linda Wegley , Donahue Megan J. , Nelson Craig E. 
Published: December 2021

AbstractWork on marine biofilms has primarily focused on host-associated habitats for their roles in larval recruitment and disease dynamics; little is known about the factors regulating the composition of reef environmental biofilms. To contrast the roles of succession, benthic communities and nutrients in structuring marine biofilms, we surveyed bacteria communities in biofilms through a six-week succession in aquaria containing macroalgae, coral, or reef sand factorially crossed with three levels of continuous nutrient enrichment. Our findings demonstrate how biofilm successional trajectories diverge from temporal dynamics of the bacterioplankton and how biofilms are structured by the surrounding benthic organisms and nutrient enrichment. We identify a suite of biofilm-associated bacteria linked with the orthogonal influences of corals, algae and nutrients and distinct from the overlying water. Our results provide a comprehensive characterization of marine biofilm successional dynamics and contextualize the impact of widespread changes in reef community composition and nutrient pollution on biofilm community structure.
Predicting the inhibition efficiencies of magnesium dissolution modulators using sparse machine learning models
Authors: Schiessler Elisabeth J. , Würger Tim , Lamaka Sviatlana V. , Meißner Robert H. , Cyron Christian J. , Zheludkevich Mikhail L. , Feiler Christian , Aydin Roland C. 
Published: December 2021

AbstractThe degradation behaviour of magnesium and its alloys can be tuned by small organic molecules. However, an automatic identification of effective organic additives within the vast chemical space of potential compounds needs sophisticated tools. Herein, we propose two systematic approaches of sparse feature selection for identifying molecular descriptors that are most relevant for the corrosion inhibition efficiency of chemical compounds. One is based on the classical statistical tool of analysis of variance, the other one based on random forests. We demonstrate how both can—when combined with deep neural networks—help to predict the corrosion inhibition efficiencies of chemical compounds for the magnesium alloy ZE41. In particular, we demonstrate that this framework outperforms predictions relying on a random selection of molecular descriptors. Finally, we point out how autoencoders could be used in the future to enable even more accurate automated predictions of corrosion inhibition efficiencies.
IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells
Authors: Ando Minami , Magi Shigeyuki , Seki Masahide , Suzuki Yutaka , Kasukawa Takeya , Lefaudeux Diane , Hoffmann Alexander , Okada Mariko 
Published: December 2021

AbstractInflammatory stimuli triggers the degradation of three inhibitory κB (IκB) proteins, allowing for nuclear translocation of nuclear factor-κB (NFκB) for transcriptional induction of its target genes. Of these three, IκBα is a well-known negative feedback regulator that limits the duration of NFκB activity. We sought to determine whether IκBα’s role in enabling or limiting NFκB activation is important for tumor necrosis factor (TNF)-induced gene expression in human breast cancer cells (MCF-7). Contrary to our expectations, many more TNF-response genes showed reduced induction than enhanced induction in IκBα knockdown cells. Mathematical modeling was used to investigate the underlying mechanism. We found that the reduced activation of some NFκB target genes in IκBα-deficient cells could be explained by the incoherent feedforward loop (IFFL) model. In addition, for a subset of genes, prolonged NFκB activity due to loss of negative feedback control did not prolong their transient activation; this implied a multi-state transcription cycle control of gene induction. Genes encoding key inflammation-related transcription factors, such asJUNBandKLF10, were found to be best represented by a model that contained both the IFFL and the transcription cycle motif. Our analysis sheds light on the regulatory strategies that safeguard inflammatory gene expression from overproduction and repositions the function of IκBα not only as a negative feedback regulator of NFκB but also as an enabler of NFκB-regulated stimulus-responsive inflammatory gene expression. This study indicates the complex involvement of IκBα in the inflammatory response to TNF that is induced by radiation therapy in breast cancer.
A temporal segmentation algorithm for restoring the controllability of networked control systems
Authors: Cui Yulong , Wu Mincheng , Shao Cunqi , He Shibo 
Published: December 2021

AbstractRestoring the controllability of networked control systems is a fundamental issue that needs to be settled, especially when malicious attacks or malfunctions occur. Previous studies tried to address such an issue by adding extra driver nodes or rewiring edges, which will inevitably change the original network structure. In this paper, an algorithm to restore the controllability of networked systems while preserving the integrity of the original network structure is proposed. Specifically, a static uncontrollable network will be transformed into a controllable temporal network by means of the cactus‐based segmentation method. The original problem will be equivalent to the classical set cover problem, which is known to be NP‐Hard, if the least number of segmentations is considered. An approximation algorithm with polynomial time complexity is proposed and it is proved that the solution to the problem is two‐optimal. Finally, simulations are carried out to verify the effectiveness and feasibility of the proposed algorithm.
Detecting hand washing activity among activities of daily living and classification of WHO hand washing techniques using wearable devices and machine learning algorithms
Authors: Zhang Yiyuan , Xue Tianwei , Liu Zhenjie , Chen Wei , Vanrumste Bart 
Published: November 2021

AbstractDuring COVID‐19, awareness of proper hand washing has increased significantly. It is critical that people learn the correct hand washing techniques and adopt good hand washing habits. Hence, this study proposes using wearable devices to detect hand washing activity among other daily living activities (ADLs) and classify steps proposed by the World Health Organization (WHO). Two experiments were conducted with 16 participants, aged from 20 to 31. The first experiment was hand washing following WHO regulation (ten participants), and the second experiment was performing eight ADLs (eight participants). All participants wore two wearable devices equipped with accelerometers and gyroscopes; one on each wrist. Four machine learning classifiers were compared in classifying hand washing steps in the leave‐one‐subject‐out (LOSO) mode. The SVM model with Gaussian kernel achieved the best performance in classifying 11 washing hands steps, with an average F1‐score of 0.8501. When detected among the other ADLs, hand washing following WHO regulation obtained the F1‐score of 0.9871. The study demonstrates that wearable devices are feasible to detect hand washing activity and the hand washing techniques as well. The classification results of getting the soap and rubbing thumbs are low, which will be the main focus in the future study.
Yeast cell detection in color microscopic images using ROC‐optimized decoloring and segmentation
Authors: Bajla Ivan , Teplan Michal 
Published: November 2021

AbstractFor the detection and evaluation of yeast cell microscopic images, decoloring and segmentation is crucial. Usually, a standard operation of color conversion to grayscale is used and subsequently, a thresholding algorithm is applied to yield the segmented cells. However, both types of these operations are controlled merely by fixed empirical parameters which are prone to inaccuracy. The authors illustrate a common problem of such a nonoptimal decoloring. They then develop a novel pipeline of algorithms for yeast cell color phantom generation. In this study, the authors extend Grundland' s decoloring approach and couple it with an adaptive thresholding operation. For the generated phantom, the parameters of these operations are optimized using the ROC‐based F1‐measure. It is showed that this measure is a better choice than the Precision and Recall measure alone. Computer experiments with various combinations of the operation coupling and different phantom backgrounds are accomplished, and the optimum values of all the controllable parameters are found. For the color phantom representing the most realistic conditions, the final fully optimized 4D combination of the improved Grundland' s decoloring and locally adaptive thresholding ensures more efficient cell detection performance than parameterless or nonoptimized combinations.
A new method to fit logistic functions with wind turbines power curves using manufacturer datasheets
Authors: Aldaoudeyeh Al‐Motasem , Alzaareer Khaled , Harasis Salman , Al‐Odat Zeyad , Obeidat Mohammad , Mansour Ayman , Wu Di , Salem Qusay 
Published: December 2021

AbstractThe literature contains different methods for estimating logistic functions parameters to fit the power‐speed characteristics of a wind turbine (WT). However, their disadvantages are: (1) they require a large amount of supervisory control and data acquisition data; (2) the parameter range needed for constrained optimization is not systematically determined; and/or (3) they do not guarantee monotonically increasing relationship between wind speed and predicted WT output power. This paper proposes a systematic approach to fitting the five‐ and the six‐parameter logistic functions to power‐speed data of WTs. The authors introduce new limits on the parameters of these functions, which guarantee their monotonicity. Most of these limits are determined analytically and are obtained from manufacturer datasheets. Afterwards, these limits are passed as optimization constraints for subspace trust region algorithm. The results show that the authors' method generally provides better accuracy with mean absolute percentage error values below 0.02 for the five‐parameter logistic function and below 0.005 for the six‐parameter logistic function. The authors present accurate fits for a group of WTs of different ratings (from 275 kW to 3000 kW) and 12 unique manufacturers, which proves the versatility of the authors' method.
Retracted: Wideband circularly polarised antenna ‘multi‐input‐multi‐output’ for wireless UWB applications
Authors: Laxman Pillalamarri , Jain Anuj 
Published: December 2021

AbstractCircularly polarised multiple‐input‐output antennas embedded in wearable wireless devices attract importance in the individual security and beauty fabric modelling industry involving technology embedded on‐clothes wearables. A circularly polarised wideband is designed and analysed in the present design‐study where a wearable application uses a multiple‐input‐output. It adds 2 symmetric ‘Multi‐Input‐Multi‐Output’ antennas that are good looking design like a swan‐shaped, and the ground plane is similar to the shape of a swan. The designed novel antenna comprises a ground plane having a line feed and a rectangular inverted L‐type micro‐strip which is supporting circular polarisation. The antenna element is spanning at 3‐DeciBell (dB) Axial Ratio Band‐Width of 5.2–7.1 GHz and an impedance bandwidth (S11 less than or equal to −10 dB) of 3.6–13 GHz. The proposed antenna manifesting a channel capacity loss less than 0.2 b/s/Hz, and envelope correlation coefficient less than the value 0.02, total active reflective coefficient less than −10 dB, and diversity gain greater than the value of 9.96, Mean Effective Gain (also represented as MEG) ratio is within ±0.5 dB. There is a twin‐sense circular polarisation in this antenna and superior isolation between resonating elements (greater than 18). The proposed antenna for human tissues specimens is also discussed with its specific absorption rate (also pronounced as SAR) in different situations that pertain to the living body. The overall size of the proposed ‘Circularly Polarised’ textile ‘Multi‐Input‐Multi‐Output’ antenna is 34:5 × 42 × 1 mm3. Because of its textile layers, reasonable performance, and compact size, the designed ‘Multi‐Input‐Multi‐Output’ antenna may be useful for wearable applications. The presented novel antenna can be made unrecognisable with a beautiful swan‐shaped design that can simply comingle with the other designs of fabric (in the fashion dress). The simulated antenna was made‐up following regular and general manual techniques and verified in the proposed conditions. The corner‐to‐corner distance between the ‘Multi‐Input‐Multi‐Output’ antennas is 14.2 mm, and the achieved isolation is beyond 18 dB after suitable adjustments of the designed final antenna.
Phäochromozytom – Modellerkrankung für die personalisierte Medizin
Authors: Remde Hanna , Nölting Svenja 
Published: November 2021

Was ist neu?
Pathophysiologie und Epidemiologie Phäochromozytome und Paragangliome (PPGL) sind Tumoren des Nebennierenmarks bzw. der Paraganglien mit malignem Potenzial. Sie lassen sich anhand der zugrunde liegenden Mutationen in Cluster unterteilen. Cluster-1-Tumoren basieren auf einer Aktivierung von Pseudohypoxie-Signalwegen, Cluster-2-Tumoren auf einer Aktivierung von Tyrosinkinase-abhängigen Signalwegen. Cluster-3-Tumore sind mit Veränderungen in Wnt-abhängigen Signalwegen assoziiert (auf Cluster 3 wird im Weiteren nicht genauer eingegangen, da vieles hierzu noch unbekannt ist). In 30–35 % der Fälle liegen (autosomal-dominant vererbte) Keimbahnmutationen vor. Weitere 35–40 % der Fälle beruhen auf somatischen Mutationen. Die Penetranz der Erkrankung ist abhängig vom betroffenen Gen, liegt jedoch bei allen Genen unter 50 %. Cluster-1-Tumoren sind häufiger extraadrenal lokalisiert und haben das höchste Metastasierungsrisiko. Cluster-2-Tumoren sind meist adrenal lokalisiert und haben ein geringes Metastasierungsrisiko.
Klinik und Diagnostik Patient*innen mit bekannter Keimbahnmutation sowie solche mit klinischen Zeichen und Symptomen eines PPGL, mit einem adrenalen Inzidentalom oder einem PPGL in der Vorgeschichte, sollten auf ein PPGL gescreent werden. Hierfür werden Metanephrin (MN), Normetanephrin (NMN) und 3-Methoxythyramin (3MT) im Plasma (optimalerweise mittels Massenspektrometrie LC/MS-MS) bestimmt. Cluster-1-Tumoren weisen ein noradrenerges, Cluster-2-Tumoren ein adrenerges Sekretionsmuster auf, wobei letztere mit einer ausgeprägteren und häufig intermittierenden Klinik (Palpitationen, Tremor, Hyperhidrosis, Angst, hypertensive Entgleisung) einhergehen. Werden deutlich erhöhte MN- und/oder NMN-Spiegel festgestellt, erfolgt eine bildgebende Tumorsuche mittels CT oder MRT, ggf. wird diese um eine funktionelle Bildgebung ergänzt.
Therapie Lokalisierte PPGL werden operativ entfernt. Dies kann meist minimalinvasiv erfolgen und sollte an einem erfahrenen Zentrum durchgeführt werden. Um Komplikationen zu vermeiden, erfolgt präoperativ eine medikamentöse α-Rezeptorblockade. Metastasierte PPGL werden derzeit mit Radionuklidtherapie, Chemotherapie oder Tyrosinkinase-Inhibitoren behandelt, auch wenn es noch keine offiziell zugelassenen Therapien gibt. Weitere neue Therapien befinden sich derzeit in der klinischen Testung.
Vor- und Nachsorge Die meisten Patient*innen, insbesondere die mit bestimmten Risikokonstellationen, benötigen aufgrund des Rezidiv- und Metastasenrisikos ein lebenslanges Follow-up, welches abhängig von der zugrunde liegenden Mutation gestaltet wird. Hierzu gehört die regelmäßige (meist jährliche) Bestimmung von MN und NMN im Plasma sowie in bestimmten Fällen auch eine Bildgebung. Da bei SDHx-Mutationen auch hormoninaktive PPGL auftreten können, werden für diese Patient*innen auch regelmäßige bildgebende Kontrollen nach einer kürzlich erschienenen Leitlinie empfohlen.
Update Großgefäßvaskulitis 2021
Authors: Czihal Michael , Hoffmann Ulrich 
Published: November 2021

Was ist neu?
Klinischer Zugang Die Bestimmung der Prätestwahrscheinlichkeit auf Basis standardisierter Scoring-Systeme kann die Testgüte bildgebender Verfahren in der Diagnostik der Riesenzellarteriitis erhöhen.
Bildgebende Diagnostik Die hochauflösende Sonografie der Gefäßwand ist das Erstlinienverfahren in der Riesenzellarteriitis-Diagnostik, falsch positive Befunde können jedoch bei kardiovaskulärem Risikoprofil, insbesondere bei Männern jenseits des 70. Lebensjahres, vorkommen.
Therapiekontrolle In der Therapiekontrolle ist Bildgebung unverzichtbar. Die PET-CT ist hier am besten untersucht, jedoch verbleiben Unklarheiten bezüglich der Befundinterpretation. Eine wertvolle alternative bzw. ergänzende Methode stellt die Kontrastmittelsonografie dar.
Fetal Profile Markers for the Detection of Robin Sequence in Fetuses with Retrognathia
Authors: Wiechers Cornelia , Poets Christian , Hoopmann Markus , Kagan Karl Oliver 
Published: December 2021

Abstract
Objective To determine whether the prefrontal space ratio (PSFR), inferior facial (IFA) and maxilla-nasion-mandible angle (MNM), and the fetal profile line (FPL) are helpful in identifying fetuses with Robin sequence (RS) in cases with isolated retrognathia, and thus better predict the likelihood of immediate need for postnatal respiratory support.
Methods This was a retrospective matched case-control study of fetuses/infants with isolated retrognathia with or without RS receiving pre- and postnatal treatment at the University Hospital of Tübingen, Germany between 2008 and 2020. The PFSR, IFA, MNM, and FPL were measured in affected and normal fetuses according to standardized protocols. Cases were stratified into isolated retrognathia and RS.
Results 21 (n=7 isolated retrognathia, n=14 RS) affected fetuses and 252 normal fetuses were included. Their median gestational age at ultrasound examination was 23.6 and 24.1 weeks, respectively. In fetuses with isolated retrognathia and RS, the PSFR, IFA, and FPL were significantly different from the normal population. At a false-positive rate of 5%, the detection rate was 76.2% for the PFSR, 85.7% for the IFA, and 90.5% for both parameters combined. However, all parameters failed to distinguish between isolated retrognathia and RS.
Conclusion PSFR and IFA are simple markers for identifying retrognathia prenatally. However, they are not helpful for the detection of RS in fetuses with isolated retrognathia. Therefore, delivery should take place in a center experienced with RS and potentially life-threatening airway obstruction immediately after birth.