bluuebunny/crossref_metadata_2025_split huggingface dataset:
Candidate resistance genes to foliar phylloxera identified at Rdv3 of hybrid grape
Authors: Yin Lu , Karn Avinash , Cadle-Davidson Lance , Zou Cheng , Londo Jason , Sun Qi , Clark Matthew D 
Published: February 2022

Abstract
The foliage of the native grape species Vitis riparia and certain cold-hardy hybrid grapes are particularly susceptible to the insect pest phylloxera, Daktulosphaira vitifoliae Fitch. A previous study using a cold-hardy hybrid grape biparental F1 population (N ~ 125) detected the first quantitative trait locus (QTL) for foliar resistance on chromosome 14, designated as resistance to Daktulosphaira vitifoliae 3 (Rdv3). This locus spans a ~ 7-Mbp (10–20 cM) region and is too wide for effective marker-assisted selection or identification of candidate genes. Therefore, we fine mapped the QTL using a larger F1 population, GE1783 (N ~ 1023), and genome-wide rhAmpSeq haplotype markers. Through three selective phenotyping experiments replicated in the greenhouse, we screened 184 potential recombinants of GE1783 using a 0 to 7 severity rating scale among other phylloxera severity traits. A 500-kb fine mapped region at 4.8 Mbp on chromosome 14 was identified. The tightly linked rhAmpSeq marker 14_4 805 213 and flanking markers can be used for future marker-assisted breeding. This region contains 36 candidate genes with predicted functions in disease resistance (R genes and Bonzai genes) and gall formation (bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase). Disease resistance genes suggest a traditional R-gene-mediated resistance mechanism often accompanied by a hypersensitive response, which has been widely studied in the plant pathology field. A novel resistance mechanism, non-responsiveness to phylloxera gall formation is proposed as a function of the bifunctional dehydratase gene, which plays a role in gallic acid biosynthesis and is important in gall formation. This study has implications for improvement of foliar phylloxera resistance in cold-hardy hybrid germplasm and is a starting place to understand the mechanism of resistance in crops to gall-forming insects.
Haplotype analyses reveal novel insights into tomato history and domestication driven by long-distance migrations and latitudinal adaptations
Authors: Blanca Jose , Sanchez-Matarredona David , Ziarsolo Peio , Montero-Pau Javier , van der Knaap Esther , Díez Ma José , Cañizares Joaquín 
Published: February 2022

AbstractA novel haplotype-based approach that uses Procrustes analysis and automatic classification was used to provide further insights into tomato history and domestication. Agrarian societies domesticated species of interest by introducing complex genetic modifications. For tomatoes, two species, one of which had two botanical varieties, are thought to be involved in its domestication: the fully wild Solanum pimpinellifolium (SP), the wild and semi-domesticated Solanum lycopersicum var. cerasiforme (SLC) and the cultivated S. l. var. lycopersicum (SLL). The Procrustes approach showed that SP evolved into SLC during a gradual migration from the Peruvian deserts to the Mexican rainforests and that Peruvian and Ecuadorian SLC populations were the result of more recent hybridizations. Our model was supported by independent evidence, including ecological data from the accession collection site and morphological data. Furthermore, we showed that photosynthesis-, and flowering time-related genes were selected during the latitudinal migrations.
Large-scale analyses of heat shock transcription factors and database construction based on whole-genome genes in horticultural and representative plants
Authors: Yu Tong , Bai Yun , Liu Zhuo , Wang Zhiyuan , Yang Qihang , Wu Tong , Feng Shuyan , Zhang Yu , Shen Shaoqin , Li Qiang , Gu Liqiang , Song Xiaoming 
Published: February 2022

Abstract
Heat shock transcription factor (Hsf) plays a critical role in regulating heat resistance. Here, 2950 Hsf family genes were identified from 111 horticultural and representative plants. More Hsf genes were detected in higher plants than in lower plants. Based on all Hsf genes, we constructed a phylogenetic tree, which indicated that Hsf genes of each branch evolved independently after species differentiation. Furthermore, we uncovered the evolutionary trajectories of Hsf genes by motif analysis. There were only six motifs (M1–M6) in lower plants, and then four novel motifs (M7–M10) appeared in higher plants. However, the motifs of some Hsf genes were lost in higher plants, indicating that Hsf genes have undergone sequence variation during their evolution. The number of Hsf genes lost was greater than the number of genes that were duplicated after whole-genome duplication in higher plants. The heat response network was constructed using 24 Hsf genes and 2421 downstream and 222 upstream genes of Arabidopsis. Further enrichment analysis revealed that Hsf genes and other transcription factors interacted with each other in the response to heat stress. Global expression maps were illustrated for Hsf genes under various abiotic and biotic stresses and several developmental stages in Arabidopsis. Syntenic and phylogenetic analyses were conducted using Hsf genes of Arabidopsis and the pan-genome of 18 Brassica rapa accessions. We also performed expression pattern analysis of Hsf and six Hsp family genes using expression values from different tissues and heat treatments in B. rapa. The interaction network between the Hsf and Hsp gene families was constructed in B. rapa, and several core genes were detected in the network. Finally, we constructed an Hsf database (http://hsfdb.bio2db.com) for researchers to retrieve Hsf gene family information. Therefore, our study will provide rich resources for the study of the evolution and function of Hsf genes.
Hierarchical transcription factor and regulatory network for drought response in Betula platyphylla
Authors: Jia Yaqi , Niu Yani , Zhao Huimin , Wang Zhibo , Gao Caiqiu , Wang Chao , Chen Su , Wang Yucheng 
Published: February 2022

Abstract
Although many genes and biological processes involved in abiotic stress responses have been identified, how they are regulated remains largely unclear. Here, to study the regulatory mechanism of birch (Betula platyphylla) responding to drought induced by polyethylene glycol 6000 (20%, w/v), a partial correlation coefficient-based algorithm for constructing a gene regulatory network (GRN) was proposed, and a three-layer hierarchical GRN was constructed, including 68 transcription factors and 252 structural genes. A total of 1448 predicted regulatory relationships are included, and most of them are novel. The reliability of the GRN was verified by chromatin immunoprecipitation (ChIP)–PCR and qRT–PCR based on transient transformation. About 55% of genes in the bottom layer of the GRN could confer drought tolerance. We selected two TFs, BpMADS11 and BpNAC090, from the top layer and characterized their function in drought tolerance. Overexpression of BpMADS11 and BpNAC090 reduces electrolyte leakage, reactive oxygen species (ROS) and malondialdehyde (MDA) contents, giving greater drought tolerance than wild-type birch. According to this GRN, the important biological processes involved in drought were identified, including ‘signaling hormone pathways’, ‘water transport’, ‘regulation of stomatal movement’, and ‘response to oxidative stress’. This work indicated that BpERF017, BpAGL61, and BpNAC090 are the key upstream regulators of birch drought tolerance. Our data clearly revealed that upstream regulators and transcription factor–DNA interaction regulate different biological processes to adapt to drought stress.
Combination of epidermal growth factor receptor mutation and the presence of high-grade patterns is associated with recurrence in resected stage I lung adenocarcinoma
Authors: Kondo Yasuto , Ichinose Junji , Ninomiya Hironori , Hashimoto Kohei , Matsuura Yosuke , Nakao Masayuki , Ishikawa Yuichi , Okumura Sakae , Satoh Yukitoshi , Mun Mingyon 
Published: February 2022

Abstract

OBJECTIVES
This study aimed to evaluate the prognostic impact of the combination of epidermal growth factor receptor (EGFR) mutation and the presence of high-grade patterns (solid or micropapillary component) in resected stage I lung adenocarcinoma.

METHODS
Patients who underwent curative resection for pathological stage I lung adenocarcinoma and EGFR mutation analysis were included in this study. The impact of the combination of EGFR mutation and the presence of &gt;5% high-grade patterns on recurrence-free survival (RFS) was retrospectively analysed using Cox proportional hazards model and propensity score-matched analysis.

RESULTS
Among the included 721 patients, EGFR mutations were positive in 380 (52.7%). In the EGFR-mutated group, cases with high-grade patterns showed poorer RFS than those without (5-year RFS, 77.7% vs 92.5%, P &lt; 0.001), whereas there were no significant prognostic differences in the EGFR wild-type group (5-year RFS, 89.8% vs 88.2%, P = 0.807). Multivariable analyses revealed that the combination of EGFR mutations and the presence of high-grade patterns was associated with poor RFS (hazard ratio = 1.655, P = 0.035). Furthermore, EGFR mutation was associated with poor RFS in the group with high-grade patterns (hazard ratio = 2.108, P = 0.008). After propensity score matching, EGFR-mutated cases with high-grade patterns showed poorer RFS (P = 0.028).

CONCLUSIONS
The combination of EGFR mutation and the presence of high-grade patterns was associated with recurrence in resected stage I lung adenocarcinoma. Histological subtypes, including minor components, should be considered when evaluating the risk of recurrence in patients with EGFR-mutated lung adenocarcinoma.
Toward a Theory of Heteronomy
Authors: Butcher Charles , Griffiths Ryan D 
Published: February 2022

AbstractIt is thought that political order in premodern Europe was characterized by overlapping and crosscutting forms of authority. Scholars have called this heteronomy, arguing that it preceded and may follow the modern sovereign state system and that it has characterized various historical locales around the world. We maintain that this conception has been under-examined, and we identity three different forms of heteronomy that existed historically. These include: (1) interstitial heteronomy, where polities with limited capacity in low-density regions experience zones of informal mixed rule on the frontier; (2) functional heteronomy, where states in thickly populated systems develop complex patterns of functional differentiation; and (3) personalistic heteronomy, where power that is invested in individuals rather than territorially defined polities can produce patterns of dual vassalage. We develop a theory of heteronomy based on the density of the system (low, high) and the nature of political relations (territorial, personal), and using the resulting two-dimensional map we explore the form of heteronomy that existed and may exist in different systems across time and space. We conclude that when scholars envisage heteronomy in the modern system, it is mostly functional, and not interstitial or personalistic heteronomy, which they have in mind.
Hourly pollutants forecasting using a deep learning approach to obtain the AQI
Authors: Moscoso-López José Antonio , González-Enrique Javier , Urda Daniel , Ruiz-Aguilar Juan Jesús , Turias Ignacio J 
Published: February 2022

AbstractThe Air Quality Index (AQI) shows the state of air pollution in a unique and more understandable way. This work aims to forecast the AQI in Algeciras (Spain) 8 hours in advance. The AQI is calculated indirectly through the predicted concentrations of five pollutants (O3, NO2, CO, SO2 and PM10) to achieve this goal. Artificial neural networks (ANNs), sequence-to-sequence long short-term memory networks (LSTMs) and a newly proposed method combing a rolling window with the latter (LSTMNA) are employed as the forecasting techniques. Besides, two input approaches are evaluated: using only the data from the own time series of the pollutant in the first case or adding exogenous variables in the second one. Several window sizes are employed (24, 28 and 72 hours) with ANNs and LSTMNAs. Additionally, several feature ranking methods are applied in the exogenous approach to select the most relevant lagged variables to feed the models. Results show how the proposed exogenous approach increases the performance of the prediction models. Besides, the newly proposed method LSTMNA provides the best performances in most of the cases evaluated. Hence, it constitutes an exciting alternative to standard LSTMs and ANNs to predict pollutants concentrations and, consequently, the AQI.
A unique case of free-floating gastric band tubing causing intraabdominal sepsis in a patient with locked-in syndrome secondary to Guillain–Barré syndrome
Authors: Cadili Lina , Davis Noelle L 
Published: February 2022

Abstract
Laparoscopic adjustable gastric banding is a known bariatric procedure that has largely fallen out of favor in our modern surgical era. Several case reports describe various complications secondary to gastric band slippage. Here we present a unique complication not related to gastric band slippage, but intraabdominal sepsis secondary to free-floating gastric band tubing after removal of the subcutaneous port in a patient with locked-in syndrome secondary to Guillain–Barré syndrome.
Cutoff Value of Qualitative HBsAg for Confirmatory HBsAg Using the Chemiluminescence Microparticle Immunoassay Method
Authors: Pasaribu Merci Monica , Wonohutomo Jessica Purwanti , Immanuel Suzanna , Kumalawati July , Indrasari Nuri Dyah , Yusra Yusra 
Published: February 2022

Abstract

Background
Confirmatory hepatitis B surface antigen (HBsAg) is an assay used to distinguish weakly reactive from false-positive HBsAg results.

Objective
To determine the signal to cutoff (S/CO) value of chemiluminescence microparticle immunoassay (CMIA) HBsAg assay that should trigger follow-up confirmatory HBsAg testing.

Methods
All specimens with an initial S/CO value of 0.90–100.00 were subjected to repeat HBsAg testing after high-speed centrifugation. The specimens with an initial S/CO value in that range remained in the same range and were then followed up with confirmatory HBsAg testing.

Result
In total, 132 specimens had an S/CO value between 0.90 and 100.00 after high-speed centrifugation, followed by confirmatory HBsAg retesting. The S/CO value of HBsAg specimens for which the results required verification with confirmatory HBsAg was 0.98 (100% sensitivity, 3.3% specificity) through 9.32 (47.1% sensitivity, 100% specificity).

Conclusion
The HBsAg S/CO values (as determined by the chemiluminescent microparticle immunoassay [CMIA] method) that should trigger confirmatory HBsAg testing are 0.98–9.32.
Proof Complexity for the Maximum Satisfiability Problem and its Use in SAT Refutations
Authors: Rollon Emma , Larrosa Javier 
Published: February 2022

Abstract
MaxSAT, the optimization version of the well-known SAT problem, has attracted a lot of research interest in the past decade. Motivated by the many important applications and inspired by the success of modern SAT solvers, researchers have developed many MaxSAT solvers. Since most research is algorithmic, its significance is mostly evaluated empirically. In this paper, we want to address MaxSAT from the more formal point of view of proof complexity. With that aim, we start providing basic definitions and proving some basic results. Then we analyse the effect of adding split and virtual, two original inference rules, to MaxSAT resolution. We show that each addition makes the resulting proof system stronger, even when virtual is restricted to empty clauses ($0$-virtual). We also analyse the power of our proof systems in the particular case of SAT refutations. We show that our strongest system, ResSV, is equivalent to circular and dual rail with split. We also analyse empirically some known gadget-based reformulations. Our results seem to indicate that the advantage of these three seemingly different systems over general resolution comes mainly from their ability of augmenting the original formula with hypothetical inconsistencies, as captured in a very simple way by the virtual rule.
Forbush decreases caused by paired interacting solar wind disturbances
Authors: Shlyk N S , Belov A V , Abunina M A , Abunin A A , Oleneva V A , Yanke V G 
Published: February 2022

ABSTRACTThe paper discusses changes in various characteristics of the solar wind, interplanetary magnetic field, geomagnetic activity, and cosmic rays during the registration of paired interacting solar wind disturbances on the Earth using the data base of Forbush effects and interplanetary disturbances – FEID. The cases of pair interaction are considered for 1995–2020: (i) successive coronal mass ejections; (ii) coronal mass ejections and high-speed streams from coronal holes; (iii) successive high-speed streams from coronal holes. It is shown that for the first events from a pair, the times for reaching the maximum values of the interplanetary magnetic field and solar wind velocity are significantly reduced, and the amplitudes of the recorded Forbush decreases decline. It is also found that the presence of interaction enriches the second event at the expense of the resources of the first, increasing geomagnetic efficiency and the degree of cosmic ray modulation for the second event in comparison with isolated events, which is especially pronounced for a pair of interacting coronal mass ejections. The existence of the described effects can be explained by the observed increase in the interplanetary magnetic field magnitude in the second events due to the presence of interaction.
Secretion and uptake of copper via a small copper carrier in blood fluid
Authors: Gioilli B D , Kidane T Z , Fieten H , Tellez M , Dalphin M , Nguyen A , Nguyen K , Linder M C 
Published: February 2022

AbstractStudies with Wilson disease model mice that accumulate excessive copper, due to a dysfunctional ATP7B “copper pump” resulting in decreased biliary excretion, showed that the compensatory increase in urinary copper loss was due to a small copper carrier (∼1 kDa) (SCC). We show here that SCC is also present in the blood plasma of normal and Wilson disease model mice and dogs, as determined by ultrafiltration and size exclusion chromatography (SEC). It is secreted by cultured hepatic and enterocytic cells, as determined by pretreatment with 67Cu nitrilotriacetate (NTA) or nonradioactive 5–10 μM Cu-NTA, and collecting and examining 3 kDa ultrafiltrates of the conditioned media, where a single major copper peak is detected by SEC. Four different cultured cell types exposed to the radiolabeled SCC all took up the 67Cu at various rates. Rates differed somewhat when uptake was from Cu-NTA. Uptake of SCC-67Cu was inhibited by excess nonradioactive Cu(I) or Ag(I) ions, suggesting competition for uptake by copper transporter 1 (CTR1). Knockout of CTR1 in fibroblasts reduced uptake rates by 60%, confirming its participation, but also involvement of other transporters. Inhibitors of endocytosis, or an excess of metal ions taken up by divalent metal transporter 1, did not decrease SCC-67Cu uptake. The results imply that SCC may play a significant role in copper transport and homeostasis, transferring copper particularly from the liver (but also intestinal cells) to other cells within the mammalian organism, as well as spilling excess into the urine in copper overload—as an alternative means of copper excretion.
Positive supercoiling favors transcription elongation through lac repressor-mediated DNA loops
Authors: Xu Wenxuan , Yan Yan , Artsimovitch Irina , Dunlap David , Finzi Laura 
Published: February 2022

Abstract
Some proteins, like the lac repressor (LacI), mediate long-range loops that alter DNA topology and create torsional barriers. During transcription, RNA polymerase generates supercoiling that may facilitate passage through such barriers. We monitored E. coli RNA polymerase progress along templates in conditions that prevented, or favored, 400 bp LacI-mediated DNA looping. Tethered particle motion measurements revealed that RNA polymerase paused longer at unlooped LacI obstacles or those barring entry to a loop than those barring exit from the loop. Enhanced dissociation of a LacI roadblock by the positive supercoiling generated ahead of a transcribing RNA polymerase within a torsion-constrained DNA loop may be responsible for this reduction in pause time. In support of this idea, RNA polymerase transcribed 6-fold more slowly through looped DNA and paused at LacI obstacles for 66% less time on positively supercoiled compared to relaxed templates, especially under increased tension (torque). Positive supercoiling propagating ahead of polymerase facilitated elongation along topologically complex, protein-coated templates.
G-quadruplex inducer/stabilizer pyridostatin targets SUB1 to promote cytotoxicity of a transplatinum complex
Authors: Hou Yinzhu , Gan Tieliang , Fang Tiantian , Zhao Yao , Luo Qun , Liu Xingkai , Qi Luyu , Zhang Yanyan , Jia Feifei , Han Juanjuan , Li Shumu , Wang Shijun , Wang Fuyi 
Published: February 2022

Abstract
Pyridostatin (PDS) is a well-known G-quadruplex (G4) inducer and stabilizer, yet its target genes have remained unclear. Herein, applying MS proteomics strategy, we revealed PDS significantly downregulated 22 proteins but upregulated 16 proteins in HeLa cancer cells, of which the genes both contain a number of G4 potential sequences, implying that PDS regulation on gene expression is far more complicated than inducing/stabilizing G4 structures. The PDS-downregulated proteins consequently upregulated 6 proteins to activate cyclin and cell cycle regulation, suggesting that PDS itself is not a potential anticancer agent, at least toward HeLa cancer cells. Importantly, SUB1, which encodes human positive cofactor and DNA lesion sensor PC4, was downregulated by 4.76-fold. Further studies demonstrated that the downregulation of PC4 dramatically promoted the cytotoxicity of trans-[PtCl2(NH3)(thiazole)] (trans-PtTz) toward HeLa cells to a similar level of cisplatin, contributable to retarding the repair of 1,3-trans-PtTz crosslinked DNA lesion mediated by PC4. These findings not only provide new insights into better understanding on the biological functions of PDS but also implicate a strategy for the rational design of novel multi-targeting platinum anticancer drugs via conjugation of PDS as a ligand to the coordination scaffold of transplatin for battling drug resistance to cisplatin.