bluuebunny/crossref_metadata_2025_split huggingface dataset:
Halotolerant biofilm-producing rhizobacteria mitigate seawater-induced salt stress and promote growth of tomato
Authors: Haque Md. Manjurul , Biswas Md. Sanaullah , Mosharaf Md Khaled , Haque Md. Amdadul , Islam Md. Shahidul , Nahar Kamrun , Islam Md. Mynul , Shozib Habibul Bari , Islam Md. Mariful , Ferdous-E-Elahi  
Published: April 2022

AbstractBiofilm-producing rhizobacteria (BPR) enhance productivity and mitigate abiotic stresses in plants. This study showed that 21 out of 65 halotolerant rhizobacteria could build biofilms. The components of the biofilm matrices i.e., extracellular polymeric substances (EPS) are proteins, curli, nanocelloluse, nucleic acids, lipids, and peptidoglycans. Various functional groups including carbonyl, carboxyl, amino, hydroxyl, and phosphate were identified. Positions of these groups were shifted by application of 5% NaCl, suggesting Na+ biosorption. By sequencing, Glutamicibacter arilaitensis (ESK1, ESM4 and ESM7), G. nicotianae (ESK19, ESM8 and ESM16), Enterobacter ludwigii (ESK15, ESK17, ESM2 and ESM17), E. cloacae (ESM5 and ESM12), Exiguobacterium acetylicum (ESM24 and ESM25), Staphylococcus saprophyticus ESK6, Leclercia adecarboxylata ESK12, Pseudomonas poae ESK16, Bacillus subtilis ESM14, and P. putida ESM17 were identified. These rhizobacteria exhibited numerous plant growth-promoting (PGP) activities including producing IAA, ACC deaminase, and siderophores, and solubilizing phosphate. Under non-stress, bacterized plants increased biomass accumulation (8–23.2% roots and 23–49.4% shoots), while under seawater-induced salt stress only ESK12, ESM4, ESM12, and ESM14 enhanced biomass production (5.8–52.9% roots and 8.8–33.4% shoots). Bacterized plants induced antioxidant defense system (19.5–142% catalase and 12.3–24.2% DPPH radical scavenging activity), retained a greater relative water content (17–124%), showed lesser membrane injuries (19.9–26.5%), and a reduced Na+ (6–24% in roots) and increased K+/Na+ ratio (78.8 and 103% in roots by ESK12 and ESM24, respectively) than the non-bacterized plants in saline conditions. Thus, native halotolerant BPR can be utilized as ameliorators of salt stress.
TIRAP-mediated activation of p38 MAPK in inflammatory signaling
Authors: Rajpoot Sajjan , Kumar Ashutosh , Zhang Kam Y. J. , Gan Siew Hua , Baig Mirza S. 
Published: April 2022

AbstractThe role of TIRAP (toll/interleukin-1 receptor (TIR) domain-containing adapter protein) in macrophage inflammatory signalling has been significantly evolved since its discovery in 2001 due to its dynamic nature and subcellular localization to regulate multiple signaling through several protein–protein interactions (PPIs). Structural analysis of these interactions can reveal a better understanding of their conformational dynamics and the nature of their binding. Tyrosine phosphorylation in the TIR domain of TIRAP is very critical for its function. In toll-like receptor (TLR) 4/2 signalling, Bruton's tyrosine kinase (BTK) and Protein kinase C delta (PKCδ) are known to phosphorylate the Y86, Y106, Y159, and Y187 of TIRAP which is crucial for the downstream function of MAPKs (mitogen-activated protein kinases) activation. The objective of this study is to understand the interaction of TIRAP with p38 MAPK through molecular docking and identify the importance of TIRAP tyrosine phosphorylation in p38 MAPK interaction. In this structural study, we performed an in-silico molecular docking using HADDOCK 2.4, pyDockWEB, ClusPro 2.0, and ZDOCK 3.0.2 tools to unravel the interaction between TIRAP and p38 MAPK. Further, manual in-silico phosphorylations of TIRAP tyrosines; Y86, Y106, Y159, and Y187 was created in the Discovery Studio tool to study the conformational changes in protein docking and their binding affinities with p38 MAPK in comparison to non-phosphorylated state. Our molecular docking and 500 ns of molecular dynamic (MD) simulation study demonstrates that the Y86 phosphorylation (pY86) in TIRAP is crucial in promoting the higher binding affinity (∆Gbind) with p38 MAPK. The conformational changes due to the tyrosine phosphorylation mainly at the Y86 site pull the TIRAP closer to the active site in the kinase domain of p38 MAPK and plays a significant role at the interface site which is reversed in its dephosphorylated state. The heatmap of interactions between the TIRAP and p38 MAPK after the MD simulation shows that the TIRAP pY86 structure makes the highest number of stable hydrogen bonds with p38 MAPK residues. Our findings may further be validated in an in-vitro system and would be crucial for targeting the TIRAP and p38 MAPK interaction for therapeutic purposes against the chronic inflammatory response and associated diseases.
Chromatic discrimination in fixed saturation levels from trichromats and subjects with congenital color vision deficiency
Authors: Igarashi Yuzo , Meireles Luiza Karina Gonçalves , Costa Brito Felipe André , da Costa Leonardo Ramos Nicolau , dos Santos Freitas Joyce , Miquilini Leticia , Portnoi Baran Luiz Claudio , Henriques Leonardo Dutra , Hauzman Einat , Oliveira Bonci Daniela Maria , Costa Marcelo Fernandes , Ventura Dora Fix , Goulart Paulo Roney Kilpp , Souza Givago Silva 
Published: April 2022

AbstractColor vision tests use estimative of threshold color discrimination or number of correct responses to evaluate performance in chromatic discrimination tasks. Both approaches have advantages and disadvantages. In the present investigation, we compared the number of errors during color discrimination task in normal trichromats and participants with color vision deficiency (CVD) using pseudoisochromatic stimuli at fixed saturation levels. We recruited 28 normal trichromats and eight participants with CVD. Cambridge Color Test was used to categorize their color vision phenotype, and those with a phenotype suggestive of color vision deficiency had their L- and M-opsin genes genotyped. Pseudoisochromatic stimuli were shown with target chromaticity in 20 vectors radiating from the background chromaticity and saturation of 0.06, 0.04, 0.03, 0.02, 0.01, and 0.005 u’v' units. Each stimulus condition appeared in four trials. The number of errors for each stimulus condition was considered an indicator of the participant's performance. At high chromatic saturation, there were fewer errors from both phenotypes. The errors of the normal trichromats had no systematic variation for high saturated stimuli, but below 0.02 u’v' units, there was a discrete prevalence of tritan errors. For participants with CVD, the errors happened mainly in red-green chromatic vectors. A three-way ANOVA showed that all factors (color vision phenotype, stimulus saturation, and chromatic vector) had statistically significant effects on the number of errors and that stimulus saturation was the most important main effect. ROC analysis indicated that the performance of the fixed saturation levels to identify CVD was better between 0.02 and 0.06 u’v’ units reaching 100%, while saturation of 0.01 and 0.005 u’v’ units decreased the accuracy of the screening of the test. We concluded that the color discrimination task using high saturated stimuli separated normal trichromats and participants with red-green color vision deficiencies with high performance, which can be considered a promising method for new color vision tests based in frequency of errors.
Elevated estradiol levels in frozen embryo transfer have different effects on pregnancy outcomes depending on the stage of transferred embryos
Authors: Li Qing , Ruan Liming , Zhu Lingling , Yang Zengyu , Zhu Maoling , Luo Yudi 
Published: April 2022

AbstractSupplementation with estradiol (E2) is routinely used in frozen embryo transfer (FET) cycles and embryo age plays an important role in conceiving. This study was to compare the effects of serum E2 levels on pregnancy outcomes between cleavage- and blastocyst-stage FET cycles using hormone replacement therapy. A total of 776 FET cycles (669 couples) performed from January 2016 to December 2019 were included in the present retrospective cohort study. Regarding cleavage-stage embryo transfers, E2 levels on progesterone initiation day were significantly lower in the ongoing pregnancy/live birth (OP/LB) group than in the non-OP/LB group (214.75 ± 173.47 vs. 253.20 ± 203.30 pg/ml; P = 0.023). In addition, there were downward trends in implantation, clinical pregnancy and OP/LB rates with increasing E2 levels. However, in blastocyst-stage embryo transfers, such trends were not observed, and E2 levels were not significant difference between the OP/LB group and the non-OP/LB group (201.66 ± 182.14 vs. 197.89 ± 212.83 pg/ml; P = 0.884). The results suggests that elevated progesterone-initiation-day E2 levels may negatively affect pregnancy outcomes during artificial cleavage-stage embryo transfers. However, it is not necessary to monitor E2 levels when transferring blastocysts in artificial FET cycles.
Reduction of pesticide application via real-time precision spraying
Authors: Zanin Alex Rogers Aguiar , Neves Danilo Carvalho , Teodoro Larissa Pereira Ribeiro , da Silva Júnior Carlos Antonio , da Silva Simone Pereira , Teodoro Paulo Eduardo , Baio Fábio Henrique Rojo 
Published: April 2022

AbstractFarmers focus on reducing the cost of production and aim to increase profit. The objective of this study was to quantify the reduction of pesticides applied to soybean (Glycine max (L.) Merrill) and maize (Zea mays L.) crops in several stages of the production cycle using a site-specific spraying application based on real-time sensors in the Brazilian Cerrado region. The sprayers were equipped with a precision spraying control system based on a real-time sensor. The spraying operations were performed not only for herbicide, but also for fungicide and insecticides applications. The maps recorded the percentage of the spray boom when the application was turned on (on/off spray system) with nozzle-to-nozzle control. The precision spraying system based on real-time sensors reduced the volume of pesticides (including herbicides, insecticides, and fungicides) applied to soybean and maize crops. There was a more significant reduction in the volume of pesticides applied post-emergence of the crops in the initial stages of soybean and maize when the crops had less leaf area or less foliage coverage between the rows. The cost reduction achieved using this technology was 2.3 times lower than the cost associated with pesticide application over the entire area using a conventional sprayer. Under the experimental conditions, there were no differences in the average crop yield, compared to the historical productivity of soybean and maize crops by applying this technology because the recommended doses were not affected and the site of application was limited to points where the presence of plants was present was detected.
A single screen-printed electrode in tandem with chemometric tools for the forensic differentiation of Brazilian beers
Authors: Mutz Yhan S. , do Rosario Denes , Silva Luiz R. G. , Galvan Diego , Janegitz Bruno C. , de Q. Ferreira Rafael , Conte-Junior Carlos A. 
Published: April 2022

AbstractIn the present study a single screen-printed carbon electrode (SPCE) and chemometric techniques were utilized for forensic differentiation of Brazilian American lager beers. To differentiate Brazilian beers at the manufacturer and brand level, the classification techniques: soft independent modeling of class analogy (SIMCA), partial least squares regression discriminant analysis (PLS-DA), and support vector machines discriminant analysis (SVM-DA) were tested. PLS-DA model presented an inconclusive assignment ratio of 20%. On the other hand, SIMCA models had a 0 inconclusive rate but an sensitivity close to 85%. While the non-linear technique (SVM-DA) showed an accuracy of 98%, with 95% sensitivity and 98% specificity. The SPCE-SVM-DA technique was then used to distinguish at brand level two highly frauded beers. The SPCE coupled with SVM-DA performed with an accuracy of 97% for the classification of both brands. Therefore, the proposed electrochemicalsensor configuration has been deemed an appropriate tool for discrimination of American lager beers according to their producer and brands.
Comparative mitogenomics and phylogenetics of the family Carangidae with special emphasis on the mitogenome of the Indian Scad Decapterus russelli
Authors: Jose Anjaly , Sukumaran Sandhya , Mukundan Lakshmi P. , Raj Neenu , Mary Sujitha , Nisha K. , Gopalakrishnan A. 
Published: April 2022

AbstractCarangids are abundant and commercially important marine fish that contribute to a significant portion of the fisheries in many parts of the world. In the present study, we characterized the complete mitogenome of the Indian scad,Decapterus russelliand performed a comprehensive comparative mitogenomic analysis of the family Carangidae. The comparative mitogenomics provided valuable insights into the structure, variability, and features of the coding and non-coding regions that evolved across species over millions of years. The structural features of tRNAs revealed changes in the frequency of mismatched and wobble base pairs, which is reflected in the base composition of H and L strands. The highly conserved sequence motif of the mTERF binding site in carangids over the ~ 400 MYA of their divergence demonstrated the functional importance of these sites. The control region of carangids was characterized by the presence of discontinuous repeat units with a high rate of sequence divergence in the form of base substitutions, insertions, and deletions. The maintenance of secondary structures in the control region independent of the rapid evolution of primary structure suggested the effect of selective constraints on their maintenance. Maximum likelihood (ML) and Bayesian inference (BI) phylogeny revealed a similar topology consistent with previous taxonomic studies. The extant carangids diverged through the evolutionary events experienced during the Cretaceous, Paleogene, and Neogene periods.
Raman spectroscopic peculiarities of Icelandic poorly crystalline minerals and their implications for Mars exploration
Authors: Muñoz-Iglesias Victoria , Sánchez-García Laura , Carrizo Daniel , Molina Antonio , Fernández-Sampedro Maite , Prieto-Ballesteros Olga 
Published: April 2022

AbstractIn this work, we have analyzed natural samples collected at three hydrothermal areas of Iceland by Raman spectroscopy. The studied high-latitude regions are considered environmentally and mineralogically appropriate Martian analogues since they are rich in weathered basalts that have been altered by hydrothermalism to mineral phases such as silica, clay minerals, sulfates, oxides, and sulfur. The main objective of this work was to assess the relation of the spectroscopic signatures of alteration to hydrothermal processes and biomediation, considering previous studies focused on the detection of lipid biomarkers in the same samples. The recorded Raman spectra, taken with optical parameters similar to the ExoMars 2022 Raman spectrometer, showed structural modifications in all secondary minerals in the form of peak shifts (in the case of sulfur and clay minerals), changes in the relative ratio intensity (in anatase) and/or shape broadening (in sulfates and hematite). These results reveal the suitability of Raman spectroscopy to examine areas rich in water-altered minerals, where a mixture of crystalline and amorphous phases can co-exist. The detection of silica is singularly interesting since, on the one hand, it can imply the past existence of hydrothermal hot springs rich in nutrient and redox gradients and, on the other hand, provides excellent matrix for biosignature preservation. The data can be helpful as an astrobiological database for the forthcoming missions to Mars, where potential upwelling groundwater systems could have altered the mineral phases in a similar way to that observed in this work.
Acquisition learning is stronger for aversive than appetitive events
Authors: van der Schaaf Marieke E. , Schmidt Katharina , Kaur Jaspreet , Gamer Matthias , Wiech Katja , Forkmann Katarina , Bingel Ulrike 
Published: April 2022

AbstractAppetitive and aversive learning are both key building blocks of adaptive behavior, yet knowledge regarding their differences is sparse. Using a capsaicin heat pain model in 36 healthy participants, this study directly compared the acquisition and extinction of conditioned stimuli (CS) predicting pain exacerbation and relief. Valence ratings show stronger acquisition during aversive compared to appetitive learning, but no differences in extinction. Skin conductance responses and contingency ratings confirmed these results. Findings were unrelated to individual differences in pain sensitivity or psychological factors. Our results support the notion of an evolutionarily hardwired preponderance to acquire aversive rather than appetitive cues as is protective for acute aversive states such as pain but may contribute to the development and maintenance of clinical conditions such as chronic pain, depression or anxiety disorders.
Bayesian networks elucidate complex genomic landscapes in cancer
Authors: Angelopoulos Nicos , Chatzipli Aikaterini , Nangalia Jyoti , Maura Francesco , Campbell Peter J. 
Published: April 2022

AbstractBayesian networks (BNs) are disciplined, explainable Artificial Intelligence models that can describe structured joint probability spaces. In the context of understanding complex relations between a number of variables in biological settings, they can be constructed from observed data and can provide a guiding, graphical tool in exploring such relations. Here we propose BNs for elucidating the relations between driver events in large cancer genomic datasets. We present a methodology that is specifically tailored to biologists and clinicians as they are the main producers of such datasets. We achieve this by using an optimal BN learning algorithm based on well established likelihood functions and by utilising just two tuning parameters, both of which are easy to set and have intuitive readings. To enhance value to clinicians, we introduce (a) the use of heatmaps for families in each network, and (b) visualising pairwise co-occurrence statistics on the network. For binary data, an optional step of fitting logic gates can be employed. We show how our methodology enhances pairwise testing and how biologists and clinicians can use BNs for discussing the main relations among driver events in large genomic cohorts. We demonstrate the utility of our methodology by applying it to 5 cancer datasets revealing complex genomic landscapes. Our networks identify central patterns in all datasets including a central 4-way mutual exclusivity between HDR, t(4,14), t(11,14) and t(14,16) in myeloma, and a 3-way mutual exclusivity of three major players: CALR, JAK2 and MPL, in myeloproliferative neoplasms. These analyses demonstrate that our methodology can play a central role in the study of large genomic cancer datasets.
Investigation of the Relation Between Tinnitus, Cognition, and the Amount of Listening Effort
Authors: Degeest Sofie , Kestens Katrien , Keppler Hannah 
Published: April 2022

Purpose:
This study aimed to investigate the effect of chronic tinnitus on measures of listening effort and cognitive performance, as well as the relation between cognitive performance and the amount of listening effort obtained by those measures.

Method:
Thirteen normal-hearing young adults with chronic tinnitus were matched with a control group. First, behavioral listening effort was measured using a dual-task paradigm in various favorable and unfavorable listening conditions. Furthermore, verbal working memory, processing speed, selective attention, and cognitive flexibility and inhibition were evaluated.

Results:
A significant and nonsignificant trend toward more listening effort in the tinnitus group was, respectively, found for the quiet listening condition and the condition with a signal-to-noise ratio of +2 dB. No significant differences in cognitive performances were found between the groups, nor were there significant relationships between the cognitive factors and listening effort scores for either the control or tinnitus group.

Conclusions:
Listening effort was increased in the tinnitus group. Although no clear differences in cognitive performance could be found between the tinnitus group and their controls, a trend could be seen whereby selective attention deficits in the subjects with tinnitus may be an important factor that affects the amount of listening effort.
Impact of Startling Acoustic Stimuli on Word Repetition in Individuals With Aphasia and Apraxia of Speech Following Stroke
Authors: Swann Zoe , Daliri Ayoub , Honeycutt Claire F. 
Published: April 2022

Purpose:
The StartReact effect, whereby movements are elicited by loud, startling acoustic stimuli (SAS), allows the evaluation of movements when initiated through involuntary circuitry, before auditory feedback. When StartReact is applied during poststroke upper extremity movements, individuals exhibit increased muscle recruitment, reaction times, and reaching distances. StartReact releases unimpaired speech with similar increases in muscle recruitment and reaction time. However, as poststroke communication disorders have divergent neural circuitry from upper extremity tasks, it is unclear if StartReact will enhance speech poststroke. Our objective is to determine if (a) StartReact is present in individuals with poststroke aphasia and apraxia and (b) SAS exposure enhances speech intelligibility.

Method:
We remotely delivered startling, 105-dB white noise bursts (SAS) and quiet, non-SAS cues to 15 individuals with poststroke aphasia and apraxia during repetition of six words. We evaluated average word intensity, pitch, pitch trajectories, vowel formants F1 and F2 (first and second formants), phonemic error rate, and percent incidence of each SAS versus non–SAS-elicited phoneme produced under each cue type.

Results:
For SAS trials compared to non-SAS, speech intensity increased (∆ + 0.6 dB), speech pitch increased (∆ + 22.7 Hz), and formants (F1 and F2) changed, resulting in a smaller vowel space after SAS. SAS affected pitch trajectories for some, but not all, words. Non-SAS trials had more stops (∆ + 4.7 utterances) while SAS trials had more sustained phonemes (fricatives, glides, affricates, liquids; ∆ + 5.4 utterances). SAS trials had fewer distortion errors but no change in substitution errors or overall error rate compared to non-SAS trials.

Conclusions:
We show that stroke-impaired speech is susceptible to StartReact, evidenced by decreased intelligibility due to altered formants, pitch trajectories, and articulation, including increased incidence of sounds that could not be produced without SAS. Future studies should examine the impact of SAS on voluntary speech intelligibility and clinical measures of aphasia and apraxia.
Implementing Speech Perception and Phonological Awareness Intervention for Children With Speech Sound Disorders
Authors: Brosseau-Lapré Françoise , Roepke Elizabeth 
Published: April 2022

Purpose:
Children with speech sound disorders have more difficulties producing speech sounds accurately than same-age peers. In addition, they often have difficulties with speech perception, and weaker phonological awareness skills than their peers and are at risk for negative long-term academic and socio-emotional outcomes. In this tutorial, we describe ways in which clinicians can target speech perception and/or phonological awareness within the context of speech production practice.

Method:
First, we briefly describe the speech perception and phonological awareness skills of children with speech sound disorders and summarize previous intervention studies that targeted speech production and speech perception and/or phonological awareness skills. Next, we demonstrate how clinicians may incorporate speech perception and phonological awareness intervention in speech therapy through example instructional objectives and activities and include a case study.

Conclusion:
Incorporating speech perception and phonological awareness into speech production intervention may improve speech and literacy outcomes for children with speech sound disorders.