Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide Analysis of Gene Expression Provides New Insights into Waterlogging Responses in Barley (Hordeum vulgare L.)

Waterlogging is a major abiotic stress causing oxygen depletion and carbon dioxide accumulation in the rhizosphere. Barley is more susceptible to waterlogging stress than other cereals. To gain a better understanding, the genome-wide gene expression responses in roots of waterlogged barley seedlings of Yerong and Deder2 were analyzed by RNA-Sequencing. A total of 6736, 5482, and 4538 differentially expressed genes (DEGs) were identified in waterlogged roots of Yerong at 72 h and Deder2 at 72 and 120 h, respectively, compared with the non-waterlogged control. Gene Ontology (GO) enrichment analyses showed that the most significant changes in GO terms, resulted from these DEGs observed under waterlogging stress, were related to primary and secondary metabolism, regulation, and oxygen carrier activity. In addition, more than 297 transcription factors, including members of MYB, AP2/EREBP, NAC, WRKY, bHLH, bZIP, and G2-like families, were identified as waterlogging responsive. Tentative important contributors to waterlogging tolerance in Deder2 might be the highest up-regulated DEGs: Trichome birefringence, α/β-Hydrolases, Xylanase inhibitor, MATE efflux, serine carboxypeptidase, and SAUR-like auxin-responsive protein. The study provides insights into the molecular mechanisms underlying the response to waterlogging in barley, which will be of benefit for future studies of molecular responses to waterlogging and will greatly assist barley genetic research and breeding.
Extracellular tRNAs and tRNA-derived fragments

ABSTRACT Fragmentation of tRNAs generates a family of small RNAs collectively known as tRNA-derived fragments. These fragments vary in sequence and size but have been shown to regulate many processes involved in cell homoeostasis and adaptations to stress. Additionally, the field of extracellular RNAs (exRNAs) is rapidly growing because exRNAs are a promising source of biomarkers in liquid biopsies, and because exRNAs seem to play key roles in intercellular and interspecies communication. Herein, we review recent descriptions of tRNA-derived fragments in the extracellular space in all domains of life, both in biofluids and in cell culture. The purpose of this review is to find consensus on which tRNA-derived fragments are more prominent in each extracellular fraction (including extracellular vesicles, lipoproteins and ribonucleoprotein complexes). We highlight what is becoming clear and what is still controversial in this field, in order to stimulate future hypothesis-driven studies which could clarify the role of full-length tRNAs and tRNA-derived fragments in the extracellular space.
Clinical Pathways for Oncological Gastrectomy: Are They a Suitable Instrument for Process Standardization to Improve Process and Outcome Quality for Patients Undergoing Gastrectomy? A Retrospective Cohort Study

(1) Background: Oncological gastrectomy requires complex multidisciplinary management. Clinical pathways (CPs) can potentially facilitate this task, but evidence related to their use in managing oncological gastrectomy is limited. This study evaluated the effect of a CP for oncological gastrectomy on process and outcome quality. (2) Methods: Consecutive patients undergoing oncological gastrectomy before (n = 64) or after (n = 62) the introduction of a CP were evaluated. Assessed parameters included catheter and drain management, postoperative mobilization, resumption of diet and length of stay. Morbidity, mortality, reoperation and readmission rates were used as indicators of outcome quality. (3) Results: Enteral nutrition was initiated significantly earlier after CP implementation (5.0 vs. 7.0 days, p < 0.0001). Readmission was more frequent before CP implementation (7.8% vs. 0.0%, p = 0.05). Incentive spirometer usage increased following CP implementation (100% vs. 90.6%, p = 0.11). Mortality, morbidity and reoperation rates remained unchanged. (4) Conclusions: After implementation of an oncological gastrectomy CP, process quality improved, while indicators of outcome quality such as mortality and reoperation rates remained unchanged. CPs are a promising tool to standardize perioperative care for oncological gastrectomy.
Effect of Substrate Conductivity on the Transient Thermal Transport of Hygroscopic Droplets during Vapor Absorption

In all kinds of liquid desiccant dehumidification systems, the temperature increase of the desiccant solution due to the effect of absorptive heating is one of the main reasons of performance deterioration. In this study, we look into the thermal effects during vapor absorption into single hygroscopic liquid desiccant droplets. Specifically, the effect of substrate conductivity on the transient heat and mass transfer process is analyzed in detail. The relative strength of the thermal effect and the solutal effect on the rate of vapor absorption is investigated and compared to the thermal effect by evaporative cooling taking place in pure water droplets. In the case of liquid desiccants, results indicate that the high thermal conductivity of copper substrates ensures more efficient heat removal, and the temperature at the droplet surface decreases more rapidly than that on Polytetrafluoroethylene (PTFE) substrates. As a result, the initial rate of vapor absorption on copper substrates slightly outweighs that on PTFE substrates. Further analysis by decomposing the vapor pressure difference indicates that the variation of vapor pressure caused by the temperature change during vapor absorption is much weaker than that induced by the concentration change. The conclusions demonstrate that a simplified isothermal model can be applied to capture the main mechanisms during vapor absorption into hygroscopic droplets even though it is evidenced to be unreliable for droplet evaporation.
Recognition of Accented Speech by Cochlear-Implant Listeners: Benefit of Audiovisual Cues

Objectives: When auditory and visual speech information are presented together, listeners obtain an audiovisual (AV) benefit or a speech understanding improvement compared with auditory-only (AO) or visual-only (VO) presentations. Cochlear-implant (CI) listeners, who receive degraded speech input and therefore understand speech using primarily temporal information, seem to readily use visual cues and can achieve a larger AV benefit than normal-hearing (NH) listeners. It is unclear, however, if the AV benefit remains relatively large for CI listeners when trying to understand foreign-accented speech when compared with unaccented speech. Accented speech can introduce changes to temporal auditory cues and visual cues, which could decrease the usefulness of AV information. Furthermore, we sought to determine if the AV benefit was relatively larger in CI compared with NH listeners for both unaccented and accented speech. Design: AV benefit was investigated for unaccented and Spanish-accented speech by presenting English sentences in AO, VO, and AV conditions to 15 CI and 15 age- and performance-matched NH listeners. Performance matching between NH and CI listeners was achieved by varying the number of channels of a noise vocoder for the NH listeners. Because of the differences in age and hearing history of the CI listeners, the effects of listener-related variables on speech understanding performance and AV benefit were also examined. Results: AV benefit was observed for both unaccented and accented conditions and for both CI and NH listeners. The two groups showed similar performance for the AO and AV conditions, and the normalized AV benefit was relatively smaller for the accented than the unaccented conditions. In the CI listeners, older age was associated with significantly poorer performance with the accented speaker compared with the unaccented speaker. The negative impact of age was somewhat reduced by a significant improvement in performance with access to AV information. Conclusions: When auditory speech information is degraded by CI sound processing, visual cues can be used to improve speech understanding, even in the presence of a Spanish accent. The AV benefit of the CI listeners closely matched that of the NH listeners presented with vocoded speech, which was unexpected given that CI listeners appear to rely more on visual information to communicate. This result is perhaps due to the one-to-one age and performance matching of the listeners. While aging decreased CI listener performance with the accented speaker, access to visual cues boosted performance and could partially overcome the age-related speech understanding deficits for the older CI listeners.
Sweet thermal taste: Perceptual characteristics in water and dependence on TAS1R2/TAS1R3.

The initial objective of this study was to determine if activation of the sweet taste receptor TAS1R2/TAS1R3 is necessary for perception of sweet thermal taste. Our approach was to inhibit the receptor with the inverse agonist lactisole using a temperature-controlled flow gustometer. Because all prior studies of thermal taste used metal thermodes to heat the tongue tip, we first investigated whether it could be generated in heated water. Experiment 1 showed that sweetness could be evoked when deionized water was heated from 20° to 35°C, and testing with static temperatures between 20° and 35°C demonstrated the importance of heating from a cool temperature. As in previous studies, thermal sweetness was reported by only a subset of participants, and replicate measurements found variability in reports of sweetness across trials and between sessions. Experiment 2 then showed that exposure to 8mM lactisole blocked perception of sweet thermal taste. Confirmation of the involvement of TAS1R2/TAS1R3 led to an investigation of possible sensory and cognitive interactions between thermal and chemical sweetness. Using sucrose as a sweet stimulus and quinine as a non-sweet control, we found that dynamic heating capable of producing thermal sweetness did not increase the sweetness of sucrose compared to static heating at 35°C. However, sweet thermal taste was disrupted if trials containing sucrose (but not quinine) were interspersed among heating-only trials. These findings provide new information relevant to understanding the perceptual processes and receptor mechanisms of sweet thermal taste, as well as the heat sensitivity of sweet taste in general.
The multifarious regulation of the apical junctional complex

Epithelial cells form highly organized polarized sheets with characteristic cell morphologies and tissue architecture. Cell–cell adhesion and intercellular communication are prerequisites of such cohesive sheets of cells, and cell connectivity is mediated through several junctional assemblies, namely desmosomes, adherens, tight and gap junctions. These cell–cell junctions form signalling hubs that not only mediate cell–cell adhesion but impact on multiple aspects of cell behaviour, helping to coordinate epithelial cell shape, polarity and function. This review will focus on the tight and adherens junctions, constituents of the apical junctional complex, and aims to provide a comprehensive overview of the complex signalling that underlies junction assembly, integrity and plasticity.
Impact of physiological noise in characterizing the functional MRI default-mode network in Alzheimer’s disease

The functional connectivity of the default-mode network (DMN) monitored by functional magnetic resonance imaging (fMRI) in Alzheimer's disease (AD) patients has been found weaker than that in healthy participants. Since breathing and heart beating can cause fluctuations in the fMRI signal, these physiological activities may affect the fMRI data differently between AD patients and healthy participants. We collected resting-state fMRI data from AD patients and age-matched healthy participants. With concurrent cardiac and respiratory recordings, we estimated both physiological responses phase-locked and non-phase-locked to heart beating and breathing. We found that the cardiac and respiratory physiological responses in AD patients were 3.00 ± 0.51 s and 3.96 ± 0.52 s later (both p < 0.0001) than those in healthy participants, respectively. After correcting the physiological noise in the resting-state fMRI data by population-specific physiological response functions, the DMN estimated by seed-correlation was more localized to the seed region. The DMN difference between AD patients and healthy controls became insignificant after suppressing physiological noise. Our results indicate the importance of controlling physiological noise in the resting-state fMRI analysis to obtain clinically related characterizations in AD.
Relationships between women’s emotional reaction to first coital experience and subsequent sexual risk-taking behaviour

Abstract Objectives: The study aimed to consider the affective reactions of young French women to their experience of first sexual intercourse and examine the relationship with subsequent risky sexual behaviours, using cluster profiles. Methods: A descriptive cross-sectional study was conducted among women in France (n = 391) (mean age 22.36 years, standard deviation 3.08). Participants completed a questionnaire with self-reported measures of emotional responses to first sexual intercourse and risky sexual behaviours. Results: Cluster analyses revealed four emotional reaction profiles: Pleasure, Guilty-pleasure, Negative-emotional and Anxiety-unpleasant. The Pleasure group reported overall and higher satisfaction and positive emotions towards first sexual intercourse; this group reported lower condom use. The Guilty-pleasure group felt pleasure tinged with guilt and reported fewer same-sex partners. The Negative-emotional profile group tended to feel major negative emotions related to initial coital experience, reporting lower or no pleasure. The Anxiety-unpleasant group reported little pleasure and major anxiety associated with first sexual intercourse. The latter two groups, respectively, reported a higher number of male sexual partners and higher alcohol consumption prior to sexual intercourse compared with the two pleasure groups. Conclusion: These results suggest that women’s emotional reactions to first sexual intercourse may be associated with subsequent healthy versus risky sexual behaviours in young adulthood.
Long-term changes in winter abundance of the barbastelle Barbastella barbastellus in Poland and the climate change – Are current monitoring schemes still reliable for cryophilic bat species?

Warmer winters may lead to changes in the hibernation behaviour of bats, such as the barbastelle Barbastella barbastellus, which prefers to hibernate at low temperatures. The species is also known for its large annual fluctuations in the number of wintering individuals, so inference about population trends should be based on long-term data. Prior to 2005, analyses indicated stable or even increasing barbastelle population in Poland. We analysed the results of 13 winter bat counts (2005–2017) of the species from 15 of the largest hibernacula, and additional site of 47 small bunkers, in Poland. The total number of wintering individuals remained stable during the study period, because the barbastelle is not a long-distance migrant, this likely reflects the national population trend. On the basis of mean winter air temperatures we divided the country into four thermal regions. Analyses of barbastelle abundance in hibernacula in the four regions revealed a 4.8% annual mean increase in numbers in the coldest region, where mean winter temperatures were below -2°C, annual mean declines of 3.3% and 3.1% in two warmer regions of western Poland, but no trend in the region of intermediate mean winter temperatures of between -1°C and -2°C. Overall, there was a significant, but weak, negative correlation between the abundance of hibernating individuals and the mean winter temperature. On the other hand, the number of individuals hibernating in small bunkers increased, even though the site was located in one of the warm regions. The results indicate a warming climate will likely reduce the use of large, well-insulated winter roosts by species that prefer colder conditions–and that this is already happening. For forest-dwelling bats, such as the barbastelle, for which monitoring schemes are primarily based on winter surveys of large hibernacula, estimations of population trends may consequently become less reliable.
Does it matter who’s at risk?: Testing message framing and narrative as moderators of the effects of self-referencing in obesity prevention messages targeting Hispanic adults living in the U.S.

Abstract This study tested whether the effect of self-referencing in a health-marketing message was amplified or attenuated when combined with message framing and narrative. Hispanic adults (N = 146) were randomly assigned to read and respond to an obesity prevention message. Self-referencing messages generated greater cognitive elaboration but only when placed in a narrative. Conversely, self-referencing messages highlighting health risks of obesity produced higher levels of involvement and intention to increase physical activity and healthy eating. Health marketing professionals can use these findings to enhance the effectiveness of obesity prevention messages that target Hispanic adults.
Oral Microbiome Profiling in Smokers with and without Head and Neck Cancer Reveals Variations Between Health and Disease

While smoking is inextricably linked to oral/head and neck cancer (HNSCC), only a small fraction of smokers develop HNSCC. Thus, we have sought to identify other factors, which may influence the development of HNSCC in smokers including microbiology. To determine microbial associations with HNSCC among tobacco users, we characterized oral microbiome composition in smokers with and without HNSCC. 16S rRNA MiSeq sequencing was used to examine the oral mucosa microbiome of 27 smokers with (cases) and 24 without HNSCC (controls). In addition, we correlated previously reported levels of DNA damage with the microbiome data. Smokers with HNSCC showed lower microbiome richness compared with controls (q = 0.012). Beta-diversity analyses, assessed as UniFrac (weighted and unweighted) and Bray–Curtis distances, showed significant differences in oral mucosal microbiome signatures between cases and controls (r2 = 0.03; P = 0.03) and higher interindividual microbiome heterogeneity in the former (q ≤ 0.01). Higher relative abundance of Stenotrophomonas and Comamonadaceae and predicted bacterial pathways mainly involved in xenobiotic and amine degradation were found in cases compared with controls. The latter, in contrast, exhibited higher abundance of common oral commensals and predicted sugar degradation pathways. Finally, levels of DNA damage in the oral cavity were correlated with the microbiome profiles above. Oral microbiome traits differ in smokers with and without HNSCC, potentially informing the risk of eventual HNSCC and shedding light into possible microbially mediated mechanisms of disease. These findings present data that may be useful in screening efforts for HNSCC among smokers who are unable to quit.
Synergistic Activity of Clofazimine and Clarithromycin in an Aerosol Mouse Model of Mycobacterium avium Infection

Infections with nontuberculous mycobacteria (NTM) have a poor prognosis in patients with underlying respiratory diseases. Clofazimine (CFZ) showed both experimental and clinical promising results against clinically relevant NTM. However, there are no data on CFZ in combination with the current recommended treatment; therefore, we aimed to study its in vivo activity in an aerosol mouse model of Mycobacterium avium. In an aerosol infection BALB/c mouse model using M. avium strain Chester, we treated 58 mice with four combinations of rifampin (RIF) at 10 mg/kg, CFZ at 25 mg/kg, and clarithromycin (CLR) and ethambutol (EMB) at 100 mg/kg. ABSTRACT Infections with nontuberculous mycobacteria (NTM) have a poor prognosis in patients with underlying respiratory diseases. Clofazimine (CFZ) showed both experimental and clinical promising results against clinically relevant NTM. However, there are no data on CFZ in combination with the current recommended treatment; therefore, we aimed to study its in vivo activity in an aerosol mouse model of Mycobacterium avium. In an aerosol infection BALB/c mouse model using M. avium strain Chester, we treated 58 mice with four combinations of rifampin (RIF) at 10 mg/kg, CFZ at 25 mg/kg, and clarithromycin (CLR) and ethambutol (EMB) at 100 mg/kg. Treatment efficacy was assessed on the basis of lung CFU counts after 2 (M2) and 4 (M4) months of treatment. At M2, CLR-RIF-EMB was slightly but significantly more efficient than CFZ-RIF-EMB (3.02 ± 0.12 versus 3.55 ± 0.28, respectively, P < 0.01), whereas CLR-CFZ-EMB and CLR-CFZ-RIF-EMB dramatically decreased lung CFU counts by 4.32 and 4.47 log10, respectively, compared to untreated group. At M4, CLR-RIF-EMB was significantly more efficient than CFZ-RIF-EMB (2 ± 0.53 versus 2.66 ± 0.22, respectively, P = 0.01). The addition of CLZ to CLR dramatically decreased the lung CFU count, with CFU counts 5.41 and 5.79 log10 lower in the CLR-CFZ-EMB and CLR-CFZ-RIF-EMB groups, respectively, than in the untreated group. The addition of CFZ to CLR seems to improve the efficacy of CLR as early as M2 and was confirmed at M4. CFZ, in addition to RIF and EMB, on the other hand, is less effective than CLR-RIF-EMB. These results need to be confirmed by similar studies along with CFZ potential for shortening treatment.