Miracle-dz/UniFAR-FTUs huggingface dataset:
Plant Health and Sound Vibration: Analyzing Implications of the Microbiome in Grape Wine Leaves

Understanding the plant microbiome is a key for plant health and controlling pathogens. Recent studies have shown that plants are responsive towards natural and synthetic sound vibration (SV) by perception and signal transduction, which resulted in resistance towards plant pathogens. However, whether or not native plant microbiomes respond to SV and the underlying mechanism thereof remains unknown. Within the present study we compared grapevine-associated microbiota that was perpetually exposed to classical music with a non-exposed control group from the same vineyard in Stellenbosch, South Africa. By analyzing the 16S rRNA gene and ITS fragment amplicon libraries we found differences between the core microbiome of SV-exposed leaves and the control group. For several of these different genera, e.g., Bacillus, Kocuria and Sphingomonas, a host-beneficial or pathogen-antagonistic effect has been well studied. Moreover, abundances of taxa identified as potential producers of volatile organic compounds that contribute to sensory characteristics of wines, e.g., Methylobacterium, Sphingomonas, Bacillus and Sporobolomyces roseus, were either increased or even unique within the core music-exposed phyllosphere population. Results show an as yet unexplored avenue for improved plant health and the terroir of wine, which are important for environmentally friendly horticulture and consumer appreciation. Although our findings explain one detail of the long-term positive experience to improve grapevine’s resilience by this unusual but innovative technique, more mechanistic studies are necessary to understand the whole interplay.
Constant‐time solution to database searching by NMR ensemble computing

Brüschweiler's Ensemble algorithm requires n = log N queries to discover the wanted object from the database of the size N. In this paper, we use a new oracle query function g(.) to improve Brüschweiler's algorithm such that only one query is needed for searching the single object. Our algorithm extends from one ancillary qubit to n ancillary qubits. We then construct the oracle query function g(.) satisfying g(x) = 0 for all input x, except for one, say x = z, where g(z) = z. We first prepare 2n qubits, including n qubits for representing the elements and n ancillary qubits for storing the result of the oracle query function. After one query, we obtain z by measuring these ancillary qubits. Our algorithm can efficiently discover the wanted object if N ≤ 230 according to current NMR spectrometer technology.
Recent results from ICRF experiments on ASDEX upgrade

ICRF has been applied at power levels up to of 4 MW for plasma heating with good results in the L‐ and H‐modes, alone and in combination with NI. Mainly minority heating has been applied so far, in some cases combined with second harmonic. Modulation experiments allowed to determine the power absorption efficiency, deposition profiles and the local heat conduction. The ICRF was also shown to have further interesting and beneficial effects on the plasma: the central impurity concentration of tungsten injected by Laser Blow Off was reduced, and a transiently improved energy confinement at the beginning of the NBI pulse was stabilized. The influence of plasma variations on the RF system and methods allowing stable operation, e.g. during the ELMy H‐mode, were studied. Coupling measurements were also used to examine SOL characteristics. Experiments comparing antennas with and without Faraday screen show only minor differences of their electrical properties and heating characteristics.
Germline MC1R variants and frequency of somatic BRAF, NRAS, and TERT mutations in melanoma: Literature review and meta‐analysis

Germline variants of the melanocortin‐1‐receptor (MC1R) gene are the most common genetic trait predisposing to cutaneous melanoma (CM). Here, we performed a literature review and meta‐analysis of the association between MC1R gene variants and the frequency of somatic mutations of the BRAF, NRAS, and TERT genes in CM patients. We included studies published until January 2020 in MEDLINE, EMBASE, Ovid Medline, and two grey literature databases. Random effect models were used to pool study‐specific estimates into summary odds ratio (SOR) and 95% confidence intervals (CIs). Subgroup and sensitivity analyses were conducted to identify potential sources of heterogeneity and assess the robustness of pooled estimates. Twelve studies published between 2006 and 2018 (encompassing 3566 CM, mostly on nonacral sites) were included. MC1R gene variants were not significantly associated with the frequency of somatic mutations of the BRAF and NRAS genes. Only three studies focused on somatic mutations of the TERT gene promoter, all of which reported moderate‐to‐strong positive associations with MC1R germline variants. MC1R gene variants appear to make only moderate changes, if any, to the risk of BRAF‐ or NRAS‐mutant CM. The association with TERT promoter mutations is suggestive, yet it warrants confirmation as it is based on a still limited number of studies
Polydatin-Induced Direct and Bystander Effects in A549 Lung Cancer Cell Line

Abstract Polydatin, a natural analogue of resveratrol, has many biological activities. The better bioavailability of polydatin than resveratrol makes it an ideal candidate for therapy. Polydatin has protective effects against various diseases (cardiovascular, neurological, inflammatory, etc.) including cancer. However, its mechanism of action has not been fully established. Therefore, the present study was initiated to explore the mechanism/s associated with chemotherapeutic effects of polydatin in in vitro using lung cancer A549 cells. The effects of polydatin on cell proliferation and metastasis were assessed using various parameters like MTT, colony formation, DNA damage, apoptosis, and wound healing. Polydatin treatment reduced the proliferation of A549 cells by inducing DNA damage and cell cycle arrest in a concentration-dependent manner. The inhibition of cell proliferation was induced by dual mechanism of senescence and apoptosis. Proteins involved in various pathways were studied using western blotting and immunocytochemistry. Interestingly, senescent and apoptotic cells induced a differential bystander response (proliferative/toxic) in naïve A549 cells. Our results show that polydatin can induce both senescence and apoptosis in A549 cells in a concentration-dependent manner and the differential bystander effects induced by polydatin are regulated by mTOR pathway.
Ocular Delivery of Polyphenols: Meeting the Unmet Needs

Nature has become one of the main sources of exploration for researchers that search for new potential molecules to be used in therapy. Polyphenols are emerging as a class of compounds that have attracted the attention of pharmaceutical and biomedical scientists. Thanks to their structural peculiarities, polyphenolic compounds are characterized as good scavengers of free radical species. This, among other medicinal effects, permits them to interfere with different molecular pathways that are involved in the inflammatory process. Unfortunately, many compounds of this class possess low solubility in aqueous solvents and low stability. Ocular pathologies are spread worldwide. It is estimated that every individual at least once in their lifetime experiences some kind of eye disorder. Oxidative stress or inflammatory processes are the basic etiological mechanisms of many ocular pathologies. A variety of polyphenolic compounds have been proved to be efficient in suppressing some of the indicators of these pathologies in in vitro and in vivo models. Further application of polyphenolic compounds in ocular therapy lacks an adequate formulation approach. Therefore, more emphasis should be put in advanced delivery strategies that will overcome the limits of the delivery site as well as the ones related to the polyphenols in use. This review analyzes different drug delivery strategies that are employed for the formulation of polyphenolic compounds when used to treat ocular pathologies related to oxidative stress and inflammation.
Etherification on Zeolites: MTBE synthesis

Although the use of methyl-tert butyl ether (MTBE) in reformulated gasoline has raised concerns due to its detection in ground water and has led to its gradual phase out in parts of the United States, the use of heavier ethers in gasoline in the future is possible. The synthesis of MTBE provides us with an insight into etherification reactions in general. This article reviews the extensive findings over the past 15 years on the application of acidic zeolites as alternative catalysts for etherification reactions and, in particular, MTBE synthesis, and compares the results with those of the commercially used ion-exchange resins. Although the resin catalysts are very active, they have some significant drawbacks (i.e., thermal fragility, sensitivity to methanol/isobutene ratios, and corrosive/disposal problems). Zeolites have been considered to be potential alternative catalysts for MTBE synthesis due to their excellent properties such as high thermal stability and modifiable acidity. The impact of various zeolite parameters, such as Si/Al ratio, type of zeolite, and the presence of extra-lattice Al, on activity is explored. Although the specific activities of most zeolites have been found to be too low to compete at low temperatures required to avoid thermodynamic limitations, H-beta zeolite has been found to be as active as the current commercial resin catalysts being used for MTBE synthesis. In addition, all zeolites studied have been found to have high selectivities to MTBE and low sensitivities to methanol/isobutene molar ratio, permitting the use of the stoichiometric reactant ratio. Application of zeolites for the synthesis of higher ethers is suggested.
Which Data Do Elementary School Teachers Use to Determine Reading Difficulties in Their Students?

Small-group interventions allow for tailored instruction for students with learning difficulties. A crucial first step is the accurate identification of students who need such an intervention. This study investigated how teachers decide whether their students need a remedial reading intervention. To this end, 64 teachers of 697 third-grade students from Germany were asked to rate whether a reading intervention for their students was “not necessary,” “potentially necessary,” or “definitely necessary. ” Independent experimenters tested the students’ reading and spelling abilities with standardized tests, and a subsample of 370 children participated in standardized tests of phonological awareness and vocabulary. Findings show that teachers’ decisions with regard to students’ needing a reading intervention overlapped more with results from standardized spelling assessments than from reading assessments. Hierarchical linear models indicated that students’ spelling abilities, along with phonological awareness and vocabulary, explained variance in teachers’ ratings over and above students’ reading skills. Teachers thus relied on proximal cues such as spelling skills to reach their decision. These findings are discussed in relation to clinical standards and educational contexts. Findings indicate that the teachers’ assignment of children to interventions might be underspecified, and starting points for specific teacher training programs are outlined.
Substrate-dependent effects of quaternary structure on RNase E activity

In this study, Moore et al. identify a mutation in the Rne protein's catalytic region (E429G), as well as a bacterial cell wall peptidoglycan hydrolase (Amidase C [AmiC]), that selectively affect the specific activity of the RNase E enzyme on long RNA substrates, but not on short synthetic oligonucleotides, by enhancing enzyme multimerization. Their findings show a previously unsuspected substrate length-dependent regulatory role for RNase E quaternary structure and identify cis-acting and trans-acting factors that mediate such regulation.
NOD2 drives early IL-33-dependent expansion of group 2 innate lymphoid cells during Crohn's disease-like ileitis.

Innate lymphoid cells (ILCs) are enriched at barrier surfaces, including the gastrointestinal tract. While most studies have focused on the balance between pathogenic group 1 ILCs (ILC1s) and protective ILC3s in maintaining gut homeostasis and during chronic intestinal inflammation, such as Crohn's disease (CD), less is known regarding ILC2s. Using an established murine model of CD-like ileitis, i.e., SAMP1/YitFc (SAMP) strain, we showed that ILC2s, compared to ILC1s and ILC3s, were increased within draining mesenteric lymph nodes and ilea of SAMP vs. AKR (parental control) mice early, during the onset of disease. Gut-derived ILC2s from Crohn's patients vs. healthy controls were also increased and expand, similar to ILC1s, in greater proportion compared to ILC3s. Importantly, we report that the intracellular bacterial-sensing protein, nucleotide-binding oligomerization domaining-containing protein-2, encoded by NOD2, the first and strongest susceptibility gene identified for CD, promoted ILC2 expansion, which was dramatically reduced in SAMP lacking NOD2 and SAMP raised under germ-free conditions. Furthermore, these effects occurred through a mechanism involving the IL-33/ST2 ligand-receptor pair. Collectively, our results indicate a functional link between NOD2 and ILC2s, regulated by the IL-33/ST2 axis, that mechanistically may contribute to early events leading to CD pathogenesis.
Differential transcription profiling of the phage LUZ19 infection process in different growth media

ABSTRACT RNA sequencing of phage-infected bacterial cultures offers a snapshot of transcriptional events occurring during the infection process, providing insights into the phage transcriptional organization as well as the bacterial response. To better mimic real environmental contexts, we performed RNA-seq of Pseudomonas aeruginosa PAO1 cultures infected with phage LUZ19 in a mammalian cell culture medium to better simulate a phage therapy event and the data were compared to lysogeny broth medium. Regardless of the media, phage LUZ19 induces significant transcriptional changes in the bacterial host over time, particularly during early infection (t = 5 min) and gradually shuts down bacterial transcription. In a common response in both media, 56 P. aeruginosa PAO1 genes are differentially transcribed and clustered into several functional categories such as metabolism, translation and transcription. Our data allowed us to tease apart a medium-specific response during infection from the identified infection-associated responses. This reinforces the concept that phages overtake bacterial transcriptome in a strict manner to gain control of the bacterial machinery and reallocate resources for infection, in this case overcoming the nutritional limitations of the mammalian cell culture medium. From a phage therapy perspective, this study contributes towards a better understanding of phage–host interaction in human physiological conditions and demonstrates the versatility of phage LUZ19 to adapt to different environments.
Chronic pain susceptibility is associated with anhedonic behavior and alterations in the accumbal ubiquitin-proteasome system.

ABSTRACT It remains unknown why upon similar acute/subacute painful conditions, pain persists in some individuals while in others it resolves. Genetic factors, mood, and functional alterations, particularly involving the mesolimbic network, appear to be key. In order to explore potential susceptibility/resistance factors, we screened a large population of rats with a peripheral neuropathy and we isolated a small subset (<15%) that presented high thresholds (HT) to mechanical allodynia (reduced pain manifestation). The phenotype was sustained over 12 weeks and was associated with higher hedonic behavior when compared with low threshold subjects (LT). The nucleus accumbens (NAc) of HT and LT animals were isolated for proteomic analysis by Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS). Two hundred and seventy-nine proteins displayed different expression between LT and HT animals/subjects. Among several protein families, the proteasome pathway repeatedly emerged in gene ontology enrichment and KEGG analyses. Several alpha and beta 20S proteasome subunits were increased in LT when compared to HT animals (e.g., PSMα1, PSMα2, and PSMβ5). On the contrary, UBA6, an upstream ubiquitin-activating enzyme, was decreased in LT animals. Altogether these observations are consistent with an overactivation of the accumbal proteasome pathway in animals that manifest pain and depressive-like behaviors after a neuropathic injury. All the proteomic data are available via ProteomeXchange with identifier PXD022478.
Expert opinion as priors for random effects in Bayesian prediction models: Subclinical ketosis in dairy cows as an example

Random effects regression models are routinely used for clustered data in etiological and intervention research. However, in prediction models, the random effects are either neglected or conventionally substituted with zero for new clusters after model development. In this study, we applied a Bayesian prediction modelling method to the subclinical ketosis data previously collected by Van der Drift et al. (2012). Using a dataset of 118 randomly selected Dutch dairy farms participating in a regular milk recording system, the authors proposed a prediction model with milk measures as well as available test-day information as predictors for the diagnosis of subclinical ketosis in dairy cows. While their original model included random effects to correct for the clustering, the random effect term was removed for their final prediction model. With the Bayesian prediction modelling approach, we first used non-informative priors for the random effects for model development as well as for prediction. This approach was evaluated by comparing it to the original frequentist model. In addition, herd level expert opinion was elicited from a bovine health specialist using three different scales of precision and incorporated in the prediction as informative priors for the random effects, resulting in three more Bayesian prediction models. Results showed that the Bayesian approach could naturally take the clustering structure of clusters into account by keeping the random effects in the prediction model. Expert opinion could be explicitly combined with individual level data for prediction. However in this dataset, when elicited expert opinion was incorporated, little improvement was seen at the individual level as well as at the herd level. When the prediction models were applied to the 118 herds, at the individual cow level, with the original frequentist approach we obtained a sensitivity of 82.4% and a specificity of 83.8% at the optimal cutoff, while with the three Bayesian models with elicited expert opinion, we obtained sensitivities ranged from 78.7% to 84.6% and specificities ranged from 75.0% to 83.6%. At the herd level, 30 out of 118 within herd prevalences were correctly predicted by the original frequentist approach, and 31 to 44 herds were correctly predicted by the three Bayesian models with elicited expert opinion. Further investigation in expert opinion and distributional assumption for the random effects was carried out and discussed.
The Role of Perfectionistic Self-Presentation in Pediatric Pain

This study sought to better understand the associations between perfectionistic self-presentation and measures of pain intensity, pain catastrophizing, pain interference, and fatigue in children and adolescents with pain. In the study, 218 adolescents responded to measures of perfectionistic self-presentation (i.e., perfectionistic self-promotion, nondisplay of imperfection and nondisclosure of imperfection), pain intensity, pain catastrophizing, pain interference, and fatigue. Four hierarchical regression analyses and three mediation analyses were conducted. Our results showed that perfectionistic self-promotion was significantly and independently associated with pain intensity and that nondisplay of imperfection was significantly and independently associated with pain catastrophizing, pain interference, and fatigue. Nondisclosure of imperfection was not significantly associated with any criterion variable. Pain catastrophizing mediated the association between both perfectionistic self-presentation and nondisplay imperfection and pain interference but not between nondisclosure of imperfection and pain interference. The findings provide new information about the role of perfectionistic self-presentation in children and adolescents’ experience of pain. These findings, if replicated, support perfectionism as a potential target of pain treatment in young people.
Warming mediates the resistance of aquatic bacteria to invasion during community coalescence

The immigration history of communities can profoundly affect community composition. For instance, early‐arriving species can have a lasting effect on community structure by reducing the invasion success of late‐arriving ones through priority effects. This can be particularly important when early‐arriving communities coalesce with another community during dispersal (mixing) events. However, the outcome of such community coalescence is unknown as we lack knowledge on how different factors influence the persistence of early‐arriving communities and the invasion success of late‐arriving taxa. Therefore, we implemented a full‐factorial experiment with aquatic bacteria where temperature and dispersal rate of a better adapted community were manipulated to test their joint effects on the resistance of early‐arriving communities to invasion, both at community and population level. Our 16S rRNA gene sequencing‐based results showed that invasion success of better adapted late‐arriving bacteria equaled or even exceeded what we expected based on the dispersal ratios of the recipient and invading communities suggesting limited priority effects on the community level. Patterns detected at the population level, however, showed that resistance of aquatic bacteria to invasion might be strengthened by warming as higher temperatures (a) increased the sum of relative abundances of persistent bacteria in the recipient communities, and (b) restricted the total relative abundance of successfully established late‐arriving bacteria. Warming‐enhanced resistance, however, was not always found and its strengths differed between recipient communities and dispersal rates. Nevertheless, our findings highlight the potential role of warming in mitigating the effects of invasion at the population level.
Robotic Partial Excision of Levator-ani Muscle (PELM) for Locally Advanced Low Rectal Cancer Invading Ipsilateral Pelvic Floor.

Purpose Tumors at the level of the anorectal junction had required APR to achieve an adequate resection margin. However, in the cases of tumor invading ipsilateral levator-ani muscle (LAM), en bloc resection of the rectum with LAM including tumor would be possible. This video is to show the critical anatomic steps of this procedure. Methods A video was produced from the robotic right PELM performed in a 57-year-old female patient with rectal cancer at 3 cm from the anal verge, invading the ipsilateral anorectal ring, who had received nCRT. Results The patient discharged at POD #8 without complication. The pathology of the surgical specimen revealed ypT3N1bM0. The secure resection margin from the tumor was achieved. Conclusion Robotic PELM is the sphincter-preserving technique that can be an alternative treatment option for low rectal cancer invading the ipsilateral LAM, which has been an indication for abdominoperineal resection (APR) or extralevator APR.