Miracle-dz/UniFAR-FTUs huggingface dataset:
Steelhead trout (Oncorhynchus mykiss) fed probiotic during the earliest developmental stages have enhanced growth rates and intestinal microbiome bacterial diversity

Sustainable aquaculture practices can help meet the increasing human demand for seafood, while easing pressures on natural fish populations. Studies aimed at increasing fish production in aquaculture have included supplementary dietary probiotics that often promote general health and enhanced growth rates by altering the microbiome of the host. Steelhead trout (Oncorhynchus mykiss) is anadromous, like salmon, and it is a subspecies of rainbow trout capable of rapid growth, making it an attractive fish to the aquaculture industry. In this study, the impact of feeding a Bacillus subtilis probiotic on the bacterial microbiome of steelhead trout was examined temporally across several stages of animal development, from eggs (day -19) through 184 days after hatching, in relation to physiological measures. Diets included: commercial feed only as a control (A), continually-fed probiotic top-coated on commercial feed (B), commercial then switch to probiotic feed (C), or probiotic then switch to commercial feed (D). Validation of probiotic concentrations on feed and in fish tissues was performed using CFU/g and qPCR, respectively. Fish growth was measured and samples for intestinal microbiome analyses were collected at multiple timepoints during fish development. Fish fed diet D yielded higher weights than the other three diets, with little impact on other biometric parameters. However, bacterial microbiome analysis indicated an increasing trend of overall alpha diversity from the egg stage to day 29 for fish fed the various diets with diet D having the highest diversity. Fish fed diets A and D maintained a high alpha diversity beyond day 29 in contrast to a decreased trend for fish still being fed probiotics in diets B and C. The fish fed diets B and C harbored a significantly higher relative abundance of Bacillus sp. in their total microbiomes (feces + mucosa). Interestingly, the mucosal-only microbiome indicated little variation between the four groups of fish. Feeding the probiotic earlier in development, during the hatchery phase, to influence bacterial microbiome composition in the intestine (rather than later after the microbiome has been established) appears to be a more effective aquaculture practice by enhancing microbiome diversity while enabling higher fish yields.
The mechanism of lncRNAs in the crosstalk between epithelial-mesenchymal transition and tumor microenvironment for early colon adenocarcinoma based on molecular subtyping

A large number of colon adenocarcinoma (COAD) patients are already advanced when diagnosed. In this study, we aimed to further understand the mechanism of tumor development in early COAD by focusing on epithelial-mesenchymal transition (EMT) and long non-coding RNAs (lncRNAs). Expression profiles of early COAD patients were obtained from public databases. EMT-related lncRNAs were used as a basis for constructing molecular subtypes through unsupervised consensus clustering. Genomic features, pathways and tumor microenvironment (TME) were compared between two subtypes. LncATLAS database was applied to analyze the relation between lncRNAs and transcription factors (TFs). First order partial correlation analysis was conducted to identify key EMT-related lncRNAs.C1 and C2 subtypes with distinct prognosis were constructed. Oncogenic pathways such as EMT, KRAS signaling, JAK-STAT signaling, and TGF-β signaling were significantly enriched in C2 subtype. Higher immune infiltration and expression of immune checkpoints were also observed in C2 subtype, suggesting the key EMT-related lncRNAs may play a critical role in the modulation of TME. In addition, JAK-STAT signaling pathway was obviously enriched in upregulated TFs in C2 subtype, which indicated a link between key lncRNAs and JAK-STAT signaling that may regulate TME. The study further expanded the research on the role of EMT-related lncRNAs in the early COAD. The six identified EMT-related lncRNAs could serve as biomarkers for early screening COAD.
The effects of graft source and orientation on outcomes after ablation of a branched peripheral nerve

Segmental peripheral nerve injuries (PNI) are the most common cause of enduring nervous system dysfunction. The peripheral nervous system (PNS) has an extensive and highly branching organization. While much is known about the factors that affect regeneration through sharp bisections and linear ablations of peripheral nerves, very little has been investigated or documented about PNIs that ablate branch points. Such injuries present additional complexity compared to linear segmental defects. This study compared outcomes following ablation of a branch point with branched grafts, specifically examining how graft source and orientation of the branched graft contributed to regeneration. The model system was Lewis rats that underwent a 2.5 cm ablation that started in the sciatic nerve trunk and included the peroneal/tibial branch point. Rats received grafts that were rat sciatic autograft, inbred sciatic allograft, and inbred femoral allograft, each of which was a branched graft of 2.5 cm. Allografts were obtained from Lewis rats, which is an inbred strain. Both branches of the sciatic grafts were mixed motor and sensory while the femoral grafts were smaller in diameter than sciatic grafts and one branch of the femoral graft is sensory and the other motor. All branched grafts were sutured into the defect in two orientations dictated by which branch in the graft was sutured to the tibial vs peroneal stumps in recipients. Outcome measures include compound muscle action potentials (CMAPs) and CatWalk gait analysis throughout the recovery period, with toluidine blue for intrinsic nerve morphometry and retrograde labeling conducted at the 36-week experimental end point. Results indicate that graft source and orientation does play a significant role earlier in the regenerative process but by 36 weeks all groups showed very similar indications of regeneration across multiple outcomes.
‘Root of all success’: Plasticity in root architecture of invasive wild radish for adaptive benefit

Successful plant establishment in a particular environment depends on the root architecture of the seedlings and the extent of edaphic resource utilization. However, diverse habitats often pose a predicament on the suitability of the fundamental root structure of a species that evolved over a long period. We hypothesized that the plasticity in the genetically controlled root architecture in variable habitats provides an adaptive advantage to worldwide-distributed wild radish (Raphanus raphanistrum, Rr) over its close relative (R. pugioniformis, Rp) that remained endemic to the East Mediterranean region. To test the hypothesis, we performed a reciprocal comparative analysis between the two species, growing in a common garden experiment on their native soils (Hamra/Sandy for Rr, Terra Rossa for Rp) and complementary controlled experiments mimicking the major soil compositions. Additionally, we analyzed the root growth kinetics via semi-automated digital profiling and compared the architecture between Rr and Rp. In both experiments, the primary roots of Rr were significantly longer, developed fewer lateral roots, and showed slower growth kinetics than Rp. Multivariate analyses of seven significant root architecture variables revealed that Rr could successfully adapt to different surrogate growth conditions by only modulating their main root length and number of lateral roots. In contrast, Rp needs to modify several other root parameters, which are very resource-intensive, to grow on non-native soil. Altogether the findings suggest an evo-devo adaptive advantage for Rr as it can potentially establish in various habitats with the minimal tweak of key root parameters, hence allocating resources for other developmental requirements.
Induction of salt tolerance in Brassica rapa by nitric oxide treatment

Salinity is one of the major plant abiotic stresses increasing over time worldwide. The most important biological role of nitric oxide (NO) in plants is related to their development and growth under abiotic conditions. The present experiment was conducted to study the effect of salt stress (0 and 100 mM) and NO (0 and 80 μM) on two different ecotypes of Brassica rapa (L.): PTWG-HL and PTWG-PK. The different growth attributes, biochemical and physiological parameters, and the mineral contents were examined. The results indicated increased hydrogen peroxide (H2O2), relative membrane permeability, malondialdehyde (MDA), and Na+ content and decreased plant biomass in both ecotypes (PTWG-PK and PTWG-HL) under salt stress. In contrast, NO treatment resulted in increased plant biomass, chlorophyll content, and total soluble proteins and decreased H2O2, relative membrane permeability, MDA, total phenolic content, catalase (CAT), peroxidase (POD), ascorbate peroxidase (APX), and Na+. The combined effect of salt stress and NO application increased the chlorophyll a content, total phenolic content, and total soluble proteins, but decreased H2O2, relative membrane permeability, MDA, and Na+. The response of carotenoids, anthocyanins, and K+, Ca2+, and Cl− ions varied in both ecotypes under all treatment conditions. The PTWG-PK ecotype showed maximum overall growth response with the application of NO. Henceforth, it is proposed that the molecular mechanisms associated with NO-induced stress tolerance in plants may be exploited to attain sustainability in agriculture under changing climate scenarios.
Exploring the relationships between team leader’s conflict management styles and team passion: From the emotional perspective

From the emotional perspective, this study explores how team leader’s conflict management styles affect team passion. A theoretical model is constructed which describes the mediating role of positive team emotional climate and the moderating impact of team emotional intelligence. We collect 101 teams paired data including 101 team leaders and 383 team members to test theoretical model. It is shown that leader’s cooperative conflict management style has a significant positive effect on both positive team emotional climate and team passion. Meanwhile, positive team emotional climate plays a mediating role between leader’s cooperative conflict management style and team passion. In addition, team emotional intelligence has a moderating effect between leader’s cooperative style and positive team emotional climate. This study not only provides a new perspective for follow-up research but also expands the research scope of impacts of conflict management styles. In addition, this study forms the underlying mechanism of team leader’s conflict management styles on team passion from the emotional perspective and investigates the mediating effect and moderating effect of emotional variable, which broadens the research on the mechanisms of conflict management styles on team outcomes to a certain extent.
Genomic characterization of intracranial teratomas using whole genome sequencing

Background Intracranial teratoma is a rare neoplasm of the central nervous system, often classified into mature and immature types and occurs mainly in children and adolescents. To date, there has been no comprehensive genomic characterization analysis of teratoma due to its rarity of the cases. Methods Forty-six patients with intracranial teratomas were collected and 22 of them underwent whole-exome sequencing, including 8 mature teratomas and 14 immature teratomas. A comprehensive analysis was performed to analyze somatic mutations, copy number variants (CNVs), mutational signatures, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway in our cohort. Results The most common somatic mutated gene in intracranial teratomas was CARD11 (18%) and IRS1 (18%), followed by PSMD11, RELN, RRAS2, SMC1A, SYNE1 and ZFHX3, with mutation rates of 14% for the latter six genes. Copy number variation was dominated by amplification, among which ARAF (50%), ATP2B3 (41%), GATA1 (41%), ATP6AP1 (36%), CCND2 (36%) and ZMYM3 (36%) were the most frequently amplified genes. Copy number deletion of SETDB2 and IL2 only appeared in immature teratoma (43% and 36%, respectively), but not in mature teratoma (p = 0.051 and 0.115, respectively). Prognostic analysis showed that TP53 mutations might be associated with poor prognosis of intracranial teratomas patients. Conclusions Our study revealed the genetic characteristics of intracranial teratoma which might be valuable for guiding future targeted therapies.
The compactness of commutators of Calderón-Zgymund operators with Dini condition

Let $T$ be the $\theta$-type Calder\'on-Zgymund operator with Dini condition. In this paper, we prove that for $b\in {\rm CMO}(\mathbb R^n)$, the commutator generated by $T$ with $b$ and the corresponding maximal commutator, are both compact operators on $L^{p}(\omega)$ spaces, where $\omega$ be the Muchenhoupt $A_p$ weight function and $1
Self-assessment of cochlear health by cochlear implant recipients

Recent technological advances in cochlear implant (CI) telemetry have enabled, for the first time, CI users to perform cochlear health (CH) measurements through self-assessment for prolonged periods of time. This is important to better understand the influence of CH on CI outcomes, and to assess the safety and efficacy of future novel treatments for deafness that will be administered as adjunctive therapies to cochlear implantation. We evaluated the feasibility of using a CI to assess CH and examined patterns of electrode impedances, electrically-evoked compound action potentials (eCAPs) and electrocochleography (ECochGs), over time, in a group of adult CI recipients. Fifteen subjects were trained to use the Active Insertion Monitoring tablet by Advanced Bionics, at home for 12 weeks to independently record impedances twice daily, eCAPs once weekly and ECochGs daily in the first week, and weekly thereafter. Participants also completed behavioral hearing and speech assessments. Group level measurement compliance was 98.9% for impedances, 100% for eCAPs and 99.6% for ECochGs. Electrode impedances remained stable over time, with only minimal variation observed. Morning impedances were significantly higher than evening measurements, and impedances increased toward the base of the cochlea. eCAP thresholds were also highly repeatable, with all subjects showing 100% measurement consistency at, at least one electrode. Just over half of all subjects showed consistently absent thresholds at one or more electrodes, potentially suggesting the existence of cochlear dead regions. All subjects met UK NICE guidelines for cochlear implantation, so were expected to have little residual hearing. ECochG thresholds were, unsurprisingly, highly erratic and did not correlate with audiometric thresholds, though lower ECochG thresholds showed more repeatability over time than higher thresholds. We conclude that it is feasible for CI users to independently record CH measurements using their CI, and electrode impedances and eCAPs are promising measurements for objectively assessing CH.
Genetic mapping of the Andean anthracnose resistance gene present in the common bean cultivar BRSMG Realce

The rajado seeded Andean bean (Phaseolus vulgaris L.) cultivar BRSMG Realce (striped seed coat) developed by Embrapa expressed a high level of anthracnose resistance, caused by Colletotrichum lindemuthianum, in field and greenhouse screenings. The main goal of this study was to evaluate the inheritance of anthracnose resistance in BRSMG Realce, map the resistance locus or major gene cluster previously named as Co-Realce, identify resistance-related positional genes, and analyze potential markers linked to the resistance allele. F2 plants derived from the cross BRSMG Realce × BRS FC104 (Mesoamerican) and from the cross BRSMG Realce × BRS Notável (Mesoamerican) were inoculated with the C. lindemuthianum races 475 and 81, respectively. The BRSMG Realce × BRS FC104 F2 population was also genotyped using the DArTseq technology. Crosses between BRSMG Realce and BAT 93 (Mesoamerican) were also conducted and resulting F2 plants were inoculated with the C. lindemuthianum races 65 and 1609, individually. The results shown that anthracnose resistance in BRSMG Realce is controlled by a single locus with complete dominance. A genetic map including 1,118 SNP markers was built and shown 78% of the markers mapped at a distances less than 5.0 cM, with a total genetic length of 4,473.4 cM. A major locus (Co-Realce) explaining 54.6% of the phenotypic variation of symptoms caused by the race 475 was identified in Pv04, flanked by the markers snp1327 and snp12782 and 4.48 cM apart each other. These SNPs are useful for marker-assisted selection, due to an estimated selection efficiency of 99.2%. The identified resistance allele segregates independently of the resistance allele Co-33 (Pv04) present in BAT 93. The mapped genomic region with 704,867 bp comprising 63 putative genes, 44 of which were related to the pathogen-host interaction. Based on all these results and evidence, anthracnose resistance in BRSMG Realce should be considered as monogenic, useful for breeding purpose. It is proposed that locus Co-Realce is unique and be provisionally designated as CoPv04R until be officially nominated in accordance with the rules established by the Bean Improvement Cooperative Genetics Committee.
Multi-Head Multi-Layer Attention to Deep Language Representations for Grammatical Error Detection

It is known that a deep neural network model pre-trained with large-scale data greatly improves the accuracy of various tasks, especially when there are resource constraints. However, the information needed to solve a given task can vary, and simply using the output of the final layer is not necessarily sufficient. Moreover, to our knowledge, exploiting large language representation models to detect grammatical errors has not yet been studied. In this work, we investigate the effect of utilizing information not only from the final layer but also from intermediate layers of a pre-trained language representation model to detect grammatical errors. We propose a multi-head multi-layer attention model that determines the appropriate layers in Bidirectional Encoder Representation from Transformers (BERT). The proposed method achieved the best scores on three datasets for grammatical error detection tasks, outperforming the current state-of-the-art method by 6.0 points on FCE, 8.2 points on CoNLL14, and 12.2 points on JFLEG in terms of F_0. 5. We also demonstrate that by using multi-head multi-layer attention, our model can exploit a broader range of information for each token in a sentence than a model that uses only the final layer's information.
A spiral interface with positive
Alt–Caffarelli–Friedman limit at the origin

We give an example of a pair of nonnegative subharmonic functions with disjoint support for which the Alt-Caffarelli-Friedman monotonicity formula has strictly positive limit at the origin, and yet the interface between their supports lacks a (unique) tangent there. This clarifies a remark appearing in the literature (see \cite{cs05}) that the positivity of the limit of the ACF formula implies unique tangents; this is true under some additional assumptions, but false in general. In our example, blow-ups converge to the expected piecewise linear two-plane function along subsequences, but the limiting function depends on the subsequence due to the spiraling nature of the interface.
Serum level of calpains product as a novel biomarker of acute lung injury following cardiopulmonary bypass

Objective The aim of this study was to test the hypothesis whether serum level of calpains could become a meaningful biomarker for diagnosis of acute lung injury (ALI) in clinical after cardiac surgery using cardiopulmonary bypass (CPB) technology. Methods and results Seventy consecutive adults underwent cardiac surgery with CPB were included in this prospective study. Based on the American-European Consensus Criteria (AECC), these patients were divided into ALI (n = 20, 28.57%) and non-ALI (n = 50, 71.43%) groups. Serum level of calpains in terms of calpains’ activity which was expressed as relative fluorescence unit (RFU) per microliter and measured at beginning of CPB (baseline), 1 h during CPB, end of CPB as well as 1, 12, and 24 h after CPB. Difference of serum level of calpains between two groups first appeared at the end of CPB and remained different at subsequent test points. Univariate and multivariate logistic regression analysis indicated that serum level of calpains 1 h after CPB was an independent predictor for postoperative ALI (OR 1.011, 95% CI 1.001, 1.021, p = 0.033) and correlated with a lower PaO2/FiO2 ratio in the first 2 days (The first day: r = -0.389, p < 0.001 and the second day: r = -0.320, p = 0.007) as well as longer mechanical ventilation time (r = 0.440, p < 0.001), intensive care unit (ICU) length of stay (LOS) (r = 0.419, p < 0.001) and hospital LOS (r = 0.297, p = 0.013). Conclusion Elevated serum level of calpains correlate with impaired lung function and poor clinical outcomes, indicating serum level of calpains could act as a potential biomarker for postoperative ALI following CPB in adults. Clinical trial registration [https://clinicaltrials.gov/show/NCT05610475], identifier [NCT05610475].
Neutrophils inhibit γδ T cell functions in the imiquimod-induced mouse model of psoriasis

Background Psoriasis is a chronic skin disease associated with deregulated interplays between immune cells and keratinocytes. Neutrophil accumulation in the skin is a histological feature that characterizes psoriasis. However, the role of neutrophils in psoriasis onset and development remains poorly understood. Methods In this study, we utilized the model of psoriasiform dermatitis, caused by the repeated topical application of an imiquimod containing cream, in neutrophil-depleted mice or in mice carrying impairment in neutrophil functions, including p47phox -/- mice (lacking a cytosolic subunit of the phagocyte nicotinamide adenine dinucleotide phosphate - NADPH - oxidase) and Sykfl/fl MRP8-cre+ mice (carrying the specific deletion of the Syk kinase in neutrophils only), to elucidate the specific contribution of neutrophils to psoriasis development. Results By analyzing disease development/progression in neutrophil-depleted mice, we now report that neutrophils act as negative modulators of disease propagation and exacerbation by inhibiting gammadelta T cell effector functions via nicotinamide adenine dinucleotide phosphate (NADPH) oxidase-mediated reactive oxygen species (ROS) production. We also report that Syk functions as a crucial molecule in determining the outcome of neutrophil and γδ T cell interactions. Accordingly, we uncover that a selective impairment of Syk-dependent signaling in neutrophils is sufficient to reproduce the enhancement of skin inflammation and γδ T cell infiltration observed in neutrophil-depleted mice. Conclusions Overall, our findings add new insights into the specific contribution of neutrophils to disease progression in the IMQ-induced mouse model of psoriasis, namely as negative regulatory cells.