Miracle-dz/UniFAR-FTUs huggingface dataset:
Overexpression of Dehydrogenase/Reductase 9 Predicts Poor Response to Concurrent Chemoradiotherapy and Poor Prognosis in Rectal Cancer Patients

Objective: To reduce the risk of locoregional recurrence, the addition of neoadjuvant concurrent chemoradiotherapy (CCRT) is recommended before surgical management for rectal cancer patients. However, despite identical tumor histology, individual patient response to neoadjuvant CCRT varies greatly. Accordingly, a comprehensive molecular characterization that is used to predict CCRT efficacy is instantly needed. Methods: Pearson’s chi-squared test was utilized to correlate dehydrogenase/reductase 9 (DHRS9) expression with clinicopathological features. Survival curves were created applying the Kaplan-Meier method, and the log-rank test was conducted to compare prognostic utility between high and low DHRS9 expression groups. Multivariate Cox proportional hazards regression analysis was applied to identify independent prognostic biomarkers based on variables with prognostic utility at the univariate level. Results: Utilizing a public transcriptome dataset, we identified that the DHRS9 gene is the most considerably upregulated gene related to epithelial cell differentiation (GO: 0030855) among rectal cancer patients with CCRT resistance. Employing immunohistochemical staining, we also demonstrated that high DHRS9 immunoexpression is considerably associated with an aggressive clinical course and CCRT resistance in our rectal cancer cohort. Among all variables with prognostic utility at the univariate level, only high DHRS9 immunoexpression was independently unfavorably prognostic of all three endpoints (all p ≤ 0.048) in the multivariate analysis. In addition, applying bioinformatic analysis, we also linked DHRS9 with unrevealed functions, such as keratan sulfate and mucin synthesis which may be implicated in CCRT resistance. Conclusion: Altogether, DHRS9 expression may serve as a helpful predictive and prognostic biomarker and assist decision-making for rectal cancer patients who underwent neoadjuvant CCRT.
Sexual reproduction and biometry of the non-zooxanthellate papillose cup coral Paracyathus pulchellus

Basic information on the reproductive biology of many scleractinian corals species is limited or entirely lacking, particularly from temperate zones, though it is essential for a better understanding of their ecology. This study describes the morphological aspects and the annual cycle of gametogenesis and biometric parameterss of the papillose cup coral Paracyathus pulchellus collected at Palinuro (Italy, Southern Tyrrhenian Sea), filling a knowledge gap about the reproductive biology of a widespread Mediterranean and Northern Atlantic coral. Samples of P. pulchellus were collected by SCUBA diving between 5- and 10-meters depth during 18 monthly collections from June 2010 to December 2011. Sexually active polyps displayed either oocytes or spermaries, indicating that P. pulchellus was gonochoric. The sex ratio of sexually active polyps was 1:1. Gametogenesis began with undifferentiated germ cells arose in the gastrodermis that migrated towards the mesoglea of the mesentery where they completed the development. During spermatogenesis, spermary diameter increased from 25 to 83 µm. Oocyte diameter ranged from 9 to 146 µm and during oogenesis the nucleus/cytoplasm ratio decreased due to the accumulation of yolk. The nucleus migrated to the periphery of the oocyte adhering closely to the cell membrane. No embryo was observed in the coelenteric cavity of the polyps, suggesting an external development of planktotrophic larvae due to the small-sized mature oocytes and a possible broadcast spawning reproductive mode. Gonadal index of both females and males increased significantly from August until November and fertilization took place from November to January. Only sexually inactive individuals were observed from February to April, suggesting a quiescence period in both males and females. Seasonal variations in water temperature and photoperiod may have a key role in regulating gametogenesis. The analysis of the main biometric parameters (polyp width, height, dry skeletal mass, volume, surface/volume ratio and bulk skeletal density) showed a negative correlation between size and skeletal density, and no sexual dimorphism.
On the role of allergen-specific IgG subclasses for blocking human basophil activation

Successful treatment of IgE mediated allergies by allergen-specific immunotherapy (AIT) usually correlates with the induction of allergen-specific IgG4. However, it is not clear whether IgG4 prevents the allergic reaction more efficiently than other IgG subclasses. Here we aimed to compare allergen-specific monoclonal IgG1 and IgG4 antibodies in their capacity to inhibit type I allergic reactions by engaging FcγRIIb. We found that IgG1, which is the dominant subclass induced by viruses, binds with a similar affinity to the FcγRIIb as IgG4 and is comparable at blocking human basophil activation from allergic patients; both by neutralizing the allergen as well as engaging the inhibitory receptor FcγRIIb. Hence, the IgG subclass plays a limited role for the protective efficacy of AIT even if IgG4 is considered the best correlate of protection, most likely simply because it is the dominant subclass induced by classical AITs.
Identification of intrinsic genes across general hypertension, hypertension with left ventricular remodeling, and uncontrolled hypertension

The purpose of the present article is to identify intrinsic genes across general hypertension (HT), hypertension with left ventricular remodeling (HT-LVR), and uncontrolled hypertension (UN-HT). In total, four microarray datasets (GSE24752, GSE75360, GSE74144, and GSE71994) were downloaded from the GEO database and were used to identify differentially expressed genes (DEGs), respectively. Furthermore, gene set enrichment analysis (GSEA) was utilized to screen for significantly enriched biological pathways across the four datasets above, respectively. Furthermore, weighted gene co-expression network analysis (WGCNA) and functional enrichment analysis were applied to screen out gene modules of interest and potential biological functions, respectively. Finally, a Metascape-based multiple gene list meta-analysis was used to investigate intrinsic genes at different stages of the progression of hypertension. A total of 75 DEGs (63 upregulated genes and 12 downregulated genes, GSE24752) and 23 DEGs (2 upregulated genes and 21 downregulated genes, GSE74144) were identified. However, there were few DEGs identified in GSE75360, GSE71994, and part of the GSE74144 datasets. GSEA and functional enrichment of gene module of interest have indicated that “Heme metabolism,” “TNF alpha/NFkB,” and “interferon alpha response signaling,” and MYC target v1/v2 were enriched significantly in different stages of hypertension progression. Significantly, findings from the multiple gene list meta-analysis suggested that FBXW4 and other 13 genes were unique to the hypertension group, and TRIM11 and other 40 genes were mainly involved in hypertension with the left ventricular remodeling group, while the other 18 genes including F13A1 significantly enriched in uncontrolled hypertension. Collectively, the precise switch of the “immune-metabolic-inflammatory” loop pathway was the most significant hallmark across different stages of hypertension, thereby providing a potential therapeutic target for uncontrolled hypertension treatment.
In vivo evidence of the prevents DSS-induced colitis of Lactiplantibacillus plantarum L15

Ulcerative colitis (UC) is challenging to treat and severely impacts patients and families. A previous study reported immunomodulatory and reduction of pro-inflammatory properties for the Lactiplantibacillus plantarum L15. This study aimed to analyze the preventive properties and mechanistic actions in an in vivo colitis model. The histopathological alteration, inflammation cytokines, and intestinal barrier function were analyzed. Subsequently, the cecal gut microbiota contents and products from different groups were detected. Finally, gene expressions related to the NF-κB signaling process were evaluated. L. plantarum L15 significantly decreased disease activity index (DAI), myeloperoxidase activity (MPO), pro-inflammatory cytokine (TNF-α, IL-1β, and IL-6) level, and increased weight change, colon length, and production of inflammation-suppressing cytokines. Furthermore, this strain supplementation substantially increased ZO-1, Occludin, and Claudin-1, and MUC2 mRNA expression levels with a corresponding decrease in serum lipopolysaccharide and D-lactic acid contents. In addition, L. plantarum L15 improved gut microbiota composition and increased short-chain fatty acid (SCFAs) in the colon content, which significantly reduced the transfer of NF-κB p65 to the nucleus. Our findings provide a theoretical basis for L. plantarum L15 as a preventive candidate for UC.
Plasma anion gap and risk of in-hospital mortality in patients with spontaneous subarachnoid hemorrhage

Background The association between the serum anion gap (AG) and prognosis of patients with spontaneous subarachnoid hemorrhage (SAH) remains unknown. Thus, this study aimed to explore the association between AG levels and mortality in patients with SAH in the intensive care unit (ICU). Methods This was a retrospective analysis of data stored in the Medical Information Mart for Intensive Care–IV and eICU Collaborative Research databases. Critically ill patients diagnosed with spontaneous SAH were included. The primary outcome measure was in-hospital all-cause mortality. A multivariate Cox proportional hazards regression model and a restricted cubic spline were used to evaluate the relationship between AG concentration and outcomes. Kaplan–Meier curves were used to compare cumulative survival among patients with AG levels. Results A total of 1,114 patients were enrolled. AG concentration was significantly associated with in-hospital all-cause mortality [hazard ratio ([HR], 1.076 (95% confidence interval (CI), 1.021–1.292; p = 0.006)]. The risk of mortality was higher in the Category 2 group (AG ≥10 mmol/L and <13 mmol/L; HR, 1.961; 95% CI, 1.157–3.324; p = 0.0) and the Category 3 group (AG ≥13 mmol/L; HR, 2.151; 95% CI, 1.198–3.864; p = 0.010) than in the Category 1 group (AG < 10 mmol/L). Cumulative survival rates were significantly lower in patients with higher AG levels (log-rank p < 0.001). Conclusions In-hospital and ICU mortalities increase with increasing AG concentration in patients with SAH. An increased serum AG level is an independent, significant, and robust predictor of all-cause mortality. Thus, serum AG levels may be used in the risk stratification of SAH.
Phytomicrobiome communications: Novel implications for stress resistance in plants

The agricultural sector is a foremost contributing factor in supplying food at the global scale. There are plethora of biotic as well as abiotic stressors that act as major constraints for the agricultural sector in terms of global food demand, quality, and security. Stresses affect rhizosphere and their communities, root growth, plant health, and productivity. They also alter numerous plant physiological and metabolic processes. Moreover, they impact transcriptomic and metabolomic changes, causing alteration in root exudates and affecting microbial communities. Since the evolution of hazardous pesticides and fertilizers, productivity has experienced elevation but at the cost of impeding soil fertility thereby causing environmental pollution. Therefore, it is crucial to develop sustainable and safe means for crop production. The emergence of various pieces of evidence depicting the alterations and abundance of microbes under stressed conditions proved to be beneficial and outstanding for maintaining plant legacy and stimulating their survival. Beneficial microbes offer a great potential for plant growth during stresses in an economical manner. Moreover, they promote plant growth with regulating phytohormones, nutrient acquisition, siderophore synthesis, and induce antioxidant system. Besides, acquired or induced systemic resistance also counteracts biotic stresses. The phytomicrobiome exploration is crucial to determine the growth-promoting traits, colonization, and protection of plants from adversities caused by stresses. Further, the intercommunications among rhizosphere through a direct/indirect manner facilitate growth and form complex network. The phytomicrobiome communications are essential for promoting sustainable agriculture where microbes act as ecological engineers for environment. In this review, we have reviewed our building knowledge about the role of microbes in plant defense and stress-mediated alterations within the phytomicrobiomes. We have depicted the defense biome concept that infers the design of phytomicrobiome communities and their fundamental knowledge about plant-microbe interactions for developing plant probiotics.
Habitat type and environmental conditions influence the age and growth of a temperate marine damselfish

Life history parameters for fishes have generally been applied to species across their entire range, however, different ecological and environmental conditions and processes (e.g., sea surface temperature, habitat, primary productivity, fishing mortality, resource availability) influence life history patterns at smaller spatial scales. By focusing on a historically protected species, we determined how environmental and ecological factors shape patterns in growth and longevity, without the impact of fishing. The Garibaldi (Hypsypops rubicundus) is a territorial marine damselfish native to the shallow rocky reefs of southern California. Garibaldi were collected from five mainland locations and five Channel Islands throughout the Southern California Bight. Paired natural reef and artificial reef habitats (i.e., breakwaters and jetties) in each mainland location were sampled. Otolith-based ageing and biological data from these populations were used to assess how age and growth vary by location, reef type (natural/artificial), island or mainland, mean annual sea surface temperature, and/or sex. The annual formation of growth increments in otoliths was validated in-situ using tetracycline mark-recapture methods to confirm that increments are formed annually. Garibaldi grew significantly larger on artificial reefs than on natural reefs but tended to live longer on paired natural reefs. Regionally, growth and longevity followed mean annual sea surface temperature gradients, consistent with Bergmann’s rule. Garibaldi exhibited clear sexual size dimorphism; males grew larger, which is uncharacteristic for both damselfish and other marine fishes from the southern California. The Garibaldi collected for this study had a maximum age of 57 years, which makes this the longest lived damselfish species by two decades.
Leaf chlorophyll parameters and photosynthetic characteristic variations with stand age in a typical desert species (Haloxylon ammodendron)

As a desert shrub, Haloxylon ammodendron combines ecological, economic, and social benefits and plays an important role in the ecological conservation of arid desert areas. Understanding its physiological characteristics and its mechanism of light energy utilization is important for the conservation and utilization of H. ammodendron. Therefore, we selected five stands (5-, 11-, 22-, 34-, and 46-year-old) of H. ammodendron as research objects in the study and measured their photosynthetic light response curves by a portable open photosynthesis system (Li-6400) with a red-blue light source (6400-02B). Then, we measured the leaf chlorophyll parameters in the laboratory, calculated the photosynthetic characteristics by using Ye Zipiao’s photosynthetic model, analyzed their variation patterns across stand ages, and explored the relationships between leaf chlorophyll parameters and photosynthetic characteristics. The results showed that leaf chlorophyll parameters and photosynthetic characteristics of H. ammodendron at different stand ages were significantly different. Chl content, P nmax, and LUEmax of H. ammodendron were V-shaped with the increase of stand age. The 5-year-old H. ammodendron was in the rapid growth period, synthesized more Chl a+b content (8.47 mg g−1) only by using a narrower range of light, and the Pnmax and LUEmax were the highest with values of 36.21 μmol m−2 s−1 and 0.0344, respectively. For the 22-year-old H. ammodendron, due to environmental stress, the values of Chl a+b content, P nmax, and LUEmax were the smallest and were 2.64 mg g−1, 25.73 μmol m−2 s−1, and 0.0264, respectively. For the older H. ammodendron, its Chl content, P nmax, and LUEmax were not significantly different and tended to stabilize but were slightly higher than those of the middle-aged H. ammodendron. On the other hand, the other photosynthetic parameters did not show significant variation patterns with stand age, such as R d, AQE, LSP, LCP, and I L-sat. In addition, we found that the relationships between Chl a+b content and P nmax and between Chl a+b content and LUEmax were highly correlated, except for the older H. ammodendron. Thus, using leaf chlorophyll content as a proxy for photosynthetic capacity and light use efficiency should be considered with caution. This work will provide a scientific reference for the sustainable management of desert ecosystems and vegetation restoration in sandy areas.
The in-session discourse of unresolved/disorganized psychotherapy patients: An exploratory study of an attachment classification

The Unresolved/disorganized (U/d) attachment classification has generated considerable interest among clinicians. This is in part based on its empirical associations with adult mental health, parenting practices, and treatment outcomes. Despite decades of theorizing, however, we have little empirical information regarding how patients with a U/d classification assigned by accredited coders actually behave or speak in psychotherapy sessions. Here, we take a step towards bridging this gap by reporting our observations of the psychotherapy session transcripts of 40 outpatients who were independently classified as U/d on the Adult Attachment Interview (AAI), the gold standard measure of adult attachment research. These patients were extracted from a larger sample of 181 and compared to others without a U/d classification. In this paper, we discuss two different discourse styles associated with a U/d classification. Some U/d patients did not seem to sufficiently elicit the therapist’s endorsement of what they said. For example, they did not justify their claims with examples or explanations, or did not consider others’ intentions or experiences. Other U/d patients were credible, but left the listener uncertain as to the underlying point of their discourse, for example, by glaringly omitting the consequences of their experiences, or interrupting their narratives mid-way. In the discussion, we place these observations in the context of recent thinking on attachment and epistemic trust, and discuss how this study may form the basis for future quantitative studies of psychotherapy.
Transcutaneous electrical nerve stimulation over acupoint for chronic obstructive pulmonary disease: A systematic review and meta-analysis

Background Transcutaneous electrical nerve stimulation over an acupoint (acu-TENS), a new technique applied in pulmonary rehabilitation programs, has been gradually used in the management of chronic obstructive pulmonary disease (COPD). However, the effects of acu-TENS have not been fully evaluated. Therefore, this review was conducted to assess the effects of acu-TENS on COPD. Methods A total of seven electronic databases were searched from their inception to September 2021 for randomized controlled trials of acu-TENS for COPD. Two investigators independently performed data extraction and methodological quality assessment. Heterogeneity was examined by Cochrane χ2 and I2 tests. The source of heterogeneity was investigated by subgroup analysis or sensitivity analysis. Results In our review, ten studies between 2008 and 2021 were included. The aggregated results indicated that acu-TENS showed positive effects in forced expiratory volume in 1 s (FEV1) [MD = 0.13 L, 95% CI (0.11–0.16), P < 0.00001], FEV1% predicted [MD = 5.92%, 95% CI (3.43–8.41), P < 0.00001], 6-min walk distance (6MWD) [MD = 14.68m, 95% CI (6.92–22.44), P = 0.0002], dyspnea visual analog scale (DVAS) [MD = −7.58, 95%CI (−14.33 to −0.84), P = 0.03], modified Borg scale (MBS) [MD = −0.46, 95% CI (−0.86 to −0.06), P = 0.03], and COPD assessment test (CAT) [MD = −4.25, 95% CI (−5.24 to −3.27), P < 0.00001]. Although six studies reported adverse effects, only one patient had shoulder pain after acu-TENS. Conclusion Acu-TENS seems to be effective in improving pulmonary function and health status in patients with COPD, with little effect on exercise capacity and dyspnea. However, this result should be interpreted with caution, and high-quality RCTs were needed for further verification.
The Entrepreneurs: Dairy farmer perspectives on finding an industry solution for the surplus calf issue—A participatory case study

Current systems for managing surplus dairy calves are wrought with ethical and animal welfare concerns. Resolving complex problems in the dairy industry requires engagement from dairy farmers and other stakeholders. The main objective of this case study was to pilot a novel methodology to deepen our understanding of how dairy producers envision the future of surplus calves in Atlantic Canada, including identifying who they felt were important to speak to as they discussed this topic. A second objective was to understand the perspectives of a key group the producers requested to speak to, representing a variety of dairy industry partners, including veterinarians, genetics companies, and animal welfare scientists amongst others (referred to as the allied industry) on the future of surplus calves. To reach these objectives, we used an inclusive participatory approach that, to our knowledge, has not yet been applied to the surplus calf issue. This approach included a series of five participatory group discussions with volunteer dairy farmers from Atlantic Canada; the allied industry group was invited to two group discussions. Participants discussed the feasibility of creating a dairy beef system as a potential solution to the surplus dairy calf issue. During the discussions, participants were encouraged to make requests to speak to individuals that would help them design a dairy beef system. Audio-recorded transcripts were subjected to inductive qualitative content analysis where short descriptors were assigned to pieces of the discussion relevant to study objectives. Four key themes from the discussions included: (1) challenges with surplus calf production on the dairy farm, such as a lack of knowledge about what type of calf would be desired by the marketplace, (2) the role of leadership and partnership in the creation of a dairy beef system, including the need to overcome communication barriers between different stakeholders, (3) post-farm gate aspects of surplus calf production, including the desire to cater to a local market, and (4) ensuring that the proposed system is economically and socially viable. Knowledge gained from this type of participatory engagement can help stakeholders align their goals to resolve complex issues such as surplus calf management.