Miracle-dz/UniFAR-FTUs huggingface dataset:
Red-crowned crane (Grus japonensis) prefers postharvest reed beds during winter period in Yancheng National Nature Reserve

Reed beds represent an important habitat for the survival of birds by providing favorable foraging and reproduction conditions. Reed management, as a traditional agricultural activity, primarily includes water level control and vegetation removal by cutting. Red-crowned crane (Grus japonensis) is one of the most endangered cranes, and their population continues to decline due to habitat loss caused by artificial activities. A lack of research relating to how reed management affects crane habitat distribution patterns throughout the wintering period hinders our ability to offer conservation recommendations. In the present study, we explored the effect of reed management on the habitat distribution patterns and analyzed the food resources of red-crowned crane in the Yancheng National Nature Reserve (YNNR). According to the reed management activities in December, we divided the wintering period into two phases: the preharvest period and the postharvest period. Throughout the wintering period, the number of cranes recorded in the common seepweed (Suaeda glauca) tidal flats remained stable, but cranes were rarely recorded in the smooth cordgrass (Spartina alterniflora) tidal flats and aquaculture fish ponds. The number of cranes, however, showed a noticeable fluctuation in the reed beds during the two periods. Before the reed harvest, only a small proportion of cranes were recorded in the reed beds (relative abundance = 2.9%). However, more cranes (relative abundance = 61.0%) were recorded after the reed harvest. Water was introduced from adjacent rivers and fish ponds to submerge the cut reed beds. Changes in potential animal food resources (items and biomass) might be one of the vital reasons for the preference of cranes to the postharvest reed beds. Our results suggest that traditional reed management in the YNNR could benefit this flagship crane species that winters in the wetland system. However, as reed harvest has been forbidden in the core zone for conservation purposes since 2016, further research is needed to verify whether forbidding the harvest of reeds is reasonable.
Contrasting drivers of community‐level trait variation for vascular plants, lichens and bryophytes across an elevational gradient

1. Across environmental gradients, community-level functional traits of plants can change due to species turnover, intraspecific variation and their covariation. Studies on vascular plants suggest that species turnover is the main driver of trait variation across gradients, although intraspecific variation can also be important. However, there is limited knowledge about whether this holds for non-vascular primary producers such as lichens and bryophytes. We hypothesized that intraspecific variation is more important for non-vascular than for vascular primary producers because they lack specialized structures to maintain homeostasis and should therefore be more responsive to extrinsic factors. 2. To assess the relative importance of species turnover versus intraspecific variation for vascular plants, lichens and bryophytes, we estimated species abundance and measured chemical (tissue nitrogen (N) and phosphorous (P) content, N:P ratio and pH) and non-chemical (specific leaf or thallus area, dry matter content and water holding capacity) functional traits along an elevational gradient in alpine southern Norway. We calculated community-weighted mean traits and quantified the relative contribution of species turnover, intraspecific variation and their covariation to total trait variation across the gradient. 3. We found mixed support for our hypothesis: the contribution of intraspecific variation to total trait variation for N and N:P was higher in lichens than in vascular plants and bryophytes, but in general the contribution of intraspecific variation differed among functional traits and producer groups. Nutrient variables (N, P and N:P) were significantly impacted by intraspecific variation for vascular plants and lichens but not for bryophytes. Non-chemical traits and pH were mainly driven by species turnover effects in all primary producer groups. 4. Our results highlight that while nearly all studies on primary producer trait variation across environments have focused on vascular plants, trait variation of other largely neglected but ecologically important producer groups, such as lichens and bryophytes, may show very different responses to the same environmental factors. In order to fully understand how future environmental changes impact on community- and ecosystem-level processes, traits of primary producers other than vascular plants-and their within-species variation-need to be considered in systems where these groups are abundant.
Assessing Paediatric Hrqol in Diabetes: Semantic and Pilot Validation Study of the Portuguese Versions of DISABKIDS-DM ConditionSpecific Module

Objective − This study aimed to semantically validate the Portuguese versions of the diabetes module of a pediatric health-related quality of life assessment instrument – DISABKIDS-DM – and to preliminarily explore their main psychometric properties. Materials and Methods − Two samples of children (8-12 yo) and adolescents (13-18 yo) with Type 1 diabetes and their caregivers participated in the semantic validation (n=36) and in the pilot study (n=160) and filled out the DISABKIDS-DM, the semantic validation questionnaires and the Strengths and Difficulties Questionnaire. Using classical statistical validation procedures, the reliability, interrater consistency, and construct, discriminant, convergent and divergent validity were analyzed. Results − The findings support the relevance, comprehensibility and adequacy of the Portuguese versions. Both the self and proxy versions exhibited adequate levels of reliability; interrater consistency; and convergent, divergent and discriminant validity. The instrument differentiated between HbA1c groups, with children/adolescents with lower levels reporting better HRQoL, and between groups with and without comorbidity, with participants with other chronic diseases showing worse HRQoL. The instrument did not discriminate between the gender and time of diagnosis categories. Children and adolescents tended to report higher levels of HRQoL than their parents. Conclusion − These results reinforce the importance of cross-cultural validation procedures to ensure the equivalence of pediatric HRQoL measures, particularly in the context of diabetes-specific instruments. More research is needed, with a larger and more diverse sample, to study the factorial structure. The use of the questionnaires should be encouraged in both pediatric clinical settings and research.
Manipulation of photoperiod perception advances gonadal growth but not laying date in the great tit

In seasonal environments, organisms use biotic and abiotic cues to time various biological processes that are crucial for growth, survival and reproductive success. Photoperiod is the best-known cue used to regulate gonadal development, migration and moult of many animal species. In birds, the relationship between photoperiod and gonadal development is clearly established, but we have little understanding on whether photoperiod also regulates actual timing of egg laying under natural conditions. Elucidating the link between photoperiod and timing of breeding is however key to understand whether an evolutionary change in sensitivity to photoperiod is a possible mechanism through which organisms could adjust their seasonal timing in response to climate warming. Here, we investigated the causal relationship between photoperiod, gonadal growth and laying date in wild female great tits. We experimentally increased the photoperiod perceived by the birds in spring by clipping head feathers, and we subsequently monitored gonadal development in the lab and egg laying dates in the wild. We show that our manipulation increased the photoperiod perceived by the birds to a level that approximately corresponds to an advancement of ten calendar days. This increase in perceived photoperiod led to an acceleration of gonadal development, but not to an advancement of egg laying dates. Our results indicate that photoperiod sensitivity is not constraining the advancement of laying date under current environmental conditions and suggest that evolution of sensitivity to other supplementary cues is necessary to advance reproduction under global warming.
Robust statistical testing of proteomics data with missing values improves detection of biologically relevant features

Statistical testing remains one of the main challenges for high-conﬁdence detection of diﬀerentially regulated proteins or peptides in large-scale quantitative proteomics experiments by mass spectrometry. Statistical tests need to be suﬃciently robust to deal with experiment intrinsic data structures and variations and often also reduced feature coverage across diﬀerent biological samples due to ubiquitous missing values. A robust statistical test provides accurate conﬁdence scores of large-scale proteomics results, regardless of instrument platform, experimental protocol and software tools. However, the multitude of diﬀerent combinations of experimental strategies, mass spectrometry techniques and in-formatics methods complicate the decision of choosing appropriate statistical approaches. We address this challenge by introducing PolySTest, a user-friendly web service for statistical testing, data browsing and data visualization. We introduce a new method, Miss test, that simultaneously tests for miss-ingness and feature abundance, thereby complementing common statistical tests by rescuing otherwise discarded data features. We demonstrate that PolySTest with integrated Miss test achieves higher con-ﬁdence and higher sensitivity for artiﬁcial and experimental proteomics data sets with known ground truth. Application of PolySTest to mass spectrometry based large-scale proteomics data obtained from diﬀerentiating muscle cells resulted in the rescue of 10%-20% additional proteins in the identiﬁed molecular networks relevant to muscle diﬀerentiation. We conclude that PolySTest is a valuable addition to existing tools and instrument enhancements that improve coverage and depth of large-scale proteomics experiments. A fully functional demo version of PolySTest and Miss test is available via http://computproteomics.bmb. sdu.dk/Apps/PolySTest .
Best Practices for Presenting Statistical Information in a Research Article

A key characteristic of scientific research is that the entire experiment (or series of experiments), including the data analyses, is reproducible. This aspect of science is increasingly emphasized. The Materials and Methods section of a scientific paper typically contains the necessary information for the research to be replicated and expanded on by other scientists. Important components are descriptions of the study design, data collection, and statistical analysis of those data, including the software used. In the Results section, statistical analyses are presented; these are usually best absorbed from figures. Model parameter estimates (including variances) and effect sizes should also be included in this section, not just results of significance tests, because they are needed for subsequent power and meta-analyses. In this article, we give key components to include in the descriptions of study design and analysis, and discuss data interpretation and presentation with examples from the horticultural sciences.
A Statistics and Analyses System of Microbial Community Level Physiological Profiles (CLPP) Based on Excel

Microbial community level physiological profiles (CLPP) assessed using Biolog MicroPlates has effectively demonstrated the metabolic activities of multiple microbes. Due to a large volume of data, and complicated calculation process, the conventional low efficiency calculations delay the study. To empower researchers to quickly tabulate, compute, analyze and present data, we introduced A Biolog EcoPlate data statistics and analyses system (A-BEP-DSAS). It is implemented with Biolog EcoPlate data tested by an ELISA microplate reader (Molecular Devices Versamax). The data input-output process and visual calculation flow are performed using Excel table linked with built-in VBA programming language. We tested A-BEP-DSAS by data from a soil sample, and rapidly and accurately obtained the average well color development (AWCD) data, carbon source utilization, six common diversity indices and other calculation results. A-BEP-DSAS is an automated program based on Microsoft Excel VBA, with the advantages of easy operation, rapid analysis, process visualization, and also allows the user to choose the data source and optimum time for analysis.
Searching for phylogenetic patterns of Symbiodiniaceae community structure among Indo-Pacific Merulinidae corals

Over half of all extant stony corals (Cnidaria: Anthozoa: Scleractinia) harbour endosymbiotic dinoflagellates of the family Symbiodiniaceae, forming the foundational species of modern shallow reefs. However, whether these associations are conserved on the coral phylogeny remains unknown. Here we aim to characterise Symbiodiniaceae communities in eight closely-related species in the genera Merulina, Goniastrea and Scapophyllia, and determine if the variation in endosymbiont community structure can be explained by the phylogenetic relatedness among hosts. We perform DNA metabarcoding of the nuclear internal transcribed spacer 2 using Symbiodiniaceae-specific primers on 30 coral colonies to recover three major endosymbiont clades represented by 23 distinct types. In agreement with previous studies on Southeast Asian corals, we find an abundance of Cladocopium and Durusdinium, but also detect Symbiodinium types in three of the eight coral host species. Interestingly, differences in endosymbiont community structure are dominated by host variation at the intraspecific level, rather than interspecific, intergeneric or among-clade levels, indicating a lack of phylogenetic constraint in the coral-endosymbiont association among host species. Furthermore, the limited geographic sampling of four localities spanning the Western and Central Indo-Pacific preliminarily hints at large-scale spatial structuring of Symbiodiniaceae communities. More extensive collections of corals from various regions and environments will help us better understand the specificity of the coral-endosymbiont relationship.
Artifact-free whole-slide imaging with structured illumination microscopy and Bayesian image reconstruction

Background Structured illumination microscopy (SIM) is a method which can be used to image biological samples and can achieve both optical sectioning and super-resolution effects. Optimization of the imaging setup and data processing methods results in high quality images without artifacts due to mosaicking or due to the use of SIM methods. Reconstruction methods based on Bayesian estimation can be used to produce images with a resolution beyond that dictated by the optical system. Findings Five complete datasets are presented including large panoramic SIM images of human tissues in pathophysiological conditions. Cancers of the prostate, skin, ovary, and breast, as well as tuberculosis of the lung, were imaged using SIM. The samples are available commercially and are standard histological preparations stained with hematoxylin and eosin. Conclusion The use of fluorescence microscopy is increasing in histopathology. There is a need for methods which reduce artifacts when employing image stitching methods or optical sectioning methods such as SIM. Stitched SIM images produce results which may be useful for intraoperative histology. Releasing high quality, full slide images and related data will aid researchers in furthering the field of fluorescent histopathology.
The complete plastome of bloodroot (Sanguinaria canadensis, Papaveraceae), a spring ephemeral from eastern North America

Abstract The complete plastome of Sanguinaria canadensis was sequenced, which is 160,117 bp in length, consisting of 87699 bp large single-copy (LSC), a 19,136 bp small single copy (SSC), and a pair of 26,638 bp inverted repeat (IR) regions. The S. canadensis plastome encodes 137 annotated genes including 37 tRNA genes, 8 rRNA genes, and 89 protein coding genes. Phylogenetic analysis strongly supported that it is a member of Chelidonieae.
Correlation between laser speckle flowgraphy and optical coherence tomography angiography measurements in normal and glaucomatous eyes

Purpose To investigate the relationship between laser speckle flowgraphy (LSFG) and optical coherence tomography angiography (OCTA) measurements of the peripapillary retina and optic nerve head (ONH) in normal eyes and eyes with primary open-angle glaucoma (POAG). Patients and methods One eye from each of 46 normal subjects and mild and moderate/advanced POAG patients were included. ONH blood flow acquired by LSFG, circumpapillary vessel density (cpVD, a 250 μm-wide elliptical annulus around the optic disc), and intra-papillary vessel density (ipVD, a 1.5×1.5 mm scan field) acquired by OCTA were measured. Their values were compared among normal controls and patients at each stage of glaucoma using one-way ANOVA, and the correlation between measurements obtained by the two methods was examined by univariate regression analysis. Results ONH tissue blood flow, tissue mean blur rate (MBR-T), and cpVD in the outer layer of the retina significantly decreased with the progression of glaucoma stage, although the latter showed no significant difference between normal subjects and mild-stage glaucoma patients. MBR-T was significantly correlated with cpVD, but not with ipVD, in the retinal outer layer. Conclusion A correlation was found only between MBR-T and cpVD in the retinal outer layer. A difference in MBR-T, but not in cpVD, was detected between normal controls and mild glaucoma patients.
DDDT_A_198874 3259..3268

Yan Song Wei Wang Yanqing Xie Bin Xiang Xuan Huang Weijie Guan Jinping Zheng 1State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, People’s Republic of China; 2Drug Research Institute of Guangzhou BaiYunShan Pharmaceutical General Factory, Guangzhou, 510515, People’s Republic of China Background: Cigarette smoke (CS) results in chronic mucus hypersecretion and airway inflammation, contributing to COPD pathogenesis. Mucin 5B (MUC5B) and mucin 5 AC (MUC5AC) are major mucins implicated in COPD pathogenesis. Carbocisteine can reduce mucus viscosity and elasticity. Although carbocisteine decreased human elastase-induced MUC5AC expression in vitro and reduced MUC5AC expression that alleviated bacteria adhesion and improved mucus clearance in vivo, the roles of carbocisteine in inducing MUC5B expression in COPD remain unclear. Methods: To investigate the Muc5b/Muc5ac ratio and the gene and protein levels of Muc5b in COPD and carbocisteine intervention models. C57B6J mice were used to develop COPD model by instilling intratracheally with lipopolysaccharide on days 1 and 14 and were exposed to CS for 2 hr twice a day for 12 weeks. Low and high doses of carbocisteine 112.5 and 225 mg/kg/d, respectively, given by gavage administration were applied for the treatment in COPD models for the same duration, and carboxymethylcellulose was used as control. Carbocisteine significantly attenuated inflammation in bronchoalveolar lavage fluid and pulmonary tissue, improved pulmonary function and protected against emphysema. Results: High-dose carbocisteine significantly decreased the overproduction of Muc5b (P<0.01) and Muc5ac (P<0.001), and restored Muc5b/Muc5ac ratio in COPD model group (P<0.001). Moreover, the Muc5b/Muc5ac ratio negatively correlated with pro-inflammatory cytokines such as IL-6 and keratinocyte-derived cytokine, mean linear intercept, functional residual capacity and airway resistance, but positively correlated with dynamic compliance. Conclusions: These findings suggest that carbocisteine attenuated Muc5b and Muc5ac secretion and restored Muc5b protein levels, which may improve mucus clearance in COPD.
Evaluation of genetic stability of sugar beet (Beta vulgaris L.) plants obtained from unfertilized ovules using RAPD markers

In order to improve the methods of embryo regeneration applied so far in in vitro cultures, a two-phased, innovative method was used. It involved using a liquid and solid media. Regeneration of ovules with the application of the gynogenesis technique took place mainly through the indirect organogenesis process during which callus got formed which was associated with the possibility of somaclonal variation occurrence. In order to identify the genetic variability taking plase during the culture, RAPD analyzes were performed. The DNA was isolated from the leaves of 10 regenerants, rooted and planted into the field. 5 of them were characterized by a haploid number of chromosomes whereas the others were of diploid nature. As a control, DNA originating from the leaves of a haploid plant growing in in vitro cultures on medium without growth regulators was used. Plants regenerated on media of various quantitative and qualitative composition in terms of phytohormonal characteristic. The results of the experiment showed that 9 out of 19 tested primers generate polymorphic bands while the remaining 10 amplify the same DNA fragments in all tested samples. The polymorphism effect was revealed in 4 plants with diploid genome and in 1 haploid plant. In total, 13 polymorphic bands were identified and 11 of them were detected in diploid DNA.