Miracle-dz/UniFAR-FTUs huggingface dataset:
16S rRNA gene-based assessment of common broiler chicken sampling methods: Evaluating intra-flock sample size, cecal pair similarity, and cloacal swab similarity to other alimentary tract locations

16S rRNA gene sequencing for characterization of microbiomes has become more common in poultry research and can be used to both answer specific research questions and help inform experimental design choices. The objective of this study was to use 16S rRNA gene sequencing to examine common sampling practices in broiler chicken studies such as: the required number of birds selected from a flock to adequately capture microbiome diversity, the differences between cecal pairs within the same bird, and whether cloacal swabs are representative of other alimentary tract (AT) locations. To do this, nine market age broilers were euthanized and immediately sampled in ten AT locations: crop, gizzard, proventriculus, duodenum, jejunum, ileum, cecal samples from each pouch, colon, and cloacal swab. DNA was extracted and subjected to 16S rRNA gene amplification and sequencing. Each location within the broiler AT hosts distinct microbial communities. When each sampling location was considered, it was found that sampling after 2.8 birds (range 2–4) resulted in less than 10% new amplicon sequencing variants (ASV) being added while sampling after 7.6 birds (range 6–10) increases new observed ASVs by less than 1%. Additionally, when cecal pairs from the same bird were evaluated, it was found that cecal pair mates are an adequate replication if interested in the total cecal microbiome but may be less useful if a rare lineage is of interest. Furthermore, when compared to other AT locations, the cecal microbiome was enriched in Firmicutes and Bacteroides while several lineages, most notably Lactobacillus, were under-represented. Finally, when cloacal swabs were compared to other AT locations, community similarity exhibited a direct distance relationship, i.e., the more aborad samples were the more similar they were to the swab. These findings indicate that while cloacal swabs can approximate overall changes in microbiome composition, they are not adequate for inferring changes to specific taxa in other parts of the AT tract—even those that are highly abundant within the microbial community. These data provide new insights guiding appropriate sample size selection within flocks and add to the consensus data regarding cecal pair similarity and destructive versus non-destructive sampling methods.
Sources of cognitive cost in scalar implicature processing: A review

Research in Experimental Pragmatics has shown that deriving scalar implicatures involves effort and processing costs. This finding was robust and replicated across a wide variety of testing techniques, logical terms, populations, and languages. However, a question that remains disputed in the literature is whether this observed processing cost is a product of the inferential process itself or other logical properties whose computation taxes cognitive resources independently of the inferential mechanism. This paper has two objectives: one is to review the previous experimental work on scalar implicatures and how it evolved in the literature, and the other is to discuss possible factors that render computing scalar implicatures cognitively effortful. Implications and directions for future research are provided.
Local-scale spatial variability in firn properties in Southwest Greenland

The increasing mass loss from the Greenland ice sheet is becoming growingly important to present-day global sea level rise. Meltwater export to the ocean may be amplified by near-surface ice layers in firn (i.e., snow that has survived at least one melt season) which prevent infiltration. Such ice layers have been documented at various sites in southwest Greenland, but little is known about the local-scale (less than 1 km) variability in firn and ice properties. Here we investigate the local variability in firn density and ice content (ice layer thickness fraction) by analyzing 45 shallow firn cores retrieved from 15 sites in southwest Greenland between 2012 and 2019. The core dataset contains groups of cores that were collected at the same site (1–632 m apart from each other) and in the same year (here referred to as same site/year cores). The two-sided Mann-Whitney U-tests suggest that most same site/year cores do not have statistically significant differences in median density or ice content over the upper 0–4.5, 4.5–9, and 9–13.5 m sections below the winter snow layer. That said, the same site/year cores still exhibit substantial density and ice content differences as well as variable ice layer stratigraphy (especially the distribution of centimeters-thick ice lenses) not explainable by measurement uncertainties. The local-scale variability in density and ice content (calculated from the same site/year cores) over the three 4.5-m sections is 4% and 19–29%, respectively. The variability is comparable to the regional gradient in our study area within an elevation difference of up to ∼200 m. The local variability is non-negligible particularly at mid- to high-elevation sites (>2,000 m a.s.l.), where firn structure changes such as ice layer formation are more recent phenomena compared to lower elevations. This study confirms that single cores can provide representative bulk statistics such as mean density and ice content of one site. However, these mean values mask substantial local variability which can compromise regional comparisons. Therefore, collection of same site/year cores and consideration of local variability are necessary for an in-depth analysis of regional variability.
Twenty-four-hour National Institute of Health Stroke Scale predicts short- and long-term outcomes of basilar artery occlusion after endovascular treatment

Background The present study aimed to evaluate the prognostic value of the 24-h National Institute of Health Stroke Scale (NIHSS) for short- and long-term outcomes of patients with basilar artery occlusion (BAO) after endovascular treatment (EVT) in daily clinical routine. Methods Patients with EVT for acute basilar artery occlusion study registry with the 24-h NIHSS, and clinical outcomes documented at 90 days and 1 year were included. The NIHSS admission, 24-h NIHSS, NIHSS delta, and NIHSS percentage change, binary definitions of early neurological improvement [ENI; improvement of 4/(common ENI)/8 (major ENI)/10 (dramatic ENI)] NIHSS points were compared to predict the favorable outcomes and mortality at 90 days and 1 year. The primary outcome was defined as favorable if the modified Rankin Scale (mRS) score was 0–3 at 90 days. Results Of the 644 patients treated with EVT, the 24-h NIHSS had the highest discriminative ability for favorable outcome prediction [receiver operator characteristic (ROC)NIHSS 24 h area under the curve (AUC): 0.92 (0.90–0.94)] at 90 days and 1 year [(ROCNIHSS 24 h AUC: 0.91 (0.89–0.94)] in comparison to the NIHSS score at admission [ROCNIHSS admission AUC at 90 days: 0.73 (0.69–0.77); 1 year: 0.74 (0.70–0.78)], NIHSS delta [ROCΔ NIHSS AUC at 90 days: 0.84 (0.81–0.87); 1 year: 0.81 (0.77–0.84)], and NIHSS percentage change [ROC%change AUC at 90 days: 0.85 (0.82–0.89); 1 year: 0.82 (0.78–0.86)]. Conclusion The 24-h NIHSS with a threshold of ≤23 points was the best surrogate for short- and long-term outcomes after EVT for BAO in the clinical routine.
Predictors for adherent behavior in the COVID-19 pandemic: A cross-sectional telephone survey

Background During the COVID-19 pandemic, protective measures have been prescribed to prevent or slow down the spread of the SARS-CoV-2 virus and protect the population. Individuals follow these measures to varying degrees. We aimed to identify factors influencing the extent to which protective measures are adhered to. Methods A cross-sectional survey (telephone interviews) was undertaken between April and June 2021 to identify factors influencing the degree to which individuals adhere to protective measures. A representative sample of 1,003 people (age >16 years) in two Austrian states (Carinthia, Vorarlberg) was interviewed. The questionnaire was based on the Health Belief Model, but also included potential response-modifying factors. Predictors for adherent behavior were identified using multiple regression analysis. All predictors were standardized so that regression coefficients (β) could be compared. Results Overall median adherence was 0.75 (IQR: 0.5–1.0). Based on a regression model, the following variables were identified as significant in raising adherence: higher age (β = 0.43, 95%CI: 0.33–0.54), social standards of acceptable behavior (β = 0.33, 95%CI: 0.27–0.40), subjective/individual assessment of an increased personal health risk (β = 0.12, 95%CI: 0.05–0.18), self-efficacy (β = 0.06, 95%CI: 0.02–0.10), female gender (β = 0.05, 95%CI: 0.01–0.08), and low corona fatigue (behavioral fatigue: β = −0.11, 95%CI: −0.18 to −0.03). The model showed that such aspects as personal trust in institutions, perceived difficulties in adopting health-promoting measures, and individual assessments of the risk of infection, had no significant influence. Conclusions This study reveals that several factors significantly influence adherence to measures aimed at controlling the COVID-19 pandemic. To enhance adherence, the government, media, and other relevant stakeholders should take the findings into consideration when formulating policy. By developing social standards and promoting self-efficacy, individuals can influence the behavior of others and contribute toward coping with the pandemic.
Research on the effects of rs1800566 C/T polymorphism of NAD(P)H quinone oxidoreductase 1 gene on cancer risk involves analysis of 43,736 cancer cases and 56,173 controls

Objective A two-electron reductase known as NQO1 [NAD(P)H quinone oxidoreductase 1] is regarded as an excellent anticancer target. Studies have found that rs1800566 polymorphism of NQO1 is linked to different cancers, but their associations remain controversial. Methods In the present work, we selected to do a comprehensive meta-analysis to analyze their correlation. We performed searches on PubMed, Embase, Google Scholar, Chinese database, and Web of Science. The results we obtained covered all publications before April 3, 2022. Results There were 176 case-control studies among them, with 56,173 corresponding controls and 43,736 cancer cases. We determined that the NQO1 rs1800566 polymorphism was not related to the cancer risk by calculating 95% confidence intervals and odds ratios. However, stratified genotyping showed that this polymorphism was protective against hepatocellular carcinoma, renal cell carcinoma, and gastric cancer. In addition, on dividing cancer into six systems, the association with gastrointestinal cancer decreased. In the race-based subgroup, a decreasing trend was observed in Asians, while an increasing trend was found among Caucasians, Africans, and mixed populations. The decreased correlation in the hospital-based subgroup was also detected. Conclusion Current study shows that rs1800566 polymorphism of NQO1 was linked to cancer susceptibility and maybe as a tumor marker in their development.
Cordyceps mushroom with increased cordycepin content by the cultivation on edible insects

Cordycepin is the major constituent of Cordyceps mushroom (or Cordyceps militaris) with therapeutic potential. Insects are the direct sources of nutrients for Cordyceps in nature. Therefore, optimized condition of Cordyceps cultivation for efficient cordycepin production was explored using six edible insects as substrates. The highest yield of cordycepin was produced by the cultivation on Allomyrina dichotoma and was 34 times that on Bombyx mori pupae. Among insect components, fat content was found to be important for cordycepin production. Especially, a positive correlation was deduced between oleic acid content and cordycepin production. The transcriptional levels of cns1 and cns2, genes involved in cordycepin biosynthesis, were higher in Cordyceps grown on A. dichotoma than on other insects tested. The addition of oleic acid to the substrates increased cordycepin production together with the transcriptional levels of cns1 and cns2. Therefore, Cordyceps with high content of cordycepin can be secured by the cultivation on insects.
Functional changes in the auditory cortex and associated regions caused by different acoustic stimuli in patients with presbycusis and tinnitus

Presbycusis and tinnitus are the two most common hearing related pathologies. Although both of these conditions presumably originate in the inner ear, there are several reports concerning their central components. Interestingly, the onset of presbycusis coincides with the highest occurrence of tinnitus. The aim of this study was to identify age, hearing loss, and tinnitus related functional changes, within the auditory system and its associated structures. Seventy-eight participants were selected for the study based on their age, hearing, and tinnitus, and they were divided into six groups: young controls (Y-NH-NT), subjects with mild presbycusis (O-NH-NT) or expressed presbycusis (O-HL-NT), young subjects with tinnitus (Y-NH-T), subjects with mild presbycusis and tinnitus (O-NH-T), and subjects with expressed presbycusis and tinnitus (O-HL-T). An MRI functional study was performed with a 3T MRI system, using an event related design (different types of acoustic and visual stimulations and their combinations). The amount of activation of the auditory cortices (ACs) was dependent on the complexity of the stimuli; higher complexity resulted in a larger area of the activated cortex. Auditory stimulation produced a slightly greater activation in the elderly, with a negative effect of hearing loss (lower activation). The congruent audiovisual stimulation led to an increased activity within the default mode network, whereas incongruent stimulation led to increased activation of the visual cortex. The presence of tinnitus increased activation of the AC, specifically in the aged population, with a slight prevalence in the left AC. The occurrence of tinnitus was accompanied by increased activity within the insula and hippocampus bilaterally. Overall, we can conclude that expressed presbycusis leads to a lower activation of the AC, compared to the elderly with normal hearing; aging itself leads to increased activity in the right AC. The complexity of acoustic stimuli plays a major role in the activation of the AC, its support by visual stimulation leads to minimal changes within the AC. Tinnitus causes changes in the activity of the limbic system, as well as in the auditory AC, where it is bound to the left hemisphere.
Wild Helianthus species: A reservoir of resistance genes for sustainable pyramidal resistance to broomrape in sunflower

Orobanche cumana Wall. , sunflower broomrape, is one of the major pests for the sunflower crop. Breeding for resistant varieties in sunflower has been the most efficient method to control this parasitic weed. However, more virulent broomrape populations continuously emerge by overcoming genetic resistance. It is thus essential to identify new broomrape resistances acting at various stages of the interaction and combine them to improve resistance durability. In this study, 71 wild sunflowers and wild relatives accessions from 16 Helianthus species were screened in pots for their resistance to broomrape at the late emergence stage. From this initial screen, 18 accessions from 9 species showing resistance, were phenotyped at early stages of the interaction: the induction of broomrape seed germination by sunflower root exudates, the attachment to the host root and the development of tubercles in rhizotron assays. We showed that wild Helianthus accessions are an important source of resistance to the most virulent broomrape races, affecting various stages of the interaction: the inability to induce broomrape seed germination, the development of incompatible attachments or necrotic tubercles, and the arrest of emerged structure growth. Cytological studies of incompatible attachments showed that several cellular mechanisms were shared among resistant Helianthus species.
Castellano and Pastor-Satorras Reply:

The Comment by Ha et al. [cond-mat/0603787] criticizes our recent result [Phys. Rev. Lett. 96, 038701 (2006)] that the contact process (CP) on uncorrelated scale-free (SF) networks does not behave according to heterogeneous mean-field (MF) theory. This claim is based in Gaussian ansatz that reproduces previously reported density fluctuations and numerical simulations for a particular value of the degree exponent $\gamma$ that seem to fit the MF prediction for the density decay exponent $\theta$ and a conjecture of the authors of the comment for the finite-size scaling exponente $\alpha=\beta/ \nu_\perp$. By means of extensive simulations of the CP on random neighbors (RN) SF networks we show that the MF prediction for $\theta4 is incorrect for small degree exponents, while the author's conjecture for $\alpha$ is at best only approximately valid for the unphysical case of uncorrelated networks with cut-off $k_c \sim N^{1/(\gamma-1)}$, which can only be constructed in the RN version of SF networks. Therefore, the main conclusion of our paper [Phys. Rev. Lett. 96, 038701 (2006)], the invalidity of MF theory for real uncorrelated SF networks, remains unchallenged.
Specialty grand challenge: Crisis/disaster management, resilience, and sustainability

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Cytological, genetic and transcriptomic characterization of a cucumber albino mutant

Photosynthesis, a fundamental process for plant growth and development, is dependent on chloroplast formation and chlorophyll synthesis. Severe disruption of chloroplast structure results in albinism of higher plants. In the present study, we report a cucumber albino alc mutant that presented white cotyledons under normal light conditions and was unable to produce first true leaf. Meanwhile, alc mutant could grow creamy green cotyledons under dim light conditions but died after exposure to normal light irradiation. No chlorophyll and carotenoid were detected in the alc mutant grown under normal light conditions. Using transmission electron microscopy, impaired chloroplasts were observed in this mutant. The genetic analysis indicated that the albino phenotype was recessively controlled by a single locus. Comparative transcriptomic analysis between the alc mutant and wild type revealed that genes involved in chlorophyll metabolism and the methylerythritol 4-phosphate pathway were affected in the alc mutant. In addition, three genes involved in chloroplast development, including two FtsH genes and one PPR gene, were found to have negligible expression in this mutant. The quality of RNA sequencing results was further confirmed by real-time quantitative PCR analysis. We also examined 12 homologous genes from alc mutant in other plant species, but no genetic variation in the coding sequences of these genes was found between alc mutant and wild type. Taken together, we characterized a cucumber albino mutant with albinism phenotype caused by chloroplast development deficiency and this mutant can pave way for future studies on plastid development.
Chronic kidney disease risk prediction scores assessment and development in Mexican adult population

Background Chronic kidney disease (CKD) is a major public health problem, with considerable growth in prevalence and mortality in recent years. Screening of CKD at primary care is crucial for the implementation of prevention strategies. The aims of this study are to assess CKD risk prediction scores and to develop a risk prediction score for the Mexican adult population. Methods Data from the Mexican National Health and Nutrition Survey 2016 was utilized and 3463 participants ≥ 20 years old were included. Reduced renal function with Glomerular filtration rate and/or the presence of albuminuria was defined as CKD. Multiple logistic regression models were performed for the creation of a training and validation model. Additionally, several models were validated in our Mexican population. Results The developed training model included sex, age, body mass index, fast plasma glucose, systolic blood pressure, and triglycerides, as did the validation model. The area under the curve (AUC) was 0.78 (95% CI: 0.72, 0.79) for training model, and 0.76 (95% CI: 0.71, 0.80) in validation model for Mexican adult population. Age, female gender, presence of diabetes and hypertension, elevated systolic and diastolic blood pressure, serum and urinary creatinine, and higher HbA1c were significantly associated with the prevalent chronic kidney disease. Previous CKD risk predictive models were evaluated with a representative sample of the Mexican adult population, their AUC was between 0.61 and 0.78. Conclusion The designed CKD risk predictive model satisfactorily predicts using simple and common variables in primary medical care. This model could have multiple benefits; such as, the identification of the population at risk, and prevention of CKD.
The focus and timing of gaze matters: Investigating collaborative knowledge construction in a simulation-based environment by combined video and eye tracking

Although eye tracking has been successfully used in science education research, exploiting its potential in collaborative knowledge construction has remained sporadic. This article presents a novel approach for studying collaborative knowledge construction in a simulation-based environment by combining both the spatial and temporal dimensions of eye-tracking data with video data. For this purpose, we have investigated two undergraduate physics student pairs solving an electrostatics problem in a simulation-based environment via Zoom. The analysis of the video data of the students’ conversations focused on the different collaborative knowledge construction levels (new idea, explication, evaluation, and non-content-related talk and silent moments), along with the temporal visualizations of the collaborative knowledge construction processes. The eye-tracking data of the students’ gaze, as analyzed by epistemic network analysis, focused on the pairs’ spatial and temporal gaze behavior. We illustrate how gaze behavior can shed light on collaborative knowledge construction in terms of the quantity of the talk (e.g., gaze behavior can shed light on the different activities of the pairs during the silent moments), quality of the talk (e.g., gaze behavior can shed light on the different approaches when constructing knowledge on physical phenomena), and temporality of collaborative knowledge construction processes [e.g., gaze behavior can shed light on (the lack of) attempts to acquire the supporting or contrasting evidence on the initial ideas on the physical phenomena]. We also discuss the possibilities and limitations of gaze behavior to reveal the critical moments in the collaborative knowledge construction processes.