Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Pathways Associated with Placental Adaptation to Maternal Nutrient Restriction in Sheep

Maternal nutrient restriction impairs placental growth and development, but available evidence suggests that adaptive mechanisms exist, in a subset of nutrient restricted (NR) ewes, that support normal fetal growth and do not result in intrauterine growth restriction (IUGR). This study utilized Affymetrix GeneChip Bovine and Ovine Genome 1.0 ST Arrays to identify novel placental genes associated with differential fetal growth rates within NR ewes. Singleton pregnancies were generated by embryo transfer and, beginning on Day 35 of pregnancy, ewes received either a 100% National Research Council (NRC) (control-fed group; n = 7) or 50% NRC (NR group; n = 24) diet until necropsy on Day 125. Fetuses from NR ewes were separated into NR non-IUGR (n = 6) and NR IUGR (n = 6) groups based on Day 125 fetal weight for microarray analysis. Of the 103 differentially expressed genes identified, 15 were upregulated and 88 were downregulated in NR non-IUGR compared to IUGR placentomes. Bioinformatics analysis revealed that upregulated gene clusters in NR non-IUGR placentomes associated with cell membranes, receptors, and signaling. Downregulated gene clusters associated with immune response, nutrient transport, and metabolism. Results illustrate that placentomal gene expression in late gestation is indicative of an altered placental immune response, which is associated with enhanced fetal growth, in a subpopulation of NR ewes.
Metabolic Responses to Arsenite Exposure Regulated through Histidine Kinases PhoR and AioS in Agrobacterium tumefaciens 5A

Arsenite (AsIII) oxidation is a microbially-catalyzed transformation that directly impacts arsenic toxicity, bioaccumulation, and bioavailability in environmental systems. The genes for AsIII oxidation (aio) encode a periplasmic AsIII sensor AioX, transmembrane histidine kinase AioS, and cognate regulatory partner AioR, which control expression of the AsIII oxidase AioBA. The aio genes are under ultimate control of the phosphate stress response via histidine kinase PhoR. To better understand the cell-wide impacts exerted by these key histidine kinases, we employed 1H nuclear magnetic resonance (1H NMR) and liquid chromatography-coupled mass spectrometry (LC-MS) metabolomics to characterize the metabolic profiles of ΔphoR and ΔaioS mutants of Agrobacterium tumefaciens 5A during AsIII oxidation. The data reveals a smaller group of metabolites impacted by the ΔaioS mutation, including hypoxanthine and various maltose derivatives, while a larger impact is observed for the ΔphoR mutation, influencing betaine, glutamate, and different sugars. The metabolomics data were integrated with previously published transcriptomics analyses to detail pathways perturbed during AsIII oxidation and those modulated by PhoR and/or AioS. The results highlight considerable disruptions in central carbon metabolism in the ΔphoR mutant. These data provide a detailed map of the metabolic impacts of AsIII, PhoR, and/or AioS, and inform current paradigms concerning arsenic–microbe interactions and nutrient cycling in contaminated environments.
Effect of Drum-Drying Conditions on the Content of Bioactive Compounds of Broccoli Pulp

This work studied the effect of drum-rotation frequency, drum temperature, and water-to-pulp ratio in a double-drum drier on the content of sulforaphane, glucoraphanin, total phenolic compounds, ascorbic acid, and antioxidant activity of broccoli pulp through a multilevel factorial design with one replicate. Drum-drying conditions did not significantly affect sulforaphane content, unlike glucoraphanin, however the poor adherence of broccoli pulp resulted in a final product with undefined shape and heterogeneous color. On the other hand, antioxidant activity was unevenly affected by drying conditions; however, drum-rotation frequency affected it in the same way that phenolic compounds and ascorbic acid, showing a concordant behavior. The ascorbic acid content decreased significantly after drying, and it was highly dependent on the experimental factors, resulting in a regression model that explained 90% of its variability. Drum-rotation frequency of 5 Hz, drum temperature of 125 °C, and water-to-pulp ratio of 0.25 resulted in an apparent increase of sulforaphane and phenolic compounds content of 13.7% and 47.6%, respectively. Drum drying has great potential to fabricate dehydrated broccoli-based foods with functional properties. Besides, since drum drying has low investment and operation costs, it represents a very attractive option for the industrialization of broccoli derivatives.
In-Service Detection and Quantification of Railway Wheel Flat by the Reflective Optical Position Sensor

Railway wheel tread flat is one of the main faults of railway wheels, which brings great harm to the safety of vehicle operation. In order to detect wheel flats dynamically and quantitatively when trains are running at high speed, a new wheel flat detection system based on the self-developed reflective optical position sensor is demonstrated in this paper. In this system, two sensors were mounted along each rail to measure the wheel-rail impact force of the entire circumference by detecting the displacement of the collimated laser spot. In order to establish a quantitative relationship between the sensor signal and the wheel flat length, a vehicle-track coupling dynamics analysis model was developed using the finite element method and multi-body dynamics method. The effects of train speed, load, wheel flat lengths, as well as the impact positions on impact forces were simulated and evaluated, and the measured data can be normalized according to the simulation results. The system was assessed through simulation and laboratory investigation, and real field tests were conducted to certify its validity and correctness. The system can determine the position of the flat wheel and can realize the quantification of the detected wheel flat, which has extensive application prospects.
Cross-sectional and Prospective Associations of Rest-Activity Rhythms With Metabolic Markers and Type 2 Diabetes in Older Men

OBJECTIVE Disruption of rest-activity rhythms is cross-sectionally associated with metabolic disorders, including type 2 diabetes, yet it remains unclear whether it predicts impaired glucose metabolism and homeostasis. The aim of this study is to examine the cross-sectional and prospective associations between rest-activity rhythm characteristics and glycemic measures in a cohort of older men. RESEARCH DESIGN AND METHODS Baseline rest-activity rhythms were derived from actigraphy with use of extended cosine model analysis. With subjects fasting, glucose, insulin, and HOMA of insulin resistance (HOMA-IR) were measured from blood at baseline and after ∼3.5 years. Type 2 diabetes was defined based on self-report, medication use, and fasting glucose. RESULTS In the cross-sectional analysis (n = 2,450), lower 24-h amplitude-to-mesor ratio (i.e., mean activity-adjusted rhythm amplitude) and reduced overall rhythmicity were associated with higher fasting insulin and HOMA-IR (all Ptrend < 0.0001), indicating increased insulin resistance. The odds of baseline type 2 diabetes were significantly higher among those in the lowest quartile of amplitude (Q1) (odds ratio [OR]Q1 vs. Q4 1.63 [95% CI 1.14, 2.30]) and late acrophase group (ORlate vs. normal 1.46 [95% CI 1.04, 2.04]). In the prospective analysis (n = 861), multiple rest-activity characteristics predicted a two- to threefold increase in type 2 diabetes risk, including a lower amplitude (ORQ1 vs. Q4 3.81 [95% CI 1.45, 10.00]) and amplitude-to-mesor ratio (OR 2.79 [95% CI 1.10, 7.07]), reduced overall rhythmicity (OR 3.49 [95% CI 1.34, 9.10]), and a late acrophase (OR 2.44 [1.09, 5.47]). CONCLUSIONS Rest-activity rhythm characteristics are associated with impaired glycemic metabolism and homeostasis and higher risk of incident type 2 diabetes.
The Accuracy of the Maximum Parsimony Method for Phylogeny Reconstruction with Morphological Characters

The accuracy of maximum parsimony for phylogeny reconstruction using morpho- logical data has never been adequately tested. In this study 128,000 known phylogenies of eight species and their associated discrete unordered character state data sets were generated by computer simulation. In order to mimic morphological data, values of the following seven simulation param- eters were varied: 1) number of characters: 2) maximum number of character states per character: 3) number of character state changes per speciation event, and 4) the probabilities of parallelisms, reversals, phyletic changes, and extinctions. Character state data for the known simulated phylog- enies were input into the program Hennig86, which found all equally parsimonious trees. The accuracy of maximum parsimony was judged primarily by the percent of time the strict consensus tree was found to be identical to the true tree. Parallelisms, reversals, phyletic changes, and ex- tinctions all significantly decrease maximum parsimony's ability to find the true phylogenetic tree. In addition, maximum parsimony is less accurate when there are fewer characters, more character states per character, and more character state changes per speciation event. For the parameter values considered, maximum parsimony did not do particularly well at finding the true phylogenetic tree. For 24.2% of the simulations, the chance that maximum parsimony found the true tree was less 25%; for 60.2% of the simulations, it was less than 50%; and for 85.2% of the simulations, it was less than 75%. In order to determine the relevance of these results to real data sets, values of the consistency index from the simulated phylogenies were compared to values reported in published plant mor- phological studies. For simulated data sets having values of the consistency index in the range reported in the literature, maximum parsimony found the true phylogenetic tree only from 0.7% to 27.8% of the time (mean = 10.3%). I advise caution, therefore, in using phylogenies reconstructed from morphological data to make inferences about biological processes or patterns that rely on knowledge of the true phylogeny. Additionally, I raise the question whether the great emphasis in systematics on phylogeny reconstruction using maximum parsimony and other cladistic methods is misplaced.
A Consent Support Resource with Benefits and Harms of Vaccination Does Not Increase Hesitancy in Parents—An Acceptability Study

It is unclear whether information given about the benefits and risks of routine childhood vaccination during consent may cue parental vaccine hesitancy. Parents were surveyed before and after reading vaccine consent information at a public expo event in Sydney, Australia. We measured vaccine hesitancy with Parent Attitudes about Childhood Vaccine Short Scale (PACV-SS), informed decision-making with Informed Subscale of the Decisional Conflict Scale (DCS-IS), items from Stage of Decision Making, Positive Attitude Assessment, Vaccine Safety and Side Effect Concern, and Vaccine Communication Framework (VCF) tools. Overall, 416 parents showed no change in vaccine hesitancy (mean PACV-SS score pre = 1.97, post = 1.94; diff = −0.02 95% CI −0.10 to 0.15) but were more informed (mean DCS-IS score pre = 29.05, post = 7.41; diff = −21.63 95% CI −24.17 to −18.56), were more positive towards vaccination (pre = 43.8% post = 50.4%; diff = 6.5% 95% CI 3.0% to 10.0%), less concerned about vaccine safety (pre = 28.5%, post = 23.0%, diff = −5.6% 95% CI −2.3% to −8.8%) and side effects (pre = 37.0%, post = 29.0%, diff = −8.0% 95% CI −4.0% to −12.0%) with no change in stage of decision-making or intention to vaccinate. Providing information about the benefits and risks of routine childhood vaccination increases parents’ informed decision-making without increasing vaccine hesitancy.
Non‐neutralizing antibody responses following A(H1N1)pdm09 influenza vaccination with or without AS03 adjuvant system

Non‐neutralizing antibodies inducing complement‐dependent lysis (CDL) and antibody‐dependent cell‐mediated cytotoxicity (ADCC) activity may contribute to protection against influenza infection. We investigated CDL and ADCC responses in healthy adults randomized to receive either non‐adjuvanted or AS03‐adjuvanted monovalent A(H1N1)pdm09 vaccine (containing 15 µg/3.75 μg of hemagglutinin, respectively) on a 2‐dose schedule 21 days apart.
Sex Differences in Intestinal Microbial Composition and Function of Hainan Special Wild Boar

Simple Summary The gut microbiome plays an important role in the health and disease status of the host. This study explores the effect of sex on intestinal microorganisms of Hainan special wild boar, hybrids of wild boar, and local sows in Hainan. Results showed that there were sex differences in the composition and function of intestinal microorganisms. Our research provides a foundational reference for the future research on Hainan special wild boars and on sex differences in the microbiomes of other species. Abstract The gut microbiome plays an important role in the health and disease status of the host. Research on the effect of sex on animal intestinal microorganisms is still limited; and the effect of castration on the gut microbiome of male pigs has not been fully investigated. In this study, 30 Hainan special wild boars at the same growth stage were divided into three groups (10 entire males, 10 females, and 10 castrated males). High-throughput 16S rRNA sequencing was used to investigate the fecal microbiota of the Hainan special wild boar. Firmicutes, Bacteroidetes, Actinobacteria, Spirochaetes, and Proteobacteria were the five dominant phyla found in the specimens. The relative abundance of Bacteroidetes was higher in the microbiota of female pigs than in male pigs, while Firmicutes was on the contrary. The percentage of Streptococcus and Lactobacillus was higher in males than females. The microbial diversity of females was significantly higher compared to males; castration increased the intestinal microbial diversity of males. Functional prediction showed that male fecal microorganisms were rich in membrane transport and carbohydrate metabolism; energy metabolism, glycan biosynthesis, and metabolism of cofactors and vitamins were rich in the female group; the fecal microorganisms of castrated males had higher membrane transport abundance.
Colocality to Cofunctionality: Eukaryotic Gene Neighborhoods as a Resource for Function Discovery

Abstract Diverging from the classic paradigm of random gene order in eukaryotes, gene proximity can be leveraged to systematically identify functionally related gene neighborhoods in eukaryotes, utilizing techniques pioneered in bacteria. Current methods of identifying gene neighborhoods typically rely on sequence similarity to characterized gene products. However, this approach is not robust for nonmodel organisms like algae, which are evolutionarily distant from well-characterized model organisms. Here, we utilize a comparative genomic approach to identify evolutionarily conserved proximal orthologous gene pairs conserved across at least two taxonomic classes of green algae. A total of 317 gene neighborhoods were identified. In some cases, gene proximity appears to have been conserved since before the streptophyte–chlorophyte split, 1,000 Ma. Using functional inferences derived from reconstructed evolutionary relationships, we identified several novel functional clusters. A putative mycosporine-like amino acid, “sunscreen,” neighborhood contains genes similar to either vertebrate or cyanobacterial pathways, suggesting a novel mosaic biosynthetic pathway in green algae. One of two putative arsenic-detoxification neighborhoods includes an organoarsenical transporter (ArsJ), a glyceraldehyde 3-phosphate dehydrogenase-like gene, homologs of which are involved in arsenic detoxification in bacteria, and a novel algal-specific phosphoglycerate kinase-like gene. Mutants of the ArsJ-like transporter and phosphoglycerate kinase-like genes in Chlamydomonas reinhardtii were found to be sensitive to arsenate, providing experimental support for the role of these identified neighbors in resistance to arsenate. Potential evolutionary origins of neighborhoods are discussed, and updated annotations for formerly poorly annotated genes are presented, highlighting the potential of this strategy for functional annotation.
Beliefs and attitudes toward endocrine therapy in patients with hormone receptor-positive breast cancer

Abstract Patients’ beliefs about medications are important predictors of medication adherence; however, the relationship between patient beliefs and adjuvant endocrine therapy (AET) adherence in patients with breast cancer remains unclear. In this study, we aimed to determine the association between patient beliefs and adherence to AET. Self-reported questionnaires covering necessity beliefs (NB), concerns beliefs (CB), and adherence were completed by 210 Korean patients with breast cancer. The rate of nonadherence was determined by calculating necessity-concern (N-C) differentials and attitudinal subgroup analysis. Multivariate logistic regression analysis was performed to determine the independent impact of patient beliefs on nonadherence. Nonadherence (Morisky Medication Adherence Scale < 8) was reported in 74.3% (n = 156) of patients and predicted by a negative balance regarding AET [odds ratio (OR) = 0.89; 95% confidence interval (CI): 0.83–0.96] and strong concerns about AET such as those in the Ambivalent (OR = 5.41; 95% CI: 1.84–15.92) and Skeptical (OR = 3.48, 95% CI: 1.14–10.65) subgroups. Patient beliefs are significantly associated with adherence to AET in Korean patients with breast cancer. NB, CB, and N-C differentials may be useful intervention targets to improve medication adherence.
Luteal Presence and Ovarian Response at the Beginning of a Timed Artificial Insemination Protocol for Lactating Dairy Cows Affect Fertility: A Meta-Analysis

Simple Summary The widespread adoption of synchronization protocols for timed artificial insemination (AI) in the dairy industry has improved reproductive performance. The most common timed AI protocol is a combination of two hormones (i.e., gonadotropin-releasing hormone and prostaglandin F 2α). Primarily, these protocols increase the insemination risk without affecting the risk of conception. Based on an advanced understanding of the underlying physiology of timed AI protocols, modifications have been developed in order to increase the conception risk. We performed a meta-analytical assessment to evaluate the effect of luteal presence and ovulatory response at the beginning of a timed AI protocol. There was a clear benefit on conception risk for cows starting a timed AI protocol with a functional corpus luteum (+10.5 percentage units) and cows ovulating at the beginning of a timed AI protocol (+11.0 percentage units). Our work highlights the importance of prerequisites for achieving excellent fertility results in timed AI protocols for lactating dairy cows. Abstract Progesterone (P4) concentration during follicular growth has a major impact on fertility response in timed artificial insemination (TAI) protocols. Luteal presence at the beginning of a TAI protocol and ovarian response after the first gonadotropin-releasing hormone (GnRH) injection (G1) affect P4 concentration and subsequently pregnancy per artificial insemination (P/AI). A systematic review of the literature and meta-analytical assessment was performed with the objective of evaluating the magnitude of the effect of luteal presence and ovarian response at the beginning of a TAI protocol on P/AI in lactating dairy cows. We considered only studies using synchronisation protocols consisting of GnRH and prostaglandin F 2α. The time interval between G1 and prostaglandin F 2α (PGF 2α) had to range from 5 to 7 d. The time interval between the PGF 2α injection and G2 had to range from 48 to 72 h. We used 28 controlled experiments from 27 published manuscripts including 16,489 cows with the objective of evaluating the effect size of having a functional corpus luteum (CL) at G1 on P/AI. Information regarding ovulatory response after G1 was available for 5676 cows. In a subset of cows (n = 4291), information was available for luteal presence and ovulatory response at the initiation of the TAI protocol. A functional CL at G1 increased (p < 0.001) the relative risk of conceiving (RR (relative risk) = 1.32; 95% CI = 1.21–1.45) in lactating dairy cows. Ovulation after G1 increased (p < 0.001) the relative risk of conceiving (RR = 1.29; 95% CI = 1.20–1.38) in lactating dairy cows. The effect of ovulatory response on P/AI after G1 was affected by luteal presence at G1. In summary, there was a clear benefit on P/AI for cows starting a TAI protocol with a functional CL (+10.5 percentage units) and cows ovulating at the beginning of a TAI protocol (+11.0 percentage units).
The Effects of Human Visual Sensory Stimuli on N1b Amplitude: An EEG Study

Sensory systems are widely known to exhibit adaptive mechanisms. Vision is no exception to input dependent changes in its sensitivity. Recent animal work demonstrates enhanced connectivity between neurons in the visual cortex. The purpose of the present experiment was to evaluate a human model that noninvasively alters the amplitude of the N1b component in the visual cortex of humans by means of rapid visual stimulation. Nineteen participants (Mage = 24 years; 52.6% male) completed a rapid visual stimulation paradigm involving black and white reversal checkerboards presented bilaterally in the visual field. EEG data was collected during the visual stimulation paradigm, which consisted of four main phases, a pre-tetanus block, photic stimulus, early post-tetanus, and late post-tetanus. The amplitude of the N1b component of the pre-tetanus, early post-tetanus and late post-tetanus visual evoked potentials were calculated. Change in N1b amplitude was calculated by subtracting pre-tetanus N1b amplitude from early and late post-tetanus. Results demonstrated a significant difference between pre-tetanus N1b (M = −0.498 µV, SD = 0.858) and early N1b (M = −1.011 µV, SD = 1.088), t (18) = 2.761, p = 0.039, d = 0.633. No difference was observed between pre-tetanus N1b and late N1b (p = 0.36). In conclusion, our findings suggest that it is possible to induce changes in the amplitude of the visually evoked potential N1b waveform in the visual cortex of humans non-invasively. Additional work is needed to corroborate that the potentiation of the N1b component observed in this study is due to similar mechanisms essential to prolonged strengthened neural connections exhibited in cognitive structures of the brain observed in prior animal research. If so, this will allow for the examination of strengthened neural connectivity and its interaction with multiple human sensory stimuli and behaviors.