Miracle-dz/UniFAR-FTUs huggingface dataset:
Association between dietary patterns and risk of breast cancer in Chinese female population: a latent class analysis

Abstract Objective: To determine if specific dietary patterns are associated with breast cancer (BC) risk in Chinese women. Design: Latent class analysis (LCA) was performed to identify generic dietary patterns based on daily food-frequency data. Setting: The Chinese Wuxi Exposure and Breast Cancer Study (2013–2014). Participants: A population-based case–control study (695 cases, 804 controls). Results: Four dietary patterns were identified, Prudent, Chinese traditional, Western and Picky; the proportion in the controls and cases was 0·30/0·32/0·16/0·23 and 0·29/0·26/0·11/0·33, respectively. Women in Picky class were characterised by higher extreme probabilities of non-consumption of specific foods, the highest probabilities of consumption of pickled foods and the lowest probabilities of consumption of cereals, soya foods and nuts. Compared with Prudent class, Picky class was associated with a higher risk (OR = 1·42, 95 % CI 1·06, 1·90), while the relevant association was only in post- (OR = 1·44, 95 % CI 1·01, 2·05) but not in premenopausal women. The Western class characterised by high-protein, high-fat and high-sugar foods, and the Chinese traditional class characterised by typical consumption of soya foods and white meat over red meat, both of them showed no difference in BC risk compared with Prudent class did. Conclusions: LCA captures the heterogeneity of individuals embedded in the population and could be a useful approach in the study of dietary pattern and disease. Our results indicated that the Picky class might have a positive association with the risk of BC.
Chromatographic Separation of Breynia retusa (Dennst.) Alston Bark, Fruit and Leaf Constituents from Bioactive Extracts

Breynia retusa (Dennst.) Alston (also known as Cup Saucer plant) is a food plant with wide applications in traditional medicine, particularly in Ayurveda. Extracts obtained with four solvents (dichloromethane, methanol, ethyl acetate and water), from three plant parts, (fruit, leaf and bark) were obtained. Extracts were tested for total phenolic, flavonoid content and antioxidant activities using a battery of assays including 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), ferric reducing antioxidant power (FRAP), cupric reducing antioxidant capacity (CUPRAC), total antioxidant capacity (TAC) (phosphomolybdenum) and metal chelating. Enzyme inhibitory effects were investigated using acetylcholinesterase (AChE), butyrylcholinesterase (BChE), tyrosinase, α-amylase and α-glucosidase as target enzymes. Results showed that the methanolic bark extract exhibited significant radical scavenging activity (DPPH: 202.09 ± 0.15; ABTS: 490.12 ± 0.18 mg Trolox equivalent (TE)/g), reducing potential (FRAP: 325.86 ± 4.36: CUPRAC: 661.82 ± 0.40 mg TE/g) and possessed the highest TAC (3.33 ± 0.13 mmol TE/g). The methanolic extracts were subjected to LC-DAD-MSn and NMR analysis. A two-column LC method was developed to separate constituents, allowing to identify and quantify forty-four and fifteen constituents in bark and fruits, respectively. Main compound in bark was epicatechin-3-O-sulphate and isolation of compound was performed to confirm its identity. Bark extract contained catechins, procyanidins, gallic acid derivatives and the sulfur containing spiroketal named breynins. Aerial parts mostly contained flavonoid glycosides. Considering the bioassays, the methanolic bark extract resulted a potent tyrosinase (152.79 ± 0.27 mg kojic acid equivalent/g), α-amylase (0.99 ± 0.01 mmol acarbose equivalent ACAE/g) and α-glucosidase (2.16 ± 0.01 mmol ACAE/g) inhibitor. In conclusion, methanol is able to extract the efficiently the phytoconstituents of B. retusa and the bark is the most valuable source of compounds.
Social Context Influences Resting Physiology in Dogs

Simple Summary Wolves became dogs over the past 35,000 years. It has been suggested that through domestication, the cooperative nature of wolves and their dependence on pack mates has been re-directed towards humans. This has also affected the social orientation of dogs towards conspecifics. In contrast to wolves, dogs in free-ranging packs are not monogamous and are less cooperative with their pack members. In a previous paper, we found that dogs resting isolated from their pack members were less relaxed/more alert than wolves in the same situation. As social context may affect such results, we replicated this study with pack-living and enclosure-kept dogs resting alone or close to pack members. Specifically, we measured heart rate and heart rate variability as physiological proxies of alertness. We found that dogs were less relaxed/more alert when resting alone than with pack members, but that this may be modulated by social status, i.e., high-ranking dogs being less relaxed than low-ranking individuals. We conclude that relaxation/alertness of dogs during rest depends on social context and that, as in wolves, conspecific pack members still have a role in this. This indicates that domestication has only partially re-directed social orientation in dogs from conspecific pack members to human partners. Abstract Domestication has affected the social life of dogs. They seem to be less dependent on their pack members than wolves, potentially causing dogs to be more alert towards their environment, especially when resting. Such a response has been found in dogs resting alone compared to wolves in the same situation. However, as this may be influenced by social context, we compared alertness (i.e., degree of activation along the sleep–wake continuum—measured via cardiac parameters) of pack-living and enclosure-kept dogs in two conditions: (1) alone, and (2) with pack members, and in two states of activation: (1) inactive wakefulness, and (2) resting. We found that when dogs were resting alone, alertness was higher than when resting in the pack; individual alertness was potentially influenced by social rank. However, alertness was similar in the two conditions during inactive wakefulness. Thus, depending on social context, familiar conspecifics may still provide support in dogs; i.e., domestication has probably only partly shifted the social orientation of dogs from conspecifics to humans. We suggest that cardiac responses of dogs may be more flexible than those of wolves because of their adaptation to the more variable presence of humans and conspecifics in their environment.
Specific Non-Reducing Ends in Heparins from Different Animal Origins: Building Blocks Analysis Using Reductive Amination Tagging by Sulfanilic Acid

Heparins are linear sulfated polysaccharides widely used as anticoagulant drugs. Their nonreducing-end (NRE) has been little investigated due to challenges in their characterization, but is known to be partly generated by enzymatic cleavage with heparanases, resulting in N-sulfated glucosamines at the NRE. Uronic NRE (specifically glucuronic acids) have been isolated from porcine heparin, with GlcA-GlcNS,3S,6S identified as a porcine-specific NRE marker. To further characterize NRE in heparinoids, a building block analysis involving exhaustive heparinase digestion and subsequent reductive amination with sulfanilic acid was performed. This study describes a new method for identifying heparin classical building blocks and novel NRE building blocks using strong anion exchange chromatography on AS11 columns for the assay, and ion-pair liquid chromatography-mass spectrometry for building block identification. Porcine, ovine, and bovine intestine heparins were analyzed. Generally, NRE on these three heparins are highly sulfated moieties, particularly with 3-O sulfates, and the observed composition of the NRE is highly dependent on heparin origin. At the highest level of specificity, the isolated marker was only detected in porcine heparin. However, the proportion of glucosamines in the NRE and the proportion of glucuronic/iduronic configurations in the NRE uronic moieties greatly varied between heparin types.
Disentangling comorbidity in chronic pain: A study in primary health care settings from India

Objectives The study examined the prevalence, sociodemographic, and clinical correlates of chronic pain among primary care patients in the state of Kerala, India. It also examined the patterns and relationships of chronic physical and mental health conditions with chronic pain. Methods This study is a cross-sectional survey conducted among 7165 adult patients selected randomly by a multi-stage stratified design from 71 primary health centers. The questionnaires administered included Chronic pain screening questionnaire, self-reported Chronic physical health condition checklist, Patient Health Questionnaire-SADS, The Alcohol Use Disorders Identification Test, Fagerström Test for Nicotine Dependence, WHO Disability Assessment Schedule and WHOQOL- BREF for Quality/Satisfaction with Life. The prevalence and comorbid patterns of chronic pain were determined. Logistic regression analysis and generalized linear mixed-effects model was employed to examine the relationship of chronic pain to socio-demographic variables and examined physical and mental health conditions. Results A total of 1831 (27%) patients reported chronic pain. Among those with chronic pain, 28.3% reported no co-occurring chronic mental or physical illness, 35.3% reported one, and 36.3% reported multi-morbidity. In the multivariate analysis, patients with chronic pain when compared to those without had higher odds of being older, female, having lower education, not living with their family, greater disability, and poor satisfaction with life. Chronic pain was independently associated with both medical (hypertension, diabetes mellitus, tuberculosis, arthritis, and other medical illnesses) and mental health conditions (depressive disorders, anxiety disorders, and tobacco dependence). It showed a varying strength of association and additive effect with increasing number of co-occurring physical and mental illnesses. Conclusions Chronic pain is a common condition among primary care attendees associated with significant burden of medical and mental health comorbidity. The findings highlight the need to incorporate treatment models that will ensure appropriate management to improve outcomes within the resource constraints.
Levels of Physical Activity in Spanish Asthmatics: A Cross-Sectional Study

Background and objectives: 339 million people in the world suffer from asthma. Regular physical activity (PA) could help in its control. Therefore, the aim of this research was to determine the level of PA in Spanish people with asthma considering variation by, age, sex, education, marital status, living together, smoking habits, alcohol intake and body mass index (BMI). Materials and Methods: 1014 Spanish people from 15 to 69 years were included in the study. Data of the Spanish Health Survey (year 2017) were analysed. PA levels were measure with the international physical activity questionnaire short version (IPAQ-SF). PA was categorized as low, moderate and high, and analyzed by sample characteristics. Mann-Whitney U test, Kruskall Wallis H and crosstabs were used to calculate statistical significance (p < 0.05). Results: On average, Spanish asthmatics engaged in a weekly volume of 2228.9 metabolic equivalent of task (MET)·min/week. Males revealed significantly higher PA than females (2516.8 vs. 2019.5 MET·min/week; p = 0.005), younger participants (<30 years) compared to people aged 30–60 years and older than 60 years (2699.0; 2243.2; 1619.3 MET·min/week; p < 0.001) and those with tertiary level of education than those without secondary (2368.3 vs. 2168.3 MET·min/week; p = 0.001). Level of PA was lower in those married (p = 0.001) and/or living together (p = 0.010). Alcohol consumers showed a higher level than the participants who did not drink (2378.3 vs. 1907.9 MET·min/week; p = 0.001), but no significant differences were found within current, past and never smokers (p = 0.890). Obese asthmatics engaged in less PA than their normal weight and overweight peers (p < 0.001). Overall, moderate level was significantly the most frequent (47.7%), but 31.6% showed a low level. Conclusions: Three out of ten Spanish people with asthma do not achieve PA recommendations, so PA programs should be executed to make people aware of its benefits in asthma control, focusing on those groups with lower PA levels.
Red LED Light Acts on the Mitochondrial Electron Chain of Mammalian Sperm via Light-Time Exposure-Dependent Mechanisms

This work analyzes the effects of red LED light on mammalian sperm mitochondrial function, using the pig as an animal model. Liquid-stored pig semen was stimulated with red-light for 1, 5 and 10 min in the presence or absence of oligomycin A, a specific inhibitor of mitochondrial ATP synthase, or carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone (FCCP), a specific disruptor of mitochondrial electron chain. Whereas exposure for 1 and 5 min significantly (p < 0.05) decreased total motility and intracellular ATP levels, irradiation for 10 min induced the opposite effect. Oligomycin A abolished the light-effects on intracellular ATP levels, O2 consumption and mitochondrial membrane potential, whereas compared to non-irradiated samples, FCCP significantly (p < 0.05) increased O2 consumption when sperm were irradiated for 1 min. Both oligomycin A and FCCP significantly (p < 0.05) decreased total motility. Red-light increased cytochrome c oxidase activity with a maximal effect after 5 min of irradiation, which was abolished by both oligomycin A and FCCP. In conclusion, red-light modulates sperm mitochondrial function via electron chain activity in an exposition, time-dependent manner.
Coping with DNA Double-Strand Breaks via ATM Signaling Pathway in Bovine Oocytes

As a common injury almost all cells face, DNA damage in oocytes—especially double-strand breaks (DSBs), which occur naturally during the first meiosis phase (meiosis I) due to synaptic complex separation—affects the fertilization ability of oocytes, instead of causing cancer (as in somatic cells). The mechanism of oocytes to effectively repair DSB damage has not yet been clearly studied, especially considering medically induced DSBs superimposed on naturally occurring DSBs in meiosis I. It was found that maturation rates decreased or increased, respectively corresponding with overexpression or interference of p21 in bovine oocytes. At the same time, the maturation rate of bovine oocytes decreased with a gradual increase in Zeocin dose, and the p21 expression in those immature oocytes changed significantly with the gradual increase in Zeocin dose (same as increased DSB intensity). Same as p21, the variation trend of ATM expression was consistent with the gradual increase in Zeocin dose. Furthermore, the oocytes demonstrated tolerance to DSBs during meiosis I, while the maturation rates decreased when the damage exceeded a certain threshold; according to which, it may be that ATM regulates the p53–p21 pathway to affect the completion of meiosis. In addition, nonhomologous recombination and cumulus cells are potentially involved in the process by which oocytes respond to DSB damage.
Contrasting community assembly processes structure lotic bacteria metacommunities along the river continuum

Summary The heterogeneous nature of lotic habitats plays an important role in the complex ecological and evolutionary processes that structure the microbial communities within them. Due to such complexity, our understanding of lotic microbial ecology still lacks conceptual frameworks for the ecological processes that shape these communities. We explored how bacterial community composition and underlying ecological assembly processes differ between lotic habitats by examining community composition and inferring community assembly processes across four major habitat types (free‐living, particle‐associated, biofilm on benthic stones and rocks, and sediment). This was conducted at 12 river sites from headwater streams to the main river in the River Thames, UK. Our results indicate that there are distinct differences in the bacterial communities between four major habitat types, with contrasting ecological processes shaping their community assembly processes. While the mobile free‐living and particle‐associated communities were consistently less diverse than the fixed sediment and biofilm communities, the latter two communities displayed higher homogeneity across the sampling sites. This indicates that the relative influence of deterministic environmental filtering is elevated in sediment and biofilm communities compared with free‐living and particle‐associated communities, where stochastic processes play a larger role.
Greater decrements in neuromuscular function following interval compared to continuous eccentric cycling

Our aim was to determine the demands and consequences of a single session of continuous (CONT) or interval (INT) eccentric cycling. Fourteen healthy males performed ‘work-matched’ CONT and INT eccentric cycling in a cross over design. Measures of maximal voluntary contraction (MVC), resting twitch force, voluntary activation (VA), muscle soreness and creatine kinase (CK) were taken at baseline, immediately post, and 24, 48 and 72 h post the first exercise bout. The second bout was used to characterise within session demands. Decreases in MVC (INT 19%, CONT 13%), twitch force (INT 31%, CONT 18%), and VA (INT 10%, CONT 6%) were observed immediately post session (p < 0.05). Reductions in twitch force were greater after INT (p < 0.05) and lasted 48 h. Muscle soreness was greater following INT, versus CONT (p < 0.05), although no differences in CK were observed. Metabolic demands (% of V̇O2peak and [BLa]) were greater during INT vs. CONT (32 ± 6% 28 ± 6%; p < 0.001), [BLa] (1.0 ± 0.4 vs. 0.8 ± 0.2 mmol·L−1; p < 0.001) and RPE (12 ± 1 vs. 11 ± 1; p < 0.001), respectively. Total time under tension was 48% greater in CONT compared to INT (p < 0.001), whereas average torque (during exercise) was 40% greater during INT compared to CONT (p < 0.001). Interval eccentric cycling exacerbates muscle soreness, decrements in muscle function and lengthens recovery compared to a work matched continuous bout, which is attributable to increased force rather than time under tension.
Epigenetic Patterns in Five-Year-Old Children Exposed to a Low Glycemic Index Dietary Intervention during Pregnancy: Results from the ROLO Kids Study

A range of in utero and early-life factors can influence offspring epigenetics, particularly DNA methylation patterns. This study aimed to investigate the influence of a dietary intervention and factors in pregnancy on offspring epigenetic profile at five years of age. We also explored associations between body composition and methylation profile in a cross-sectional analysis. Sixty-three five-year-olds were selected from the ROLO Kids Study, a Randomized controlled trial Of a LOw glycemic index dietary intervention from the second trimester of pregnancy. DNA methylation was investigated in 780,501 CpG sites in DNA isolated from saliva. Principal component analysis identified no association between maternal age, weight, or body mass index (BMI) during pregnancy and offspring DNA methylation (p > 0.01). There was no association with the dietary intervention during pregnancy, however, gene pathway analysis identified functional clusters involved in insulin secretion and resistance that differed between the intervention and control. There were no associations with child weight or adiposity at five years of age; however, change in weight from six months was associated with variation in methylation. We identified no evidence of long-lasting influences of maternal diet or factors on DNA methylation at age five years. However, changes in child weight were associated with the methylome in childhood.
The Promise of Optogenetics for Bioproduction: Dynamic Control Strategies and Scale-Up Instruments

Progress in metabolic engineering and synthetic and systems biology has made bioproduction an increasingly attractive and competitive strategy for synthesizing biomolecules, recombinant proteins and biofuels from renewable feedstocks. Yet, due to poor productivity, it remains difficult to make a bioproduction process economically viable at large scale. Achieving dynamic control of cellular processes could lead to even better yields by balancing the two characteristic phases of bioproduction, namely, growth versus production, which lie at the heart of a trade-off that substantially impacts productivity. The versatility and controllability offered by light will be a key element in attaining the level of control desired. The popularity of light-mediated control is increasing, with an expanding repertoire of optogenetic systems for novel applications, and many optogenetic devices have been designed to test optogenetic strains at various culture scales for bioproduction objectives. In this review, we aim to highlight the most important advances in this direction. We discuss how optogenetics is currently applied to control metabolism in the context of bioproduction, describe the optogenetic instruments and devices used at the laboratory scale for strain development, and explore how current industrial-scale bioproduction processes could be adapted for optogenetics or could benefit from existing photobioreactor designs. We then draw attention to the steps that must be undertaken to further optimize the control of biological systems in order to take full advantage of the potential offered by microbial factories.
Proteomic analyses identify differentially expressed proteins and pathways between low-risk and high-risk subtypes of early-stage lung adenocarcinoma and their prognostic impacts.

The histopathological subtype of lung adenocarcinoma (LUAD) is closely associated with prognosis. Micropapillary or solid predominant LUAD tends to relapse after surgery at an early stage, whereas lepidic pattern shows a favorable outcome. However, the molecular mechanism underlying this phenomenon remains unknown. Here, we recruited 31 lepidic predominant LUADs (LR: low-risk subtype group) and 28 micropapillary or solid predominant LUADs (HR: high-risk subtype group). Tissues of these cases were obtained and label-free quantitative proteomic and bioinformatic analyses were performed. Additionally, prognostic impact of targeted proteins was validated using The Cancer Genome Atlas databases (n=492) and tissue microarrays composed of early-stage LUADs (n=228). A total of 192 differentially expressed proteins were identified between tumor tissues of LR and HR and three clusters were identified via hierarchical clustering excluding eight proteins. Cluster 1 (65 proteins) showed a sequential decrease in expression from normal tissues to tumor tissues of LR and then to HR and was predominantly enriched in pathways such as tyrosine metabolism and ECM-receptor interaction, and increased matched mRNA expression of 18 proteins from this cluster predicted favorable prognosis. Cluster 2 (70 proteins) demonstrated a sequential increase in expression from normal tissues to tumor tissues of LR and then to HR and was mainly enriched in pathways such as extracellular organization, DNA replication and cell cycle, and high matched mRNA expression of 25 proteins indicated poor prognosis. Cluster 3 (49 proteins) showed high expression only in LR, with high matched mRNA expression of 20 proteins in this cluster indicating favorable prognosis. Furthermore, high expression of ERO1A and FEN1 at protein level predicted poor prognosis in early-stage LUAD, supporting the mRNA results. In conclusion, we discovered key differentially expressed proteins and pathways between low-risk and high-risk subtypes of early-stage LUAD. Some of these proteins could serve as potential biomarkers in prognostic evaluation.