Miracle-dz/UniFAR-FTUs huggingface dataset:
Complete Genome Sequencing of Influenza A Viruses within Swine Farrow-to-Wean Farms Reveals the Emergence, Persistence, and Subsidence of Diverse Viral Genotypes

ABSTRACT Influenza A viruses (IAVs) are endemic in swine and represent a public health risk. However, there is limited information on the genetic diversity of swine IAVs within farrow-to-wean farms, which is where most pigs are born. In this longitudinal study, we sampled 5 farrow-to-wean farms for a year and collected 4,190 individual nasal swabs from three distinct pig subpopulations. Of these, 207 (4.9%) samples tested PCR positive for IAV, and 124 IAVs were isolated. We sequenced the complete genomes of 123 IAV isolates and found 31 H1N1, 26 H1N2, 63 H3N2, and 3 mixed IAVs. Based on the IAV hemagglutinin, seven different influenza A viral groups (VGs) were identified. Most of the remaining IAV gene segments allowed us to differentiate the same VGs, although an additional viral group was identified for gene segment 3 (PA). Moreover, the codetection of more than one IAV VG was documented at different levels (farm, subpopulation, and individual pigs), highlighting the environment for potential IAV reassortment. Additionally, 3 out of 5 farms contained IAV isolates (n = 5) with gene segments from more than one VG, and 79% of all the IAVs sequenced contained a signature mutation (S31N) in the matrix gene that has been associated with resistance to the antiviral amantadine. Within farms, some IAVs were detected only once, while others were detected for 283 days. Our results illustrate the maintenance and subsidence of different IAVs within swine farrow-to-wean farms over time, demonstrating that pig subpopulation dynamics are important to better understand the diversity and epidemiology of swine IAVs. IMPORTANCE On a global scale, swine are one of the main reservoir species for influenza A viruses (IAVs) and play a key role in the transmission of IAVs between species. Additionally, the 2009 IAV pandemics highlighted the role of pigs in the emergence of IAVs with pandemic potential. However, limited information is available regarding the diversity and distribution of swine IAVs on farrow-to-wean farms, where novel IAVs can emerge. In this study, we studied 5 swine farrow-to-wean farms for a year and characterized the genetic diversity of IAVs among three different pig subpopulations commonly housed on this type of farm. Using next-generation-sequencing technologies, we demonstrated the complex distribution and diversity of IAVs among the pig subpopulations studied. Our results demonstrated the dynamic evolution of IAVs within farrow-to-wean farms, which is crucial to improve health interventions to reduce the risk of transmission between pigs and from pigs to people.
Identification, Classification and Differential Expression of Oleosin Genes in Tung Tree (Vernicia fordii)

Triacylglycerols (TAG) are the major molecules of energy storage in eukaryotes. TAG are packed in subcellular structures called oil bodies or lipid droplets. Oleosins (OLE) are the major proteins in plant oil bodies. Multiple isoforms of OLE are present in plants such as tung tree (Vernicia fordii), whose seeds are rich in novel TAG with a wide range of industrial applications. The objectives of this study were to identify OLE genes, classify OLE proteins and analyze OLE gene expression in tung trees. We identified five tung tree OLE genes coding for small hydrophobic proteins. Genome-wide phylogenetic analysis and multiple sequence alignment demonstrated that the five tung OLE genes represented the five OLE subfamilies and all contained the “proline knot” motif (PX5SPX3P) shared among 65 OLE from 19 tree species, including the sequenced genomes of Prunus persica (peach), Populus trichocarpa (poplar), Ricinus communis (castor bean), Theobroma cacao (cacao) and Vitis vinifera (grapevine). Tung OLE1, OLE2 and OLE3 belong to the S type and OLE4 and OLE5 belong to the SM type of Arabidopsis OLE. TaqMan and SYBR Green qPCR methods were used to study the differential expression of OLE genes in tung tree tissues. Expression results demonstrated that 1) All five OLE genes were expressed in developing tung seeds, leaves and flowers; 2) OLE mRNA levels were much higher in seeds than leaves or flowers; 3) OLE1, OLE2 and OLE3 genes were expressed in tung seeds at much higher levels than OLE4 and OLE5 genes; 4) OLE mRNA levels rapidly increased during seed development; and 5) OLE gene expression was well-coordinated with tung oil accumulation in the seeds. These results suggest that tung OLE genes 1–3 probably play major roles in tung oil accumulation and/or oil body development. Therefore, they might be preferred targets for tung oil engineering in transgenic plants.
Preventing (impulsive) errors: Electrophysiological evidence for online inhibitory control over incorrect responses

Abstract In a rich environment, with multiple action affordances, selective action inhibition is critical in preventing the execution of inappropriate responses. Here, we studied the origin and the dynamics of incorrect response inhibition and how it can be modulated by task demands. We used EEG in a conflict task where the probability of compatible and incompatible trials was varied. This allowed us to modulate the strength of the prepotent response, and hence to increase the risk of errors, while keeping the probability of the two responses equal. The correct response activation and execution was not affected by compatibility or by probability. In contrast, incorrect response inhibition in the primary motor cortex ipsilateral to the correct response was more pronounced on incompatible trials, especially in the condition where most of the trials were compatible, indicating a modulation of inhibitory strength within the course of the action. Two prefrontal activities, one medial and one lateral, were also observed before the response, and their potential links with the observed inhibitory pattern observed are discussed.
A Comprehensive Multi-Illuminant Dataset for Benchmarking of the Intrinsic Image Algorithms

In this paper, we provide a new, real photo dataset with precise ground-truth for intrinsic image research. Prior ground-truth datasets have been restricted to rather simple illumination conditions and scene geometries, or have been enhanced using image synthesis methods. The dataset provided in this paper is based on complex multi-illuminant scenarios under multi-colored illumination conditions and challenging cast shadows. We provide full per-pixel intrinsic ground-truth data for these scenarios, i.e. reflectance, specularity, shading, and illumination for scenes as well as preliminary depth information. Furthermore, we evaluate 3 state-of-the-art intrinsic image recovery methods, using our dataset.
Niche Partitioning in Sympatric Gorilla and Pan from Cameroon: Implications for Life History Strategies and for Reconstructing the Evolution of Hominin Life History

Factors influencing the hominoid life histories are poorly understood, and little is known about how ecological conditions modulate the pace of their development. Yet our limited understanding of these interactions underpins life history interpretations in extinct hominins. Here we determined the synchronisation of dental mineralization/eruption with brain size in a 20th century museum collection of sympatric Gorilla gorilla and Pan troglodytes from Central Cameroon. Using δ13C and δ15N of individuals’ hair, we assessed whether and how differences in diet and habitat use may have impacted on ape development. The results show that, overall, gorilla hair δ13C and δ15N values are more variable than those of chimpanzees, and that gorillas are consistently lower in δ13C and δ15N compared to chimpanzees. Within a restricted, isotopically-constrained area, gorilla brain development appears delayed relative to dental mineralization/eruption [or dental development is accelerated relative to brains]: only about 87.8% of adult brain size is attained by the time first permanent molars come into occlusion, whereas it is 92.3% in chimpanzees. Even when M1s are already in full functional occlusion, gorilla brains lag behind those of chimpanzee (91% versus 96.4%), relative to tooth development. Both bootstrap analyses and stable isotope results confirm that these results are unlikely due to sampling error. Rather, δ15N values imply that gorillas are not fully weaned (physiologically mature) until well after M1 are in full functional occlusion. In chimpanzees the transition from infant to adult feeding appears (a) more gradual and (b) earlier relative to somatic development. Taken together, the findings are consistent with life history theory that predicts delayed development when non-density dependent mortality is low, i.e. in closed habitats, and with the “risk aversion” hypothesis for frugivorous species as a means to avert starvation. Furthermore, the results highlight the complexity and plasticity of hominoid/hominin development.
Circadian hemodynamics in men and women with high blood pressure: dipper vs. nondipper and racial differences

Objective: The ‘nondipping’ pattern of circadian blood pressure (BP) variation is an established independent predictor of adverse cardiovascular outcomes. Although this phenomenon has been widely studied, its underlying circadian hemodynamics of cardiac output and systemic vascular resistance (SVR) have not been well characterized. We evaluated the hypothesis that BP nondipping would be associated with a blunted night-time reduction in SVR in a biracial sample of 140 (63 African-American and 77 white) men and women with elevated clinic BP (130–159/85–99 mmHg). Methods and results: Twenty-four-hour ambulatory hemodynamics were assessed using standard ambulatory BP monitoring coupled with synchronized ambulatory impedance cardiography. Using the criterion of less than 10% dip in SBP, there were 51 nondippers (SBP dip = 7.3 ± 2.6%) and 89 dippers (SBP dip = 15.5 ± 3.4%). There was minimal change in cardiac output from daytime to night-time in both dippers and nondippers. However, SVR decreased from daytime to night-time, but nondippers compared with dippers exhibited a significantly attenuated decrease in SVR from daytime to night-time (7.8 vs. 16.1%, P < 0.001). Relative to their white counterparts, African-Americans also exhibited blunted SBP dipping (10.9 vs. 14.6%, P < 0.001) as well as an attenuated decrease in SVR (10.8 vs. 15.6%, P < 0.001). Conclusion: Overall, these findings indicate that blunted night-time BP dipping is associated with impairment of the systemic vasodilation that is characteristic of the night-time sleep period and is especially prominent among African-Americans. In the context of high BP, these findings suggest that nondipping may be a manifestation, or marker, of more advanced vascular disease.
Axillary Skip Metastases and the False-Negative Rate of Sentinel Lymph Node Biopsy in Patients With Breast Cancer Are Related to Negative ALDH-1 Expression and Ki-67 Expression

Breast cancer stem cells (CSCs) have been hypothesized to be the driving force behind tumorigenesis and metastasis. In this study, we evaluated the relationships between CSC expressions in primary breast cancers and corresponding metastatic sentinel and nonsentinel lymph nodes (SLNs and NSLNs). The clinical implications of these relationships were also investigated. CSC expressions were evaluated in 167 breast cancer specimens and associated lymph node biopsies (when present). We used double immunohistochemistry of CD44/CD24 and single immunohistochemistry of ALDH-1 on paraffin-embedded breast tissue, SLN, and NSLN specimens. Seven cases had metastatic NSLNs without SLN involvement—so-called “skip metastasis. ” Fifty cases of SLNs (29.9%) and 33 cases of NSLNs (25.7%) had metastases. In the breast cancers, metastatic SLNs, and NSLNs, the expression rates of CD44+/CD24− were 47.9%, 26.1%, and 34.6 %, respectively, while the expression rates of ALDH-1+ were 42.5%, 36.4%, and 33.3%, respectively. Significant relationships were not observed between CSC expressions in breast cancer and metastatic SLNs or NSLNs. The presence of skip metastasis correlated with negative ALDH-1 in breast cancer (P = .04), as well as several clinicopathologic factors: age >50 years (P = .004), negative lymphovascular tumor emboli (P = .02), and high Ki-67 expression (P = .04). Axillary lymph node metastasis showed no significant relationship with any CSC marker. However, CD44+/CD24− and ALDH-1 expressions of metastatic SLNs correlated with CSCs of primary breast cancers. In summary, skip metastasis correlated with negative expression of ALDH-1 in primary breast cancers, which could be promising as a means of assessing the risk of skip metastasis.
Development of a Web-Based Survey for Monitoring Daily Health and its Application in an Epidemiological Survey

Background Early detection of symptoms arising from exposure to pathogens, harmful substances, or environmental changes is required for timely intervention. The administration of Web-based questionnaires is a potential method for collecting information from a sample population. Objective The objective of our study was to develop a Web-based daily questionnaire for health (WDQH) for symptomatic surveillance. Methods We adopted two different survey methods to develop the WDQH: an Internet panel survey, which included participants already registered with an Internet survey company, and the Tokyo Consumers’ Co-operative Union (TCCU) Internet survey, in cooperation with the Japanese Consumers’ Co-operative Union, which recruited participants by website advertising. The Internet panel survey participants were given a fee every day for providing answers, and the survey was repeated twice with modified surveys and collection methods: Internet Panel Survey I was conducted every day, and Internet Panel Survey II was conducted every 3 days to reduce costs. We examined whether the survey remained valid by reporting health conditions on day 1 over a 3-day period, and whether the response rate would vary among groups with different incentives. In the TCCU survey, participants were given a fee only for initially registering, and health information was provided in return for survey completion. The WDQH included the demographic details of participants and prompted them to answer questions about the presence of various symptoms by email. Health information collected by the WDQH was then used for the syndromic surveillance of infection. Results Response rates averaged 47.3% for Internet Panel Survey I, 42.7% for Internet Panel Survey II, and 40.1% for the TCCU survey. During a seasonal influenza epidemic, the WDQH detected a rapid increase in the number of participants with fever through the early aberration reporting system. Conclusions We developed a health observation method based on self-reporting by participants via the Internet. We validated the usefulness of the WDQH by its practical use in syndromic surveillance.
Enhanced control of Mycobacterium tuberculosis extrapulmonary dissemination in mice by an arabinomannan-protein conjugate vaccine

Currently there are a dozen or so of new vaccine candidates in clinical trials for prevention of tuberculosis (TB) and each formulation attempts to elicit protection by enhancement of cell-mediated immunity (CMI). In contrast, most approved vaccines against other bacterial pathogens are believed to mediate protection by eliciting antibody responses. However, it has been difficult to apply this formula to TB because of the difficulty in reliably eliciting protective antibodies. Here, we developed capsular polysaccharide conjugates by linking mycobacterial capsular arabinomannan (AM) to either Mtb Ag85b or B. anthracis protective antigen (PA). Further, we studied their immunogenicity by ELISA and AM glycan microarrays and protection efficacy in mice. Immunization with either Abg85b-AM or PA-AM conjugates elicited an AM-specific antibody response in mice. AM binding antibodies stimulated transcriptional changes in Mtb. Sera from AM conjugate immunized mice reacted against a broad spectrum of AM structural variants and specifically recognized arabinan fragments. Conjugate vaccine immunized mice infected with Mtb had lower bacterial numbers in lungs and spleen, and lived longer than control mice. These findings provide additional evidence that humoral immunity can contribute to protection against Mtb.
PROCESSABILITIES AND MECHANICAL-PROPERTIES OF SURLYN-TREATED STARCH/LDPE BLENDS

The esterification of the hydroxyl group of starch with DuPont Surlyn was considered as pretreatment method of starch before blending with polyolefins. In treating starch with Surlyn, two different reaction conditions were taken to optimize reaction conditions. First, the esterification reaction was carried out in 110°C xylene with oleic acid as a catalyst. Second, the reaction was carried out in a 90°C mixture of deionized water and xylene with ceric ammonium nitrate (CAN) as an initiator. Starch granules would be swollen above the gelatinization temperature in water. In both cases, starch was modified by Surlyn to have good compatibility with low-density polyethylene (LDPE). The mechanical and rheological properties were examined for blends of the treated starch and LDPE. This system may be one of the biodegradable polymer blends that sufficiently retain properties as a packaging film.
Healthy Workplaces? A Survey of Massachusetts Employers

Purpose. This study examines worksite health promotion (WHP) and occupational health and safety (OHS) activities by Massachusetts employers, and the extent to which workplaces with programming in one domain were more likely to have the other as well. Design. In 2008, the Massachusetts Department of Public Health surveyed a stratified sample of Massachusetts worksites. Setting. A mailed questionnaire to be completed by workplace representatives. Subjects. Massachusetts worksites returning the questionnaire. Measures. Questionnaire items about worksite characteristics, WHP, and some OHS practices. Analysis. We scored levels of WHP and OHS activity; examined the relationship between activities in the two domains by employer characteristics; and assessed self-reported coordination between them. Results. The 890 responding worksites had higher scores for OHS (mean = 48% of practices, SD = 24%) than WHP (mean = 20%, SD = 12%). The difference between these scores varied by a factor of two across industry sectors and was smallest for workforces of 100+ employees (p = .001). Employers with no unionized workers reported fewer activities in both domains (p < .0001). Only 28% of respondents reported always/often coordinating OHS and WHP efforts; these organizations had more activities overall in both domains. Conclusion. Larger and unionized workplaces in Massachusetts were more likely to offer both WHP and OHS programming. Self-reported coordination was somewhat associated with more activity in both domains, although levels of WHP activity varied widely.
The zinc-finger transcription factor Hindsight regulates ovulation competency of Drosophila follicles

Follicle rupture, the final step in ovulation, utilizes conserved molecular mechanisms including matrix metalloproteinases (Mmps), steroid signaling, and adrenergic signaling. It is still unknown how follicles become competent for follicle rupture/ovulation. Here, we identify a zinc-finger transcription factor Hindsight (Hnt) as the first transcription factor regulating follicle’s competency for ovulation in Drosophila. Hnt is not expressed in immature stage-13 follicle cells but is upregulated in mature stage-14 follicle cells, which is essential for follicle rupture/ovulation. Hnt upregulates Mmp2 expression in posterior follicle cells (essential for the breakdown of the follicle wall) and Oamb expression in all follicle cells (the receptor for receiving adrenergic signaling and inducing Mmp2 activation). Hnt’s role in regulating Mmp2 and Oamb can be replaced by its human homolog Ras-responsive element-binding protein 1 (RREB-1). Our data suggest that Hnt/RREB-1 plays conserved role in regulating follicle maturation and competency for ovulation.
Tai Chi Chuan and Baduanjin Mind-Body Training Changes Resting-State Low-Frequency Fluctuations in the Frontal Lobe of Older Adults: A Resting-State fMRI Study

Age-related cognitive decline is a significant public health concern. Recently, non-pharmacological methods, such as physical activity and mental training practices, have emerged as promising low-cost methods to slow the progression of age-related memory decline. In this study, we investigated if Tai Chi Chuan (TCC) and Baduanjin modulated the fractional amplitude of low-frequency fluctuations (fALFF) in different frequency bands (low-frequency: 0.01–0.08 Hz; slow-5: 0.01–0.027 Hz; slow-4: 0.027–0.073 Hz) and improved memory function. Older adults were recruited for the randomized study. Participants in the TCC and Baduanjin groups received 12 weeks of training (1 h/day for 5 days/week). Participants in the control group received basic health education. Each subject participated in memory tests and fMRI scans at the beginning and end of the experiment. We found that compared to the control group: (1) TCC and Baduanjin groups demonstrated significant improvements in memory function; (2) TCC increased fALFF in the dorsolateral prefrontal cortex (DLPFC) in the slow-5 and low-frequency bands; and (3) Baduanjin increased fALFF in the medial PFC in the slow-5 and low-frequency bands. This increase was positively associated with memory function improvement in the slow-5 and low-frequency bands across the TCC and Baduanjin groups. Our results suggest that TCC and Baduanjin may work through different brain mechanisms to prevent memory decline due to aging.
Hybrid Docking-QSAR Studies of 1, 4-dihydropyridine-3, 5-Dicarboxamides as Potential Antitubercular Agents.

BACKGROUND Tuberculosis is one of the main medical problems and some people are suffering still from this infectious disease. 1, 4-dihydropyridines are multi-target ligands that recently are recognized as anti-tubercular agents. METHODS In the current research, computational studies were conducted of some synthesized 1, 4- dihydropyridine-3, 5-dicarboxamides in non-hydrolyzed and hydrolyzed forms to find the drugreceptor interactions profile. RESULTS Among equations obtained for non-hydrolyzed compounds, the model with better statistical parameters such as R2= 0.9462, q2 of LOO= 0.8318 and q2 of LMO= 0.7987 was considered as the best one and EEig08d, LAI, Mor23m, GATS3e, Mor28m descriptors were identified as the most significant factors that affect the biological activity of non-hydrolyzed compounds. CONCLUSION In the hydrolyzed compounds, the model which has R2= 0.9731, q2 of LOO= 0.91154462 and q2 of LMO= 0.742 was considered as the best one and Mor27e and BEHv2 were also revealed as the most important descriptors in hydrolyzed compounds.