Miracle-dz/UniFAR-FTUs huggingface dataset:
13:Bacterial Degradation of Archaeological Wood in Anoxic Waterlogged Environments

Anoxic ecosystems offer extreme environmental conditions and under these conditions wood can be preserved for thousands of years. The recalcitrant nature of wood is not only controlled by the anoxic environment but also by the structure and organisation of the cell wall components. The decay mechanisms acting in anoxic ecosystems are though not fully understood. Preserved archaeological wood objects are due to their age, archaeological, and cultural record well suited for studying the degradation of biogenic carbon in anoxic environments. Erosion bacteria are the main degraders of waterlogged archaeological wood but it has so far not been possible to isolate or explicitly identify the bacteria species. The typical erosion bacteria decay pattern is a mixture of sound and decayed cell wall areas. The cellulose rich secondary cell wall is decayed and an amorphous residual material is left behind. The lignin rich compound middle lamella and often also parts of the S1 and S3 cell wall is preserved. The ultrastructural decay pattern corresponds well with the general observation that cellulose and hemicellulose is lost in preference to lignin. Hemicellulose is decayed in preference to cellulose. The degree of polymerisation is reduced for the remaining carbohydrates in waterlogged wood. Decayed cell wall areas have lost birefringence due to loss of crystalline cellulose, but the crystallinity of the remaining cellulose microfibrils is not significantly changed compared to sound reference wood. The lignin degradation is minor and incomplete.
Soft drink consumption in Pacific Island countries and territories: a review of trade data.

INTRODUCTION Pacific Islands Countries and Territories (PICTs) have some of the highest rates of obesity and diabetes in the world. Research has demonstrated a strong link between sugar-sweetened beverage (SSB) consumption and subsequent risk of overweight, obesity, dental caries and type II diabetes. To address the impact of SSBs on noncommunicable diseases, it is crucial to understand the level of SSB consumption in PICTs. METHODS The volume of soft drinks imported and exported was requested from PICTs to estimate the litres of soft drink consumption per head of population. Analysis was confined to PICTs who did not produce their own soft drinks because production data was limited. The Harmonised Commodity Description and Coding System (HS) category 22.02 was used which includes both diet and sugar-sweetened soft drinks. The trade data estimates were then compared with school survey data to explore how the data sources corresponded given the strengths and weaknesses of each. RESULTS Soft drink import volumes were a feasible way of estimating total soft drink consumption in PICTs and look at trends over time. Seven out of eleven non-producing PICTs contacted were able to provide volume of soft drinks imported. In 2011, estimates of soft drink consumption per person were 84L in Palau, 47L in the Commonwealth of the Northern Mariana Islands (CNMI), 41L in Niue, 31L in Tonga, 22L in Federates States of Micronesia, 8L in Tuvalu and 1L in Kiribati. CONCLUSIONS Trade data is a feasible way of monitoring soft drink consumption and may be useful to evaluate the impact of changes in government policy on importation of soft drinks. Data quality could be maximised by including export data, adjusting for visitor numbers and cross-checking exports from corresponding countries. To monitor SSB consumption, a wider range of categories could be included such as categories for sugar-sweetened juice and sweetened-milk drinks.
Role of Race/Ethnicity, Language, and Insurance in Use of Cervical Cancer Prevention Services Among Low-Income Hispanic Women, 2009–2013

Introduction Hispanic women in the United States have an elevated risk of cervical cancer, but the existing literature does not reveal why this disparity persists. Methods We performed a retrospective cohort analysis of 17,828 low-income women aged 21 to 64 years seeking care at Oregon community health centers served by a hosted, linked electronic health record during 2009 through 2013. We assessed the odds of having had Papanicolaou (Pap) tests and receiving human papillomavirus (HPV) vaccine, by race/ethnicity, insurance status, and language. Results Hispanic women, regardless of pregnancy status or insurance, had greater odds of having had Pap tests than non-Hispanic white women during the study period. English-preferring Hispanic women had higher odds of having had Pap tests than Spanish-preferring Hispanic women (OR, 2.08; 95% confidence interval [CI], 1.63–2.66) but lower odds of having received HPV vaccination (OR, 0.21; 95% CI, 0.12–0.38). Uninsured patients, regardless of race/ethnicity, had lower odds of HPV vaccine initiation than insured patients did. Once a single dose was received, there were no significant racial/ethnic differences in vaccine series completion. Conclusion In this sample of low-income women seeking care at Oregon community health centers, we found minimal racial/ethnic disparities in the receipt of cervical cancer prevention services. Inequities by insurance status, especially in the receipt of HPV vaccine, persist. Community health center–based care may be a useful model to address racial/ethnic disparities in prevention, but this model would need further population-wide study.
Negative Regulation of Meiotic Gene Expression by the Nuclear Poly(a)-binding Protein in Fission Yeast*

Meiosis is a cellular differentiation process in which hundreds of genes are temporally induced. Because the expression of meiotic genes during mitosis is detrimental to proliferation, meiotic genes must be negatively regulated in the mitotic cell cycle. Yet, little is known about mechanisms used by mitotic cells to repress meiosis-specific genes. Here we show that the poly(A)-binding protein Pab2, the fission yeast homolog of mammalian PABPN1, controls the expression of several meiotic transcripts during mitotic division. Our results from chromatin immunoprecipitation and promoter-swapping experiments indicate that Pab2 controls meiotic genes post-transcriptionally. Consistently, we show that the nuclear exosome complex cooperates with Pab2 in the negative regulation of meiotic genes. We also found that Pab2 plays a role in the RNA decay pathway orchestrated by Mmi1, a previously described factor that functions in the post-transcriptional elimination of meiotic transcripts. Our results support a model in which Mmi1 selectively targets meiotic transcripts for degradation via Pab2 and the exosome. Our findings have therefore uncovered a mode of gene regulation whereby a poly(A)-binding protein promotes RNA degradation in the nucleus to prevent untimely expression.
Number of T Reg Cells That Differentiate Does Not Increase upon Encounter of Agonist Ligand on Thymic Epithelial Cells

It has been reported that the differentiation of CD4+CD25+ regulatory T cells (T reg cells) can be induced by agonist peptide/major histocompatibility complex ligands in the thymus. Exploiting a transgenic mouse line wherein expression of a particular T cell epitope can be controlled temporally and quantitatively, we found that diversion of differentiating thymocytes into the FoxP3 T reg cell pathway by this agonist ligand was essentially nonexistent. However, CD4+CD25+ thymocytes were much less sensitive than their CD4+CD25− companions, by two to three orders of magnitude, to agonist-induced clonal deletion, such that their proportion increased, giving the false impression of induced differentiation. To account for these and prior observations, one can propose that differentiation along the CD4+CD25+ pathway is induced by cues other than recognition of self-agonist cues, which are poorly read by thymocytes, whose T cell receptors are conducive to selection toward the conventional CD4+CD25− lineage. Thus, selective survival, rather than induced differentiation, may explain the apparent enrichment observed here and in previous studies.
Structural basis for complement factor H–linked age-related macular degeneration

Nearly 50 million people worldwide suffer from age-related macular degeneration (AMD), which causes severe loss of central vision. A single-nucleotide polymorphism in the gene for the complement regulator factor H (FH), which causes a Tyr-to-His substitution at position 402, is linked to ∼50% of attributable risks for AMD. We present the crystal structure of the region of FH containing the polymorphic amino acid His402 in complex with an analogue of the glycosaminoglycans (GAGs) that localize the complement regulator on the cell surface. The structure demonstrates direct coordination of ligand by the disease-associated polymorphic residue, providing a molecular explanation of the genetic observation. This glycan-binding site occupies the center of an extended interaction groove on the regulator's surface, implying multivalent binding of sulfated GAGs. This finding is confirmed by structure-based site-directed mutagenesis, nuclear magnetic resonance–monitored binding experiments performed for both H402 and Y402 variants with this and another model GAG, and analysis of an extended GAG–FH complex.
Stimulation of Dopamine Receptor D5 Expressed on Dendritic Cells Potentiates Th17-Mediated Immunity

Dendritic cells (DCs) are responsible for priming T cells and for promoting their differentiation from naive T cells into appropriate effector cells. Emerging evidence suggests that neurotransmitters can modulate T cell-mediated immunity. However, the involvement of specific neurotransmitters or receptors remains poorly understood. In this study, we analyzed the role of dopamine in the regulation of DC function. We found that DCs express dopamine receptors as well as the machinery necessary to synthesize, store, and degrade dopamine. Notably, the expression of D5R decreased upon LPS-induced DC maturation. Deficiency of D5R on the surface of DCs impaired LPS-induced IL-23 and IL-12 production and consequently attenuated the activation and proliferation of Ag-specific CD4+ T cells. To determine the relevance of D5R expressed on DCs in vivo, we studied the role of this receptor in the modulation of a CD4+ T cell-driven autoimmunity model. Importantly, D5R-deficient DCs prophylactically transferred into wild-type recipients were able to reduce the severity of experimental autoimmune encephalomyelitis. Furthermore, mice transferred with D5R-deficient DCs displayed a significant reduction in the percentage of Th17 cells infiltrating the CNS without differences in the percentage of Th1 cells compared with animals transferred with wild-type DCs. Our findings demonstrate that by contributing to CD4+ T cell activation and differentiation to Th17 phenotype, D5R expressed on DCs is able to modulate the development of an autoimmune response in vivo.
Predictors of improvement in a cognitive-behavioral intervention for women with rheumatoid arthritis

In this article we present a secondary analysis of data from a brief cognitive—behavioral intervention for women with rheumatoid arthritis that resulted in significant overall improvements in personal coping resources, pain coping behaviors, psychological well-being, and fatigue. Not every participant, however, improved during the intervention. Establishing predictors of improvement in brief interventions is important to optimize the cost-effective use of these resources. In search of predictors of improvement, we examined demographic and background variables, personal coping resources, pain coping behaviors, and social support. Both linear and quadratic effects were analyzed, comparing baseline measures to both immediate postintervention and 3-month follow-up outcomes using standardized indexes of predictors and criteria variables. After removing the effects of baseline scores on the outcomes index, significant predictors of improvement included length of time since diagnosis, personal coping resources, and maladaptive and adaptive pain coping behaviors. Both linear and quadratic effects were found, although this varied as a function of type of predictor.
Unsupervised Neural-Symbolic Integration

Symbolic has been long considered as a language of human intelligence while neural networks have advantages of robust computation and dealing with noisy data. The integration of neural-symbolic can offer better learning and reasoning while providing a means for interpretability through the representation of symbolic knowledge. Although previous works focus intensively on supervised feedforward neural networks, little has been done for the unsupervised counterparts. In this paper we show how to integrate symbolic knowledge into unsupervised neural networks. We exemplify our approach with knowledge in different forms, including propositional logic for DNA promoter prediction and first-order logic for understanding family relationship.
International Journal of Behavioral Nutrition and Physical Activity Predicting Short-term Weight Loss Using Four Leading Health Behavior Change Theories

Background: This study was conceived to analyze how exercise and weight management psychosocial variables, derived from several health behavior change theories, predict weight change in a short-term intervention. The theories under analysis were the Social Cognitive Theory, the Transtheoretical Model, the Theory of Planned Behavior, and Self-Determination Theory.
Restriction Spectrum Imaging As a Potential Measure of Cortical Neurite Density in Autism

Autism postmortem studies have shown various cytoarchitectural anomalies in cortical and limbic areas including increased cell packing density, laminar disorganization, and narrowed minicolumns. However, there is little evidence on dendritic and axonal organization in ASD. Recent imaging techniques have the potential for non-invasive, in vivo studies of small-scale structure in the human brain, including gray matter. Here, Restriction Spectrum Imaging (RSI), a multi-shell diffusion-weighted imaging technique, was used to examine gray matter microstructure in 24 children with ASD (5 female) and 20 matched typically developing (TD) participants (2 female), ages 7–17 years. RSI extends the spherical deconvolution model to multiple length scales to characterize neurite density (ND) and organization. Measures were examined in 48 cortical regions of interest per hemisphere. To our knowledge, this is the first time that a multi-compartmental diffusion model has been applied to cortical gray matter in ASD. The ND measure detected robust age effects showing a significant positive relationship to age in all lobes except left temporal when groups were combined. Results were also suggestive of group differences (ASDTD) in bilateral parietal regions as well as widespread age effects were detected. Our findings support the value of multi-shell diffusion imaging for assays of cortical gray matter. This approach has the potential to add to postmortem literature, examining intracortical organization, intracortical axonal content, myelination, or caliber. Robust age effects further support the validity of the ND metric for in vivo examination of gray matter microstructure in ASD and across development. While diffusion MRI does not approach the precision of histological studies, in vivo imaging measures of microstructure can complement postmortem studies, by allowing access to large sample sizes, a whole-brain field of view, longitudinal designs, and combination with behavioral and functional assays. This makes multi-shell diffusion imaging a promising technique for understanding the underlying cytoarchitecture of the disorder.
Implementation of a physician assistant/hospitalist service in an academic medical center: impact on efficiency and patient outcomes.

BACKGROUND Accreditation Council on Graduate Medical Education (ACGME) duty hour restrictions have led to the widespread implementation of non-house staff services in academic medical centers, yet little is known about the quality and efficiency of patient care on such services. OBJECTIVE To evaluate the quality and efficiency of patient care on a physician assistant/hospitalist service compared with that of traditional house staff services. DESIGN Retrospective cohort study. SETTING Inpatient general medicine service of a 747-bed academic medical center. PATIENTS A total of 5194 consecutive patients admitted to the general medical service from July 2005 to June 2006, including 992 patients on the physician assistant/hospitalist service and 4202 patients on a traditional house staff service. INTERVENTION A geographically localized service staffed with physician assistants and supervised by hospitalists. MEASUREMENTS Length of stay (LOS), cost of care, inpatient mortality, intensive care unit (ICU) transfers, readmissions, and patient satisfaction. RESULTS Patients admitted to the study service were younger, had lower comorbidity scores, and were more likely to be admitted at night. After adjustment for these and other factors, and for clustering by attending physician, total cost of care was marginally lower on the study service (adjusted costs 3.9% lower; 95% confidence interval [CI] -7.5% to -0.3%), but LOS was not significantly different (adjusted LOS 5.0% higher; 95% CI, -0.4% to +10%) as compared with house staff services. No difference was seen in inpatient mortality, ICU transfers, readmissions, or patient satisfaction. CONCLUSIONS For general medicine inpatients admitted to an academic medical center, a service staffed by hospitalists and physician assistants can provide a safe alternative to house staff services, with comparable efficiency.
Oxidative Stress and Amyloid Toxicity: Insights From Yeast

Alzheimer's disease is the most common neurodegenerative disorder. One of the factors that promotes neurodegeneration is the accumulation of senile plaques formed by Aβ peptide. In this paper, it was analyzed that if oxidative stress is cause or consequence of amyloid cascade and the role of antioxidant defense system in this process, using S. cerevisiae (with a multicopy plasmid containing the Aβ1‐42 sequence) as experimental model. Cells grown on glycerol were more tolerant than when grown on glucose, strengthening the role of the antioxidant defense system against Aβ accumulation. Antioxidant defense deficiency did not change the pattern of amyloid aggregation. On the other hand, the presence of Aβ increased the level of intracellular oxidation and induced the activity of catalase, superoxide dismutase, and aconitase. Peroxissomal catalase deficient cells (Δcta1), were more sensitive to Aβ toxicity than the wild type strain, while mitochondrial superoxide dismutase (Sod2) deficient cells displayed the highest frequency of petites. Besides, Aβ alters the oxygen consumption and the activity of complex III and IV. Taken together, our results point out that the Aβ toxicity mechanism involves an oxidative stress induction by increasing ROS production into the mitochondria, where Cta1 and Sod2 play a crucial role in the regulation of the redox balance. J. Cell. Biochem. 118: 1442–1452, 2017. © 2016 Wiley Periodicals, Inc.
The temporal primacy of self-related stimuli and negative stimuli: an ERP-based comparative study

ABSTRACT Numerous studies have shown there exist attention biases for self-related and negative stimuli. Few studies, however, have been carried out to compare the effects of such stimuli on the neural mechanisms of early attentional alertness and subsequent cognitive processing. The purpose of the present study was to examine the temporal primacy of both self-related stimuli and negative stimuli in the neurophysiologic level. In a modified oddball task, event-related potentials of the deviant stimuli (i.e., self-face, negative face and neutral face) were recorded. Results revealed that larger P2 amplitudes were elicited by self-related and negative stimuli than by neutral stimuli. Negative stimuli, however, elicited shorter P2 latencies than self-related and neutral stimuli. As for the N2 component, self-related and negative stimuli elicited smaller amplitudes and shorter latencies than neutral stimuli, but otherwise did not differ. Self-related stimuli also elicited larger P3 and late positive component (LPC) amplitudes than negative and neutral stimuli. The pattern of results suggests that the primacy of negative stimuli occurred at an early attention stage of processing, while the primacy of self-related stimuli occurred at the subsequent cognitive evaluation and memory stage.
Preliminary Development of a Wearable Device for Dynamic Pressure Measurement in Garments

During activity, the body’s limbs experience significant anthropometrical changes as muscles and tendons exert force for motion and stability. This dynamic motion is of interest to sports compression garment manufacturers who seek to enhance sports performance through gradient compression garment design. Existing devices for measuring garment pressure are generally not well suited to dynamic pressure measurement during sports activities due to limited portability, memory, communication and power capacity. A wearable wireless monitoring device was constructed, which included six 18mm diameter low profile pressure sensors that were placed on the body at various positions, e.g. on the calf, thigh, and buttocks regions, to sense garment pressure in the range of 5 – 50mmHg. The accuracy and precision of the wearable dynamic pressure monitoring device was explored using a series of step changes in pressure effected through the placement of a series of known masses. Similar tests were also conducted with the Kikuhime TM and PicoPress TM for comparison. Further tests to explore the performance of the wearable dynamic pressure monitoring device to monitor changes in pressure between a subject and garment during various activities were also performed. The performance of the wearable dynamic pressure monitoring device is discussed in terms of portability, dynamic response, accuracy, precision, resolution and general utility. It was generally found to be acceptable for further field studies. Wireless dynamic pressure monitoring devices represent a tool that could be utilised to help further understand and characterise dynamic compression in various sports activities. Such a device would enable functional testing and provide valuable information on dynamic compression values and the physiological efficacy of gradient compression garment design. © 2009 Published by Elsevier Ltd.
Imaging analysis of the interface between osteoblasts and microrough surfaces of laser‐sintered titanium alloy constructs

Previous work using focused ion beam (FIB) analysis of osteoblasts on smooth and microrough Ti surfaces showed that the average cell aspect ratio and distance from the surface are greater on the rough surface. In order to better interrogate the relationship between individual cells and their substrate using multiple imaging modalities, we developed a method that tracks the same cell across confocal laser scanning microscopy (CLSM) to correlate surface microroughness with cell morphology and cytoskeleton; scanning electron microscopy (SEM) to provide higher resolution for observation of nanoroughness as well as chemical mapping via energy dispersive X‐ray spectroscopy; and transmission electron microscopy (TEM) for high‐resolution imaging. FIB was used to prepare thin sections of the cell‐material interface for TEM, or for three‐dimensional electron tomography. Cells were cultured on laser‐sintered Ti‐6Al‐4V substrates with polished or etched surfaces. Direct cell to surface attachments were observed across surfaces, though bridging across macroscale surface features occurred on rough substrates. Our results show that surface roughness, cell cytoskeleton and gross morphology can be correlated with the cell‐material cross‐sectional interface at the single cell level across multiple high‐resolution imaging modalities. This work provides a platform method for further investigating mechanisms of the cell‐material interface.