Miracle-dz/UniFAR-FTUs huggingface dataset:
Metabolic engineering of Escherichia coli to produce succinate from soybean hydrolysate under anaerobic conditions

It is of great economic interest to produce succinate from low‐grade carbon sources, which can enhance the competitiveness of the biological route. In this study, succinate producer Escherichia coli CT550/pHL413KF1 was further engineered to efficiently use the mixed sugars from non‐food based soybean hydrolysate to produce succinate under anaerobic conditions. Since many common E. coli strains fail to use galactose anaerobically even if they can use it aerobically, the glucose, and galactose related sugar transporters were deactivated individually and evaluated. The PTS system was found to be important for utilization of mixed sugars, and galactose uptake was activated by deactivating ptsG. In the ptsG− strain, glucose, and galactose were used simultaneously. Glucose was assimilated mainly through the mannose PTS system while galactose was transferred mainly through GalP in a ptsG− strain. A new succinate producing strain, FZ591C which can efficiently produce succinate from the mixed sugars present in soybean hydrolysate was constructed by integration of the high succinate yield producing module and the galactose utilization module into the chromosome of the CT550 ptsG− strain. The succinate yield reached 1.64 mol/mol hexose consumed (95% of maximum theoretical yield) when a mixed sugars feedstock was used as a carbon source. Based on the three monitored sugars, a nominal succinate yield of 1.95 mol/mol was observed as the strain can apparently also use some other minor sugars in the hydrolysate. In this study, we demonstrate that FZ591C can use soybean hydrolysate as an inexpensive carbon source for high yield succinate production under anaerobic conditions, giving it the potential for industrial application.
Performance of Calculated and Directly Measured Low-Density Lipoprotein Cholesterol in a Pediatric Population

Objectives An assessment of methods for the accurate measurement of low-density lipoprotein cholesterol (LDL-C) at decreased concentrations has not yet been carried out. We evaluated the performance of the Friedewald equation, a direct enzymatic assay, and a novel equation for determining LDL-C levels in a pediatric population with elevated triglycerides and reduced LDL-C levels. Methods LDL-C concentrations of 127 pediatric patients were determined by the Friedewald equation, a direct enzymatic assay, and a novel equation. The bias of each approach was assessed at selected LDL-C cutoffs and after stratifying samples by triglyceride content. The concordance of each approach, relative to the reference method, was determined at LDL-C cut-points of less than 70, 70 to 99, and 100 to 129 mg/dL. Results The Friedewald equation substantially underestimated pediatric LDL-C concentrations below 100 mg/dL in the presence of elevated triglycerides. The Ortho Clinical Diagnostics (Raritan, NJ) direct LDL assay was positively biased at low LDL-C levels. The novel equation most effectively reduced the bias of the Friedewald equation at all LDL-C concentrations and increased the concordance of sample classification to the reference method. Conclusions The novel equation should be used for accurate measurement of pediatric LDL-C when the concentration is below 100 mg/dL in the presence of elevated triglycerides (150-399 mg/dL).
Evaluation of Cerebral White Matter in Prelingually Deaf Children Using Diffusion Tensor Imaging

This study compared white matter development in prelingually deaf and normal-hearing children using a tract-based spatial statistics (TBSS) method. Diffusion tensor imaging (DTI) was performed in 21 prelingually deaf (DEAF group) and 20 normal-hearing (HEAR group) subjects aged from 1.7 to 7.7 years. Using TBSS, we evaluated the regions of significant difference in fractional anisotropy (FA) between the groups. Correlations between FA values and age in each group were also analyzed using voxel-wise correlation analyses on the TBSS skeleton. Lower FA values of the white matter tract of Heschl's gyrus, the inferior frontooccipital fasciculus, the uncinate fasciculus, the superior longitudinal fasciculus, and the forceps major were evident in the DEAF group compared with those in the HEAR group below 4 years of age, while the difference was not significant in older subjects. We also found that age-related development of the white matter tracts may continue until 8 years of age in deaf children. These results imply that development of the cerebral white matter tracts is delayed in prelingually deaf children.
Surgical treatment for isolated mitral valve endocarditis: a 16-year single-centre experience

OBJECTIVES Despite progress in management, mitral valve endocarditis (MVE) is still a life-threatening disease. We report our experience in surgical treatment of infective isolated MVE. METHODS A total of 140 operations in 128 patients for MVE performed between January 2000 and December 2015 were included in a retrospective study. There were 109 (78%) operations for native and 31 (22%) operations for prosthetic valve endocarditis. Preoperative and postoperative characteristics and mortality of patients were registered. Cox regression identified factors associated with mortality. Mean follow-up period was 68 months (range 1-168 months) and 100% complete. RESULTS There were 13 deaths within 30 days after the 140 operations (9%). Severe perioperative complications occurred in 59 (42%) operations. Overall cumulative survival was 73% ± 4 at 5 years and 62 ± 5% at 10 years after the first operation. Age, diabetes, EuroSCORE II and perivalvular abscess were independent predictors for long-term mortality. Valve repair was performed in 76 (54%) operations and replacement in 64 (46%) operations. Thirty-day mortality for repair was 1%, and 5-year and 10-year cumulative survival was 86 ± 4% and 77 ± 6%, respectively. In the replacement group the 30-day mortality was 19% and cumulative survival at 5 years and 10 years was 55 ± 7% and 41 ± 8%, respectively. Postoperative complications occurred in 21% and 67%, respectively, after operations for repair and replacement. Ten (8%) patients had 12 reoperations for recurrent endocarditis. CONCLUSIONS MVE requiring surgical treatment is a challenging disease with high hospital mortality after valve replacement. Mitral valve repair can be performed in suitable endocarditis patients with excellent results. Age, diabetes and EuroSCORE were independently associated with mortality in a multivariable model.
Molecular Biomarkers for Weight Control in Obese Individuals Subjected to a Multiphase Dietary Intervention

Context Although calorie restriction has proven beneficial for weight loss, long-term weight control is variable between individuals. Objective To identify biomarkers of successful weight control during a dietary intervention (DI). Design, Setting, and Participants Adipose tissue (AT) transcriptomes were compared between 21 obese individuals who either maintained weight loss or regained weight during the DI. Results were validated on 310 individuals from the same study using quantitative reverse transcription polymerase chain reaction and protein levels of potential circulating biomarkers measured by enzyme-linked immunosorbent assay. Intervention Individuals underwent 8 weeks of low-calorie diet, then 6 months of ad libitum diet. Outcome Measure Weight changes at the end of the DI. Results We evaluated six genes that had altered expression during DI, encode secreted proteins, and have not previously been implicated in weight control (EGFL6, FSTL3, CRYAB, TNMD, SPARC, IGFBP3), as well as genes for which baseline expression differed between those with good and poor weight control (ASPN, USP53). Changes in plasma concentrations of EGFL6, FSTL3, and CRYAB mirrored AT messenger RNA expression; all decreased during DI in individuals with good weight control. ASPN and USP53 had higher baseline expression in individuals who went on to have good weight control. Expression quantitative trait loci analysis found polymorphisms associated with expression levels of USP53 in AT. A regulatory network was identified in which transforming growth factor β1 (TGF-β1) was responsible for downregulation of certain genes during DI in good controllers. Interestingly, ASPN is a TGF-β1 inhibitor. Conclusions We found circulating biomarkers associated with weight control that could influence weight management strategies and genes that may be prognostic for successful weight control.
Soft shadows from extended light sources with penumbra deep shadow maps

This paper presents a new method of precomputing high-quality soft shadows that can be cast on a static scene as well as on dynamic objects added to that scene. The method efficiently merges the visibility computed from many shadow maps into a penumbra deep shadow map (PDSM) structure. The resulting structure effectively captures the changes of attenuation in each PDSM pixel, and therefore constitutes an accurate representation of light attenuation. By taking advantage of the visibility coherence, the method is able to store a compact representation of the visibility for every location within the field of view of the PDSM. Modern programmable graphics hardware technology is used by the method to cast real-time complex soft shadows.
Periodontal Disease Assessed Using Clinical Dental Measurements and Cancer Risk in the ARIC Study

Background While evidence is increasingly consistent with a positive association between periodontitis and cancer risk, most studies have relied on self-reported periodontitis. In this study, we prospectively evaluated the association of periodontal disease severity with cancer risk in black and white older adults in a cohort study that included a dental examination. Methods Included were 7466 participants in the Atherosclerosis Risk in Communities study cohort who at visit 4 (1996-1998) reported being edentulous or underwent the dental examination. Probing depth and gingival recession were measured at six sites on all teeth; these measurements were used to define periodontal disease severity. Incident cancers (n = 1648) and cancer deaths (n = 547) were ascertained during a median of 14.7 years of follow-up. All statistical tests were two-sided. Results An increased risk of total cancer (hazard ratio [HR] = 1.24, 95% confidence interval [CI] = 1.07 to 1.44, Ptrend = .004) was observed for severe periodontitis (>30% of sites with attachment loss >3 mm) compared with no/mild periodontitis (<10% of sites with attachment loss >3 mm), adjusting for smoking and other factors. Strong associations were observed for lung cancer (HR = 2.33, 95% CI = 1.51 to 3.60, Ptrend < .001), and elevated risks were noted for colorectal cancer for severe periodontitis, which were significant among never smokers (HR = 2.12, 95% CI = 1.00 to 4.47). Associations were generally weaker, or not apparent among black participants, except for lung and colorectal cancers, where associations were similar by race. No associations were observed for breast, prostate, or hematopoietic and lymphatic cancer risk. Conclusions This study provides additional evidence that cancer risk, especially for lung and colorectal cancer, is elevated in individuals with periodontitis. Additional research is needed to understand cancer site-specific and racial differences in findings.
[18F]FDG positron emission tomography in patients presenting with suspicion of giant cell arteritis—lessons from a vasculitis clinic

Aims The usefulness of [18F] fluorodeoxyglucose-positron emission tomography/computed tomography ([18F]FDG-PET/CT) for diagnosing giant cell arteritis (GCA) has been previously reported. Yet, the interpretation of PET scans is not clear-cut. The present study aimed at determining the best method to analyse PET/CT in a large, real-life cohort of patients presenting with suspicion of GCA. Methods and results One hundred and three patients with clinical suspicion of GCA undergoing PET/CT between 2006 and 2012 were included. Clinical data were retrieved from patients' charts. PET/CT was categorized by visual scoring of the uptake and by the artery/liver standardized uptake values (SUV) ratios. Diagnosis of GCA was confirmed in 68 patients and excluded in 35 patients, which served as the controls. GCA patients were older (median age 75 vs. 68 years), and presented more often with ischaemic symptoms. The best discrimination between GCA patients and controls was achieved for PET/CT findings within the supra-aortic arteries (sensitivity 0.71, specificity 0.91 for a SUV/LE cut-off value of 1.0). Specificity of PET/CT for the aorta and the iliofemoral arteries was lower (<0.34). Visual scoring correlated poorly to SUV measurements (Kendall Tau-b 0.13-0.55) and had a lower diagnostic accuracy (sensitivity 0.77, specificity 0.75). Prednisone treatment for ≥10 days significantly reduced PET/CT sensitivity (P = 0.009). Conclusion SUV based analysis of PET/CT enhances diagnostic accuracy with best discrimination in the supra-aortic region, particularly in steroid naïve patients. For discrimination based on the aorta and the iliofemoral region, higher cut-off values have to be applied, resulting in lower sensitivities for diagnosing GCA.
Thermoregulation of Biofilm Formation in Burkholderia pseudomallei Is Disrupted by Mutation of a Putative Diguanylate Cyclase

ABSTRACT Burkholderia pseudomallei, a tier 1 select agent and the etiological agent of melioidosis, transitions from soil and aquatic environments to infect a variety of vertebrate and invertebrate hosts. During the transition from an environmental saprophyte to a mammalian pathogen, B. pseudomallei encounters and responds to rapidly changing environmental conditions. Environmental sensing systems that control cellular levels of cyclic di-GMP promote pathogen survival in diverse environments. Cyclic di-GMP controls biofilm production, virulence factors, and motility in many bacteria. This study is an evaluation of cyclic di-GMP-associated genes that are predicted to metabolize and interact with cyclic di-GMP as identified from the annotated genome of B. pseudomallei 1026b. Mutants containing transposon disruptions in each of these genes were characterized for biofilm formation and motility at two temperatures that reflect conditions that the bacteria encounter in the environment and during the infection of a mammalian host. Mutants with transposon insertions in a known phosphodiesterase (cdpA) and a predicted hydrolase (Bp1026b_I2285) gene exhibited decreased motility regardless of temperature. In contrast, the phenotypes exhibited by mutants with transposon insertion mutations in a predicted diguanylate cyclase gene (Bp1026b_II2523) were strikingly influenced by temperature and were dependent on a conserved GG(D/E)EF motif. The transposon insertion mutant exhibited enhanced biofilm formation at 37°C but impaired biofilm formation at 30°C. These studies illustrate the importance of studying behaviors regulated by cyclic di-GMP under varied environmental conditions in order to better understand cyclic di-GMP signaling in bacterial pathogens. IMPORTANCE This report evaluates predicted cyclic di-GMP binding and metabolic proteins from Burkholderia pseudomallei 1026b, a tier 1 select agent and the etiologic agent of melioidosis. Transposon insertion mutants with disruptions in each of the genes encoding these predicted proteins were characterized in order to identify key components of the B. pseudomallei cyclic di-GMP-signaling network. A predicted hydrolase and a phosphodiesterase that modulate swimming motility were identified, in addition to a diguanylate cyclase that modulates biofilm formation and motility in response to temperature. These studies warrant further evaluation of the contribution of cyclic di-GMP to melioidosis in the context of pathogen acquisition from environmental reservoirs and subsequent colonization, dissemination, and persistence within the host.
In situ embolism induction reveals vessel refilling in a natural aspen stand

Little is known about the ability of trees to recover hydraulic conductance (k) within a growing season by regrowth or refilling of embolized conduits. Recovery of k lost to drought or other causes would prevent chronic reductions in gas exchange and productivity. To test recovery ability we conducted a 2-year experiment (2014-15) on a cohort of aspen ramets (Populus tremuloides, Michx.). Whole-tree k was measured from mid-June through September from sapflow (Q) and pre-dawn and mid-day xylem pressure. We induced embolism in the treatment group with high air pressure delivered by a split pressure chamber sealed around the main trunk. Successful treatments reduced k and Q by 50% or more without causing rapid desiccation. The majority of trees recovered following treatment, rising to control levels of k and Q between 12 and 17 days. Failure to recover was correlated with drier climate conditions. The growing-season recovery of k was attributed to refilling of embolized vessels, based on the absence of diameter growth. Pre-dawn xylem pressures during recovery were similar to the threshold needed to passively collapse emboli. Successful recovery during the 2-year study was consistent with no reduction in cumulative Q or canopy area in treatment vs controls. However, non-recovering trees in 2014 exhibited lower basal area growth at the start of the 2015 growing season, suggesting a linkage between recovery ability and productivity. This study provides evidence for the potential of trees to recover xylem function by refilling during the growing season.
Mice lacking BCAS1, a novel myelin‐associated protein, display hypomyelination, schizophrenia‐like abnormal behaviors, and upregulation of inflammatory genes in the brain

The abnormal expression and function of myelin‐related proteins contribute to nervous system dysfunction associated with neuropsychiatric disorders; however, the underlying mechanism of this remains unclear. We found here that breast carcinoma amplified sequence 1 (BCAS1), a basic protein abundant in the brain, was expressed specifically in oligodendrocytes and Schwann cells, and that its expression level was decreased by demyelination. This suggests that BCAS1 is a novel myelin‐associated protein. BCAS1 knockout mice displayed schizophrenia‐like behavioral abnormalities and a tendency toward reduced anxiety‐like behaviors. Moreover, we found that the loss of BCAS1 specifically induced hypomyelination and the expression of inflammation‐related genes in the brain. These observations provide a novel insight into the functional link between oligodendrocytes and inflammation and/or abnormal behaviors.
Polarization, Partisanship and Junk News Consumption over Social Media in the US

What kinds of social media users read junk news? We examine the distribution of the most significant sources of junk news in the three months before President Donald Trump first State of the Union Address. Drawing on a list of sources that consistently publish political news and information that is extremist, sensationalist, conspiratorial, masked commentary, fake news and other forms of junk news, we find that the distribution of such content is unevenly spread across the ideological spectrum. We demonstrate that (1) on Twitter, a network of Trump supporters shares the widest range of known junk news sources and circulates more junk news than all the other groups put together; (2) on Facebook, extreme hard right pages, distinct from Republican pages, share the widest range of known junk news sources and circulate more junk news than all the other audiences put together; (3) on average, the audiences for junk news on Twitter share a wider range of known junk news sources than audiences on Facebook public pages.
Chronic Stress Alters Behavior in the Forced Swim Test and Underlying Neural Activity in Animals Exposed to Alcohol Prenatally: Sex- and Time-Dependent Effects

Dysregulation of the hypothalamic-pituitary-adrenal (HPA) stress response has been suggested to play a role in vulnerability to stress-related disorders, such as depression. Prenatal alcohol exposure (PAE) may result in HPA dysregulation, which in turn may predispose individuals to the effects of stress exposure throughout life, and increase their risk of developing depression compared to unexposed individuals. We examined the immediate and delayed effects of chronic unpredictable stress (CUS) in adulthood on behavior of PAE animals in the forced swim test (FST) and the neurocircuitry underlying behavioral, emotional, and stress regulation. Adult male and female offspring from PAE and control conditions were tested for 2 days in the FST, with testing initiated either 1 day (CUS-1; immediate) or 14 days (CUS-14; delayed) post-CUS. Following testing, c-fos mRNA expression of the medial prefrontal cortex (mPFC), amygdala, hippocampal formation, and the paraventricular nucleus of the hypothalamus was assessed. Our results indicate that PAE and CUS interact to differentially alter FST behaviors and neural activation of several brain areas in males and females, and effects may depend on whether testing is immediate or delayed post-CUS. PAE males showed decreased time immobile (Day 1 of FST) following immediate testing, while PAE females showed increased time immobile (Day 2 of FST) following delayed testing compared to their respective control counterparts. Moreover, in males, PAE decreased c-fos mRNA expression in the lateral and central nuclei of the amygdala in the non-CUS condition, and increased c-fos mRNA expression in the CA1 in the CUS-14 condition. By contrast in females, c-fos mRNA expression in the Cg1 was decreased in PAE animals (independent of CUS) and decreased in all mPFC subregions in CUS-14 animals (independent of prenatal treatment). Constrained principal component analysis, used to identify neural and behavioral networks, revealed that PAE altered the activation of these networks and modulated the effects of CUS on these networks in a sex- and time-dependent manner. This dysregulation of the neurocircuitry underlying behavioral, emotional and stress regulation, may ultimately contribute to an increased vulnerability to psychopathologies, such as depression, that are often observed following PAE.
A Semantic++ MapReduce Parallel Programming Model

Big data is playing a more and more important role in every area such as medical health, internet finance, culture and education etc. How to process these big data efficiently is a huge challenge. MapReduce is a good parallel programming language to process big data. However, it has lots of shortcomings. For example, it cannot process complex computing. It cannot suit real-time computing. In order to overcome these shortcomings of MapReduce and its variants, in this paper, we propose a Semantic++ MapReduce parallel programming model. This study includes the following parts. (1) Semantic++ MapReduce parallel programming model. It includes physical framework of semantic++ MapReduce parallel programming model and logic framework of semantic++ MapReduce parallel programming model; (2) Semantic++ extraction and management method for big data; (3) Semantic++ MapReduce parallel programming computing framework. It includes semantic++ map, semantic++ reduce and semantic++ shuffle; (4) Semantic++ MapReduce for multi-data centers. It includes basic framework of semantic++ MapReduce for multi-data centers and semantic++ MapReduce application framework for multi-data centers; (5) A Case Study of semantic++ MapReduce across multi-data centers.