Miracle-dz/UniFAR-FTUs huggingface dataset:
Three-Dimensional Model of Salmonella’s Needle Complex at Subnanometer Resolution

A cryo–electron microscopy structure of a bacterial secretion complex reveals threefold symmetry. Type III secretion systems (T3SSs) are essential virulence factors used by many Gram-negative bacteria to inject proteins that make eukaryotic host cells accessible to invasion. The T3SS core structure, the needle complex (NC), is a ~3.5 megadalton-sized, oligomeric, membrane-embedded complex. Analyzing cryo–electron microscopy images of top views of NCs or NC substructures from Salmonella typhimurium revealed a 24-fold symmetry for the inner rings and a 15-fold symmetry for the outer rings, giving an overall C3 symmetry. Local refinement and averaging showed the organization of the central core and allowed us to reconstruct a subnanometer composite structure of the NC, which together with confident docking of atomic structures reveal insights into its overall organization and structural requirements during assembly.
First Principles Investigation on the Structural, Electronic and Optical Properties of Amorphous Silica Glass

The structural, electronic, and optical properties of an amorphous SiO2 (a-SiO2) model is investigated by using first-principles calculation. Most research works used beta-cristobalite glass structure as a reference to amorphous silica structure. However, only the electronic properties were been presented without any link towards the optical properties. Here, we demonstrate simultaneous electronic and optical properties, which closely matched to a-SiO2 properties by generating small sample of amorphous quartz glass. Using the Rietveld refinement, amorphous silica structure was generated and optimized using density functional theory in CASTEP computer code. A thorough analysis of the amorphous quartz structure obtained from different thermal treatment was carried out. The structure of amorphous silica was validated with previous theoretical and experimental works. It is shown that small sample of amorphous silica have similar structural, electronic and optical properties with a larger sample. The calculated optical and electronic properties from the a-SiO2 glass match closely to previous theoretical and experimental data from others. The a-SiO2 band gap of 5.853 eV is found to be smaller than the experimental value of ~9 eV. This is due to the underestimation and assumption made in DFT. However, the band gap value is in good agreement with the other theoretical works. Apart from the absorption edge at around 6.5 eV, the refractive index is 1.5 at 0eV. Therefore, this atomic structure can served as a reference model for future research works on amorphous structures.
Changes of Physical Properties of Soils by Organic Material application

The objective of this study was to investigate the effect of organic materials (compost, straw, green manure, pig manure, seed production oil cake, and industrial by products including municipal sewage sludge, industrial sewage sludge, leather processing sludge, and alcohol fermentation processing sludge) on physical properties of soils in seven paddy and four upland fields with differential soil textures, sandy loam, loam, or clay loam, etc. The investigated physical parameters were bulk density (BD), air permeability (AP), macroporosity, hardness, shear resistance, frictional resistance, water stability aggregate (WSA), and Middleton's dispersion ratio. Except for coarse sandy loam field with weak structure, a decrease in BD and shear resistance, and an increase in macroporosity and AP in plots with applying organic materials compared to plots without applying organic materials appeared. In upland fields, the positive effect of organic materials on WSA, BD, and air permeability was higher than in paddy fields. The combined plot of NPK and compost had lower BD, hardness, and shear resistance, and higher macroporosity and WSA than plot with compost. Green manure had higher positive effect on physical properties of soils compared to other organic materials and the extent of positive effect had no significant correlation with soil organic matter content. Of industrial byproducts applied in coarse sandy loam soil under upland condition, municipal sewage sludge and pig manure compost had higher effect on increase of WSA than leather processing sludge and alcohol fermentation processing sludge. Unlike WSA, there were no significant differences between industrial byproduct types in other physical properties. in silty clay loam soil under the upland condition, straw had more positive effect on soil physical parameters than hairy vetch and pig manure. Therefore, different organic materials had differently active effect on physical parameters depending on types of soil and land use. Especially, it could be thought that well-decomposed organic materials have the advantage of an increase in organic matter content, while coarse organic materials of an increase in WSA.
Long-Term Outcomes after Imatinib Mesylate Discontinuation in Chronic Myeloid Leukemia Patients with Undetectable Minimal Residual Disease

Background: Imatinib mesylate (IM) discontinuation is under active investigation in chronic myeloid leukemia-chronic phase (CML-CP) patients with undetectable minimal residual disease (UMRD). However, limited data exist on the long-term outcomes following IM discontinuation in patients treated with frontline IM therapy. Methods: We consecutively enrolled patients with CML-CP who discontinued IM after achieving UMRD for ≥12 months between June 2009 and January 2013. Results: Nineteen patients (8 male, 11 female) were included. After IM discontinuation, 14 patients (74%) lost UMRD after a median of 4.0 months. Of the 14 patients with molecular relapses, 12 (86%) relapsed within the first 9 months after IM discontinuation and 2 (14%) relapsed at 20.5 and 22.8 months, respectively. No molecular relapse was observed after 2 years of IM discontinuation. With a median follow-up of 58.1 months (range 23.0-66.5), the estimated UMRD persistence rate at 5 years was 23.7%. IM was readministered in all patients with molecular relapse, and 12 patients (86%) reachieved UMRD at a median of 5.3 months. A high-risk Sokal score, delayed UMRD achievement and short-term IM therapy were significantly associated with molecular relapse. Conclusion: These findings suggest that IM discontinuation in patients who achieved UMRD after frontline IM therapy resulted in favorable long-term outcomes in terms of safety and feasibility.
Endoscopic tri-modal imaging is more effective than standard endoscopy in identifying early-stage neoplasia in Barrett's esophagus.

BACKGROUND & AIMS Endoscopic tri-modal imaging (ETMI) incorporates high-resolution endoscopy (HRE), autofluorescence imaging (AFI), and narrow band imaging (NBI). A recent uncontrolled study found that ETMI improved the detection of high-grade dysplasia (HGD) and early carcinoma (Ca) in Barrett's esophagus (BE). The aim was to compare ETMI with standard video endoscopy (SVE) for the detection of HGD/Ca with the use of a randomized cross-over design. METHODS Patients referred for work-up of inconspicuous HGD/Ca were eligible and underwent both SVE and ETMI in randomized order within an interval of 6-12 weeks. During ETMI, inspection with HRE was followed by AFI. Detected lesions were inspected in detail with NBI and biopsied, followed by random biopsies. During SVE, any visible lesion was biopsied followed by random biopsies. RESULTS Eighty-seven patients with BE underwent ETMI and SVE. No significant difference was observed in overall histologic yield between ETMI and SVE. ETMI had a significantly higher targeted yield compared with SVE because of AFI. However, the yield of targeted biopsies of ETMI was significantly inferior to the overall yield of SVE. Detailed inspection with NBI reduced the false-positive rate of HRE + AFI from 71% to 48% but misclassified 17% of HGD/Ca lesions as not suspicious. CONCLUSIONS ETMI statistically significant improves the targeted detection of HGD/Ca compared with SVE. Subsequent characterization of lesions with NBI appears to be of limited value. At this stage, ETMI cannot replace random biopsies for detection of lesions or targeted biopsies for characterization of lesions in a high-risk population.
Conscious Knowledge and Decision Making Under Ambiguity in Mild Cognitive Impairment and Alzheimer Disease

Older adults face many situations that require them to make important decisions. Decision making is a broad and complex construct. One conceptualization of decision making is the somatic marker hypothesis developed by Bechara et al.1 These authors state that the experience of emotion that operates unconsciously is tied to the decisionmaking processes. Empirical support for the somatic marker hypothesis is largely based on performance on the Iowa Gambling Task (IGT), a paradigm designed to stimulate decisions in terms of uncertainty (ie, implicit rules), reward, and punishment. According to Bechara et al,2 normal participants started to make the right selections in that card game before they had conscious knowledge that those were the best selections. In this task, healthy controls demonstrate an anticipatory electrodermal response (ie, unconscious and automatic bodily signals) to card selection; before selecting a risky choice, they show a physiological reaction indicating that they are bodily experiencing the anticipated risk even before conscious knowledge is available. Since the seminal work of Bechara et al,2 some authors have suggested that an explicit/analytical understanding can be sufficient to guide advantageous decision making measured by the IGT.3 In fact, healthy individuals with higher levels of conscious explicit knowledge of the advantageous strategy during the IGT also have better decision performance on the task2,3 and there was no significant association between level of explicit knowledge and development of anticipatory skin conductance responses for these individuals.2 Advantageous decision making therefore seems to be associated with 2 distinct, namely implicit and explicit, systems. Patients with mild cognitive impairments (MCI) and Alzheimer disease (AD) typically perform less well on decision-making tasks than do healthy controls.4,5 To the best of our knowledge, however, no study has directly compared decision-making performances of older adults with MCI and AD in ambiguous context. Furthermore, there are no data available on the relationship between conscious knowledge of contingencies and decision-making performances under conditions of uncertainty in AD and MCI. In the present study, we investigated these 2 questions and hypothesized that decision-making performances would be impaired in both MCI and AD patients. Explicit knowledge would be associated with advantageous decision-making performance under conditions of uncertainty in both AD and MCI.
Why do so many petals have conical epidermal cells?

BACKGROUND The conical epidermal cells found on the petals of most Angiosperm species are so widespread that they have been used as markers of petal identity, but their function has only been analysed in recent years. This review brings together diverse data on the role of these cells in pollination biology. SCOPE The published effects of conical cells on petal colour, petal reflexing, scent production, petal wettability and pollinator grip on the flower surface are considered. Of these factors, pollinator grip has been shown to be of most significance in the well-studied Antirrhinum majus/bumble-bee system. Published data on the relationship between epidermal cell morphology and floral temperature were limited, so an analysis of the effects of cell shape on floral temperature in Antirrhinum is presented here. Statistically significant warming by conical cells was not detected, although insignificant trends towards faster warming at dawn were found, and it was also found that flat-celled flowers could be warmer on warm days. The warming observed is less significant than that achieved by varying pigment content. However, the possibility that the effect of conical cells on temperature might be biologically significant in certain specific instances such as marginal habitats or weather conditions cannot be ruled out. CONCLUSIONS Conical epidermal cells can influence a diverse set of petal properties. The fitness benefits they provide to plants are likely to vary with pollinator and habitat, and models are now required to understand how these different factors interact.
Resveratrol Potentiates Vitamin D and Nuclear Receptor Signaling

The 1,25‐dihydroxyvitamin D3 (1,25D) hormone is derived from vitamin D generated in skin or obtained from the diet, and binds to and activates the vitamin D receptor (VDR) in target tissues including kidney, colon/small intestine, and bone/muscle. We tested resveratrol for its ability to modulate VDR signaling, using vitamin D responsive element (VDRE) and mammalian 2‐hybrid (M2H) transcriptional system technology. Via VDRE‐based assays in kidney, colon and myoblast cells, VDR‐mediated transcription was activated by resveratrol, and a cooperative effect on transactivation was observed with resveratrol plus 1,25D. The M2H assay revealed a modest, resveratrol‐induced dimerization of VDR with its retinoid X receptor (RXR) heteropartner. Cells treated with both resveratrol and 1,25D displayed synergistic stimulation of VDR–RXR heterodimerization, while resveratrol antagonized rexinoid‐mediated RXR‐RXR homodimerization. Increased transactivation in response to resveratrol was also observed with a subset of other nuclear receptors and their respective cognate responsive elements. Evaluation of wild‐type versus a ligand‐binding domain mutant VDR revealed that hormone‐responsiveness to 1,25D was severely depressed, while the response to resveratrol was only moderately attenuated. Moreover, radiolabeled 1,25D‐displacement assays demonstrated an increase in VDR‐bound 1,25D in the presence of resveratrol. Thus, resveratrol may affect VDR and other nuclear receptors indirectly, likely via the ability of resveratrol to: (1) potentiate 1,25D binding to VDR; (2) activate RXR; and/or (3) stimulate SIRT1, an enzyme known to deacetylate nuclear receptors. The results of this study elucidate a possible pathway for crosstalk between two nutritionally derived lipids, vitamin D and resveratrol, both of which converge on VDR signaling. J. Cell. Biochem. 116: 1130–1143, 2015. © 2014 Wiley Periodicals, Inc.
Sources of small-scale variation in the invertebrate communities of headwater streams

SUMMARY 1. Our objective was to investigate the associations between benthic macroinvertebrate communities and environmental factors described at three spatial scales: local, reach and catchment. Differences in these associations, because of local topography, were determined by categorising sites into those having a large or small ‘reach contributing area’ (RCA), which is the lateral area of land contributing surface and subsurface flow of water, nutrients, organic and inorganic materials to a stream reach independent of catchment size and upstream contributions, and created by local topography. 2. Twenty-three sites were sampled in the Lake Nipigon Forest in north-western Ontario. Local variables included hydrological metrics and stream morphology characteristics. Terrestrial reach and catchment variables included forest characteristics, topography and geomorphology. Invertebrates were identified and classified into functional feeding guilds. Canonical correspondence analysis and redundancy analysis were used to determine which variables contributed most to macro-invertebrate community structure and how the RCA influenced those associations. 3. Overall, local-scale variables explained most variation in taxonomic and functional community structure (51.6 and 59.1%). Catchment-scale variables explained more variation in the community (43.9 and 43.5%) than reach-scale variables. In sites with a large RCA, the reach-scale variables accounted for almost 10% more variability in taxonomic structure than the catchment-scale variables, and in sites with a small RCA, catchment-scale variables explained almost 23% more variation in feeding guild structure than reach-scale variables. 4. Topography was important at both the reach and the catchment scales. Variables at the reach scale most associated with invertebrate community tended to be related to forest cover, whereas important variables at the catchment scale were related to topography, wetlands and lakes. 5. The difference in associations between invertebrate communities and environmental factors based on RCA indicates the influence of local topography on the linkage between aquatic habitats and the surrounding terrestrial environment. Understanding how these linkages affect aquatic communities can help to develop more effective predictive models of invertebrate community and more prescriptive conservation and management strategies for small streams.
Smoking and mortality: A prospective study

The mortality experience of 68,153 men, 35 to 64 years of age, over a period representing 482,658 person‐years of observation during which 4,706 known deaths occurred is related to their cigarette smoking habits. The findings are compared to the several other prospective studies reported in recent years relating mortality to cigarette smoking. All studies are in essential agreement that cigarette smoking increases the risk for cancer of the mouth, larynx, esophagus, lung, kidney, and bladder. A few other tissue sites appear to carry increased risk of cancer as a result of cigarette smoking in one or another study but without unanimity. The risk gradient for lung cancer by age and amount of smoking increases in successive 10‐year age groups to be maximal at 55 to 64 years in our study. Other diseases related to cigarette smoking in this and other prospective studies are gastric ulcer, emphysema, aneurysm, general arteriosclerosis, and arteriosclerotic heart disease. The latter is especially important because of the large number of deaths involved. The relative risk gradient for arteriosclerotic heart disease by age and amount of cigarette smoking was found to be maximum in the youngest age group comprising men 35 to 44 years of age and lessens with increasing age. Future studies should be directed toward identifying other variables with which cigarette smoking interacts in those individuals developing disease.
Success rate of terbutaline in inhibiting preterm labor for 48 h

Abstract Objective: To determine terbutaline success rate in postponing preterm labor for 48 h and to identify factors associated with its efficacy, side effects, maternal and neonatal outcomes. Methods: A retrospective study analyzing data from pregnant women suffering from preterm labor who had received terbutaline for inhibition of labor from January 2007 to December 2013. Results: A total of 385 cases were analyzed; there were 321 cases (83.4%) delivered ≥48 h and 64 cases (16.6%) delivered before 48 h. The factors that affect the success rate of terbutaline administration in singleton pregnancy were cervical dilatation (ORs 0.37; 95% CI 0.18–0.79) and cervical effacement (ORs 0.36; 95% CI 0.17–0.75). The most common side effect of terbutaline was tachycardia (95.1%), but there were no serious cardiovascular events and maternal death. Mean neonatal birth weight was 2.294. 3 ± 638.4 g. Neonatal complications included respiratory distress syndrome (RDS) 16.2%, intraventricular hemorrhage (IVH) 1.4%, necrotizing enterocolitis (NEC) 0.7%, sepsis 5.3%, and neonatal death 0.9%. Conclusions: The success rate of terbutaline in treatment of preterm labor was high whereas side effects were tolerable. Neonatal outcome was good. The factors that significantly affect the success rate of terbutaline administration in singleton pregnancy were cervical dilatation and cervical effacement. Thus, terbutaline can be used safely for short-term treatment of preterm labor.
Investigation of residual hepatitis C virus in presumed recovered subjects

Recent studies have found hepatitis C virus (HCV) RNA in peripheral blood mononuclear cells (PBMCs) of the majority of presumed recovered subjects. We investigated this unexpected finding using samples from patients whose HCV RNA and anti‐HCV status had been serially confirmed. HCV RNA was detected in PBMCs from 66 of 67 chronic HCV carriers. Subpopulation analysis revealed that the viral load (log copies/106 cells) in B cells (4.14 ± 0.71) was higher than in total PBMCs (3.62 ± 0.71; P < 0.05), T cells (1.67 ± 0.88; P < 0.05), and non‐B/T cells (2.48 ± 1.15; P < 0.05). HCV negative‐strand RNA was not detected in PBMCs from any of 25 chronically infected patients. No residual viral RNA was detected in total PBMCs or plasma of 59 presumed recovered subjects (11 spontaneous and 48 treatment induced) using nested real‐time polymerase chain reaction with a detection limit of 2 copies/μg RNA (from ∼1 × 106 cells). PBMCs from 2 healthy HCV‐negative blood donors became HCV RNA positive, with B‐cell predominance, when mixed in vitro with HCV RNA–positive plasma, thus passively mimicking cells from chronic HCV carriers. No residual HCV was detected in liver or other tissues from 2 spontaneously recovered chimpanzees. Conclusion: (1) HCV RNA was detected in PBMCs of most chronic HCV carriers and was predominant in the B‐cell subpopulation; (2) HCV detected in PBMCs was in a nonreplicative form; (3) HCV passively adsorbed to PBMCs of healthy controls in vitro, becoming indistinguishable from PBMCs of chronic HCV carriers; and (4) residual HCV was not detected in plasma or PBMCs of any spontaneous or treatment‐recovered subjects or in chimpanzee liver, suggesting that the classic pattern of recovery from HCV infection is generally equivalent to viral eradication. (HEPATOLOGY 2013)
Oxidative stress parameters after combined fluoxetine and acetylsalicylic acid therapy in depressive patients

There are numerous reports indicating disturbed equilibrium between oxidative processes and antioxidative defense in patients with depression. Moreover, depressive patients are characterized by the presence of elements of an inflammatory process, which is one of the sources of reactive oxygen species (ROS). In view of the above, it was decided to study both the effect of fluoxetine monotherapy and that of fluoxetine co‐administered with acetylsalicylic acid on lipid peroxidation and antioxidative defense in patients with the first depressive episode in their life.
Auditory Space-Time Receptive Field Dynamics Revealed by Spherical White-Noise Analysis

Numerous studies have investigated the spatial sensitivity of cat auditory cortical neurons, but possible dynamic properties of the spatial receptive fields have been largely ignored. Given the considerable amount of evidence that implicates the primary auditory field in the neural pathways responsible for the perception of sound source location, a logical extension to earlier observations of spectrotemporal receptive fields, which characterize the dynamics of frequency tuning, is a description that uses sound source direction, rather than sound frequency, to examine the evolution of spatial tuning over time. The object of this study was to describe auditory space-time receptive field dynamics using a new method based on cross-correlational techniques and white-noise analysis in spherical auditory space. This resulted in a characterization of auditory receptive fields in two spherical dimensions of space (azimuth and elevation) plus a third dimension of time. Further analysis has revealed that spatial receptive fields of neurons in auditory cortex, like those in the visual system, are not static but can exhibit marked temporal dynamics. This might result, for example, in a neuron becoming selective for the direction and speed of moving auditory sound sources. Our results show that ∼14% of AI neurons evidence significant space-time interaction (inseparability).