Miracle-dz/UniFAR-FTUs huggingface dataset:
The Probe Profile and Lateral Resolution of Scanning Transmission Electron Microscopy of Thick Specimens

Abstract Lateral profiles of the electron probe of scanning transmission electron microscopy (STEM) were simulated at different vertical positions in a micrometers-thick carbon sample. The simulations were carried out using the Monte Carlo method in CASINO software. A model was developed to fit the probe profiles. The model consisted of the sum of a Gaussian function describing the central peak of the profile and two exponential decay functions describing the tail of the profile. Calculations were performed to investigate the fraction of unscattered electrons as a function of the vertical position of the probe in the sample. Line scans were also simulated over gold nanoparticles at the bottom of a carbon film to calculate the achievable resolution as a function of the sample thickness and the number of electrons. The resolution was shown to be noise limited for film thicknesses less than 1 μm. Probe broadening limited the resolution for thicker films. The validity of the simulation method was verified by comparing simulated data with experimental data. The simulation method can be used as quantitative method to predict STEM performance or to interpret STEM images of thick specimens.
Characterizing freezing of gait in Parkinson's disease: Models of an episodic phenomenon

Freezing of gait (FOG) is a very disabling and common gait disorder in Parkinson's disease (PD). The first aim of this article was to provide a methodological and critical review of the most common research approach to understand FOG, ie, comparing the behavior of freezers with that of non‐freezers. The review demonstrates that studies often fall short in clearly defining the freezer\non‐freezer groups and in controlling for disease severity and other confounders. These problems complicate data interpretation on FOG. The second aim of this article was to summarize the literature on the potential mechanisms behind the episodic nature of FOG in the following four models: (1) The threshold model assumes that FOG occurs when the accumulation of various motor deficits reinforce each other to a point of motor breakdown; (2) the interference model proposes that FOG represents an inability to deal with concurrent cognitive, limbic, and motor input, causing an interruption of locomotion; (3) the cognitive model views FOG as induced by a failure to process response conflict, leading to behavioral indecision; and (4) the decoupling model sees FOG as a disconnection between preparatory programming and the intended motor response as a result of which automatic movement generation gets stuck. These four theoretical premises are still incomplete and do not fully explain FOG. The depletion of motor and cognitive reserves and an increasingly complex response to levodopa with disease progression will also have an impact on the emergence of FOG episodes. © 2013 International Parkinson and Movement Disorder Society
Evaluation of potential GPRS 900/1800-MHz and WCDMA 1900-MHz interference to consumer electronics

This study assessed the potential for interference to consumer electronics from radio frequency (RF) fields radiated by general packet radio service (GPRS) 900/1800-MHz and wideband code division multiple access (WCDMA) 1900-MHz handsets. The study was enhanced by additional testing with fields that were characteristic of radio transmissions from GSM 900/1800-MHz handsets and 900/1800-MHz fields that comply with the requirements of the international immunity standard to RF fields, IEC 61000-4-3. Four examples of consumer electronics were tested-a television, radio, CD player, and telephone. Generally, each device exhibited some form of interference at most of the test field levels (1, 3, 10, and 30 V/m). GPRS/GSM 1800-MHz and WCDMA signals never caused interference to any device at 1 V/m. The IEC 61000-4-3-specified test signal consistently produced more audio/visual interference than GPRS- or GSM-type signals at the same test frequency and carrier field strength level. Audio/visual interference produced by WCDMA signals was generally lower than that produced by GPRS. These results, combined with the inherently lower maximum output power of WCDMA, indicate that WCDMA will usually pose a lower risk of interference compared with GPRS for similar separation distances between handsets and common items of consumer electronics.
Cerebral Electromagnetic Activity in the Subdelta Range

The frequency range between 0.1 and 0.9 Hz was investigated with magnetoelectroencephalography-EEG coregistration in 10 adult patients with epilepsy and five children with other neurologic conditions. In all instances, a dominant rhythm between 0.2 and 0.4 Hz could be observed in the waking and sleeping states. It showed a waxing and waning quality and was unrelated to eye opening or closing but increased in amplitude during sleep. The maximum was usually in the occipital areas but occasionally in the frontal regions. The rhythm was more persistent and better seen in the magnetoelectroencephalogram, but subdelta activity was also discernible in the EEG. The magnetoelectroencephalographic rhythmicity and frequency suggested possible respiration artifact. Two normal control subjects were therefore investigated by electroencephalography while respirations were monitored. A clear relation to respiration was established. It persisted during breath-holding, albeit at lower amplitude. Larger amplitude transients occurred before and at the cessation of breath-holding as well as hyperventilation. An observed frequency increase before voluntary hyperventilation suggests a relation to the readiness potential and event-related desynchronization as well as synchronization. Subdelta frequencies, which can be readily recorded without special DC amplifiers, provide additional information for clinical as well as research data. They may also be an interface between autonomic and voluntary functions, especially in regard to respiration.
Modeling the utilization of starch by activated sludge for simultaneous substrate storage and microbial growth

This paper presents a mechanistic model incorporating microbial growth on external substrate with simultaneous formation of storage biopolymers (activated sludge model for growth and storage‐ASMGS) for the utilization of starch by activated sludge. Model description and calibration utilized experimental data of an SBR fed with particulate native potato starch (NPS) and soluble starch (SolS) selected as model substrates. The fate of starch was monitored in a cycle together with glycogen and oxygen uptake rate (OUR) profiles. In the experiments, glycogen formation was significantly lower than predicted by total conversion of starch to glycogen, justifying the need to account for primary growth on starch. The proposed model basically modified Activated Sludge Model No.3 (ASM3), to include adsorption of starch, its hydrolysis and simultaneous growth and glycogen formation using the hydrolysis products, which was mainly maltose. Model simulations indicated hydrolysis of the adsorbed starch as the rate limiting process. The proposed model calibrated well the fate of all major model components, namely, starch, glycogen, and OUR. Particulate NPS and SolS were hydrolyzed with similar rates; however, primary and secondary growth processes on SolS were more efficient, with higher yields, due to the more easily utilizable products of SolS, both in terms of extracellular hydrolysis and of stored poly‐glucose. Modeling with ASM3, assuming starch as either readily or slowly biodegradable, did not provide an equally acceptable fit for the glycogen and OUR curves; supporting the need to consider primary growth together with storage as defined in the proposed model. © 2006 Wiley Periodicals, Inc.
Proinflammatory Role of Monocyte-Derived CX3CR1int Macrophages in Helicobacter hepaticus-Induced Colitis

ABSTRACT Cells of the monocyte/macrophage lineage play important roles in the pathogenesis of inflammatory bowel diseases, but they are also present in the normal healthy intestine, where they are critical for maintaining homeostasis. It has been unclear whether the proinflammatory roles of intestinal macrophages reflect altered behavior of the existing resident cells, or whether they involve recruitment of a distinct cell type. Here, we have explored these ideas using the model of colitis induced by Helicobacter hepaticus in the context of neutralization or deletion of interleukin-10 (IL-10). Granulocytes and monocytes made up most of the inflammatory myeloid infiltrates found in the colon of H. hepaticus-infected colitic mice, rising to a peak within 2 weeks of H. hepaticus inoculation but taking several months to resolve completely. The inflammatory response was dependent on the combined presence of H. hepaticus and absence of IL-10 and was accompanied by increased production of inflammatory mediators such as IL-1β, tumor necrosis factor alpha (TNF-α), IL-6, and IL-23p19 by infiltrating myeloid cells, mostly relatively immature cells of the macrophage lineage that express intermediate levels of CX3CR1. In contrast, the population of mature CX3CR1hi macrophages did not expand as markedly during colitis, and these cells made little contribution to inflammatory mediator production. Taking into account their numerical dominance in the myeloid compartment, we conclude that newly recruited monocytes are the main source of proinflammatory mediators in colitis induced in the absence of IL-10 signaling and that altered behavior of mature macrophages is not a major component of this pathology.
Suppression of Wnt Signaling by the Green Tea Compound (–)-Epigallocatechin 3-Gallate (EGCG) in Invasive Breast Cancer Cells

Genetic and biochemical de-regulation of Wnt signaling is correlated with breast and other cancers. Our goal was to identify compounds that block Wnt signaling as a first step toward investigating new strategies for suppression of invasive and other breast cancers. In a limited phytonutrient screen, EGCG ((–)-epigallocatechin 3-gallate), the major phytochemical in green tea, emerged as an intriguing candidate. Epidemiological studies have associated green tea consumption with reduced recurrence of invasive and other breast cancers. Wnt signaling was inhibited by EGCG in a dose-dependent manner in breast cancer cells. The apparent mechanism targeted the HBP1 transcriptional repressor, which we had previously characterized as a suppressor of Wnt signaling. EGCG treatment induced HBP1 transcriptional repressor levels through an increase in HBP1 mRNA stability, but not transcriptional initiation. To test functionality, DNA-based short hairpin RNA (shRNA) was used to knockdown the endogenous HBP1 gene. Consistently, the HBP1 knockdown lines had reduced sensitivity to EGCG in the suppression of Wnt signaling and of a target gene (c-MYC). Because our ongoing studies clinically link abrogation of HBP1 with invasive breast cancer, we tested if EGCG also regulated biological functions associated with de-regulated Wnt signaling and with invasive breast cancer. EGCG reduced both breast cancer cell tumorigenic proliferation and invasiveness in an HBP1-dependent manner. Together, the emerging mechanism is that EGCG blocks Wnt signaling by inducing the HBP1 transcriptional repressor and inhibits aspects of invasive breast cancer. These studies provide a framework for considering future studies in breast cancer treatment and prevention.
Apparent Diffusion Coefficient Decreases and Magnetic Resonance Imaging Perfusion Parameters are Associated in Ischemic Tissue of Acute Stroke Patients

Perfusion-and diffusion-weighted magnetic resonance imaging scans are thought to allow the characterization of tissue at risk of infarction. The authors tested the hypothesis that the apparent diffusion coefficient (ADC) decrease should be associated with the severity of the perfusion deficit in ischemic tissue of acute stroke patients. Perfusion-and diffusion-weighted scans were performed in 11 patients with sudden onset of neurologic deficits within the last 6 hours and T2-weighted magnetic resonance imaging scans were obtained after 6 days. Parameter images of the maximum of the contrast agent concentration, time to peak, relative cerebral blood volume, relative cerebral blood flow, and relative mean transit time were computed from the perfusion-weighted data. A threshold function was used to identify tissue volumes with stepwise ADC decreases. An onionlike distribution of successively decreasing ADC values was found, with the lowest ADC in the center of the ischemic region. Correspondingly, tissue perfusion decreased progressively from the periphery toward the ischemic core. This effect was most pronounced in the time-to-peak maps, with a linear association between ADC decrease and time-to-peak increase. Apparent diffusion coefficient values decreased from the periphery toward the ischemic core, and this distribution of ADC values was strongly associated with the severity of the perfusion deficit.
Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers

Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria, Chloroflexi, and Firmicutes increased whereas Cyanobacteria, β-proteobacteria, and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils.
Occupational radiation exposure from C arm fluoroscopy during common orthopaedic surgical procedures and its prevention.

BACKGROUND Image intensifiers have become popular due to the concept of minimally invasive surgeries leading to decreasing invasiveness, decreased operative time, and less morbidity. The drawback, however, is an increased risk of radiation exposure to surgeon, patient and theatre staff. These exposures have been of concern due to their potential ability to produce biological effects. The present study was embarked upon to analyse the amount of radiation received by orthopedic surgeons in India using standard precautionary measures and also to bring awareness about the use of image intensifier safety in everyday practice. MATERIALS AND METHODS Twelve right-handed male orthopedic surgeons (4 senior consultants, 5 junior consultants and 3 residents) were included in a three month prospective study for radiation exposure measurement with adequate protection measures in all procedures requiring C Arm fluoroscopy. Each surgeon was provided with 5 Thermo Luminescent Dosimeter (TLD) badges which were tagged at the level of neck, chest, gonads and both wrists. Operative time and exposure time of each procedure was recorded. Exposure dose of each badge at the end of the study was obtained and the results were analysed. RESULTS Mean radiation exposure to all the parts were well within permissible limits. There was a significantly positive correlation between the exposure time and the exposure dose for the left wrist (r=0.735, p<0.01) and right wrist (r=0.58, p<0.05). The dominant hand had the maximum exposure overall. CONCLUSION Orthopaedic surgeons are not classified radiation workers. The mean exposure doses to all parts of the body were well within permissible limits. Nothing conclusive, however, can be said about the stochastic effects (chance effects like cancers). Any amount of radiation taken is bound to pose an additional occupational hazard. It is thus desirable that radiation safety precautions should be taken and exposures regularly monitored with at least one dosimeter for monitoring the whole-body dose.
Effects of Interrupted Wetness Periods on Conidial Germination, Germ Tube Elongation and Infection Periods of Botryosphaeria dothidea Causing Apple White Rot

Responses of Botryosphaeria dothidea to interrupted wetness periods were investigated under in vivo and in vitro conditions. Conidia of B. dothidea were allowed to germinate on apple fruits under wetting condition at 25ºC for 5 hr. They were air-dried for 0, 1, 2 or 4 hr, and then rewetted at 25ºC for 5 hr. Following an initial wetness period of 5 hr, 83% of the conidia germinated. The percent conidial germination increased to 96% when wetting was extended continuously another 5 hr. However, no further conidial germination was observed when wetting was interrupted by dry periods of 1, 2 and 4 hr, resulting in 83, 81 and 82%, respectively. The mean length of the germ tubes was 37 μm after 5 hr of wetting and elongated to 157 μm after 10 hr of continuous wetting. On the other hand, interruption of wetting by a dry period of 1 hr or longer after the 5 hr of initial wetting arrested the germ tube elongation at approximately 42 μm long. Prolonged rewetting up to 40 hr did not restore germ tube elongation on slide glasses under substrate treatments. Model simulation using weather data sets revealed that ending infection periods by a dry period of at least 1 hr decreased the daily infection periods, avoiding the overestimation of infection warning. This information can be incorpo- rated into infection models for scheduling fungicide sprays to control apple white rot with fewer fungicide applications.
Monotic Versus Dichotic Multiple-Stimulus Auditory Steady State Responses in Young Children

In their recent study on infant multiple auditory steady state responses (ASSR), the authors found that ASSR amplitudes unexpectedly decreased when switching from 1-ear stimulation to 2-ear stimulation, a result not present in adults. In addition, residual EEG noise levels increased in the 2-ear condition. In the present study, to determine whether to use 1-ear or 2-ear multiple ASSR Protocols clinically, the authors tested a new group of 19 young children to determine whether these unexpected findings could be replicated. ASSR amplitude and EEG noise were compared for 1-ear (4 stimuli) versus 2-ear (8 stimuli) multiple stimuli presented at 60 dBHL. Results indicated a small but significant decrease in amplitudes going from 1-ear (40.1 nV) to 2-ear (37.9 nV) multiple stimuli. EEG noise was not significantly different between the 2 conditions. Despite small amplitude decreases, the 2-ear stimulus condition was more efficient for infants and young children with normal hearing.
The Eighth FIII Domain of Human Fibronectin Promotes Integrin α5β1 Binding via Stabilization of the Ninth FIII Domain*

Binding of the extracellular matrix molecule fibronectin to the integrin receptor α5β1 elicits downstream signaling pathways that modulate cell function. Fibronectin-α5β1 interaction occurs via the conserved RGD sequence in the tenth FIII (FIII10) domain of fibronectin. A synergistic site containing the sequence PHSRN in the adjacent FIII9 domain has also been identified. Here we investigate the function of the eighth FIII domain in integrin-mediated cell adhesion using a wide range of methods, including biochemical, biological, and biophysical assays of integrin binding, cell adhesion, and protein denaturation. Mutation of the FIII9 synergistic site (PHSRN to PHAAA) in FIII9-10 reduced the binding activity for integrin α5β1 to levels observed for FIII10 alone, but the corresponding mutant in FIII8-9-10 showed no loss of binding activity. Cell adhesion assays also demonstrated enhanced functional activity of constructs containing FIII8. Equilibrium chemical denaturation studies indicated that FIII8 confers conformational stability upon FIII9, but only if the exposed loops, PHSRN and VKNEED on FIII9 and FIII8, respectively, are intact. These results demonstrate that the loss of integrin binding activity, observed upon alteration of the PHSRN synergistic site of FIII9-10, results partly from a loss of conformational stability of FIII9. Our data suggest a mechanism for integrin α5β1-fibronectin interaction, which in addition to the primary RGD binding event, involves a conformation-sensitive scanning by the integrin for accessible sites on the ligand, whereupon full activation of downstream signaling occurs.
Antiproliferative effects of heparin on vascular smooth muscle cells are reversed by epidermal growth factor

Heparin and related glycosaminoglycans are potent inhibitors of both in vivo and in vitro smooth muscle cell (SMC) proliferation. We have found that epidermal growth factor (EGF) reverses the antiproliferative effects of heparin. Other known SMC mitogens, including platelet‐derived growth factor (PDGF), insulin‐like growth factor‐1 (IGF‐1), and thrombin, were unable to prevent heparin action. The EGF specificity was further demonstrated by developing a biological growth assay in which EGF or PDGF, at concentrations as low as 1 ng/ml, stimulated SMC growth in the absence of other serum components. Under these conditions, EGF, but not PDGF, suppressed heparin inhibition as well. The ability of EGF to reverse heparin inhibition was only observed when mitogen and glycosaminoglycan were added to SMC at similar times. If SMC were pretreated with heparin for 48 hours prior to EGF addition, the protective effects of EGF were lost. Heparin did not directly prevent 125I‐EGF or platelet‐derived EGF‐like peptides from binding to the EGF receptor on SMC. However, cultures that were pretreated with heparin for 48 hours bound 49% less 125I‐EGF than cultures that had been pretreated with the mucopolysac‐charide for only 2 hours or that had not been preexposed to heparin. In previous studies, we have established that heparin exerts its maximal inhibitory activity after a 48‐hour treatment of SMC (Reilly et al. 1986). Taken together, these data suggest that heparin may exert its antiproliferative potential by slowly and specifically altering SMC response to EGF‐like mitogens of platelet origin.