Miracle-dz/UniFAR-FTUs huggingface dataset:
Super-resolution imaging of C-type lectin spatial rearrangement within the dendritic cell plasma membrane at fungal microbe contact sites

Dendritic cells express DC-SIGN and CD206, C-type lectins (CTLs) that bind a variety of pathogens and may facilitate pathogen uptake for subsequent antigen presentation. Both proteins form punctate membrane nanodomains (∼80 nm) on naïve cells. We analyzed the spatiotemporal distribution of CTLs following host-fungal particle contact using confocal microscopy and three distinct methods of cluster identification and measurement of receptor clusters in super-resolution datasets: DBSCAN, Pair Correlation and a custom implementation of the Getis spatial statistic. Quantitative analysis of confocal and super-resolution images demonstrated that CTL nanodomains become concentrated in the contact site relative to non-contact membrane after the first hour of exposure and established that this recruitment is sustained out to 4 h. DC-SIGN nanodomains in fungal contact sites exhibit a 70% area increase and a 38% decrease in interdomain separation. Contact site CD206 nanodomains possess 90% greater area and 42% lower interdomain separation relative to non-contact regions. Contact site CTL clusters appear as disk-shaped domains of approximately 150-175 nm in diameter. The increase in length scale of CTL nanostructure in contact sites suggests that the smaller nanodomains on resting membranes may merge during fungal recognition, or that they become packed closely enough to achieve sub-resolution inter-domain edge separations of <30 nm. This study provides evidence of local receptor spatial rearrangements on the nanoscale that occur in the plasma membrane upon pathogen binding and may direct important signaling interactions required to recognize and respond to the presence of a relatively large pathogen.
Lumbar Sympathectomy Increases Blood Flow in a Dog Model of Chronic Cauda Equina Compression

Objective: This study was designed to assess changes in blood flow of the dog cauda equina after lumbar sympathectomy using an experimental chronic cauda compression model. Methods: The cauda equina was compressed at 10 mm Hg with a plastic balloon in all animals (n = 12). One week later, bilateral lumbar sympathectomy was carried out in the LSX group (n = 7), and vessels of the cauda equina were thereafter observed for 90 minutes using a specially designed microscope supplied with a video camera. Five animals did not undergo sympathectomy and were used as controls. The volume of blood flow was calculated from two parameters: velocity (mm/s) and diameter (μm) of a vessel observed in each animal. Results: The increment in vessel diameter in the LSX group was pronounced at 30 and 45 minutes after sympathectomy compared with the control group (P < 0.05). Blood flow in the LSX group was increased at 30 minutes depending on dilation of the vessel diameter compared with the control group (P < 0.05). The velocity in the observed vessels remained unchanged throughout the measurements. Conclusions: These data suggest that lumbar sympathectomy could induce an increase in blood flow of the compressed cauda equina. As lumbar sympathetic block increases blood flow not only in the lower limbs but also in the cauda equina, it might be evaluated for a conservative treatment of intermittent claudication due to lumbar spinal canal stenosis.
Positive and Negative Coupling of the Metabotropic Glutamate Receptors to a G Protein–activated K+ Channel, GIRK, in Xenopus Oocytes

Metabotropic glutamate receptors (mGluRs) control intracellular signaling cascades through activation of G proteins. The inwardly rectifying K+ channel, GIRK, is activated by the βγ subunits of Gi proteins and is widely expressed in the brain. We investigated whether an interaction between mGluRs and GIRK is possible, using Xenopus oocytes expressing mGluRs and a cardiac/brain subunit of GIRK, GIRK1, with or without another brain subunit, GIRK2. mGluRs known to inhibit adenylyl cyclase (types 2, 3, 4, 6, and 7) activated the GIRK channel. The strongest response was observed with mGluR2; it was inhibited by pertussis toxin (PTX). This is consistent with the activation of GIRK by Gi/Go-coupled receptors. In contrast, mGluR1a and mGluR5 receptors known to activate phospholipase C, presumably via G proteins of the Gq class, inhibited the channel's activity. The inhibition was preceded by an initial weak activation, which was more prominent at higher levels of mGluR1a expression. The inhibition of GIRK activity by mGluR1a was suppressed by a broad-specificity protein kinase inhibitor, staurosporine, and by a specific protein kinase C (PKC) inhibitor, bis-indolylmaleimide, but not by PTX, Ca2+ chelation, or calphostin C. Thus, mGluR1a inhibits the GIRK channel primarily via a pathway involving activation of a PTX-insensitive G protein and, eventually, of a subtype of PKC, possibly PKC-μ. In contrast, the initial activation of GIRK1 caused by mGluR1a was suppressed by PTX but not by the protein kinase inhibitors. Thus, this activation probably results from a promiscuous coupling of mGluR1a to a Gi/Go protein. The observed modulations may be involved in the mGluRs' effects on neuronal excitability in the brain. Inhibition of GIRK by phospholipase C–activating mGluRs bears upon the problem of specificity of G protein (GIRK interaction) helping to explain why receptors coupled to Gq are inefficient in activating GIRK.
The Cfr rRNA Methyltransferase Confers Resistance to Phenicols, Lincosamides, Oxazolidinones, Pleuromutilins, and Streptogramin A Antibiotics

ABSTRACT A novel multidrug resistance phenotype mediated by the Cfr rRNA methyltransferase is observed in Staphylococcus aureus and Escherichia coli. The cfr gene has previously been identified as a phenicol and lincosamide resistance gene on plasmids isolated from Staphylococcus spp. of animal origin and recently shown to encode a methyltransferase that modifies 23S rRNA at A2503. Antimicrobial susceptibility testing shows that S. aureus and E. coli strains expressing the cfr gene exhibit elevated MICs to a number of chemically unrelated drugs. The phenotype is named PhLOPSA for resistance to the following drug classes: Phenicols, Lincosamides, Oxazolidinones, Pleuromutilins, and Streptogramin A antibiotics. Each of these five drug classes contains important antimicrobial agents that are currently used in human and/or veterinary medicine. We find that binding of the PhLOPSA drugs, which bind to overlapping sites at the peptidyl transferase center that abut nucleotide A2503, is perturbed upon Cfr-mediated methylation. Decreased drug binding to Cfr-methylated ribosomes has been confirmed by footprinting analysis. No other rRNA methyltransferase is known to confer resistance to five chemically distinct classes of antimicrobials. In addition, the findings described in this study represent the first report of a gene conferring transferable resistance to pleuromutilins and oxazolidinones.
Stop Signals Provide Cross Inhibition in Collective Decision-Making by Honeybee Swarms

Stop, Don't Go There Decision-making in complex brains requires the reaching of a consensus based on information relayed by multiple neurons. A similar situation occurs in the decision-making process of swarming bees, where multiple individuals relay information about suitable hive sites, but a single site is chosen by the swarm. Seeley et al. (p. 108, published online 8 December; see the Perspective by Niven ) show that consensus in this system is reached as information from scouting bees accumulates within the hive. Stop signals were given by scout bees from a particular site to those scout bees signaling from other sites. As the signals accumulate, scouting ceases and the bees prepare to swarm to the site that was best represented among the scouts. When this process was simulated, the results indicated that cross-inhibition among the bees functions similarly to that which occurs among neurons within complex brains. In both cases, such cross-inhibition prevents the overall system from coming to an impasse. Scout bees bring about nest-site decisions by targeting stop signals at bees with other candidate sites. Honeybee swarms and complex brains show many parallels in how they make decisions. In both, separate populations of units (bees or neurons) integrate noisy evidence for alternatives, and, when one population exceeds a threshold, the alternative it represents is chosen. We show that a key feature of a brain—cross inhibition between the evidence-accumulating populations—also exists in a swarm as it chooses its nesting site. Nest-site scouts send inhibitory stop signals to other scouts producing waggle dances, causing them to cease dancing, and each scout targets scouts’ reporting sites other than her own. An analytic model shows that cross inhibition between populations of scout bees increases the reliability of swarm decision-making by solving the problem of deadlock over equal sites.
DUSTY Mg ii ABSORBERS: IMPLICATIONS FOR THE GAMMA-RAY BURST/QUASAR INCIDENCE DISCREPANCY

There is nearly a factor of 4 difference in the number density of intervening Mg ii absorbers as determined from gamma-ray burst (GRB) and quasar lines of sight. We use a Monte Carlo simulation to test if a dust extinction bias can account for this discrepancy. We apply an empirically determined relationship between the dust column density and Mg ii rest equivalent width to simulated quasar sight lines and model the underlying number of quasars that must be present to explain the published magnitude distribution of Sloan Digital Sky Survey quasars. We find that an input Mg ii number density dn/dz of 0.273 ± 0.002 over the range 0.4 ⩽ z ⩽ 2.0 and with Mg ii equivalent width W0 ⩾ 1.0 Å accurately reproduces observed distributions. From this value, we conclude that a dust obstruction bias cannot be the sole cause of the observed discrepancy between GRB and quasar sight lines: this bias is likely to reduce the discrepancy only by ∼10%.
Influence of the cycle length on the production of PHA and polyglucose from glycerol by bacterial enrichments in sequencing batch reactors

PHA, a naturally occurring biopolymer produced by a wide range of microorganisms, is known for its applications as bioplastic. In recent years the use of agro‐industrial wastewater as substrate for PHA production by bacterial enrichments has attracted considerable research attention. Crude glycerol as generated during biodiesel production is a waste stream that due to its high organic matter content and low price could be an interesting substrate for PHA production. Previously we have demonstrated that when glycerol is used as substrate in a feast‐famine regime, PHA and polyglucose are simultaneously produced as storage polymers. The work described in this paper aimed at understanding the effect of the cycle length on the bacterial enrichment process with emphasis on the distribution of glycerol towards PHA and polyglucose. Two sequencing batch reactors where operated with the same hydraulic and biomass retention time. A short cycle length (6 h) favored polyglucose production over PHA, whereas at long cycle length (24 h) PHA was more favored. In both communities the same microorganism appeared dominating, suggesting a metabolic rather than a microbial competition response. Moreover, the presence of ammonium during polymer accumulation did not influence the maximum amount of PHA that was attained. Biotechnol. Bioeng. 2013;110: 3148–3155. © 2013 Wiley Periodicals, Inc.
An instruction-level energy model for embedded VLIW architectures

In this paper, an instruction-level energy model is proposed for the data-path of very long instruction word (VLIW) pipelined processors that can be used to provide accurate power consumption information during either an instruction-level simulation or power-oriented scheduling at compile time. The analytical model takes into account several software-level parameters (such as instruction ordering, pipeline stall probability, and instruction cache miss probability) as well as microarchitectural-level ones (such as pipeline stage power consumption per instruction) providing an efficient pipeline-aware instruction-level power estimation, whose accuracy is very close to those given by RT or gate-level simulations. The problem of instruction-level power characterization of a K-issue VLIW processor is O(N/sup 2K/) where N is the number of operations in the ISA and K is the number of parallel instructions composing the very long instruction. One of the advantages of the proposed model consists of reducing the complexity of the characterization problem to O(K/spl times/N/sup 2/). The proposed model has been used to characterize a four-issue VLIW core with a six-stage pipeline.
Incidence, Event Rates, and Early Outcome of Stroke in Dublin, Ireland: The North Dublin Population Stroke Study

Background and Purpose— The World Health Organization has emphasized the importance of international population-based data for unbiased surveillance of stroke incidence and outcome. To date, few such studies have been conducted using recommended gold-standard ascertainment methods. We conducted a large, population-based stroke study in Dublin, Ireland. Methods— Using gold-standard ascertainment methods, individuals with stroke and transient ischemic attack occurring over a 12-month period (December 1, 2005–November 30, 2006) in North Dublin were identified. Disability was assessed using the modified Rankin score and stroke severity (<72 hours) by the National Institutes of Health Stroke Scale. Stroke-related deaths were confirmed by review of medical files, death certificates, pathology, and coroner's records. Crude and standardized (to European and World Health Organization standard populations) rates of incidence, risk factors, severity, and early outcome (mortality, case-fatality, disability) were calculated, assuming a Poisson distribution for the number of events. Results— Seven hundred one patients with new stroke or transient ischemic attack were ascertained (485 first-ever stroke patients, 83 recurrent stroke patients, 133 first-ever transient ischemic attack patients). Crude frequency rates (all rates per 1000 person-years) were: 1.65 (95% CI, 1.5–1.79; first-ever stroke), 0.28 (95% CI, 0.22–0.35; recurrent stroke), and 0.45 (95% CI, 0.37–0.53; first-ever transient ischemic attack). Age-adjusted stroke rates were higher than those in 9 other recent population-based samples from high-income countries. High rates of subtype-specific risk factors were observed (atrial fibrillation, 31.3% and smoking, 29.1% in ischemic stroke; warfarin use, 21.2% in primary intracerebral hemorrhage; smoking, 53.9% in subarachnoid hemorrhage; P<0.01 for all compared with other subtypes). Compared with recent studies, 28-day case-fatality rates for primary intracerebral hemorrhage (41%; 95% CI, 29.2%–54.1%) and subarachnoid hemorrhage (46%; 95% CI, 28.8%–64.5%) were greater in Dublin. Conclusions— Using gold-standard methods for case ascertainment, we found high incidence rates of stroke in Dublin compared with those in similar high-income countries; this is likely explained in part by high rates of subtype-specific risk factors.
Temperature‐Dependence of the Rates of Reaction of Trifluoroacetic Acid with Criegee Intermediates

Abstract The rate coefficients for gas‐phase reaction of trifluoroacetic acid (TFA) with two Criegee intermediates, formaldehyde oxide and acetone oxide, decrease with increasing temperature in the range 240–340 K. The rate coefficients k(CH2OO + CF3COOH)=(3.4±0.3)×10−10 cm3 s−1 and k((CH3)2COO + CF3COOH)=(6.1±0.2)×10−10 cm3 s−1 at 294 K exceed estimates for collision‐limited values, suggesting rate enhancement by capture mechanisms because of the large permanent dipole moments of the two reactants. The observed temperature dependence is attributed to competitive stabilization of a pre‐reactive complex. Fits to a model incorporating this complex formation give k [cm3 s−1]=(3.8±2.6)×10−18 T2 exp((1620±180)/T) + 2.5×10−10 and k [cm3 s−1]=(4.9±4.1)×10−18 T2 exp((1620±230)/T) + 5.2×10−10 for the CH2OO + CF3COOH and (CH3)2COO + CF3COOH reactions, respectively. The consequences are explored for removal of TFA from the atmosphere by reaction with biogenic Criegee intermediates.
Autonomic Cardiac Regulation During Spontaneous Nocturnal Hypoglycemia in Patients With Type 1 Diabetes

OBJECTIVE Experimental clamp studies have suggested that hypoglycemia evokes a reduction of cardiac vagal control in patients with type 1 diabetes. However, there are limited data on the influence of spontaneous nocturnal hypoglycemia on cardiac autonomic regulation. RESEARCH DESIGN AND METHODS Adults with type 1 diabetes (n = 37) underwent continuous glucose monitoring via a subcutaneous sensor as well as recording of R-R interval or electrocardiogram for 3 nights. Heart rate (HR) variability was analyzed during periods of hypoglycemia (glucose <3.5 mmol/L) (minimum length of 20 min) and a control nonhypoglycemic period (glucose >3.9 mmol/L) of equal duration and at the same time of night. RESULTS The duration of hypoglycemic and control episodes (n = 18) ranged from 20 to 190 min (mean 71 min). HR (62 ± 7 vs. 63 ± 9 beats per min; P = 0.30) or the high-frequency component of HR power spectrum (2,002 ± 1,965 vs. 1,336 ± 1,506 ms2; P = 0.26) did not change during hypoglycemia. Hypoglycemia resulted in a significant decrease in the low-frequency component of HR variability (2,134 ± 1,635 vs. 1,169 ± 1,029 ms2, respectively; P = 0.006). The decline in the glucose concentration displayed a significant positive correlation with the decrease of the low-frequency component of HR variability (r = 0.48; P = 0.04). The latter was closely related to an increase in muscle sympathetic nerve activity recorded in 10 subjects during controlled sympathetic activation. CONCLUSIONS Spontaneous nocturnal hypoglycemia in patients with type 1 diabetes results in a reduction of the low-frequency component of HR, which is best explained by excessive sympathetic activation without a concomitant withdrawal of vagal outflow.
Semi-automatic object segmentation using colour invariance and Graph cuts

Conventional semi-automatic or interactive methods, which require a small amount of user inputs for region segmentation of objects, have obtained the best segmentation results. A new semi-automatic segmentation technique by using coloured scale-invariant feature transform (CSIFT) to extract seed pixels in Graph Cuts is introduced here. First, CSIFT is used to extract feature points of objects in the image. Then, a voting process is used to extract the matched points as object seeds. The detailed technique via s–t Graph Cuts has been presented, and a new segmentation energy cost function with two colour-invariant descriptors has been proposed: colour-name descriptor and colour-shade descriptor. The colour-name descriptor introduces high-level considerations resembling top-down intervention, and the colour-shade descriptor allows us to include physical consideration derived from the image formation model capturing gradual colour surface variations and provides congruencies in the presence of shadows and highlights in the segmentation. The experimental results prove that the proposed method provides high-quality segmentations with object details.
Optimal control of autonomous linear systems switched with a pre-assigned finite sequence

The paper deals with the optimal control of switched piecewise linear autonomous systems, where the objective is to minimize the performance index over an infinite time horizon. We assume that the switching sequence has a finite length and is pre-assigned, while the unknown switching times are the optimization parameters. We also assume that at each switch a jump in the state space may occur and that a cost may be associated to each switch. The optimal control for this class of systems takes the form of a state feedback, i.e., it is possible to identify a region of the state space such that an optimal switch should occur if and only if the present state belongs to this region. We show how such a region can be computed with a numerical procedure and show that, in the particular case in which the switching costs is null, the region is homogeneous.
Matrix Assessment of the Articular Cartilage Surface after Chondroplasty with the Holmium:Yttrium-Aluminum-Garnet Laser

A long-term in vivo study was performed to assess biochemical changes after laser repair of articular cartilage. Forty New Zealand White rabbits were sacrificed 26 weeks after undergoing an articular cartilage chondroplasty with use of a holmium:yttrium-aluminum-garnet laser at 0.8 joules per pulse and a rate of 10 Hz. Glycosaminoglycan content in the repaired tissue decreased significantly with both perpendicular (19.59 ± 5.6 μg hexosamin/mg of dry tissue) and tangential delivery (14.78 ± 4.5 μg/mg) compared with the sham-treated tissue (39.6 ± 5.0 μg/mg). Cellular viability was also significantly decreased. Sulfate incorporation was decreased to 203 ± 142 cpm/mg of dry cartilage in the tangential mode and 461 ± 209 cpm/mg in the tangential mode, compared with the sham at 1845 cpm/mg. Uptake of [3H]thymidine decreased to 463 ± 473 cpm/mg of dry tissue and 455 ± 170 cpm/mg in the tangential and perpendicular modes, respectively, compared with 2465 cpm/mg in the sham tissue. There were no significant differences between the tangential and perpendicular delivery modes in any assessments performed. The short-term chondrocyte destruction previously noted in a 12-week study after laser treatment was not reversed during a longer-term 26-week study, and cellular viability was not recovered, suggesting that the loss of chondrocyte function may be permanent.
Intensity discrimination and detection of amplitude modulation.

Thresholds for detection of low-rate sinusoidal amplitude modulation and for detection of intensity increments were measured over a wide range of levels in an examination of the relationship between these fundamental aspects of intensity processing. As expected, thresholds measured with a continuous 1-kHz tone decrease with increasing carrier/pedestal level. For levels between 6 and 85 dB SPL the data are well described by 10 log delta I/I = 0.44. (20 log m) + D(fm), where delta I/I is the Weber fraction for increment detection, m is the modulation index at threshold, and D(fm) depends on modulation rate (fm). The relationship between the psychometric functions for modulation and increment detection is also consistent with this equation. The data indicate a clear relationship between modulation and increment detection and thus provide an important additional consideration for models of modulation processing. No existing models provide an adequate account of this relationship.