Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of NADPH Phagocyte Oxidase in Host Defense against Acute Respiratory Acinetobacter baumannii Infection in Mice

ABSTRACT Acinetobacter baumannii is an emerging bacterial pathogen that rapidly develops multiple-drug resistance and is responsible for many nosocomial pulmonary infections. This study investigated the role of the NADPH phagocyte oxidase (phox) and inducible nitric oxide synthase (NOS2) in the host defense against respiratory infection with A. baumannii in mouse models of intranasal A. baumannii infection. gp91phox−/− mice showed higher susceptibility to A. baumannii infection than wild-type (WT) C57BL/6 mice, with significantly greater bacterial counts in their lungs (1,000-fold) (P < 0.005) and spleens (10-fold) (P < 0.05). Moreover, all of the gp91phox−/− mice succumbed to infection within 48 h. In contrast, only a moderate increase in bacterial burdens was detected in the lungs of NOS2−/− mice, and all NOS2−/− mice survived infection. Compared to WT mice, the pulmonary influx of inflammatory cells and serum and local inflammatory cytokine/chemokine responses were not obviously impaired at 4 h and were significantly higher at 24 h (P < 0.05) in gp91phox−/− mice, but NADPH-deficient neutrophils were unable to control bacterial replication and extrapulmonary dissemination. Thus, NADPH phagocyte oxidase appears to play a crucial role in the neutrophil-mediated host defense against A. baumannii.
Selecting Relevant Web Trained Concepts for Automated Event Retrieval

Complex event retrieval is a challenging research problem, especially when no training videos are available. An alternative to collecting training videos is to train a large semantic concept bank a priori. Given a text description of an event, event retrieval is performed by selecting concepts linguistically related to the event description and fusing the concept responses on unseen videos. However, defining an exhaustive concept lexicon and pre-training it requires vast computational resources. Therefore, recent approaches automate concept discovery and training by leveraging large amounts of weakly annotated web data. Compact visually salient concepts are automatically obtained by the use of concept pairs or, more generally, n-grams. However, not all visually salient n-grams are necessarily useful for an event query -- some combinations of concepts may be visually compact but irrelevant -- and this drastically affects performance. We propose an event retrieval algorithm that constructs pairs of automatically discovered concepts and then prunes those concepts that are unlikely to be helpful for retrieval. Pruning depends both on the query and on the specific video instance being evaluated. Our approach also addresses calibration and domain adaptation issues that arise when applying concept detectors to unseen videos. We demonstrate large improvements over other vision based systems on the TRECVID MED 13 dataset.
Effect of Isovolemic, Isothermic Hemodialysis on Cerebral Perfusion and Vascular Stiffness Using Contrast Computed Tomography and Pulse Wave Velocity

Background Patients undergoing hemodialysis treatment have a six-fold increased risk for stroke relative to the general population. However, the effect of hemodialysis on cerebral blood flow is poorly studied and confounding factors like blood pressure and ultrafiltration as well as temperature changes have rarely been accounted for. The aim of our study was to use state-of-the-art technology to evaluate the effect of a single dialysis session on cerebral perfusion as well as on vascular stiffness. Methods Chronic hemodialysis patients (7 male/3 female, mean age 58 years) were recruited. Cerebral blood flow and arterial pulse wave velocity were measured before and immediately after a hemodialysis session. To exclude effects of volume changes we kept ultrafiltration to a minimum, allowing no change in body weight. Isothermic conditions were maintained by using the GENIUS single-pass batch-dialysis system with a high-flux polysulfone dialyser. Cerebral blood flow was measured by contrast-enhanced computed tomography. Pulse wave velocity was measured using the SphygmoCor (AtCor Medical, USA) device by a single operator. Results This study shows for the first time that isovolemic, isothermic hemodialysis neither affected blood pressure or heart rate, nor total or regional cerebral perfusion. There was also no change in pulse wave velocity. Conclusions Mechanisms other than the dialysis procedure itself might be causative for the high incidence of ischemic strokes in this patient population. Moreover, the sole removal of uremic toxins does not lead to short-term effects on vascular stiffness, underlying the importance of volume control in this patient population.
Formulating tightest bounds on causal effects in studies with unmeasured confounders

This paper considers the problem of evaluating the causal effect of an exposure on an outcome in observational studies with both measured and unmeasured confounders between the exposure and the outcome. Under such a situation, MacLehose et al. (Epidemiology 2005; 16:548–555) applied linear programming optimization software to find the minimum and maximum possible values of the causal effect for specific numerical data. In this paper, we apply the symbolic Balke–Pearl linear programming method (Probabilistic counterfactuals: semantics, computation, and applications. Ph.D. Thesis, UCLA Cognitive Systems Laboratory, 1995; J. Amer. Statist. Assoc. 1997; 92:1172–1176) to derive the simple closed‐form expressions for the lower and upper bounds on causal effects under various assumptions of monotonicity. These universal bounds enable epidemiologists and medical researchers to assess causal effects from observed data with minimum computational effort, and they further shed light on the accuracy of the assessment. Copyright © 2008 John Wiley & Sons, Ltd.
Differences in the Angiographic Evaluation of Coiled Cerebral Aneurysms between a Core Laboratory Reader and Operators: Results of the Cerecyte Coil Trial

BACKGROUND AND PURPOSE: Independent evaluation of angiographic images is becoming widely applied in the assessment of treatment outcomes of cerebral aneurysms. In the current study, we assessed the agreement between an independent core laboratory and the operators regarding angiographic appearance in a recent randomized, controlled trial. MATERIALS AND METHODS: Data were derived from the Cerecyte Coil Trial. Angiographic images of each coiled aneurysm, taken immediately after embolization and at 5- to 7-month follow-up, were evaluated by the operator at the treating center and by an independent neuroradiologist at the core laboratory. For the purpose of this study, images were interpreted on a 3-point scale to provide uniformity for analysis; grade 1: complete occlusion, grade 2: neck remnant; and grade 3: sac filling. “Unfavorable angiographic appearance” was defined as grade 3 at follow-up or interval worsening of grade between the 2 time points. RESULTS: The study included 434 aneurysms. Immediately after embolization, grade 3 was reported by operators in 39 (9%) compared with 52 (12%) by the core laboratory (P = .159). On follow-up, grade 3 was reported by operators in 44 (10%) compared with 81 (19%) by the core laboratory (P < .0001). Overall, operators noted unfavorable angiographic appearance in 78 (18%) compared with 134 (31%) by the core laboratory (P < .0001). At every time point, agreement between the core laboratory and the operators was slight. CONCLUSIONS: Unfavorable angiographic appearance was noted almost twice as frequently by an independent core laboratory as compared with the operators. Planning of trials and interpretation of published studies should be done with careful attention to the mode of angiographic appearance interpretation.
Alcohol consumption among low-income pregnant Latinas.

BACKGROUND Due to changing cultural norms, Latinas of childbearing age residing in the U.S. may be at increasing risk of drinking harmful levels of alcohol during pregnancy, and may also be unaware of the risks for Fetal Alcohol Spectrum Disorders associated with this behavior. We assessed the prevalence of alcohol consumption in a sample of low-income pregnant Latinas and examined risk factors for alcohol use in the periconceptional period. METHODS As part of a larger intervention trial, a cross-sectional in-home interview study was conducted among a sample of 100 pregnant low-income Latinas receiving services from the Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) in San Diego County, California. RESULTS Fifty-seven percent of respondents indicated they were either life-time abstainers or had not consumed any alcohol in the periconceptional period. Forty-three percent reported some alcohol use in the three months prior to recognition of the current pregnancy, and 20% reported at least one binge episode of four or more standard drinks during that time frame. Five percent reported drinking seven or more drinks per week, and 8% continued drinking alcohol after recognition of pregnancy. Significant predictors of any alcohol use in the periconceptional period included English language/higher level of acculturation, younger maternal age, lower parity, higher level of education, younger age at first drink, and having ever smoked. Women who were aware of alcohol warning messages and /or had more knowledge of the Fetal Alcohol Syndrome (FAS) were significantly more likely to have consumed alcohol in the periconceptional period. Frequency of periconceptional use of alcohol did not differ between women who planned or did not plan the pregnancy. CONCLUSION The prevalence and pattern of early pregnancy alcohol consumption in this sample of Latinas is similar to patterns noted in other race/ethnic groups in the U.S. Level of knowledge about FAS and awareness of warning messages was not protective for early pregnancy alcohol consumption, suggesting that specific knowledge was insufficient to prevent exposure or that other factors reinforce maintenance of alcohol consumption in early pregnancy. Selective interventions in low-income Latinas are warranted, and should be focused on women of reproductive age who are binge or frequent drinkers and who are at risk of becoming pregnant.
Using the Electromyogram to Anticipate Torques About the Elbow

Processed (i.e., rectified, smoothed) electromyogram (EMG) activity from skeletal muscles precedes mechanical tension by 50-100 ms. This property can be exploited to anticipate muscle mechanical activity. Thus, we investigated the ability of surface EMG to estimate joint torque at future times, up to 750 ms. EMG recorded from the biceps and triceps muscles of 54 subjects during constant-posture, force-varying contractions was related to elbow torque. Higher-order FIR models, combined with advanced EMG processing (whitening; four EMG channels per muscle), provided a nearly identical minimum error of 5.48 ±2.21% MVCF (flexion maximum voluntary contraction) over the time advance range of 0-60 ms. Error grew for larger time advances. The more common method of filtering EMG amplitude with a Butterworth filter (second-order, 1.5 Hz cutoff frequency) produced a statistically inferior (p <; 10-6) minimum torque error of 6.90 ±2.39% MVCF, with an error nadir at a time advance of 60 ms. Error was progressively poorer at all other time advances. Lower-order FIR models mimicked the poorer performance of the Butterworth models. The more advanced models provide lower estimation error, require no selection of an electromechanical delay term and maintain their lowest error over a substantial range of advance times.
Leukocyte Telomere Length is Associated with Abdominal Aortic Aneurysm ( AAA )

1078-5884/$36 a 2010 European Socie doi:10.1016/j.ejvs. 2010.01. 013 Abstract Objective: Telomeres are specialised DNA structures present at the ends of linear chromosomes, which shorten with each successive cell division and the length of which represents cellular biological age. The aim of this study was to determine the relationship between abdominal aortic aneurysm (AAA) and white cell telomere length. Methods: Peripheral blood samples were collected from 190 patients with AAA and 183 controls. Genomic DNA was extracted from white cells and telomere lengths determined using a chemiluminescence technique. Results: The mean white cell telomere length was significantly lower in AAA patients compared to controls (median age 66 years in both groups), with a mean difference of 189 base pairs (bp) (95% confidence interval 77 bp to 301 bp, P Z 0.005). This relationship between caseecontrol status and mean telomere restriction fragment (TRF) length did not change after adding other risk factors into a multiple regression model. The risk of having AAA doubled in patients with a mean TRF length in the lowest quartile compared to patients with a mean TRF length in the highest quartile (odds ratio 2.30, 95% Confidence Interval 1.28e4.13, P Z 0.005). Conclusion: Our data show that patients with AAA have shorter leukocyte telomere length compared to controls. This suggests that vascular biological aging may have a role in the pathogenesis of AAA. a 2010 European Society for Vascular Surgery. Published by Elsevier Ltd. All rights reserved.
Dynein light chain regulates axonal trafficking and synaptic levels of Bassoon

Bassoon and the related protein Piccolo are core components of the presynaptic cytomatrix at the active zone of neurotransmitter release. They are transported on Golgi-derived membranous organelles, called Piccolo-Bassoon transport vesicles (PTVs), from the neuronal soma to distal axonal locations, where they participate in assembling new synapses. Despite their net anterograde transport, PTVs move in both directions within the axon. How PTVs are linked to retrograde motors and the functional significance of their bidirectional transport are unclear. In this study, we report the direct interaction of Bassoon with dynein light chains (DLCs) DLC1 and DLC2, which potentially link PTVs to dynein and myosin V motor complexes. We demonstrate that Bassoon functions as a cargo adapter for retrograde transport and that disruption of the Bassoon–DLC interactions leads to impaired trafficking of Bassoon in neurons and affects the distribution of Bassoon and Piccolo among synapses. These findings reveal a novel function for Bassoon in trafficking and synaptic delivery of active zone material.
Mitochondrial permeability transition in pH-dependent reperfusion injury to rat hepatocytes.

To simulate ischemia and reperfusion, cultured rat hepatocytes were incubated in anoxic buffer at pH 6.2 for 4 h and reoxygenated at pH 7.4. During anoxia, intracellular pH (pHi) decreased to 6.3, mitochondria depolarized, and ATP decreased to <1% of basal values, but the mitochondrial permeability transition (MPT) did not occur as assessed by confocal microscopy from the redistribution of cytosolic calcein into mitochondria. Moreover, cell viability remained >90%. After reperfusion at pH 7.4, pHi returned to pH 7.2, the MPT occurred, and most hepatocytes lost viability. In contrast, after reperfusion at pH 6.2 or with Na+-free buffer at pH 7.4, pHi did not rise and cell viability remained >80%. After acidotic reperfusion, the MPT did not occur. When hepatocytes were reperfused with cyclosporin A (0.5-1 μM) at pH 7.4, the MPT was prevented and cell viability remained >80%, although pHi increased to 7.2. Reperfusion with glycine (5 mM) also prevented cell killing but did not block recovery of pHi or the MPT. Retention of cell viability was associated with recovery of 30-40% of ATP. In conclusion, preventing the rise of pHi after reperfusion blocked the MPT, improved ATP recovery, and prevented cell death. Cyclosporin A also prevented cell killing by blocking the MPT without blocking recovery of pHi. Glycine prevented cell killing but did not inhibit recovery of pHi or the MPT.
The Wiek Fault System east of Rügen Island: origin, tectonic phases and its relationship to the Trans-European Suture Zone

Abstract The Tornquist Fan, reflecting the northern part of the Trans-European Suture Zone, comprises a series of fault zones and major single faults, striking mainly subparallel to the SW margin of the Fennoscandian Shield. The deep-seated faults of Wiek, Nord Jasmund and Schaabe, which cross the northern part of Rügen Island and areas of the adjacent Baltic Sea from NW to SE, originated in the late Paleozoic. They are accompanied by younger faults, especially in the Pomeranian Bay, that were formed by Mesozoic tectonic processes. Based on reprocessed offshore seismic lines east of Rügen, a polyphase evolution for the Wiek Fault System is proposed. It implies changes in the stress field since the Caledonian Orogeny. Crustal extension in the Middle Devonian led to the formation of basins along the SW margin of Laurussia. Subsequent compressional movements, induced by the distant Variscan Orogeny, resulted in segmentation and block faulting of the Rügen Basin prior to the late Carboniferous. These Paleozoic faults were reactivated by Mesozoic extensional stress regimes. In addition, new en echelon faults were generated, contemporaneously with the formation of the Western Pomeranian Fault System. Since the Late Cretaceous (Africa–Iberia–Europe convergence), selected major normal faults have been reactivated as reverse faults.
Oxidant Trade-Offs in Immunity: An Experimental Test in a Lizard

Immune system functioning and maintenance entails costs which may limit investment into other processes such as reproduction. Yet, the proximate mechanisms and ‘currencies’ mediating the costs of immune responses remain elusive. In vertebrates, up-regulation of the innate immune system is associated with rapid phagocytic production of pro-oxidant molecules (so-called ‘oxidative burst’ responses). Oxidative burst responses are intended to eliminate pathogens but may also constitute an immunopathological risk as they may induce oxidative damage to self cells. To minimize the risk of infection and, at the same time, damage to self, oxidative burst activity must be carefully balanced. The current levels of pro- and antioxidants (i.e. the individual oxidative state) is likely to be a critical factor affecting this balance, but this has not yet been evaluated. Here, we perform an experiment on wild-caught painted dragon lizards (Ctenophorus pictus) to examine how the strength of immune-stimulated oxidative burst responses of phagocytes in whole blood relates to individual oxidative status under control conditions and during an in vivo immune challenge with Escherichia coli lipopolysaccharide (LPS). Under control conditions, oxidative burst responses were not predicted by the oxidative status of the lizards. LPS-injected individuals showed a strong increase in pro-oxidant levels and a strong decrease in antioxidant levels compared to control individuals demonstrating a shift in the pro-/antioxidant balance. Oxidative burst responses in LPS-injected lizards were positively related to post-challenge extracellular pro-oxidants (reflecting the level of cell activation) and negatively related to pre-challenge levels of mitochondrial superoxide (suggesting an immunoregulatory effect of this pro-oxidant). LPS-challenged males had higher oxidative burst responses than females, and in females oxidative burst responses seemed to depend more strongly on antioxidant status than in males. Our results confirm the idea that oxidative state may constrain the activity of the innate immune system. These constraints may have important consequences for the way selection acts on pro-oxidant generating processes.
Infrared Spectroscopy of Substellar Objects in Orion

We present broad band spectra of a sample of 21 low luminosity sources in the Trapezium Cluster, with masses in the range 0.008 - 0.10 M⊙ (assuming an age of 1 Myr). These were selected for low extinction in most cases and are located west of the brighter nebulosity. The spectra are in the H bandpass (1.4-1.95 µm) and K bandpass (1.9-2.5 µm) also for most of the brighter sources, with a resolution of 50 nm. They were taken with the United Kingdom Infrared Telescope (UKIRT) using the CGS4 spectrometer. Absorption by water vapour bands is detected in all the substellar candidates except one, which is a highly reddened object with strong H2 emission and an anomalously blue (I-J) colour, implying that it is a very young cluster member with circumstellar matter. The observation of prominent water vapour bands confirms the low Effective Temperatures implied by our (I-J) colour measurements in an earlier paper and would imply late M or L spectral types if these were older field dwarfs. However, the profiles of the H bandpass spectra are very different from those of field dwarfs with similar water absorption strength, demonstrating that they are not foreground or background objects. In addition, the CO absorption bands at 2.3 µm and the NaI absorption feature at 2.21 µm are very weak for such cool sources. All these features are quite well reproduced by the AMES-Dusty-1999 model atmospheres of Allard et al.(2000,2001), and arise from the much lower gravities predicted for the Trapezium sources (3.5 < log(g) < 4.0) compared to evolved objects (log g � 5.5), This represents a new proof of the substellar status of our sources, independent of the statistical arguments for low contamination, which are reexamined here. The very late spectral types of the planetary mass objects and very low mass brown dwarfs demonstrate that they are cluster members, since they are too luminous to be field dwarfs in the background. We also present additional UKIRT photometry of a small region in the south of the Trapezium cluster where the extinction and nebular brightness are low, which permitted the detection of objects with 1 Myr masses slightly lower than our previous least massive source at 8 MJup. Following a minor update to our previous J band photometry, due to a new UKIRT filter calibration, there are � 15 planetary mass candidates in the full dataset.
Correlations Between Macular, Skin, and Serum Carotenoids

Purpose Ocular and systemic measurement and imaging of the macular carotenoids lutein and zeaxanthin have been employed extensively as potential biomarkers of AMD risk. In this study, we systematically compare dual wavelength retinal autofluorescence imaging (AFI) of macular pigment with skin resonance Raman spectroscopy (RRS) and serum carotenoid levels in a clinic-based population. Methods Eighty-eight patients were recruited from retina and general ophthalmology practices from a tertiary referral center and excluded only if they did not have all three modalities tested, had a diagnosis of macular telangiectasia (MacTel) or Stargardt disease, or had poor AFI image quality. Skin, macular, and serum carotenoid levels were measured by RRS, AFI, and HPLC, respectively. Results Skin RRS measurements and serum zeaxanthin concentrations correlated most strongly with AFI macular pigment volume under the curve (MPVUC) measurements up to 9° eccentricity relative to MPVUC or rotationally averaged macular pigment optical density (MPOD) measurements at smaller eccentricities. These measurements were reproducible and not significantly affected by cataracts. We also found that these techniques could readily identify subjects taking oral carotenoid-containing supplements. Conclusions Larger macular pigment volume AFI and skin RRS measurements are noninvasive, objective, and reliable methods to assess ocular and systemic carotenoid levels. They are an attractive alternative to psychophysical and optical methods that measure MPOD at a limited number of eccentricities. Consequently, skin RRS and MPVUC at 9° are both reasonable biomarkers of macular carotenoid status that could be readily adapted to research and clinical settings.