Miracle-dz/UniFAR-FTUs huggingface dataset:
Interspecific Hybridization and Mitochondrial Introgression in Invasive Carcinus Shore Crabs

Interspecific hybridization plays an important role in facilitating adaptive evolutionary change. More specifically, recent studies have demonstrated that hybridization may dramatically influence the establishment, spread, and impact of invasive populations. In Japan, previous genetic evidence for the presence of two non-native congeners, the European green crab Carcinus maenas and the Mediterranean green crab C. aestuarii, has raised questions regarding the possibility of hybridization between these sister species. Here I present analysis based on both nuclear microsatellites and the mitochondrial cytochrome C oxidase subunit I (COI) gene which unambiguously argues for a hybrid origin of Japanese Carcinus. Despite the presence of mitochondrial lineages derived from both C. maenas and C. aestuarii, the Japanese population is panmictic at nuclear loci and has achieved cytonuclear equilibrium throughout the sampled range in Japan. Furthermore, analysis of admixture at nuclear loci indicates dramatic introgression of the C. maenas mitochondrial genome into a predominantly C. aestuarii nuclear background. These patterns, along with inferences drawn from the observational record, argue for a hybridization event pre-dating the arrival of Carcinus in Japan. The clarification of both invasion history and evolutionary history afforded by genetic analysis provides information that may be critically important to future studies aimed at assessing risks posed by invasive Carcinus populations to Japan and the surrounding region.
Thoracic electrical impedance tomographic measurements during volume controlled ventilation-effects of tidal volume and positive end-expiratory pressure

The aim of the study was to analyze thoracic electrical impedance tomographic (EIT) measurements accomplished under conditions comparable with clinical situations during artificial ventilation. Multiple EIT measurements were performed in pigs in three transverse thoracic planes during the volume controlled mode of mechanical ventilation at various tidal volumes (V/sub T/) and positive end-expiratory pressures (PEEP). The protocol comprised following ventilatory patterns: (1) V/sub T/ (400, 500, 600, 700 ml) was varied in a random order at various constant PEEP levels and (2) PEEP (2, 5, 8, 11, 14 cm H/sub 2/O) was randomly modified during ventilation with a constant V/sub T/. The EIT technique was used to generate cross-sectional images of (1) regional lung ventilation and (2) regional shifts in lung volume with PEEP. The quantitative analysis was performed in terms of the tidal amplitude of the impedance change, reflecting the volume of delivered gas at various preset V/sub T/ and the end-expiratory impedance change, revealing the variation of the lung volume at various PEEP levels. The results showed: (1) an increase in the tidal amplitude of the impedance change, proportional to the delivered V/sub T/ at all constant PEEP levels, (2) a rising end-expiratory impedance change, with PEEP reflecting an increase in gas volume, and (3) a PEEP-dependent redistribution of the ventilated gas between the planes. The generated images and the quantitative results indicate the ability of EIT to identify regional changes in V/sub T/ and lung volume during mechanical ventilation.
IMPACT OF LAND USE CHANGE ON EROSION RISK: AN INTEGRATED REMOTE SENSING, GEOGRAPHIC INFORMATION SYSTEM AND MODELING METHODOLOGY

The objective of this study was to evaluate the impact of rapidly changing land use on erosion and sedimentation in a mixed land use watershed in the Ozark Highlands of the USA. The research combines a geographic information system‐based soil erosion modeling approach with land use change detection to quantify the influence of changing land use on erosion risk. Five land use/land cover maps were generated or acquired for a 20‐year period (1986 through 2006) at approximately 5‐year intervals to assess land use change and to predict a projected (2030) land use scenario for the West Fork White River watershed in Northwest Arkansas. The Unit Stream Power based Erosion/Deposition model was applied to the observed and predicted land use to assess the impact on erosion. Total erosion from urban areas was predicted to increase by a factor of six between 1986 and 2030 based on the projected 2030 land use. Results support previous reports of increased urbanization leading to increased soil erosion risk. This study highlights the interaction of changes in land use with soil erosion potential. Soil erosion risk on a landscape can be quantified by incorporating commonly available biophysical data with geographic information system and remote sensing, which could serve as a land/watershed management tool for the rapid assessment of the effects of environmental change on erosion risk. Copyright © 2011 John Wiley & Sons, Ltd.
Letter and symbol identification: No evidence for letter-specific crowding mechanisms

It has been proposed that letters, as opposed to symbols, trigger specialized crowding processes, boosting identification of the first and last letters of words. This hypothesis is based on evidence that single-letter accuracy as a function of within-string position has a W shape (the classic serial position function [SPF] in psycholinguistics) whereas an inverted V shape is obtained when measured with symbols. Our main goal was to test the robustness of the latter result. Our hypothesis was that any letter/symbol difference might result from short-term visual memory processes (due to the partial report [PR] procedures used in SPF studies) rather than from crowding. We therefore removed the involvement of short-term memory by precueing targetitem position and compared SPFs with precueing and postcueing. Perimetric complexity was stringently matched between letters and symbols. In postcueing conditions similar to previous studies, we did not reproduce the inverted V shape for symbols: Clear-cut W shapes were observed with an overall smaller accuracy for symbols compared to letters. This letter/symbol difference was dramatically reduced in precueing conditions in keeping with our prediction. Our results are not consistent with the claim that letter strings trigger specialized crowding processes. We argue that PR procedures are not fit to isolate crowding processes.
Regulatory Risk, Market Risk and Capital Structure: Evidence from U.S. Electric Utilities

There is a sharp contrast when one compares firm leverage ratios between U.S. and British electric utilities, which have both been deregulated in the past decade. In the U.S., leverage ratios have been declining while in the U.K., they show a marked increase. To better understand the decline in leverage of U.S. investor owned electric utilities, this paper investigates the impact of deregulation on the capital structure decisions of these firms. We find that the heightened uncertainty created by the deregulation process and the associated increase in both regulatory and market risks have resulted in firms reducing their leverage ratios. Specifically, we find that the most important factors that impact capital structure are: 1) the stranded cost recovery and divestiture policies and 2) the potential loss of market share due to competition and fears of downward pressure on prices i.e. market risk. We also find that belonging to a holding company lowers leverage while the possibility of a merger decreases leverage. Identifying the importance of these variables for a firm's financing decisions not only furthers our understanding of capital structure choice but also sheds light on the financial effects of deregulation, which have not been previously documented.
Impact of hot compressed water pretreatment on the structural changes of woody biomass for bioethanol production

As an initial step in an alternative use of woody biomass to produce bioethanol, this work was aimed at investigating the effect of hot compressed water (HCW) pretreatment within the temperature range 100 to 200 °C in a batch-type reactor on the structural changes of Tamarix ramosissima. The untreated and pretreated solid residues were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), r transform infrared spectroscopy (FT-IR), solid-state cross polarization/magic angle spinning (CP/MAS), 13C NMR spectroscopy, and thermogravimetric analysis (TGA), as well as chemical methods. The results showed that HCW pretreatment solubilized mainly hemicelluloses and resulted in enriched cellulose and lignin content in the pretreated solids. It was found that the deposition of lignin droplets on the residual surfaces was produced during pretreatment under the hot water conditions above 140 °C. In addition, the removal of hemicelluloses and lignin re-localisation as a result of condensation reactions under the severe pretreatment condition may lead to an increase in cellulose crystallinity and thermal stability of biomass solid residues, thus consequently influencing the downstream digestibility of biomass for sugars and bioethanol production.
Accuracy of Saturated Soil Hydraulic Conductivity Estimated from Numerically Simulated Single‐Ring Infiltrations

The accuracy of the PI method in estimating soil Ks was tested by numerical simulations. Estimated Ks using two‐ponding‐depth and multiple‐ponding‐depth infiltration were compared. Transient and steady‐state infiltration data for six soils were used to estimate Ks. The PI should yield more accurate Ks estimates in coarse‐ than fine‐textured soils. The transient method does not solve the Ks inaccuracy problems in fine‐textured soils.
Molecular Typing of Selected Enterococcus faecalis Isolates: Pilot Study Using Multilocus Sequence Typing and Pulsed-Field Gel Electrophoresis

ABSTRACT The present study compared the recently developed multilocus sequence typing (MLST) approach with a well-established molecular typing technique, pulsed-field gel electrophoresis (PFGE), for subspecies differentiation of Enterococcus faecalis isolates. We sequenced intragenic regions of three E. faecalis antigen-encoding genes (ace, encoding a collagen and laminin adhesin; efaA, encoding an endocarditis antigen; and salA, encoding a cell wall associated antigen) and one housekeeping gene (pyrC) of 22 E. faecalis isolates chosen largely for their temporal and geographical diversity, but also including some outbreak isolates. MLST analysis of polymorphic regions of these four genes identified 13 distinct sequence types (STs) with different allelic profiles; the composite sequences generated from the four sequenced gene fragments of individual isolates showed 98.3 to 100% identity among the 22 isolates. We also found that the allelic profiles from two sequences, ace and salA, were sufficient to distinguish all 13 STs of this study. The 13 STs corresponded to 12 different PFGE types, with one previously designated PFGE clone (a widespread U.S. clone of β-lactamase-producing isolates) being classified into two highly related STs which differed at 2 of 2,894 bases, both in the same allele. MLST also confirmed the clonal relationships among the isolates of two other PFGE clonal groups, including vancomycin resistant isolates. Thus, this pilot study with representative E. faecalis isolates suggests that, similar to PFGE, the sequence-based typing method may be useful for differentiating isolates of E. faecalis to the subspecies level in addition to identifying outbreak isolates.
The use of electrophysiological monitoring in the intraoperative management of intracranial aneurysms

OBJECTIVES Somatosensory evoked potentials (SSEPs) and brainstem auditory evoked potentials (BAEPs) have been increasingly utilised during surgery for intracranial aneurysms to identify cerebral ischaemia. Between July 1994 and April 1996, we surgically treated 70 aneurysms in 49 consecutive patients (58 operations) with the aid of intraoperative evoked potential monitoring. This study sought to evaluate the usefulness of SSEP and BAEP monitoring during intracranial aneurysm surgery. METHODS Mean patient age was 51.9 (range 18–79) years. The sizes of the aneurysms were 3–4 mm (15), 5–9 mm (26), 10–14 mm (11), 15–19 mm (seven), 20–24 mm (six), and >25 mm (five). SSEPs were monitored in 58 procedures (100%) and BAEPs in 15 (26%). The neurological status of the patients was evaluated before and after surgery. RESULTS Thirteen of the 58 procedures (22%) monitored with SSEPs had SSEP changes (12 transient, one persistent); 45 (78%) had no SSEP changes. Three of 15 patients (20%) monitored with BAEPs had changes (two transient, one persistent); 12 (80%) had no BAEP changes. Of the 14 patients with transient SSEP or BAEP changes, these changes resolved with adjustment or removal of aneurysm clips (nine), elevating MAP (four), or retractor adjustment (one). Mean time from precipitating event to electrophysiological change was 8.9 minutes (range 3–32), and the mean time for recovery of potentials in patients with transient changes was 20.2 minutes (range 3–60). Clinical outcome was excellent in 39 patients, good in five, and poor in three (two patients died), and was largely related to pretreatment grade. CONCLUSIONS SSEPs and BAEPs are useful in preventing clinical neurological injury during surgery for intracranial aneurysms and in predicting which patients will have unfavourable outcomes.
PKCγ participates in food entrainment by regulating BMAL1

Temporally restricted feeding (RF) can phase reset the circadian clocks in numerous tissues in mammals, contributing to altered timing of behavioral and physiological rhythms. However, little is known regarding the underlying molecular mechanism. Here we demonstrate a role for the gamma isotype of protein kinase C (PKCγ) in food-mediated entrainment of behavior and the molecular clock. We found that daytime RF reduced late-night activity in wild-type mice but not mice homozygous for a null mutation of PKCγ (PKCγ−/−). Molecular analysis revealed that PKCγ exhibited RF-induced changes in activation patterns in the cerebral cortex and that RF failed to substantially phase shift the oscillation of clock gene transcripts in the absence of PKCγ. PKCγ exerts effects on the clock, at least in part, by stabilizing the core clock component brain and muscle aryl hydrocarbon receptor nuclear translocator like 1 (BMAL1) and reducing its ubiquitylation in a deubiquitination-dependent manner. Taken together, these results suggest that PKCγ plays a role in food entrainment by regulating BMAL1 stability.
Variable outcome and methylation status according to CEBPA mutant type in double-mutated acute myeloid leukemia patients and the possible implications for treatment

Although CEBPA double-mutated (CEBPADM) acute myeloid leukemia is considered to be a favorable-risk disease, relapse remains a major cause of treatment failure. Most CEBPADM patients have a classic biallelic mutant combination with an N-terminal mutation leading to production of p30 protein plus a C-terminal loss-of-function in-frame indel mutation (CEBPAClassic-DM), but approximately one-third of cases have one or more non-classic mutations, with diverse combinations reported, and there is little information on the consequences of such mutants. We evaluated outcome in a cohort of 104 CEBPADM patients, 79 CEBPAClassic-DM and 25 with non-classic mutants, and found that the latter may have poorer survival (5-year overall survival 64% vs. 46%; P=0.05), particularly post relapse (41% vs. 0%; P=0.02). However, for this analysis, all non-classic cases were grouped together, irrespective of mutant combination. As CEBPADM cases have been reported to be hypermethylated, we used methylation profiling to assess whether this could segregate the different mutants. We developed a CEBPAClassic-DM methylation signature from a preliminary cohort of 10 CEBPADM (including 8 CEBPAClassic-DM) and 30 CEBPA wild-type (CEBPAWT) samples, and independently validated the signature in 17 CEBPAClassic-DM cases. Assessment of the signature in 16 CEBPADM cases with different non-classic mutant combinations showed that only 31% had a methylation profile equivalent to CEBPAClassic-DM whereas for 69% the profile was either intermediate between CEBPAClassic-DM and CEBPAWT or equivalent to CEBPAWT. These results suggest that CEBPADM cases with non-classic mutants may be functionally different from those with CEBPAClassic-DM mutants, and should not automatically be included in the same prognostic group. (AML12 is registered under ISRCTN17833622 and AML15 under ISRCTN17161961).
Empirical Evaluation of MPEG-7 Texture Descriptors with A Large-Scale Experiment

This paper conducts an empirical evaluation of the MPEG-7 texture descriptors and the LBP (Local Binary Pattern) operator. The experiment involves 319 textures from the Outex texture database, which makes it one of the largest experiments found in the literature, if not the largest, in terms of the number of texture classes. The descriptors are evaluated with respect to retrieval performance and computational complexity. Experimental results show that the LBP operator outperforms MPEG-7 texture descriptors on both accounts.
Role of the Methoxy Group in Immune Responses to mPEG-Protein Conjugates

Anti-PEG antibodies have been reported to mediate the accelerated clearance of PEG-conjugated proteins and liposomes, all of which contain methoxyPEG (mPEG). The goal of this research was to assess the role of the methoxy group in the immune responses to mPEG conjugates and the potential advantages of replacing mPEG with hydroxyPEG (HO-PEG). Rabbits were immunized with mPEG, HO-PEG, or t-butoxyPEG (t-BuO-PEG) conjugates of human serum albumin, human interferon-α, or porcine uricase as adjuvant emulsions. Assay plates for enzyme-linked immunosorbent assays (ELISAs) were coated with mPEG, HO-PEG, or t-BuO-PEG conjugates of the non-cross-reacting protein, porcine superoxide dismutase (SOD). In sera from rabbits immunized with HO-PEG conjugates of interferon-α or uricase, the ratio of titers of anti-PEG antibodies detected on mPEG-SOD over HO-PEG-SOD (“relative titer”) had a median of 1.1 (range 0.9–1.5). In contrast, sera from rabbits immunized with mPEG conjugates of three proteins had relative titers with a median of 3.0 (range 1.1–20). Analyses of sera from rabbits immunized with t-BuO-PEG-albumin showed that t-butoxy groups are more immunogenic than methoxy groups. Adding Tween 20 or Tween 80 to buffers used to wash the assay plates, as is often done in ELISAs, greatly reduced the sensitivity of detection of anti-PEG antibodies. Competitive ELISAs revealed that the affinities of antibodies raised against mPEG-uricase were c. 70 times higher for 10 kDa mPEG than for 10 kDa PEG diol and that anti-PEG antibodies raised against mPEG conjugates of three proteins had >1000 times higher affinities for albumin conjugates with c. 20 mPEGs than for analogous HO-PEG-albumin conjugates. Overall, these results are consistent with the hypothesis that antibodies with high affinity for methoxy groups contribute to the loss of efficacy of mPEG conjugates, especially if multiply-PEGylated. Using monofunctionally activated HO-PEG instead of mPEG in preparing conjugates for clinical use might decrease this undesirable effect.
Free and total p-cresol sulfate levels and infectious hospitalizations in hemodialysis patients in CHOICE and HEMO

Abstract The uremic syndrome is attributed to progressive retention of compounds that, under normal conditions, are excreted by the healthy kidneys. p-cresol sulfate (PCS), a prototype protein-bound uremic retention solute, has been shown to exert toxic effects in vitro. Recent studies have identified relations between increased levels of PCS and indoxyl sulfate (IS) and adverse clinical outcomes in hemodialysis patients. We explored the relationship between free and total PCS and IS with infection-related hospitalizations (IH) and septicemia in 2 cohorts, Choices for Healthy Outcomes in Caring for end-stage renal disease (ESRD) Study (CHOICE) and Hemodialysis Study (HEMO). We measured free and total levels of PCS and IS in stored specimens in CHOICE, a cohort of 464 incident hemodialysis patients enrolled in 1995 to 1998 and followed for an average of 3.4 years and in a prevalent dialysis cohort of 495 patients enrolled in HEMO from 1995 to 2000 and followed for an average of 4.4 years. We measured free PCS and IS using mass spectroscopy. The 2 cohorts were linked to United States Renal Data System (USRDS) Medicare billing records to ascertain IH over follow-up. We examined the association of free and total levels of PCS and IS with IH and septicemia using multilevel Poisson regression models adjusted for demographics, comorbidities, clinical factors, and laboratory tests including residual kidney function. We stratified patients a priori based on gastrointestinal (GI) disease as PCS and IS are produced in colon. In CHOICE, highest tertile of free PCS in multivariable model was associated with 50% higher risk of IH [95% CI = 1.01–2.23] compared with lowest tertile in patients with no-GI disease. A significant trend was noted between greater levels of free PCS and septicemia in no-GI disease group in both cohorts, while no association was noted in GI disease group. Total PCS concentrations were not associated with either IH or septicemia in either cohort. No significant risk of IH or septicemia was noted with higher levels of free or total IS in either GI or no-GI disease group. These results suggest an association between higher concentrations of free PCS and infection-related and sepsis-related hospitalizations in hemodialysis patients. Better methods of dialysis should be developed to evaluate the utility of removing PCS and its effect on the outcome and also therapies to decrease gastrointestinal tract production of uremic solutes.
Pharmacodynamic Evaluation of the Intracellular Activities of Antibiotics against Staphylococcus aureus in a Model of THP-1 Macrophages

ABSTRACT The pharmacodynamic properties governing the activities of antibiotics against intracellular Staphylococcus aureus are still largely undetermined. Sixteen antibiotics of seven different pharmacological classes (azithromycin and telithromycin [macrolides]; gentamicin [an aminoglycoside]; linezolid [an oxazolidinone]; penicillin V, nafcillin, ampicillin, and oxacillin [β-lactams]; teicoplanin, vancomycin, and oritavancin [glycopeptides]; rifampin [an ansamycin]; and ciprofloxacin, levofloxacin, garenoxacin, and moxifloxacin [quinolones]) have been examined for their activities against S. aureus (ATCC 25923) in human THP-1 macrophages (intracellular) versus that in culture medium (extracellular) by using a 0- to 24-h exposure time and a wide range of extracellular concentrations (including the range of the MIC to the maximum concentration in serum [Cmax; total drug] of humans). All molecules except the macrolides caused a net reduction in bacterial counts that was time and concentration/MIC ratio dependent (four molecules tested in detail [gentamicin, oxacillin, moxifloxacin, and oritavancin] showed typical sigmoidal dose-response curves at 24 h). Maximal intracellular activities remained consistently lower than extracellular activities, irrespective of the level of drug accumulation and of the pharmacological class. Relative potencies (50% effective concentration or at a fixed extracellular concentration/MIC ratio) were also decreased, but to different extents. At an extracellular concentration corresponding to their Cmaxs (total drug) in humans, only oxacillin, levofloxacin, garenoxacin, moxifloxacin, and oritavancin had truly intracellular bactericidal effects (2-log decrease or more, as defined by the Clinical and Laboratory Standards Institute guidelines). The intracellular activities of antibiotics against S. aureus (i) are critically dependent upon their extracellular concentrations and the duration of cell exposure (within the 0- to 24-h time frame) to antibiotics and (ii) are always lower than those that can be observed extracellularly. This model may help in rationalizing the choice of antibiotic for the treatment of S. aureus intracellular infections.