Miracle-dz/UniFAR-FTUs huggingface dataset:
Distribution of Protozoa in Subsurface Sediments of a Pristine Groundwater Study Site in Oklahoma

Sediment core samples were obtained at a groundwater study site in Oklahoma in January and June 1985. Most-probable-number estimates showed that protozoan numbers declined steeply with depth in subsoil. Flagellates and amoebae dominated the protozoan population, which declined to a most probable number of 28 · g (dry weight)−1 in a clay loam layer at the bottom of the unsaturated zone. Samples from a texturally variable interface zone between 3 and 4 m down also were variable in their content of protozoa. Four contiguous clay loam samples in a single core from this zone contained variable numbers of amoebae ranging from 0.2 to 44 · g (dry weight)−1. However, a sandy clay loam layer at the bottom of the core contained a mixture of flagellates and amoebae with a combined population density of 67 · g (dry weight)−1. A slow-growing filose amoeba was isolated from interface zone samples and was tentatively classified in a new family in the order Aconchulinida. Protozoa were not detected in the saturated zone except in a very permeable gravelly, loamy sand layer at a depth of approximately 7.5 m. Low numbers (4 to 6 · g [dry weight]−1) of surface-type flagellates and amoebae, as well as the filose amoeba seen in the interface zone, were observed in this layer. Acid-treated and untreated samples contained equivalent numbers of protozoa, showing that the majority of protozoa in the layer at 7.5 m and the interface zone samples were encysted. Increased numbers of bacteria also were found in the layer at 7.5 m, indicating that it was biologically more active than other saturated-zone layers. Cyanobacteria grew in illuminated samples from this layer, suggesting that it may be connected hydrologically to a nearby river.
A transgenic model of autoimmune hemolytic anemia

We made double transgenic mice bearing immunoglobulin heavy and light chain genes encoding an autoantibody against the mouse erythrocyte by the cross of C57BL/6 mice carrying the transgene for each chain of the immunoglobulin. Although no obvious disorders were found in the single- chain transgenic mice, severely anemic symptoms were found in some of the double transgenic mice, in which most B cells express, at least on their surface, the autoantibody reactive to self-antigens on the erythrocyte. Individual double-transgenic mice showed a wide variation of phenotypes between severe anemia and no symptoms. Both deletion and anergy of autoreactive B cells were seen in each individual mouse, but their relative contribution to self-tolerance was variable and not directly related to the severity of anemia or the amount of the autoantibody produced. This transgenic system provides a good autoimmune disease model for exploring its onset mechanism, and means of its treatment and prevention.
Survival of blacks and whites after a cancer diagnosis.

CONTEXT In recent years a theory that cancer biology is different in blacks and whites has gained prominence in reaction to epidemiologic observations that blacks have poorer survival than whites, even when diagnosed with cancer of similar severity. Yet, few studies have evaluated whether lower-quality treatment and shorter overall life expectancy due to a greater burden of other illnesses may explain the survival discrepancy. OBJECTIVE To estimate the magnitude of overall and cancer-specific survival differences between blacks and whites who receive comparable treatment for similar-stage cancer. DATA SOURCES We searched MEDLINE for English-language articles published from 1966 to January 2002 that reported on overall survival for black and white patients treated similarly for cancer. STUDY SELECTION The abstracts or titles for 891 citations were independently examined by 2 authors. The full text was retrieved if the abstract mentioned both black and white patients, made some comment regarding either similarity of treatment received or presented an analysis based on the treatment received, and commented on survival. Studies were included if they included data for at least 10 black and 10 white patients; specified the cohort ascertainment method and what measures were undertaken to minimize loss to follow-up; summarized survival of both blacks and whites using actuarial measures; presented outcomes within stage, adjusted for stage, or based on cohorts with balanced stage distributions; and specified that blacks and whites in the study received similar treatment. We identified 89 unique cohorts in 54 articles that met our inclusion criteria. DATA EXTRACTION Overall survival rates and hazard ratios (HRs) for death for blacks relative to whites were calculated. These were subsequently adjusted for rates of death due to causes other than the cancer under study to determine cancer-specific survival and cancer-specific HRs. DATA SYNTHESIS Results represent 189 877 white and 32 004 black patients with 14 different cancers. Compared with whites, blacks had an overall excess risk of death (HR, 1.16; 95% confidence interval [CI], 1.12-1.20). After correction for deaths due to other causes, the cancer-specific HR was 1.07 (95% CI, 1.02-1.13). Of the 14 cancers, blacks were at a significantly higher risk of cancer-specific death only for cancer of the breast, uterus, or bladder. CONCLUSIONS Only modest cancer-specific survival differences are evident for blacks and whites treated comparably for similar-stage cancer. Therefore, differences in cancer biology between racial groups are unlikely to be responsible for a substantial portion of the survival discrepancy. Differences in treatment, stage at presentation, and mortality from other diseases should represent the primary targets of research and interventions designed to reduce disparities in cancer outcomes.
Fungicide activity through activation of a fungal signalling pathway

Fungicides generally inhibit enzymatic reactions involved in fungal cellular biosynthesis. Here we report, for the first time, an example of fungicidal effects through hyperactivation of a fungal signal transduction pathway. The OSC1 gene, encoding a MAP kinase (MAPK) related to yeast Hog1, was isolated from the fungal pathogen Colletotrichum lagenarium that causes cucumber anthracnose. The osc1 knockout mutants were sensitive to high osmotic stress and showed increased resistance to the fungicide fludioxonil, indicating that Osc1 is involved in responses to hyperosmotic stress and sensitivity to fludioxonil. The Osc1 MAPK is phosphorylated under high osmotic conditions, indicating activation of Osc1 by high osmotic stress. Importantly, fludioxonil treatment also activates phosphorylation of Osc1, suggesting that improper activation of Osc1 by fludioxonil has negative effects on fungal growth. In the presence of fludioxonil, the wild‐type fungus was not able to infect the host plant because of a failure of appressorium‐mediated penetration, whereas osc1 mutants successfully infected plants. Analysis using a OSC1‐GFP fusion gene indicated that Osc1 is rapidly translocated to the nucleus in appressorial cells after the addition of fludioxonil, suggesting that fludioxonil impairs the function of infection structures by activation of Osc1. Furthermore, fludioxonil activates Hog1‐type MAPKs in the plant pathogenic fungi Cochliobolus heterostrophus and Botrytis cinerea. These results strongly suggest that fludioxonil acts as a fungicide, in part, through activation of the MAPK cascade in fungal pathogens.
Study of rod- and cone-driven oscillatory potentials in mice.

PURPOSE To characterize rod- and cone-driven oscillatory potentials (OPs) in mice. METHODS Dark- and light-adapted electroretinograms (ERGs) were obtained in three mouse models: wild-type C57BL/6J mouse, cone photoreceptor function loss 1 (cpfl1) mouse, and rhodopsin knockout (rho-/-) mouse. A Butterworth filter was used to extract OPs from ERG signals. Latencies were calculated from the extracted OPs. Major frequency components were determined from OP power spectra computed using fast Fourier transform (FFT). The total power of the OP signal (an alternative measurement of amplitude) was calculated by numerically integrating the area enclosed by its frequency spectra, which is analogous to the total energy of mechanical vibration. RESULTS In C57BL/6J mice, dark- and light-adapted OPs had distinctly different peak frequencies (100 to 120 Hz and 70 to 85 Hz, respectively). In cpfl1 mice which possess pure rod ERGs, dark-adapted OPs had a peak frequency similar to those of the wild-type mice, whereas light-adapted ERGs and OPs were not detectable. In rho-/- mice with pure cone functions, both dark-adapted and light-adapted OPs had peak frequencies of 70 to 90 Hz, which were similar to those obtained from light-adapted OPs in wild-type mice. The total power of cone-driven OPs was less than 5% that of rod-driven OPs. In time-domain, cone-driven OPs occurred approximately 13 ms after rod-driven OPs. CONCLUSIONS Cone- and rod-driven OPs exhibit significantly different characteristics in peak frequency, latency, and total power. By using these characteristics, it is possible to differentiate cone- and rod-driven OPs in mouse models. Understanding these OP features is essential for analyzing OPs.
Emergency transcatheter aortic valve replacement in patients with cardiogenic shock due to acutely decompensated aortic stenosis.

AIMS To assess outcomes of TAVR as a rescue therapy in patients with cardiogenic shock due to acutely decompensated aortic stenosis. METHODS AND RESULTS Of 771 high-risk patients who underwent TAVR, 27 (3.5%; 78±9 years; 12 men) were treated emergently due to acutely decompensated aortic stenosis with cardiogenic shock. SAPIEN and CoreValve prostheses were implanted in 11 and 16 patients, respectively: the transfemoral access route was used in 25. Three patients died within 72 hours of successful valve deployment, and a further six died within a month, giving a 30-day mortality of 33.3%, which was significantly higher than in electively treated patients (7.7%, p<0.0001). Univariate predictors of 30-day mortality in cardiogenic-shock patients were baseline cardiac output <3.0 l/min, reduced cardiac power index, impaired renal function, and mechanical ventilation, as well as severe acute kidney injury after TAVR. Estimated one-year survival was 59.3% in emergently and 82.7% in electively treated patients (p=0.0009). However, 30-day landmark analysis showed no difference in cumulative survival between TAVR modalities. In cardiogenic-shock patients without concomitant reduced cardiac output and impaired renal function at baseline (n=22), estimated one-year survival was 72.7%. CONCLUSIONS TAVR should be considered a reasonable rescue therapy in patients with cardiogenic shock secondary to decompensated aortic stenosis.
ALIMENTARY TRACT: ESOPHAGUS Motor and Sensory Function of the Esophagus Revelations Through Ultrasound Imaging

Catheter based high frequency intraluminal ultrasound (HFIUS) imaging is a powerful tool to study esophageal sensory and motor function and dysfunction in vivo in humans. It has provided a number of important insights into the longitudinal muscle function of the esophagus. Based on the ultrasound images and intraluminal pressure recordings, it is clear that there is synchrony in the timing as well as the amplitude of contraction between the circular and the longitudinal muscle layers of the esophagus in normal subjects. On the other hand, in patients with spastic disorders of the esophagus, there is an asynchrony of contraction related to the timing and amplitude of contraction of the two muscle layers during peristalsis. Achalasia, diffuse esophageal spasm, and nutcracker esophagus (spastic motor disorders of the esophagus) are associated with hypertrophy of the circular as well as longitudinal muscle layers. A sustained contraction of the longitudinal muscle of the esophagus is temporally related to chest pain and heartburn and may very well be the cause of symptoms. Longitudinal muscle function of the esophagus can be studied in vivo in humans using dynamic ultrasound imaging. Longitudinal muscle dysfunction appears to be important in the motor and sensory disorders of the esophagus.
Neurocognitive profiles in help-seeking individuals: comparison of risk for psychosis and bipolar disorder criteria

Background. Neurocognitive deficits are important aspects of the schizophrenic disorders because they have a strong impact on social and vocational outcomes. We expanded on previous research by focusing on the neurocognitive profiles of persons at high risk (HR) or ultra-high risk (UHR) for schizophrenic and affective psychoses. Our main aim was to determine whether neurocognitive measures are sufficiently sensitive to predict a group affiliation based on deficits in functional domains. Method. This study included 207 help-seeking individuals identified as HR (n = 75), UHR (n = 102) or at high risk for bipolar disorder (HRBip; n = 30), who were compared with persons comprising a matched, healthy control group (CG; n = 50). Neuropsychological variables were sorted according to their load in a factor analysis and were compared among groups. In addition, the likelihood of group membership was estimated using logistic regression analyses. Results. The performance of HR and HRBip participants was comparable, and intermediate between the controls and UHR. The domain of processing speed was most sensitive in discriminating HR and UHR [odds ratio (OR) 0.48, 95% confidence interval (CI) 0.28–0.78, p = 0.004] whereas learning and memory deficits predicted a conversion to schizophrenic psychosis (OR 0.47, 95% CI 0.25–0.87, p = 0.01). Conclusions. Performances on neurocognitive tests differed among our three at-risk groups and may therefore be useful in predicting psychosis. Overall, cognition had a profound effect on the extent of general functioning and satisfaction with life for subjects at risk of psychosis. Thus, this factor should become a treatment target in itself.
QTL controlling grain filling under terminal drought stress in a set of wild barley introgression lines

Drought is a major abiotic stress impeding the yield of cereal crops globally. Particularly in Mediterranean environments, water becomes a limiting factor during the reproductive developmental stage, causing yield losses. The wild progenitor of cultivated barley Hordeum vulgare ssp spontaneum (Hsp) is a potentially useful source of drought tolerance alleles. Wild barley introgression lines like the S42IL library may facilitate the introduction of favorable exotic alleles into breeding material. The complete set of 83 S42ILs was genotyped with the barley 9k iSelect platform in order to complete genetic information obtained in previous studies. The new map comprises 2,487 SNPs, spanning 989.8 cM and covering 94.5% of the Hsp genome. Extent and positions of introgressions were confirmed and new information for ten additional S42ILs was collected. A subset of 49 S42ILs was evaluated for drought response in four greenhouse experiments. Plants were grown under well-watered conditions until ten days post anthesis. Subsequently drought treatment was applied by reducing the available water. Several morphological and harvest parameters were evaluated. Under drought treatment, trait performance was reduced. However, there was no interaction effect between genotype and treatment, indicating that genotypes, which performed best under control treatment, also performed best under drought treatment. In total, 40 QTL for seven traits were detected in this study. For instance, favorable Hsp effects were found for thousand grain weight (TGW) and number of grains per ear under drought stress. In particular, line S42IL-121 is a promising candidate for breeding improved malting cultivars, displaying a TGW, which was increased by 17% under terminal drought stress due to the presence of an unknown wild barley QTL allele on chromosome 4H. The introgression line showed a similar advantage in previous field experiments and in greenhouse experiments under early drought stress. We, thus, recommend using S42IL-121 in barley breeding programs to enhance terminal drought tolerance.
Hyperechogenic Bowel: Etiologies, Management, and Outcome according to Gestational Age at Diagnosis in 279 Consecutive Cases in a Single Center

Abstract Introduction The aim of the study was to investigate perinatal outcome of fetuses with hyperechogenic bowel (HB) in relation to gestational age at diagnosis. Materials and Methods This is a retrospective observational study of fetal HB cases from 2002 to 2012. Patients were divided into three groups according to trimester at diagnosis. For each group, data from fetal ultrasound examination, fetal medicine investigations, intrapartum cares, and neonatal outcome were obtained. Results A diagnosis of HB was made in 279 fetuses among them 17 (6%) during the first trimester, 186 (67%) during the second trimester, and 75 (27%) during the third trimester. A significant prevalence of maternal comorbidities was noticed in group 1 (12%: p = 0.02). A chromosomal defect was identified in 13% of the fetuses without difference among the three groups. HB was associated with prenatal infection in 11.5% (n = 32) of the cases, with an equal distribution between groups 2 and 3. Intrauterine growth retardation was noticed in 23% (n = 64) of the cases with a slightly high prevalence in groups 1 (35%). HB was the only ultrasonographic intestinal soft marker in 80% (n = 223) of the fetuses, two-third of them were detected during the first and the second trimesters (p = 0.001). However, HB was associated with bowel dilation in 33% of the cases diagnosed during the third trimester (p = 001). Ultrasonographic extraintestinal anomalies were identified in 30% of the fetuses with a higher prevalence in group 1 (59%). HB resolved spontaneously in 55 (19.7%) cases—without difference among the three groups. In group 1 we recorded a significant prevalence of intrauterine demise (23.5%, p = 0.004). Two hundred twenty-seven (81.3%) pregnancies resulted in live-born neonates; among them gastrointestinal anomalies were noticed in 12.5% with a significant prevalence in group 3 (36%) compared with 6 and 5.4% in groups 1 and 2, respectively (p = 0.001). Extraintestinal anomalies were confirmed in 27% of the cases, whereas postnatal mortality rate was of 7% without differences between the three groups. Conclusion Detection of HB during the first trimester is associated with an increased risk for maternal comorbidities, intrauterine growth retardation, and adverse pregnancy outcome. Moreover, if HB is detected during the second trimester, it is associated with a favorable prognosis. Otherwise, HB detected during the third trimester is associated with a significant risk of gastrointestinal anomaly.
[Evaluation of clinical significance of chronic obstructive pulmonary disease assessment test].

OBJECTIVE To determine the reliability and validity of the COPD assessment test (CAT) Chinese version in patients with chronic obstructive pulmonary disease (COPD), and to study its value in evaluating quality of life in Chinese patients. METHODS One hundred and thirty-five patients with COPD in stable condition from Peking Union Medical College Hospital were assessed by interview with CAT Chinese version, and underwent pulmonary function test on the same day. The validity was documented by performing correlation analysis, and Pearson's correlation coefficients were calculated. The stages of COPD determined by CAT score and lung function were compared to observe the value of CAT in determining disease severity. RESULTS Cronbach's alpha of CAT Chinese version was 0.805. CAT score increased with the severity of the disease, and was negatively correlated to FEV(1)% of predicted (r = -0.567, P < 0.01). CAT score varied significantly in patients (10 ± 5, 16 ± 6, 21 ± 7 and 23 ± 6), with different severity of COPD (χ(2) = 48.437, P < 0.01). There was a high degree of consistency between the stages of COPD determined by CAT score and lung function. CONCLUSIONS The Chinese version of the CAT had good internal consistency reliability and validity, and can be used to assess the quality of life for Chinese COPD patients. It provided a simple, valid and standardized measurement of COPD health status.
Assessment of 3D motion increases the applicability of accelerometers for monitoring left ventricular function.

OBJECTIVES Miniaturized accelerometers attached to the epicardium have been shown to provide useful clinical information. However, attachment of such a sensor has been cumbersome due to requirement of aligning the three sensor axes with the cardiac coordinate axes, limiting clinical utility. We propose a new method to process the three-dimensional (3D) accelerometer signal that does not require such alignment. METHODS In 20 open-chest pigs, miniaturized 3D accelerometers were fixated on the epicardium in apical and basal regions of left ventricle. Accelerations in circumferential, longitudinal and radial directions were measured and a 3D velocity vector was calculated. Systolic velocity along the 3D vector and velocities in circumferential, longitudinal and radial directions were compared with the positive time derivate of left ventricular pressure during changes in global left ventricular function (epinephrine, esmolol and fluid loading) and to strain echocardiography during left anterior descending artery occlusion. RESULTS Distinct changes in all accelerometer velocities were observed during alterations on global and regional left ventricular function. Accelerometer 3D and circumferential systolic velocities in apical region best reflected left ventricular function during interventions on global function by correlating significantly with the positive time derivate of left ventricular pressure, r = 0.83 and r = 0.86, respectively. The accelerometer 3D velocity also demonstrated equally good capacity as circumferential velocity in discriminating coronary occlusion from interventions on global left ventricular function with sensitivity/specificity of 0.90/0.83 and 0.90/0.86, respectively. CONCLUSIONS Accelerometer 3D systolic velocity showed very good correspondence to changes in global and regional left ventricular function. Our results demonstrate that by the use of the accelerometer 3D motion vector, no alignment of the sensor with the cardiac coordinate axes was required. This increases potential clinical applicability of the accelerometer in cardiac surgery.
Cholesterol-dependent Syntaxin-4 and SNAP-23 Clustering Regulates Caveolar Fusion with the Endothelial Plasma Membrane*

We determined the organization of target (t) SNARE proteins on the basolateral endothelial plasma membrane (PM) and their role in the mechanism of caveolar fusion. Studies were performed in a cell-free system involving endothelial PM sheets and isolated biotin-labeled caveolae. We monitored the fusion of caveolae with the PM by the detection of biotin-streptavidin complexes using correlative high resolution fluorescence microscopy and gold labeling electron microscopy on ultrathin sections of PM sheets. Imaging of PM sheets demonstrated and biochemical findings showed that the t-SNARE proteins present in endothelial cells (SNAP-23 and syntaxin-4) formed cholesterol-dependent clusters in discrete areas of the PM. Upon fusion of caveolae with the target PM, 50% of the caveolae co-localized with the t-SNARE clusters, indicating that these caveolae were at the peak of the fusion reaction. Fluorescent streptavidin staining of PM sheets correlated with the ultrastructure in the same area. These findings demonstrate that t-SNARE clusters in the endothelial target PM serve as the fusion sites for caveolae during exocytosis.