Miracle-dz/UniFAR-FTUs huggingface dataset:
The OECD program to validate the rat uterotrophic bioassay. Phase 2: dietary phytoestrogen analyses.

Many commercial laboratory diets have detectable levels of isoflavones (e.g., phytoestrogens such as genistein [GN]) that have weak estrogenic activity both in vitro and in vivo. During validation studies of the uterotrophic bioassay, diet samples from 20 participating laboratories were collected and analyzed for three major phytoestrogens: GN, daidzein (DN), and coumestrol (CM). Soy phytoestrogens GN and DN were found at total phytoestrogen levels from 100 to 540 microg/g laboratory diet; a forage phytoestrogen, CM, ranged from nondetectable to 4 microg/g laboratory diet. The phytoestrogen levels were compared with both baseline uterine weights of the control groups and with the relative uterine weight increase of groups administered two weak estrogen agonists: bisphenol A (BPA) and nonylphenol (NP). The comparison uses a working assumption of additivity among the phytoestrogens, despite several significant qualifications to this assumption, to estimate total genistein equivalents (TGE). Some evidence was found that phytoestrogen levels in the diet > 325-350 microg/g TGE could diminish the responsiveness of the uterotrophic bioassay to weak agonists. This was especially true for the case of the intact, immature female version of the uterotrophic bioassay, where higher food consumption relative to body weight leads to higher intakes of dietary phytoestrogens versus ovariectomized adults. This dietary level is sufficient in the immature female to approach a biological lowest observable effect level for GN of 40-50 mg/kg/day. These same data, however, show that low to moderate levels of dietary phytoestrogens do not substantially affect the responsiveness of the assay with weak estrogen receptor agonists such as NP and BPA. Therefore, laboratories conducting the uterotrophic bioassay for either research or regulatory purposes may routinely use diets containing levels of phytoestrogens < 325-350 microg/g TGE without impairing the responsiveness of the bioassay.
Extreme Rainfall and Flooding from Supercell Thunderstorms

Supercell thunderstorms, the storm systems responsible for most tornadoes, have often been dismissed as flood hazards. The role of supercell thunderstorms as flood agents is examined through analyses of storm systems that occurred in Texas (5‐6 May 1995), Florida (26 March 1992), Nebraska (20‐21 June 1996), and Pennsylvania (18‐19 July 1996). Particular attention is given to the ‘‘Dallas Supercell,’’ which resulted in 16 deaths from flash flooding and more than $1 billion in property damage during the evening of 5 May 1995. Rainfall analyses using Weather Surveillance Radar-1988 Doppler (WSR-88D) reflectivity observations and special mesonet rain gauge observations from Dallas, Texas, show that catastrophic flash flooding resulted from exceptional rainfall rates at 5‐60-min timescales. The spatial structure of extreme rainfall was linked to supercell structure and motion. The ‘‘Orlando Supercell’’ produced extreme rainfall rates (greater than 300 mm h 21) at 1‐5-min timescales over a dense rain gauge network. The Nebraska and Pennsylvania storm systems produced record flooding over larger spatial scales than the Texas and Florida storms, by virtue of organization and motion of multiple storms over the same region. For both the Nebraska and Pennsylvania storms, extreme rainfall and tornadoes occurred in tandem. Severe rainfall measurement problems arise for supercell thunderstorms, both from conventional gauge networks and weather radar. It is hypothesized that supercell storms play a significant role in the ‘‘climatology’’ of extreme rainfall rates (100-yr return interval and greater) at short time intervals (1‐60 min) in much of the central and eastern United States.
Anatomical Information Content in the Ediacaran Fossils and Their Possible Zoological Affinities1

Abstract Various modes of preservation of Ediacaran fossils in different sediments, quartz sand at Zimnie Gory in northern Russia and lime mud at Khorbusuonka in northern Yakutia, show that the sediment was liquid long after formation of the imprints and that its mineralogy did not matter. A laminated 2 mm thick microbial mat is preserved intact at Zimnie Gory. It stabilized the sediment surface allowing formation of imprints on it. The soft body impressions on the under surface of the sand bed and within it developed owing to formation of a less than 1 mm thin “death mask” by precipitation of iron sulfide in the sediment. Fossils of the same species or even parts of the same organism may be preserved differently. Internal organs either collapsed, their cavities being filled with sediment from above, or resisted compression more effectively than the rest of the body. This allows restoration of the original internal anatomy of Ediacaran organisms. At Zimnie Gory numerous series of imprints of Yorgia on the clay bottom surface with the collapsed body at their end represent death tracks. The environment of formation of the Ediacaran fossils was thus inhospitable to most organisms. Those adapted to it, namely the radially organized frondose Petalonamae (of possible ctenophoran affinities), anchored in the mat with their basal bulbs. They evolved towards sessile life possibly in symbiosis with photo- or chemoautotrophic microorganisms. Vagile Ediacaran organisms belong mostly to the Dipleurozoa (somewhat resembling chordates and nemerteans), characterized by a segmented dorsal hydraulic skeleton, intestine with metameric caeca, and serial gonads. Only a fraction of the actual Precambrian faunal diversity is represented in the Ediacaran biota.
Depressive Symptom Clusters and 5-Year Incidence of Coronary Artery Calcification: The Coronary Artery Risk Development in Young Adults Study

Background— Because depression is a multidimensional construct and few studies have compared the relative importance of its facets in predicting cardiovascular risk, we evaluated the utility of depressive symptom clusters in predicting the 5-year incidence of coronary artery calcification (CAC). Methods and Results— Participants were 2171 middle-aged adults (58% female; 43% black) from the Coronary Artery Risk Development in Young Adults (CARDIA) study who were free of cardiovascular disease. Depressive symptom clusters (z scores) were measured by questionnaires in 2000 to 2001, and CAC was measured by electron beam computed tomography in 2000 to 2001 and 2005 to 2006. There were 243 cases (11%) of incident CAC, defined as the absence of CAC at baseline and the presence of CAC at follow-up. Total depressive symptoms (odds ratio, 1.16; 95% confidence interval, 1.02–1.33; P=0.03) and the depressed affect cluster (odds ratio, 1.17; 95% confidence interval, 1.03–1.33; P=0.02) predicted incident CAC; however, the somatic, interpersonal distress, low positive affect, and pessimism clusters did not. The depressed affect–incident CAC relationship was independent of age, sex, race, education, and antidepressant use; was similar across sex and racial groups; and was partially accounted for by tobacco use and mean arterial pressure. Conclusions— In contrast to recent results indicating that the somatic cluster is the most predictive of cardiovascular outcomes, we found that the prospective association between depressive symptoms and incident CAC was driven by the depressed affect cluster. Our findings raise the possibility that there may not be 1 facet of depression that is the most cardiotoxic across all contexts.
Distribution of calretinin‐immunoreactivity in the rat entorhinal cortex: Coexistence with GABA

Inhibitory neurons in the entorhinal cortex control information flow between the cortical areas and the hippocampus. We characterized the inhibitory circuits in the rat entorhinal cortex by analyzing the distribution of calretinin‐immunoreactivity and its colocalization with glutamate decarboxylase (GAD) and gamma‐aminobutyric acid (GABA). The location of calretinin‐immunoreactive (IR) neurons and terminals varies between the different layers and subfields of the entorhinal cortex. The immunopositive neurons can be divided into two major morphological classes: bipolar and multipolar, which have two or more long, aspiny or sparsely spiny dendrites that extend through several layers. In addition, there are unclassified immunopositive neurons that have large lightly stained somata. They are located primarily in layer V. Colocalization analyses with GAD and GABA revealed that approximately 40% (657 out of 1,777) of all calretinin‐IR cells within the entorhinal cortex contain GAD or GABA. In layers I–III, over 90% of the calretinin‐IR neurons contain GAD or GABA. In layers V–VI, however, most of the calretinin‐IR neurons do not colocalize with either GAD or GABA. The distribution patterns of calretinin‐immunoreactivity in the entorhinal cortex is consistent with the partitioning of the rat entorhinal cortex into six subfields. Furthermore, calretinin is expressed in a morphologically heterogeneous population of cells in the rat entorhinal cortex which includes both GABAergic and non‐GABAergic neurons. J. Comp. Neurol. 378:363–378, 1997. © 1997 Wiley‐Liss, Inc.
Application of Thoracoscopic Hybrid Surgery in the Treatment of Stage III Tuberculous Empyema.

BACKGROUND To investigate the efficacy and value of thoracoscopic hybrid surgery in the treatment of stage III chronic tuberculous empyema (CTE). METHODS 48 patients diagnosed as CTE with pleural thickening and encysted abscess cavity from were treated by hybrid operation (HO). Small incision operation was first used for resection of thickening pleural fibreboard and decortication of parietal pleura. Then, thoracoscopy was guided into chest to decorticate the visceral pleurali. Additional 25 patients with open operation of pleurectomy were set as control. RESULTS The average operation time of HO group was 70 ± 22 min compared to 130 ± 32 min of control. The amount of bleeding, hospitalization time and chest tube drainage of HO group (200 ± 55 ml, 18 ± 1.2 days, 3.5 ± 1.5 days) were significantly decreased compared to control (400 ± 45 ml, 28 ± 4.5 days, 6.5 ± 2.5 days). Post operation complications occurred in 5 (10.42%) and 3 (12%) cases for HO group and control, respectively. CONCLUSIONS In stage III CTE, the small incision assisted thoracoscopic hybrid surgery help to remove thickening parietal pleura, promote the application of thoracoscopy, which has obvious advantages compared to traditional surgery.
The Next Generation Sky Survey and the Quest for Cooler Brown Dwarfs

The Next Generation Sky Survey (NGSS) is a proposed NASA MIDEX mission to map the entire sky in four infrared bandpasses - 3.5, 4.7, 12, and 23 um. The seven-month mission will use a 50-cm telescope and four-channel imager to survey the sky from a circular orbit above the Earth. Expected sensitivities will be half a million times that of COBE/DIRBE at 3.5 and 4.7 um and a thousand times that of IRAS at 12 and 23 um. NGSS will be particularly sensitive to brown dwarfs cooler than those presently known. Deep absorption in the methane fundamental band at 3.3 um and a predicted 5-um overluminosity will produce uniquely red 3.5-to-4.7 um colors for such objects. For a limiting volume of 25 pc, NGSS will completely inventory the Solar Neighborhood for brown dwarfs as cool as Gl 229B. At 10 pc, the census will be complete to 500 K. Assuming a field mass function with alpha = 1, there could be one or more brown dwarfs warmer than 150 K lying closer to the Sun than Proxima Centauri and detectable primarily at NGSS wavelengths. NGSS will enable estimates of the brown dwarf mass and luminosity functions to very cool temperatures and will provide both astrometric references and science targets for NGST.
Parasite identification, succession and infection pathways in perch fry (Perca fluviatilis): new insights through a combined morphological and genetic approach

SUMMARY Identification of parasite species is particularly challenging in larval and juvenile hosts, and this hampers the understanding of parasite acquisition in early life. The work described here employs a new combination of methods to identify parasite species and study parasite succession in fry of perch (Perca fluviatilis) from Lake Constance, Germany. Classical morphological diagnostics are combined with sequence comparisons between parasite life-stages collected from various hosts within the same ecosystem. In perch fry at different stages of development, 13 different parasite species were found. Incomplete morphological identifications of cestodes of the order Proteocephalidea, and trematodes of the family Diplostomatidae were complemented with sequences of mitochondrial DNA (cytochrome oxidase 1) and/or nuclear (28 s rDNA) genes. Sequences were compared to published data and used to link the parasites in perch to stages from molluscs, arthropods and more easily identifiable developmental stages from other fishes collected in Lake Constance, which both aided parasite identification and clarified transmission pathways. There were distinct changes in parasite community composition and abundance associated with perch fry age and habitat shifts. Some parasites became more abundant in older fish, whereas the composition of parasite communities was more strongly affected by the ontogenetic shifts from the pelagic to the littoral zone.
Noninvasive Ultrasound Molecular Imaging of the Effect of Statins on Endothelial Inflammatory Phenotype in Early Atherosclerosis

Background/Objectives Inflammatory changes on the endothelium are responsible for leukocyte recruitment to plaques in atherosclerosis. Noninvasive assessment of treatment-effects on endothelial inflammation may be of use for managing medical therapy and developing novel therapies. We hypothesized that molecular imaging of vascular cell adhesion molecule-1 (VCAM-1) with contrast enhanced ultrasound (CEU) could assess treatment effects on endothelial phenotype in early atherosclerosis. Methods Mice with atherosclerosis produced by gene deletion of the LDL-receptor and Apobec-1-editing protein were studied. At 12 weeks of age, mice received 8 weeks of regular chow or atorvastatin-enriched chow (10 mg/kg/day). At 20 weeks, CEU molecular imaging for aortic endothelial VCAM-1 expression was performed with VCAM-1-targeted (MBVCAM) and control microbubbles (MBCtr). Aortic wall thickness was assessed with high frequency ultrasound. Histology, immunohistology and Western blot were used to assess plaque burden and VCAM-1 expression. Results Plaque burden was reduced on histology, and VCAM-1 was reduced on Western blot by atorvastatin, which corresponded to less endothelial expression of VCAM-1 on immunohistology. High frequency ultrasound did not detect differences in aortic wall thickness between groups. In contrast, CEU molecular imaging demonstrated selective signal enhancement for MBVCAM in non-treated animals (MBVCAM 2±0.3 vs MBCtr 0.7±0.2, p<0.01), but not in statin-treated animals (MBVCAM 0.8±0.2 vs MBCtr 1.0±0.2, p = ns; p<0.01 for the effect of statin on MBVCAM signal). Conclusions Non-invasive CEU molecular imaging detects the effects of anti-inflammatory treatment on endothelial inflammation in early atherosclerosis. This easily accessible, low-cost technique may be useful in assessing treatment effects in preclinical research and in patients.
Rocket‐borne spectroscopic measurements in the ultraviolet aurora: The Lyman‐Birge‐Hopfield bands

Ultraviolet emissions from Earth's aurora were observed at wavelengths between 1,675 and 2,075 {angstrom} by a sounding rocket payload launched at Churchill, Canada, on March 28, 1980. The emissions from the Lyman-Birge-Hopfield (LBH) and Vegard-Kaplan (VK) bands of N{sub 2} were observed and analyzed to determine the relative populations of the {nu}{prime} = 0-6 levels of the {alpha}{sup 1}{pi}{sub g} state and the {nu}{prime} = 4, 6, 7, and 8 levels of the {Alpha}{sup 3}{Sigma}{sub g}{sup +} state, respectively. The relative population of higher vibrational levels of the {Alpha}{sup 3}{Sigma}{sub g}{sup +} state are consistent with direct excitation and cascade. The relative populations of the vibrational levels of the {alpha}{sup 1}{pi}{sub g} state peak at {nu}{prime} = 2. Such a distribution has not been observed previously in the aurora.
Expression levels of adiponectin receptors and periodontitis.

BACKGROUND AND OBJECTIVE We recently showed that adiponectin, an adipocyte-derived cytokine, may function as a negative regulator of the Toll-like receptor signaling pathway and of osteoclast formation in periodontal disease. In this study, we investigated whether the expression levels of adiponectin receptors (AdipoR1 and AdipoR2) are related to the presence of periodontitis. MATERIAL AND METHODS We initially examined, using RT-PCR, the expression of the AdipoR1 and AdipoR2 genes at the mRNA level in several oral tissues of C57BL mice. Next, we investigated (using real-time PCR assays) whether inflammatory cytokines, such as tumor necrosis factor-alpha, could affect the expression levels of these genes in human gingival fibroblasts. Lastly, we compared the expression levels of these receptor proteins in gingival tissues between two healthy subjects and five patients with severe periodontal disease using western blotting analysis. RESULTS The AdipoR1 and AdipoR2 receptors were ubiquitously expressed in the oral tissues of mice. We observed that treatment with tumor necrosis factor-alpha could significantly reduce the expression levels of both AdipoR1 and AdipoR2 genes in human gingival fibroblasts. Moreover, we found that the expression of both receptors was lower in periodontal tissues from patients with severe periodontitis than in patients with healthy periodontal tissues. CONCLUSION These observations suggest that adiponectin may not function efficiently in sites of periodontal disease because of a decrease in the number of its receptors, and this probable dysfunction may play a role in worsening periodontitis in patients.
Future Perspectives of ERAS: A Narrative Review on the New Applications of an Established Approach

ERAS approach (Enhanced Recovery After Surgery) is a multimodal, perioperative pathway designed to achieve early recovery after surgery. ERAS has shown documented efficacy in elective surgery, and the concept of “multimodal” and “multidisciplinary” approach seems still to be of higher importance than each single item within ERAS protocols. New perspectives include the use of ERAS in emergency surgery, where efficacy and safety on outcome have been documented, and flexibility of traditional items may add benefits for traditionally high-risk patients. Obstetric surgery, as well, may open wide horizons for future research, since extremely poor data are currently available, and ERAS benefits may translate even on the baby. Finally, the concept of “outcome” may be extended when considering the specific setting of cancer surgery, in which variables like cancer recurrence, early access to adjuvant therapies, and, finally, long-term survival are as important as the reduced perioperative complications. In this perspective, different items within ERAS protocols should be reinterpreted and eventually integrated towards “protective” techniques, to develop cancer-specific ERAS approaches keeping pace with the specific aims of oncologic surgery.
The Bavieca open-source speech recognition toolkit

This article describes the design of Bavieca, an open-source speech recognition toolkit intended for speech research and system development. The toolkit supports lattice-based discriminative training, wide phonetic-context, efficient acoustic scoring, large n-gram language models, and the most common feature and model transformations. Bavieca is written entirely in C++ and presents a simple and modular design with an emphasis on scalability and reusability. Bavieca achieves competitive results in standard benchmarks. The toolkit is distributed under the highly unrestricted Apache 2.0 license, and is freely available on SourceForge.
Fronts in anomalous diffusion–reaction systems

A review of recent developments in the field of front dynamics in anomalous diffusion–reaction systems is presented. Both fronts between stable phases and those propagating into an unstable phase are considered. A number of models of anomalous diffusion with reaction are discussed, including models with Lévy flights, truncated Lévy flights, subdiffusion-limited reactions and models with intertwined subdiffusion and reaction operators.
Enteral nutritional intake in adult korean intensive care patients.

BACKGROUND Nutritional support is important for maximizing clinical outcomes in critically ill patients, but enteral nutritional intake is often inadequate. OBJECTIVE To assess the nutritional intake of energy and protein during the first 4 days after initiation of enteral feeding and to examine the relationship between intake and interruptions of enteral feeding in Korean patients in intensive care. METHODS A cohort of 34 critically ill adults who had a primary medical diagnosis and received bolus enteral feeding were studied prospectively. Energy and protein requirements were determined by using the Harris-Benedict equation and the American Dietetic Association equation. Energy and protein intake prescribed and received and the reasons for and lengths of feeding interruptions were recorded for 4 consecutive days immediately after enteral feeding began. RESULTS Although the differences between requirements and intakes of energy and protein decreased significantly, patients did not receive required energy and protein intake during the 4 days of the study. Energy intake prescribed was consistently less than required on each of the 4 days. Enteral nutrition was withheld for a mean of 6 hours per patient for the 4 days. Prolonged feeding interruptions due to gastrointestinal intolerance (r= -0.874; P < .001) and procedures (r= -0.839; P = .005) were negatively associated with the percentage of prescribed energy received. CONCLUSIONS Enteral nutritional intake was insufficient in bolus-fed Korean intensive care patients because of prolonged feeding interruptions and underprescription of enteral nutrition. Feeding interruptions due to gastrointestinal intolerance and procedures were the main contributors to inadequate energy intake.
Cultural selection drives the evolution of human communication systems

Human communication systems evolve culturally, but the evolutionary mechanisms that drive this evolution are not well understood. Against a baseline that communication variants spread in a population following neutral evolutionary dynamics (also known as drift models), we tested the role of two cultural selection models: coordination- and content-biased. We constructed a parametrized mixed probabilistic model of the spread of communicative variants in four 8-person laboratory micro-societies engaged in a simple communication game. We found that selectionist models, working in combination, explain the majority of the empirical data. The best-fitting parameter setting includes an egocentric bias and a content bias, suggesting that participants retained their own previously used communicative variants unless they encountered a superior (content-biased) variant, in which case it was adopted. This novel pattern of results suggests that (i) a theory of the cultural evolution of human communication systems must integrate selectionist models and (ii) human communication systems are functionally adaptive complex systems.
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

We describe the testing and release of AutoDock4 and the accompanying graphical user interface AutoDockTools. AutoDock4 incorporates limited flexibility in the receptor. Several tests are reported here, including a redocking experiment with 188 diverse ligand‐protein complexes and a cross‐docking experiment using flexible sidechains in 87 HIV protease complexes. We also report its utility in analysis of covalently bound ligands, using both a grid‐based docking method and a modification of the flexible sidechain technique. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009