Miracle-dz/UniFAR-FTUs huggingface dataset:
Cranial nerves of the coelacanth, Latimeria chalumnae [Osteichthyes: Sarcopterygii: Actinistia], and comparisons with other craniata.

We reconstructed the cranial nerves of a serially sectioned prenatal coelacanth, Latimeria chalumnae. This allowed us to correct several mistakes in the literature and to make broad phylogenetic comparisons with other craniates. The genera surveyed in our phylogenetic analysis were Eptatretus, Myxine, Petromyzon, Lampetra, Chimaera, Hydrolagus, Squalus, Mustelus, Polypterus, Acipenser, Lepisosteus, Amia, Neoceratodus, Protopterus, Lepidosiren, Latimeria and Ambystoma. Cladistic analysis of our data shows that Latimeria shares with Ambystoma two characters of the cranial nerves. Our chief findings are: 1) Latimeria possesses an external nasal papilla and pedunculated olfactory bulbs but lacks a discrete terminal nerve. In other respects its olfactory system resembles the plesiomorphic pattern for craniates. 2) The optic nerve is plicated, a character found in many but not all gnathostomes. Latimeria retains an interdigitated partial decussation of the optic nerves, a character found in all craniates surveyed. 3) The oculomotor nerve supplies the same extrinsic eye muscles as in lampreys and gnathostomes. As in gnathostomes generally, Latimeria has a ciliary ganglion but its cells are located intracranially in the root of the oculomotor nerve, and their processes reach the eye via oculomotor and profundal rami. 4) The trochlear nerve supplies the superior oblique muscle as in all craniates that have not secondarily reduced the eye and its extrinsic musculature. 5) The profundal ganglion and ramus are entirely separate from the trigeminal system, with no exchange of fibers. This character has an interesting phylogenetic distribution: in hagfishes, lampreys, lungfishes and tetrapods, the profundal and trigeminal ganglia are fused, whereas in other taxa surveyed the ganglia are separate. The principal tissues innervated by the profundal nerve are the membranous walls of the tubes of the rostral organ. 6) As in lampreys and gnathostomes, the trigeminal nerve has maxillary and mandibular rami. Unlike all other gnathostomes surveyed, the trigeminal nerve of Latimeria lacks a sizable superficial ophthalmic ramus. Thus, Latimeria lacks the well-developed superficial ophthalmic complex reported in most other fishes. As in gnathostomes generally, the maxillary ramus of the trigeminal nerve fuses with the buccal ramus of the anterodorsal lateral line nerve to form the buccal+maxillary complex. We reject the term 'Gasserian ganglion', which is often applied to the fused profundal and trigeminal ganglion of tetrapods. 7) The abducent nerve innervates not only the lateral rectus muscle (a character common to myopterygians) but also the basicranial muscle. As we previously reported, it is probable that the basicranial muscle of Latimeria is homologous to the ocular retracter muscle of amphibians. (ABSTRACT TRUNCATED AT 400 WORDS)
ST6Gal-I sialyltransferase promotes tumor necrosis factor (TNF)-mediated cancer cell survival via sialylation of the TNF receptor 1 (TNFR1) death receptor

Activation of the tumor necrosis factor receptor 1 (TNFR1) death receptor by TNF induces either cell survival or cell death. However, the mechanisms mediating these distinct outcomes remain poorly understood. In this study, we report that the ST6Gal-I sialyltransferase, an enzyme up-regulated in numerous cancers, sialylates TNFR1 and thereby protects tumor cells from TNF-induced apoptosis. Using pancreatic and ovarian cancer cells with ST6Gal-I knockdown or overexpression, we determined that α2-6 sialylation of TNFR1 had no effect on early TNF-induced signaling events, including the rapid activation of NF-κB, c-Jun N-terminal kinase (JNK), extracellular signal-regulated kinase (ERK), and Akt (occurring within 15 min). However, upon extended TNF treatment (6–24 h), cells with high ST6Gal-I levels exhibited resistance to TNF-induced apoptosis, as indicated by morphological evidence of cell death and decreased activation of caspases 8 and 3. Correspondingly, at these later time points, high ST6Gal-I expressers displayed sustained activation of the survival molecules Akt and NF-κB. Additionally, extended TNF treatment resulted in the selective enrichment of clonal variants with high ST6Gal-I expression, further substantiating a role for ST6Gal-I in cell survival. Given that TNFR1 internalization is known to be essential for apoptosis induction, whereas survival signaling is initiated by TNFR1 at the plasma membrane, we examined TNFR1 localization. The α2-6 sialylation of TNFR1 was found to inhibit TNF-induced TNFR1 internalization. Thus, by restraining TNFR1 at the cell surface via sialylation, ST6Gal-I acts as a functional switch to divert signaling toward survival. These collective findings point to a novel glycosylation-dependent mechanism that regulates the cellular response to TNF and may promote cancer cell survival within TNF-rich tumor microenvironments.
The Best Predictors of Survival: Do They Vary by Age, Sex, and Race?

We consider a broad set of variables used by social scientists and clinicians to identify the leading predictors of five-year survival among American adults. We address a question not considered in earlier research: Do the strongest predictors of survival vary by age, sex or race/ethnicity? The analysis uses hazard models with 30 well-established predictors to examine five-year survival in the National Health and Nutrition Examination Survey. We find that the simple measure of self-assessed health and self-reported measures of functional ability and disability are the strongest predictors in all demographic groups, and are generally ranked considerably higher than biomarkers. Among the biomarkers, serum albumin is highly ranked in most demographic groups, whereas clinical measures of cardiovascular and metabolic function are consistently among the weakest predictors. Despite these similarities, there is substantial variation in the leading predictors across demographic groups, most notably by race and ethnicity
Arsenic exposure assists ccm3 genetic polymorphism in elevating blood pressure

Epidemiologic study has suggested that arsenic exposure is positively related to increased blood pressure. However, the underlying mechanism concerning interaction between genetic polymorphisms and arsenic exposure remains unclear. In present study, within 395 Chinese, the effects of interaction between arsenic exposure and CCM3 gene polymorphisms on elevation of blood pressure were probed by multiple Logistic regression models after adjusting for confounding factors. Firstly, we found that serum arsenic was positively associated with blood pressure, cholesterol, glucose and C-reactive protein. Then, adjusted for confounding factors of age, gender, smoking, alcohol consumption, BMI and degree of education, arsenic exposure incurred the hazard of increased systolic pressure and diastolic pressure, with odds ratios (ORs) being 1.725 and 1.425, respectively. Distinctly, we found that interactions between rs3804610* rs9818496, rs6784267*rs9818496, and rs3804610* rs6784267 variant genotype can increase significantly risks of SBP. Additionally, interactions between rs9818496, rs3804610 and rs6784267 genotypic variantions and arsenic exposure boosted the hazard of increased systolic pressure, with ORs being 1.496, 1.496 and 1.312. In conclusion, our fingdings suggest that As exposure of population can assist CCM3 polymorphism in elevating SBP.
Accurate gradient computations at interfaces using finite element methods

Abstract New finite element methods are proposed for elliptic interface problems in one and two dimensions. The main motivation is to get not only an accurate solution, but also an accurate first order derivative at the interface (from each side). The key in 1D is to use the idea of Wheeler (1974). For 2D interface problems, the point is to introduce a small tube near the interface and propose the gradient as part of unknowns, which is similar to a mixed finite element method, but only at the interface. Thus the computational cost is just slightly higher than in the standard finite element method. We present a rigorous one dimensional analysis, which shows a second order convergence order for both the solution and the gradient in 1D. For two dimensional problems, we present numerical results and observe second order convergence for the solution, and super-convergence for the gradient at the interface.
Globalization and the Environmental Impact of FDI

We analyze the environmental impact of capital inflows and investigate the halo effect (FDI improves the environment). We control for the type of FDI inflows, the EKC (Environmental Kuznets Curve) effect and country income level, and find (i) a differential industry effect: while total foreign investment in aggregate has a negative effect on all countries, this can be traced in particular to capital flows to manufacturing and nonfinancial services sectors. ; (ii) an income inequality effect: foreign investment flowing into poorer countries has harmful effects on environment consistent with the race-to-the bottom argument, while capital flowing to richer countries has a beneficial effect and supports the halo effect; (iii) the EKC effect depends on the sector absorbing the FDI and again income level of the country. We show that studies relying only on firm level or aggregate data, miss the sectoral spillovers, and thus may lead to misleading conclusions. Nadia Doytch Department of Economics, School of Business Brooklyn College City University of New York ndoytch@brooklyn.cuny. edu Merih Uctum Ph. D. Program in Economics Graduate Center, CUNY 365 5th Avenue New York, NY 10016 muctum@gc.cuny. edu
Application of Classification Tree and Neural Network Algorithms to the Identification of Serological Liver Marker Profiles for the Diagnosis of Hepatocellular Carcinoma

Objective: Although many attempts have been made to identify tumour-specific α-fetoprotein (AFP) glycoforms or other serological markers for the diagnosis of hepatocellular carcinoma (HCC), none of the available markers has, so far, shown satisfactory sensitivity and specificity. Here we aimed to apply classification tree and neural network algorithms to interpret the levels of multiple serological liver markers to improve overall specificity and sensitivity, particularly with a view to discriminating between liver cirrhosis with and without HCC. Methods: We developed classification trees and neural networks that identified serological liver marker profiles comprising AFP, α1-antitrypsin (A1AT), α2-macroglobulin (A2MG), thyroxine-binding globulin (TBG), transferrin and albumin as well as sex and age, which might permit the diagnosis of HCC. Data were collected from 65 HCC patients, 51 patients with liver cirrhosis alone (LC) and 51 normal healthy subjects. Results: The generated classification trees and neural networks showed similar diagnostic values in differentiating HCC from LC. The classification trees identified AFP, A1AT and albumin as the most important classification parameters, whereas the neural networks identified A2MG, AFP, A1AT and albumin as the predominant factors. The classification logic of the classification trees indicated that more HCC cases could be identified among cases with slightly elevated AFP levels by using the serum levels of A1AT and albumin. The neural networks were also useful for the identification of the HCC cases when the AFP levels were below 500 ng/ml (p < 0.005). The neural networks could identify HCC cases with AFP levels within the normal range, but the classification trees could not. By combining the conventional AFP test and the neural networks, the overall diagnostic sensitivity for HCC was significantly increased from 60.0 to 73.8% (p < 0.05) while maintaining a high specificity (88.2%). The sensitivities for tumors of different sizes were similar. Conclusion: The neural network algorithm appeared to be more powerful than the classification tree algorithm in the identification of the distinctive serological liver marker profiles for the diagnosis of the HCC subgroup without significant elevation in serum AFP levels. By incorporating serological levels of other liver markers and including data from a large number of patients and control subjects, it should prove possible to develop a versatile neural network for early diagnosis of HCC.
The Association of Race/Ethnicity and Patch Test Results: North American Contact Dermatitis Group, 1998–2006

BackgroundThe North American Contact Dermatitis Group patch tests patients with suspected allergic contact dermatitis (ACD) to a broad series of screening allergens and publishes periodic reports. We have previously reported on the association of race and ethnicity with the rates of positive responses to standard patch test allergens. This report extends those observations. ObjectiveThe aim of the study was to report the North American Contact Dermatitis Group patch testing results from January 1, 1998, to December 31, 2006, comparing the frequency of positive reactions between white and black subjects. Methods and MaterialsStandardized patch testing with 45 allergens was used at 13 centers in North America. &khgr;2 analysis of results in black subjects as compared with whites was examined. ResultsA total of 19,457 patients were tested; 92.9% (17,803) were white and 7.1% (1,360) were black. The final diagnoses of ACD (whites, 45.9%; blacks, 43.6%) and irritant contact dermatitis (13.0%/13.3%) were similar in the 2 groups. The diagnosis of atopic dermatitis was less common in the white patients (8.9%) as compared with the black patients (13.3%). Positive patch test reactions rates were similar for most allergens. However, statistically, blacks reacted more frequently to p-phenylenediamine (7.0% vs 4.4%, P < 0.001), bacitracin (11.6% vs 8.3%, P = 0.0004), as well as specific rubber accelerators mercaptobenzothiazole (2.7% vs 1.8%), thiuram (6.2% vs 4.3%), and mercapto mix (1.9% vs 0.8%, P < 0.001). Whites had an increase in positive reactions to fragrances (12.12% vs 6.77%, P < 0.0001), formaldehyde (9.25% vs 5.45%, P < 0.0001), and some formaldehyde releaser preservatives used in personal care products and textile resins (9.80% vs 6.18%, P < 0.0001). ConclusionsThere were statistically different rates of positive patch test reactions to specific allergens between black and white patients suspected of having ACD. The etiology of these differences is unclear but probably relates to culturally determined exposure patterns rather than genetic differences.
Investigation of mtDNA control region sequences in a Tibetan population sample from China

Abstract Mitochondrial hypervariable region sequences including HVI and HVII (15,751–520) were investigated from 174 unrelated Tibetan individuals living in Tibet Autonomous Region in People’s Republic of China. The resulted sequences were aligned and compared with revised Cambridge sequence (rCRS). This sequence variability rendered a high gene diversity value (0.9940 ± 0.0021) and a high random match probability (0.0118) was determined with PIC of 0.9882. Among a total of 174 samples, 217 polymorphic sites were identified, which defined 135 haplotypes. A total of 135 different haplotypes were detected, 113 of them were unique and 22 were shared. The most common haplogroup was M9a1a1c1b1 (16.09%), followed by A11 (6.32%), A (5.17%), R (4.60%), A15 (4.60%), and G3a1 (3.45). The proportions of macro-haplogroups M, N, and L were 54.60%, 42.53%, and 2.87%, respectively. By principal component analysis (PCA), there was no special cluster between Tibetans and other populations except that the structure of Tibetans closely resembled that of Uygur in component 2.
USTUR WHOLE-BODY CASE 0212: 17-YEAR FOLLOW-UP OF PLUTONIUM CONTAMINATED WOUND

The National Council of Radiation Protection and Measurements' (NCRP) wound model was applied to the bioassay data from a United States Transuranium and Uranium Registries' whole-body tissue donor, Case 0212. This individual was exposed to plutonium nitrate as a result of an occupational wound injury and he underwent extensive chelation treatment with Ca-DTPA. All major soft tissues and bones were collected post-mortem and radiochemically analyzed for 238Pu, 239,240Pu and 241Am. The 239,240Pu activity in the total body was estimated to be 232.0 Bq, with 80.3 Bq retained in the liver, 115.1 Bq in the skeleton and 14.3 Bq in the wound. The maximum likelihood method was used to simultaneously fit the 'post-treatment' urinary excretion and post-mortem liver and skeleton retention data. It was demonstrated that the deposited material was predominantly a strongly retained soluble compound (nitrate) with a 22% fraction of plutonium particles. The residual intake, the amount of plutonium deposited in the wound that was not removed from the system by Ca-DTPA, was estimated to be 288 Bq. The resulting committed effective dose was 134 mSv. Accounting for plutonium eliminated in the urine during chelation therapy, the actual 'untreated' intake was 1204 Bq, and the projected committed effective dose was 567 mSv. Hence, DTPA treatment reduced the dose by a factor of 4.
Graptolite community responses to global climate change and the Late Ordovician mass extinction

Significance Climate change during Late Ordovician mass extinction drove an ecologically selective decline in the abundance of deep-water macrozooplankton, accompanied by a shift to simpler, less even communities. These results indicate that the species abundance structure of planktic communities may be a leading indicator of the effects of climate change on biodiversity and a more sensitive gauge of those effects than taxonomic diversity change alone. Additionally, we present a Bayesian likelihood method of habitat inference that may be applicable to other similar cases. Mass extinctions disrupt ecological communities. Although climate changes produce stress in ecological communities, few paleobiological studies have systematically addressed the impact of global climate changes on the fine details of community structure with a view to understanding how changes in community structure presage, or even cause, biodiversity decline during mass extinctions. Based on a novel Bayesian approach to biotope assessment, we present a study of changes in species abundance distribution patterns of macroplanktonic graptolite faunas (∼447–444 Ma) leading into the Late Ordovician mass extinction. Communities at two contrasting sites exhibit significant decreases in complexity and evenness as a consequence of the preferential decline in abundance of dysaerobic zone specialist species. The observed changes in community complexity and evenness commenced well before the dramatic population depletions that mark the tipping point of the extinction event. Initially, community changes tracked changes in the oceanic water masses, but these relations broke down during the onset of mass extinction. Environmental isotope and biomarker data suggest that sea surface temperature and nutrient cycling in the paleotropical oceans changed sharply during the latest Katian time, with consequent changes in the extent of the oxygen minimum zone and phytoplankton community composition. Although many impacted species persisted in ephemeral populations, increased extinction risk selectively depleted the diversity of paleotropical graptolite species during the latest Katian and early Hirnantian. The effects of long-term climate change on habitats can thus degrade populations in ways that cascade through communities, with effects that culminate in mass extinction.
Validation of ACE-FTS N 2 O measurements

The Atmospheric Chemistry Experiment (ACE), also known as SCISAT, was launched on 12 August 2003, carrying two instruments that measure vertical profiles of atmospheric constituents using the solar occultation technique. One of these instruments, the ACE Fourier Transform Spectrometer (ACE-FTS), is measuring volume mixing ratio (VMR) profiles of nitrous oxide (N 2 O) from the upper troposphere to the lower mesosphere at a vertical resolution of about 3–4 km. In this study, the quality of the ACE-FTS version 2.2 N 2 O data is assessed through comparisons with coincident measurements made by other satellite, balloon-borne, aircraft, and ground-based instruments. These consist of vertical profile comparisons with the SMR, MLS, and MIPAS satellite instruments, multiple aircraft flights of ASUR, and single balloon flights of SPIRALE and FIRS-2, and partial column comparisons with a network of ground-based Fourier Transform InfraRed spectrometers (FTIRs). Overall, the quality of the ACE-FTS version 2.2 N 2 O VMR profiles is good over the entire altitude range from 5 to 60 km. Between 6 and 30 km, the mean absolute differences for the satellite comparisons lie between -42 ppbv and +17 ppbv, with most within ±20 ppbv. This corresponds to relative deviations from the mean that are within ±15%, except for comparisons with MIPAS near 30 km, for which they are as large as 22.5%. Between 18 and 30 km, the mean absolute differences are generally within ±10 ppbv, again excluding the aircraft and balloon comparisons. From 30 to 60 km, the mean absolute differences are within ±4 ppbv, and are mostly between -2 and +1 ppbv. Given the small N 2 O VMR in this region, the relative deviations from the mean are therefore large at these altitudes, with most suggesting a negative bias in the ACE-FTS data between 30 and 50 km. In the comparisons with the FTIRs, the mean relative differences between the ACE-FTS and FTIR partial columns are within ±6.6% for eleven of the twelve contributing stations. This mean relative difference is negative at ten stations, suggesting a small negative bias in the ACE-FTS partial columns over the altitude regions compared. Excellent correlation ( R =0.964) is observed between the ACE-FTS and FTIR partial columns, with a slope of 1.01 and an intercept of -0.20 on the line fitted to the data.
Impairment of tubular secretion of urate in renal transplant patients on cyclosporine.

The prevalence of hyperuricemia was investigated in 214 kidney allograft recipients, 81 were on azathioprine and steroids and 133 on cyclosprine (CyA) and low-dose steroids or on triple therapy. All had stable renal function, serum creatinine < 2.5 mg/dl, and a follow-up between 12 and 120 months. At the time of the study, blood and urine samples were obtained to perform tests of renal function. The renal handling of urate was evaluated by a combined pyrazinamide and probenecid test in 35 selected patients (12 normouricemic on azathioprine, 9 normouricemic on CyA and 14 hyperuricemic on CyA). The prevalence of hyperuricemia was higher in the group of patients on CyA (19.7 vs. 66.9%, p < 0.001), as well as the concentration of serum urate (6.1 +/- 1.9 vs. 7.6 +/- 1.7, p < 0.001), and serum creatinine (1.2 +/- 0.3 vs. 1.4 +/- 0.4, p < 0.001). In patients on CyA, multivariate analysis showed that the most important predictive variables of hyperuricemia were: serum creatinine, FEurate, diuretic use and CyA blood levels (r = 0.73, p < 0.0001). Thirteen patients on CyA (9.9%) had at least one episode of gouty arthritis. Those patients were older than the hyperuricemic patients without gout (45.7 +/- 6.7 vs. 37.1 +/- 13.5 years, p < 0.01), had worse renal function (serum creatinine 1.9 +/- 0.4 vs. 1.5 +/- 0.4 mg/dl, p < 0.01), and higher prevalence of hypertension (100 vs. 63.1%, p < 0.05). (ABSTRACT TRUNCATED AT 250 WORDS)