Miracle-dz/UniFAR-FTUs huggingface dataset:
The Deep Roots of the Rings of Life

Reconstructing early evolutionary events like the origins of informational and operational genes, membranes, and photophosphorylation is difficult because early evolutionary events can be masked by subsequent gene flows. Furthermore, as evolution progresses through both Darwinian survival of the fittest (tree-like evolution) and symbiotic/endosymbiotic cooperation (ring-like evolution), trees alone are not adequate to represent Earth’s evolutionary history. Here, we reconstruct and root the New Rings of Life and use it as a framework for interpreting early events in the evolution of life. Unlike the three-domain hypothesis, the rings do not fit all life into one of three immutable categories, but rather accommodate new gene flows as novel organisms are discovered. A draft of the Rooted Rings of Life is reconstructed by analyzing the phylogenetic distributions of indels (insertions/deletions) and genes coding for fundamental molecular processes. Their phylogenetic distributions are inconsistent with all trees. Hypergeometric distribution analyses of them strongly localize the root of the rings to a segment of the deepest ring (P < 10−21 and P < 10−194), and whole-genome analyses independently confirm the topology of the rooted rings (P < 7.1 × 10−6). The rings identify several large gene flows, including a flow of a thousand genes into the Halobacteria and the Eubacteria, the related photocyte flow, the flow of genes into the last common ancestor of the eocytes and the eukaryotes, and the informational and operational gene flows into the eukaryotes. The rooted rings also chronologically order steps in the evolution of extant taxa, that is, phototrophy evolved from Halobacteria (photophosphorylation) → Heliobacteria (photosynthesis) → Cyanobacteria (oxygenic photosynthesis).
Kinetics of transforming growth factor‐β1 and extracellular matrix in renal tubulointerstitial lesions of mercuric chloride‐treated Brown Norway rats

Renal tubulointerstitial lesions in mercuric chloride(HgCl2)‐treated Brown Norway rats were investigated focusing on the kinetics of transforming growth factor‐β1(TGF‐β1) and extracellular matrix (ECM). Rats were injected with 1 mg/kg b.w. of HgCl2 at days 0, 2, and 4, and 5 rats were killed at days 2, 4, 6, 8, 10, and 20, respectively. TGF‐β1 mRNA expression in the renal cortex measured by competitive RT‐PCR method reached a peak at day 6, mildly decreased at days 8 and 10, and increased again toward day 20. Signals of TGF‐β1 mRNA examined by in situ hybridization method were recognized in the regenerative tubular epithelium at day 6, and in both tubular epithelium and infiltrated mononuclear cells at day 20. After tubular injury, strong immunoreactivity to TGF‐β1 protein was found in desquamated tubular epithelial cells. Then, positive staining was found in the regenerative tubular epithelial cells. Later, infiltrated mononuclear cells also became positive for TGF‐β1 protein. In the ECM, deposition of fibronectin was prominent throughout the experimental period. In conclusion, this strongly suggests that TGF‐β1 derived from tubular epithelial cells and some macrophages might be related to the development of renal interstitial fibrosis in HgCl2‐treated BN rats.
Cyclic AMP Signaling Inhibits Megakaryocytic Differentiation by Targeting Transcription Factor 3 (E2A) Cyclin-dependent Kinase Inhibitor 1A (CDKN1A) Transcriptional Axis*

Background: Cyclic AMP signaling impairs megakaryopoiesis through an unknown mechanism. Results: cAMP transcriptionally represses the transcription factor E2A with resultant impairment in the expression of its target CDKN1A. Conclusion: In discovering a mechanism for cAMP-induced inhibition, E2A is identified clearly as critical megakaryocytic factor. Significance: Elucidating the repertoire of necessary transcription factors is crucial for understanding control of megakaryocytic lineage. Signaling via the intracellular second messenger cyclic AMP (cAMP) has long been implicated in the repression of megakaryocytic differentiation. However, the mechanisms by which cAMP signaling impairs megakaryopoiesis have never been elucidated. In a human CD34+ cell culture model, we show that the adenylyl cyclase agonist forskolin inhibits megakaryocytic differentiation in a protein kinase A-dependent manner. Using this system to screen for downstream effectors, we identified the transcription factor E2A as a key target in a novel repressive signaling pathway. Specifically, forskolin acting through protein kinase A-induced E2A down-regulation and enforced expression of E2A overrode the inhibitory effects of forskolin on megakaryopoiesis. The dependence of megakaryopoiesis on critical thresholds of E2A expression was confirmed in vivo in haploinsufficient mice and ex vivo using shRNA knockdown in human progenitors. Using a variety of approaches, we further identified p21 (encoded by CDKN1A) as a functionally important megakaryopoietic regulator residing downstream of E2A. These results thus implicate the E2A-CDKN1A transcriptional axis in the control of megakaryopoiesis and reveal the lineage-selective inhibition of this axis as a likely mechanistic basis for the inhibitory effects of cAMP signaling.
Direct Inhibition of TNF-α Promoter Activity by Fanconi Anemia Protein FANCD2

Fanconi anemia (FA), an inherited disease, is associated with progressive bone marrow failure, predisposition to cancer, and genomic instability. Genes corresponding to 15 identified FA complementation groups have been cloned, and each gene product functions in the response to DNA damage induced by cross-linking agents and/or in protection against genome instability. Interestingly, overproduction of inflammatory cytokines such as tumor necrosis factor alpha (TNF-α) and aberrant activation of NF-κB-dependent transcriptional activity have been observed in FA cells. Here we demonstrated that FANCD2 protein inhibits NF-κB activity in its monoubiquitination-dependent manner. Furthermore, we detected a specific association between FANCD2 and an NF-κB consensus element in the TNF-α promoter by electrophoretic mobility shift assays (EMSA) and chromatin immunoprecipitation (ChIP) assay. Therefore, we propose FANCD2 deficiency promotes transcriptional activity of the TNF-α promoter and induces overproduction of TNF-which then sustains prolonged inflammatory responses. These results also suggest that artificial modulation of TNFα production could be a promising therapeutic approach to FA.
Viscoplastic Anand model for solder alloys and its application

A viscoplastic constitutive model, the Anand model, in which plasticity and creep are unified and described by the same set of flow and evolutionary relations, was applied to represent the inelastic deformation behavior for solder alloys. After conducting creep tests and constant strain rate tests, the material parameters for the Anand model of the Pb‐rich content solder 92.5Pb5Sn2. 5Ag were determined from the experimental data using a nonlinear fitting method. The material parameters for 60Sn40Pb, 62Sn36Pb2Ag and 96.5Sn3. 5Ag solders were fitted from the conventional model in the literature where plasticity and creep are artificially separated. Model simulations and verifications reveal that there is good agreement between the model predictions and experimental data. Some discussion on this unified model is also presented. This viscoplastic constitutive model for solder alloys possesses some advantages over the separated model. The achieved Anand model has been applied in finite element simulation of stress/strain responses in solder joints for chip component, thin quad flat pack and flip‐chip assembly. The simulation results are in good agreement with the results in the literature. It is concluded that the Anand model could be recommended as a useful material model for solder alloys and can be used in the finite element simulation of solder joint reliability in electronic packaging and surface mount technology.
Effects of protein, monounsaturated fat, and carbohydrate intake on blood pressure and serum lipids: results of the OmniHeart randomized trial.

CONTEXT Reduced intake of saturated fat is widely recommended for prevention of cardiovascular disease. The type of macronutrient that should replace saturated fat remains uncertain. OBJECTIVE To compare the effects of 3 healthful diets, each with reduced saturated fat intake, on blood pressure and serum lipids. DESIGN, SETTING, AND PARTICIPANTS Randomized, 3-period, crossover feeding study (April 2003 to June 2005) conducted in Baltimore, Md, and Boston, Mass. Participants were 164 adults with prehypertension or stage 1 hypertension. Each feeding period lasted 6 weeks and body weight was kept constant. INTERVENTIONS A diet rich in carbohydrates; a diet rich in protein, about half from plant sources; and a diet rich in unsaturated fat, predominantly monounsaturated fat. MAIN OUTCOME MEASURES Systolic blood pressure and low-density lipoprotein cholesterol. RESULTS Blood pressure, low-density lipoprotein cholesterol, and estimated coronary heart disease risk were lower on each diet compared with baseline. Compared with the carbohydrate diet, the protein diet further decreased mean systolic blood pressure by 1.4 mm Hg (P = .002) and by 3.5 mm Hg (P = .006) among those with hypertension and decreased low-density lipoprotein cholesterol by 3.3 mg/dL (0.09 mmol/L; P = .01), high-density lipoprotein cholesterol by 1.3 mg/dL (0.03 mmol/L; P = .02), and triglycerides by 15.7 mg/dL (0.18 mmol/L; P<.001). Compared with the carbohydrate diet, the unsaturated fat diet decreased systolic blood pressure by 1.3 mm Hg (P = .005) and by 2.9 mm Hg among those with hypertension (P = .02), had no significant effect on low-density lipoprotein cholesterol, increased high-density lipoprotein cholesterol by 1.1 mg/dL (0.03 mmol/L; P = .03), and lowered triglycerides by 9.6 mg/dL (0.11 mmol/L; P = .02). Compared with the carbohydrate diet, estimated 10-year coronary heart disease risk was lower and similar on the protein and unsaturated fat diets. CONCLUSION In the setting of a healthful diet, partial substitution of carbohydrate with either protein or monounsaturated fat can further lower blood pressure, improve lipid levels, and reduce estimated cardiovascular risk. Clinical Trials Registration ClinicalTrials.gov Identifier: NCT00051350.
Structural analysis of wild-type and mutant human immunodeficiency virus type 1 Tat proteins

We expressed the human immunodeficiency virus type 1 transactivator protein, Tat, in the wheat germ cell-free translation system and found it to exist as a monomer. The first coding exon (residues 1 to 72) of wheat germ-expressed Tat was resistant to trypsin digestion, indicating that it is a highly folded, independently structured protein domain. Several mutant Tat proteins were dramatically more sensitive to trypsin than the wild type was, suggesting that their reduced transactivation activities are the result of destabilized structures. Mutant proteins with single-amino-acid substitutions were also identified that had reduced transactivation activities but wild-type structures in the trypsin assay. These mutants clustered in two regions of Tat, at acidic residues 2 and 5 in the amino terminus and between residues 18 and 32. These mutants, wild type in structure but reduced in activity, identify residues in the wild-type protein that may directly contact other molecules during Tat function.
An Informative Feature Selection Method Based on Sparse PCA for VHR Scene Classification

Understanding the scenes provided by very high resolution satellite (VHR) imagery has become a critical task. In this letter, we propose a new informative feature selection method for VHR scene classification. First, scale-invariant feature transform and speeded up robust feature operators are used to extract local features from the original VHR images to construct a visual dictionary. A sparse principal component analysis (sPCA) is then adopted to learn a set of informative features from the visual dictionary for each category. Finally, the scenes are represented by sparse informative low-level features. We conducted experiments on the University of California at Merced data set containing 21 different areal scene categories with submeter resolution and the Sydney data set containing seven land-use categories with 0.5-m spatial resolution. The experimental results demonstrate that the proposed method outperforms the state-of-the-art methods even without saliency detection.
Cardiac Sarcoid: A Clinicopathologic Study of 84 Unselected Patients with Systemic Sarcoidosis

SUMMARY Although sarcoid may involve the myocardium, there is little information on its incidence or significance. We studied 84 consecutive autopsied patients with sarcoidosis. The patients ranged in age from 18-80 years (average 46 years) and 61% were women; 23 (27%) of them had myocardial granulomas. In eight (35%) these were clinically silent, and in 15 (65%) there was a history of heart failure and/or arrhythmias and conduction defects. Of the 23 patients, only four (17%) had grossly evident, widespread myocardial lesions: three of these four (75%) had documented arrhythmias. All four had sudden, unexpected death at an average age of 36 years; in only two had sarcoid been suspected during life. The other 19 patients (83%) had microscopically evident granulomatous involvement. Of these, eight (42%) had a rhythm or conduction disturbance and three (16%) sudden death, although none of those who suffered sudden death had a recognized rhythm or conduction disturbance. Nine (15%) of those without cardiac sarcoidosis had a rhythm or conduction disturbance and eight (13%) suffered a sudden death.The results show that although myocardial involvement occurs in at least 25% of patients with sarcoid, it most often involves a small portion of myocardium and is clinically silent. Since some of the 61 patients in whom myocardial lesions were not identified may still have had small microscopic granulomas, the true incidence of myocardial sarcoid may be even greater than suggested here. Rhythm and conduction disturbances are more common in the cardiac sarcoid group, but the findings suggest that only the small subset of patients with severe, grossly evident myocardial sarcoid are at increased risk for sudden death.
Quantum Cascade Laser Absorption Spectroscopy as a Plasma Diagnostic Tool: An Overview

The recent availability of thermoelectrically cooled pulsed and continuous wave quantum and inter-band cascade lasers in the mid-infrared spectral region has led to significant improvements and new developments in chemical sensing techniques using in-situ laser absorption spectroscopy for plasma diagnostic purposes. The aim of this article is therefore two-fold: (i) to summarize the challenges which arise in the application of quantum cascade lasers in such environments, and, (ii) to provide an overview of recent spectroscopic results (encompassing cavity enhanced methods) obtained in different kinds of plasma used in both research and industry.
The Heat-Shock Response: Its Variation, Regulation and Ecological Importance in Intertidal Gastropods (genus Tegula)1

Abstract The enhanced synthesis of heat-shock proteins (hsps), called the heat-shock (or stress) response, is activated when environmental stress denatures proteins. Hsp synthesis is activated at the upper temperatures of an organism's thermal range and is therefore thought to be critical for enhancing thermal tolerance limits in ectothermic animals. Here I show that the two temperate sister species T. brunnea and T. montereyi that occupy the subtidal and low-intertidal zone differ from the low- to mid-intertidal T. funebralis (and the subtropical mid-intertidal T. rugosa) in (i) heat tolerance, (ii) the onset temperature of their main hsp, hsp70 (70 kDa), (iii) the temperature of maximal hsp70 synthesis, (iv) the upper temperature of hsp synthesis, and (v) the recovery from a thermal stress typical for the mid-intertidal zone. A regulatory model in which hsps themselves regulate their own transcription and synthesis through a negative autoregulatory feedback mechanism can explain acclimation-induced but not interspecific variation in the onset temperature of hsp70 synthesis. Transplanting species across their vertical distribution limits showed that interspecific differences in the stress response are likely to prevent species occurring lower from inhabiting sites higher in the rocky intertidal zone. Endogenous levels of a hsp of a molecular mass of 72 kDa, hsp72, changed little with heat stress in a species' native thermal environment. The results therefore confirm the importance of interspecific differences in the stress response for setting limits to an organism's thermal environment. However, the role of hsps as short-term indicators of sublethal heat stress within a species' native thermal environment may be limited without a better understanding of their functional and regulatory characteristics.
Market Failures and Misallocation

I develop a method to measure and separate the production misallocation caused by failures in factor markets versus financial markets. When I apply the method to rice farming villages in Thailand I find surprisingly little misallocation. Optimal reallocation would increase output in most villages by less than 15 percent. By 2006 most misallocation comes from factor market failures. I derive a decomposition of aggregate growth that accounts for misallocation. Declining misallocation contributes little to growth compared to factor accumulation and rising farm productivity. I use a government credit intervention to test my measures. I confirm that credit causes a statistically significant decrease in only financial market misallocation.
Effect of Graphic Cigarette Warnings on Smoking Intentions in Young Adults

Introduction Graphic warnings (GWs) on cigarette packs are widely used internationally and perhaps will be in the US but their impact is not well understood. This study tested support for competing hypotheses in different subgroups of young adults defined by their history of cigarette smoking and individual difference variables (e.g., psychological reactance). One hypothesis predicted adaptive responding (GWs would lower smoking-related intentions) and another predicted defensive responding (GWs would raise smoking-related intentions). Methods Participants were an online sample of 1,169 Americans ages 18–24, who were randomly assigned either to view nine GWs designed by the FDA or to a no-label control. Both the intention to smoke in the future and the intention to quit smoking (among smokers) were assessed before and after message exposure. Results GWs lowered intention to smoke in the future among those with a moderate lifetime smoking history (between 1 and 100 cigarettes), and they increased intention to quit smoking among those with a heavy lifetime smoking history (more than 100 cigarettes). Both effects were limited to individuals who had smoked in some but not all of the prior 30 days (i.e., occasional smokers). No evidence of defensive “boomerang effects” on intention was observed in any subgroup. Conclusion Graphic warnings can reduce interest in smoking among occasional smokers, a finding that supports the adaptive-change hypothesis. GWs that target occasional smokers might be more effective at reducing cigarette smoking in young adults.
Neurologic Recovery According to Early Magnetic Resonance Imaging Findings in Traumatic Cervical Spinal Cord Injuries

The aim of this study was to determine the usefulness of early magnetic resonance imaging findings in predicting neurologic recovery at or below the injured level in traumatic cervical spinal cord injuries. Thirty patients with traumatic cervical spinal cord injuries were included. All of the patients received a magnetic resonance imaging and a neurologic examination in the emergency room, within 7 days of injury and at 6 months following the injury. To quantify neurologic recovery below the injured level, we modified clinical scales, particularly the motor ratio and the sensory ratio. We used the neurologic level to quantify recovery around the injured level. We assessed neurologic recovery according to MRI patterns and lesion extents. The pure hemorrhagic MRI pattern was not observed. In edematous and mixed types, the improvement of neurologic levels was not significantly different. The motor ratio and sensory ratio improved significantly more in edematous type patients than in mixed type patients. Based on MRI lesion extent, the improvement of neurologic levels was not significantly different, and motor ratio and sensory ratio improved significantly more in those with one or two segments involved than in those with more than two segments involved. In conclusion, early MRI pattern and lesion extent after traumatic cervical spinal cord injury may provide important information to help predict neurologic recovery, especially below the injured level.
Asymptotic Growth Rates and Strong Bending of Turbulent Flame Speeds of G-Equation in Steady Two-Dimensional Incompressible Periodic Flows

The study of turbulent flame speeds (the large time front speeds) is a fundamental problem in turbulent combustion theory. A significant project is to understand how the turbulent flame speed ($s_T$) depends on the flow intensity ($A$). The G-equation is a very popular level set flame propagation model in the turbulent combustion community. The main purpose of this paper is to study properties of $\lim_{A\to +\infty} \frac{s_T}{A}$ and $\lim_{A\to +\infty}\, s_T$ (if finite, or strong bending) in the G-equation model for two-dimensional (2D) divergence-free periodic flows. Our analysis is based on the invariant measures and rotation vectors of the 2D flows and the travel times of the associated flow trajectories under control. Optimal linear/sublinear growth and strong bending conditions are precisely given in terms of rotation vectors and periodic orbits. A strong bending formula of $s_T$ in the cat's-eye flow is discovered by averaging the controlled characteristics of the G-equation. The growth rate of.
Mammographic Breast Density, Dense Area, and Breast Area Differences by Phase in the Menstrual Cycle

Background: Mammographic breast density may be greater in the luteal phase (days 15-30) than the follicular phase (days 1-14) of the menstrual cycle; this may have implications for when mammography screening should occur. Objective: Examine whether percent breast density, breast area, or dense area differ by menstrual phase. Methods: We identified 204 premenopausal women with regular periods who were <55 years (mean = 45.0 years) and had two screening mammograms within 9 to 18 months, with one screening between days 9 and 14, and one screening between days 22 and 35 of the menstrual cycle. We measured percent breast density, breast area, and dense area using the Cumulus software. We used linear regression to test for differences in breast density, breast area, and dense area from follicular to luteal phase, adjusting for change in weight and time between exams. Results: The mean (SD) percent breast density was 35.8% (21.3) in the follicular phase and 36.7% (21.3) in the luteal phase. Multivariable analyses showed small but not statistically significant increases in percent density [1.1%; 95% confidence interval (95% CI), −0.2% to 2.3%] and breast area (16.7 cm2; 95% CI, −2.8 to 36.2) and a statistically significant increase in dense area (13.1 cm2; 95% CI, 0.1-26.1) in the luteal compared with the follicular phase. Conclusions: Breast density, breast area, and dense area have small, but probably not clinically meaningful, increases in the luteal phase of the menstrual cycle. However, there are other factors that may differ by menstrual cycle phase that we were unable to assess (e.g., breast compression), which may ultimately influence mammographic sensitivity by menstrual cycle phase. (Cancer Epidemiol Biomarkers Prev 2006;15(11):2303–6)