Miracle-dz/UniFAR-FTUs huggingface dataset:
Solar exposure and residential geographic history in relation to exfoliation syndrome in the United States and Israel.

IMPORTANCE Residential (geographic) history and extent of solar exposure may be important risk factors for exfoliation syndrome (XFS) but, to our knowledge, detailed lifetime solar exposure has not been previously evaluated in XFS. OBJECTIVE To assess the relation between residential history, solar exposure, and XFS. DESIGN, SETTING, AND PARTICIPANTS This clinic-based case-control study was conducted in the United States and Israel. It involved XFS cases and control individuals (all ≥ 60-year-old white individuals) enrolled from 2010 to 2012 (United States: 118 cases and 106 control participants; Israel: 67 cases and 72 control participants). MAIN OUTCOMES AND MEASURES Weighted lifetime average latitude of residence and average number of hours per week spent outdoors as determined by validated questionnaires. RESULTS In multivariable analyses, each degree of weighted lifetime average residential latitude away from the equator was associated with 11% increased odds of XFS (pooled odds ratio [OR], 1.11; 95% CI, 1.05-1.17; P < .001). Furthermore, every hour per week spent outdoors during the summer, averaged over a lifetime, was associated with 4% increased odds of XFS (pooled OR, 1.04; 95% CI, 1.00-1.07; P = .03). For every 1% of average lifetime summer time between 10 am and 4 pm that sunglasses were worn, the odds of XFS decreased by 2% (OR, 0.98; 95% CI, 0.97-0.99; P < .001) in the United States but not in Israel (OR, 1.00; 95% CI, 0.99-1.01; P = .92; P for heterogeneity = .005). In the United States, after controlling for important environmental covariates, history of work over water or snow was associated with increased odds of XFS (OR, 3.86; 95% CI, 1.36-10.9); in Israel, there were too few people with such history for analysis. We did not identify an association between brimmed hat wear and XFS (P > .57). CONCLUSIONS AND RELEVANCE Lifetime outdoor activities may contribute to XFS. The association with work over snow or water and the lack of association with brimmed hat wear suggests that ocular exposure to light from reflective surfaces may be an important type of exposure in XFS etiology.
Agent-Based Modeling and Simulation for Supply Chain Risk Management - A Survey of the State-of-the-Art

Due to the complex nature and numerous interacting factors that contributes to the increased vulnerability of supply chains, traditional methods have been found to be inadequate for Supply Chain Risk Management (SCRM). Agent-Based Modeling and Simulation (ABMS), an agent-oriented approach to model and simulate complex adaptive systems, represents a recent development in supply chain planning that has been regarded highly appropriate for studying risk management [1-4]. The objective of this paper is to provide a multi-perspective survey of the state-of-the-art agent based modeling and simulation approaches for SCRM.
Applicability of International Harvesting Equipment Productivity Studies in Maine, USA: A Literature Review

Harvesting equipment productivity studies have been conducted in many countries around the world spanning over 25 years. These studies have shown that many factors influence individual machine productivity. These factors include stand and site conditions, equipment configuration, management objectives, and operator experience. Productivity can increase or decrease with slight changes in any of these factors. This literature review also highlights the variety of experimental designs and data collection methods encountered in a cross section of those studies. It further shows the variation in species composition, stand density, tree diameter, and harvest prescription. Although studies that include the influence of operator performance on harvest equipment productivity are limited, they were included in this review where appropriate and available. It is clear that productivity equations should be developed using population-level data with several operators. Some studies were conducted in stands similar to Maine, but they used harvesting equipment that is not commonly used in logging operations in this state. Therefore the applicability of existing studies to the logging industry in Maine, USA, is very limited. Our conclusion is that in order to accurately predict harvesting productivity it is necessary to develop regional harvesting productivity equations using harvesting equipment commonly used in Maine. Forest operations researchers in other regions will be able to use this summary to explore the difficulty of applying productivity information to regional logging operations.
Dietary Fat Elevates Hepatic ApoA-I Production by Increasing the Fraction of Apolipoprotein A-I mRNA in the Translating Pool (*)

Elevated plasma high density lipoprotein cholesterol (HDL-C) levels are associated with a decreased risk for coronary heart disease. Ironically, diets enriched in saturated fat and cholesterol (HF/HC diets), which tend to accelerate atherosclerotic processes by increasing LDL cholesterol levels, also raise HDL-C. We have recently reported, using a human apoA-I (hapoA-1) transgenic mouse model, that the elevation of HDL-C by a HF/HC diet is attributable, in part, to an increase in the hepatic production of hapoA-1. To further define the hepatocellular processes associated with this induction, we have prepared primary hepatocytes from hapoA-1 transgenic mice. Rates of hapoA-1 secretion were 40% greater from cells prepared from animals fed the HF/HC relative to a low fat-low cholesterol (LF/LC) control diet. The abundance of hapoA-1 mRNA in these cells was similar between hepatocytes prepared from the HF/HC and LF/LC diet fed animals, suggesting a post-transcriptional mechanism that does not involve mRNA stability. Inhibition of secretion using brefeldin A revealed an increase in cellular hapoA-1 accumulation. Thus, the HF/HC diet apparently affects hepatic hapoA-1 production via a mechanism that is manifest prior to the exit of newly synthesized hapoA-1 from the Golgi. Pulse-chase experiments revealed a 39% greater peak hapoA-1 synthesis, with no difference in the degradation of total labeled hapoA-1 protein, as a result of the HF/HC diet feeding. Finally, resolution of liver S10 extracts via sucrose density sedimentation and metrizamide density equilibrium gradient centrifugation analyses both revealed similar increases (31 and 24%, respectively) in the relative percentage of hapoA-1 mRNA associated with the translating polysomal fractions as a result of the HF/HC feeding. Together, these data suggest that the HF/HC diet affects hepatic hapoA-1 production via a specific modulation in the relative amount of hapoA-1 mRNA in the polysomal pool. These observations provide an opportunity to explore a new mechanism regulating apoA-1 production and might lead to the development of novel therapies to elevate plasma HDL-C levels.
Regulation of immune responses to protein therapeutics by transplacental induction of T cell tolerance

Transplacental modulation of T cell repertoire during immune ontogeny leads to antigen-specific immune tolerance to an immunogenic protein therapeutic. Can’t we all get along? The past century brought great advances for the treatment of some genetic disorders caused by single protein deficiencies. In particular, hemophilia A, which is caused by a deficiency of coagulation factor VIII, can now be treated by replacing the missing factor. Unfortunately, the most severely affected patients, who completely lack endogenous factor VIII, often develop antibodies against the replacement protein because their bodies recognize it as a foreign substance. To overcome this problem, Gupta et al. have now developed a method for transplacental exposure of fetuses to the missing antigen, thus ensuring immune tolerance for protein therapy that will be delivered after birth. Central tolerance plays a key role in modulating immune responses to self and exogenous antigens. The absence of self-antigen expression, as in patients with genetic deficiencies, prevents the development of antigen-specific immune tolerance. Hence, a substantial number of patients develop neutralizing antibodies to the corresponding protein therapeutics after replacement treatment. In this context, the administration of missing antigens during fetal development, a key period for self-tolerance establishment, should confer early and long-lasting antigen-specific tolerance. To this end, we exploited the physiological pathway of the neonatal Fc receptor (FcRn) through which maternal immunoglobulins are transplacentally transferred to fetuses. We demonstrate that Fc-fused antigens administered to pregnant mice reach fetal lymphoid organs in an FcRn-dependent manner, accumulate in antigen-presenting cells of myeloid origin, and promote the generation of both thymic and peripheral antigen-specific regulatory T cells. This strategy was successfully pursued in a mouse model of hemophilia A, where maternofetal transfer of the Fc-fused immunodominant domains of coagulation factor VIII conferred antigen-specific tolerance. Transplacental tolerance induction with Fc-fused proteins may thus prove valuable to prevent alloimmunization after replacement protein therapy for congenital deficiencies.
A MCMC Approach to Hierarchical Mixture Modelling

There are many hierarchical clustering algorithms available, but these lack a firm statistical basis. Here we set up a hierarchical probabilistic mixture model, where data is generated in a hierarchical tree-structured manner. Markov chain Monte Carlo (MCMC) methods are demonstrated which can be used to sample from the posterior distribution over trees containing variable numbers of hidden units.
Molecular Mechanisms Underlying Renin-Angiotensin-Aldosterone System Mediated Regulation of BK Channels

Large-conductance calcium-activated potassium channels (BK channels) belong to a family of Ca2+-sensitive voltage-dependent potassium channels and play a vital role in various physiological activities in the human body. The renin-angiotensin-aldosterone system is acknowledged as being vital in the body's hormone system and plays a fundamental role in the maintenance of water and electrolyte balance and blood pressure regulation. There is growing evidence that the renin-angiotensin-aldosterone system has profound influences on the expression and bioactivity of BK channels. In this review, we focus on the molecular mechanisms underlying the regulation of BK channels mediated by the renin-angiotensin-aldosterone system and its potential as a target for clinical drugs.
p53, a Target of Estrogen Receptor (ER) α, Modulates DNA Damage-induced Growth Suppression in ER-positive Breast Cancer Cells*

Background: ERα and p53 are transcription factors that play important roles in breast cancer. Results: ERα transcriptionally regulates p53, which then modulates DNA damage-induced growth suppression. Conclusion: p53 is a target of ERα and is responsible for the sensitivity of ERα-positive breast cancer cells to DNA damage. Significance: Loss of ERα, causing a decrease in p53 expression, could lead to tumors resistant to both antiestrogen and chemotherapy. In response to genotoxic stress, the p53 tumor suppressor induces target genes for cell cycle arrest, apoptosis, and DNA repair. Although p53 is the most commonly mutated gene in all human cancers, it is only mutated in about 20% of breast cancers. 70% of all breast cancer cases are estrogen receptor (ER)-positive and express ERα. ER-positive breast cancer generally indicates good patient prognosis and treatment responsiveness with antiestrogens, such as tamoxifen. However, ER-positive breast cancer patients can experience loss or a reduction in ERα, which is associated with aggressive tumor growth, increased invasiveness, poor prognosis, and loss of p53 function. Consistent with this, we found that p53 is a target gene of ERα. Specifically, we found that knockdown of ERα decreases expression of p53 and its downstream targets, MDM2 and p21. In addition, we found that ERα activates p53 transcription via binding to estrogen response element half-sites within the p53 promoter. Moreover, we found that loss of ERα desensitizes, whereas ectopic expression of ERα sensitizes, breast cancer cells to DNA damage-induced growth suppression in a p53-dependent manner. Altogether, this study provides an insight into a feedback loop between ERα and p53 and a biological role of p53 in the DNA damage response in ER-positive breast cancers.
A Molecular and Morphological Reassessment of Diademaceae

We revisit the family Diademaceae based on available sequence data and morphology. Diademaceae is characterized by ascomata opening with a flat circular lid and fissitunicate, short orbicular frequently cylindrical, pedicellate asci. Ascospores are frequently circular in section but narrowing to one end with three or more transverse septa, without longitudinal septa, and mostly with a thick sheath. In recent treatments Clathrospora, Comoclathris, Diadema, Diademosa, and Graphyllium were placed in the family. Following molecular and morphological study, Clathrospora, Comoclathris, and Diademosa, are excluded from the family and referred to Pleosporaceae. Graphyllium is excluded from Diademaceae, based on hysterothecium-like ascomata with a longitudinal opening, and tentatively placed in Hysteriaceae with uncertainty; species with hysterothecia have now been accommodated in at least five families. The study accepts only Diadema in the family. The status of Diademaceae as a distinct family, based on the ascomata opening by a flat circular lid, is thought to be doubtful. Fresh collections of Diadema are needed for epitypification and to obtain sequence data to establish if this is a well-resolved family.
Treatment-related myelodysplastic syndrome: molecular characteristics and therapy

Purpose of reviewTreatment-related myelodysplastic syndrome (t-MDS) is a serious complication of cancer treatment. Here we review recent advances in knowledge of the risk factors, pathogenesis, and treatment of t-MDS. Recent findingsRecent studies have provided important new information regarding genetic risk factors that may predispose individual patients to develop t-MDS after exposure to cytotoxic therapeutic agents and that may be used to predict individuals at enhanced risk for this complication. The role of specific candidate genes associated with commonly involved genetic lesions in the pathogenesis of t-MDS has also been investigated. Finally, factors determining outcomes of transplantation treatment for this disorder have been elucidated. Hematopoietic cell transplantation provides potentially curative therapy for t-MDS, but additional improvements are necessary to improve outcomes. SummaryImproved understanding of genetic risk factors is expected to facilitate early identification of patients at risk for t-MDS, guiding therapeutic decision making, and allowing early application of preventive or therapeutic strategies.
Olfactory relationships of the telencephlaon and diencephalon in the rabbit. 1. An autoradiographic study of the efferent connections of the main and accessory olfactory bulbs

The efferent connections of the main and accessory olfactory bulbs in the female albino rabbit have been studied using the autoradiographic method for tracing axonal pathways. Following unilateral injections of 3H‐leucine into the main olfactory bulb, radioactively labeled material transported intraaxonally by axoplasmic flow in an anterograde direction from soma to axon terminal is present ipsilaterally in the superficial half of the plexiform layer (IA) of: the entire circumference of the olfactory peduncle, the tenia tecta, the full mediolateral extent of the olfactory tubercle, the entire length of the prepyriform cortex, a transition area between the prepyriform cortex and the horizontal limb of the nucleus of the diagonal band, the nucleus of the lateral olfactory tract, the anterior cortical and posterolateral cortical amygdaloid nuclei (periamygdaloid areas 1, rostral half of 2, 5 of Rose, '31), and the ventrolateral entorhinal cortex (entorhinal areas 1, 2, 4, 5, 7 of Rose, '31). No subcortical or contralateral projection of main bulb efferents was found.
Detrimental effects of Bartonella henselae are counteracted by l-arginine and nitric oxide in human endothelial progenitor cells

The recruitment of circulating endothelial progenitor cells (EPCs) might have a beneficial effect on the clinical course of several diseases. Endothelial damage and detachment of endothelial cells are known to occur in infection, tissue ischemia, and sepsis. These detrimental effects in EPCs are unknown. Here we elucidated whether human EPCs internalize Bartonella henselae constituting a circulating niche of the pathogen. B. henselae invades EPCs as shown by gentamicin protection assays and transmission electron microscopy (TEM). Dil-Ac-LDL/lectin double immunostaining and fluorescence-activated cell sorting (FACS) analysis of EPCs revealed EPC bioactivity after infection with B. henselae. Nitric oxide (NO) and its precursor l-arginine (l-arg) exert a plethora of beneficial effects on vascular function and modulation of immune response. Therefore, we tested also the hypothesis that l-arg (1–30 mM) would affect the infection of B. henselae or tumor necrosis factor (TNF) in EPCs. Our data provide evidence that l-arg counteracts detrimental effects induced by TNF or Bartonella infections via NO (confirmed by DETA-NO and L-NMMA experiments) and by modulation of p38 kinase phosphorylation. Microarray analysis indicated several genes involved in immune response were differentially expressed in Bartonella-infected EPCs, whereas these genes returned in steady state when cells were exposed to sustained doses of l-arg. This mechanism may have broad therapeutic applications in tissue ischemia, angiogenesis, immune response, and sepsis.
Appropriate probe search method to specify groups in higher taxonomic ranks

A new method for procedures using a computer to find out useful candidates for probes discriminating a certain group in higher ranks of bacteria is presented. In order to make the search of the probes systematic, two indices are proposed, i.e., Coincidence Ratio Inside Group (CRIG) and Coincidence Number Outside Group (CNOG), which indicate the rate of matching of probes inside or outside group respectively. Using two indices, allowance grades indicating usefulness of arbitrary sequence as a probe are defined from 9 (5 in species) to 0. Its application to the 16S rRNA gene of 2206 bacterial species selected from the Ribosomal Database Project (RDP‐II) (J.R. Cole et al., Nucleic Acids Res. 31: 442–443, 2003) is shown. Small nucleotide sequences of the length L (L = 15, 19, 23) were searched from about 550 bases. As a result of computer calculations, appropriate probes are found in all taxonomic ranks, in addition, it is found that 95% of genera can be identified uniquely. The method is useful for DNA chips or targeted PCR which can select a desirable bacteria set in any taxonomic rank. The method is in principle deterministic, and widely applied to any type of nucleotide sequences. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Stress Influences on Anoikis

It long has been suspected that psychosocial factors affect cancer development and progression. Although the connections between stress and cancer causation are not strong, epidemiologic and clinical studies have provided strong links between cancer progression and several stress-related factors including chronic stress, depression, and social isolation. Recent molecular and biological studies have identified specific signaling pathways that influence cancer growth and metastasis. In particular, stress hormones can have a significant impact on protecting cancer cells from undergoing the anoikis form of programmed cell death, thus, providing a mechanistic advantage for metastasis. This review provides an overview of the relationship between psychosocial factors and the avoidance of anoikis by cancer cells. Cancer Prev Res; 4(4); 481–5. ©2011 AACR.
Accelerating Irregular Algorithms on GPGPUs Using Fine-Grain Hardware Worklists

Although GPGPUs are traditionally used to accelerate workloads with regular control and memory-access structure, recent work has shown that GPGPUs can also achieve significant speedups on more irregular algorithms. Data-driven implementations of irregular algorithms are algorithmically more efficient than topology-driven implementations, but issues with memory contention and memory-access irregularity can make the former perform worse in certain cases. In this paper, we propose a novel fine-grain hardware work list for GPGPUs that addresses the weaknesses of data-driven implementations. We detail multiple work redistribution schemes of varying complexity that can be employed to improve load balancing. Furthermore, a virtualization mechanism supports seamless work spilling to memory. A convenient shared work list software API is provided to simplify using our proposed mechanisms when implementing irregular algorithms. We evaluate challenging irregular algorithms from the Lonestar GPU benchmark suite on a cycle-level simulator. Our findings show that data-driven implementations running on a GPGPU using the hardware work list outperform highly optimized software-based implementations of these benchmarks running on a baseline GPGPU with speedups ranging from 1.2 - 2.4× and marginal area overhead.
Olga - a conversational agent with gestures

The Olga project has developed an animated agent interface for information services. The interface combines a graphical interface, spoken dialogue and an animated 3D ‘human-like’ character for multimodal input and output. The interaction is intelligently managed using techniques derived from spoken dialogue but extended for the graphical modality. The Olga agent is innovative in combining a spoken dialogue system with a 3-D animated character using lip-synthronized synthetic speech and gesturing. Particular attention has been paid to ensuring that the behaviour of the agent is immediately comprehensible for the user. Synchronizing speech with mouth movements increases intelligibility, while facial and gesturing realize the agent’s internal states and focus of the dialogue.
Effect of ionizing radiation on cellular procoagulability and co-ordinated gene alterations.

BACKGROUND AND OBJECTIVES Ionizing radiation (IR) is associated with thrombotic vascular occlusion predicting a poor clinical outcome. Our study examined whether IR induced tissue factor (TF) expression and procoagulability. We further investigated coordinated gene alterations associated with TF upregulation in the myelomonocytic leukemia THP-1 cells. DESIGN AND METHODS TF expression was determined by quantitative Reverse Transcriptase (TaqMan) PCR, TF ELISA and TF activity by a two stage chromogenic assay in the time course of days 1, 3, 7, 10, and 17 post IR. To detect IR-induced alterations in gene expression, Affymetrix HG U133 Plus 2.0 microarrays were used. RESULTS IR induced a significant increase in TF/GAPDH mRNA ratios and cellular TF protein on days 3 and 7 post IR (20 Gy [p>or=0.01] and 40 Gy [p <or=0.01 vs. control]), suggesting a late and persistent induction of TF. An increase in cellular TF activity was already found 1 day post IR (20 Gy and 40 Gy [p>or=0.001] vs. control respectively), suggesting IR immediately alters the cellular thrombogenicity. TF upregulation post IR was confirmed in PBMNCs. Gene expression profiling showed IR increased the expression of inflammatory and apoptosis-related pathways known to be involved in the regulation of TF expression. INTERPRETATION AND CONCLUSIONS TF upregulation together with inflammation and apoptosis may increase the thrombogenicity of tissues. The demonstrated upregulation of TF might play a pivotal role in radiation associated thrombosis.