Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient representation as a design principle for neural coding and computation

Does the brain construct an efficient representation of the sensory world? We review progress on this question, focusing on a series of experiments in the last decade which use fly vision as a model system in which theory and experiment can confront each other. Although the idea of efficient representation has been productive, clearly it is incomplete since it doesn't tell us which bits of sensory information are most valuable to the organism. We argue that, in fact, an organism which maximizes the (biologically meaningful) adaptive value of its actions given fixed resources must have internal representations of the outside world that are optimal in a very specific information theoretic sense: they maximize the information about the future of sensory inputs at a fixed value of the information about their past. This principle contains as special cases computations which the brain seems to carry out, and it should be possible to test this optimization directly. We return to the fly visual system and report the results of preliminary experiments that are in very suggestive agreement with theory
Phase Variable O Antigen Biosynthetic Genes Control Expression of the Major Protective Antigen and Bacteriophage Receptor in Vibrio cholerae O1

The Vibrio cholerae lipopolysaccharide O1 antigen is a major target of bacteriophages and the human immune system and is of critical importance for vaccine design. We used an O1-specific lytic bacteriophage as a tool to probe the capacity of V. cholerae to alter its O1 antigen and identified a novel mechanism by which this organism can modulate O antigen expression and exhibit intra-strain heterogeneity. We identified two phase variable genes required for O1 antigen biosynthesis, manA and wbeL. manA resides outside of the previously recognized O1 antigen biosynthetic locus, and encodes for a phosphomannose isomerase critical for the initial step in O1 antigen biosynthesis. We determined that manA and wbeL phase variants are attenuated for virulence, providing functional evidence to further support the critical role of the O1 antigen for infectivity. We provide the first report of phase variation modulating O1 antigen expression in V. cholerae, and show that the maintenance of these phase variable loci is an important means by which this facultative pathogen can generate the diverse subpopulations of cells needed for infecting the host intestinal tract and for escaping predation by an O1-specific phage.
B-lymphopoiesis is stopped by mobilizing doses of G-CSF and is rescued by overexpression of the anti-apoptotic protein Bcl2

Osteoblasts are necessary to B lymphopoiesis and mobilizing doses of G-CSF or cyclophosphamide inhibit osteoblasts, whereas AMD3100/Plerixafor does not. However, the effect of these mobilizing agents on B lymphopoiesis has not been reported. Mice (wild-type, knocked-out for TNF-α and TRAIL, or over-expressing Bcl-2) were mobilized with G-CSF, cyclophosphamide, or AMD3100. Bone marrow, blood, spleen and lymph node content in B cells was measured. G-CSF stopped medullar B lymphopoiesis with concomitant loss of B-cell colony-forming units, pre-pro-B, pro-B, pre-B and mature B cells and increased B-cell apoptosis by an indirect mechanism. Overexpression of the anti-apoptotic protein Bcl2 in transgenic mice rescued B-cell colony forming units and pre-pro-B cells in the marrow, and prevented loss of all B cells in marrow, blood and spleen. Blockade of endogenous soluble TNF-α with Etanercept, or combined deletion of the TNF-α and TRAIL genes did not prevent B lymphopoiesis arrest in response to G-CSF. Unlike G-CSF, treatments with cyclophosphamide or AMD3100 did not suppress B lymphopoiesis but caused instead robust B-cell mobilization. G-CSF, cyclophosphamide and AMD3100 have distinct effects on B lymphopoiesis and B-cell mobilization with: 1) G-CSF inhibiting medullar B lymphopoiesis without mobilizing B cells in a mechanism distinct from the TNF-α-mediated loss of B lymphopoiesis observed during inflammation or viral infections; 2) CYP mobilizing B cells but blocking their maturation; and 3) AMD3100 mobilizing B cells without affecting B lymphopoiesis. These results suggest that blood mobilized with these three agents may have distinct immune properties.
Conservation of a stress response: human heat shock transcription factors functionally substitute for yeast HSF

Heat shock factors (HSF) are important eukaryotic stress responsive transcription factors which are highly structurally conserved from yeast to mammals. HSFs bind as homotrimers to conserved promoter DNA recognition sites called HSEs. The baker's yeast Saccharomyces cerevisiae possesses a single essential HSF gene, while distinct HSF isoforms have been identified in humans. To ascertain the degree of functional similarity between the yeast and human HSF proteins, human HSF1 and HSF2 were expressed in yeast cells lacking the endogenous HSF gene. We demonstrate that human HSF2, but not HSF1, homotrimerizes and functionally complements the viability defect associated with a deletion of the yeast HSF gene. However, derivatives of hHSF1 that give rise to a trimerized protein, through disruption of a carboxyl‐ or amino‐terminal coiled‐coil domain thought to engage in intra‐molecular interactions that maintain the protein in a monomeric state, functionally substitute for yeast HSF. Surprisingly, hHSF2 expressed in yeast activates target gene transcription in response to thermal stress. Moreover, hHSF1 and hHSF2 exhibit selectivity for transcriptional activation of two distinct yeast heat shock responsive genes, which correlate with previously established mammalian HSF DNA binding preferences in vitro. These results provide new insight into the function of human HSF isoforms, and demonstrate the remarkable functional conservation between yeast and human HSFs, critical transcription factors required for responses to physiological, pharmacological and environmental stresses.
Computing the q-index for Tsallis Nonextensive Image Segmentation

The concept of entropy based on Shannon Theory of Information has been applied in the field of image processing and analysis since the work of T. Pun [1]. This concept is based on the traditional Boltzaman-Gibbs entropy, proposed under the classical thermodynamic. On the other hand, it is well known that this old formalism fails to explain some physical system if they have complex behavior such as long rang interactions and long time memories. Recently, studies in mechanical statistics have proposed a new kind of entropy, called Tsallis entropy (or non-extensive entropy), which has been considered with promising results on several applications in order to explain such phenomena. The main feature of Tsallis entropy is the $q$-index parameter, which is close related to the degree of system nonextensivity. In 2004 was proposed[2] the first algorithm for image segmentation based on Tsallis entropy. However, the computation of the q-index was already an open problem. On the other hand, in the field of image segmentation it is not an easy task to compare the quality of segmentation results. This is mainly due to the lack of an image ground truth based on human reasoning. In this paper, we propose the first methodology in the field of image segmentation for q-index computation and compare it with other similar approaches using a human based segmentation ground truth. The results suggest that our approach is a forward step for image segmentation algorithms based on Information Theory.
Numerical study on upper-millimeter wave to terahertz devices using PBG waveguiding structure

The photonic crystal device is potentially important for upper-millimeter and terahertz applications and will create a new breakthrough in modern electromagnetic wave circuits. The propagation loss of photonic crystal waveguides, which is related to the confinement property of guided mode, is thought one of key factors in device designs. The dispersion characteristics of the PhC structure are firstly calculated by using the plane wave expansion method. Then the wave propagation properties of the PhC straight waveguides, T-junctions are numerically investigated as well as a bandpass filter based on microcavity.
Trends in total hospital financial performance under the prospective payment system

In this article, the author examines trends in determinants of total hospital facility revenues, expenses, and net profits during the period 1977-89. Measures of change in transaction prices are developed, which enable an analysis of trends in real hospital outputs and total factor productivity. The main source of hospital spending growth in excess of the gross national product is identified as growth in hospital employee compensation.
PPARγ Inhibitors as Novel Tubulin-Targeting Agents

The microtubule-targeting agents (MTAs) are a very successful class of cancer drugs with therapeutic benefits in both hematopoietic and solid tumors. However, resistance to these drugs is a significant problem. Current MTAs bind to microtubules, and/or to their constituent tubulin heterodimers, and affect microtubule polymerization and dynamics. The PPARγ inhibitor T0070907 can reduce tubulin levels in colorectal cancer cell lines and suppress tumor growth in a murine xenograft model. T0070907 does not alter microtubule polymerization in vitro, and does not appear to work by triggering modulation of tubulin RNA levels subsequent to decreased polymerization. This observation suggests the possible development of antimicrotubule drugs that work by a novel mechanism, and implies the presence of cancer therapeutic targets that have not yet been exploited. This review summarizes what is known about PPARγ inhibitors and cancer cell death, with emphasis on the tubulin phenotype and PPAR-dependence, and identifies potential mechanisms of action.
Explaining the Migration of Stocks from Exchanges in Emerging Economies to International Center

The authors study the determinants of the growing migration of stock market activity to international financial centers. They use a sample of 77 countries and document that higher economic growth and more macroeconomic stability help stock market development. Countries with higher income per capita, sounder macroeconomic policies, more efficient legal systems, better shareholder protection, and more open financial markets tend to have larger and more liquid stock markets. The authors show that these factors also drive the degree with which capital raising, listing, and trading have been migrating to international financial centers. As fundamentals improve and technology advances, this migration will likely increase and domestic stock market activity may become too little to support local markets. For many emerging economies, the best policy is to establish sound fundamentals but not necessarily the trading, or even listing of securities locally.
Temperature and rainfall control of outflow from the Scott Glacier catchment (Svalbard) in the summers of 2005 and 2006

The article examines characteristics of meteorological and runoff time-series collected from the Scott Glacier catchment, Svalbard, during 2005 and 2006. The river discharge of Scottelva (Scott River) was monitored at a gauging station situated near the mouth of Recherche Fjord. Meteorological time-series (i.e. air temperature and precipitation) were monitored in Calypsobyen. The analysis shows interrelationships between meteorological and hydrological time-series, and that the runoff of Scottelva depends on the amount and intensity of glacial ablation. Total ablation for the Scott Glacier was estimated at 63.9 cm water equivalent in the 2005 season and 98.2 cm water equivalent in the 2006 season. A total of 64% and 72% of the discharge from the Scottelva in the respective 2005 and 2006 seasons came from surface ablation of the glacier.
Mitochondrial DNA as a biomarker for in-vitro fertilization outcome

Purpose of review This article discusses the use of mitochondrial DNA (mtDNA) copy number as a potential biomarker for embryo viability in assisted reproduction. Recent findings Mitochondria have a well-established role in regulating embryo energy metabolism, and their efficiency has significant implications for reproductive success. Two recent studies suggested that elevated mtDNA copy number is associated with decreased implantation potential in human embryos generated by IVF. In the first study, Fragouli et al. reported that blastocysts that are aneuploid and those obtained from older reproductive age women have a higher mtDNA copy number. In addition, euploid blastocysts that failed to implant had a higher mtDNA copy number; and pregnancy did not occur when mtDNA copy number was above a threshold. In a subsequent study, Diez-Juan et al. found that mtDNA copy number inversely correlates with implantation potential of euploid embryos, not only for blastocysts but also for cleavage stage embryos. Instead of a threshold model, they proposed a score for embryos based on mtDNA copy number, which would be indicative of implantation potential. Unlike the previous study, Diez-Juan et al. did not find an age-associated decrease in mtDNA copy number in day 3 or day 5 embryos. Summary Recent reports suggest that mtDNA copy number may be used as a biomarker for embryo viability. Further studies are necessary to determine whether mtDNA copy number constitutes a parameter independent of morphology and preimplantation genetic screening and whether its use may result in higher IVF pregnancy rates.
Early Tertiary magmatism in NE Greenland

Abstract Between 73° and 74°N in NE Greenland, a Lower Series of quartz tholeiite lavas is overlain by an Upper Series which varies from quartz tholeiitic to basanitic. The Lower Series basalts are attributed to large melt fractions produced east of the present outcrop where lithospheric thinning permitted the Iceland plume to ascend to shallow levels. Relocation of eruption sites up to 150 km (? ) further west, preceeded Upper Series activity. In this, small-degree melts, generated principally from garnet-lherzolite facies sources, were followed by products of more extensive, shallower melting which gave rise successively to the Upper Series lavas, a post-Upper Series basaltic dyke swarm and its associated caldera complex. Palaeomagnetic observations and 40Ar/39Ar dating suggest that the Lower Series (and part of the Upper Series) erupted in C24r at 58–57 Ma. Rejuvenescent activity at c. 32 Ma, marking the termination of volcanism, may relate to decompressive mantle melting associated with late regional uplift.
Obesity and the electrocardiogram

Obesity is associated with a wide variety of electrocardiographic (ECG) abnormalities. Most of these reflect alterations in cardiac morphology. Some serve as markers of risk for sudden death. Key ECG abnormalities or alterations occurring with disproportionately high frequency in obese subjects include: leftward shifts of the P wave QRS and T wave axes, various changes in P wave morphology, low QRS voltage, various markers of left ventricular hypertrophy (particularly the Cornell voltage and product), T wave flattening in the inferior and lateral leads, lengthening of the corrected QT interval and prolonged QT interval duration. Alterations in the signal‐averaged ECG and in heart rate variability may be arrhythmogenic. Cardiac arrhythmias have been described in obese subjects, but are often accompanied by left ventricular hypertrophy or the sleep apnea syndrome. Many of these ECG abnormalities are reversible with substantial weight loss. Thus, obesity is associated with a wide variety of ECG abnormalities, many of which are corrected by weight loss.
A peptide antigen derived from EGFR T790M is immunogenic in non-small cell lung cancer

Lung cancer is the leading cause of cancer-related deaths worldwide. Epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs), such as gefitinib and erlotinib, have demonstrated marked clinical activity against non-small cell lung cancer (NSCLC) harboring activating epidermal growth factor receptor (EGFR) mutations. However, in most cases, patients develop acquired resistance to EGFR-TKI therapy. The threonine to methionine change at codon 790 of EGFR (EGFR T790M) mutation is the most common acquired resistance mutation, and is present in ~50% cases of TKI resistance. New treatment strategies for NSCLC patients harboring the EGFR T790M mutation are required. We evaluated the immunogenicity of an antigen derived from EGFR with the T790M mutation. Using BIMAS we selected several EGFR T790M-derived peptides bound to human leukocyte antigen (HLA)-A*02:01. T790M-A peptide (789–797) (IMQLMPFGC)-specific cytotoxic T lymphocytes (CTLs) were induced from peripheral blood mononuclear cells (PBMCs) of HLA-A2+ healthy donors. An established T790M-A-specific CTL line showed reactivity against the NCSLC cell line, H1975-A2 (HLA-A2+, T790M+), but not H1975 (HLA-A2−, T790M+), and the corresponding wild-type peptide (ITQLMPFGC)-pulsed T2 cells using an interferon-γ (IFN-γ) enzyme-linked immuno spot (ELISPOT) assay. This CTL line also demonstrated peptide-specific cytotoxicity against H1975-A2 cells. This finding suggests that the EGFR T790M mutation-derived antigen could be a new target for cancer immunotherapy.
Multiethnic differences in smoking in Israel: pooled analysis from three national surveys.

BACKGROUND Smoking is a major public health risk and information regarding high-risk groups is needed to plan, implement and evaluate interventions aimed at lowering the number of smokers. METHODS During the years 1999-2001 data was collected regarding the smoking behaviour of the Israeli population in three national surveys. All three surveys included ages 25-64 and two included also ages 21-25 and over 64. RESULTS Smoking was associated with age, sex, ethnicity, education and religiosity after adjusting for the various demographic characteristics of the survey population. The prevalence of smoking among Arab and immigrant men from the former Soviet Union is higher than among Jewish men. Among women the opposite association exists. The older, religious and more educated reported smoking less frequently. In the Jewish population respondents, defining themselves as secular, reported higher rates of smoking. Only in women was marital status associated with smoking. A few specific high-risk groups for smoking can be identified such as young, less educated men, Arab men, single Jewish women and young immigrant men and women. CONCLUSIONS The three ethnic groups residing in Israel differ in the prevalence of smoking; each has a distinct pattern of smoking, positioning them at different stages within the conceptual framework of the larger smoking pandemic. Ethnicity, religiosity, age and education are associated with smoking in both sexes. This calls for specific tailored interventions aimed at younger men with less education, Arab men, and young immigrants.
Genetic Algorithm Based Wavelength Division Multiplexing Networks Planning

This paper presents a new heuristic algorithm useful for long-term planning of survivable WDM networks. A multi-period model is formulated that combines network topology design and capacity expansion. The ability to determine network expansion schedules of this type becomes increasingly important to the telecommunications industry and to its customers. The solution technique consists of a Genetic Algorithm that allows generating several network alternatives for each time period simultaneously and shortest-path techniques to deduce from these alternatives a least-cost network expansion plan over all time periods. The multi-period planning approach is illustrated on a realistic network example. Extensive simulations on a wide range of problem instances are carried out to assess the cost savings that can be expected by choosing a multi-period planning approach instead of an iterative network expansion design method. Keywords—Wavelength Division Multiplexing, Genetic Algorithm, Network topology, Multi-period reliable network planning
Panaché: A Scalable Distributed Index for Keyword Search

The primary challenge in developing a peer-to-peer file sharing system is implementing an efficient keyword search mechanism. This paper presents Panache, a distributed inverted index that scales well with the number of nodes in the network. Panache addresses three critical needs for searching peer-topeer file sharing systems—efficient use of bandwidth, relevant search results and accommodation for graceful node transience. To achieve these needs, Panache aggregates popularity information and builds upon other peer-to-peer systems that distribute index information by keyword. Relying on a combination of Bloom filtering, query ordering, and truncated results based on popularity data, Panache can be shown to use significantly less bandwidth than Gnutella using realworld estimates of network parameters, while retaining high quality search results. Simulation experiments demonstrate that Panache may be viable for Internet deployment, although more comprehensive testing is needed. Panache provides an exciting starting point for future development and optimization.
Ice particles in stratiform clouds in the Arctic and possible mechanisms for the production of high ice concentrations

The presence of ice particles in clouds affects precipitation processes, the radiative properties of the clouds, and the derivation of cloud properties from remote sensing measurements. High ice particle concentrations occur often in slightly to moderately supercooled clouds in the Arctic. This paper combines data collected in a common type of ice-producing arctic cloud (stratocumulus) with calculations based on laboratory experiments to elucidate mechanisms that might be responsible for the ice. Ice splinters produced during riming could account for the relatively high concentrations of ice particles in clouds that encompass temperatures between −2.5°C and −8°C. However, it has generally been assumed that ice splinters grow into pristine ice crystal habits, whereas detailed measurements in an arctic stratocumulus cloud showed that only 32% of the ice particles were pristine crystals (needles, sheaths, short columns, and plates) and 10% were broken pieces of needles or sheaths. Thirty-seven percent of the ice particles were not identifiable crystal types, 20% were frozen drops, and 1% were aggregates and graupel. The large numbers of unidentifiable ice particles could have originated from the fragmentation of delicate ice crystals and the shattering of some drops during freezing in free fall. These two mechanisms may also play a role in the production of relatively high ice particle concentrations in moderately supercooled arctic clouds that lie outside of the temperature zone where ice splinter production by riming occurs.