Miracle-dz/UniFAR-FTUs huggingface dataset:
Physical evidence for distinct mechanisms of translational control by upstream open reading frames

The Saccharomyces cerevisiae GCN4 mRNA 5′‐leader contains four upstream open reading frames (uORFs) and the CPA1 leader contains a single uORF. To determine how these uORFs control translation, we examined mRNAs containing these leaders in cell‐free translation extracts to determine where ribosomes were loaded first and where they were loaded during steady‐state translation. Ribosomes predominantly loaded first at GCN4 uORF1. Following its translation, but not the translation of uORF4, they efficiently reinitiated protein synthesis at Gcn4p. Adding purified eIF2 increased reinitiation at uORFs 3 or 4 and reduced reinitiation at Gcn4p. This indicates that eIF2 affects the site of reinitiation following translation of GCN4 uORF1 in vitro. In contrast, for mRNA containing the CPA1 uORF, ribosomes reached the downstream start codon by scanning past the uORF. Addition of arginine caused ribosomes that had synthesized the uORF polypeptide to stall at its termination codon, reducing loading at the downstream start codon, apparently by blocking scanning ribosomes, and not by affecting reinitiation. The GCN4 and CPA1 uORFs thus control translation in fundamentally different ways.
Kinetic-energy functional of the electron density.

A kinetic-energy functional of the electronic density is presented. This functional is based on an integral form and is correct through second order in the response. The formulas are compared numerically with the Thomas\char21{}Fermi\char21{}von Weizs\"acker\char21{}like formulas and favorable results are found. These formulas correctly give both shell structures in the electron densities of atoms and bond charges in the electron densities of solids. This quantum oscillation in the electron density is lacking in the densities of previous kinetic-energy functionals and is regarded as the major achievement of the current approach.
Astrocyte CD38: Links to Neuroinflammation in HAND

Central nervous system (CNS) HIV-1 infection can lead to encephalitis (HIVE), which compromises brain function and presents clinically as HIV-associated dementia [HAD, (Navia et al., 1986; Price et al., 1988; Wiley and Achim, 1994; Brew et al., 1995; Grant, 2008; Letendre et al., 2008; Price and Spudich, 2008)], the most serious form of HIV-associated neurocognitive disorders [HAND, (Grant, 2008; Letendre et al., 2008)]. HAND is associated with various cognitive, behavioral and motor dysfunctions [for details refer (Ances and Ellis, 2007; Grant, 2008)]. Although initiation of combined antiretroviral therapy (cART) has been linked to cognitive improvement and decreased incidence of HAD (Brodt et al., 1997; Sacktor et al., 1999; Foley et al., 2008), the yearly incidence rates for milder forms of HAND are still as high as 10-25% (Woods et al., 2009), and the prevalence of HAD is on the rise due to longer life expectancy of HIV-1-infected individuals (Lindl et al., 2010). The neuroinflammatory cascade associated with HAND, beginning with the infiltration of HIV-1-infected macrophages and immune activated microglial cells, likely reaches the endpoint of neurodegeneration via glial activation and changes in glial inflammatory responses (Kaul and Lipton, 2006). Reactive astrogliosis, the recruitment to and proliferation of astroglial cells at injury sites, is commonly observed during HIVE (Gonzales and Davis, 1988; Persidsky et al., 1996; Ridet et al., 1997; Wu and Schwartz, 1998; Petito et al., 1999). Astrocytes are the most abundant cell type in the CNS; and yet, their specific roles continue to be unraveled. Thus, characterization of molecules/pathways involving the activated astrocytes during HIVE and HAND, is of high interest. CD38 expression on peripheral T lymphocytes is a marker for disease progression in HIV-1infected patients (Savarino et al., 2000; Vigano et al., 2000; Kolber, 2008; Sinclair et al., 2008). CD38 is a 45-kD ectoenzyme involved in the synthesis of potent calcium(Ca2+) mobilizing agents, cyclic ADP ribose (cADPR) and nicotinic acid adenine dinucleotide phosphate (NAADP+) (Heidemann et al., 2005b; Banerjee et al., 2008). CD38 expression has been detected both in neurons and astrocytes in the cerebral cortex (Mizuguchi et al., 1995; Yamada et al., 1997), while it is primarily expressed by astrocytes in culture (Pawlikowska et al., 1996). Our group has shown that CD38 is one of the most upregulated molecules in IL1-activated astroglial cells in vitro and is also expressed by astrocytes in HIVE brain tissues
Compact Modeling of a Magnetic Tunnel Junction Based on Spin Orbit Torque

High endurance, high speed, scalability, low voltage, and CMOS-compatibility are the ideal attributes of memories that any integrated circuit designer dreams about. Adding non-volatility to all these features makes the magnetic tunnel junctions (MTJs) an ultimate candidate to efficiently build a hybrid MTJ/CMOS technology. Two-terminal MTJs based on spin-transfer torque (STT) switching have been intensively investigated in literature with a variety of model proposals. Despite the attractive potential of the STT devices, the issue of the common writing/reading path decreases their reliability dramatically. A three-terminal MTJ based on the spin-orbit torque (SOT) approach represents a pioneering way to triumph over current two-terminal MTJs by separating the reading and the writing paths. In this paper, we introduce the first compact model, which describes the SOT-MTJ device based on recently fabricated samples. The model has been developed in Verilog-A language, implemented on Cadence Virtuoso platform and validated with Spectre simulator. For optimized simulation accuracy, many experimental parameters are included in this model. Simulations prove the capability of the model to be efficiently used to design hybrid MTJ/CMOS circuits. Innovative logic circuits based on the SOT-MTJ device, modeled in this paper, are already in progress.
Advantages of allowing Hexagonal Pixels to be used as a Boundary Description Format

This paper considers some algorithmic extensions and some speci(cid:2)c advantages when using a hexagonal pixel array as compared with the usual practice of using a rectangular or square pixel raster array. Discussed are some of the algorithmic changes that are required when using pixels arranged within a hexagonal matrix. The use of a boundary hexagonal description format is considered from the point of view of; hexagonal six-connected contour edge encoding as compared with square four-connected and eight-connected descriptors, ef(cid:2)cient probability autocorrelation analysis, direct image manipulation and algorithmic simpli(cid:2)cation. Hardware and software conversion techniques for hexagonal pixels are now being seriously considered especially with the potential emergence of hexagonal CCD censor arrangements for cameras; for example this includes a recent patent with Fuji Photo Film Co.Ltd. (US patent number 6882364 Apr 19 2005) incorporating a bidirectional honeycomb pattern.
Epidemiology of Genital Herpes Simplex Virus Type 1 and 2 Infections in Southwestern Finland During a 10-Year Period (2003–2012)

Background The objective of this study was to analyze the proportion of herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) in genital infections during a 10-year period (2003–2012) among outpatients of a clinic of sexually transmitted disease in Southwestern Finland. Methods We analyzed prospectively the proportion of HSV-1– or HSV-2–positive culture samples from our sexually transmitted disease clinic outpatients with genital herpes infection during the years 2003 to 2012 and compared the proportions of positive HSV-1 and HSV-2 findings with the age and sex of the patients. Results Herpes simplex virus type 2 was typed in 66.4% (557/839) and HSV-1 in 33.6% (282/839) of the patients during the entire study period. The mean age of male patients (26.3 years) with a laboratory-confirmed HSV-1 infection was significantly lower than that in male patients with an HSV-2 infection in 2003 to 2007 (26.3 vs. 32.9 years), with P < 0.0001, and (28.6 vs. 34.0) P < 0.0019 in 2008 to 2012, respectively. More female than male patients had HSV-1 infection; in the first study period (2003–2007), 58% were female, and in 2008 to 2012, it was again 63.6%. There was no significant difference between the age of female patients with HSV-1 and those with HSV-2. Conclusions Herpes simplex virus type 2 was still the most common causative agent of genital herpes in Southwestern Finland, but the proportion of HSV-1 was increasingly high. The age difference between male patients with HSV-1 and HSV-2 narrowed during the years studied.
Large-eddy simulation of a turbulent piloted methane/air diffusion flame (Sandia flame D)

The Lagrangian Flamelet Model is formulated as a combustion model for large-eddy simulations of turbulent jet diffusion flames. The model is applied in a large-eddy simulation of a piloted partially premixed methane/air diffusion flame (Sandia flame D). The results of the simulation are compared to experimental data of the mean and RMS of the axial velocity and the mixture fraction and the unconditional and conditional averages of temperature and various species mass fractions, including CO and NO. All quantities are in good agreement with the experiments. The results indicate in accordance with experimental findings that regions of high strain appear in layer like structures, which are directed inwards and tend to align with the reaction zone, where the turbulence is fully developed. The analysis of the conditional temperature and mass fractions reveals a strong influence of the partial premixing of the fuel.
Comparison of periodontal microbiological patterns in Italian spouses.

PURPOSE The aim of this study is to evaluate whether periodontopathogens are transmitted from husband to wife or vice versa. MATERIALS AND METHODS We tested the microbiological profile of 9 couples married for at least 10 years suffering from periodontitis. The microbiological analysis provides the quantification by Real-Time PCR of six main periodontopathogens, including P. gingivalis, T. denticola, T. forsythia, F. nucleatum ssp. polymorphum, P. intermedia, A. actinomycetemcomitans and genotype of P. gingivalis FimA in 90 subgingival plaque samples. RESULTS The microbiological profiles highlighted a quite similar composition of oral microbial flora among husband and wife. Statistical results revealed a very high Pearson correlation values for the microbiological profiles in all 9 spouses. Additionally, five couples out of nine showed statistically similar values for the microbiological profile as determined by the Wilcoxon rank Sign test. We provided also a strong validation for the horizontal transmission of oral pathogens in the detection of the same genotype of P. gingivalis FimA in the spouses. CONCLUSIONS The presence of periodontitis in one member of the couple is a strong indicator of risk for the colonization of the spouse by periodontophatic bacteria. This study confirms that periodontal disease can be transmitted suggesting the importance of an early detection of oral pathogens in familial pattern of periodontitis to clarify the source of infection in order to assess correct prevention protocols based on potential infectivity within spouses.
Supplementary Material : Discovering the Building Blocks of Atomistic Systems

The length of SOAP vectors is determined by a radial basis cutoff nmax and an angular basis (spherical harmonic) cutoff lmax. We tuned the SOAP parameters to produce the best predictive results for GB energy using a grid search over radial cutoff values from 3.5 : 0.5 : 6.0 (from next-nearest neighbor shell up to fifth-nearest neighbors), lmax ∈ [8, 20], and nmax ∈ [8, 20]. The best performance of the ASR machine learning was obtained for cutoff of 5Å and lmax = 18 with nmax = 18. The same parameters were used for all other results of this work. Once the smallest features in the overlap of atomic environments have been resolved, increasing the values for lmax and nmax does not improve performance, but does incur additional computational cost.
Zyklusabhängigkeit mimischer Reaktionen auf erotische Bilder

Übersicht: Fünfunddreißig gesunde Frauen nahmen an einer Elektromyografie-Studie (EMG) zur Untersuchung des mimischen Ausdrucks des Grundgefühls „Freude“ in Abhängigkeit von visuellen Stimuli teil. Die elektrische Aktivität des Musculus zygomaticus major (kurz Zygomaticus; hebt die Mundwinkel beim Lächeln und ist entscheidend am mimischen Ausdruck von Freude beteiligt) wurde gemessen. Die untersuchten Frauen zeigten bei der Präsentation erotischer Stimuli in der follikulären Phase häufiger Zygomaticus-Reaktionen als in der lutealen Phase, während es unter der Kontrollbedingung keinen Phasenunterschied gab. Die Autoren folgern daraus, dass die Neigung, auf erotische Reize mit dem Ausdruck von Freude zu reagieren, ein bedeutsamer Faktor zur Koordination des Sexualverhaltens sei, der dazu dienen könnte, die Wahrscheinlichkeit von Geschlechtsverkehr während der empfängnisbereiten Tage zu erhöhen. Die Zyklusabhängigkeit weiblichen sexuellen Verlangens wird von den Autoren vor dem Hintergrund evolutionspsychologischer Theorien als ein adaptiver psychologischer Mechanismus betrachtet. Dieser trage über die Koordination sexuellen Verhaltens zum Reproduktionserfolg bei.
Climate Change and Human Health: Estimating Avoidable Deaths and Disease

Human population health has always been central in the justification for sustainable development but nearly invisible in the United Nations Framework Convention on Climate Change negotiations. Current scientific evidence indicates that climate change will contribute to the global burden of disease through increases in diarrhoeal disease, vector‐borne disease, and malnutrition, and the health impacts of extreme weather and climate events. A few studies have estimated future potential health impacts of climate change but often generate little policy‐relevant information. Robust estimates of future health impacts rely on robust projections of future disease patterns. The application of a standardized and established methodology has been developed to quantify the impact of climate change in relation to different greenhouse gas emission scenarios. All health risk assessments are necessarily biased toward conservative best‐estimates of health effects that are easily measured. Global, regional, and national risk assessments can take no account of irreversibility, or plausible low‐probability events with potentially very high burdens on human health. There is no “safe limit” of climate change with respect to health impacts as health systems in some regions do not adequately cope with the current climate variability. Current scientific methods cannot identify global threshold health effects in order for policymakers to regulate a “tolerable” amount of climate change. We argue for the need for more research to reduce the potential impacts of climate change on human health, including the development of improved methods for quantitative risk assessment. The large uncertainty about the future effects of climate change on human population health should be a reason to reduce greenhouse gas emissions, and not a reason for inaction.
A Novel Isoform of Met Receptor Tyrosine Kinase Blocks Hepatocyte Growth Factor/Met Signaling and Stimulates Skeletal Muscle Cell Differentiation*

Background: Alternative splicing gives a variation from the same gene. Results: A novel alternative splicing form of Met exists in human skeletal muscle, and its depletion decreases muscle differentiation, whereas its overexpression acts oppositely. Conclusion: A novel alternative splicing form of Met regulates skeletal muscle differentiation. Significance: This is an example of regulation by alternative splicing, which affects skeletal muscle differentiation. Hepatocyte growth factor (HGF) and its receptor, Met, regulate skeletal muscle differentiation. In the present study, we identified a novel alternatively spliced isoform of Met lacking exon 13 (designated Δ13Met), which is expressed mainly in human skeletal muscle. Alternative splicing yielded a truncated Met having extracellular domain only, suggesting an inhibitory role. Indeed, Δ13Met expression led to a decrease in HGF-induced tyrosine phosphorylation of Met and ERK phosphorylation, as well as cell proliferation and migration via sequestration of HGF. Interestingly, in human primary myoblasts undergoing differentiation, Δ13Met mRNA and protein levels were rapidly increased, concomitantly with a decrease in wild type Met mRNA and protein. Inhibition of Δ13Met with siRNA led to a decreased differentiation, whereas its overexpression potentiated differentiation of human primary myoblasts. Furthermore, in notexin-induced mouse injury model, exogenous Δ13Met expression enhanced regeneration of skeletal muscle, further confirming a stimulatory role of the isoform in muscle cell differentiation. In summary, we identified a novel alternatively spliced inhibitory isoform of Met that stimulates muscle cell differentiation, which confers a new means to control muscle differentiation and/or regeneration.
A real time urban flood monitoring system for metro Manila

A real time urban flood monitoring system was deployed into two streets (Earnshaw and San Diego Streets) on España Boulevard, Manila. The system consists of a ground-based pressure sensor and a rain gauge connected to a locally designed data logger with telemetry capabilites using GPRS network. Data from the stations are received by a TCP server and is processed in order to provide visual information and realtime flood updates through mobile and web services. An ahead of time flood estimation system was implemented using a Random Forest algorithm in order to provide an early warning advisory to motorist and users of the system. Results from the test validation show that the resulting prediction model indicates a strong predictive performance without relying on rainfall-runoff model obtained through geological and hydrological surveys.
The molecular basis of sulfonylurea herbicide resistance in tobacco

The enzyme acetolactate synthase (ALS) is the target enzyme for the sulfonylurea and imidazolinone herbicides. We describe the isolation and characterization of the ALS genes from two herbicide‐resistant mutants, C3 and S4‐Hra, of Nicotiana tabacum. There are two distinct ALS genes in tobacco which are 0.7% divergent at the amino acid sequence level. The C3 mutant has a single Pro–Gln replacement at amino acid 196 in one ALS gene. This gene is termed the class I gene and is equivalent to the SuRA locus. The S4‐Hra mutant has two amino acid changes in the other ALS gene. This gene is termed the class II gene or the SuRB locus. The S4‐Hra mutant includes a Pro–Ala substitution at amino acid 196 and a Trp–Leu substitution at amino acid 573. Gene reintroduction experiments have confirmed that these amino acid substitutions are responsible for the herbicide resistance phenotypes. Transgenic plants carrying these genes are highly resistant to sulfonylurea herbicide applications.
Towards improving the utility of fine‐needle aspiration biopsy for the diagnosis of thyroid tumours

Thyroid nodules are quite common with approximately 5% of the population, and approximately 10% of older individuals, having palpable thyroid nodules (Mazzaferri, 1993). Between 30 and 50% of people living in the United States and Europe have thyroid nodules noted on ultrasound examination. Fine-needle aspiration biopsy (FNAB) has become the mainstay of thyroid nodule evaluation. While the overall accuracy of FNAB is excellent, an indeterminate or suspicious biopsy can pose a diagnostic and management dilemma. Some of these issues are illustrated in the following patient vignettes.
Hormonal Contraceptive Use and Discontinuation Among HIV-Infected Women in Uganda and Zimbabwe

Background: Hormonal contraception (HC) use by HIV-infected women has been identified by the World Health Organization as an important strategy for reducing vertical HIV transmission. Little is known about the factors associated with HC discontinuation among HIV-infected women. Methods: We analyzed data from a prospective study of HC use among 231 HIV-infected users with oral contraceptive (OC) or injectable depot medroxyprogesterone acetate (DMPA) in Uganda and Zimbabwe. We used Kaplan–Meier survival curves to estimate the median duration of OC and DMPA use and use of any highly effective contraceptive method. Cox proportional hazards models were used to investigate factors associated with HC discontinuation. Results: Median duration was 36 months [95% confidence interval (CI): 14 to 61] for OC use and 19 months (95% CI: 14 to 24) for DMPA use. Median duration of any highly effective method was 36 months (95% CI: 26 to N/A) for OC users and 22 months (95% CI: 14 to 38) for DMPA users. In multivariable analyses, living in Zimbabwe [hazard ratio (HR): 0.39; 95% CI: 0.18 to 0.83], no partner (HR: 7.18; 95% CI: 3.05 to 16.88), and cervical infection (HR: 1.99; 95% CI: 0.90 to 4.41) were associated with OC discontinuation. No partner (HR: 2.00; 95% CI: 1.12 to 3.58), nausea (HR: 1.84; 95% CI: 1.02 to 3.34), and excessive night sweats (HR: 1.80; 95% CI: 0.95 to 3.40) were associated with DMPA discontinuation. Conclusion: Long-term use of HC methods is acceptable to HIV-infected women. Women discontinue for a variety of reasons, primarily unrelated to HIV. Alternative methods and ongoing contraceptive counseling is essential to reduce unplanned pregnancies and vertical HIV transmission.
Lessons from the evolution of an anatomical facial muscle model

Recently, Industrial Light & Magic has begun exploring facial muscle simulation as a means of augmenting our blendshape-based facial animation workflow in order to attain higher quality results. During this process, we discovered that a precise and accurate model of the underlying facial anatomy is key to obtaining high-quality facial simulation results that can be used for photorealistic hero characters. We present an overview of our workflow for developing such a model along with some of the key anatomical lessons that were essential to the process.
Weighing Up the Risks: The Challenge of Studying ‘Risk’ in Empirical Research

Studying multifaceted risks that are simultaneously and differently perceived and experienced presents significant challenges, but gaining insight into multiple realities and rationalities is crucial for achieving effective and collaborative governance. This article describes the challenges of a recent study that looked at how different actors, ranging from smallholder farmers to international biotechnology development projects, weigh up the risks associated with the uncertain future of maize agriculture in Kenya. It presents personal reflections on a 12‐month experience of applying a multi‐sited, ethnographic research approach in Kenya and the UK, in an attempt to observe the creation, perception and experience of risks. The article demonstrates the importance of history, knowledge, social and institutional settings, trust and politics in the ways that risks are created, perceived and experienced by these different actors, and argues for the necessity of engaging with these highly contextualised processes at individual, local and institutional levels.