Miracle-dz/UniFAR-FTUs huggingface dataset:
A hybrid CPU-GPU implementation to accelerate multiple pairwise protein sequence alignment

Bioinformatics is an interdisciplinary field that applies techniques from computer science, statistics and engineering to guide in the study of large biological data. Protein structure and sequence analysis is very important in bioinformatics mainly in understanding cellular processes which helps in simplifying the development of drugs for metabolic pathways. Protein sequence alignment is a technique that is concerned with identifying the similarities among different protein structures in order to discover the relationships among them. These kinds of techniques are computationally extensive which hinders their applicability. In this paper, we propose a parallel approach to speed up the computational time of two sequence alignment algorithms using a hybrid implementation that combines the power of multicore CPUs and that of contemporary GPUs. Our study shows that the hybrid approach solves the problem much faster than its sequential counterpart.
Opn5 is a UV-sensitive bistable pigment that couples with Gi subtype of G protein

Opn5 (neuropsin) belongs to an independent group separated from the other six groups in the phylogenetic tree of opsins, for which little information of absorption characteristics and molecular properties of the members is available. Here we show that the chicken Opn5 (cOpn5m) is a UV-sensitive bistable pigment that couples with Gi subtype of G protein. The recombinant expression of cOpn5m in HEK 293s cells followed by the addition of 11-cis- and all-trans-retinal produced UV light-absorbing and visible light-absorbing forms, respectively. These forms were interconvertible by UV and visible light irradiations, respectively, indicating that cOpn5m is a bistable pigment. The absorption maxima of these forms were estimated to be 360 and 474 nm, respectively. The GTPγS binding assay clearly showed that the visible light-absorbing form having all-trans-retinal activates Gi type of G protein, whereas no Gt or Gq activation ability was observed. Immunohistochemical studies using an antibody against cOpn5m clearly showed that this pigment is localized within some types of amacrine cells and some cells in the ganglion cell layer of the retinas, the vast majority of cells in the pineal gland and serotonin-positive cells in the paraventricular organ. Because cOpn5m is the only UV-sensitive opsin among the opsins found so far in chicken, this study provides the molecular basis for UV reception in chicken.
Uncertain Booms and Fragility

I develop a framework of the buildup and outbreak of financial crises in an asymmetric information setting. In equilibrium, two distinct economic states arise endogenously: ? normal times,? periods of modest investment, and ? booms,? periods of expansionary investment. Normal times occur when the intermediary sector realizes moderate investment opportunities. Booms occur when the intermediary sector realizes many investment opportunities, but also occur when it realizes very few opportunities. As a result, investors face greater uncertainty in booms. During a boom, subsequent arrival of negative information about an intermediary asset results in large downward shifts in investors? confidence about the underlying quality of long-term assets. A crisis of confidence ensues. Investors collectively force costly early liquidation of the intermediated assets and move capital to safe assets, in a flight-to-quality episode.
Collagen Formation and Endochondral Ossification in Estrogen Treated Mice.∗

Summary The effect of estrogen on rate of collagen synthesis and new bone formation in the mouse was investigated by high resolution autoradiographic methods. H 3 -proline and H3-glycine were administered on the first and seventh days, respectively, following estrogen treatment, and the mice were sacrificed at various intervals during the 24 hours following each tracer injection. The position of the radioproline label on metaphyseal tra-beculae indicated that the control bones grew in length 135 μ/day, whereas the bones from mice injected with estrogen 24 hours previously grew only 66 μ/day. Grain counts indicated that (a) uptake of the labeled amino acids by osteoblasts, and (b) subsequent transfer of the label with time after injection to surfaces of newly forming metaphyseal and endosteal bone were not affected by prior estrogen treatment. Silver grains were observed over the bone 16-24 hours after tracer administration. It was concluded that estrogen stimulates the processes which promote the differentiation of osteoblasts in the bones of mice, and that the hormone has no effect on the functional capacity of individual osteoblasts to synthesize and form collagen.
Neurotoxic Effects and Biomarkers of Lead Exposure: A Review

Lead, a systemic toxicant affecting virtually every organ system, primarily affects the central nervous system, particularly the developing brain. Consequently, children are at a greater risk than adults of suffering from the neurotoxic effects of lead. To date, no safe lead-exposure threshold has been identified. The ability of lead to pass through the blood-brain barrier is due in large part to its ability to substitute for calcium ions. Within the brain, lead-induced damage in the prefrontal cerebral cortex, hippocampus, and cerebellum can lead to a variety of neurologic disorders. At the molecular level, lead interferes with the regulatory action of calcium on cell functions and disrupts many intracellular biological activities. Experimental studies have also shown that lead exposure may have genotoxic effects, especially in the brain, bone marrow, liver, and lung cells. Knowledge of the neurotoxicology of lead has advanced in recent decades due to new information on its toxic mechanisms and cellular specificity. This paper presents an overview, updated to January 2009, of the neurotoxic effects of lead with regard to children, adults, and experimental animals at both cellular and molecular levels, and discusses the biomarkers of lead exposure that are useful for risk assessment in the field of environmental health.
Recognition of pre-formed and flexible elements of an RNA stem-loop by nucleolin.

Nucleolin is an abundant nucleolar protein which is essential for ribosome biogenesis. The first two of its four tandem RNA-binding domains (RBD12) specifically recognize a stem-loop structure containing a conserved UCCCGA sequence in the loop called the nucleolin-recognition element (NRE). We have determined the structure of the consensus SELEX NRE (sNRE) by NMR spectroscopy. In both the free and bound RNA the top part of the stem forms a loop E (or S-turn) motif. In the absence of protein, the structure of the hairpin loop is not well defined due to conformational heterogeneity, and appears to be in equilibrium between two families of conformations. Titrations of RBD1, RBD2, and RBD12 with the sNRE show that specific binding requires RBD12. In complex with RBD12, the hairpin loop interacts specifically with the protein and adopts a well-defined structure which shares some of the features of the free form. The loop E motif also has specific interactions with the protein. Implications of these findings for the mechanism of recognition of RNA structures by modular proteins are discussed.
Explaining the EU's Policy Portfolio: Applying a Federal Integration Approach to EU Cohesion Policy. Bruges Political Research Paper No. 20, December 2011

This paper engages with the debate about why the nature of the EU's policy portfolio is as it is. It does so by taking cohesion policy and asking the question, why has it come to occupy so important a position in the EU‟s policy portfolio? It is argued that the two most common conceptually-based approaches applied to cohesion policy – intergovernmentalism and multilevel governance – do not adequately explain either the timing or the dynamic of cohesion policy. A model that combines economic integration approaches and federal approaches is developed in the paper to provide a basis for a new explanatory framework for the prominent position of cohesion in the portfolio. We suggest that our approach – which we call a federal integration approach – has the potential to be applied to other policy areas.
Does Upregulation of Inducible Nitric Oxide Synthase Play a Role in Hepatic Injury?

Lipopolysaccharide (LPS) and gut ischemia/reperfusion (I/R) injury cause reversible liver injury. Because nitric oxide (NO) can have both beneficial and deleterious effects in the gastrointestinal tract, and because the role of NO in gut I/R-induced hepatic injury is unknown, this study examined its role in LPS and gut I/R-induced hepatic injury in the rat. Both LPS and gut I/R caused a similar increase in serum hepatocellular enzymes. LPS but not gut I/R caused a significant increase in upregulation of hepatic inducible NO synthase (iNOS) according to quantitative real-time RT-PCR and Western immunoblot analysis. Aminoguanidine, a selective iNOS inhibitor, attenuated LPS-induced hepatic injury and hypotension, but did not prevent gut I/R-induced hepatic injury. In contrast, the non-selective NOS inhibitor NG-nitro-L-arginine methyl ester aggravated liver damage from both LPS and gut I/R. These data indicate that iNOS plays a role in mediating LPS-induced hepatic injury, but not gut I/R-induced hepatic injury. The data also suggest that the constitutive isoforms of NOS play a hepatoprotective role in both models of hepatic injury.
Spectrin repeat proteins in the nucleus

Spectrin repeat sequences are among the more common repeat elements identified in proteins, typically occurring in large structural proteins. Examples of spectrin repeat‐containing proteins include dystrophin, α‐actinin and spectrin itself—all proteins with well‐demonstrated roles of establishing and maintaining cell structure. Over the past decade, it has become clear that, although these proteins display a cytoplasmic and plasma membrane distribution, several are also found both at the nuclear envelope, and within the intranuclear space. In this review, we provide an overview of recent work regarding various spectrin repeat‐containing structural proteins in the nucleus. As well, we hypothesize about the regulation of their nuclear localization and possible nuclear functions based on domain architecture, known interacting proteins and evolutionary relationships. Given their large size, and their potential for interacting with multiple proteins and with chromatin, spectrin repeat‐containing proteins represent strong candidates for important organizational proteins within the nucleus. Supplementary material for this article can be found on the BioEssays website (http://www.interscience.wiley.com/jpages/0265‐9247/suppmat/index.html). BioEssays 27:144–152, 2005. © 2005 Wiley Periodicals, Inc.
Reactivation of Latent Human Cytomegalovirus in CD14+ Monocytes Is Differentiation Dependent

ABSTRACT We have previously demonstrated reactivation of latent human cytomegalovirus (HCMV) in myeloid lineage cells obtained from healthy donors. Virus was obtained from allogenically stimulated monocyte-derived macrophages (Allo-MDM), but not from macrophages differentiated by mitogenic stimulation (ConA-MDM). In the present study, the cellular and cytokine components essential for HCMV replication and reactivation were examined in Allo-MDM. The importance of both CD4+ and CD8+ T cells in the generation of HCMV-permissive Allo-MDM was demonstrated by negative selection or blocking experiments using antibodies directed against both HLA class I and HLA class II molecules. Interestingly, contact of monocytes with CD4 or CD8 T cells was not essential for reactivation of HCMV, since virus was observed in macrophages derived from CD14+monocytes stimulated by supernatants produced by allogeneic stimulation of peripheral blood mononuclear cells. Examination of the cytokines produced in Allo-MDM and ConA-MDM cultures indicated a significant difference in the kinetics of production and quantity of these factors. Further examination of the cytokines essential for the generation of HCMV-permissive Allo-MDM identified gamma interferon (IFN-γ) but not interleukin-1 or -2, tumor necrosis factor alpha, or granulocyte-macrophage colony-stimulating factor as critical components in the generation of these macrophages. In addition, although IFN-γ was crucial for reactivation of latent HCMV, addition of IFN-γ to unstimulated macrophage cultures was insufficient to reactivate virus. Thus, this study characterizes two distinct monocyte-derived cell types which can be distinguished by their ability to reactivate and support HCMV replication and identifies the critical importance of IFN-γ in the reactivation of HCMV.
Escherichia coli Hsp31 functions as a holding chaperone that cooperates with the DnaK‐DnaJ‐GrpE system in the management of protein misfolding under severe stress conditions

Escherichia coli Hsp31 is a homodimeric protein that exhibits chaperone activity in vitro and is a representative member of a recently recognized family of heat shock proteins (Hsps). To gain insights on Hsp31 cellular function, we deleted the hchA gene from the MC4100 chromosome and combined the resulting null allele with lesions in other cytoplasmic chaperones. Although the hchA mutant only exhibited growth defects when cultivated at 48°C, loss of Hsp31 had a strong deleterious effect on the ability of cells to survive and recover from transient exposure to 50°C, and led to the enhanced aggregation of a subset of host proteins at this temperature. The absence of Hsp31 did not significantly affect the ability of the ClpB‐DnaK‐DnaJ‐GrpE system to clear thermally aggregated proteins at 30°C suggesting that Hsp31 does not possess disaggregase activity. Although it had no effect on the growth of groES30, ΔclpB or ΔibpAB cells at high temperatures, the hchA deletion aggravated the temperature sensitive phenotype of dnaK756 and grpE280 mutants and led to increased aggregation in stressed dnaK756 cells. On the basis of biochemical, structural and genetic data, we propose that Hsp31 acts as a modified holding chaperone that captures early unfolding intermediates under prolonged conditions of severe stress and releases them when cells return to physiological conditions. This additional line of defence would complement the roles of DnaK‐DnaJ‐GrpE, ClpB and IbpB in the management of thermally induced cellular protein misfolding.
Beauty in the Eye of the Home-Owner: Aesthetic Zoning and Residential Property Values: Beauty in the Eye of the Home-Owner

This paper empirically confirms one core motivation for architectural zoning: Shape homogeneity among neighboring homes increases the value of residential buildings. Drawing on large-scale shape and transaction data, this study first develops a data-driven measure of architectural similarity, condensing three-dimensional shapes to univariate shape distributions. These algorithm-based similarity estimates are good predictors of human perceptions of shape similarity and are linked to property attributes and transaction prices. For the city of Rotterdam, a price premium of approximately 3.5 percent is estimated for row houses within very homogeneous ensembles over buildings facing heterogeneous neighbors. This article is protected by copyright. All rights reserved
A Novel Type of 0-dB Directional Coupler for Microwave Integrated Circuits

A novel planar configuration of 0-dB directional coupler is presented as a single-layer crossover in microwave integrated circuits. Results of detailed structure analysis are discussed. Some design recommendations are given. A higher device performance in comparison with convenient 0-dB planar directional couplers is illustrated by results of numerical simulation and experimental investigation.
Rapid Urinary Trypsinogen-2 Test Strip in the Diagnosis of Acute Pancreatitis

Objectives: Early diagnosis of acute pancreatitis remains a challenge. A rapid dipstick screening test for acute pancreatitis has been developed. This prospective study was designed to evaluate the diagnostic value and time course of the rapid urinary trypsinogen-2 test strip in acute pancreatitis, with comparisons with serum amylase and serum lipase. Methods: A total of 165 patients with acute abdominal pain (67 with acute pancreatitis and 98 with other acute abdominal diseases) attending our emergency unit were included. All patients were tested with the urinary trypsinogen-2 test strip, and serum amylase and serum lipase concentrations were determined simultaneously. To measure the time course of the urinary trypsinogen-2 test, 32 patients with acute pancreatitis were tested with a urinary trypsinogen-2 test strip on days 1, 2, 3, and 4 after admission. Results: Using a cutoff level of 50 μg/L for urinary trypsinogen-2, the sensitivity, specificity, and accuracy of the urinary trypsinogen-2 test strip for recognition of acute pancreatitis were 89.6%, 85.7%, and 87.3%, respectively. The diagnostic accuracy rates of serum amylase and serum lipase were 88.5% and 93.3%, using cutoff values of 3 times the upper normal limits for serum amylase and serum lipase, respectively. All but one of the 17 patients with severe acute pancreatitis was detected by the test strip (sensitivity, 94.1%). The time-course study of the urinary trypsinogen-2 test strip revealed that the sensitivity on days 1, 2, 3, and 4 was 90.6%, 81.2%, 59.4%, and 50%, respectively. There was no significant difference in the sensitivity between urinary trypsinogen-2 and serum lipase; however, the sensitivity values of serum lipase were significantly higher than those of serum amylase from days 1 to 4. Conclusion: The rapid urinary trypsinogen-2 test is a reliable and simple method for the early diagnosis of acute pancreatitis. A positive test identifies patients in need of further diagnostic measures. The urinary trypsinogen-2 test can be performed in health care units where laboratory testing facilities are not immediately available.
Preventing diabetic foot ulcers.

Approximately 6% of the U.S. diabetic population (14 million) experiences lower extremity amputation due to diabetic foot ulcers. Investigators have demonstrated that the amputation rate can be reduced through specific preventive measures. However, these findings are not consistent across studies. Integration of research findings into the model of care for the chronically ill suggests that the inconsistency may be due to the lack of inclusion of key individual and environmental variables. In this critical review of the literature, a model of care for the chronically ill is provided to direct prevention, diagnosis, and treatment of diabetic foot ulcers.
Fibre optic sensor for non‐invasive monitoring of blood pressure during MRI scanning

This report focuses on designing and implementing a non‐invasive blood pressure (NIBP) measuring device capable of being used during magnetic resonance imaging (MRI). Based on measuring pulse wave velocity in arterial blood, the device uses the obtained result to estimate diastolic blood pressure. Pulse transit times are measured by two fibre optical accelerometers placed over the chest and carotid artery. The fabricated accelerometer contains two static fibres and a cantilever beam, whose free end is angled at 90 degrees to act as a reflecting surface. Optical fibres are used for both illuminating the surface and receiving the reflected light. When acceleration is applied to the sensor, it causes a deflection in the beam, thereby changing the amount of reflected light. The sensor's output voltage is proportional to the intensity of the reflected light. Tests conducted on the electronics and sensors inside an MRI room during scanning proved that the device is MR‐ compatible. No artifacts or distortions were detected. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Maternal infection with toxoplasma gondii in pregnancy and the risk of hearing loss in the offspring

Abstract The aim of this study was to investigate the association between maternal infection with Toxoplasma gondii (T. gondii) in pregnancy and subsequent risk of hearing loss in the offspring. The study included 27 727 children born in Norway 1992–1994. Maternal toxoplasma infection during pregnancy was ascertained by serological examination and fetal infection was ascertained by parasite detection in amniotic fluid and/or postnatal serological examination. Hearing loss was defined as mean hearing loss >35 dB HL in the better ear averaged over the pure-tone hearing thresholds at 500, 1000, and 2000 Hz, and the children were identified through linkage to the Norwegian Registry of Hearing Loss in Children. Twenty-two of the 27 727 children (0.08%) were diagnosed with hearing loss. Forty women had primary T. gondii infection in pregnancy. None of their offspring had hearing loss. There was also no association between T. gondii infection prior to pregnancy and hearing loss in the offspring. Hence, we did not find any association between T. gondii infection in pregnancy and hearing loss in the offspring. Sumario El propósito de este estudio fue investigar la asociación entre la infección materna con Toxoplasma gondii (T. Gondii) en el embarazo y el riesgo subsiguiente de pérdida auditiva en el bebé. El estudio incluyó 27.727 niños nacidos en Noruega entre 1992 y 1994. La infección materna por toxoplasma durante el embarazo fue evaluada por examen serológico y la infección fetal fue evaluada por detección del parásito en el líquido amniótico y/o por examen serológico post-natal. La pérdida auditiva fue definida como una hipoacusia media de > 35 dB en el mejor oído, promediado con base en los umbrales auditivos de tonos puros en 500, 1000 y 2000 Hz, y los niños fueron identificados a través de contacto con el Registro Noruego de Hipoacusia en Niños. Veintidós de los 27.727 niños (0.08%) se diagnosticaron con una pérdida auditiva. Cuarenta mujeres tuvi-eron infección primaria por T. Gondii durante el embarazo. Ninguno de sus hijos exhibieron una pérdida auditiva. No existió asociación entre la infección por T. Gondii antes del embarazo y la hipoacusia en el producto. Por tanto, no encontramos ninguna asociación entre la infección por T. Gondii en el embarazo y la aparición de una pérdida auditiva en el producto.
ON PHASE THREE OF THE SHIFTING‐BALANCE THEORY

A common conclusion in several recent publications devoted to the deterministic analysis of the third phase of Wright's shifting‐balance theory is that under reasonable conditions phase three should proceed easily. I argue that the mathematical equations analyzed in these papers do not correspond to the biological situation they were meant to describe. I present a more appropriate study of the third phase of the shifting balance. My results show that the third phase can proceed only under much more restricted conditions than the previous studies suggested. Migration should be neither too strong not too weak relative to selection. The higher peak should be sufficiently dominant over the lower peak. Recombination can greatly reduce the plausibility of this phase or completely preclude peak shifts. A very important determinant of the ultimate outcome of the competition between different peaks is the topological structure of the network of demes. Peak shifts in two‐dimensional networks of demes are more difficult than in one‐dimensional networks. Phase three can be accomplished easiest if it is initiated in one of the peripheral demes.