Miracle-dz/UniFAR-FTUs huggingface dataset:
RAS/Cyclic AMP and Transcription Factor Msn2 Regulate Mating and Mating-Type Switching in the Yeast Kluyveromyces lactis

ABSTRACT In response to harsh environmental conditions, ascomycetes produce stress-resistant spores to promote survival. As sporulation requires a diploid DNA content, species with a haploid lifestyle, such as Kluyveromyces lactis, first induce mating in response to stress. In K. lactis, mating and mating-type switching are induced by the DNA-binding protein Mts1. Mts1 expression is known to be upregulated by nutrient limitation, but the mechanism is unknown. We show that a ras2 mutation results in a hyperswitching phenotype. In contrast, strains lacking the phosphodiesterase Pde2 had lower switching rates compared to that of the wild type (WT). As Ras2 promotes cyclic AMP (cAMP) production and Pde2 degrades cAMP, these data suggest that low cAMP levels induce switching. Because the MTS1 regulatory region contains several Msn2 binding sites and Msn2 is a transcription factor that is activated by low cAMP levels, we investigated if Msn2 regulates MTS1 transcription. Consistently with this idea, an msn2 mutant strain displayed lower switching rates than the WT strain. The transcription of MTS1 is highly induced in the ras2 mutant strain. In contrast, an msn2 ras2 double mutant strain displays WT levels of the MTS1 transcript, showing that Msn2 is a critical inducer of MTS1 transcription. Strains lacking Msn2 and Pde2 also exhibit mating defects that can be complemented by the ectopic expression of Mts1. Finally, we show that MTS1 is subjected to negative autoregulation, presumably adding robustness to the mating and switching responses. We suggest a model in which Ras2/cAMP/Msn2 mediates the stress-induced mating and mating-type switching responses in K. lactis.
Observation of Correlated Particle-Hole Pairs and String Order in Low-Dimensional Mott Insulators

Parity correlations in a one-dimensional Bose gas in an optical lattice reveal a hidden “string order. ” Quantum phases of matter are characterized by the underlying correlations of the many-body system. Although this is typically captured by a local order parameter, it has been shown that a broad class of many-body systems possesses a hidden nonlocal order. In the case of bosonic Mott insulators, the ground state properties are governed by quantum fluctuations in the form of correlated particle-hole pairs that lead to the emergence of a nonlocal string order in one dimension. By using high-resolution imaging of low-dimensional quantum gases in an optical lattice, we directly detect these pairs with single-site and single-particle sensitivity and observe string order in the one-dimensional case.
Molecular determination of carriage of the mecA locus in coagulase negative staphylococci in screening swabs from patients in an intensive care unit

Staphylococci are important nosocomial pathogens, which are easily transmitted from patient to patient, and there is concern over the recent emergence of antibiotic resistance to the β lactam class of antimicrobial drugs, particularly within methicillin resistant Staphylococcus aureus (MRSA). Coagulase negative staphylococci, although relatively less pathogenic than S aureus, are important pathogens, particularly in immunocompromised or immunosuppressed patients, where they can cause line associated bacteraemia and infections of prosthetic devices, such as heart valves. Recently, several studies have suggested that S aureus may acquire the mecA locus through the horizontal gene transfer of this locus from methicillin resistant (mecA +ve) coagulase negative staphylococci to methicillin sensitive S aureus , thus resulting in the emergence of MRSA phenotypes.1,2 Therefore, the aim of our study was to determine the incidence of carriage of the mecA locus in coagulase negative staphylococci isolated from screening swabs from an intensive care unit (ICU) in a large acute teaching hospital. Seventy five patients within the ICU at Belfast City Hospital …
The Polycomb-Group GeneEzh2 Is Required for Early Mouse Development

ABSTRACT Polycomb-group (Pc-G) genes are required for the stable repression of the homeotic selector genes and other developmentally regulated genes, presumably through the modulation of chromatin domains. Among the Drosophila Pc-G genes,Enhancer of zeste [E(z)] merits special consideration since it represents one of the Pc-G genes most conserved through evolution. In addition, the E(Z) protein family contains the SET domain, which has recently been linked with histone methyltransferase (HMTase) activity. Although E(Z)-related proteins have not (yet) been directly associated with HMTase activity, mammalian Ezh2 is a member of a histone deacetylase complex. To investigate its in vivo function, we generated mice deficient for Ezh2. The Ezh2 null mutation results in lethality at early stages of mouse development. Ezh2 mutant mice either cease developing after implantation or initiate but fail to complete gastrulation. Moreover, Ezh2-deficient blastocysts display an impaired potential for outgrowth, preventing the establishment of Ezh2-null embryonic stem cells. Interestingly, Ezh2 is up-regulated upon fertilization and remains highly expressed at the preimplantation stages of mouse development. Together, these data suggest an essential role forEzh2 during early mouse development and genetically linkEzh2 with eed and YY1, the only other early-acting Pc-G genes.
Endophytic Chaetomium sp . from Michelia champaca L . and its taxol production

The study of naturally occurring compounds from plants has progressed to its present state of development by passing through a long time. Fungi have an excellent record in producing novel bioactive compounds and many of these presently have important medicinal properties. We subsequently isolated few endophytic fungi from plant parts and tested for the production of taxol like compound. Medicinal plants produce bioactive constituents capable of preventing and curing illnesses. They also provide a unique environment for endophytes. Diverse fungal endophytes exist within plant tissues, with a global estimate of upto a million species. These endophytes presumably occur in a mutualistic association with the host plants, such as enhancing hosts competitive abilities by excreting some bioactive metabolites. Fungal endophytes residing in medicinal plants have been recognized to be a likely source of novel metabolites of pharmaceutical importance. However, these special fungi have not been systematically characterized. In this paper, an endophytic Chaetomium sp. from Michelia champaca L. was investigated for taxol, an anti-cancer compound and its molecular characterization.
GPU System Calls

GPUs are becoming first-class compute citizens and are being tasked to perform increasingly complex work. Modern GPUs increasingly support programmabilityenhancing features such as shared virtual memory and hardware cache coherence, enabling them to run a wider variety of programs. But a key aspect of general-purpose programming where GPUs are still found lacking is the ability to invoke system calls. We explore how to directly invoke generic system calls in GPU programs. We examine how system calls should be meshed with prevailing GPGPU programming models, where thousands of threads are organized in a hierarchy of execution groups: Should a system call be invoked at the individual GPU task, or at different execution group levels? What are reasonable ordering semantics for GPU system calls across these hierarchy of execution groups? To study these questions, we implemented GENESYS – a mechanism to allow GPU programs to invoke system calls in the Linux operating system. Numerous subtle changes to Linux were necessary, as the existing kernel assumes that only CPUs invoke system calls. We analyze the performance of GENESYS using micro-benchmarks and three applications that exercise the filesystem, networking, and memory allocation subsystems of the kernel. We conclude by analyzing the suitability of all of Linux’s system calls for the GPU.
Role of lysosomes and cathepsin inhibitor in plasma during pneumococcal infection.

Infecting microorganisms may directly affect metabolic processes by competition for substrate or they may release toxins which may affect specific metabolic pathways. Alternatively, substances causing an adverse effect upon biochemical mechanisms may be released by the host in response to infection. Since DeDuve and his associates described lysosomes [1], many workers have attributed a major role to acid hydrolases in inflammatory and toxic phenomena. It has been postulated that bacterial lipopolysaccharides, acidosis of tissues, and hypoxia disrupt lysosomes; the ensuing release of acid hydrolases then alters cellular metabolism and causes cellular death [2-4]. However, the role of lysosomes and lysosomal enzymes in the pathogenesis of infection is unknown. The following studies were designed to determine the role of lysosomes and their enzymes in the pathogenesis of lethal pneumococcal infection.
Weight typology: An Optimality theoretic approach

This paper reviews the descriptive generalizations regarding segment weight, and provides an Optimality Theory (OT) analysis that both confirms and challenges traditional typological expectations. Ultimately, the predictions of factorial ranking provide a means by which to examine the adequacy of individual OT analyses and a metric by which to re-examine our assumptions about linguistic patterns and the nature of phonological typology. Descriptively, weight is shown to come in two flavors, coerced and distinctive. Each is relevant to both consonants and vowels, and each has its own generalizations - an implicational relationship between coerced weight and segment sonority, but no such relationship between distinctive weight and sonority. Theoretically, the factorial ranking of a small set of constraints not only explains the descriptive generalizations, but also results in some unexpected predictions that are, in fact, empirically supported.
Study of aortic- common iliac bifurcation and its clinical significance.

OBJECTIVE To determine the position of the aortic bifurcation, angle of aortic-common iliac bifurcation in relation to the lumbar vertebra, diameter of distal aorta, length of common iliac, diameter of iliac at bifurcation in cadavers. MATERIALS AND METHODS The present study was done on 25 cadavers (16 males, 9 females) used for the dissection by 1st year MBBS students. The dissections were performed by anterior approach to the lumbar vertebra. The position of the aortic bifurcation, aortic bifurcation angle were measured in relation to lumbar vertebra. The remaining parameters were measured with the help of digital vernier caliper. RESULTS The aortic bifurcation was seen in between L3 and L5 vertebra in all the cases. In majority of cases, 16 (64%), the bifurcation was observed at the level of L4 vertebra. During statistical analysis, significant differences were observed in the mean values of aortic-iliac take off angles and in mean diameter of distal aorta. CONCLUSION The exact location of aortic bifurcation is useful when invasive procedures are performed in the pelvis, laproscopic lumbar discectomy and lumbosacral total disc arthroplasty. The aortic bifurcation mostly found at the level of L4 vertebra in the present study similar to previous studies. The aortic bifurcation can be a reliable landmark for determining the lumbar vertebral segments on MRI or CT.
Modelo adaptativo para Organizaciones virtuales de agentes

[ES] Cada vez gana mas fuerza la idea de que modelar las interacciones de un sistema multi-agente no puede estar relacionado solamente con el propio agente y sus capacidades de comunicacion, si no que es necesario utilizar los conceptos de una ingenieria organizacional. Es posible establecer distintos tipos de organizaciones de agentes dependiendo del tipo de comunicacion, del modo de coordinacion entre agentes, asi como del tipo de agentes que conforman el grupo. Cada organizacion necesita de un soporte de coordinacion que determine explicitamente como deben organizarse los agentes y llevar a cabo las acciones y tareas asignadas dentro de la misma. En este estudio se presenta un nuevo modelo de coordinacion para una organizacion de agentes. La principal novedad del modelo consistira en la capacidad de planificacion dinamica y adaptativa para llevar a cabo una distribucion optima de las tareas de los agentes miembros de la organizacion. Se trata de un modelo unico en su concepcion, que permite dotar a una organizacion de capacidades auto-adaptativas en tiempo de ejecucion para entornos altamente dinamicos. De esta forma, el comportamiento de un agente estara determinado por las metas que desee alcanzar, pero teniendo en cuenta el resto de metas de los agentes companeros y los cambios en el entorno. Complementariamente el modelo es evaluado en un sistema multi-agente desarrollado dentro de la arquitectura orientada a organizaciones THOMAS y simulado en un entorno virtual. ; [EN] An idea that seems to be gaining considerable ground is that modeling the interactions of a multi-agent system cannot be related exclusively to the actual agent and its communication capabilities, but must involve the use of concepts found in organizational engineering as well. It is possible to establish different types of agent organizations according to the type of communication, the coordination among agents, and the type of agents that comprise the group. Each organization needs to be supported by a coordinated effort that explicitly determines how the agents should be organized and carry out the actions and tasks assigned to them. This thesis work presents a new global coordination model for an agent organization. The primary novelty of the model consists of the dynamic and adaptive planning capability to distribute tasks among the agent members of the organization as effectively as possible. This model is unique in its conception, allowing an organization in a highly dynamic environment to employ self-adaptive capabilities in execution time. This allows for the behavior of an agent to be determined by the goals it wishes to reach, while still giving consideration to the goals of other agents and any changes in the environment. The model is evaluated in a multi-agent system developed within an architecture oriented towards THOMAS organizations and simulated in a virtual environment.
Subfoveal Choroidal Thickness Changes Following Anti-Vascular Endothelial Growth Factor Therapy in Myopic Choroidal Neovascularization.

PURPOSE To investigate subfoveal choroidal thickness (SFCT) changes following intravitreal anti-vascular endothelial growth factor (anti-VEGF) therapy and to identify clinical and choroidal parameters associated with visual outcome in eyes with myopic choroidal neovascularization (CNV). METHODS In 60 eyes of 54 patients who were treated with anti-VEGF injections for myopic CNV, SFCT was measured using enhanced depth imaging optical coherence tomography at baseline, at 1, 3, and 6 months after initial anti-VEGF therapy, and at the final visit. Subfoveal choroidal thickness was compared between visits in subgroups separated based on anatomic outcome, recurrence, or resolution. Univariate and multivariate regression analyses were performed to identify factors associated with final best-corrected visual acuity (BCVA). RESULTS At baseline, the mean SFCT was 47.6 ± 24.7 μm, significantly lower than that of the contralateral eyes (59.8 ± 34.4 μm, P = 0.022). The thickness significantly decreased to 45.2 ± 24.0 μm (P = 0.027) 1 month after the anti-VEGF therapy. In the recurrent cases, the SFCT significantly increased from 46.1 ± 25.5 μm at month 1 to 52.4 ± 25.8 μm at the time of recurrence (P = 0.020); however, no significant change in the SFCT was noted in the nonrecurrent cases. In the regression analyses, the baseline BCVA (P < 0.001) and central macular thickness (CMT; P = 0.003) significantly correlated with the final BCVA, whereas SFCT or its change was not significantly associated with final BCVA. CONCLUSIONS Subfoveal choroidal thicknesss significantly decreased following anti-VEGF therapy in myopic CNV, but showed a subsequent increase in recurrence. Subfoveal choroidal thickness may reflect disease activity and aid decision making regarding retreatment in myopic CNV for recurrent cases.
Probing Conservation of HAMP Linker Structure and Signal Transduction Mechanism through Analysis of Hybrid Sensor Kinases

ABSTRACT The HAMP linker, a predicted structural element observed in many sensor kinases and methyl-accepting chemotaxis proteins, transmits signals between sensory input modules and output modules. HAMP linkers are located immediately inside the cytoplasmic membrane and are predicted to form two short amphipathic α-helices (AS-1 and AS-2) joined by an unstructured connector. HAMP linkers are found in the Escherichia coli nitrate- and nitrite-responsive sensor kinases NarX and NarQ (which respond to ligand by increasing kinase activity) and the sensor kinase CpxA (which responds to ligand by decreasing kinase activity). We constructed a series of hybrids with fusion points throughout the HAMP linker, in which the sensory modules of NarX or NarQ are fused to the transmitter modules of NarX, NarQ, or CpxA. A hybrid of the NarX sensor module and the CpxA HAMP linker and transmitter module (NarX-CpxA-1) responded to nitrate by decreasing kinase activity, whereas a hybrid in which the HAMP linker of NarX was replaced by that of CpxA (NarX-CpxA-NarX-1) responded to nitrate by increasing kinase activity. However, sequence variations between HAMP linkers do not allow free exchange of HAMP linkers or their components. Certain deletions in the NarX HAMP linker resulted in characteristic abnormal responses to ligand; similar deletions in the NarQ and NarX-CpxA-1 HAMP linkers resulted in responses to ligand generally similar to those seen in NarX. We conclude that the structure and action of the HAMP linker are conserved and that the HAMP linker transmits a signal to the output domain that ligand is bound.
FDA approach to evaluation of pathogen reduction technology

athogen reduction (PR) is a novel approach to decreasing pathogen transmission by blood transfusion. It has the potential to inactivate a broad range of pathogens that could be found in donated blood products and thus it would complement existing methods to prevent or decrease the presence of pathogens. The current methods include donor selection, skin disinfection, diversion of initial collection, and testing for specific agents. The concept of PR holds great promise. Ideally, PR methods should inactivate all pathogens found in blood products, not damage the transfusion product, and be safe to be administered to all patients. In reality, PR methodology is in its infancy and has yet to reach its true potential. In their current form, PR treatments are unlikely to sterilize the transfusion product. This results from large loads of certain pathogens that could overwhelm the capacity of the treatment, resistant forms of pathogens, inaccessible pathogens due to interference from storage bag geometry, poor light energy delivery due to interfering substances, and the potential for human error during processing. The PR methods are not strictly pathogen specific and produce collateral damage to the transfusion products that is often evident by the decreased retention of these products in circulation. In addition, the toxicity of PR chemicals and their metabolites and adducts may not be realized until a large-scale patient population is exposed to them. The FDA will evaluate PR treatments for their efficacy in decreasing pathogens in blood products, their effect on the transfusion product, and their safety to the recipient of treated products.
Molecular mechanisms of neurotransmitter release

The release of neurotransmitter from neurons represents one of the pivotal events in synaptic transmission. Neurotransmitters are released from synaptic vesicles in presynaptic neurons in response to neural activity, diffuse across the synaptic cleft, and bind specific receptors in order to bring about changes in postsynaptic neurons. Some of the molecular processes that govern neurotransmitter release are now becoming better understood. The steps involved can be broken down into two partially overlapping presynaptic cycles, the neurotransmitter cycle and the synaptic vesicle cycle. The neurotransmitter cycle involves transmitter biosynthesis, storage, reuptake, and degradation. The synaptic vesicle cycle involves targeting to the nerve terminal, docking, fusion, endocytosis, and recycling. Biochemical and structural studies have yielded important insight into our understanding of each of these two cycles. Further, both pharmacological and genetic interference with either of these cycles results in profound alterations in synaptic transmission and behavior, demonstrating the crucial role of neurotransmitter release. © 2001 John Wiley & Sons, Inc. Muscle Nerve 24: 581–601, 2001
Efficacy of IDET for Relief of Leg Pain Associated with Discogenic Low Back Pain

Abstract: Intradiscal electrothermal annuloplasty (IDET) is an effective treatment for chronic discogenic low back pain (LBP). However, efficacy of IDET for the treatment of referred leg pain has not been examined. This study was performed to assess the long‐term efficacy of IDET for the treatment of referred leg pain in chronic discogenic LBP patients. Data were retrospectively analyzed as an IDET case series from January 1999 to December 2000. The IDET procedure was performed at 1–3 symptomatic levels confirmed by pressure‐controlled discography. General pain outcome was evaluated by Visual Analog Scale (VAS). LBP and leg pain were assessed separately using five‐point pain scales (subsets of the North American Spine Society [NASS] LBP outcome assessment instrument: 0 = no pain, 4 = worst pain) at the 18‐month follow‐up. Among 129 patients who underwent IDET, 30 patients underwent subsequent back surgery and were excluded from the study, giving a total of 99 patients. Eighty‐three patients (83.8%) had leg pain without sciatica. Fifty‐two (52.5%), 21 (21.2%), and 8 (8.0%) patients showed LBP > leg pain, LBP = leg pain and LBP < leg pain, respectively. Fifty‐three out of 83 patients (63.9%) showed post‐IDET improvement in pain, with a mean VAS score of 3.28 ± 2.31. Thirty patients (36.1%) showed no improvement. A statistically significant (P < 0.05) improvement in subjective back and referred leg pain was observed. Improvements in back and referred leg pain were well‐correlated (r = 0.721, P < 0.01). A relatively large number of LBP patients who underwent IDET (84%) presented with referred leg pain without sciatica. The IDET procedure afforded improvements in leg pain that correlated well with improvements in back pain (0.75/4 and 0.88/4, respectively). These data suggest that IDET may relieve associated limb pain in chronic discogenic LBP patients.