Miracle-dz/UniFAR-FTUs huggingface dataset:
Association of Stomatin with Lipid Bodies*

The oligomeric lipid raft-associated integral protein stomatin normally localizes to the plasma membrane and the late endosomal compartment. Similar to the caveolins, it is targeted to lipid bodies (LBs) on overexpression. Endogenous stomatin also associates with LBs to a small extent. Green fluorescent protein-tagged stomatin (StomGFP) and the dominant-negative caveolin-3 mutant DGV(cav3)HA occupy distinct domains on LB surfaces but eventually intermix. Studies of StomGFP deletion mutants reveal that the region for membrane association but not oligomerization and raft association is essential for LB targeting. Blocking protein synthesis leads to the redistribution of StomGFP from LBs to LysoTracker-positive vesicles indicating a connection with the late endosomal/lysosomal pathway. Live microscopy of StomGFP reveals multiple interactions between LBs and microtubule-associated vesicles possibly representing signaling events and/or the exchange of cargo. Proteomic analysis of isolated LBs identifies adipophilin and TIP47, various lipid-specific enzymes, cytoskeletal components, chaperones, Ras-related proteins, protein kinase D2, and other regulatory proteins. The association of the Rab proteins 1, 6, 7, 10, and 18 with LBs indicates various connections to other compartments. Our data suggest that LBs are not only involved in the storage of lipids but also participate actively in the cellular signaling network and the homeostasis of lipids.
A congruent phylogenomic signal places eukaryotes within the Archaea

Determining the relationships among the major groups of cellular life is important for understanding the evolution of biological diversity, but is difficult given the enormous time spans involved. In the textbook ‘three domains’ tree based on informational genes, eukaryotes and Archaea share a common ancestor to the exclusion of Bacteria. However, some phylogenetic analyses of the same data have placed eukaryotes within the Archaea, as the nearest relatives of different archaeal lineages. We compared the support for these competing hypotheses using sophisticated phylogenetic methods and an improved sampling of archaeal biodiversity. We also employed both new and existing tests of phylogenetic congruence to explore the level of uncertainty and conflict in the data. Our analyses suggested that much of the observed incongruence is weakly supported or associated with poorly fitting evolutionary models. All of our phylogenetic analyses, whether on small subunit and large subunit ribosomal RNA or concatenated protein-coding genes, recovered a monophyletic group containing eukaryotes and the TACK archaeal superphylum comprising the Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota. Hence, while our results provide no support for the iconic three-domain tree of life, they are consistent with an extended eocyte hypothesis whereby vital components of the eukaryotic nuclear lineage originated from within the archaeal radiation.
Throughput Maximization in Software-Defined Networks with Consolidated Middleboxes

Today's computer networks rely on a wide spectrum of specialized middleboxes to improve their security and performance. Traditional middleboxes that are implemented by dedicated hardware are expensive and hard to manage. A promising technique of consolidated middleboxes - implementing traditional middleboxes in Virtual Machines (VMs) - offers economical yet simplified management of middleboxes in Software-Defined Networks (SDNs). However there are still challenges to realizing user routing requests with network function enforcement (a sequence of middleboxes) while maximizing the network throughput, due to various resource constraints on SDNs, such as forwarding table capacity at each switch, bandwidth resource capacity at each link, and computing resource capacity at each server (Physical Machine). In this paper, we study the problem of maximizing the network throughput of an SDN by admitting as many user requests as possible, where each user request has both bandwidth and computing resource demands to implement its network functions (consolidated middleboxes). We first formulate the problem as a novel network throughput maximization problem. We then provide an Integer Linear Program (ILP) solution for it if the problem size is small, otherwise, we devise two heuristics that strive for the fine tradeoff between the accuracy of solutions and the running times of achieving the solutions. We finally evaluate the performance of the proposed algorithms by simulations, based on real and synthetic network topologies. Experimental results demonstrate that the proposed algorithms are very promising.
Examining the impact of shallow groundwater on evapotranspiration from uncultivated land in Colorado's Lower Arkansas River Valley

iii List of Figures: . vi List of Tables: . vii Justification of Work Performed . 1 Review of Methods Used . 4 Study Sites and Well Locations . 4 Estimation of ET . 6 Measurement of Potential Explanatory Variables . 8 Discussion of Results . 14 Basic Hydrologic Behavior of Field Sites . 14 Factors Most Associated with Space-Time ET Variations . 14 Spatial Variations of ET, Water Table Depth, and NDVI . 19 Contribution of Groundwater Upflux to Total ET . 25 Summary and Conclusions. 28 References . 30
Análisis estructural y tectosedimentario de la subcuenca de rincón blanco, precordillera occidental, provincia de San Juan

En la region del rio Los Patos, provincia de San Juan, aflora un serie triasica asociada al hemigraben mas septentrional de la cuenca Cuyana. Este ha sido identificado como Rincon Blanco y reune los depositos de Barreal, Hilario, Rincon Blanco, quebradas El Salto, El Tigre y Cerro Puntudo. El area de estudio forma parte de la faja corrida y plegada de la Precordillera en donde la deformacion compresiva dio lugar al desarrollo de estructuras complejas y fenomenos de inversion tectonica que dificultan el analisis del rift, la historia de su relleno y consecuentemente la correlacion a traves de la subcuenca. Sin embargo, el mapeo detallado de las estructuras, el estudio cinematico de las fallas y el analisis de la evolucion de los ambientes sedimentarios posibilitaron la elaboracion de un modelo simplicado del periodo extensional de la subcuenca. La sedimentacion fue continental, epiclastica y piroclastica y tuvo lugar en depocentros aislados que formaron un hemigraben asimetrico con polaridad este. El margen activo corresponde a la zona de Rincon Blanco mientras que la rampa corresponde a la zona de Barreal - Hilario. La evolucion del relleno estuvo marcada por un fuerte control tectonico y climatico que le imprimieron a las secuencias rasgos distintivos. Estas caracteristicas permitieron aplicar los conceptos de la estratigrafia secuencial, asi se identificaron tres secuencias depositacionales en terminos de espacio de acomodacion, que representan dos estadios de rifting (sinrift I y II) y sus correspondientes sags. Los resultados obtenidos correlacionan muy bien con lo observado en la rampa y con lo propuesto por otros autores para el depocentro Uspallata. El interesante contenido fosil compuesto por flora, fauna invertebrada, en especial de trazas fosiles, y vertebrada dada por la presencia de icnitas de tetrapados se utilizo para reconstruir la paleogeografia de la cuenca, al mismo tiempo que constituyo una herramienta de gran valor para ajustar la propuesta estratigrafica secuencial lograda a traves de los conceptos tectosedimentarios. El estudio detallado de la asociacion de tetrapodos de la Formacion Corral de Piedra, asimismo senala que por sus caracteristicas constituyen hasta el momento el registro mas antiguo de este grupo de dinosaurios en el mundo. Finalmente el analisis estructural y tectosedimentario permitieron ver que la secuencia aflorante sobre la margen oriental de la cuenca no esta directamente relacionada al Grupo Rincon Blanco y hasta tanto no se cuente con un dato preciso de edad, se la ha identificado como Unidad Marachemill.
Semi-transparent central stop in high-resolution X-ray ptychography using Kirkpatrick–Baez focusing

A semi-transparent central stop has been used for ptychographic coherent diffractive imaging to increase the effective dynamic range in the recording of the far-field diffraction patterns. In this way, the high flux density provided by nano-focusing Kirkpatrick–Baez mirrors can be fully exploited for high resolution and quantitative phase reconstructions.
Optical interconnection networks based on microring resonators

Optical microring resonators can be integrated on a chip to perform switching operations directly in the optical domain. Thus they become a building block to create switching elements in on-chip optical interconnection networks, which promise to overcome some of the limitations of current electronic networks. However, the peculiar asymmetric power losses of microring resonators impose new constraints on the design and control of on-chip optical networks. In this work, we study the design of multistage interconnection networks optimized for a particular metric that we name the degradation index, which characterizes the asymmetric behavior of microrings. We also propose a routing control algorithm to maximize the overall throughput, considering the maximum allowed degradation index as a constraint.
Sociodemographic characteristics associated with blindness in a Nile Delta governorate of Egypt

Background: Globally, blindness is associated with old age and being female. Other sociodemographic and socioeconomic status characteristics associated with blindness have included educational attainment, and occupation. These factors reflect exposure to specific risk factors for blinding eye diseases and utilisation of preventive and curative services by specific sectors of the population. Methods: A population based survey of blindness and trachoma was conducted in Menofiya governorate in Egypt. 3322 adults 50 years of age and over were sampled from throughout the governorate (population 2.7 million). Visual acuity and clinical conditions were recorded and interviews with respondents were conducted. Results: Overall, blindness (<6/60 presenting vision in the better eye) was recorded in 13% of the study population. Besides age and sex, other factors associated with blindness (logistic regression) were marital status and poor sanitation in the household. Conclusion: Socioeconomic status does not appear to be a significant factor associated with blindness in adults in this setting. Instead, sociocultural factors, in particular, characteristics associated with gender sensitive decision making within households, are likely to be more important considerations in understanding blindness in these communities. Successfully combating blindness in the Nile Delta of Egypt will require gender sensitive efforts aimed at timely and effective utilisation of eye care services.
Revisiting Hypergraph Models for Sparse Matrix Partitioning

We provide an exposition of hypergraph models for parallelizing sparse matrix-vector multiplies. Our aim is to emphasize the expressive power of hypergraph models. First, we set forth an elementary hypergraph model for the parallel matrix-vector multiply based on one-dimensional (1D) matrix partitioning. In the elementary model, the vertices represent the data of a matrix-vector multiply, and the nets encode dependencies among the data. We then apply a recently proposed hypergraph transformation operation to devise models for 1D sparse matrix partitioning. The resulting 1D partitioning models are equivalent to the previously proposed computational hypergraph models and are not meant to be replacements for them. Nevertheless, the new models give us insights into the previous ones and help us explain a subtle requirement, known as the consistency condition, of hypergraph partitioning models. Later, we demonstrate the flexibility of the elementary model on a few 1D partitioning problems that are hard to solve using the previously proposed models. We also discuss extensions of the proposed elementary model to two-dimensional matrix partitioning.
Mycoplasma salivarium as a Dominant Coloniser of Fanconi Anaemia Associated Oral Carcinoma

Mycoplasma salivarium belongs to the class of the smallest self-replicating Tenericutes and is predominantly found in the oral cavity of humans. In general it is considered as a non-pathogenic commensal. However, some reports point to an association with human diseases. M. salivarium was found e.g. as causative agent of a submasseteric abscess, in necrotic dental pulp, in brain abscess and clogged biliary stent. Here we describe the detection of M. salivarium on the surface of a squamous cell carcinoma of the tongue of a patient with Fanconi anaemia (FA). FA is an inherited bone marrow failure syndrome based on defective DNA-repair that increases the risk of carcinomas especially oral squamous cell carcinoma. Employing high coverage, massive parallel Roche/454-next-generation-sequencing of 16S rRNA gene amplicons we analysed the oral microbiome of this FA patient in comparison to that of an FA patient with a benign leukoplakia and five healthy individuals. The microbiota of the FA patient with leukoplakia correlated well with that of the healthy controls. A dominance of Streptococcus, Veillonella and Neisseria species was typically observed. In contrast, the microbiome of the cancer bearing FA patient was dominated by Pseudomonas aeruginosa at the healthy sites, which changed to a predominance of 98% M. salivarium on the tumour surface. Quantification of the mycoplasma load in five healthy, two tumour- and two leukoplakia-FA patients by TaqMan-PCR confirmed the prevalence of M. salivarium at the tumour sites. These new findings suggest that this mycoplasma species with its reduced coding capacity found ideal breeding grounds at the tumour sites. Interestingly, the oral cavity of all FA patients and especially samples at the tumour sites were in addition positive for Candida albicans. It remains to be elucidated in further studies whether M. salivarium can be used as a predictive biomarker for tumour development in these patients.
Simulated Procedure Rehearsal Is More Effective Than a Preoperative Generic Warm-Up for Endovascular Procedures

Introduction:Patient-specific simulated rehearsal (PsR) of a carotid artery stenting procedure (CAS) enables the interventionalist to rehearse the case before performing the procedure on the actual patient by incorporating patient-specific computed tomographic data into the simulation software. This study aimed to evaluate whether PsR of a CAS procedure can enhance the operative performance versus a virtual reality (VR) generic CAS warm-up procedure or no preparation at all. Methods:During a 10-session cognitive/technical VR course, medical residents were trained in CAS. Thereafter, in a randomized crossover study, each participant performed a patient-specific CAS case 3 times on the simulator, preceded by 3 different tasks: a PsR, a generic case, or no preparation. Technical performances were assessed using simulator-based metrics and expert-based ratings. Results:Twenty medical residents (surgery, cardiology, radiology) were recruited. Training plateaus were observed after 10 sessions for all participants. Performances were significantly better after PsR than after a generic warm-up or no warm-up for total procedure time (16.3 ± 0.6 vs 19.7 ± 1.0 vs 20.9 ± 1.1 minutes, P = 0.001) and fluoroscopy time (9.3 ± 0.1 vs 11.2 ± 0.6 vs 11.2 ± 0.5 minutes, P = 0.022) but did not influence contrast volume or number of roadmaps used during the “real” case. PsR significantly improved the quality of performance as measured by the expert-based ratings (scores 28 vs 25 vs 25, P = 0.020). Conclusions:Patient-specific simulated rehearsal of a CAS procedure significantly improves operative performance, compared to a generic VR warm-up or no warm-up. This technology requires further investigation with respect to improved outcomes on patients in the clinical setting.
Seroprevalence of measles, mumps and rubella antibodies in Luxembourg: results from a national cross-sectional study

A serological prevalence survey was carried out in Luxembourg during 2000–2001 to determine the antibody status of the Luxembourg population against vaccine-preventable infections. Blood samples of children and adolescents were collected prospectively in randomly selected schools. Samples of adults were obtained through volunteer patients of the national health laboratory or of the mandatory pre-nuptial test. Measles, mumps and rubella (MMR) virus antibody concentrations were measured using commercial ELISA tests. Age-standardized prevalence of measles, mumps and rubella virus antibodies was found to be 96·58, 75·40 and 95·69% respectively. Significant age-dependence of serology was observed for all three infections, with study participants born after the introduction of the MMR vaccine experiencing a gradual decline of antibodies following vaccination in childhood. Older study participants who were more likely to have antibodies from natural infection had consistently higher titres than younger individuals. Present vaccination coverage with MMR appears to be sufficient to prevent large local outbreaks of measles and rubella, but probably not mumps.
Choline intake influences phosphatidylcholine DHA enrichment in nonpregnant women but not in pregnant women in the third trimester.

BACKGROUND Phosphatidylcholine (PC) produced via the S-adenosylmethionine-dependent phosphatidylethanolamine (PE) N-methyltransferase (PEMT) pathway is enriched with docosahexaenoic acid (DHA). DHA plays a critical role in fetal development and is linked to health endpoints in adulthood. It is unknown whether choline, which can serve as a source of S-adenosylmethionine methyl groups, influences PC-DHA or the PC:PE ratio in pregnant and nonpregnant women. OBJECTIVE This study tested whether choline intake affects indicators of choline-related lipid metabolism, including erythrocyte and plasma PC-DHA and PC:PE ratios, in pregnant women in the third trimester and nonpregnant women. DESIGN Pregnant (n = 26) and nonpregnant (n = 21) women consumed 480 or 930 mg choline/d and a daily DHA supplement for 12 wk. Blood was collected at baseline and at the midpoint and end of the study. PC-DHA was analyzed as the proportion of total PC fatty acids. RESULTS Pregnant women had greater (P = 0.002) PC-DHA concentrations than did nonpregnant women at baseline. The proportion of erythrocyte and plasma PC-DHA increased (P ≤ 0.002) in pregnant and nonpregnant women regardless of choline intake. However, in nonpregnant women, consumption of 930 mg choline/d led to greater (P < 0.001) erythrocyte PC-DHA and a more rapid increase (P < 0.001) in plasma PC-DHA. Lower (P = 0.001-0.024) erythrocyte and plasma PC:PE in pregnant women was not modified by choline intake. CONCLUSIONS A higher choline intake may increase PEMT activity, resulting in greater PC-DHA enrichment of the PC molecule in nonpregnant women. Increased production of PC-DHA during pregnancy indicates elevated PEMT activity and a higher demand for methyl donors. This trial was registered at clinicaltrials.gov as NCT01127022.
ACTIVE REGION TRANSITION REGION LOOP POPULATIONS AND THEIR RELATIONSHIP TO THE CORONA

The relationships among coronal loop structures at different temperatures are not settled. Previous studies have suggested that coronal loops in the core of an active region (AR) are not seen cooling through lower temperatures and therefore are steadily heated. If loops were cooling, the transition region would be an ideal temperature regime to look for a signature of their evolution. The Extreme-ultraviolet Imaging Spectrometer on Hinode provides monochromatic images of the solar transition region and corona at an unprecedented cadence and spatial resolution, making it an ideal instrument to shed light on this issue. Analysis of observations of AR 10978 taken in 2007 December 8–19 indicates that there are two dominant loop populations in the AR: (1) core multitemperature loops that undergo a continuous process of heating and cooling in the full observed temperature range 0.4–2.5 MK and even higher as shown by the X-Ray Telescope and (2) peripheral loops which evolve mostly in the temperature range 0.4–1.3 MK. Loops at transition region temperatures can reach heights of 150 Mm in the corona above the limb and develop downflows with velocities in the range of 39–105 km s−1.
Numerical solution of an inverse problem in size-structured population dynamics

We consider a size-structured model for cell division and address the question of determining the division (birth) rate from the measured stable size distribution of the population. We propose a new regularization technique based on a filtering approach. We prove convergence of the algorithm and validate the theoretical results by implementing numerical simulations, based on classical techniques. We compare the results for direct and inverse problems, for the filtering method and for the quasi-reversibility method proposed in Perthame and Zubelli (2007 Inverse Problems 23 1037).
On non-Gaussianities in single-field inflation

We study the impact of higher dimension operators in the inflaton Lagrangian on the non-Gaussianity of the scalar spectrum. These terms can strongly enhance the effect without spoiling slow-roll, though it is difficult to exceed fNL~1, because the scale which suppresses the operators cannot be too low, if we want the effective field theory description to make sense. In particular we explicitly calculate the three-point function given by an higher derivative interaction of the form (∇)4, which is expected to give the most important contribution. The angular dependence of the result turns out to be quite different from the minimal case without higher dimension operators.
Did the Hartz Reforms Speed-Up Job Creation? A Macro-Evaluation Using Empirical Matching Functions

Starting in January 2003, Germany implemented the first two so-called Hartz reforms, followed by the third and fourth packages of Hartz reforms in January 2004 and January 2005, respectively. The aim of these reforms was to accelerate labor market flows and reduce unemployment duration. Without attempting to evaluate the specific components of these Hartz reforms, this paper provides a first attempt to evaluate the overall effectiveness of the first two reform waves, Hartz I/II and III, in speeding up the matching process between unemployed and vacant jobs. The analysis is conceptually rooted in the flow-based view underlying the reforms, estimating the structural features of the matching process. The results indicate that the reforms indeed had an impact in making the labor market more dynamic and accelerating the matching process.
RFID opportunity analysis for leaner manufacturing

Although RFID is seen by many as a revolutionary enabler of automated data capture, confusion still remains as to how manufacturing organisations can identify cost-effective opportunities for its use. Managers view promotional business case estimates as unjustified, simulation based analysis and analytical models as secondary modes of analysis, and case studies are scarce. Further, there is a lack of simple tools to understand how RFID can help to achieve a leaner manufacturing environment, after the use of which practitioners can be routed to grounded forms of analysis. The purpose of this paper is to provide and test such a toolset, which uses the seven Toyota Production System wastes as a template. In our approach, RFID technology is viewed as a vehicle to achieve leaner manufacturing through automated data collection, assurance of data dependencies, and improvements in production and inventory visibility. The toolset is tested on case examples from two push-based, multi-national fast moving consumer goods manufacturing companies. The opportunity analysis is shown to identify not only initially suspected areas of improvement, but also other areas of value.