Miracle-dz/UniFAR-FTUs huggingface dataset:
P29: a novel tyrosine-phosphorylated membrane protein present in small clear vesicles of neurons and endocrine cells

A novel membrane protein from rat brain synaptic vesicles with an apparent 29,000 Mr (p29) was characterized. Using monospecific polyclonal antibodies, the distribution of p29 was studied in a variety of tissues by light and electron microscopy and immunoblot analysis. Within the nervous system, p29 was present in virtually all nerve terminals. It was selectively associated with small synaptic vesicles and a perinuclear region corresponding to the area of the Golgi complex. P29 was not detected in any other subcellular organelles including large dense-core vesicles. The distribution of p29 in various subcellular fractions from rat brain was very similar to that of synaptophysin and synaptobrevin. The highest enrichment occurred in purified small synaptic vesicles. Outside the nervous system, p29 was found only in endocrine cell types specialized for peptide hormone secretion. In these cells, p29 had a distribution very similar to that of synaptophysin. It was associated with microvesicles of heterogeneous size and shape that are primarily concentrated in the centrosomal-Golgi complex area. Secretory granules were mostly unlabeled, but their membrane occasionally contained small labeled evaginations. Immunoisolation of subcellular organelles from undifferentiated PC12 cells with antisynaptophysin antibodies led to a concomitant enrichment of p29, synaptobrevin, and synaptophysin, further supporting a colocalization of all three proteins. P29 has an isoelectric point of approximately 5.0 and is not N-glycosylated. It is an integral membrane protein and all antibody binding sites are exposed on the cytoplasmic side of the vesicles. Two monoclonal antibodies raised against p29 cross reacted with synaptophysin, indicating the presence of related epitopes. P29, like synaptophysin, was phosphorylated on tyrosine residues by endogenous tyrosine kinase activity in intact vesicles.
Cheko : Aspect-Oriented Runtime Monitor Certification via Model-Checking ( Extended Version )

In-lining runtime monitors into untrusted binary programs via aspectweaving is an increasingly popular technique for efficiently and flexibly securing untrusted mobile code. However, the complexity of the monitor implementation and in-lining process in these frameworks can lead to vulnerabilities and low assurance for code-consumers. This paper presents a machine-verification technique for aspect-oriented in-lined reference monitors based on abstract interpretation and model-checking. Rather than relying upon trusted advice, the system verifies semantic properties expressed in a purely declarative policy specification language. Experiments on a variety of real-world policies and Java applications demonstrate that the approach is practical and effective.
First full investigation of levels of microplastics on sandy beaches in Malta

This paper will report on the first full investigations on the level of occurrence and qualitative/quantitative profiles of microplastics, MP, (1-5mm) in a number of saudy beaches in Malta, (Central MeditelTanean). Five popular beaches were investigated, including Ghadira Bay, Golden Bay, St. George's Bay, Ghajn Tuftieha Bay and Pretty Bay. Samples for all bays were collected in Tuffieha and Pretty Bay, samples were also collected from a 40cm depth. MP were extracted from sand through wet sieving, and then sorted and characterized according to size, colour, shape, and polymer type. Several parameters including degree of sea exposure and sand properties were reeorded. Full beach profiles for all locations are available. Identification of polymer type was carried out by means of qualitative density tests. 2015, the highest levels of MP were reported ill Pretty Bay at 10.81 itemsllO,OOcm o of wet sand with the lowest being in Ghajn Tuffiet1. , at 0.72 items/lOOO em'. In levels ofMP in the dlY season were found to be higher than those in the wet season (winter), Higher MP concentration was at 10 m up-shore as opposed to the strandline. Furthermore, surface sands comained a higher concentration ofrvIP when corr:. pared with the sEbsurface sediments: though this was not was no! the case at Pretty Bay in winter. These results are interpreted in terms of different beach profiles, beach dynamics, sand propel1ies and potential sources ofl'vlP. The local level of occurrence of ! viP seems to be lower when compared to other European locations studied so far. The fact that in this study, MP below Irnm were not included in the data, as well as the lack of rivers in the Maltese isimlds, regular beach clean ups and other factors may explain this. Data on the characterisation of ! viP found are provided. For example, polyethylene and polypropylene were the most common polymers recorded at Gnajn Tuftleha Bay whereas polyethylene and paint fragments were the most common 'MP recorded at Pretty Bay, This investigation is a contribution to our knowledge of how levels of ! vIP in sandy beaches may be affected by sand propel1ies and dynamics, beach profiles and other factors.
Distributed control algorithm and experiment of multi-agents in a non-rectangular bounded space

In this paper, we consider coordinated motion and cooperative control of multi-agents in a non-rectangular bounded space, and present a velocity consensus algorithm for the agents with double-integrator dynamics. The traditional consensus algorithm for bounded space is only applied to rectangular bouncing boundaries, not suitable for non-rectangular space. Therefore, we introduce the concept of the mirrored velocity that not only can convert the discontinuous real velocity into the continuous mirrored velocity, but also can expand a bounded space into an infinite space, and eventually the velocity of multi-agents asymptotically converge to the same values, respectively. Finally, the effectiveness of the proposed consensus algorithm is examined by numerical simulations. Moreover, we pave the way from theoretical design to practical implementation by performing an experiment in a real multi-robot system.
[Effect of simvastatin on residual ridge resorption after tooth extraction].

OBJECTIVE To observe the effect of simvastatin carried by poly (lactide-co-glycolide) (PLGA) on residual ridge resorption following tooth extraction. METHODS Sixty male Wistar rats were divided into experimental groups and control groups (30 rats/group). PLGA was immediately implanted with or without simvastatin into extraction sockets of the mandibular incisors. Soft X-ray photography, bone mineral density (BMD) and histopathologic study were conducted at 7, 14, 28, 56, and 84 days after implantation. RESULTS The relative length values of residual alveolar ridge of the experimental groups were greater than those of the controls at 14, 28, 56, and 84 days after implantation, and there was a significant difference between the experimental and control groups (P < 0.05). The BMD of the specific region was higher in the experimental groups [(7.101 +/- 0.025), (7.178 +/- 0.039), and (7.162 +/- 0.052) g/cm(2)] than that in the control groups [(7.074 +/- 0.014), (7.117 +/- 0.012), and (7.059 +/- 0.037) g/cm(2)] (P < 0.05) after 28, 56, and 84 days. Light microscopy showed that bone formation rate and quality of the experimental group were better than those in the control group at the same time. CONCLUSIONS Simvastatin carried by PLGA could induce bone formation of tooth socket. Local application of simvastatin would be potential to preserve the length and bone volume of alveolar ridge after tooth extraction.
High temperature and hospitalizations for cardiovascular and respiratory causes in 12 European cities.

RATIONALE Episode analyses of heat waves have documented a comparatively higher impact on mortality than on morbidity (hospital admissions) in European cities. The evidence from daily time series studies is scarce and inconsistent. OBJECTIVES To evaluate the impact of high environmental temperatures on hospital admissions during April to September in 12 European cities participating in the Assessment and Prevention of Acute Health Effects of Weather Conditions in Europe (PHEWE) project. METHODS For each city, time series analysis was used to model the relationship between maximum apparent temperature (lag 0-3 days) and daily hospital admissions for cardiovascular, cerebrovascular, and respiratory causes by age (all ages, 65-74 age group, and 75+ age group), and the city-specific estimates were pooled for two geographical groupings of cities. MEASUREMENTS AND MAIN RESULTS For respiratory admissions, there was a positive association that was heterogeneous between cities. For a 1 degrees C increase in maximum apparent temperature above a threshold, respiratory admissions increased by +4.5% (95% confidence interval, 1.9-7.3) and +3.1% (95% confidence interval, 0.8-5.5) in the 75+ age group in Mediterranean and North-Continental cities, respectively. In contrast, the association between temperature and cardiovascular and cerebrovascular admissions tended to be negative and did not reach statistical significance. CONCLUSIONS High temperatures have a specific impact on respiratory admissions, particularly in the elderly population, but the underlying mechanisms are poorly understood. Why high temperature increases cardiovascular mortality but not cardiovascular admissions is also unclear. The impact of extreme heat events on respiratory admissions is expected to increase in European cities as a result of global warming and progressive population aging.
Augmentation of Postnatal Neovascularization With Autologous Bone Marrow Transplantation

Background —Endothelial progenitor cells (EPCs) have been identified in adult human peripheral blood. Because circulating EPCs should originate from bone marrow (BM), we examined whether BM mononuclear cells (BM-MNCs) can give rise to functional EPCs and whether transplantation of autologous BM-MNCs might augment angiogenesis and collateral vessel formation in a rabbit model of hindlimb ischemia. Methods and Results —Rabbit BM-MNCs were isolated by centrifugation through a Histopaque density gradient and cultured on fibronectin. EPCs developed from BM-MNCs in vitro, as assessed by acetylated LDL incorporation, nitric oxide (NO) release, and expression of von Willebrand factor and lectin binding. Unilateral hindlimb ischemia was surgically induced in rabbits (n=8), and fluorescence-labeled autologous BM-MNCs were transplanted into the ischemic tissues. Two weeks after transplantation, fluorescence microscopy revealed that transplanted cells were incorporated into the capillary network among preserved skeletal myocytes. In contrast, transplanted autologous BM-fibroblasts did not participate in EC capillary network formation (n=5). Then, in an additional 27 rabbits, saline (control; n=8), autologous BM-MNCs (n=13; 6.9±2.2×106 cells/animal), or BM-fibroblasts (n=6; 6.5±1.5×106 cells/animal) were injected into the ischemic tissues at postoperative day 7. Four weeks after transplantation, the BM-MNC–transplanted group had more angiographically detectable collateral vessels (angiographic score: 1.5±0.34 versus 0.94±0.26 and 1.1±0.14;P <0.05), a higher capillary density (23±5.8 versus 10±1.9 and 11±0.8 per field;P <0.001), and a greater laser Doppler blood perfusion index (505±155 versus 361±35 and 358±22 U;P <0.05) than the control and BM-fibroblast–transplanted groups. Conclusions —Direct local transplantation of autologous BM-MNCs seems to be a useful strategy for therapeutic neovascularization in ischemic tissues in adults, consistent with “therapeutic vasculogenesis. ”
Study of the optimization of gold ore concentration using gravity separator (shaking table): case study for LS epithermal gold deposit in Artisanal Small scale Gold Mining (ASGM) Paningkaban, Banyumas, Central Java

Aiming to increase the concentration of gold ore from LS epithermal gold deposit Paningkaban, Banyumas, Central Java related to its characteristic, shaking table has been applied in the development of non-amalgamation technique for artisanal miners. Many parameters affect the results of processing the gold concentration using a shaking table. The parameters studied in this research are gold grain size fraction, water flow rate, and shaking table speed. With an objective to determine the optimum condition, this study was designed using statistical approach Response Surface Method (RSM) at which all of the variables were varied altogether. The research method is to process the gold using shaking table with three levels approach, so that in total there were 27 concentrates to analyze using Fire Assay (FA) and further assessed using RSM to distinguish the interaction among parameters and the optimum condition. For the gold ore deposit from Artisanal Small scale Gold Mining (ASGM) in Paningkaban, Banyumas, Central Java with the formation of low sulfidation epithermal, the results showed that the highest gold was 3688 ppm with operating conditions ie gold grain size fraction of -100 + 200 mesh (-149 + 74 micron), water flow rate of 18 l / min and shaking speed of 100 rpm. From the RSM assessment it was obtained that optimum operating conditions is on gold grain size of -100+ 200 mesh (87,2576 micron), water flow rate of 9 l / min and shaking speed of 100 rpm. Thus, shaking table could be an alternative non-amalgamation technique to process LS epithermal gold ore in Paningkaban creating a sustainable ASGM.
Robotic homing through a noisy potential field using information entropy

For a robot navigation system used in an unpredictable environment, it is generally effective to create a pathway that robots can track for carrying out a given task, such as reaching a goal. In the biological world, ants construct a foraging path using a volatile substance called pheromone, which has been widely studied and whose characteristics have been used in a transportation network model. When a navigation path is constructed by autonomous agents using this pheromone model, the created potential field can be very noisy, with many local peaks due to the unsynchronized updates of the field. In this paper, a new robotic homing algorithm is proposed. The algorithm minimizes information entropy and can track dynamic and noisy potential fields. The proposed algorithm is evaluated through a computer simulation.
Conversion of a Semiarid Nevada Soil to Irrigated Agriculture Preferentially Removes Labile Carbon

Due to the scarcity of arable land, semiarid rangelands are often converted to irrigated croplands, which is likely to affect soil organic carbon (SOC) due to changes in C inputs into the soil and environmental factors regulating decomposition. In this study, soil density and particle size fractions as well as their C and N contents, stable isotopic composition, and chemical characterization by mid-infrared spectroscopy were measured in a native shrubland and an adjacent agricultural site under alfalfa cultivation for at least 50 years in western Nevada. Cultivation significantly reduced the amount of C and N in the surface soils and the proportion of C present in the labile fractions. The δ13C and δ15N values of the SOC reflected dominant vegetation types at each site, and suggested most SOC was root-derived. The potential decomposition rate of SOC was higher in the shrubland than in the alfalfa surface soil reflecting the larger amount of labile C present in the shrubland soils. Spectroscopy results suggested that the greater recalcitrance of the alfalfa soils was due to insoluble SOC moieties. Additional analyses of buried, SOC-rich, A horizons at both sites showed that slower decomposition of ‘deep’ SOC was due to lower substrate quality supported by fractionation and spectroscopy data. The results of this study showed that converting a semiarid shrubland into irrigated cropland significantly reduced SOC content but increased overall stability of residual SOC.
Autoregulation of Nisin Biosynthesis in Lactococcus lactis by Signal Transduction (*)

The post-translationally modified, antimicrobial peptide nisin is secreted by strains of Lactococcus lactis that contain the chromosomally located nisin biosynthetic gene cluster nisABTCIPRKFEG. When a 4-base pair deletion is introduced into the structural nisA gene (ΔnisA), transcription of ΔnisA is abolished. Transcription of the ΔnisA gene is restored by adding subinhibitory amounts of nisin, nisin mutants, or nisin analogs to the culture medium, but not by the unmodified precursor peptide or by several other antimicrobial peptides. Upon disruption of the nisK gene, which encodes a putative sensor protein that belongs to the class of two-component regulators, transcription of ΔnisA was no longer inducible by nisin. Fusion of a nisA promoter fragment to the promoterless reporter gene gusA resulted in expression of gusA in L. lactis NZ9800 (ΔnisA) only upon induction with nisin species. The expression level of gusA was directly related to the amount of inducer that was added extracellularly. These results provide insight into a new mechanism of autoregulation through signal transduction in prokaryotes and demonstrate that antimicrobial peptides can exert a second function as signaling molecules.
An abacus turn model for time/space-efficient reconfigurable routing

Applications' traffic tends to be bursty and the location of hot-spot nodes moves as time goes by. This will significantly aggregate the blocking problem of wormhole-routed Network-on-Chip (NoC). Most of state-of-the-art traffic balancing solutions are based on fully adaptive routing algorithms which may introduce large time/space overhead to routers. Partially adaptive routing algorithms, on the other hand, are time/space efficient, but lack of even or sufficient routing adaptiveness. Reconfigurable routing algorithms could provide on-demand routing adaptiveness for reducing blocking, but most of them are off-line solutions due to the lack of a practical model to dynamically generate deadlock-free routing algorithms. In this paper, we propose the abacus-turn-model (AbTM) for designing time/space-efficient reconfigurable wormhole routing algorithms. Unlike the original turn model, AbTM exploits dynamic communication patterns in applications to reduce the routing latency and chip area requirements. We apply forbidden turns dynamically to preserve deadlock-free operations. Our AbTM routing architecture has two distinct advantages: First, the AbTM leads to a new router architecture without adding virtual channels and routing table. This reconfigurable architecture updates the routing path once the communication pattern changes, and always provides full adaptiveness to hot-spot directions to reduce network blocking. Secondly, the reconfiguration scheme has a good scalability because all operations are carried out between neighbors. We demonstrate these advantages through extensive simulation experiments. The experimental results are indeed encouraging and prove its applicability with scalable performance in large-scale NoC applications.
Monobloc and Midface Distraction Osteogenesis in Pediatric Patients with Severe Syndromal Craniosynostosis

We present 2 children with severe syndromal craniosynostosis who were in need of urgent midface advancement surgery due to recurrent ocular dislocations (Pfeiffer’s syndrome type II) or severe upper respiratory obstruction (Crouzon’s syndrome). They were operated using distraction osteogenesis, with gradual midface or monobloc advancements. In the Pfeiffer patient, a maxillary distraction of 25 mm achieved effective cessation of ocular dislocations, whereas a 23-mm monobloc advancement in the Crouzon patient achieved cessation of nocturnal arterial desaturations. No major postoperative complications were recorded. Distraction osteogenesis has become a versatile and safe technique that allows for large skeletal advancements.
MINS2: Revisiting the molecular code for transmembrane-helix recognition by the Sec61 translocon

UNLABELLED To be fully functional, membrane proteins should not only fold, but also get inserted into the membrane, which is mediated by the Sec61 translocon. Recent experimental studies have attempted to elucidate how the Sec61 translocon accomplishes this delicate task by measuring the translocon-mediated membrane insertion free energies of 357 systematically designed peptides. On the basis of this data set, we have developed MINS2, a novel sequence-based computational method for predicting the membrane insertion free energies of protein sequences. A benchmark analysis of MINS2 shows that MINS2 signi.cantly outperforms previously proposed methods. Importantly, the application of MINS2 to known membrane protein structures shows that a better prediction of membrane insertion free energies does not lead to a better prediction of transmembrane segments of polytopic membrane proteins. AVAILABILITY A web server for MINS2 is publicly available at http://service.bioinformatik. uni-saarland.de/mins. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Uranium (U)-Tolerant Bacterial Diversity from U Ore Deposit of Domiasiat in North-East India and Its Prospective Utilisation in Bioremediation

Uranium (U)-tolerant aerobic chemo-heterotrophic bacteria were isolated from the sub-surface soils of U-rich deposits in Domiasiat, North East India. The bacterial community explored at molecular level by amplified ribosomal DNA restriction analysis (ARDRA) resulted in 51 distinct phylotypes. Bacterial community assemblages at the U mining site with the concentration of U ranging from 20 to 100 ppm, were found to be most diverse. Representative bacteria analysed by 16S rRNA gene sequencing were affiliated to Firmicutes (51%), Gammaproteobacteria (26%), Actinobacteria (11%), Bacteroidetes (10%) and Betaproteobacteria (2%). Representative strains removed more than 90% and 53% of U from 100 μM and 2 mM uranyl nitrate solutions, respectively, at pH 3.5 within 10 min of exposure and the activity was retained until 24 h. Overall, 76% of characterized isolates possessed phosphatase enzyme and 53% had PIB-type ATPase genes. This study generated baseline information on the diverse indigenous U-tolerant bacteria which could serve as an indicator to estimate the environmental impact expected to be caused by mining in the future. Also, these natural isolates efficient in uranium binding and harbouring phosphatase enzyme and metal-transporting genes could possibly play a vital role in the bioremediation of metal-/radionuclide-contaminated environments.
Biodiversity Strategy Improved in Ethiopia by Using Optimal Control System

Biodiversity Strategy (BS) explains conserving biodiversity is not just a matter of protecting wildlife in nature reserves. It is also about safeguarding the natural systems of the Earth that are our life support systems, purifying the waters, recycling oxygen, carbon and other essential elements, maintaining the fertility of the soil, providing food from the land, freshwaters, and seas, yielding medicines and safeguarding the genetic richness on which we depend in the creaseless struggle to improve our crops and livestock. Biodiversity can be divided into three hierarchical categories – Genes, species and ecosystems that describe quite different aspects of living systems and that scientists’ measure in different ways. We tried to measure BS with suitable parameters by using Optimal Control Systems including Hamiltonian – Jacobi – Bellman Equation (HJBE) and state, costate with control aimed at to improve BS in Ethiopia and explain how to improve and implemented it in Ethiopia in future properly.