Miracle-dz/UniFAR-FTUs huggingface dataset:
Large-scale circuit reconstruction in medial entorhinal cortex

The mechanisms by which the electrical activity of ensembles of neurons in the brain give rise to an individual’s behavior are still largely unknown. Navigation in space is one important capacity of the brain, for which the medial entorhinal cortex (MEC) is a pivotal structure in mammals. At the cellular level, neurons that represent the surrounding space in a grid-like fashion have been identified in MEC. These so-called grid cells are located predominantly in layer 2 of the MEC. The detailed neuronal circuits underlying this unique activity pattern are still poorly understood. This thesis comprises a group of studies contributing to a mechanistic description of the synaptic architecture in layer 2 of the MEC in rat. First, this thesis describes the discovery of hexagonally arranged cell clusters. Furthermore, anatomical data on the dichotomy of the two principle cell types in layer 2 of the MEC is presented. In the second part of this thesis, the first connectomic study of the MEC is reported which provides a detailed picture of the circuit structure in MEC layer 2. An analysis of the axonal architecture of excitatory neurons revealed synaptic positional sorting along axons, integrated into precise microcircuits. These microcircuits were found to involve interneurons with a surprising degree of axonal specialization for effective and fast inhibition. Together, these results contribute to a detailed understanding of the circuitry in MEC. They provide the first description of highly precise synaptic arrangements along axons in the cerebral cortex of mammals. The functional implications of these anatomical features were explored using numerical simulations, suggesting effects on the propagation of synchronous activity in layer 2 of the MEC. These findings motivate future investigations to clarify the contribution of precise synaptic architecture to computations underlying spatial navigation. Further studies are required to understand whether the reported synaptic specializations are specific for the MEC or represent a general wiring principle in the mammalian cortex.
Air‐Sea Gas Transfer: Determining Bubble Fluxes With In Situ N
 2
 Observations

Oxygen measurements by in situ sensors on remote platforms are used to determine net biological oxygen ﬂ uxes in the surface ocean. On an annual basis these ﬂ uxes are stoichiometrically related to the export of organic carbon from the upper ocean (the ocean's biological carbon pump). In situ measurements on remote platforms make it feasible to observe the annual biological oxygen ﬂ ux globally, but the accuracy of these estimates during periods of high winds depends on model ‐ determined ﬂ uxes by bubble processes created by breaking waves. We verify the importance of bubble processes in the gas exchange model of Liang et al. (2013, using surface ‐ ocean N 2 gas measurements determined from observations of dissolved gas pressure and oxygen concentrations every 3 hr on a mooring in the northeast subarctic Paci ﬁ c at Ocean Station Papa. The changes in N 2 concentration during 10 separate monthlong periods in the winters between 2007 and 2016 indicate that bubble processes in the gas exchange model are over predicted by about a factor of 3 at this location. (The bubble mass transfer coef ﬁ cients must be multiplied by 0.37 ± 0.14 to match the observations.) These results can be used to adjust model ‐ determined bubble ﬂ uxes to yield more accurate measurements of net biological oxygen production until the next generation gas ‐ exchange models are developed. of the oxygen ﬂ ux, the models must be able to evaluate physical ﬂ uxes of gas transfer caused by bubbles that result from breaking waves at high wind speeds. Our paper uses measurements of nitrogen gas on a surface mooring in the northeast Paci ﬁ c Ocean to evaluate the role of bubbles in air ‐ sea gas exchange. With the information provided here oceanographers can use the veri ﬁ ed gas exchange models to accurately determine biologically produced air ‐ sea oxygen ﬂ uxes. This advance will make it possible to verify biological ﬂ uxes that are critical for determining the ocean's role in climate, predicted in global circulation models.
Age‐related optimization of screw placement for reduced loosening risk in locked plating

When using locked plating for bone fracture fixation, screw loosening is reported as one of the most frequent complications and is commonly attributed to an incorrect choice of screw configuration. Choosing a patient‐optimized screw configuration is not straightforward as there are many interdependent variables that affect device performance. The aim of the study was to evaluate the influence that locking screw configuration has on loosening risk and how this is influenced by bone quality. This study uses finite element models that incorporate cortical bone heterogeneity, orthotropy, and geometrical nonlinearity to examine the effect of screw configuration on variables associated with loosening and interfragmentary motion. Strain levels within the bone were used as indicators of regions that may undergo loosening. The study found that, in healthy bone under axial loading, the most important variables influencing strain levels within the bone were the size of the bridging span (working length) and the plate rigidity. Unlike healthy bone, osteoporotic bone was found to be particularly sensitive to the spacing of the screws within the plate. Using two empty screw holes between the screws closest to the fracture was found to reduce the strain levels at the first screw by 49% in osteoporotic bone (compared to only 2.4% in healthy bone). The study also found that under torsional loading the total number of screws used was the most important variable with a 59% reduction in the strain around the screws closest to the fracture when using six rather than four screws in osteoporotic bone. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 34:1856–1864, 2016.
Weed Dynamics, Productivity and Profitability of Green Chilli as Influenced by Different Weed Control Measures

Chilli, claimed as red gold, is one of the important spices as well as vegetable crops of the country grown over an area of 37,958 ha with a production of 5.54 lakh tonnes with a productivity of 14.59 t ha -1 in Karnataka (Anon, 2012). In Hyderabad Karnataka region especially, TBP and UKP irrigation commands of state crop is cultivated on large area under irrigation much of which finds its way to Kerala market for export and export International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 6 Number 10 (2017) pp. 3358-3365 Journal homepage: http://www.ijcmas. com
Simulating Opportunistic Networks: Survey and Future Directions

Simulation is one of the most powerful tools we have for evaluating the performance of opportunistic networks (OppNets). In this paper, we focus on available tools and models, compare their performance and precision and experimentally show the scalability of different simulators. We also perform a gap analysis of state-of-the-art OppNet simulations and sketch out possible further development and lines of research. This paper is targeted at students starting work and research in this area while also serving as a valuable source of information for experienced researchers.
CD9 tetraspanin generates fusion competent sites on the egg membrane for mammalian fertilization

CD9 tetraspanin is the only egg membrane protein known to be essential for fertilization. To investigate its role, we have measured, on a unique acrosome reacted sperm brought in contact with an egg, the adhesion probability and strength with a sensitivity of a single molecule attachment. Probing the binding events at different locations of wild-type egg we described different modes of interaction. Here, we show that more gamete adhesion events occur on Cd9 null eggs but that the strongest interaction mode disappears. We propose that sperm–egg fusion is a direct consequence of CD9 controlled sperm–egg adhesion properties. CD9 generates adhesion sites responsible for the strongest of the observed gamete interaction. These strong adhesion sites impose, during the whole interaction lifetime, a tight proximity of the gamete membranes, which is a requirement for fusion to take place. The CD9-induced adhesion sites would be the actual location where fusion occurs.
The Role of Monthly Updated Climate Forecasts in Improving Intraseasonal Water Allocation

Seasonal streamflow forecasts contingent on climate information are essential for short-term planning (e.g., water allocation) and for setting up contingency measures during extreme years. However, the water allocated based on the climate forecasts issued at the beginning of the season needs to be revised using the updated climate forecasts throughout the season. In this study, reservoir inflow forecasts downscaled from monthly updated precipitation forecasts from ECHAM4.5 forced with ‘‘persisted’’ SSTs were used to improve both seasonal and intraseasonal water allocation during the October‐February season for the Angat reservoir, a multipurpose system, in the Philippines. Monthly updated reservoir inflow forecasts are ingested into a reservoir simulation model to allocate water for multiple uses by ensuring a high probability of meeting the end-of-season target storage that is required to meet the summer (March‐May) demand. The forecastbased allocation is combined with the observed inflows during the season to estimate storages, spill, and generated hydropower from the system. The performance of the reservoir is compared under three scenarios: forecasts issued at the beginning of the season, monthly updated forecasts during the season, and use of climatological values. Retrospective reservoir analysis shows that the operation of a reservoir by using monthly updated inflow forecasts reduces the spill considerably by increasing the allocation for hydropower during above-normal-inflow years. During below-normal-inflow years, monthly updated streamflow forecasts could be effectively used for ensuring enough water for the summer season by meeting the end-of-season target storage. These analyses suggest the importance of performing experimental reservoir analyses to understand the potential challenges and opportunities in improving seasonal and intraseasonal water allocation by using real-time climate forecasts.
Effect of Flood Peak Discharge Control by a Small Reservoir in an Urbanized Area—Case Study in the Kurabe River Basin, Japan

Recently severe damage of flooding by urbanization was frequently occurred. To prevent this damage, small reservoir was constructed in the urbanized residential area. This paper describes an effect of flood peak discharge control by a small reservoir (control reservoir) caused by rapidly developed urbanization. Although work for this purpose was conducted, research on the effects of the control reservoir was not conducted until now. This research, conducted by simulation, was a case study in the Kurabe River Basin in the Tedori River Alluvial Fan Area, Japan, based on the precise investigation of the reservoir in the actual field. The study was conducted to determine not only the actual control reservoir capacity for the newly developed residential area but also the ideal capacity for all present residential areas and the largest capacity allowable for a maximum rainfall event that recently occurred. The control reservoir effects between individual blocks and the entire basin area were compared by dividing the test basin into 15 blocks (sub-basins). The results showed that the effects on the capacity per unit area of the residential area in blocks have close relationship with the decreasing ratio of peak discharge in blocks. Consequently, the effects of control reservoir capacity and the limitation were clarified. In the future, control reservoirs should be constructed for all of the already developed residential areas, for example, by utilizing underground car parking lot. The results of this research can contribute to the design of the control reservoir for protection against flooding damage in urbanized areas.
Low complexity Kolmogorov-Smirnov modulation classification

Kolmogorov-Smirnov (K-S) test–a non-parametric method to measure the goodness of fit, is applied for automatic modulation classification (AMC) in this paper. The basic procedure involves computing the empirical cumulative distribution function (ECDF) of some decision statistic derived from the received signal, and comparing it with the CDFs of the signal under each candidate modulation format. The K-S-based modulation classifier is first developed for AWGN channel, then it is applied to OFDM-SDMA systems to cancel multiuser interference. Regarding the complexity issue of K-S modulation classification, we propose a low-complexity method based on the robustness of the K-S classifier. Extensive simulation results demonstrate that compared with the traditional cumulant-based classifiers, the proposed K-S classifier offers superior classification performance and requires less number of signal samples (thus is fast).
Adjuvant Epirubicin With or Without Ifosfamide for Adult Soft-Tissue Sarcoma

This randomized study compared the efficacy of epirubicin-based adjuvant chemotherapy on the disease-free interval (DFI) and overall survival of patients with high-risk soft-tissue sarcomas. After curative surgery, 43 of the 88 enrolled patients were assigned to surgery with or without radiotherapy and 45 to surgery plus chemotherapy (26 epirubicin, 19 epirubicin + ifosfamide) with or without radiotherapy. The trial closed prematurely because of poor patient accrual. There was a statistical significant difference in the 5-year disease-free survival of the patients receiving adjuvant chemotherapy with or without radiotherapy (69%) and that of those treated with surgery with or without radiotherapy (44%) (p = 0.01). The 5-year survival of the patients treated with adjuvant chemotherapy with or without radiotherapy was 72% as against 47% of those treated with surgery with or without radiotherapy (p = 0.06). The power of the study was 0.65 for both the DFI and overall survival. The results of the study suggest a possible advantage of epirubicin-based adjuvant chemotherapy in patients with soft-tissue sarcoma at high risk of relapse.
Terrestrial colonization of the Balearic Islands: New evidence for the Mediterranean sea-level drawdown during the Messinian Salinity Crisis

Guillem Mas1*, Agnès Maillard2, Josep A. Alcover3, Joan J. Fornós1, Pere Bover3, and Enric Torres-Roig3 1Grup de Recerca Ciències de la Terra, Universitat de les Illes Balears, E-07122 Palma (Mallorca), Spain 2Géosciences Environnement Toulouse–Observatoire Midi-Pyrénées (GET-OMP), Université Paul Sabatier, F-31400 Toulouse, France 3Departament de Biodiversitat Animal i Microbiana, IMEDEA (CSIC-UIB), E-07190 Esporles (Mallorca), Spain
Dietary fibre and risk of colorectal cancer in the Breast Cancer Detection Demonstration Project (BCDDP) follow-up cohort.

BACKGROUND The hypothesis that increased intake of dietary fibre lowers the risk of colorectal cancer (CRC) has recently been weakened by results from cohort and intervention studies that did not detect such an association. We investigated the association between dietary fibre intake and risk of CRC in a cohort of women that prospectively answered a food frequency questionnaire (FFQ). METHODS We studied 45 491 women in the Breast Cancer Detection Demonstration Project (BCDDP) follow-up cohort. A 62-item FFQ was administered from 1987 and 1989 to assess dietary intake. Participants received follow-up questionnaires (in 1992-1995 and 1995-1998) on which they reported incident cancers. Cases were also identified through searches of the National Death Index and state cancer registries. Cox proportional hazard regression was used to generate risk ratios and 95% CI for quintiles of total fibre intake and fibre subtypes. RESULTS During a mean follow-up time of 8.5 years we identified 487 colorectal cancer cases. The 10th and 90th percentiles of dietary fibre intake were 5.4 g and 18.2 g respectively. For total fibre we observed no association with colorectal cancer (fifth versus first quintile, RR = 0.94, 95% CI: 0.71-1.23). Analyses by subgroup of fibre and by anatomical subsite did not reveal any stronger inverse associations. CONCLUSIONS Within a cohort of older women characterized by a relatively low fibre intake, there was little evidence that dietary fibre intake lowers the risk of colorectal cancer.
Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads

Recent improvements in technology have made DNA sequencing dramatically faster and more efficient than ever before. The new technologies produce highly accurate sequences, but one drawback is that the most efficient technology produces the shortest read lengths. Short-read sequencing has been applied successfully to resequence the human genome and those of other species but not to whole-genome sequencing of novel organisms. Here we describe the sequencing and assembly of a novel clinical isolate of Pseudomonas aeruginosa, strain PAb1, using very short read technology. From 8,627,900 reads, each 33 nucleotides in length, we assembled the genome into one scaffold of 76 ordered contiguous sequences containing 6,290,005 nucleotides, including one contig spanning 512,638 nucleotides, plus an additional 436 unordered contigs containing 416,897 nucleotides. Our method includes a novel gene-boosting algorithm that uses amino acid sequences from predicted proteins to build a better assembly. This study demonstrates the feasibility of very short read sequencing for the sequencing of bacterial genomes, particularly those for which a related species has been sequenced previously, and expands the potential application of this new technology to most known prokaryotic species.
Sphingosine 1-Phosphate Transactivates the Platelet-Derived Growth Factor β Receptor and Epidermal Growth Factor Receptor in Vascular Smooth Muscle Cells

Abstract— Sphingosine 1-phosphate (S1P) is a bioactive lipid generated during vascular injury that regulates cell growth, differentiation, survival, and motility via endothelial differentiation gene (EDG) family G protein–coupled receptors. Although several G protein–coupled receptor ligands transactivate receptor tyrosine kinases, such as the epidermal growth factor receptor (EGFR), S1P-stimulated receptor tyrosine kinase transactivation has not been well studied. We show that platelet-derived growth factor β receptor (PDGFβR) and EGFR are tyrosine phosphorylated in response to S1P in rat aortic vascular smooth muscle cells (VSMCs). S1P-stimulated transactivation of PDGFβR and EGFR was mediated via Gi-coupled EDG receptors. S1P-stimulated transactivation of EGFR and PDGFβR was dependent on Src, reactive oxygen species, and cholesterol-rich membranes. A phosphoinositide 3-kinase–Akt pathway was activated by S1P and blocked by AG1296 and AG1478. Activation of extracellular signal–regulated kinase (ERK) 1 and ERK2 pathway by S1P was blocked only by AG1478. In Chinese hamster ovary cells that expressed exogenous EDG-1, activation of Akt and ERK1/2 in response to S1P was observed and was enhanced by coexpression of PDGFβR or EGFR. S1P-mediated VSMC proliferation was shown to be secondary to transactivation, because it was suppressed by AG1296 and AG1478. These data establish S1P as an important stimulus for EGFR and PDGFβR activation in VSMCs that may have important implications for the vessel response to injury.
Oxide based nanoscale analog synapse device for neural signal recognition system

We report oxide based analog synpase for neuromorphic system. By optimizing redox reaction at the metal/oxide interface, we can obtain stable analog synapse characteristics and wafer scale switching uniformity. We have confirmed the feasibility of neuromorphic hardware system with oxide synapse array device which recognizes the electroencephalogram (EEG) signal and rat's neural signal.
Enhancing object-based system composition through per-object mixins

The management of complexity in large systems is traditionally focused on the modeling and management of classes and hierarchies of classes. In order to improve the compositional flexibility in large systems, this paper turns the focus on objects rather than classes. It demonstrates that a more powerful object system can ease the development of large systems and can improve the degree of code reuse. The paper introduces per-object mixins as a new object-level language construct for object-based system composition. Per-object mixins are implemented in the scripting language XOT/sub CL/ as a straightforward extension of its method chaining mechanism and enables the developer to mix classes into the precedence order of an arbitrary object. Per-object mixins can be used to implement state-specific behavior changes in a clean way. We present per-object mixins as a general approach to hide object specifics from client objects transparently.
Predicting Success: Patterns of Cortical Activation and Deactivation Prior to Response Inhibition

The present study investigated the relationships between attention and other preparatory processes prior to a response inhibition task and the processes involved in the inhibition itself. To achieve this, a mixed fMRI design was employed to identify the functional areas activated during both inhibition decision events and the block of trials following a visual cue introduced 2 to 7 sec prior (cue period). Preparing for successful performance produced increases in activation for both the cue period and the inhibition itself in the frontoparietal cortical network. Furthermore, preparation produced activation decreases in midline areas (insula and medial prefrontal) argued to be responsible for monitoring internal emotional states, and these cue period deactivations alone predicted subsequent success or failure. The results suggest that when cues are provided to signify the imminent requirement for behavioral control, successful performance results from a coordinated pattern of preparatory activation in task-relevant areas and deactivation of task-irrelevant ones.
Retrieving Compatible Web Services

Service retrieval holds a central role during the development of Web services and Service-Based Applications (SBAs). The higher the number of available services, the more complex it becomes to locate the service closer to the developer needs. The complexity increases further with the number of available service versions that could also be suitable for this purpose. Existing approaches on service retrieval use a similarity measure between service interfaces to identify potentially relevant services. In this work we focus on introducing information about the compatibility of services while calculating their similarity as the means for providing more suitable results. For this purpose we update and extend an existing Web services matchmaker called UDDI Registry by Example (URBE).