Miracle-dz/UniFAR-FTUs huggingface dataset:
Connectomics of synaptic microcircuits: lessons from the outer retina

Photoreceptors form a sophisticated synaptic complex with bipolar and horizontal cells, transmitting the signals generated by the phototransduction cascade to downstream retinal circuitry. The cone photoreceptor synapse shows several characteristic anatomical connectivity motifs that shape signal transfer: typically, ON‐cone bipolar cells receive photoreceptor input through invaginating synapses; OFF‐cone bipolar cells form basal synapses with photoreceptors. Both ON‐ and OFF‐cone bipolar cells are believed to sample from all cone photoreceptors within their dendritic span. Electron microscopy and immunolabelling studies have established the robustness of these motifs, but have been limited by trade‐offs in sample size and spatial resolution, respectively, constraining precise quantitative investigation to a few individual cells. 3D‐serial electron microscopy overcomes these limitations and has permitted complete sets of neurons to be reconstructed over a comparatively large section of retinal tissue. Although the published mouse dataset lacks labels for synaptic structures, the characteristic anatomical motifs at the photoreceptor synapse can be exploited to identify putative synaptic contacts, which has enabled the development of a quantitative description of outer retinal connectivity. This revealed unexpected exceptions to classical motifs, including substantial interaction between rod and cone pathways at the photoreceptor synapse, sparse photoreceptor sampling and atypical contacts. Here, we summarize what was learned from this study in a more general context: we consider both the implications and limitations of the study and identify promising avenues for future research.
Sex differences may indeed exist for 3-D navigational abilities: But was sexual selection responsible?

Polygyny does not necessarily entail sexual selection of men. All factors that affect the operational sex ratio must be considered. Data from contemporary hunter-gatherers indicate higher mortality rates in men than in women, and lost female reproductive time. If sexual selection did occur in ancestral hunter-gatherers, it was probably men selecting women and not women selecting men.
Nanostructured polyaniline-coated anode for improving microbial fuel cell power output

An approach for improving the power generation of a dual-chamber microbial fuel cell by using a nanostructured polyaniline (PANI)-modified glassy carbon anode was investigated. Modification of the glassy carbon anode was achieved by the electrochemical polymerisation of aniline in 1 M H2SO4 solution. The MFC reactor showed power densities of 0.082 mW cm−2 and 0.031 mW cm−2 for the nano- and microstructured PANI anode, respectively. The results from electron microscopy scanning confirmed formation of the nanostructured PANI film on the anode surface and the results from electrochemical experiments confirmed that the electrochemical activity of the anode was significantly enhanced after modification by nanostructured PANI. Electrochemical impedance spectroscopic results proved that the charge transfer would be facilitated after anode modification with nanostructured PANI.
The Five-Minute Rule 20 Years Later: and How Flash Memory Changes the Rules

In 1987, Jim Gray and Gianfranco Putzolu published their now-famous five-minute rule for trading off memory and I/O capacity. Their calculation compares the cost of holding a record (or page) permanently in memory with the cost of performing disk I/O each time the record (or page) is accessed, using appropriate fractions of prices for RAM chips and disk drives. The name of their rule refers to the break-even interval between accesses. If a record (or page) is accessed more often, it should be kept in memory; otherwise, it should remain on disk and read when needed.
Global Optimization of Transmitter Placement in Wireless Communication Systems

This paper explores the application of a global optimization technique to solve the optimal transmitter placement problem in wireless system design. An efficient pattern search algorithm—DIRECT (DIviding RECTangles) of Jones, Perttunen, and Stuckman (1993)—has been connected to a parallel 3D radio propagation ray tracing modeler running on a 200-node Beowulf cluster of workstations. The algorithm optimizes, for a given computational investment, the locations of a specified number of transmitters across the feasible region of the design space. The focus of the paper is on the implementations of the DIRECT algorithm and the parallel 3D ray tracing propagation model. Both simulation results and site measurement data are presented in support of the effectiveness of the present work.
A framework for customizable schema evolution in object-oriented databases

This paper describes an evolution framework supporting customization of the schema evolution and instance adaptation approaches in an object database management system. The framework is implemented as an integral part of an interpreter for a language with a versioned type system and employs concepts from object-oriented frameworks and aspect-oriented programming to support flexible changes. Some example customizations currently implemented with the framework are also described.
Dock180 and ELMO1 Proteins Cooperate to Promote Evolutionarily Conserved Rac-dependent Cell Migration*

Cell migration is essential throughout embryonic and adult life. In numerous cell systems, the small GTPase Rac is required for lamellipodia formation at the leading edge and movement ability. However, the molecular mechanisms leading to Rac activation during migration are still unclear. Recently, a mammalian superfamily of proteins related to the prototype member Dock180 has been identified with homologues in Drosophila and Caenorhabditis elegans. Here, we addressed the role of Dock180 and ELMO1 proteins, which function as a complex to mediate Rac activation, in mammalian cell migration. Using mutants of Dock180 and ELMO1 in a Transwell assay as well as transgenic rescue of a C. elegans mutant lacking CED-5 (Dock180 homologue), we identified specific regions of Dock180 and ELMO1 required for migration in vitro and in a whole animal model. In both systems, the Dock180·ELMO1 complex formation and the ability to activate Rac were required. We also found that ELMO1 regulated multiple Dock180 superfamily members to promote migration. Interestingly, deletion mutants of ELMO1 missing their first 531 or first 330 amino acids that can still bind and cooperate with Dock180 in Rac activation failed to promote migration, which correlated with the inability to localize to lamellipodia. This finding suggests that Rac activation by the ELMO·Dock180 complex at discrete intracellular locations mediated by the N-terminal 330 amino acids of ELMO1 rather than generalized Rac activation plays a role in cell migration.
Human Transporter Database: Comprehensive Knowledge and Discovery Tools in the Human Transporter Genes

Transporters are essential in homeostatic exchange of endogenous and exogenous substances at the systematic, organic, cellular, and subcellular levels. Gene mutations of transporters are often related to pharmacogenetics traits. Recent developments in high throughput technologies on genomics, transcriptomics and proteomics allow in depth studies of transporter genes in normal cellular processes and diverse disease conditions. The flood of high throughput data have resulted in urgent need for an updated knowledgebase with curated, organized, and annotated human transporters in an easily accessible way. Using a pipeline with the combination of automated keywords query, sequence similarity search and manual curation on transporters, we collected 1,555 human non-redundant transporter genes to develop the Human Transporter Database (HTD) (http://htd.cbi.pku.edu.cn). Based on the extensive annotations, global properties of the transporter genes were illustrated, such as expression patterns and polymorphisms in relationships with their ligands. We noted that the human transporters were enriched in many fundamental biological processes such as oxidative phosphorylation and cardiac muscle contraction, and significantly associated with Mendelian and complex diseases such as epilepsy and sudden infant death syndrome. Overall, HTD provides a well-organized interface to facilitate research communities to search detailed molecular and genetic information of transporters for development of personalized medicine.
Fabrication and characterization of a low-temperature hermetic MEMS package bonded by a closed loop AuSn solder-line

This paper presents a hermetic MEMS package bonded by a closed-loop AuSn solder-line. We design three different test specimens including substrate heated specimen without interconnection-line (SHX), substrate heated specimen with interconnection-line (SHI) and locally heated specimen with interconnection-line (LHI). Pressurized helium leak tests are carried out for hermetic seal evaluation with the critical pressure test for bonding strength measurement. In hermeticity tests, SHX, SHI and LHI show leak rates of 8.4/spl plusmn/6.7/spl times/10/sup -10/ mbar-l/s, 13.5/spl plusmn/9.8/spl times/10/sup -10/ mbar-l/s and 18.8/spl plusmn/9.9/spl times/10/sup -10/ mbar-l/s with the same internal volume of 6.89/spl plusmn/0.2/spl times/10/sup -6/ l, respectively. The specimens of SHX and SHI, bonded by the substrate heater, show leak rates lower than that of LHI. However, the three test specimens satisfy MIL-STD-883E for hermeticity test of microcircuits. In the additional critical pressure test, no fracture is found in the bonded specimens at applied pressure of 1/spl plusmn/0.1MPa. From these results, we approximately extract the bonding strength of the test specimen of 3.53/spl plusmn/0.07 MPa. We experimentally verify that the LHI shows potential for hermetic MEMS packaging with interconnection-line and short-time bonding processes for mass production.
Observations of Barnacle Detachment from Silicones using High-Speed Video

ABSTRACT The detachment of barnacles (under shear and tensile loads) from silicone was investigated with the aid of high-speed digital video recording. A handheld probe was used to apply loads to the shells of barnacles attached to three clear silicone-elastomer coatings of known thickness applied to glass plates. The tests were performed in the laboratory in air and underwater. Representative data are presented as a qualitative description of separation at the barnacle adhesive–silicone interface. Detailed examination of adhesive separation during detachment provided new insight into the nature of a marine biological adhesive on a low modulus, artificial surface. The visible response of the barnacle adhesive on silicone under external shear and tensile loading was suggestive of the viscous fingering seen in Saffman–Taylor instabilities. Complex branching separation occurred in rapid progression, usually within 100 ms. The results suggest that the barnacle adhesive exhibits rheological responses of a viscous material at the interface with silicone surfaces. Additional experiments with time-lapse photography demonstrated that the adhesive was stable underwater but became dehydrated or coalesced when exposed directly to air. A simple model of the adhesive system of a barnacle in contact with silicone based upon Balanus eburneus is proposed to assist in the development of a more complete understanding of barnacle adhesion.
Mutation of the slow myosin heavy chain rod domain underlies hyaline body myopathy

Objective: To identify the gene and specific mutation underlying hyaline body myopathy in the family studied. Methods: A microsatellite-based whole genome scan was performed. Linkage analysis assumed autosomal dominant inheritance and equal allele frequencies. A candidate gene approach within the linked interval and direct sequencing were used for mutation detection. Results: Initial analysis indicated a maximum lod score of 3.01 at D14S1280. High-density mapping surrounding the linked locus was performed. Multipoint analysis showed that the linked region with a maximum lod score of 3.01 extended from D14S742 to D14S608 with a peak non-parametric linkage (NPL) score of 3.75 at D14S608. The myosin heavy chain genes MYH6 and MYH7 map to the region between D14S742 and D14S1280. Sequence analysis of the coding regions of MYH7 revealed an A→T transversion at nucleotide position 25596 (M57965) resulting in a histidine-to-leucine amino acid change at residue 1904 (H1904L). Conclusion: Pathogenicity of the MYH7 H1904L mutation most likely results from disruption of myosin heavy chain assembly or stability of the sarcomeric protein. The MYH7 tail domain mutation results in an inclusion body myopathy with an apparent absence of hypertrophic cardiomyopathy usually associated with mutations of this gene.
Comparison of inertial mechanization approaches for inertial aided monocular EKF-SLAM

Localization of pedestrians becomes a difficult task in situations where no measurements with respect to an established reference system, as it is provided by satellites when using GPS, are available. One possible approach to tackle this problem is to attach a suitable sensor to pedestrians and then to run a simultaneous localization and mapping (SLAM) algorithm in order to localize the sensor. A combination of an inertial measurement unit (IMU) with a monocular camera is a promising choice of sensors for an indoor pedestrian localization system since these sensors provide complementary measurements. This paper discusses two approaches to integrate visual and inertial information which differ mainly in the choice of reference coordinate system. A detailed description of both approaches is given and they are compared with respect to their performance on simulated and real measurement data.
Electrospun core–sheath fibers for integrating the biocompatibility of silk fibroin and the mechanical properties of PLCL

In the process of preparing core–sheath fibers via coaxial electrospinning, the relative evaporation rates of core and sheath solvents play a key role in the formation of the core–sheath structure of the fiber. Both silk fibroin (SF) and poly(lactide-co-e-caprolactone) (PLCL) have good biocompatibility and biodegradability. SF has better cell affinity than PLCL, whereas PLCL has higher breaking strength and elongation than SF. In this work, hexafluoroisopropanol (HFIP)-formic acid (volume ratio 8:2), HFIP and HFIP–dichloromethane (volume ratio 8:2) were used to dissolve PLCL as the core solutions, and HFIP was used to dissolve SF as the sheath solution. Then, core–sheath structured SF/PLCL (C-SF/PLCL) fibers were prepared by coaxial electrospinning with the core and sheath solutions. Transmission electron microscopy images indicated the existence of the core–shell structure of the fibers, and energy dispersive X-ray analysis results revealed that the fiber mat with the greatest content of core–shell structure fibers was obtained when the core solvent was HFIP–dichloromethane (volume ratio 8:2). Tensile tests showed that the C-SF/PLCL fiber mat displayed improved tensile properties, with strength and elongation that were significantly higher than those of the pure SF mat. The C-SF/PLCL fiber mat was further investigated as a scaffold for culturing EA.hy926 cells, and the results showed that the fiber mat permitted cellular adhesion, proliferation and spreading in a manner similar to that of the pure SF fiber mat. These results indicated that the coaxial electrospun SF/PLCL fiber mat could be considered a promising candidate for tissue engineering scaffolds for blood vessels. Copyright © 2014 John Wiley & Sons, Ltd.
IEDB-3D: structural data within the immune epitope database

IEDB-3D is the 3D structural component of the Immune Epitope Database (IEDB) available via the ‘Browse by 3D Structure’ page at http://www.iedb. org. IEDB-3D catalogs B- and T-cell epitopes and Major Histocompatibility Complex (MHC) ligands for which 3D structures of complexes with antibodies, T-cell receptors or MHC molecules are available in the Protein Data Bank (PDB). Journal articles that are primary citations of PDB structures and that define immune epitopes are curated within IEDB as any other reference along with accompanying functional assays and immunologically relevant information. For each curated structure, IEDB-3D provides calculated data on intermolecular contacts and interface areas and includes an application, EpitopeViewer, to visualize the structures. IEDB-3D is fully embedded within IEDB, thus allowing structural data, both curated and calculated, and all accompanying information to be queried using multiple search interfaces. These include queries for epitopes recognized in different pathogens, eliciting different functional immune responses, and recognized by different components of the immune system. The query results can be downloaded in Microsoft Excel format, or the entire database, together with structural data both curated and calculated, can be downloaded in either XML or MySQL formats.
Smart views for analyzing problem reports: tool demo

Issue tracking repositories contain a wealth of information for reasoning about various aspects of software development processes. In this paper, we focus on bug triaging and provide visual means to explore the effort estimation quality and the bug life-cycle of reported problems. Our approach uses a combination of graphical views to investigate details of individual problem reports while maintaining the context provided by the surrounding data population. This enables the detection and detailed analysis of hidden patterns and facilitates the analysis of problem report outliers.
Effects of a diisocyanate compatibilizer on the properties of citric acid modified thermoplastic starch/poly(lactic acid) blends

In this article, for the first time in the literature effects of phenylene diisocyanate (PDI)-based compatibilizer on the physical and chemical properties of citric acid (CA) modified thermoplastic starch (TPS)/poly(lactic acid) (PLA) blends were investigated with respect to PDI and CA content and blend composition. The blends were prepared by melt compounding in a laboratory microcompounder. Fourier transformation infrared spectroscopy results showed that CA interacted with starch and PDI interacted by both starch and PLA through the hydroxyl groups. It was revealed from SEM micrographs that combinatorial usage of CA and PDI resulted in an improved, finer distribution of TPS in PLA matrix. This improvement affected the mechanical properties of blend, especially the toughness related properties such as impact strength and elongation at break. The thermal properties such as Tg and Tm revealed from differential scanning calorimeter analysis were in line with the morphological structure of the blends by suggesting the compatibilization phenomena in the presence of PDI and CA together. Thermogravimetric analysis showed that compatibilization of two phases improved the thermal stability of the blends. As a general conclusion, the combinatorial usage of PDI and CA can be utilized to obtain tougher PLA/TPS blends-based materials to overcome the brittleness problem. POLYM. ENG. SCI., 53:2183–2193, 2013. © 2013 Society of Plastics Engineers
Cascade of Current-Starved Pseudo Floating-Gate inverters

In this paper we investigate the result of implementing series connected current-starved pseudo floating-gate (CSPFG) inverters in filter design. These inverters are suited for designing high quality filters where sharp transition band, high gain, low power consumption and high speed is the main goal. We show that CSPFG inverters have 1 order behaviour and a cascade of inverters can be used to increases the order of these circuits. AC simulation of the series connected inverters is presented to show how this effect. Linearity simulations of the series connected inverters are also presented to show the good transient properties suited for designing high gain filters. Typical applications are detection of high frequency components in sensor signals, i.e. airbag sensors or in high frequency radio design.
A Snapshot of Two DARPA Speech and Natural Language Programs

DARPA is investing in speech and natural language processing research to ensure the availability of key technology needed by the Department of Defense for a wide variety of applications. The research programs aim (a) to develop enabling component technology that can be integrated on demand and/or rapidly tailored for specific applications and (b) to demonstrate that technology in limited prototypes. The programs are highly synergistic and emphasize objective performance evaluation.
A genetic dichotomy model for the inheritance of Alzheimer's disease and common age-related disorders.

Alzheimer’s disease (AD), already one of the most serious health problems in the U.S., will carry an ever burgeoning impact as the proportion of elderly continues to increase. Clinically, AD is a progressive neurodegenerative disorder characterized by global cognitive decline. Neuropathologically, the brains of AD patients contain abundant amounts of neurofibrillary tangles (NFT) and β-amyloid in the form of senile plaques (SP) and blood vessel deposits. While the etiological events that lead to AD have not been clearly resolved, genetic factors clearly play a major role; there is an emerging consensus that AD is a complex and genetically heterogeneous disorder that is best explained by an age-dependent dichotomous model. On one hand, early-onset (<60) AD is caused by defects in any of three different genes: presenilin 1 (PSEN1) on chromosome 14 (1), presenilin 2 (PSEN2) on chromosome 1 (2), and the amyloid β protein precursor (APP) on chromosome 21 (3). On the other hand, late-onset AD is associated with genetic polymorphisms that appear to operate as risk factors and/or genetic modifiers.
Simulation of Optical Properties of Ni-Doped ZnO Based on Density Functional Theory

The semiconductor ZnO has gained substantial interest in the research community in part because of its large exciton binding energy (60 meV). Based on first-principles spin-density functional calculations, the electronic structures and reflectivity of pure ZnO have been calculated. We find that theory calculated peaks basal consistent with the experiment results. The absorbing properties of Ni doped ZnO have also been calculated and the relationships between electronic structures and absorbing properties are investigated. The results show that the absorbing properties of Co doped ZnO improved significantly compared to pure ZnO system. Absorption frequency peak moves to low frequency and one absorption band appear at 1236.9nm. The theoretical results have offered a direction for the designing and application of ZnO which could lead to lasing action based on exciton recombination even above room temperature.