Miracle-dz/UniFAR-FTUs huggingface dataset:
Three-dimensional culture systems for the expansion of pluripotent embryonic stem cells

Mouse embryonic stem cell (ESC) lines, and more recently human ESC lines, have become valuable tools for studying early mammalian development. Increasing interest in ESCs and their differentiated progeny in drug discovery and as potential therapeutic agents has highlighted the fact that current two‐dimensional (2D) static culturing techniques are inadequate for large‐scale production. The culture of mammalian cells in three‐dimensional (3D) agitated systems has been shown to overcome many of the restrictions of 2D and is therefore likely to be effective for ESC proliferation. Using murine ESCs as our initial model, we investigated the effectiveness of different 3D culture environments for the expansion of pluripotent ESCs. Solohill Collagen, Solohill FACT, and Cultispher‐S microcarriers were employed and used in conjunction with stirred bioreactors. Initial seeding parameters, including cell number and agitation conditions, were found to be critical in promoting attachment to microcarriers and minimizing the size of aggregates formed. While all microcarriers supported the growth of undifferentiated mESCs, Cultispher‐S out‐performed the Solohill microcarriers. When cultured for successive passages on Cultispher‐S microcarriers, mESCs maintained their pluripotency, demonstrated by self‐renewal, expression of pluripotency markers and the ability to undergo multi‐lineage differentiation. When these optimized conditions were applied to unweaned human ESCs, Cultispher‐S microcarriers supported the growth of hESCs that retained expression of pluripotency markers including SSEA4, Tra‐1–60, NANOG, and OCT‐4. Our study highlights the importance of optimization of initial seeding parameters and provides proof‐of‐concept data demonstrating the utility of microcarriers and bioreactors for the expansion of hESCs. Biotechnol. Bioeng. 2010;107:683–695. © 2010 Wiley Periodicals, Inc.
Description of the UAM system for generating very short summaries at DUC-2004 ∗

This paper describes the techniques used for producing very short summaries (around 75 bytes) of single documents. As in last year’s version, the processing has been divided into two separate steps: firstly, a sentence extractor selects the most relevant sentences from the document; and, next, portions of those sentences are put together in order to produce the final headline. The main novelty is the way in which the text chunks have been weighted, and completed with keywords and noun phrases obtained from the documents. Our runs are ranked in the 12 and 13 positions with respect to unigram recall (ROUGE-1), but failed to identify bigrams, trigrams and four-grams as accurately as most of the other systems.
Middleware for Embedded Adaptive Dependability

The Middleware for Embedded Adaptive Dependability (MEAD) infrastructure enhances large-scale distributed real-time embedded middleware applications with novel capabilities, including (i) transparent, yet tunable, fault tolerance in real time, (ii) proactive dependability, (iii) resource-aware system adaptation to crash, communication, partitioning and timing faults with (iv) scalable and fast fault-detection and fault-recovery.
Alcohol and Crime

The author of this posthumously published article was a Fellow of the American Psychiatric Association, Executive Director of the National Committee on Alcohol Hygiene, Medical Consultant to the Canadian National Committee for Education on Alcoholism, Inc., Chief Psychiatrist in the Neuropsychiatric Institute of Baltimore, and Assistant Neurology, in the Johns Hopkins Medical School and Hospital. Other articles by Dr. Seliger may be found in our Vol. 38, Pages 425ff. and in Vol. 41, Pages 24ff. -EDITOR.
Redox centers evolution in phospho-olivine type (LiFe0.5Mn0.5 PO4) nanoplatelets with uniform cation distribution.

In phospho-olivine type structures with mixed cations (LiM1M2PO4), the octahedral M1 and M2 sites that dictate the degree of intersites order/disorder play a key role in determining their electrochemical redox potentials. In the case of LiFexMn1-xPO4, for example, in micrometer-sized particles synthesized via hydrothermal route, two separate redox centers corresponding to Fe(2+)/Fe(3+) (3.5 V vs Li/Li(+)) and Mn(2+)/Mn(3+) (4.1 V vs Li/Li(+)), due to the collective Mn-O-Fe interactions in the olivine lattice, are commonly observed in the electrochemical measurements. These two redox processes are directly reflected as two distinct peak potentials in cyclic voltammetry (CV) and equivalently as two voltage plateaus in their standard charge/discharge characteristics (in Li ion batteries). On the contrary, we observed a single broad peak in CV from LiFe0.5Mn0. 5PO4 platelet-shaped (∼10 nm thick) nanocrystals that we are reporting in this work. Structural and compositional analysis showed that in these nanoplatelets the cations (Fe, Mn) are rather homogeneously distributed in the lattice, which is apparently the reason for a synergetic effect on the redox potentials, in contrast to LiFe0.5Mn0. 5PO4 samples obtained via hydrothermal routes. After a typical carbon-coating process in a reducing atmosphere (Ar/H2), these LiFe0.5Mn0. 5PO4 nanoplatelets undergo a rearrangement of their cations into Mn-rich and Fe-rich domains. Only after such cation rearrangement (via segregation) in the nanocrystals, the redox processes evolved at two distinct potentials, corresponding to the standard Fe(2+)/Fe(3+) and Mn(2+)/Mn(3+) redox centers. Our experimental findings provide new insight into mixed-cation olivine structures in which the degree of cations mixing in the olivine lattice directly influences the redox potentials, which in turn determine their charge/discharge characteristics.
Structural and Biophysical Characterization of the Cytoplasmic Domains of Human BAP29 and BAP31

Two members of the B-cell associated 31 (BAP31) family are found in humans; BAP29 and BAP31. These are ubiquitously expressed receptors residing in the endoplasmic reticulum. BAP31 functions in sorting of membrane proteins and in caspase-8 mediated apoptosis, while BAP29 appears to mainly corroborate with BAP31 in sorting. The N-terminal half of these proteins is membrane-bound while the C-terminal half is cytoplasmic. The latter include the so called variant of death effector domain (vDED), which shares weak sequence homology with DED domains. Here we present two structures of BAP31 vDED determined from a single and a twinned crystal, grown at pH 8.0 and pH 4.2, respectively. These structures show that BAP31 vDED forms a dimeric parallel coiled coil with no structural similarity to DED domains. Solution studies support this conclusion and strongly suggest that an additional α-helical domain is present in the C-terminal cytoplasmic region, probably forming a second coiled coil. The thermal stability of BAP31 vDED is quite modest at neutral pH, suggesting that it may assemble in a dynamic fashion in vivo. Surprisingly, BAP29 vDED is partially unfolded at pH 7, while a coiled coil is formed at pH 4.2 in vitro. It is however likely that folding of the domain is triggered by other factors than low pH in vivo. We found no evidence for direct interaction of the cytoplasmic domains of BAP29 and BAP31.
Retinal Nerve Fiber Layer Thickness Changes in Parkinson Disease: A Meta-Analysis

Background Parkinson disease (PD) is a neurodegenerative process that leads to a selective loss of dopaminergic neurons, mainly in the basal ganglia of the brain. Numerous studies have analyzed the ability of optical coherence tomography (OCT) to detect retinal nerve fiber layer (RNFL) thickness abnormalities and changes in PD, but the results have not always been consistent. Therefore, we carried out a meta-analysis to evaluate the RNFL thickness measured with OCT in PD. Methods and Findings Case-control studies were selected through an electronic search of the Cochrane Controlled Trials Register, PUBMED and EMBASE. For the continuous outcomes, we calculated the weighted mean difference (WMD) and 95% confidence interval (CI). The statistical analysis was performed by RevMan 5.0 software. Thirteen case-control studies were included in the present meta-analysis, containing a total of 644 eyes in PD patients and 604 eyes in healthy controls. The results of our study showed that there was a significant reduction in average RNFL thickness in patients with PD compared to healthy controls (WMD = −5.76, 95% CI: −8.99 to −2.53, P = 0.0005). Additionally, differences of RNFL thickness in superior quadrant (WMD = −4.44, 95% CI: −6.93 to −1.94, P = 0.0005), inferior quadrant (WMD = −7.56, 95% CI: −11.33 to −3.78, P<0.0001), nasal quadrant (WMD = −3.12, 95% CI: −5.63 to −0.61, P = 0.01) and temporal quadrant (WMD = −4.63, 95% CI: −7.20 to −2.06, P = 0.0004) were all significant between the two groups. Conclusion In view of these results and the noninvasive nature of OCT technology, we surmise that OCT could be a useful tool for evaluating the progression of the Parkinson disease. Trial Registration ClinicalTrials.gov NCT01928212
A Finite Element Method for Interactive Physically Based Shape Modelling with Quadratic Tetrahedra

We present an alternative approach to standard geometric shape editing using physically-based simulation. With our technique, the user can deform complex objects in real-time. The enabling technology of this approach is a fast and accurate finite element implementation of an elasto-plastic material model, specifically designed for interactive shape manipulation. Using quadratic shape functions, we avoid the inherent drawback of volume locking exhibited by methods based on linear finite elements. The physical simulation uses a tetrahedral mesh, which is constructed from a coarser approximation of the detailed surface. Having computed a deformed state of the tetrahedral mesh, the deformation is transferred back to the high detail surface. This can be accomplished in an accurate and efficient way using the quadratic shape functions. In order to guarantee stability and real-time frame rates during the simulation, we cast the elasto-plastic problem into a linear formulation. For this purpose, we present a corotational formulation for quadratic finite elements. We demonstrate the versatility of our approach in interactive manipulation sessions and show that our animation system can be coupled with further physics-based animations like, e.g. fluids and cloth, in a bi-directional way. CR Categories: I.3. 5 [Computer Graphics]: Physically based modeling
Balancing Generality and Specificity in Document Management Systems

This paper describes an experiment to extend the reach of the document-centric metaphors of computing to new physical and virtual objects in the workplace. By bringing these entities into the sphere of electronic documents, we leverage users’ knowledge and expectations about how documents work, and also leverage existing tools and applications that understand and manipulate documents. Being able to use generalpurpose tools on semantically-loaded content types can be useful, but there are potential pitfalls with the loss of the functionality provided by special-purpose applications. We investigate a solution to this problem that strikes a balance between generality and specificity by allowing application functionality and user interface components to be associated with the document and used by general-purpose applications that operate on that document.
Supervised learning through the lens of compression

This work continues the study of the relationship between sample compression schemes and statistical learning, which has been mostly investigated within the framework of binary classification. We first extend the investigation to multiclass categorization: we prove that in this case learnability is equivalent to compression of logarithmic sample size and that the uniform convergence property implies compression of constant size. We use the compressibility-learnability equivalence to show that (i) for multiclass categorization, PAC and agnostic PAC learnability are equivalent, and (ii) to derive a compactness theorem for learnability. We then consider supervised learning under general loss functions: we show that in this case, in order to maintain the compressibility-learnability equivalence, it is necessary to consider an approximate variant of compression. We use it to show that PAC and agnostic PAC are not equivalent, even when the loss function has only three values.
Design of 2D Time-Varying Vector Fields

Design of time-varying vector fields, i.e., vector fields that can change over time, has a wide variety of important applications in computer graphics. Existing vector field design techniques do not address time-varying vector fields. In this paper, we present a framework for the design of time-varying vector fields, both for planar domains as well as manifold surfaces. Our system supports the creation and modification of various time-varying vector fields with desired spatial and temporal characteristics through several design metaphors, including streamlines, pathlines, singularity paths, and bifurcations. These design metaphors are integrated into an element-based design to generate the time-varying vector fields via a sequence of basis field summations or spatial constrained optimizations at the sampled times. The key-frame design and field deformation are also introduced to support other user design scenarios. Accordingly, a spatial-temporal constrained optimization and the time-varying transformation are employed to generate the desired fields for these two design scenarios, respectively. We apply the time-varying vector fields generated using our design system to a number of important computer graphics applications that require controllable dynamic effects, such as evolving surface appearance, dynamic scene design, steerable crowd movement, and painterly animation. Many of these are difficult or impossible to achieve via prior simulation-based methods. In these applications, the time-varying vector fields have been applied as either orientation fields or advection fields to control the instantaneous appearance or evolving trajectories of the dynamic effects.
Anatomically Discrete Sex Differences in Neuroplasticity in Zebra Finches as Reflected by Perineuronal Nets

Large morphological sex differences in the vertebrate brain were initially identified in song control nuclei of oscines. Besides gross differences between volumes of nuclei in males and females, sex differences also concern the size and dendritic arborization of neurons and various neurochemical markers, such as the calcium-binding protein parvalbumin (PV). Perineuronal nets (PNN) of the extracellular matrix are aggregates of different compounds, mainly chondroitin sulfate proteoglycans, that surround subsets of neurons, often expressing PV. PNN develop in zebra finches song control nuclei around the end of the sensitive period for song learning and tutor deprivation, known to delay the end of the song learning sensitive period, decreases the numbers of PNN in HVC. We demonstrate here the existence in zebra finches of a major sex difference (males > females) affecting the number of PNN (especially those surrounding PV-positive cells) in HVC and to a smaller extent the robust nucleus of the arcopallium, RA, the two main nuclei controlling song production. These differences were not present in Area X and LMAN, the lateral magnocellular nucleus of the anterior nidopallium. A dense expression of material immunoreactive for chondroitin sulfate was also detected in several nuclei of the auditory and visual pathways. This material was often organized in perineuronal rings but quantification of these PNN did not reveal any sex difference with the exception that the percentage of PNN surrounding PV-ir cells in the dorsal lateral mesencephalic nucleus, MLd, was larger in females than in males, a sex difference in the opposite direction compared to what is seen in HVC and RA. These data confirm and extend previous studies demonstrating the sex difference affecting PNN in HVC-RA by showing that this sex difference is anatomically specific and does not concern visual or auditory pathways.
DSP Online Algorithms for The ATLAS TileCal Read-Out Drivers

TileCal is the hadronic tile calorimeter of the ATLAS experiment at LHC/CERN. The central element of the back-end system of the TileCal detector is the read-out driver (ROD). The main components of the TileCal ROD are the Digital Signal Processors (DSPs) placed on the processing unit (PU) daughterboards. This paper presents a detailed description of the code developed for the DSPs. The code is divided into two different parts: the first part contains the core functionalities and the second part the reconstruction algorithms. The core acts as an operating system and controls configuration, data reception and transmission and synchronization between front-end data and the timing, trigger and control (TTC) information. The reconstruction algorithms implemented on the DSP are the optimal filtering (OF), muon tagging (MTag) and missing calculation. The OF algorithm reconstructs the deposited energy and the phase of the signal for every calorimeter channel within a front-end module. This reconstructed energy is used by the MTag algorithm to tag low transverse momentum muons that may escape the ATLAS muon spectrometer Level 1 trigger whereas the Missing algorithm computes the total transverse energy and the projection on and axis for the entire module that will be used by the Level 2 trigger system.
Optimal transmission radius for energy efficient broadcasting protocols in ad hoc and sensor networks

We investigate the problem of minimum energy broadcasting in ad hoc networks where nodes have capability to adjust their transmission range. The minimal transmission energy needed for correct reception by neighbor at distance r is proportional to ralpha+ce , alpha and ce being two environment-dependent constants. We demonstrate the existence of an optimal transmission radius, computed with a hexagonal tiling of the network area, that minimizes the total power consumption for a broadcasting task. This theoretically computed value is experimentally confirmed. The existing localized protocols are inferior to existing centralized protocols for dense networks. We present two localized broadcasting protocols, based on derived "target" radius, that remain competitive for all network densities. The first one, TR-LBOP, computes the minimal radius needed for connectivity and increases it up to the target one after having applied a neighbor elimination scheme on a reduced subset of direct neighbors. In the second one, TRDS, each node first considers only neighbors whose distance is no greater than the target radius (which depends on the power consumption model used), and neighbors in a localized connected topological structure such as RNG or LMST. Then, a connected dominating set is constructed using this subgraph. Nodes not selected for the set may be sent to sleep mode. Nodes in selected dominating set apply TR-LBOP. This protocol is the first one to consider both activity scheduling and minimum energy consumption as one combined problem. Finally, some experimental results for both protocols are given, as well as comparisons with other existing protocols. Our analysis and protocols remain valid if energy needed for packet receptions is charged
Full‐length von Willebrand factor (vWF) cDNA encodes a highly repetitive protein considerably larger than the mature vWF subunit.

Full‐length human von Willebrand factor (vWF) cDNA was assembled from partial, overlapping vWF cDNAs. This cDNA construct includes a coding sequence of 8439 nucleotides which encode a single‐chain precursor of 2813 amino‐acid residues, representing a putative signal peptide, a prosequence and mature vWF of 22, 741 and 2050 amino acids, respectively. This represents the longest coding sequence determined to date. In‐vitro expression of full‐length vWF cDNA revealed the synthesis of a polypeptide with a mol. wt corresponding with that of the unglycosylated precursor. The precursor is a highly repetitive protein which consists of two duplicated (B, C), a triplicated (A), a quadruplicated (D) and a partly duplicated domain (D'), in the following order: H‐D1‐D2‐D'‐D3‐A1‐A2‐A3‐D4‐B1‐B2‐C1‐C2‐OH. Both the prosequence, composed of two D domains (D1, D2), and mature vWF harbor an arg‐gly‐asp (‘R‐G‐D’) sequence which has been implicated in cell‐attachment functions. It is argued that the pro‐sequence is equivalent to von Willebrand Antigen II (vW AgII).
Editorial: Special Issue on High‐Permittivity Dielectric Oxides

High-permittivity dielectric oxides is the theme of this Special Issue of Chemical Vapor Deposition. In this Editorial, Tony Jones recaps the search for an alternative to SiO2 as a dielectric layer for the electronics industry, and introduces the papers presented in the Special Issue as an overview of current research directions in the MOCVD and ALD of a wide range of high-k dielectric oxides. The breadth of materials and resultant electronic properties reported confirm that the jury is still out regarding the final choice of oxide for the next generation of microelectronics.
Chemoprevention of Colorectal Cancer

Colorectal cancer has become one of the most prevalent malignant diseases for both men and women. Patients with inflammatory bowel diseases or certain inherited cancer syndromes are at high risk of developing colorectal cancer and have naturally the highest need for cancer prevention. In familial adenomatous polyposis (FAP) and Lynch syndrome, most of the underlying germline mutations can be detected by DNA sequencing, and medical counselling of affected individuals involves both surveillance tests and chemopreventive measures. However, as the mechanisms leading to colorectal cancer differ in these high-risk groups, the molecular action of chemopreventive drugs needs to be adjusted to the certain pathway of carcinogenesis. In the last decades, a number of drugs have been tested, including sulindac, aspirin, celecoxib, and mesalazine, but some of them are still controversially discussed. This review summarizes the advances and current standards of colorectal cancer prevention in patients with inflammatory bowel disease, FAP and Lynch syndrome.
Cooperative μUAV-UGV autonomous indoor surveillance

In this paper, we present a heterogenous UGV-UAV system cooperatively solving tasks of periodical surveillance in indoor environments. In the proposed scenario, the UGV is equipped with an interactive helipad and it acts as a carrier of the UAV. The UAV is a light-weight quadro-rotor helicopter equipped with two cameras, which are used to inspect locations inaccessible for the UGV. The paper is focused on the most crucial aspects of the proposed UAV-UGV periodical surveillance that are visual navigation, localization and autonomous landing that need to be done periodically. We propose two concepts of mobile helipads employed for correction of imprecise landing of the UAV. Beside the description of the visual navigation, relative localization and both helipads, a study of landing performance is provided. The performance of the complex system is proven by an experiment of autonomous periodical surveillance in a changing environment with presence of people.