Miracle-dz/UniFAR-FTUs huggingface dataset:
Heparin/Heparan Sulfate Proteoglycans Glycomic Interactome in Angiogenesis: Biological Implications and Therapeutical Use

Angiogenesis, the process of formation of new blood vessel from pre-existing ones, is involved in various intertwined pathological processes including virus infection, inflammation and oncogenesis, making it a promising target for the development of novel strategies for various interventions. To induce angiogenesis, angiogenic growth factors (AGFs) must interact with pro-angiogenic receptors to induce proliferation, protease production and migration of endothelial cells (ECs). The action of AGFs is counteracted by antiangiogenic modulators whose main mechanism of action is to bind (thus sequestering or masking) AGFs or their receptors. Many sugars, either free or associated to proteins, are involved in these interactions, thus exerting a tight regulation of the neovascularization process. Heparin and heparan sulfate proteoglycans undoubtedly play a pivotal role in this context since they bind to almost all the known AGFs, to several pro-angiogenic receptors and even to angiogenic inhibitors, originating an intricate network of interaction, the so called “angiogenesis glycomic interactome”. The decoding of the angiogenesis glycomic interactome, achievable by a systematic study of the interactions occurring among angiogenic modulators and sugars, may help to design novel antiangiogenic therapies with implications in the cure of angiogenesis-dependent diseases.
Regularized Auto-Encoders Estimate Local Statistics

What do auto-encoders learn about the underlying data generating distribution? Recent work suggests that some auto-encoder variants do a good job of capturing the local manifold structure of the unknown data generating density. This paper clarifies some of these previous intuitive observations by showing that minimizing a particular form of regularized reconstruction error yields a reconstruction function that locally characterizes the shape of the data generating density. More precisely, we show that the auto-encoder captures the score (derivative of the logdensity with respect to the input) or the local mean associated with the unknown data-generating density. This is the second result linking denoising auto-encoders and score matching, but in way that is different from previous work, and can be applied to the case when the auto-encoder reconstruction function does not necessarily correspond to the derivative of an energy function. The theorems provided here are completely generic and do not depend on the parametrization of the autoencoder: they show what the auto-encoder would tend to if given enough capacity and examples. These results are for a contractive training criterion we show to be similar to the denoising auto-encoder training criterion with small corruption noise, but with contraction applied on the whole reconstruction function rather than just encoder. Similarly to score matching, one can consider the proposed training criterion as a convenient alternative to maximum likelihood, i.e., one not involving a partition function. Finally, we make the connection to existing sampling algorithms for such autoencoders, based on an MCMC walking near the high-density manifold.
A Fast Algorithm for Computing the Closest Point and Distance Transform

This paper presents a new algorithm for computing the closest point transform to a manifold on a rectilinear grid in low dimensional spaces. The closest point transform finds the closest point on a manifold and the Euclidean distance to a manifold for all the points in a grid, (or the grid points within a specified distance of the manifold). We consider manifolds composed of simple geometric shapes, such as, a set of points, piecewise linear curves or triangle meshes. The algorithm computes the closest point on and distance to the manifold by solving the Eikonal equation |∇u| = 1 by the method of characteristics. The method of characteristics is implemented efficiently with the aid of computational geometry and polygon/polyhedron scan conversion. The computed distance is accurate to within machine precision. The computational complexity of the algorithm is linear in both the number of grid points and the complexity of the manifold. Thus it has optimal computational complexity. Examples are presented for piecewise linear curves in 2D and triangle meshes in 3D. 1 The Closest Point Transform Let u(x), x ∈ R, be the distance from the point x to a manifold S. If dim(S) = n − 1, (for example curves in 2D or surfaces in 3D), then the distance is signed. The orientation of the manifold determines the sign of the distance. One can adopt the convention that the outward normals point in the direction of positive or negative distance. In order for the distance to be well-defined, the manifold must be orientable and have a consistent orientation. A Klein bottle in 3D for example is not orientable. Two concentric circles in 2D have consistent orientations only if the normals of the inner circle point “inward” and the normals of the outer circle point “outward”, or vice-versa. Otherwise the distance would be ill-defined in the region between the circles. For manifolds which are not closed, the distance is ill-defined in any neighborhood of the boundary. However, the distance is well-defined in neighborhoods of the manifold which do not contain the boundary. If dim(S) < n− 1, (for example a set of points in 2D or a curve in 3D), the distance is unsigned, (non-negative).
Expression in Escherichia coli of a New Multidrug Efflux Pump, MexXY, from Pseudomonas aeruginosa

ABSTRACT Two new genes (mexXY) similar to mexAB,mexCD, and mexEF and mediating multidrug resistance were cloned from the chromosome of Pseudomonas aeruginosa. Elevated ethidium extrusion was observed withEscherichia coli cells harboring the plasmid carryingmexXY. This MexXY system confers higher resistance to fluoroquinolones than the MexAB and MexCD systems, and E. coli TolC or P. aeruginosa OprM is necessary for the function of the MexXY system.
Deep Brain Recordings in Parkinson's Disease: Processing, Analysis and Fusion with Anatomical Models

This thesis presents several novel techniques and tools for automatic classification and analysis of highly detailed invasive recordings of the brain activity in patients with Parkinson’s disease (PD). By utilizing machine learning concepts, we approach three of the principal questions, central to modern treatment and understanding of the PD: i) What information about patient’s state can be derived from recorded brain activity? By identifying patterns characteristic for tremor onset in signals recorded through deep brain stimulation electrodes, we show that an adaptive system, modifying treatment parameters to match current state of its bearer, is feasible. ii) How to obtain trustworthy answers to scientific questions from noisy microelectrode activity recordings? We show that undesirable noise is highly prevalent in intraoperative microelectrode recordings and provide the sigInspect: a GUI tool for annotation of microelectrode signals. The tool includes a set of well-performing classifiers for automatic artifact identification, validated on an extensive multi-center database of manually labeled data. iii) Where exactly in the target nucleus were the signals recorded? This question is vital for appropriate stimulation electrode placement as well as for better understanding of possible side effects. We propose a novel probabilistic model for fitting a 3D anatomical atlas of the subthalamic nucleus based solely on the recorded electrophysiological activity and show that such approach may lead to more accurate localization of recording sites during and after the surgery.
Selection of IgG Variants with Increased FcRn Binding Using Random and Directed Mutagenesis: Impact on Effector Functions

Despite the reasonably long half-life of immunoglogulin G (IgGs), market pressure for higher patient convenience while conserving efficacy continues to drive IgG half-life improvement. IgG half-life is dependent on the neonatal Fc receptor (FcRn), which among other functions, protects IgG from catabolism. FcRn binds the Fc domain of IgG at an acidic pH ensuring that endocytosed IgG will not be degraded in lysosomal compartments and will then be released into the bloodstream. Consistent with this mechanism of action, several Fc-engineered IgG with increased FcRn affinity and conserved pH dependency were designed and resulted in longer half-life in vivo in human FcRn-transgenic mice (hFcRn), cynomolgus monkeys, and recently in healthy humans. These IgG variants were usually obtained by in silico approaches or directed mutagenesis in the FcRn-binding site. Using random mutagenesis, combined with a pH-dependent phage display selection process, we isolated IgG variants with improved FcRn-binding, which exhibited longer in vivo half-life in hFcRn mice. Interestingly, many mutations enhancing Fc/FcRn interaction were located at a distance from the FcRn-binding site validating our random molecular approach. Directed mutagenesis was then applied to generate new variants to further characterize our IgG variants and the effect of the mutations selected. Since these mutations are distributed over the whole Fc sequence, binding to other Fc effectors, such as complement C1q and FcγRs, was dramatically modified, even by mutations distant from these effectors’ binding sites. Hence, we obtained numerous IgG variants with increased FcRn-binding and different binding patterns to other Fc effectors, including variants without any effector function, providing distinct “fit-for-purpose” Fc molecules. We therefore provide evidence that half-life and effector functions should be optimized simultaneously as mutations can have unexpected effects on all Fc receptors that are critical for IgG therapeutic efficacy.
A Modified Bird-Mating Optimization with Hill-Climbing for Connection Decisions of Transformers

This paper endeavors to apply a hybrid bird-mating optimization approach to connection decisions of distribution transformers. It is expected that with the aid of hybrid bird-mating approach, the voltage imbalance and deviation can be mitigated, hence ensuring a satisfactory supplying power more effectively. To evaluate the effectiveness of this method, it has been tested through practical distribution systems with comparisons to other methods. Test results help confirm the feasibility of the approach, serving as beneficial references for the improvement of electric power grid operations.
Multichannel Consistent Sampling and Reconstruction Associated With Linear Canonical Transform

Multichannel sampling is fundamental in the theory of multichannel parallel analog-to-digital converters and multiplexing wireless communication. This letter investigates the multichannel consistent sampling theory associated with the linear canonical transform, which can combine the reconstruction of the signal and the correction of sensor distortions. The consistency requests that a resampling of the reconstruction by the original sampling operation yields the same measurements as before. The consistent sampling is applicable to an arbitrary finite energy signal and without the constraint such as band-limiting. Under this circumstance, two effective reconstruction methods based on the shift-invariant reconstruction space and the linear canonical basis functions space are developed. Finally, the reconstruction experiment of the radar echo signal is presented.
The Role of Destination’s Built Environment on Nonmotorized Travel Behavior: A Case of Long Beach, California

This study examines how built environment factors at trip destinations influence nonmotorized travel behavior in the City of Long Beach, California. Using 2008–2009 National Household Travel Survey with California Add-Ons, we found that nonmotorized users tend to choose more clustered destinations than motorized users, and that density, diversity, and design at destinations significantly affect mode choice decisions. Transportation networks and nonmotorized facilities at trip destinations are especially important factors for nonmotorized mode choice. Future policy and research need to consider built environment factors at trip destinations to effectively accommodate nonmotorized travel within a city.
Assure High Quality Code Using Refactoring and Obfuscation Techniques

Nowadays, software refactoring techniques are widely adopted to enhance the quality of software by improving its understandability, performance, as well as other quality related design attributes. On the other hand, various kinds of software obfuscation methods have been proposed to protect security-sensitive information involved in software implementations. This paper analyzes how refactoring and obfuscation use reverse transformations to improve quality and security of software code, and proposes a systematic modeling approach based on i* to support the selection of refactoring techniques and obfuscation methods under different social, environmental and operational situations. First, top-level softgoals guiding designer’s decision making are identified and analyzed; next accidental programming “bad smells” and intentional code cracker’s threats to these softgoals are identified and analyzed; then refactoring and obfuscation transformations are modeled as countermeasures for these threats; eventually their reversal relations and counteracting patterns are examined using example code segments.
UTAPS: An Underlying Topology-Aware Peer Selection Algorithm in BitTorrent

BitTorrent is one of the most well known peer-to-peer file sharing applications, accounting for a significant proportion of Internet traffic. Current BitTorrent system builds its overlay network by randomly selecting peers, a fact that has the potential to seriously handicap both individual performance and generate a significant amount of cross-ISP traffic. In this paper, we propose a novel peer selection algorithm called UTAPS which could selects peers within small hop counts and low round trip time (RTT) range by utilizing the knowledge of underlying topology. Consequently, the proximities among peers in the P2P overlay network are enhanced. Simulation results show that the UTAPS algorithm can achieve better individual performance in sense of low download time and reduce the traffics which are injected into ISP backbones.
A Hybrid Model for Web Image Annotation

Retrieving images in response to textual queries requires some knowledge of the semantic of images. Accordingly, an efficient image annotation and retrieval system is highly desired for this purpose. However, current image annotation technique is not satisfying which often includes noisy keywords. To improve image annotation, we propose a hybrid Web image annotation model (HIAM) consisting of two basic submodules, HMIAM and IARM. The former, based on hidden Markov model, associates an image with some keywords like other traditional models, while the latter utilizes textual information in Web documents to evaluate each keyword's importance to image semantics: each keyword is associated with certain weight to quantify its similarity to image semantics. Then keywords with low weight can be removed as noisy data. The experimental results show that the post-processed annotations by our model are better than original ones.
Histopathologic evaluation of postmortem autolytic changes in bluegill (Lepomis macrohirus) and crappie (Pomoxis anularis) at varied time intervals and storage temperatures

Information is lacking on preserving fish carcasses to minimize postmortem autolysis artifacts when a necropsy cannot be performed immediately. The purpose of this study was to qualitatively identify and score histologic postmortem changes in two species of freshwater fish (bluegill—Lepomis macrochirus; crappie—Pomoxis annularis), at varied time intervals and storage temperatures, to assess the histologic quality of collected samples. A pooled sample of 36 mix sex individuals of healthy bluegill and crappie were euthanized, stored either at room temperature, refrigerated at 4 °C, or frozen at −20 °C, and then necropsied at 0, 4, 24, and 48 h intervals. Histologic specimens were evaluated by light microscopy. Data showed that immediate harvesting of fresh samples provides the best quality and refrigeration would be the preferred method of storage if sample collection had to be delayed for up to 24 h. When sample collection must be delayed more than 24 h, the preferred method of storage to minimize autolysis artifacts is freezing if evaluation of the gastrointestinal tract is most important, or refrigeration if gill histology is most important. The gill arch, intestinal tract, followed by the liver and kidney were the most sensitive organs to autolysis.
Out of Africa, the Nile Valley and the Northern Route

Hypotheses on the dispersal patterns of modern humans out of Africa have undergone much change in the past decade, with new ideas on the routes and geographic extent of movements proposed. New data and perspectives from the Nile Valley necessitate reassessment of the role of the Northern Route. Here, fossil evidence and technological strategies followed in the Nile Valley between 200 000 to 300 000 years ago, and its relevance to dispersal patterns are discussed. Most of the sites in the Nile Valley relate to extensive quarrying activities associated with sophisticated logistical strategies. Early Middle Stone Age Sangoan assemblages already show complex adaptive patterns in the exploita tion of colorants and hafting of typical core-axes. The MIS 6 Lupemban consisting of non-Levallois systems, symmetrical lanceolate foliate tools and blades from volumetric cores are succeeded by the Early Nubian Complex of the early Last Interglacial. One of the typological elements that sets the early Nubian Complex apart, is triangular or leaf-shaped bifacial foliates, associated with Nubian point production. There are ephemeral traces of occupation in the drier periods of MIS 5, followed by the much more visible Nubian Complex sensu stricto, mainly a MIS 5a phenomenon. Bifacial foliates disappear from the typological inventory, but Nubian points still occur. Around 60 000 years ago technological goals are geared towards increased productiv ity, as evidenced in the Lower Nile Valley Complex (LNVC) and the Taramsan. The Taramsan is transitional to the Upper Palaeolithic in the Nile Valley and by 40 000 years ago fully Upper Palaeolithic indus tries occur here. The human fossil remains from Singa, Taramsa 1 and Nazlet Khater contribute valuable perspectives on the phylogenetic history of the Middle and Late Pleistocene populations from North
Pneumonia surveillance in Thailand: current practice and future needs.

We reviewed reported pneumonia cases and deaths in Thailand since 1975 to evaluate the pneumonia surveillance system. In Sa Kaeo Province, we analyzed 3 years in detail (1999--2001) from electronic surveillance data, and compared deaths reported through surveillance to death certificate data in 1999 and 2000. In addition, we interviewed surveillance personnel who collected the data from all 7 hospitals and from a 10% random sample of health centers. Since the mid-1980s, reported illnesses and deaths from pneumonia have been increasing. In Sa Kaeo, an average of 925 pneumonia cases were reported each year, for an estimated average annual incidence of 211 per 100,000. The age-specific incidence peaked at 1,418 per 100,000 in children less than 5 years. In 1999 and 2000, there were 7 and 6 pneumonia deaths, respectively, reported through the surveillance system, compared with 28 and 53, respectively, reported by death certificate. Sixty-two (82%) of the 72 surveillance personnel reported receiving some training, but most of this was informal. Although written criteria to diagnose pneumonia were established in 1996, those who report cases did not know these criteria. A combination of physician, nurse, and public health workers diagnoses were used. According to the written criteria, cases of suspect or rule out pneumonia should be reported, but when asked about specific examples only 79% of persons interviewed said they would report "tuberculosis with pneumonia" and 44% would report "bronchitis, rule out pneumonia. " Seventy-four percent of persons interviewed completed the surveillance report within one day of patient admission.
Optimization of percussive mechanism in rotary-percussion drill for lunar exploration

Rotary-percussive Drill (RPD) has been widely employed in extraterrestrial exploration as a main drilling and sampling device. Percussive mechanism, as an inevitable part of RPD, is commonly utilized to exert percussion onto drill stem to improve drilling performance once hard rock is encountered. However, since driving resource provided by the probe is limited in lunar exploration, outputs of percussive mechanism-impact energy and percussive frequency-which are restricted by system power affect the drilling efficiency greatly. In order to maximize the percussive performance under a limited power resource, this paper presents a kind of feasible optimization approach aiming at optimizing the design parameter matches of percussive mechanism. The optimized result is compared with a group of randomly-selected parameters match to emphasize the advantage of optimization. Experiments are conducted on a Drilling and Coring Test-bed (DCTB) to verify the optimized result.
The Influence of Reference Frame Selection on Spatial Template Construction

Abstract The use of spatial relational terms requires the selection of a reference frame and the construction of a spatial template. The reference frame divides up space, indicating above/below, front/back, and left/right directions. Spatial templates are applied to reference frames and define regions in space that correspond to good, acceptable, and bad uses of particular spatial relations. In two experiments we examined whether reference frame selection influences the spatial templates that are constructed for the spatial relations “above” and “below. ” Results indicated two such influences, one operating across trials and one operating within a trial. Across trials, the preferences for using the different types of reference frames directly influenced the parsing of space, such that when multiple spatial templates were constructed, they were combined to form a composite template. Spatial templates constructed for the different reference frames were very similar, indicating that the type of reference frame did not alter the overall shape or relative sizes of the regions within the spatial template. Within a trial, the activation of multiple reference frames during reference frame selection resulted in the construction of multiple spatial templates, even when instructions were given to respond on the basis of a single reference frame.