Miracle-dz/UniFAR-FTUs huggingface dataset:
Rare Functional Variants in Complement Genes and Anti-FH Autoantibodies-Associated aHUS

Atypical hemolytic uremic syndrome (aHUS) is a rare disease characterized by microangiopathic hemolytic anemia, thrombocytopenia and renal failure. It is caused by genetic or acquired defects of the complement alternative pathway. Factor H autoantibodies (anti-FHs) have been reported in 10% of aHUS patients and are associated with the deficiency of factor H-related 1 (FHR1). However, FHR1 deficiency is not enough to cause aHUS, since it is also present in about 5% of Caucasian healthy subjects. In this study we evaluated the prevalence of genetic variants in CFH, CD46, CFI, CFB, C3, and THBD in aHUS patients with anti-FHs, using healthy subjects with FHR1 deficiency, here defined “supercontrols,” as a reference group. “Supercontrols” are more informative than general population because they share at least one risk factor (FHR1 deficiency) with aHUS patients. We analyzed anti-FHs in 305 patients and 30 were positive. The large majority were children (median age: 7.7 [IQR, 6.6–9.9] years) and 83% lacked FHR1 (n = 25, cases) due to the homozygous CFHR3-CFHR1 deletion (n = 20), or the compound heterozygous CFHR3-CFHR1 and CFHR1-CFHR4 deletions (n = 4), or the heterozygous CFHR3-CFHR1 deletion combined with a frameshift mutation in CFHR1 that generates a premature stop codon (n = 1). Of the 960 healthy adult subjects 48 had the FHR1 deficiency (“supercontrols”). Rare likely pathogenetic variants in CFH, THBD, and C3 were found in 24% of cases (n = 6) compared to 2.1% of the “supercontrols” (P-value = 0.005). We also found that the CFH H3 and the CD46GGAAC haplotypes are not associated with anti-FHs aHUS, whereas these haplotypes are enriched in aHUS patients without anti-FHs, which highlights the differences in the genetic basis of the two forms of the disease. Finally, we confirm that common infections are environmental factors that contribute to the development of anti-FHs aHUS in genetically predisposed individuals, which fits with the sharp peak of incidence during scholar-age. Further studies are needed to fully elucidate the complex genetic and environmental factors underlying anti-FHs aHUS and to establish whether the combination of anti-FHs with likely pathogenetic variants or other risk factors influences disease outcome and response to therapies.
Reduction of Periodic Motion Artifacts in Photoplethysmography

Periodic motion artifacts affect photoplethysmography (PPG) signals in activities of daily living (ADL), cardiopulmonary exercise testing (CPX), and cardiopulmonary resuscitation (CPR). This hampers measurement of interbeat intervals (IBIs) and oxygen saturation (SpO2). Our objective was to develop a generic algorithm to remove periodic motion artifacts, recovering artifact-reduced PPG signals for beat-to-beat analysis. Methods: The algorithm was retrospectively evaluated on forehead PPG signals measured while walking on a treadmill. The step rate was tracked in a motion reference signal via a second-order generalized integrator with a frequency-locked loop. Two reference signals were compared: sensor motion relative to the skin (Δx[n]) measured via self-mixing interferometry and head motion (av[n]) measured via accelerometry. The step rate was used in a quadrature harmonic model to estimate the artifacts. Quadrature components need only two coefficients per frequency leading to a short filter and prevent undesired frequency-shifted components in the artifact estimate. Subtracting the estimate from the measured signal reduced the artifacts. Results: Compared to Δx[n], av[n] had a better signal-to-noise ratio and more consistently contained a component at the step rate. Artifact reduction was effective for distinct step rate and pulse rate, since the artifact-reduced signals provided more stable IBI and SpO2 measurements. Conclusion: Accelerometry provided a more reliable motion reference signal. The proposed algorithm can be of significance for monitoring in ADL, CPX, or CPR, by providing artifact-reduced PPG signals for improved IBI and SpO2 measurements during periodic motion.
P-Channels: Robust Multivariate M-Estimation of Large Datasets

In this paper we introduce a new technique that allows to estimate modes of a high-dimensional probability density function with linear time-complexity in the number of dimensions and the number of samples. The method can be implemented in an order-independent incremental way, such that the space-complexity is linear in the number of dimensions and the number of modes. The number of required samples to get reliable estimates depends linearly on the number of dimensions even if we replace the assumption of independent stochastic variables with the weaker assumption of data clustered in submanifolds. These submanifolds need not to be known, but smoothness assumptions are made. The new technique is based on representing data in what we call P-channels
Line-Based Registration of Panoramic Images and LiDAR Point Clouds for Mobile Mapping

For multi-sensor integrated systems, such as the mobile mapping system (MMS), data fusion at sensor-level, i.e., the 2D-3D registration between an optical camera and LiDAR, is a prerequisite for higher level fusion and further applications. This paper proposes a line-based registration method for panoramic images and a LiDAR point cloud collected by a MMS. We first introduce the system configuration and specification, including the coordinate systems of the MMS, the 3D LiDAR scanners, and the two panoramic camera models. We then establish the line-based transformation model for the panoramic camera. Finally, the proposed registration method is evaluated for two types of camera models by visual inspection and quantitative comparison. The results demonstrate that the line-based registration method can significantly improve the alignment of the panoramic image and the LiDAR datasets under either the ideal spherical or the rigorous panoramic camera model, with the latter being more reliable.
Sequence analysis Efficient peptide – MHC-I binding prediction for alleles with few known binders

Motivation: In silico methods for the prediction of antigenic peptides binding to MHC class I molecules play an increasingly important role in the identification of T-cell epitopes. Statistical and machine learning methods in particular are widely used to score candidate binders based on their similarity with known binders and non-binders. The genes coding for the MHC molecules, however, are highly polymorphic, and statistical methods have difficulties building models for alleles with few known binders. In this context, recent work has demonstrated the utility of leveraging information across alleles to improve the performance of the prediction. Results: We design a support vector machine algorithm that is able to learn peptide–MHC-I binding models for many alleles simultaneously, by sharing binding information across alleles. The sharing of information is controlled by a user-defined measure of similarity between alleles. We show that this similarity can be defined in terms of supertypes, or more directly by comparing key residues known to play a role in the peptide–MHC binding. We illustrate the potential of this approach on various benchmark experiments where it outperforms other state-of-the-art methods. Availability: The method is implemented on a web server: http:// cbio.ensmp.fr/kiss. All data and codes are freely and publicly available from the authors. Contact: laurent.jacob@ensmp.fr Supplementary information: Supplementary data are available at Bioinformatics online.
uPAR-targeted Optical Imaging Contrasts as Theranostic Agents for Tumor Margin Detection

Complete removal of tumors by surgery is the most important prognostic factor for cancer patients with the early stage cancers. The ability to identify invasive tumor edges of the primary tumor, locally invaded small tumor lesions, and drug resistant residual tumors following neoadjuvant therapy during surgery should significantly reduce the incidence of local tumor recurrence and improve survival of cancer patients. In this study, we report that urokinase plasminogen activator (uPA) and its receptor (uPAR) are the ligand/cell surface target pair for the development of targeted optical imaging probes for enhancing imaging contrasts in the tumor border. Recombinant peptides of the amino terminal fragment (ATF) of the receptor binding domain of uPA were labeled with near infrared fluorescence (NIR) dye molecules either as peptide-imaging or peptide-conjugated nanoparticle imaging probes. Systemic delivery of the uPAR-targeted imaging probes in mice bearing orthotopic human breast or pancreatic tumor xenografts or mouse mammary tumors led to the accumulation of the probes in the tumor and stromal cells, resulting in strong signals for optical imaging of tumors and identification of tumor margins. Histological analysis showed that a high level of uPAR-targeted nanoparticles was present in the tumor edge or active tumor stroma immediately adjacent to the tumor cells. Furthermore, following targeted therapy using uPAR-targeted theranostic nanoparticles, residual tumors were detectable by optical imaging through the imaging contrasts produced by NIR-dye-labeled theranostic nanoparticles in drug resistant tumor cells. Therefore, results of our study support the potential of the development of uPAR-targeted imaging and theranostic agents for image-guided surgery.
A segmentation-free approach to Arabic and Urdu OCR

In this paper, we present a generic Optical Character Recognition system for Arabic script languages called Nabocr. Nabocr uses OCR approaches specific for Arabic script recognition. Performing recognition on Arabic script text is relatively more difficult than Latin text due to the nature of Arabic script, which is cursive and context sensitive. Moreover, Arabic script has different writing styles that vary in complexity. Nabocr is initially trained to recognize both Urdu Nastaleeq and Arabic Naskh fonts. However, it can be trained by users to be used for other Arabic script languages. We have evaluated our system's performance for both Urdu and Arabic. In order to evaluate Urdu recognition, we have generated a dataset of Urdu text called UPTI (Urdu Printed Text Image Database), which measures different aspects of a recognition system. The performance of our system for Urdu clean text is 91%. For Arabic clean text, the performance is 86%. Moreover, we have compared the performance of our system against Tesseract's newly released Arabic recognition, and the performance of both systems on clean images is almost the same.
A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads

MOTIVATION G → A hypermutation is an innate antiviral defense mechanism, mediated by host enzymes, which leads to the mutational impairment of viruses. Sensitive and specific identification of host-mediated G → A hypermutation is a novel sequence analysis challenge, particularly for viral deep sequencing studies. For example, two of the most common hepatitis B virus (HBV) reverse transcriptase (RT) drug-resistance mutations, A181T and M204I, arise from G → A changes and are routinely detected as low-abundance variants in nearly all HBV deep sequencing samples. RESULTS We developed a classification model using measures of G → A excess and predicted indicators of lethal mutation and applied this model to 325 920 unique deep sequencing reads from plasma virus samples from 45 drug treatment-naïve HBV-infected individuals. The 2.9% of sequence reads that were classified as hypermutated by our model included most of the reads with A181T and/or M204I, indicating the usefulness of this model for distinguishing viral adaptive changes from host-mediated viral editing. AVAILABILITY Source code and sequence data are available at http://hivdb.stanford. edu/pages/resources.html. CONTACT ereuman@stanfordalumni.org SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Development of a metrological scanning probe microscope incorporating a quartz tuning fork sensor and heterodyne laser interferometry

We present an overview of the design of the metrological scanning probe microscope (mSPM) currently under development at the National Measurement Institute Australia (NMIA) and report on preliminary results on the characterization of key components. The mSPM is being developed as part of the nanometrology program at NMIA and will provide dimensional measurements made at the nanometer scale that are traceable to the realization of the SI meter at NMIA. The instrument will provide an addressable measurement volume of 100 μm × 100 μm × 25 μm with a target uncertainty of 1 nm for the position measurement. It incorporates a quartz tuning fork (QTF) detector and a high-performance heterodyne laser interferometer system.
Frameworks = (components + patterns)

nition we use most is “a framework is a reusable design of all or part of a system that is represented by a set of abstract classes and the way their instances interact. ” Another common definition is “a framework is the skeleton of an application that can be customized by an application developer. ” These are not conflicting definitions; the first describes the structure of a framework while the second describes its purpose. Nevertheless, they point out the difficulty of defining frameworks clearly. Frameworks are important, and continually become more important. Systems like OLE, OpenDoc, and DSOM are frameworks; Java is spreading new frameworks like AWT and Beans. Most commercially available frameworks seem to be for technical domains such as user interfaces or distribution, and most applicationspecific frameworks are proprietary. But the steady rise of frameworks means every software developer should know what they are and how to deal with them. The ideal reuse technology provides components that can be easily connected to make a new system. The software developer does not have to know how the component is implemented, and it is easy for the developer to learn how to use it. The resulting system will be efficient, easy to maintain, and reliable. The electric power system is like that; you can buy a toaster from one store and a television from another, and they will both work at either your home or office. Most people do not know Ohm’s Law, yet they have no trouble connecting a new toaster to the power system. Unfortunately, software is not nearly as composable as the electric power system. The original vision of software reuse was based on components. In the beginning, commercial interest in object-oriented technology also focused on reusable Ralph E. Johnson Frameworks= (Components+Patterns)
Arabidopsis PPR40 Connects Abiotic Stress Responses to Mitochondrial Electron Transport1[W][OA]

Oxidative respiration produces adenosine triphosphate through the mitochondrial electron transport system controlling the energy supply of plant cells. Here we describe a mitochondrial pentatricopeptide repeat (PPR) domain protein, PPR40, which provides a signaling link between mitochondrial electron transport and regulation of stress and hormonal responses in Arabidopsis (Arabidopsis thaliana). Insertion mutations inactivating PPR40 result in semidwarf growth habit and enhanced sensitivity to salt, abscisic acid, and oxidative stress. Genetic complementation by overexpression of PPR40 complementary DNA restores the ppr40 mutant phenotype to wild type. The PPR40 protein is localized in the mitochondria and found in association with Complex III of the electron transport system. In the ppr40-1 mutant the electron transport through Complex III is strongly reduced, whereas Complex IV is functional, indicating that PPR40 is important for the ubiqinol-cytochrome c oxidoreductase activity of Complex III. Enhanced stress sensitivity of the ppr40-1 mutant is accompanied by accumulation of reactive oxygen species, enhanced lipid peroxidation, higher superoxide dismutase activity, and altered activation of several stress-responsive genes including the alternative oxidase AOX1d. These results suggest a close link between regulation of oxidative respiration and environmental adaptation in Arabidopsis.
Interpopulation and context-related differences in responses of a marine gastropod to predation risk

We conducted laboratory experiments to investigate interpopulation differences in the behavioural responses of the whelk Buccinum undatum to the predatory lobster Homarus americanus and the asteroid Leptasterias polaris, both in the absence and presence of feeding opportunities. Whelks from three populations in the eastern North Atlantic (1) responded to lobsters by displaying avoidance behaviours (burrowing in the sediments or retreating inside their shell), (2) responded to asteroids by displaying escape responses (rapid crawling, shell rocking behaviour or foot contortions), and (3) more often refrained from feeding in the presence of a lobster than in the presence of an asteroid. Although whelks from the three populations responded similarly to lobsters and asteroids, interpopulation differences were evident. Thus, whelks from populations sympatric with a given predator more frequently displayed 'appropriate' antipredator behaviours (i.e. avoidance in the presence of a lobster, and escape in the presence of an asteroid) than did whelks allopatric with that predator. Also, whelks from a population sympatric with both predators fed less readily in the presence of a given predator than did whelks allopatric with that predator. However, the presence of a lobster or an asteroid had the same impact on the feeding response of whelks from two populations with contrasting predator fields, one sympatric with lobsters, but allopatric with asteroids, and one sympatric with asteroids, but allopatric with lobsters. The results of our study indicate that coexistence (over evolutionary or ecological time) with lobsters and asteroids increases the propensity of the whelk to display avoidance and escape behaviours in the presence of lobsters and asteroids, respectively, but has a less predictable effect on how whelks trade off predation risk and food acquisition. Studies are needed to investigate the roles of inheritance and experience on the development of antipredator behaviours and decision making by prey animals when predation risk conflicts with other fitness-related activities such as the acquisition of food or reproductive opportunities. Copyright 1999 The Association for the Study of Animal Behaviour.
Exploring Interaction Fidelity in Virtual Reality: Object Manipulation and Whole-Body Movements

High degrees of interaction fidelity (IF) in virtual reality (VR) are said to improve user experience and immersion, but there is also evidence of low IF providing comparable experiences. VR games are now increasingly prevalent, yet we still do not fully understand the trade-off between realism and abstraction in this context. We conducted a lab study comparing high and low IF for object manipulation tasks in a VR game. In a second study, we investigated players' experiences of IF for whole-body movements in a VR game that allowed players to crawl underneath virtual boulders and "dangle'' along monkey bars. Our findings show that high IF is preferred for object manipulation, but for whole-body movements, moderate IF can suffice, as there is a trade-off with usability and social factors. We provide guidelines for the development of VR games based on our results.
Do Doctors Prescribe Antibiotics Out of Fear of Malpractice?

This paper investigates whether doctors prescribe antibiotics to protect themselves against potential malpractice claims. Using data from the National Ambulatory Medical Care Survey on more than half a million outpatient visits between 1993 and 2011, I find that doctors are 6% less likely to prescribe antibiotics after the introduction of a cap on noneconomic damages. Over 140 million discharge records from the Nationwide Inpatient Sample do not reveal a corresponding change in hospital stays for conditions that can potentially be avoided through antibiotic use in the outpatient setting. These findings, as well as a stylized model of antibiotic prescribing under the threat of malpractice, suggest that liability-reducing tort reforms can decrease the amount of antibiotics that are inappropriately prescribed for defensive reasons.
Automated Robot with Object Recognition and Handling Features

With the advent of new technologies, eve ry industry is moving towards automation. A large number of jobs in industries, such as Manufacturing, are performed repeatedly. These jobs require a lot of human effort. In such cases, there is a need of an automated robot which can perform the repetitive task more efficiently. This pap er is about a robot which has object recognition and handling features. The robot will optically recognize the objects and pick and place them as per the hand gestures given by the user. It will have a camera to capture image of the objects and one arm to perform the pick and place function.
Abstraction and Performance from Explicit Monadic Reflectio n

Most of the existing literature about monadic programming focuses on theory but does not address issues of software engineering. Using monadic parsing as a running example, we demonstrate monadic programs written in a typical style, recognize how they violate abstraction boundaries, and recover clean abstraction crossings through monadic reflection. Once monadic reflection is made explicit, it is possible to construct a grammar for monadic programming that is independent of domain-specific operations. This grammar, in turn, enables the redefinition of the monadic operators as macros that eliminate at expansion time the overhead imposed by functional representations. The results are very efficient monadic programs; for parsing, the output code is competitive with good hand-crafted parsers.
Monoclonal antibody and an antibody-toxin conjugate to a cell surface proteoglycan of melanoma cells suppress in vivo tumor growth.

A monoclonal antibody directed against a cell surface chondroitin sulfate proteoglycan of human melanoma cells, 9.2. 27, and its diphtheria toxin A chain (DTA) conjugate were investigated for their effects on in vitro protein synthesis and in vivo tumor growth of human melanoma cells. The 9.2. 27 IgG and its DTA conjugate display similar serological activities against melanoma target cells but only the conjugate can induce consistent in vitro inhibition of protein synthesis and toxicity in M21 melanoma cells. However, both 9.2. 27 IgG and its DTA conjugate effect significant suppression of M21 tumor growth in vivo in an immunotherapy model of a rapidly growing tumor in athymic nu/nu mice, suggesting that other host mechanisms may mediate monoclonal antibody-induced tumor suppression.
An intuitive explanation of graph signal processing-based electrical load disaggregation

Graph Signal Processing (GSP)-based techniques for disaggregation are obtained as a solution of appropriately formulated optimization problem. There is a possibility to work out the intuitive steps behind this solution to gain insights on improvising the existing algorithm and building new ones. In this direction, the paper presents an attempt made to bring out the intuitive explanation of the GSP-based disaggregation solution in a clear manner. Additionally, the promising results obtained by extending the existing GSP-based solution for 15 minutes sampled power data are presented. Also captured are the results towards disaggregating the loads of interest when unknown high power loads are present in the aggregate power data.