gebhart/patrepeval huggingface dataset:
Microtubulin configuration and mitochondrial distribution after ultra‐rapid cooling of bovine oocytes (2002)

Considerable attention has been focused on the cryopreservation of mammalian oocytes, as a consequence of poor development of cryopreserved bovine oocytes in vitro, in order to enhance the application of genetic engineering. Experiments were carried out to evaluate the viability and ultra-structural changes of bovine oocytes cryopreserved by ultra rapid cooling methods. Oocytes that had been allowed to mature for 22 hr were exposed to a mixture of cryoprotectants (3.2 M ethylene glycol, 2.36 M dimethyl sulfoxide (DMSO), 0.6 M sucrose), and were cryopreserved by very rapid cooling either within glass capillaries or as droplets on copper electron microscope grids. After being warmed, the oocytes were cultured in in vitro maturation (IVM) medium for an additional 2 hr. Viability was assessed by determining the development rate after fertilization with frozen-thawed semen from which motile sperm had been recovered using a Percoll density gradient, and by immunochemical evaluation of microtubule and mitochondrial morphology. Cleavage and development rates were significantly (P < 0.05) lower in oocytes cryopreserved by vitrification than in in vitro fertilization (IVF) control group, but did not differ in the open-pulled glass (OPG) or copper grid (CG) groups. In most oocytes cryopreserved by vitrification, the microtubules were partially or completely broken. Similarly mitochondria appeared to be abnormal compared to that of unfrozen oocytes. Oocytes cultured in IVM medium supplemented with both cytochalasin B (a protein synthesis inhibitor) and 2-mercaptoethanol (an antioxidant) showed less damage to microtubules, but not to mitochondria after cryopreservation. In conclusion, this study showed that bovine oocytes can be cryopreserved by vitrification within small droplets using CGs. While damage to microtubules and mitochondria may be involved in reduced viability, supplementation of IVM medium with cytochalasin B appears to enhance stabilization of microtubules during oocyte cryopreservation.
Neutrophil degranulation, NETosis and platelet degranulation pathway genes are co-induced in whole blood up to six months before tuberculosis diagnosis (2022)

Abstract Mycobacterium tuberculosis ( M.tb ) causes tuberculosis (TB) and remains one of the leading causes of mortality due to an infectious pathogen. Host immune responses have been implicated in driving the progression from infection to severe lung disease. We analyzed longitudinal RNA sequencing (RNAseq) data from the whole blood of 74 TB progressors whose samples were grouped into four six-month intervals preceding diagnosis (the GC6-74 study). We additionally analyzed RNAseq data from an independent cohort of 90 TB patients with positron emission tomography-computed tomography (PET-CT) scan results which were used to categorize them into groups with high and low levels of lung damage (the Catalysis TB Biomarker study). These groups were compared to non-TB controls to obtain a complete whole blood transcriptional profile for individuals spanning from early stages of M.tb infection to TB diagnosis. The results revealed a steady increase in the number of genes that were differentially expressed in progressors at time points closer to diagnosis with 278 genes at 13–18 months, 742 at 7–12 months and 5,131 detected 1–6 months before diagnosis and 9,205 detected in TB patients. A total of 2,144 differentially expressed genes were detected when comparing TB patients with high and low levels of lung damage. There was a large overlap in the genes upregulated in progressors 1–6 months before diagnosis (86%) with those in TB patients. A comprehensive pathway analysis revealed a potent activation of neutrophil and platelet mediated defenses including neutrophil and platelet degranulation, and NET formation at both time points. These pathways were also enriched in TB patients with high levels of lung damage compared to those with low. These findings suggest that neutrophils and platelets play a critical role in TB pathogenesis, and provide details of the timing of specific effector mechanisms that may contribute to TB lung pathology. Author summary Mycobacterium tuberculosis ( M.tb ) causes tuberculosis (TB) and remains one of the leading causes of mortality due to an infectious pathogen. Human immune responses must be balanced to inhibit disease progression while limiting self-damage, however in defense against M.tb host responses have been implicated in lung damage and in driving progression of M.tb infection to severe lung disease. The identification of immune responses that are activated during the development of TB could provide potential targets for interventions that might suppress disease progression, and possibly limit tissue damage. Here we identify a subset of genes that function in several biological processes that are strongly activated in the late stages of TB development and in TB patients. The proteins encoded by these genes are known to degrade lung tissue and contribute to severe lung disease.
Pose and Joint-Aware Action Recognition (2022)

Recent progress on action recognition has mainly focused on RGB and optical flow features. In this paper, we approach the problem of joint-based action recognition. Unlike other modalities, constellation of joints and their motion generate models with succinct human motion information for activity recognition. We present a new model for joint-based action recognition, which first extracts motion features from each joint separately through a shared motion encoder before performing collective reasoning. Our joint selector module re-weights the joint information to select the most discriminative joints for the task. We also propose a novel joint-contrastive loss that pulls together groups of joint features which convey the same action. We strengthen the joint-based representations by using a geometry-aware data augmentation technique which jitters pose heatmaps while retaining the dynamics of the action. We show large improvements over the current state-of-the-art joint-based approaches on JHMDB, HMDB, Charades, AVA action recognition datasets. A late fusion with RGB and Flow-based approaches yields additional improvements. Our model also outperforms the existing baseline on Mimetics, a dataset with out-of-context actions.
Why colour order systems? (1984)

Abstract In this introductory lecture to the AIC Forsius Symposium on Colour Order Systems, the author reviews color order systems from a historical point of view as samplings of the World of Colour, seeking with each example to find an answer to the question posed in the title.
Small size single and multiband antenna arrays with diversity capabilities for portable devices (2002)

Two techniques to reduce the physical size of circular and rectangular microstrip patch antennas are presented. The antenna elements are orientated orthogonally to each other to form multielement antennas (MEAs) to realize diversity antennas. The reduced size and thin substrate thicknesses will allow compatibility with portable communications systems.
Introduction. Machine learning in neurosurgery: transitioning to a new era of contemporary medicine (2023)

Rapid technological evolution has transformed clinical practice, constituting big data and artificial intelligence as omnipresent tools in the medical arsenal and creating extraordinary potential and unprecedented challenges.The paradigm shift witnessed by the healthcare sector as a result of the mass digitization of information has organically permeated neurosurgery.In recent years, surgical innovation compounded by clinical expertise, in conjunction with novel data-processing techniques, has enabled meaningful advancements in the application of machine learning in neurosurgery.This issue of Neurosurgical Focus embodies a representation of the progress in translating machine learning algorithms into clinical practice.The articles included in this issue invariably resonate with the drive to recruit artificial intelligence to address impactful questions, derive meaningful outcomes, and achieve personalized patient management.The authors study current machine learning models, evaluate novel algorithms, and discuss approaches to appraising machine learning techniques in neurosurgery.Machine learning in neurosurgery extends beyond the mere synthesis of existing research and exemplifies the power of merging information technology with medical science to transition clinical practice to a new era of contemporary medicine.In our attempt to open this Pandora's box, we hope to provide a long-lasting reference for clinicians and scientists, stimulate scientific thought, and provide a framework for a fruitful conversation on a highly complicated and challenging topic.We immensely appreciate the contributing authors' work in undertaking the formidable task of unraveling the highly convoluted role of machine learning in neurosurgery.
ChemInform Abstract: SYNTHESIS OF TRIAMANTANE (1981)

Abstract Norbornadien (I) liefert das Dimere Binor S (II), aus dem bei der Behandlung mit Silberperchlorat in hohenAusbeuten die beiden Olefine (III) und (IV) entstehen.
Chitosan biohydrogel beads: A recyclable, biodegradable, heterogeneous catalyst for the regioselective synthesis of 5-aryl-2-oxazolidinones from carbon dioxide and aziridines at mild conditions (2012)

In the search for efficient catalysts for a reaction under mild conditions, cycloaddition reactions of carbon dioxide with various aziridines catalyzed by chitosan biohydrogel beads without additional solvent and metal co-catalyst to form five-membered 5-aryl-2-oxazolidinones in high yields and selectivity has been studied. Reaction rate, conversion and selectivity are studied as a function of a series of input variables including catalyst loading, temperature, pressure and solvent system. The catalyst is easily recovered and has been reused in five consecutive cycles without any significant loss of its catalytic activity and selectivity. The catalyst, chitosan biohydrogel beads, has been characterized by a variety of techniques, namely, scanning electron microscopy and Fourier transform infrared spectroscopy. A plausible reaction mechanism for the hydrogen-bond assisted ring-opening of aziridine to five-membered 5-aryl-2-oxazolidinones is also proposed.
Cycles, Compartments, and Polymerization (2019)

The two quotes in the epigraph, in juxtaposition, always make me smile, and I tried to keep them in mind while writing this chapter. The first eight chapters of this book have the effect of eliminating the impossible by investigating the facts to which Twain is referring. Perhaps he would consider them trifling, but I doubt that Twain ever performed an experiment to test an idea. Every working scientist knows that science is not just a set of facts but is also a set of questions. The best way to begin answering a question is to pose a hypothesis and that hypothesis begins as a conjecture. Only when we have a hypothesis, can we design experiments to test it, and if we are lucky, the results of those experiments lead us a little closer to the truth. This chapter summarizes facts that lead to an alternative scenario for life’s origin in freshwater hydrothermal conditions rather than a marine origin in saltwater hydrothermal vents. As stated in the introduction to this book, when assumptions are part of the story they will be made explicit so that the logic that arises from them will be clear. What follows in this overview is a list of ten prerequisites we assume are necessary for cellular life to begin, followed by eight assumptions underlying the scenario to be presented here. Prerequisite conditions for life to begin: Dilute solutions of potential reactants are available, together with a process by which they can be sufficiently concentrated to react. Energy sources available in the environment can drive reactions such as carbon fixation, primitive metabolism, and polymerization. Products of reactions accumulate within the site rather than dispersing into the bulk phase environment. Amphiphiles assemble into membranous compartments over the range of temperatures, salt concentrations, and pH values related to each site. Biologically relevant polymers are synthesized with chain lengths sufficient to act as catalysts or incorporate genetic information. A plausible physical mechanism can produce encapsulated polymers as protocells then subject them to combinatorial selection. Organic solutes in aqueous solutions become biochemical solutes within protocells and then substrates supporting a primitive metabolism.
Evaluation of the Lipid-binding Properties of Recombinant Dystrophin Spectrin-like Repeat Domains R1-3 (2021)

Recombinant micro-dystrophin genes are designed to treat Duchenne muscular dystrophy (DMD) by retaining dystrophin domains believed to play key functional roles while fitting the packaging capacity of adeno-associated virus vectors. Domains R1-3 are important for muscle force generation and for association with the sarcolemma, but the nature of this interaction is not fully understood. We measured lipid-binding affinity of 3 peptides containing different spectrin-like repeat modules (R1-3; R1-2; and R1, 2, 22). Lipid-binding affinity was highest with R1-3, suggesting that the complete R1-R3 region could be beneficial and should be considered for inclusion in micro-dystrophin constructs.
Erratum to: a SNP profiling panel for sample tracking in whole-exome sequencing studies (2015)

This is an Erratum to Genome Medicine 2013, 5:89, highlighting an error in Table 1 of the original article. Please see related article: http://genomemedicine.com/content/5/9/89.[This corrects the article DOI: 10.1186/gm492.].
<title>Statistical analysis of fMRI data using orthogonal filterbanks</title> (1999)

Functional magnetic resonance imaging is a recent technique that allows the measurement of brain metabolism (local concentration of deoxyhemoglobin using BOLD contrast) while subjects are performing a specific task. A block paradigm produces alternating sequences of images (e.g., rest versus motor task). In order to detect and localize areas of cerebral activation, one analyzes the data using paired differences at the voxel level. As an alternative to the traditional approach which uses Gaussian spatial filtering to reduce measurement noise, we propose to analyze the data using an orthogonal filterbank. This procedure is intended to simplify and eventually improve the statistical analysis. The system is designed to concentrate the signal into a fewer number of components thereby improving the signal-to- noise ratio. Thanks to the orthogonality property, we can test the filtered components independently on a voxel-by- voxel basis; this testing procedure is optimal for i.i.d. measurement noise. The number of components to test is also reduced because of down-sampling. This offers a straightforward approach to increasing the sensitivity of the analysis (lower detection threshold) while applying the standard Bonferroni correction for multiple statistical tests. We present experimental results to illustrate the procedure. In addition, we discuss filter design issues. In particular, we introduce a family of orthogonal filters which are such that any integer reduction m can be implemented as a succession of elementary reductions m<SUB>1</SUB> to m<SUB>p</SUB> where m equals m<SUB>1</SUB>...m<SUB>p</SUB> is a prime number factorization of m.
Stakeholder engagement in methodological research: Development of a clinical decision support tool (2019)

Methodological research has the opportunity to benefit from stakeholder engagement by ensuring that the perspectives of those most impacted by the results are involved in study design and conduct. While additional planning and investments in maintaining stakeholder knowledge and trust may be needed, they are offset by the valuable insights gained.
Generalization of metric classification algorithms for sequences classification and labelling (2016)

The article deals with the issue of modification of metric classification algorithms. In particular, it studies the algorithm k-Nearest Neighbours for its application to sequential data. A method of generalization of metric classification algorithms is proposed. As a part of it, there has been developed an algorithm for solving the problem of classification and labelling of sequential data. The advantages of the developed algorithm of classification in comparison with the existing one are also discussed in the article. There is a comparison of the effectiveness of the proposed algorithm with the algorithm of CRF in the task of chunking in the open data set CoNLL2000.
On the Use of HF Surface Wave Radar in Congested Waters: Influence of Masking Effect on Detection of Small Ships (2006)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> In this paper, we assess the capability of a high- frequency surface wave radar (HFSWR) to detect a small fast boat moving behind a ship, the dimensions of which are comparable to the wavelength. We show that, in the HF-band, the scattered field in the shadow region of the large ship is significant enough to induce strong coupling between the two vessels. This results in fluctuations in the radar cross section (RCS) values of the small boat of about 12 dB at 10 MHz, for instance. We also introduce a complete simulation tool to account for the environment and, thus, to be able to simulate real scenes. We have validated these results through anechoic chamber measurements, with two different masking vessels and three different masked ships. The measurements have shown both the low-attenuation results and the RCS fluctuations. </para>
Molecular tracing of the emergence, diversification, and transmission of S. aureus sequence type 8 in a New York community (2014)

During the last 2 decades, community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) strains have dramatically increased the global burden of S. aureus infections. The pandemic sequence type (ST)8/pulsed-field gel type USA300 is the dominant CA-MRSA clone in the United States, but its evolutionary history and basis for biological success are incompletely understood. Here, we use whole-genome sequencing of 387 ST8 isolates drawn from an epidemiological network of CA-MRSA infections and colonizations in northern Manhattan to explore short-term evolution and transmission patterns. Phylogenetic analysis predicted that USA300 diverged from a most common recent ancestor around 1993. We found evidence for multiple introductions of USA300 and reconstructed the phylogeographic spread of isolates across neighborhoods. Using pair-wise single-nucleotide polymorphism distances as a measure of genetic relatedness between isolates, we observed that most USA300 isolates had become endemic in households, indicating their critical role as reservoirs for transmission and diversification. Using the maximum single-nucleotide polymorphism variability of isolates from within households as a threshold, we identified several possible transmission networks beyond households. Our study also revealed the evolution of a fluoroquinolone-resistant subpopulation in the mid-1990s and its subsequent expansion at a time of high-frequency outpatient antibiotic use. This high-resolution phylogenetic analysis of ST8 has documented the genomic changes associated with USA300 evolution and how some of its recent evolution has been shaped by antibiotic use. By integrating whole-genome sequencing with detailed epidemiological analyses, our study provides an important framework for delineating the full diversity and spread of USA300 and other emerging pathogens in large urban community populations.
State estimation for a class of discrete nonlinear systems with randomly occurring uncertainties and distributed sensor delays (2014)

In this paper, the state estimation problem is investigated for a class of discrete nonlinear systems with randomly occurring uncertainties and distributed sensor delays. The norm-bounded uncertainties enter into the system in a randomly way, and such randomly occurring uncertainties (ROUs) obey certain Bernoulli distributed white noise sequence with known conditional probability. By constructing a new Lyapunov–Krasovskii functional, sufficient conditions are proposed to guarantee the convergence of the estimation error for all discrete time-varying delays, ROUs and distributed sensor delays. Subsequently, the explicit form of the estimator parameter is derived by solving two linear matrix inequalities (LMIs) which can be easily tested by using standard numerical software. Finally, a simulation example is given to illustrate the feasibility and effectiveness of the proposed estimation scheme.
Light focusing microprobes for biomedical and photonics applications based on integrated microsphere arrays (2010)

The task of development of compact light-focusing tools for biomedical and photonics applications is challenging due to the multimodal structure of beams propagating in flexible delivery systems of such devices. In this study it is shown that integration of microspheres inside hollow waveguides or capillaries permits compact focusing of light from multimodal sources. Experimental studies were performed for variety of spheres with sizes from 10 to 300 μm with refraction indices ranging from 1.47 to 1.9. It is shown that for high index (1.9) spheres the smallest focused spots can be obtained in chains containing odd number of spheres. It is also demonstrated that increasing the length of such chains generally provides smaller focused spot sizes at the expense of the transmitted power. The underlying optical properties are shown to be based on the filtering of the modes with the best focusing properties in such structures. It is demonstrated that under contact with tissue such structures allow obtaining focused beams with high throughput and wavelength-scale dimensions that can be used for developing novel ultra-precise laser surgical tools.
Carbon nanotube based sensors for DNA detection (2009)

In this study, comparsion between the performances of carbon nanotube based random network field-effect transistors and resistors were made in DNA sensing, in order to establish which device has greater sensitivity towards biosensing applications. In resistor devices, P2A and P3 carbon nanotube solution were sprayed onto cheap and flexible polyethylene terephthalate substrate with uniform conductivity. This method is suitable for bulk production of devices compared to chemical vapour grown carbon nanotubes on field effect transistors. The effect of P2A and P3 carbon nanotube based resistors in DNA sensing were taken into account and the sensitivity of resistors towards biosening were evaluated. Label-free DNA sensing was achieved by comparing the effectiveness of intercalators used, N,N'Bis(3-propylimidazole)-1,4,5,8-naphthalene Diimide- [Os(bpy)2Cl]+ (PIND-Os) and N,N'Bis(3-propylimidazole)-1,4,5,8-naphthalene Diimide- [Ru(bpy)2Cl]+ (PIND-Ru).
Electric Wrist Rotation in Proportional-Controlled Systems (1998)

The purpose of this study was to define specifically the functional usage of electric wrist rotation (EWR), and assess its value to persons with an amputation wearing proportional-controlled prostheses. Key Points: Survey results of 32 persons with an amputation who were fitted with EWR included data on extent of usage, battery usage, specific tasks performed, and advantages and disadvantages. Conclusions: A strong majority of the wearers surveyed used the EWR effectively, and preferred the component to its absence. Surprisingly, both persons with unilateral and bilateral amputation used the EWR for active rotation and prepositioning. Use of the EWR correlated highly with the extent of usage of the prosthesis that is, those who use their prosthesis extensively also will tend to use electric wrist rotation.