gebhart/patrepeval huggingface dataset:
Developmental expression of a unique carbohydrate antigen, Tn antigen, in mouse central nervous tissues (2001)

Using an anti-Tn monoclonal antibody, the Tn antigen was detected immunohistochemically in prenatal and early postnatal central nervous tissues. On embryonic day 9 (E9), the antigen was distributed throughout the single neuroepithelial layer in the neocortex and then became more prominent in the preplate than in the ventricular zone along with formation of the preplate. Following division of the preplate and concomitant formation of the cortical plate, distinct labeling of the neocortex occurred in the marginal, subplate and intermediate zones, whereas in the cortical plate and ventricular zone were virtually not immunostained. It is notable that thalamocortical afferent fibers were also immunostained specifically on E14. After birth, the localization of the antigen became less noticeable and by 3 weeks after birth, the antigen had substantially disappeared. In the developing cerebellum, prominent labeling was also observed in the molecular layer and outskirts of the cerebellar nuclei on early postnatal days. To characterize the glycoprotein bearing the Tn antigen biochemically, immunoblot analysis was performed. The glycoprotein, most of which was extracted with a salt solution, migrated as a broad smeared band corresponding to a molecular weight of about 250 kDa on SDS-PAGE. Among the various tissues examined, this glycoprotein was only detected in the brain and its amount increased until an early postnatal stage with a peak on postnatal day 3 (P3), and then decreased gradually with age. This spatially and developmentally regulated expression of the Tn antigen suggests that this antigen plays a significant role in brain development.
Segmentation of the Optic Disc, Macula and Vascular Arch in Fundus Photographs (2007)

An automatic system is presented to find the location of the major anatomical structures in color fundus photographs; the optic disc, the macula, and the vascular arch. These structures are found by fitting a single point-distribution-model to the image, that contains points on each structure. The method can handle optic disc and macula centered images of both the left and the right eye. The system uses a cost function, which is based on a combination of both global and local cues, to find the correct position of the model points. The global terms in the cost function are based on the orientation and width of the vascular pattern in the image. The local term is derived from the image structure around the points of the model. To optimize the fit of the point-distribution-model to an image, a sophisticated combination of optimization processes is proposed which combines optimization in the parameter space of the model and in the image space, where points are moved directly. Experimental results are presented demonstrating that our specific choices for the cost function components and optimization scheme are needed to obtain good results. The system was developed and trained on a set of 500 screening images, and tested on a completely independent set of 500 screening images. In addition to this the system was also tested on a separate set of 100 pathological images. In the screening set it was able to find the vascular arch in 93.2%, the macula in 94.4%, the optic disc location in 98.4% and whether it is dealing with a left or right eye in 100% of all tested cases. For the pathological images test set, this was 77.0%, 92.0%, 94.0%, and 100% respectively.
Physics and Dosimetric Principles of SRS and SBRT (2019)

This paper reviews the radiation physics and dosimetric principles of stereotactic radiosurgery (SRS) and stereotactic body radiotherapy (SBRT). Recent radiation therapy physics and technology developments are reviewed followed by a brief description of the equipment available for SRS and SBRT. The treatment planning process and beam orientation optimization for SRS and SBRT are discussed. The dose calculation algorithms for radiation therapy are described including simple correction-based methods, advanced model-based algorithms and Monte Carlo simulations. Guidelines for SRS and SBRT treatment planning and plan evaluation are summarized including detailed dose prescription, organ dose tolerance and plan acceptance criteria. Finally, dosimetry measurements for SRS and SBRT are discussed with a focus on small field dosimetry.
Reversible Conversion Bismuth Fluoride and Oxyfluoride Nanocomposites for Li Batteries (2006)

Abstract not Available.
Impacts of video Quality of Experience on User Engagement in a live event (2014)

In order to understand the effects of QoE (Quality of Experience) on User Engagement, we measured QoE metrics on client side during Roland Garros 2013, an international tennis tournament broadcast live over the Internet. We analyze the impacts of four metrics on User Engagement: the video startup time, buffering ratio, average bitrate and content popularity. Our results demonstrate that video buffering is a critical parameter which impacts end-user satisfaction. We show also that content popularity is an important parameter of our analysis, whereas the video startup time is less significant. We highlight the relationship between the average bitrate and User Engagement in the case of popular content. Finally we confirm a correlation between metrics.
Design and simulation of artificial fish lateral line (2019)

Fishes can avoid colliding with obstacles and track baits depending on the lateral distributed sense nodes which can sense the pressure variances of the surrounding flow field. Fish often uses the lateral-line system as their only means for navigation, especially under poor visual conditions. This sensing mechanism provides a new perspective for researchers and engineers to build such a sensing system that could be applied to control and near field navigation for underwater robots and vehicles. In this article, a pressure-sensing-based is proposed, with 10 pressure sensors acting as lateral line and use the three-dimensional printer to print the fish structure and install the artificial lateral line on it. Through preliminary experiments and numerical simulation, we obtain the pressure sensor data. By comparing the experimental data with the numerical simulation data, it can be verified that the pressure variation of the pressure sensor in the numerical simulation data is consistent with that in the experimental data. The artificial lateral line provides a new sense to man-made underwater vehicles and marine robots, so that they can sense like fish.
Overview of 40 Years' Chemical Study (2009)

1,6-Dihydro-3(2H)-pyridinone, designed as a common synthon for synthesis of various natural products, was found to be easily prepared in large scale and successfully used to synthesize a variety of alkaloids such as ibogamine, quinine and tecomanine. A tricyclo[3.3.0.0(2.8)]octane was also served as a common synthon for several sesquiterpenes such as pentalenene and quadrone. Synthetic studies by using sulfinyl chirality via an intramolecular Michael addition gave the novel route to construct spiro-ketal moiety in enantiomerically pure form. By applying this method, many natural spiro-ketal compounds were asymmetrically synthesized effectively. 3-Sulfinylated 1,4-dihydropyridine, a chiral NADH model compound, reduced activated ketones such as methyl benzoylformate to give the corresponding alcohols in excellent optical yields. A kind of 3-O-substituted pyridoxal chiral model compound was useful for preparation of alpha,alpha-dialkylated alpha-amino acids by asymmetric alpha-alkylation of alpha-amino acids. 2'-O,4'-C-Bridged nucleic acid analogs, BNAs, developed as novel type of artificial nucleic acids, showed an extraordinarily high binding affinity toward single stranded RNA and double stranded DNA complements along with excellent nuclease-resistant ability. Oligonucleotides containing BNA monomer units were proved to be very useful for various biotechnologies, such as antisense and antigene methodologies.
A Query Language Solution for Fastest Flight Connections. (2004)

This paper discusses how to extend the applicability of the recursive cascade update command of the Xplain query language. This command guarantees termination because cycle detection is included, which is in favor of end user computing. The execution of this command is based on graph reduction; therefore it can only be applied to acyclic graphs. Because flights constitute cycles between airports, it seemed impossible to specify a query language solution for shortest flight connections between two arbitrary airports. However, on a time scale cyclic connections between successive flights cannot exist at all. Therefore we designed an appropriate semantic data model for feasible connections between successive flights. Using this extended data model, the cascade command still enables end users to specify recursive queries for the fastest series of flights between any pair of airports. KEY WORDS shortest path, recursive query, semantic model, transitive closure 1.
Four distinct alpha satellite subfamilies shared by human chromosomes 13, 14 and 21 (1991)

We describe the characterisation of four alpha satellite sequences which are found on a subset of the human acrocentric chromosomes. Direct sequence study, and analysis of somatic cell hybrids carrying specific human chromosomes indicate a unique 'higher-order structure' for each of the four sequences, suggesting that they belong to different subfamilies of alpha DNA. Under very high stringency of Southern hybridisation conditions, all four subfamilies were detected on chromosomes 13, 14 and 21, with 13 and 21 showing a slightly greater sequence homology in comparison to chromosome 14. None of these subfamilies were detected on chromosomes 15 and 22. In addition, we report preliminary evidence for a new alphoid subfamily that is specific for human chromosome 14. These results, together with those of earlier published work, indicate that the centromeres of the five acrocentric chromosomes are characterised by a number of clearly defined alphoid subfamilies or microdomains (with at least 5, 7, 3, 5 and 2 different ones on chromosomes 13, 14, 15, 21 and 22, respectively). These microdomains must impose a relatively stringent subregional pairing of the centromeres of two homologous chromosomes. The different alphoid subfamilies reported should serve as useful markers to allow further 'dissection' of the structure of the human centromere as well as the investigation of how the different nonhomologous chromosomes may interact in the aetiology of aberrations involving these chromosomes.
Automatic Injection of Chicken Parts with Polyphosphate (1976)

Broiler parts were treated with Kena(R) (sodium tripolyphosphate and sodium hexametaphosphate) using overnight marination or two types of automatic injection equipment and compared with control (no treatment). After treatment, parts were water cooked, battered and breaded, fried, and held refrigerated for up to 3 days or frozen for up to 9 months. One set was frozen uncoated directly after water cooking. Significant improvements in cook yield, thiobarbituric acid (TBA) values and taste panel ratings for flavor and rancidity were found in polyphosphate treated parts compared to control parts. Organoleptic and TBA differences became significant after 1–3 days refrigerated storage. Organoleptic differences became significant after 3 months uncoated frozen and 6 months battered and breaded frozen storage. No significant differences among polyphosphate treatment methods were found.
Characterization of an Acyclovir‐Resistant Herpes Simplex Virus Type 2 Strain Isolated from a Premature Neonate (2000)

Acyclovir resistance is not a recognized problem among neonates with perinatal herpes simplex virus (HSV) infection. A premature newborn with neurocutaneous HSV infection was treated for 21 days with acyclovir. Disseminated disease recurred 8 days later. A recurrent isolate was resistant to acyclovir and lacked thymidine kinase activity on the basis of a frameshift mutation in the thymidine kinase (tk) gene. Compared with the sensitive isolate obtained during primary infection, replication of the resistant isolate was reduced on primary and permanent cells and even further impaired on cells deleted for cellular tk. The resistant isolate lacked virulence in a murine model of genital infection. Acyclovir-resistant HSV-2 mutants can develop rapidly in neonatal infection and cause clinically significant disease, despite decreased replication in vitro and attenuated virulence in an animal model.
Genes for resistance to plant viruses (1986)

Although many cases are known of plant genes conferring resistance to particular viruses, in no case is the mechanism of gene action fully understood. The complementary phenomenon of virulence in the virus, whereby an altered form may overcome a particular resistance gene, also awaits explanation. This article reviews current knowledge of genetic aspects of control of resistance and virulence, and draws attention to common features of mechanisms in different species. The evidence for polygenic resistance and “modifier” genes is critically assessed, and possible overlap between resistance and mechanisms of nonhost immunity examined. Theoretical models of resistance gene action and of the interaction between resistance and virulence genes are described and developed. The extent to which known mechanisms fit these models is tested. Current and future possibilities for exploiting resistance genes in crop protection using techniques of cell and genetic manipulation are discussed.
Compact Surface-mount UWB Monopole Antenna for Mobile Applications (2006)

In this paper, a novel surface-mount ultra-wideband (UWB) monopole antenna with a compact size of only 12:5 £ 9 £ 1:5mm 3 is obtained by folding a metal-plate onto a low-proflle rectangular-box foam base. By carefully adding a matching slit on the upper side of metal-plate, the antenna can achieve good impedance matching over a very wide bandwidth of about 7.97GHz (3.03{11.0GHz, deflned by 2:1 VSWR). Experimental results of a constructed prototype of the proposed antenna are presented.
Improvements in BBN's HMM-Based Offline Arabic Handwriting Recognition System (2009)

Offline handwriting recognition of free-flowing Arabic text is a challenging task due to the plethora of factors that contribute to the variability in the data. In this paper, we address some of these sources of variability, and present experimental results on a large corpus of handwritten documents. Specific techniques such as the application of context-dependent Hidden Markov Models (HMMs) for the cursive Arabic script, unsupervised adaptation to account for the stylistic variations across scribes, and image pre-processing to remove ruled-lines are explored. In particular, we proposed a novel integration of structural features in the HMM framework which exclusively results in a 9% relative improvement in performance. Overall, we demonstrate a relative reduction of 17% in word error rate over our baseline Arabic handwriting recognition system.
Fully Microfabricated and Integrated SU-8-Based Capillary Electrophoresis-Electrospray Ionization Microchips for Mass Spectrometry (2007)

We present a fully microfabricated and monolithically integrated capillary electrophoresis (CE)-electrospray ionization (ESI) chip for coupling with high-throughput mass spectrometric (MS) analysis. The chips are fabricated fully of a negative photoresist SU-8 by a standard lithographic process which enables straightforward batch fabrication of multiple chips with precisely controlled dimensions and, thus, reproducible analytical performance from chip to chip. As the coaxial sheath flow interface is patterned as an integral part of the SU-8 chip, the fluidic design is dead-volume-free. No significant peak broadening occurs so that very narrow peak widths (down to 2-3 s) are obtained. The sheath flow interface also enables comprehensive optimization of both the CE and the ESI conditions separately so that the same chip design is adaptable to diverse analytical conditions. Plate numbers of the order of 105 m-1 and good resolution are routinely reached for small molecules and peptides within a 2 cm separation length and a typical cycle time of only 30-90 s per sample. In addition, a limit of detection of 100 nM corresponding to a total amount of only 4.5 amol (per injection volume of 45 pL) and excellent quantitative linearity (R2 = 0.9999; 100 nM to 100 microM) were obtained in small-molecule analysis using verapamil as a test compound. The quantitative repeatability was proven good (8.5-21.4% relative standard deviation, peak area) also for the other drug substances and peptides tested.
Diffusion Basis Functions Decomposition for Estimating White Matter Intravoxel Fiber Geometry (2007)

In this paper, we present a new formulation for recovering the fiber tract geometry within a voxel from diffusion weighted magnetic resonance imaging (MRI) data, in the presence of single or multiple neuronal fibers. To this end, we define a discrete set of diffusion basis functions. The intravoxel information is recovered at voxels containing fiber crossings or bifurcations via the use of a linear combination of the above mentioned basis functions. Then, the parametric representation of the intravoxel fiber geometry is a discrete mixture of Gaussians. Our synthetic experiments depict several advantages by using this discrete schema: the approach uses a small number of diffusion weighted images (23) and relatively small b values (1250 s/mm2), i.e., the intravoxel information can be inferred at a fraction of the acquisition time required for datasets involving a large number of diffusion gradient orientations. Moreover our method is robust in the presence of more than two fibers within a voxel, improving the state-of-the-art of such parametric models. We present two algorithmic solutions to our formulation: by solving a linear program or by minimizing a quadratic cost function (both with non-negativity constraints). Such minimizations are efficiently achieved with standard iterative deterministic algorithms. Finally, we present results of applying the algorithms to synthetic as well as real data.
Optimal actuator placement on an active reflector using a modified simulated annealing technique (1991)

The development of a lightweight actuation system for maintaining the surface accuracy of a composite honeycomb panel using piezoelectric actuators is discussed. A modified simulated annealing technique is used to optimize the problem with both combinatorial and continuous criteria and with inequality constraints. Near optimal solutions for the location of the actuators, using combinatorial optimization, and for the required actuator forces, employing continuous optimization, are sought by means of the modified simulated annealing technique. The actuator locations are determined by first seeking a near optimum solution using the modified simulated annealing technique. The final actuator configuration consists of an arrangement wherein the piezoelectric actuators are placed along six radial lines. Numerical results showing the achievable surface correction by means of this configuration are presented.
Inhibition of CFTR channels by a peptide toxin of scorpion venom (2004)

Peptide toxins have been valuable probes in efforts to identify amino acid residues that line the permeation pathway of cation-selective channels. However, no peptide toxins have been identified that interact with known anion-selective channels such as the cystic fibrosis transmembrane conductance regulator (CFTR). CFTR channels are expressed in epithelial cells and are associated with several genetic disorders, including cystic fibrosis and polycystic kidney disease. Several organic inhibitors have been used to investigate the structure of the Cl- permeation pathway in CFTR. However, investigations of the wider cytoplasmic vestibule have been hindered by the lack of a high-affinity blocker that interacts with residues in this area. In this study we show that venom of the scorpion Leiurus quinquestriatus hebraeus reversibly inhibits CFTR, in a voltage-independent manner, by decreasing single-channel mean burst duration and open probability only when applied to the cytoplasmic surface of phosphorylated channels. Venom was able to decrease burst duration and open probability even when CFTR channels were locked open by treatment with either vanadate or adenosine 5'-(beta,gamma-imido)triphosphate, and block was strengthened on reduction of extracellular Cl- concentration, suggesting inhibition by a pore-block mechanism. Venom had no effect on ATP-dependent macroscopic opening rate in channels studied by inside-out macropatches. Interestingly, the inhibitory activity was abolished by proteinase treatment. We conclude that a peptide toxin contained in the scorpion venom inhibits CFTR channels by a pore-block mechanism; these experiments provide the first step toward isolation of the active component, which would be highly valuable as a probe for CFTR structure and function.
Helicase–Primase Inhibitor Pritelivir for HSV-2 Infection (2014)

Pritelivir reduced the rates of genital HSV shedding and days with lesions in a dose-dependent manner in otherwise healthy men and women with genital herpes. (Funded by AiCuris; ClinicalTrials.gov number, NCT01047540.).
Safe and efficient hybrid memory management for Java (2015)

Java uses automatic memory management, usually implemented as a garbage-collected heap. That lifts the burden of manually allocating and deallocating memory, but it can incur significant runtime overhead and increase the memory footprint of applications. We propose a hybrid memory management scheme that utilizes region-based memory management to deallocate objects automatically on region exits. Static program analysis detects allocation sites that are safe for region allocation, i.e., the static analysis proves that the objects allocated at such a site are not reachable after the region exit. A regular garbage-collected heap is used for objects that are not region allocatable. The region allocation exploits the temporal locality of object allocation. Our analysis uses coarse-grain source code annotations to disambiguate objects with non-overlapping lifetimes, and maps them to different memory scopes. Region-allocated memory does not require garbage collection as the regions are simply deallocated when they go out of scope. The region allocation technique is backed by a garbage collector that manages memory that is not region allocated. We provide a detailed description of the analysis, provide experimental results showing that as much as 78% of the memory is region allocatable and discuss how our hybrid memory management system can be implemented efficiently with respect to both space and time.
Design of optimal excitation signals (1990)

This paper studies the problem of designing optimal excitations to measure linear systems. The measurement accuracy is to be maximum for a specified peak value of the excitation signal. The study is limited to SISO systems, but the results can be generalized to MIMO signals without fundamental problems. Optimization can be performed either in the time domain or in the frequency domain. A first approach maximizes the power of the excitation signal by reducing the crest factor of a signal with a specified power spectrum. The frequency-domain approach optimizes the power spectrum of the excitation signal resulting in a maximal information matrix for a specified input power. The general solution consists of the combined problem of designing a signal resulting in a maximum information matrix for a specified peak value of the excitation. The authors study both problems separately and then propose a suboptimal solution for the general problem.