gebhart/patrepeval huggingface dataset:
Antibodies to plasmodium falciparum glutamic acid rich protein (PfGARP) inhibit parasite growth by arresting trophozoite development (2016)

Background: Malaria affects almost one-half of the world's population and causes more than 600,000 deaths annually. Young children in malaria endemic areas of Africa have the highest mortality rate because of their immature immune systems. In previous vaccine discovery efforts, we developed a differential screening method using plasma from children who were resistant or susceptible to falciparum malaria. Using this approach, we discovered PfSEA-1. Antibodies to PfSEA-1 predict resistance to severe disease in two yr old children, block schizont egress from infected RBC in vitro, and vaccination with rPbSEA-1A protects mice from P. berghei ANKA challenge (Raj et. al Science 2014). Methods & Materials: We have now adapted our differential screening method to field parasite-derived phage display libraries. In differential bio-panning assays, PfGARP (aa 410-673) was recognized by plasma pooled from resistant (n=11) but not susceptible (n=14) children participating in our birth cohort in Muheza, Tanzania. To further characterize PfGARP, we generated mouse antibodies against this immuno-relevant, highly invariant region (PfGARP-A) and performed growth inhibition (GIA) and immunolocalization studies. For GIA, 3D7 parasites were synchronized to the ring stage and plated at 0.3-0.4% parasitemia in the presence of anti-PfGARP-A or pre-immune sera (1:10 dilution). Parasites were cultured for 48 hrs and ring and early trohozoite stage parasites were enumerated. Schematic of phase display technique Results: Anti-PfGARP-A inhibited parasite growth by 99% compared to controls (P < 0.001). In confocal studies, PfGARP localized to the RBC membrane in trophozoite and early schizont infected RBCs, but not to other parasite stages or uninfected RBC. To determine the mechanism of growth inhibition we performed trophozoite arrest assays (TAA) using anti-PfGARP-A. For TAA, 3D7 parasites were synchronized to the ring stage and plated at 5% parasitemia in the presence of anti-PfGARP-A or pre-immune mouse sera (1:10 dilution). Parasites were cultured for 36 hrs and trophozoite stage parasites were enumerated. Anti-PfGARP-A arrested trophozoite progression by 99% compared to controls (P < 0.001) Localization of PfGARP Growth Inhibition Assay Conclusion: These data support Pf-GARP as a novel vaccine candidate for pediatric falciparum malaria. By blocking trophozoite development, PfGARP may synergize with vaccines targeting hepatocyte and red cell invasion and schizont egress.
Hybrid Metasurfaces : From Optoelectronics to Nonlinear Optics. (2020)

Abstract not provided.
Apoptosis of ventricular and atrial myocytes from pacing-induced canine heart failure (2001)

We have identified components of the signalling pathways along which apoptosis proceeds following the induction of heart failure in dogs. Apoptosis was also detected in the atria raising the possibility that, like human dilated cardiomyopathy, the molecular changes are global.
Grow with the Flow: When Morphogenesis Meets Microfluidics (2019)

Developmental biology has advanced the understanding of the intricate and dynamic processes involved in the formation of an organism from a single cell. However, many gaps remain in the knowledge of embryonic development, especially regarding tissue morphogenesis. A possible approach to mimic such phenomena uses pluripotent stem cells in in vitro morphogenetic models. Herein, these systems are summarized with emphasis on the ability to better manipulate and control cellular interfaces with either liquid or solid materials using microengineered tools, which is critical for attaining deeper insights into pattern formation and stem cell differentiation during organogenesis. The role of conventional and customized cell-culture systems in supporting important advances in the field of morphogenesis is discussed, and the fascinating role that material sciences and microengineering currently play and are expected to play in the future is highlighted. In conclusion, it is proffered that continued microfluidics innovations when applied to morphogenesis promise to provide important insights to advance many multidisciplinary fields, including regenerative medicine.
Scalable Bandwidth-Tunable Micro-Ring Filter Based on Multi-Channel-Spectrum Combination (2018)

We propose and experimentally demonstrate a scalable bandwidth-tunable bandpass filter on silicon. Its spectrum is combined by that of four channels and each channel is formed by two cascaded micro-ring resonators (MRRs). By tuning the center wavelength spacing of the eight MRRs and the phase shifts of four channels, a wide bandwidth tuning range from 37.5 GHz to 227.5 GHz can be achieved with a shape factor between 0.2 and 0.73 and an in-band ripple less than 1 dB. By comparing with the performance of three-channel and two-channel structures, we can draw the conclusion that inducing more channels can effectively improve the bandwidth tunability. The filter also has a wide free spectral range (about 1.2 THz) and small footprint (0.12 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ).
Calcific aortic valve disease: Is it another face of atherosclerosis? (2015)

Calcific aortic valve disease (CAVD) is the most common valvular heart disease in the elderly. As life expectancy increases, prevalence of CAVD is expected to rise. CAVD is characterized by progressive dystrophic calcification of aortic cusps. In the initial stages, the pathogenesis is similar to atherosclerosis, characterized by basement membrane disruption, inflammation, cell infiltration, lipid deposition, and calcification. Presence of osteopontin in calcified aortic valves suggests pathological calcification and bone formation in these calcified valves. Historical, experimental, genetic, and clinical evidences suggest that CAVD and atherosclerosis share the same pathological sequences with common risk factors. Understanding the two faces of atherosclerosis, the vascular and valvular, will help us to prevent progression of aortic sclerosis to aortic stenosis, by controlling modifiable risk factors and by initiating statin therapy in them. However, the knowledge about these preventive measures and drugs is scanty. In this review article, an attempt is made to unfurl the relation between atherosclerosis and CAVD.
Detailed Images of Asteroid 25143 Itokawa from Hayabusa (2006)

Rendezvous of the Japanese spacecraft Hayabusa with the near-Earth asteroid 25143 Itokawa took place during the interval September through November 2005. The onboard camera imaged the solid surface of this tiny asteroid (535 meters by 294 meters by 209 meters) with a spatial resolution of 70 centimeters per pixel, revealing diverse surface morphologies. Unlike previously explored asteroids, the surface of Itokawa reveals both rough and smooth terrains. Craters generally show unclear morphologies. Numerous boulders on Itokawa's surface suggest a rubble-pile structure.
AIM: Adaptive integral method for solving large‐scale electromagnetic scattering and radiation problems (1996)

We describe basic elements and implementation of the adaptive integral method (AIM): a fast iterative integral‐equation solver applicable to large‐scale electromagnetic scattering and radiation problems. As compared to the conventional method of moments, the AIM solver provides (for typical geometries) significantly reduced storage and solution time already for problems involving 2,000 unknowns. This reduction is achieved through a compression of the impedance matrix, split into near‐field and far‐field components. The near‐field component is computed by using the Galerkin method employing a set of N arbitrary basis functions. The far‐field matrix elements are calculated by using the Galerkin method as well, with a set of N auxiliary basis functions. The auxiliary basis functions are constructed as superpositions of pointlike current elements located on uniformly spaced Cartesian grid nodes and are required to reproduce, with a prescribed accuracy, the far field generated by the original basis functions. Algebraically, the resulting near‐field component of the impedance matrix is sparse, while its far‐field component is a product of two sparse matrices and a three‐level Toeplitz matrix. These Toeplitz properties are exploited, by using discrete fast Fourier transforms, to carry out matrix‐vector multiplications with O ( N 3/2 log N ) and O ( N log N ) serial complexities for surface and volumetric scattering problems, respectively. The corresponding storage requirements are O ( N 3/2 ) and O ( N ). In the domain‐decomposed parallelized implementation of the solver, with the number Np of processors equal to the number of domains, the total memory required in surface problems is reduced to O ( N 3/2 / N P 1/2 ). The speedup factor in matrix‐vector multiplication is equal to the number of processors N p . We present a detailed analysis of the errors introduced by the use of the auxiliary basis functions in computing far‐field impedance matrix elements. We also discuss the algorithm complexity and some aspects of its implementation and applications.
Force-guided robotic assembly based on perturbation/correlation (2002)

Summary form only given as follows. Force guided robot control is a control scheme based on the interpretation of measured force acting on the robot end effector. In the traditional force-guided control schemes, the contact force measured by a force sensor is directly fed back to a feedback controller to generate a motion correction signal. In this paper, instead of simply measuring contact forces, we take positive actions by giving perturbation to the end effector and observing the reaction forces to the perturbation in order to obtain much richer and more reliable information. By taking the correlation between the input perturbation and the resultant reaction forces, we can determine the gradient of the force profile and guide the part correctly. This algorithm is applied to a pipe insertion task, in which the insertion force is minimized during the insertion. Based on the process model and stability analysis using the Popov stability criterion, conditions for stable, successful insertion despite nonlinearities and uncertainties in the environment are obtained. The theoretical results are verified using the experimental data. To generate high frequency perturbation, a vibratory end effector using piezoelectric actuators is designed and built.
Temporal Analysis of Language through Neural Language Models (2014)

We provide a method for automatically detecting change in language across time through a chronologically trained neural language model. We train the model on the Google Books Ngram corpus to obtain word vector representations specific to each year, and identify words that have changed significantly from 1900 to 2009. The model identifies words such as "cell" and "gay" as having changed during that time period. The model simultaneously identifies the specific years during which such words underwent change.
Using Deep Learning for Arabic Writer Identification (2020)

Identification of persons is mainly through the physiological characteristics like fingerprints, face, iris, retina, and hand geometry and the behavioral characteristics like a voice, signature, and handwriting. Identifying the author of a handwritten document has been an active field of research over the past few years and it used in many applications as in biometrics, forensics and historical document analysis. This research presents the study and implementation of the stages of writer identification, starting from data acquisition, and then augmente the data through programming an algorithm that generate a large number of texts from the set of texts available within the database, finally building a convolutional Neural Network (CNN)) Which is useful for extracting features information and then classification the data, therefore, the features are not needed to pre-define. The experiments in this study were conducted on images of Arabic handwritten documents from ICFHR2012 dataset of 202 writer, and each writer have 3 text. The proposed method achieved a classification accuracy of 98.2426%.
Classification of faults in synchronous sequential circuits (1993)

Undetectable and redundant faults in synchronous sequential circuits are analyzed. A distinction is drawn between undetectable faults and faults that are never manifested as output errors. The latter are classified as redundant. It is shown that there are faults for which a test sequence does not exist; however, under certain initial conditions (or initial states) of the circuit, faulty behavior may be observed. Such faults are called partially detectable faults. A partially detectable fault is undetectable, but is not redundant, as it affects circuit operation under some conditions. The author observes that the notion of redundancy cannot be separated from the mode of operation of the circuit. Two modes of operation are considered, representative of common modes, called the synchronization mode and the free mode. Accordingly, the identification of redundant faults calls for different test generation strategies. Two test strategies to generate tests for detectable faults and partial tests for partially detectable faults are defined, called the restricted test strategy and the unrestricted test strategy.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Surgical Treatment of Gastric Gastrointestinal Stromal Tumor (2013)

Gastrointestinal stromal tumor is the most common mesenchymal tumor in the gastrointestinal tract and is most frequently developed in the stomach in the form of submucosal tumor. The incidence of gastric gastrointestinal stromal tumor is estimated to be as high as 25% of the population when all small and asymptomatic tumors are included. Because gastric gastrointestinal stromal tumor is not completely distinguished from other submucosal tumors, a surgical excisional biopsy is recommended for tumors >2 cm. The surgical principles of gastrointestinal stromal tumor are composed of an R0 resection with a normal mucosa margin, no systemic lymph node dissection, and avoidance of perforation, which results in peritoneal seeding even in cases with otherwise low risk profiles. Laparoscopic surgery has been indicated for gastrointestinal stromal tumors <5 cm, and the indication for laparoscopic surgery is expanded to larger tumors if the above mentioned surgical principles can be maintained. A simple exogastric resection and various transgastric resection techniques are used for gastrointestinal stromal tumors in favorable locations (the fundus, body, greater curvature side). For a lesion at the gastroesophageal junction in the posterior wall of the stomach, enucleation techniques have been tried preserve the organ's function. Those methods have a theoretical risk of seeding a ruptured tumor, but this risk has not been evaluated by well-designed clinical trials. While some clinical trials are still on-going, neoadjuvant imatinib is suggested when marginally unresectable or multiorgan resection is anticipated to reduce the extent of surgery and the chance of incomplete resection, rupture or bleeding.
Effective nebulization of interferon-γ using a novel vibrating mesh (2019)

It is possible to nebulize IFN-γ effectively with vibrating mesh nebulizer devices without compromising its stability. The PDAP allows for generation of IFN-γ aerosols with improved aerodynamic properties thereby increasing its potential efficiency for lower respiratory tract deposition over current technology, whilst maintaining the integrity and bioactivity of IFN-γ. This delivery modality therefore offers a rational means of facilitating the clinical translation of inhaled IFN-γ.
A 10b, 0.7ps resolution coarse-fine time-to-digital converter in 65nm CMOS using a time residue amplifier (2015)

This paper presents a TA based coarse-fine TDC with high resolution. The new design contains a half-pass judger to measure the relative position of the stop edge in the subrange of the delayed sequence. The extra operation helps to limit the range of time residue sent to the fine stage by one half. With the limitation, TA can achieve a high gain, ensuring the two-stage TDC with a high resolution. Besides, a new MUX structure is designed, and the signal ports are well arranged to improve the reaction speed and to reduce the power consumption. Experiment results show that resolution of the proposed circuit is 0.7ps, and the measurement range can reach 1ns. The DNL and INL are measured as 0.5LSB and 2LSB, respectively. Better linearity can be achieved by using INL lookup table and adding compensated blocks.
Functional Specialization and Evolution of Leader Proteinases in the Family <i>Closteroviridae</i> (2001)

Members of the Closteroviridae and Potyviridae families of the plant positive-strand RNA viruses encode one or two papain-like leader proteinases. In addition to a C-terminal proteolytic domain, each of these proteinases possesses a nonproteolytic N-terminal domain. We compared functions of the several leader proteinases using a gene swapping approach. The leader proteinase (L-Pro) of Beet yellows virus (BYV; a closterovirus) was replaced with L1 or L2 proteinases of Citrus tristeza virus (CTV; another closterovirus), P-Pro proteinase of Lettuce infectious yellows virus (LIYV; a crinivirus), and HC-Pro proteinase of Tobacco etch virus (a potyvirus). Each foreign proteinase efficiently processed the chimeric BYV polyprotein in vitro. However, only L1 and P-Pro, not L2 and HC-Pro, were able to rescue the amplification of the chimeric BYV variants. The combined expression of L1 and L2 resulted in an increased RNA accumulation compared to that of the parental BYV. Remarkably, this L1-L2 chimera exhibited reduced invasiveness and inability to move from cell to cell. Similar analyses of the BYV hybrids, in which only the papain-like domain of L-Pro was replaced with those derived from L1, L2, P-Pro, and HC-Pro, also revealed functional specialization of these domains. In subcellular-localization experiments, distinct patterns were observed for the leader proteinases of BYV, CTV, and LIYV. Taken together, these results demonstrated that, in addition to a common proteolytic activity, the leader proteinases of closteroviruses possess specialized functions in virus RNA amplification, virus invasion, and cell-to-cell movement. The phylogenetic analysis suggested that functionally distinct L1 and L2 of CTV originated by a gene duplication event.
Current Status of Fibroblast Growth Factor Receptors Targeted Therapies in Breast Cancer (2018)

Breast cancer (BC) is the most common malignancy and second only to lung cancer in terms of mortality in women. Despite the incredible progress made in this field, the metastatic breast cancer leaves a poor prognosis. In an era of personalized medicine, there is an urgent need for a better knowledge of the biology leading to the disease, which can lead to the design of always more accurate drugs against patients&rsquo; specific molecular aberrations. Among one of the actionable targets is the Fibroblast Growth Factor Receptor (FGFR) pathway, triggered by specific ligands. The FGFRs/FGFs axis offers interesting molecular targets to be pursued in clinical development. This mini-review will focus on the current knowledge of the FGFRs mutations leading to tumour formation and summarizes the state-of-the-art of therapeutic strategies for targeted treatments against the FGFRs/FGFs axis in the context of BC.
Vasoactive intestinal polypeptide and the ocular innervation. (1986)

The indirect immunofluorescence technique with antisera to vasoactive intestinal polypeptide (VIP) stains peripheral nerve fibers in both the anterior segment and the posterior segment of rat, guinea pig, cat, and rhesus monkey eyes. While immunoreactive corneal nerves are lacking, all four species have a prominent innervation of the superficial limbal blood vessels. The aqueous humor outflow apparatus of the rat, guinea pig, and cat, but not the monkey, contain VIP-like immunoreactive nerves. All four animals have immunoreactive iris nerve fibers, tending either to surround large blood vessels or to lie as free stromal nerves. Only in the cat are immunoreactive nerve fibers seen within the iris muscles. A modest number of VIP-like immunoreactive nerves are present in the ciliary body of all four animals; immunoreactive nerve fibers within the ciliary processes occur only in the rat and guinea pig. VIP-like immunoreactive nerves are found in the choroid of all four animals. An association of immunoreactive nerve fibers to uveal melanocytes also is apparent. The present findings expand several prior immunohistochemical studies of mammalian eyes in which the VIP-like immunoreactive nerves to the choroid was emphasized.
Pharmacological treatment for uterine leiomyosarcomas (2014)

DOX alone, gemcitabine alone, DOX + dacarbazine and gemcitabine + docetaxel may be treatment options for first-line and second-line therapies. However, the clinical benefit of the combination chemotherapy versus single-agent chemotherapy is still debated. Trabectedin is a promising agent for recurrent uterine LMS, able to obtain a prolonged disease control, with 3-month and 6-month progression-free survival rates exceeding 50 and 30%, respectively, and with sometimes unexpectedly durable responses. Pazopanib is the only approved targeted therapy. Hormone therapy with aromatase inhibitors may be a therapeutic option in heavily treated patients with slowly progressive, steroid receptor-positive tumors. Whenever possible, women with recurrent uterine LMS should be encouraged to enter well-designed clinical trials aimed to detect novel active agents.
A survey on time series data mining (2017)

In this paper, an overview on existing data mining techniques for time series modeling and analysis will be provided. Classification of available literature on time series data mining shows that the main research orientations can be divided into three subfields: Dimensionality Reduction (Time Series Representation), Similarity Measures and Data Mining Tasks.
A tRNA gene mapping within the chloroplast rDNA cluster is differentially expressed during the development of<i>Daucus carota</i> (1994)

In vivo analysis of expression of the chloroplast rDNA cluster during somatic embryogenesis of Daucus carota (D.carota) was performed by Northern-blot analysis with different DNA probes, spanning both the 16S rRNA gene, the 16S-23S rRNA spacer, which contains the two mosaic tRNA genes tRNA(Ile) and tRNA(Ala), and the region upstream of the 16S rRNA gene, where a tRNA(Val) maps. We show that expression both of the spacer tRNAs tRNA(Ile) and tRNA(Ala) is not significantly regulated during development whereas the amount of the transcript corresponding to tRNA(Val) is not detectable during early embryonic stages and progressively accumulates during late phases. Multiple transcription start sites have been identified upstream of the tRNA(Val) gene by S1 mapping analysis, which are activated late during the embryogenesis. These data indicate that developmental control mechanisms act on plastid gene expression during embryogenesis in carrot.