gebhart/patrepeval huggingface dataset:
Transferable Visual Words: Exploiting the Semantics of Anatomical Patterns for Self-Supervised Learning (2021)

This paper introduces a new concept called "transferable visual words" (TransVW), aiming to achieve annotation efficiency for deep learning in medical image analysis. Medical imaging-focusing on particular parts of the body for defined clinical purposes-generates images of great similarity in anatomy across patients and yields sophisticated anatomical patterns across images, which are associated with rich semantics about human anatomy and which are natural visual words. We show that these visual words can be automatically harvested according to anatomical consistency via self-discovery, and that the self-discovered visual words can serve as strong yet free supervision signals for deep models to learn semantics-enriched generic image representation via self-supervision (self-classification and self-restoration). Our extensive experiments demonstrate the annotation efficiency of TransVW by offering higher performance and faster convergence with reduced annotation cost in several applications. Our TransVW has several important advantages, including (1) TransVW is a fully autodidactic scheme, which exploits the semantics of visual words for self-supervised learning, requiring no expert annotation; (2) visual word learning is an add-on strategy, which complements existing self-supervised methods, boosting their performance; and (3) the learned image representation is semantics-enriched models, which have proven to be more robust and generalizable, saving annotation efforts for a variety of applications through transfer learning. Our code, pre-trained models, and curated visual words are available at https://github.com/JLiangLab/TransVW.
Initialization of iterative refinement clustering algorithms (1998)

Iterative refinement clustering algorithms (e.g. K-Means, EM) converge to one of numerous local minima. It is known that they are especially sensitive to initial conditions. We present a procedure for computing a refined starting condition from a given initial one that is based on an efficient technique for estimating the modes of a distribution. The refined initial starting condition leads to convergence to &quot;better&quot; local minima. The procedure is applicable to a wide class of clustering algorithms for both discrete and continuous data. We demonstrate the application of this method to the Expectation Maximization (EM) clustering algorithm and show that refined initial points indeed lead to improved solutions. Refinement run time is considerably lower than the time required to cluster the full database. The method is scalable and can be coupled with a scalable clustering algorithm to address the large-scale clustering in data mining. 1 Background Clustering has been formulated in var...
On-chip sensor for light direction detection (2013)

We present an on-chip optical sensor capable of detecting the direction of incident light. No off-chip optical or mechanical components or modifications—for example, baffles, slit structures, mirrors, etc.—are needed. The sensor was implemented in a standard 0.5 μm complementary metal-oxide semiconductor process. A pair of on-chip photodiodes separated by a metal “wall” (created by stacking all metal layers, contacts, and vias available in the process) is used to detect the direction of the incident light. This metal stack wall creates on-chip shadowing to facilitate detection so that the two photodiodes produce different amounts of photocurrent. A model for this device is presented. The analysis indicts that the ratio of the difference of these two currents to the larger of the two currents has a linear relationship with the angle of the incident light. Moreover, we also demonstrate this ratio is almost independent of the incident light intensity. Test results verify these two conclusions and show good sensitivity to light direction and immunity to light intensity. An accuracy of 1.6 deg over a 100 deg range is achieved by the linear relationship.
From nonpeptide toward noncarbon protease inhibitors: Metallacarboranes as specific and potent inhibitors of HIV protease (2005)

HIV protease (PR) represents a prime target for rational drug design, and protease inhibitors (PI) are powerful antiviral drugs. Most of the current PIs are pseudopeptide compounds with limited bioavailability and stability, and their use is compromised by high costs, side effects, and development of resistant strains. In our search for novel PI structures, we have identified a group of inorganic compounds, icosahedral metallacarboranes, as candidates for a novel class of nonpeptidic PIs. Here, we report the potent, specific, and selective competitive inhibition of HIV PR by substituted metallacarboranes. The most active compound, sodium hydrogen butylimino bis-8,8-[5-(3-oxa-pentoxy)-3-cobalt bis(1,2-dicarbollide)]di-ate, exhibited a K(i) value of 2.2 nM and a submicromolar EC(50) in antiviral tests, showed no toxicity in tissue culture, weakly inhibited human cathepsin D and pepsin, and was inactive against trypsin, papain, and amylase. The structure of the parent cobalt bis(1,2-dicarbollide) in complex with HIV PR was determined at 2.15 A resolution by protein crystallography and represents the first carborane-protein complex structure determined. It shows the following mode of PR inhibition: two molecules of the parent compound bind to the hydrophobic pockets in the flap-proximal region of the S3 and S3' subsites of PR. We suggest, therefore, that these compounds block flap closure in addition to filling the corresponding binding pockets as conventional PIs. This type of binding and inhibition, chemical and biological stability, low toxicity, and the possibility to introduce various modifications make boron clusters attractive pharmacophores for potent and specific enzyme inhibition.
Detection theory for accurate and non-invasive skin cancer diagnosis using dynamic thermal imaging (2017)

Skin cancer is the most common cancer in the United States with over 3.5M annual cases. Presently, visual inspection by a dermatologist has good sensitivity (> 90%) but poor specificity (< 10%), especially for melanoma, which leads to a high number of unnecessary biopsies. Here we use dynamic thermal imaging (DTI) to demonstrate a rapid, accurate and non-invasive imaging system for detection of skin cancer. In DTI, the lesion is cooled down and the thermal recovery is recorded using infrared imaging. The thermal recovery curves of the suspected lesions are then utilized in the context of continuous-time detection theory in order to define an optimal statistical decision rule such that the sensitivity of the algorithm is guaranteed to be at a maximum for every prescribed false-alarm probability. The proposed methodology was tested in a pilot study including 140 human subjects demonstrating a sensitivity in excess of 99% for a prescribed specificity in excess of 99% for detection of skin cancer. To the best of our knowledge, this is the highest reported accuracy for any non-invasive skin cancer diagnosis method.
Development of a Bead-Based Multiplex Genotyping Method for Diagnostic Characterization of HPV Infection (2012)

The accurate genotyping of human papillomavirus (HPV) is clinically important because the oncogenic potential of HPV is dependent on specific genotypes. Here, we described the development of a bead-based multiplex HPV genotyping (MPG) method which is able to detect 20 types of HPV (15 high-risk HPV types 16, 18, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68 and 5 low-risk HPV types 6, 11, 40, 55, 70) and evaluated its accuracy with sequencing. A total of 890 clinical samples were studied. Among these samples, 484 were HPV positive and 406 were HPV negative by consensus primer (PGMY09/11) directed PCR. The genotyping of 484 HPV positive samples was carried out by the bead-based MPG method. The accuracy was 93.5% (95% CI, 91.0-96.0), 80.1% (95% CI, 72.3-87.9) for single and multiple infections, respectively, while a complete type mismatch was observed only in one sample. The MPG method indiscriminately detected dysplasia of several cytological grades including 71.8% (95% CI, 61.5-82.3) of ASCUS (atypical squamous cells of undetermined significance) and more specific for high grade lesions. For women with HSIL (high grade squamous intraepithelial lesion) and SCC diagnosis, 32 women showed a PPV (positive predictive value) of 77.3% (95% CI, 64.8-89.8). Among women >40 years of age, 22 women with histological cervical cancer lesions showed a PPV of 88% (95% CI, 75.3-100). Of the highest risk HPV types including HPV-16, 18 and 31 positive women of the same age groups, 34 women with histological cervical cancer lesions showed a PPV of 77.3% (95% CI, 65.0-89.6). Taken together, the bead-based MPG method could successfully detect high-grade lesions and high-risk HPV types with a high degree of accuracy in clinical samples.
Amine-Based Ionic Liquid for CO<sub>2</sub> Capture and Electrochemical or Thermal Regeneration (2020)

An ethylenediamine-functionalized ionic liquid (IL) was synthesized for CO2 capture from industrial gases, with good CO2 absorption capacity of around 0.95 mmol (42 mg) of CO2/g of IL at 35 °C. In contrast to conventional gas desorption via utilization of an energy intensive thermal swing, CO2 was released on competitive complexation of the amines with cupric ions introduced to the ionic liquid electrolyte by the oxidation of a copper electrode. The electrolyte was regenerated by electrodeposition of cupric ions at the cathode. This work emphasizes the importance of electrodeposition from metal-containing ILs and the potential for new recyclable catalysts.
3D Echo Planar Time-resolved Imaging (3D-EPTI) for ultrafast multi-parametric quantitative MRI (2021)

Abstract Multi-parametric quantitative MRI has shown great potential to improve the sensitivity and specificity of clinical diagnosis and to enhance our understanding of complex brain processes, but suffers from long scan time especially at high spatial resolution. To address this long-standing challenge, we introduce a novel approach, termed 3D Echo Planar Time-resolved Imaging (3D-EPTI), which significantly increases the acceleration capacity of MRI sampling, and provides high acquisition efficiency for multi-parametric MRI. This is achieved by exploiting the spatiotemporal correlation of MRI data at multiple timescales through new encoding strategies within and between efficient continuous readouts. Specifically, an optimized spatiotemporal CAIPI encoding within the readouts combined with a radial-block sampling strategy across the readouts enables an acceleration rate of 800 folds in the k-t space. A subspace reconstruction was employed to resolve thousands of artifact-free high-quality multi-contrast images spaced at a time interval of ~1 ms. We have demonstrated the ability of 3D-EPTI to provide robust and repeatable whole-brain simultaneous T 1 , T 2 , T 2 *, PD and B 1 + mapping at high isotropic resolution within minutes (e.g., 1-mm isotropic resolution in 3 minutes), and to enable submillimeter multi-parametric imaging to study detailed brain structures. Highlights Ultra-fast acquisition for 3D multi-parametric quantitative MRI. Simultaneous T 1 T 2 T 2 * PD and B 1 + mapping. 3-minute scan at 1-mm isotropic resolution with whole-brain coverage. Multi-parametric mapping at 700-μm isotropic resolution in 10 minutes. Repeatable quantification and cortical-depth analysis.
WDM up-conversion employing frequency quadrupling in optical modulator (2009)

This work presents an optical up-conversion system with frequency quadrupling for wavelength-division-multiplexing (WDM) communication systems using a dual-parallel Mach-Zehnder modulator without optical filtering. Four-channel 1.25-Gb/s wired fiber-to-the-x (FTTx) and wireless radio-over-fiber (RoF) signals are generated and transmitted simultaneously. Moreover, the decline in receiver sensitivities due to Mach-Zehnder modulator bias drifts is also investigated. Receiver power penalties of the 20-GHz up-converted WDM signals and baseband (BB) FTTx signals are less than 1 dB when bias deviation voltage is less the 20% of the half-wave voltage. After transmission over a 50-km SSMF, the receiver power penalties of both the BB and 20-GHz RF OOK signals are less than 1 dB. Notably, 60-GHz optical up-conversion can be achieved using 15-GHz radio frequency (RF) components and equipment.
Electromagnetic inverse scattering based object imaging and characterization (2014)

Summary form only given. Object imaging and object characterization based on electromagnetic inverse scattering involves retrieving the equivalent source from the scattered field measured outside the source region due to a known incident field. The solution to the inverse equivalent source problem is not unique. In (S. Shahir, M. Mohajer, A. Rohani, and S. Safavi-Naeini, “Permittivity profile estimation based on nonradiating equivalent source,” Progress in Electromagnetic Research B, Vol. 50, pp. 157-175, 2013), we estimated uniquely the scatterer permittivity profiles by minimizing the non-radiating objective function and applying the information of the scatterer locations and boundaries.Object imaging and object characterization of one and two dielectric cylinders are reported by Zakaria (A. Zakaria, I. Jeffrey, M. Ostadrahimi, M. Asefi and J. LoVetri, "A Novel 3D Near-field Microwave Imaging System," IEEE international symposium on Antennas and Propagation, pp. 816-817, 2013). Zakaria has been able to reconstruct the scatterers' cross sections. Some artifacts can be observed in the results. The reconstructed cross section of the circular cylinder is not circular. Ostadrahimi has done initial calibration by using a PEC circular cylinder to work around the issue (M. Ostadrahimi, A. Zakaria, J. LoVetri, and L. Shafai, "A Near-Field Dual Polarized Microwave Imaging System," IEEE Transactions on Microwave Theory and Techniques, Vol. 61, No. 3, 2013). In the aforementioned experiments, the mutual coupling between the adjacent probes was unavoidable, and the objects under test were small in terms of wavelength. We are going to present our experimental results for object imaging and characterization at 75-110 GHz. By calibrating the electromagnetic inverse scattering system accurately, we have successfully been able to reconstruct the large-size object images. The reconstructed objects are also to be characterized by minimizing the non-radiating objective function.
Controlled Stoichiometry for Quaternary CuIn<sub><i>x</i></sub>Ga<sub>1−<i>x</i></sub>S<sub>2</sub>Chalcopyrite Nanoparticles from Single-Source Precursors via Microwave Irradiation (2010)

We report the synthesis of quaternary CuInxGa1−xS2 (0 ≤ x ≤1) chalcopyrite nanoparticles from decomposition of two molecular single source precursors (SSPs), (Ph3P)2Cu(μ-SEt)2In(SEt)2 (1) and (Ph3P)2Cu(μ-SEt)2Ga(SEt)2 (2), via microwave irradiation. We were able to precisely control stoichiometry and bandgaps of quaternary CuInxGa1−xS2 nanoparticles ranging from 1.40 to 2.30 eV.
Polymerizable viscoelastic fluids (1990)

Abstract Rheological, elongational flow, and scanning electron microscopy measurements have been performed on cationic monomers associated with specific counterions. The monomers are formed through the reaction of allyl bromide and a variety of dimethylalkylamine derivatives. The results show that above a specific monomer–counterion concentration, highly elongated structures are formed in solution. These structures are adequately described as polymerizable rod‐like micelles. The physical properties of these fluids are interpreted in terms of a micellar sphere to rod transition which gradually occurs over a specific concentration range (>1g/dL, in general). At higher concentrations, these rod‐like entities are capable of interacting with each other. Therefore, even though the forces holding the structures together are certainly weaker than a chemical bond, polymeric‐like properties are observed in these polymerizable viscoelastic fluids.
Loop-free convergence using oFIB (2012)

This draft describes a mechanism for use in conjunction with link
state routing protocols which prevents the transient loops which would
otherwise occur during topology changes. It does this by correctly
sequencing the FIB updates on the routers. This mechanism can be used
in the case of non-urgent link or node shutdowns and restarts or link
metric changes. It can also be used in conjunction with a FRR
mechanism which converts a sudden link or node failure into a non-
urgent topology change. This is possible where a complete repair path
is provided for all affected destinations. After a non-urgent
topology change, each router computes a rank that defines the time at
which it can safely update its FIB. A method for accelerating this
loop-free convergence process by the use of completion messages is
also described.
A Study of Wireless Power Transfer and Loss in Seawater With High Transfer Efficiency and Positional Degree of Freedom for Small AUVs (2020)

The seas around Japan are rich in energy and mineral resources. Autonomous Underwater Vehicles (AUVs) that can move freely in the sea are effective for efficient investigation and utilization of these resources. AUVs are battery capacity-dependent and have a short time of activity, and must be pulled out of the sea each time they are recharged. This paper has examined the wireless power transfer technology in the sea for the efficient operation of AUVs. Experiments on wireless power transfer of high power in salt water have been conducted using a metal pressure vessel such as an AUV and transfer and receiving coils. We have shown that the proposal method has high degree of freedom of position and transfer efficiency. We also have studied the loss of wireless power transfer in the sea by simulation.
Prevention by anti-LFA-1 of acute myoblast death following transplantation (1997)

Myoblast transplantation is a potential treatment for Duchenne muscular dystrophy. One of the problems possibly responsible for the limited success of clinical trials is the rapid death of the myoblasts after transplantation. To investigate this problem, myoblasts expressing beta-galactosidase were injected in the tibialis anterior muscles of mice. Beta-galactosidase activity was reduced by 74.7% after 3 days. Myoblast death observed at 3 days was reduced to 57.2% when the hosts were irradiated. This result suggested that host cells were contributing to this phenomenon. Transplantation in SCID and FK506-treated mice did not reduce cell death, indicating that mortality was not due to an acute specific reaction. In contrast, administration of the anti-LFA-1 (TIB-213) mAb markedly reduced myoblast death at 3 days without altering leukocyte tissue infiltration. We postulated that neutrophils were mediating myoblast mortality by an LFA-1-dependent mechanism. To test this hypothesis, IL-1beta-activated myoblasts were loaded with 6-carboxy-2',7'-dichlorodihydrofluorescein diacetate, di(acetoxymethylester) (DCFH), a marker for oxidative stress. Addition of neutrophils and zymosan-activated serum resulted in a time-dependent DCFH fluorescence; this neutrophil-induced oxidation was considerably inhibited by TIB-213. These results indicate that an effective control of the inflammatory reaction will be necessary for any new clinical trials of myoblast transplantation and suggest that neutrophil-mediated myoblast injury occurs by an LFA-1-dependent pathway.
Molecular cloning of a putative receptor protein kinase gene encoded at the self-incompatibility locus of Brassica oleracea. (1991)

Self-recognition between pollen and stigma during pollination in Brassica oleracea is genetically controlled by the multiallelic self-incompatibility locus (S). We describe the S receptor kinase (SRK) gene, a previously uncharacterized gene that resides at the S locus. The nucleotide sequences of genomic DNA and of cDNAs corresponding to SRK predict a putative transmembrane receptor having serine/threonine-specific protein kinase activity. Its extracellular domain exhibits striking homology to the secreted product of the S-locus glycoprotein (SLG) gene and is connected via a single pass transmembrane domain to a protein kinase catalytic center. SRK alleles derived from different S-locus genotypes are highly polymorphic and have apparently evolved in unison with genetically linked alleles of SLG. SRK directs the synthesis of several alternative transcripts, which potentially encode different protein products, and these transcripts were detected exclusively in reproductive organs. The identification of SRK may provide new perspectives into the signal transduction mechanism underlying pollen recognition.
Mixture of mixture n-gram language models (2013)

This paper presents a language model adaptation technique to build a single static language model from a set of language models each trained on a separate text corpus while aiming to maximize the likelihood of an adaptation data set given as a development set of sentences. The proposed model can be considered as a mixture of mixture language models. The mixture model at the top level is a sentence-level mixture model where each sentence is assumed to be drawn from one of a discrete set of topic or task clusters. After selecting a cluster, each n-gram is assumed to be drawn from one of the given n-gram language models. We estimate cluster mixture weights and n-gram language model mixture weights for each cluster using the expectation-maximization (EM) algorithm to seek the parameter estimates maximizing the likelihood of the development sentences. This mixture of mixture models can be represented efficiently as a static n-gram language model using the previously proposed Bayesian language model interpolation technique. We show a significant improvement with this technique (both perplexity and WER) compared to the standard one level interpolation scheme.
Bias in Ligation-Based Small RNA Sequencing Library Construction Is Determined by Adaptor and RNA Structure (2015)

High-throughput sequencing (HTS) has become a powerful tool for the detection of and sequence characterization of microRNAs (miRNA) and other small RNAs (sRNA). Unfortunately, the use of HTS data to determine the relative quantity of different miRNAs in a sample has been shown to be inconsistent with quantitative PCR and Northern Blot results. Several recent studies have concluded that the major contributor to this inconsistency is bias introduced during the construction of sRNA libraries for HTS and that the bias is primarily derived from the adaptor ligation steps, specifically where single stranded adaptors are sequentially ligated to the 3' and 5'-end of sRNAs using T4 RNA ligases. In this study we investigated the effects of ligation bias by using a pool of randomized ligation substrates, defined mixtures of miRNA sequences and several combinations of adaptors in HTS library construction. We show that like the 3' adaptor ligation step, the 5' adaptor ligation is also biased, not because of primary sequence, but instead due to secondary structures of the two ligation substrates. We find that multiple secondary structural factors influence final representation in HTS results. Our results provide insight about the nature of ligation bias and allowed us to design adaptors that reduce ligation bias and produce HTS results that more accurately reflect the actual concentrations of miRNAs in the defined starting material.