gebhart/patrepeval huggingface dataset:
Incorporating Prior Knowledge on Class Probabilities into Local Similarity Measures for Intermodality Image Registration (2009)

We present a methodology for incorporating prior knowledge on class probabilities into the registration process. By using knowledge from the imaging modality, pre-segmentations, and/or probabilistic atlases, we construct vectors of class probabilities for each image voxel. By defining new image similarity measures for distribution-valued images, we show how the class probability images can be nonrigidly registered in a variational framework. An experiment on nonrigid registration of MR and CT full-body scans illustrates that the proposed technique outperforms standard mutual information (MI) and normalized mutual information (NMI) based registration techniques when measured in terms of target registration error (TRE) of manually labeled fiducials.
The Informed Wall: applying additive digital fabrication techniques on architecture (2006)

In this work in progress report we present the results of a four week design studio with graduate students as part of a broader research project on investigating digital additive fabrication processes and their implications on architectural design.In a simple test arrangement we realized the digital design and additive fabrication of two by three meters brick walls. The use of bricks, being the primary module for construction, and at a relatively coarse resolution, allowed us to concentrate on the design of completely programmed walls encompassing material-dependent parameters. The resulting prototypes depict the great potential of the integration of the design and the fabrication process. Non-standardized solutions can be easily accomplished as the design data is directly used to control the fabrication process. In using an additive digital fabrication process, a novel architectural product of the kind Âbrick wallÂ emerged, which could not have been conceived or fabricated manually.
Oxide–Polymer Heterojunction Diodes with a Nanoscopic Phase-Separated Insulating Layer (2018)

Organic semiconductor-insulator blend films are widely explored for high-performance electronic devices enabled by unique phase-separation and self-assembly phenomena at key device interfaces. Here we report the first demonstration of high-performance hybrid diodes based on p- n junctions formed by a p-type poly(3-hexylthiophene) (P3HT)-poly(methyl methacrylate) (PMMA) blend and n-type indium-gallium-zinc oxide (IGZO). The thin film morphology, microstructure, and vertical phase-separation behavior of the P3HT films with varying contents of PMMA are systematically analyzed. Microstructural and charge transport evaluation indicates that the polymer insulator component positively impacts the morphology, molecular orientation, and effective conjugation length of the P3HT films, thereby enhancing the heterojunction performance. Furthermore, the data suggest that PMMA phase segregation creates a continuous nanoscopic interlayer between the P3HT and IGZO layers, playing an important role in enhancing diode performance. Thus, the diode based on an optimal P3HT-PMMA blend exhibits a remarkable 10-fold increase in forward current versus that of a neat P3HT diode, yielding an ideality factor value as low as 2.5, and a moderate effective barrier height with an excellent rectification ratio. These results offer a new approach to simplified manufacturing of low-cost, large-area hybrid inorganic-organic electronics technologies.
Pd-Catalyzed N-Arylation of Secondary Acyclic Amides: Catalyst Development, Scope, and Computational Study (2009)

We report the efficient N-arylation of acyclic secondary amides and related nucleophiles with aryl nonaflates, triflates, and chlorides. This method allows for easy variation of the aromatic component in tertiary aryl amides. A new biaryl phosphine with P-bound 3,5-(bis)trifluoromethylphenyl groups was found to be uniquely effective for this amidation. The critical aspects of the ligand were explored through synthetic, mechanistic, and computational studies. Systematic variation of the ligand revealed the importance of (1) a methoxy group on the aromatic carbon of the “top ring” &lt;i&gt;ortho&lt;/i&gt; to the phosphorus and (2) two highly electron-withdrawing P-bound 3,5-(bis)trifluoromethylphenyl groups. Computational studies suggest the electron-deficient nature of the ligand is important in facilitating amide binding to the LPd(II)(Ph)(X) intermediate.
CALLUS-MEDIATED PLANT REGENERATION FROM MORPHOLOGICALLY CHANGED PETALS PRODUCED BY MUTAGEN-TREATED APICAL ROSE BUDS (2015)

The apical buds of lateral rose branches (Rosa hybrida âCarl Redâ) were asexually propagated by cutting and treatment with chemical mutagens (N-methyl-Nâ-nitro-N-nitrosoguanidine, ethyl methane sulfonate, 6-azacytidine, and acridine orange), and the growth and differentiation or morphological alterations of the mutagen-treated buds were traced in developed flowers. Variations in size, shape, colour, and the number of petals were detected most frequently in flowers produced from apical buds treated with 100 I¼g/ml N-methyl-Nâ-nitro-N-nitrosoguanidine. The variant petals were cultured on Murashige and Skoog medium supplemented with I±-naphthalene acetic acid and 6-benzylaminopurine for in vitro isolation and the reproduction of morphologically altered rose plants. Embryogenic calli were obtained from adventitious roots induced from the petals and were successfully differentiated into intact plants. Consequently, the regenerated plants produced flowers that were different from those originally used for tissue culture. The appearance of the flowers in these rose plants was highly consistent through repeated cycles of cutting, suggesting that the present approach is an easy and rapid procedure for mutation breeding in rose in combination with tissue culture techniques for the in situ isolation and propagation of variant plants. This approach is expected to provide an effective method for easily and rapidly inducing variations in rose flowers and for in vitro morphogenesis through their regeneration.
The POU domain: a large conserved region in the mammalian pit-1, oct-1, oct-2, and Caenorhabditis elegans unc-86 gene products. (1988)

The POU domain: a large conserved region in
Genetic Design via Combinatorial Constraint Specification (2017)

We present a formal language for specifying via constraints a "design space" of DNA constructs composed of genetic parts, and an algorithm for automatically and correctly creating a novel representation of the space of satisfying designs. The language is simple, captures a large class of design spaces, and possesses algorithms for common operations on design spaces. The flexibility of this approach is demonstrated using a 16-gene nitrogen fixation pathway and genetic logic circuits.
A simulation study on the topochemical and statistical distribution of the activity in particulate solids (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA simulation study on the topochemical and statistical distribution of the activity in particulate solidsMasataka Machida and Mamoru SennaCite this: J. Phys. Chem. 1986, 90, 21, 5329–5333Publication Date (Print):October 1, 1986Publication History Published online1 May 2002Published inissue 1 October 1986https://pubs.acs.org/doi/10.1021/j100412a085https://doi.org/10.1021/j100412a085research-articleACS PublicationsRequest reuse permissionsArticle Views22Altmetric-Citations2LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Antibody Therapy in the Management of Shiga Toxin-Induced Hemolytic Uremic Syndrome (2004)

Hemolytic uremic syndrome (HUS) is a disease that can lead to acute renal failure and often to other serious sequelae, including death. The majority of cases are attributed to infections with Escherichia coli, serotype O157:H7 strains in particular, which cause bloody diarrhea and liberate one or two toxins known as Shiga toxins 1 and 2. These toxins are thought to directly be responsible for the manifestations of HUS. Currently, supportive nonspecific treatment is the only available option for the management of individuals presenting with HUS. The benefit of antimicrobial therapy remains uncertain because of several reports which claim that such intervention can in fact exacerbate the syndrome. There have been only a few specific therapies directed against neutralizing the activities of these toxins, but none so far has been shown to be effective. This article reviews the literature on the mechanism of action of these toxins and the clinical manifestations and current management and treatment of HUS. The major focus of the article, however, is the development and rationale for using neutralizing human antibodies to combat this toxin-induced disease. Several groups are currently pursuing this approach with either humanized, chimeric, or human antitoxin antibodies produced in transgenic mice. They are at different phases of development, ranging from preclinical evaluation to human clinical trials. The information available from preclinical studies indicates that neutralizing specific antibodies directed against the A subunit of the toxin can be highly protective. Such antibodies, even when administered well after exposure to bacterial infection and onset of diarrhea, can prevent the occurrence of systemic complications.
Pulse train control in an excitable micropillar laser with delayed optical feedback (Conference Presentation) (2018)

Recent experiments with an excitable VCSEL micropillar laser with delayed optical feedback demonstrated that the system is able to sustain trains of optical pulses. The laser has two layers of gain and one layer of absorption in the VCSEL cavity, and it is an excitable single longitudinal and transverse mode laser. With optical feedback, a past pulse can trigger a new pulse, creating a pulse train with repetition rate given by the delay time. It is possible to trigger and retime pulses by appropriate external perturbations, in the form of appropriately timed short optical pulses. In particular, several pulse trains can be triggered independently by optical perturbations, and sustained simultaneously in the external cavity, with different timing in between pulses. Such dynamics are also called localised structures, and are investigated here theoretically. It has been verified experimentally and theoretically that the phase of the electric field is not relevant. The Yamada model – a well-established system of ordinary differential equations for intensity, gain and absorption – is thus a suitable model. As we show, the Yamada model with delayed intensity feedback describes the pulsing micropillar laser system in good agreement with the experiment. A bifurcation analysis of this model shows that several pulsing periodic solution with different repetition rates coexist and are stable. Although coexisting pulse trains can seem independent on the timescale of the experiment, we show that they correspond here to extremely long transient dynamics toward one of the stable periodic solutions, with equidistant pulses.
Comparison of Anterior Cruciate Ligament Tunnel Position and Graft Obliquity With Transtibial and Anteromedial Portal Femoral Tunnel Reaming Techniques Using High‐Resolution Magnetic Resonance Imaging (2011)

Level III, retrospective comparative study.
One step ultra-high-throughput sequencing of the paired antibody VH:VL and TCRβ:α repertoires using cell lysate resistant xenopolymerase in emulsion (2020)

Abstract Antibodies and T cell receptors (TCRs) have critical roles in adaptive immunity and thus the determination of their sequences is essential for understanding immune responses in infections or vaccinations, for the discovery of therapeutic antibodies, and for the engineered T cell therapies. Antibodies are composed of variable heavy (VH) and light (VL) chains, and TCRs are composed of variable TCRα/γ and TCRβ/δ chains. Since those chains are encoded by two different transcripts, the determination of functional sequences requires single-cell sequencing. Emulsification of single-cells followed by barcoding of the transcripts or fusion of VH:VL or TCRβ:α transcripts using overlap extension RT-PCR allows high-throughput single-cell sequencing; however, because cell lysate in emulsion inhibits the RT-PCR reaction, these methods require complex microfluidics devices to bypass the inhibition which most of biomedical laboratories cannot access. We discovered recently engineered xenopolymerase, RTX, has an exceptional cell lysate resistance that can overcome this limitation. By employing this unique feature of RTX, we have developed a one-step emulsion-based ultra-high-throughput sequencing method for paired antibody VH:VL and TCRβ:α repertoires not requiring microfluidics or any other specialized equipment. Using this methodology, we obtained high yields (5,000 to &amp;gt;20,000/sample) of paired VH:VL or TCRβ:α clonotypes at low cost. As a demonstration, we applied the methodology to the peripheral blood plasmablasts and T follicular helper (TFH) cells from a seasonal influenza vaccine recipient and discovered high-affinity influenza-specific antibodies and TCRβ:α.
An Integrative Multiomics Framework for Identification of Therapeutic Targets in Pulmonary Fibrosis (2023)

Pulmonary fibrosis (PF) is a heterogeneous disease with a poor prognosis. Therefore, identifying additional therapeutic modalities is required to improve outcome. However, the lack of biomarkers of disease progression hampers the preclinical to clinical translational process. Here, this work assesses and identifies progressive alterations in pulmonary function, transcriptomics, and metabolomics in the mouse lung at 7, 14, 21, and 28 days after a single dose of oropharyngeal bleomycin. By integrating multi-omics data, this work identifies two central gene subnetworks associated with multiple critical pathological changes in transcriptomics and metabolomics as well as pulmonary function. This work presents a multi-omics-based framework to establish a translational link between the bleomycin-induced PF model in mice and human idiopathic pulmonary fibrosis to identify druggable targets and test therapeutic candidates. This work also indicates peripheral cannabinoid receptor 1 (CB<sub>1</sub> R) antagonism as a rational therapeutic target for clinical translation in PF. Mouse Lung Fibrosis Atlas can be accessed freely at https://niaaa.nih.gov/mouselungfibrosisatlas.
Characterizing spatial distribution of ink-jet printed horseradish peroxidase on paper substrates (2008)

In solid phase bioanalysis, bioagents are incorporated onto solid materials to give them the ability to detect and/or quantify specific target analytes. Previous research has shown that the enzyme horseradish peroxidase (HRP) can be printed on paper without significant inactivation using piezoelectric ink-jet technologies. However, bioanalytical performance of the resulting bioactive papers can be affected not only by the printing conditions and quantity of enzyme deposited, but also by the enzyme spatial distribution and printed enzyme stability. In this study, confocal laser scanning microscopy (CLSM) is used to characterize the inplane and cross-sectional localized enzyme activity of HRP ink-jet printed on fibrous supports with different surface chemistry and composition. Key paper attributes that can affect the analytical performance are identified.
Surgical Management for Peyronie's Disease (2013)

Peyronie's disease is a common debilitating condition for both men and their partners that results in penile deformity and compromises sexual functioning. While there are a myriad of medical therapeutic options, these have not been demonstrated to correct the deformity and restore sexual function definitively. As such, surgery is the mainstay of treatment for this disease, and multiple surgical approaches may be considered depending on disease characteristics, patient co-morbidity, and findings on preoperative diagnostic testing. The purpose of this review is to highlight the different surgical approaches and different procedures within each approach, and to examine important issues for surgeons to consider for administering the best treatment that restores function while reconciling patient expectations.
LRIG1 regulates cadherin‐dependent contact inhibition directing epithelial homeostasis and pre‐invasive squamous cell carcinoma development (2012)

Epidermal growth factor receptor (EGFR) pathway activation is a frequent event in human carcinomas. Mutations in EGFR itself are, however, rare, and the mechanisms regulating EGFR activation remain elusive. Leucine-rich immunoglobulin repeats-1 (LRIG1), an inhibitor of EGFR activity, is one of four genes identified that predict patient survival across solid tumour types including breast, lung, melanoma, glioma, and bladder. We show that deletion of Lrig1 is sufficient to promote murine airway hyperplasia through loss of contact inhibition and that re-expression of LRIG1 in human lung cancer cells inhibits tumourigenesis. LRIG1 regulation of contact inhibition occurs via ternary complex formation with EGFR and E-cadherin with downstream modulation of EGFR activity. We find that LRIG1 LOH is frequent across cancers and its loss is an early event in the development of human squamous carcinomas. Our findings imply that the early stages of squamous carcinoma development are driven by a change in amplitude of EGFR signalling governed by the loss of contact inhibition.
Efficient Global String Kernel with Random Features (2019)

Analysis of large-scale sequential data has been one of the most crucial tasks in areas such as bioinformatics, text, and audio mining. Existing string kernels, however, either (i) rely on local features of short substructures in the string, which hardly capture long discriminative patterns, (ii) sum over too many substructures, such as all possible subsequences, which leads to diagonal dominance of the kernel matrix, or (iii) rely on non-positive-definite similarity measures derived from the edit distance. Furthermore, while there have been works addressing the computational challenge with respect to the length of string, most of them still experience quadratic complexity in terms of the number of training samples when used in a kernel-based classifier. In this paper, we present a new class of global string kernels that aims to (i) discover global properties hidden in the strings through global alignments, (ii) maintain positive-definiteness of the kernel, without introducing a diagonal dominant kernel matrix, and (iii) have a training cost linear with respect to not only the length of the string but also the number of training string samples. To this end, the proposed kernels are explicitly defined through a series of different random feature maps, each corresponding to a distribution of random strings. We show that kernels defined this way are always positive-definite, and exhibit computational benefits as they always produce Random String Embeddings (RSE) that can be directly used in any linear classification models. Our extensive experiments on nine benchmark datasets corroborate that RSE achieves better or comparable accuracy in comparison to state-of-the-art baselines, especially with the strings of longer lengths. In addition, we empirically show that RSE scales linearly with the increase of the number and the length of string.
Adaptive Parameter EXploration (APEX): Adaptation of robot autonomy from human participation (2014)

The problem of Adaptation from Participation (AfP) aims to improve the efficiency of a human-robot team by adapting a robot's autonomous systems and behaviors based on command-level input from a human supervisor. As a solution to AfP, the Adaptive Parameter EXploration (APEX) algorithm continuously explores the space of all possible parameter configurations for the robot's autonomous system in an online and anytime manner. Guided by information deduced from the human's latest intervening commands, APEX is capable of adapting an arbitrary robot system to dynamic changes in task objectives and conditions during a session. We explore this framework within visual navigation contexts where the humanrobot team is tasked with covering or patrolling over multiple terrain boundaries such as coastlines and roads. We present empirical evaluations of two separate APEX-enabled systems: the first, deployed on an aerial robot within a controlled environment, and the second, on a wheeled robot operating within a challenging university campus setting.
Identification of a novel viral protein in infectious bursal disease virus-infected cells (1995)

Infectious bursal disease virus (IBDV), a member of the Birnaviridae, specifies two genomic double-stranded RNAs, segment A and segment B. Segment A encodes a 110 kDa polyprotein which is processed into virus proteins VP2, VP3 and VP4. A second open reading frame (ORF), designated ORF A-2, immediately preceding and partially overlapping the 110 kDa protein gene has also been described. After prokaryotic expression of this ORF and immunization of rabbits with the expressed protein we obtained reagents that allowed the identification of the ORF A-2 gene product in IBDV-infected cells. The ORF A-2 protein exhibits an apparent molecular mass of 21 kDa which is larger than the size of 16.5 kDa calculated from the deduced amino acid sequence. Immunofluorescence studies demonstrated the presence of the ORF A-2 protein in bursa samples from IBDV-infected chicken. In summary, the IBDV ORF A-2 product represents the fifth IBDV protein described. Therefore, we propose to designate it as IBDV VP5.
A planar passive dual band array feed antenna for Ku band satellite communication terminals (2012)

A planar passive array feed antenna for bidirectional Ku band satellite communication was designed, fabricated and measured. The feed antenna achieved 50 dB isolation between transmit and receive ports across the transmitting band. An on-reflector test was conducted by mounting the array feed with external low noise amplifier and block downconverter (LNB) on a 90 cm dish to verify the feed radiation efficiency and illumination pattern. The measured signal to noise ratio (SNR) with the planar feed including loss in test connectors was within 2 dB of that of a commercial horn feed.