gebhart/patrepeval huggingface dataset:
Binding of Bruton's tyrosine kinase to Fyn, Lyn, or Hck through a Src homology 3 domain-mediated interaction. (1994)

Bruton's tyrosine kinase (Btk) is a recently described B-cell-specific tyrosine kinase. Mutations in this gene lead to human X chromosome-linked agammaglobulinemia and murine X-linked immunodeficiency. Although genetic evidence strongly suggests that Btk plays a crucial role in B-lymphocyte differentiation and activation, its precise mechanism of action remains unknown, primarily because the proteins that it interacts with have not yet been identified. Here, we show that Btk interacts with Src homology 3 domains of Fyn, Lyn, and Hck, protein-tyrosine kinases that get activated upon stimulation of B- and T-cell receptors. These interactions are mediated by two 10-aa motifs in Btk. An analogous site with the same specificity is also present in Itk, the T-cell-specific homologue of Btk. Our data extend the range of interactions mediated by Src homology 3 domains and provide an indication of a link between Btk and established signaling pathways in B lymphocytes.
Adhesion of Biologically Inspired Polymer Microfibers on Soft Surfaces (2009)

Polymer microfiber arrays with mushroom-shaped tips are shown to adhere well to a soft, smooth substrate. An existing model describing the effect of backing layer thickness is also shown to be applicable to the adhesion of fibrillar arrays on soft surfaces. Simulations showed that adhesion can be enhanced by increasing the compliance of the microfibers in addition to maximizing single-fiber adhesion. This model can be used to guide the development of optimized microfiber adhesives for use on soft surfaces such as biological tissues or textiles.
Generative Adversarial Networks (2022)

The Science of Deep Learning emerged from courses taught by the author that have provided thousands of students with training and experience for their academic studies, and prepared them for careers in deep learning, machine learning, and artificial intelligence in top companies in industry and academia. The book begins by covering the foundations of deep learning, followed by key deep learning architectures. Subsequent parts on generative models and reinforcement learning may be used as part of a deep learning course or as part of a course on each topic. The book includes state-of-the-art topics such as Transformers, graph neural networks, variational autoencoders, and deep reinforcement learning, with a broad range of applications. The appendices provide equations for computing gradients in backpropagation and optimization, and best practices in scientific writing and reviewing. The text presents an up-to-date guide to the field built upon clear visualizations using a unified notation and equations, lowering the barrier to entry for the reader. The accompanying website provides complementary code and hundreds of exercises with solutions.
Improvement of the Gate Oxide Integrity by Modifying Crystal Pulling and Its Impact on Device Failures (1994)

Czochralski single‐crystal wafers grown with different pulling rates using various hot zone modifications were analyzed with respect to grown‐in defects and gate oxide integrity (GOI). The quality of the wafers characterized by crystal defect density as well as by GOI yield was found to be related strongly with the pulling conditions. Depending on the growth rate two concentric regions, characterized by different GOI and grown‐in defect levels and separated by a ring‐like area with high stacking fault density, were found on the wafers. The single‐bit failure rate in some dynamic random access memory (DRAM) reliability tests turned out to correlate with GOI yield. Thus it is clearly shown that the bulk quality related with crystal pulling conditions correlates with the DRAM reliability.
Ethylene Synthesis and Regulated Expression of Recombinant Protein in Synechocystis sp. PCC 6803 (2012)

The ethylene-forming enzyme (EFE) from Pseudomonas syringae catalyzes the synthesis of ethylene which can be easily detected in the headspace of closed cultures. A synthetic codon-optimized gene encoding N-terminal His-tagged EFE (EFEh) was expressed in Synechocystis sp. PCC 6803 (Synechocystis) and Escherichia coli (E. coli) under the control of diverse promoters in a self-replicating broad host-range plasmid. Ethylene synthesis was stably maintained in both organisms in contrast to earlier work in Synechococcus elongatus PCC 7942. The rate of ethylene accumulation was used as a reporter for protein expression in order to assess promoter strength and inducibility with the different expression systems. Several metal-inducible cyanobacterial promoters did not function in E. coli but were well-regulated in cyanobacteria, albeit at a low level of expression. The E. coli promoter P(trc) resulted in constitutive expression in cyanobacteria regardless of whether IPTG was added or not. In contrast, a Lac promoter variant, P(A1lacO-1), induced EFE-expression in Synechocystis at a level of expression as high as the Trc promoter and allowed a fine level of IPTG-dependent regulation of protein-expression. The regulation was tight at low cell density and became more relaxed in more dense cultures. A synthetic quorum-sensing promoter system was also constructed and shown to function well in E. coli, however, only a very low level of EFE-activity was observed in Synechocystis, independent of cell density.
Functions of the α, β, and γ Subunits of UDP-GlcNAc:Lysosomal Enzyme N-Acetylglucosamine-1-phosphotransferase (2009)

UDP-GlcNAc:lysosomal enzyme N-acetylglucosamine-1-phosphotransferase is an alpha(2)beta(2)gamma(2) hexamer that mediates the first step in the synthesis of the mannose 6-phosphate recognition marker on lysosomal acid hydrolases. Using a multifaceted approach, including analysis of acid hydrolase phosphorylation in mice and fibroblasts lacking the gamma subunit along with kinetic studies of recombinant alpha(2)beta(2)gamma(2) and alpha(2)beta(2) forms of the transferase, we have explored the function of the alpha/beta and gamma subunits. The findings demonstrate that the alpha/beta subunits recognize the protein determinant of acid hydrolases in addition to mediating the catalytic function of the transferase. In mouse brain, the alpha/beta subunits phosphorylate about one-third of the acid hydrolases at close to wild-type levels but require the gamma subunit for optimal phosphorylation of the rest of the acid hydrolases. In addition to enhancing the activity of the alpha/beta subunits toward a subset of the acid hydrolases, the gamma subunit facilitates the addition of the second GlcNAc-P to high mannose oligosaccharides of these substrates. We postulate that the mannose 6-phosphate receptor homology domain of the gamma subunit binds and presents the high mannose glycans of the acceptor to the alpha/beta catalytic site in a favorable manner.
[Early detection of non-palpable (T0) breast cancer: the diagnostic procedure for pathological discharge from the nipple]. (1994)

Detection of non-palpable (T0) breast cancer by pathological nipple discharge is possible 3 years or more earlier than tumorous breast cancer. However, the definite diagnosis of T0 breast cancer has been considered to be very difficult because the standard diagnostic method such as exfoliative cytology and ductography were not totally reliable. In 1985 we first demonstrated the significance of CEA measurement in nipple discharge for diagnosis of T0 breast cancer. Since then CEA activity in nipple discharge was estimated in 60 patients with breast diseases by means of enzyme immunoassay using monoclonal anti CEA antibody. They include 17 with T0 breast cancer, 9 with borderline lesion, 20 with intraductal papilloma and 14 with fibrocystic diseases. When the cut off value of CEA concentration was set at 600 ng/ml, the sensitivity, specificity and accuracy were 76.5%, 100% and 92.2%, respectively. These levels were higher than those for mammography or cytology. In the past 7 years, 13 cases of T0 breast cancer were detected in our hospital. They accounted for 2.5% of total breast cancer cases. In conclusion, CEA measurement in nipple discharge is a useful method for the diagnosis of non-palpable breast cancer.
Xenopus embryos regulate the nuclear localization of XMyoD. (1994)

Injection of Xenopus myoD mRNA into Xenopus embryos leads to only a modest activation of myogenic markers. In contrast, we show that injected mouse myoD mRNA leads to a potent activation. We postulate that XMyoD is under negative control in frog embryos, but because of slight sequence differences, mouse MyoD fails to see the negative signal. Whereas mMyoD is constitutively nuclear, XMyoD is largely cytoplasmic except in a region of the embryo that includes the location where mesoderm induction occurs; there, it is nuclear. At MBT, endogenous XmyoD mRNA is expressed ubiquitously in the frog embryo. Our results suggest that this expression would lead to cytoplasmic XMyoD protein. Among other events, muscle induction might remove this negative regulation, allow MyoD to enter the nucleus, and establish an autoregulatory loop that could commit cells to myogenesis.
Dimensional variation tolerant silicon-on-insulator directional couplers (2014)

We design silicon ridge/rib waveguide directional couplers which are simultaneously tolerant to width, height, coupling gap, and etch depth variations. Using wafer-scale measurements of structures fabricated in the IMEC Standard Passives process, we demonstrate the normalized standard deviation in the per-length coupling coefficient (a metric for the splitting ratio variation) of the variation-tolerant directional couplers is up to 4 times smaller than that of strip waveguide designs. The variation-tolerant couplers are also the most broadband and the deviation in the coupling coefficient shows the lowest spectral dependence.
Sticky Situations: Key Components That Control Bacterial Surface Attachment (2012)

The formation of bacterial biofilms is initiated by cells transitioning from the free-swimming mode of growth to a surface. This review is aimed at highlighting the common themes that have emerged in recent research regarding the key components, signals, and cues that aid in the transition and those involved in establishing a more permanent surface association during initial attachment.
A low glitch 10-bit 75-MHz CMOS video D/A converter (1995)

A low glitch 10-bit 75-MHz CMOS current-output video digital-to-analog Converter (DAC) for high-definition television (HDTV) applications is described. In order to achieve monotonicity and low glitch, a special segmented antisymmetric switching sequence and an innovative asymmetrical switching buffer have been used. The video DAC has been fabricated by using 0.8 /spl mu/m single-poly double-metal CMOS technology. Experimental results indicated that the conversion rate is above 75 MHz, and nearly 50% of samples have differential and integral linearity errors less than 0.24 LSB and 0.6 LSB, respectively. The glitch has been reduced to be less than 3.9 pV/spl middot/s and the settling time within /spl plusmn/0.1% of the final value is less than 13 ns. The video DAC is operated by a single 5 V power supply and dissipates 1.70 mW at 75 MHz conversion rate (140 mW in the DAC portion). The chip size of video DAC is 1.75 mm/spl times/1.2 mm (1.75 mm/spl times/0.7 mm for the DAC portion).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Placebo-Controlled Trial of Tofacitinib Monotherapy in Rheumatoid Arthritis (2012)

In patients with active rheumatoid arthritis, tofacitinib monotherapy was associated with reductions in signs and symptoms of rheumatoid arthritis and improvement in physical function. (Funded by Pfizer; ORAL Solo ClinicalTrials.gov number, NCT00814307.).
The synthesis and absolute configuration of mycosporins. A novel application of the Staudinger reaction (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe synthesis and absolute configuration of mycosporins. A novel application of the Staudinger reactionJames D. White, Janice H. Cammack, and Kazuhiko SakumaCite this: J. Am. Chem. Soc. 1989, 111, 24, 8970–8972Publication Date (Print):November 1, 1989Publication History Published online1 May 2002Published inissue 1 November 1989https://pubs.acs.org/doi/10.1021/ja00206a059https://doi.org/10.1021/ja00206a059research-articleACS PublicationsRequest reuse permissionsArticle Views894Altmetric-Citations32LEARN 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 optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Biosynthesis of aminocyclitol-aminoglycoside antibiotics and related compounds (2007)

This review covers the biosynthesis of aminocyclitol-aminoglycoside antibiotics and related compounds, particularly from the molecular genetic perspectives. 195 references are cited.
FEMTOLITER MICRODROPLET ARRAY DEVICE FOR SINGLE-MOLECULE DIGITAL ENZYME-LINKED IMMUNOSORBENT ASSAY (2011)

Single-molecule biomarkers captured on beads are successfully isolated and detected within femtoliter water-in-oil microdroplet array on hydrophilic-in-hydrophobic micropatterned surface in a flow cell. Enclosure of single bead into each droplet was efficiently achieved by sequentially injecting aqueous solution with beads and oil using micropipette. The feasibility of our device is demonstrated by detecting streptavidin-biotin interaction of which limit of detection was 78 zM. Such simple and efficient approach promises the development of highly sensitive and potable Enzyme-linked immunosorbent assay device by direct coupling with CMOS image sensor of which each pixel has comparable dimension with individual microdroplet.
Face detection and tracking in a video by propagating detection probabilities (2003)

This paper presents a new probabilistic method for detecting and tracking multiple faces in a video sequence. The proposed method integrates the information of face probabilities provided by the detector and the temporal information provided by the tracker to produce a method superior to the available detection and tracking methods. The three novel contributions of the paper are: 1) Accumulation of probabilities of detection over a sequence. This leads to coherent detection over time and, thus, improves detection results. 2) Prediction of the detection parameters which are position, scale, and pose. This guarantees the accuracy of accumulation as well as a continuous detection. 3) The representation of pose is based on the combination of two detectors, one for frontal views and one for profiles. Face detection is fully automatic and is based on the method developed by Schneiderman and Kanade (2000). It uses local histograms of wavelet coefficients represented with respect to a coordinate frame fixed to the object. A probability of detection is obtained for each image position and at several scales and poses. The probabilities of detection are propagated over time using a Condensation filter and factored sampling. Prediction is based on a zero order model for position, scale, and pose; update uses the probability maps produced by the detection routine. The proposed method can handle multiple faces, appearing/disappearing faces as well as changing scale and pose. Experiments carried out on a large number of sequences taken from commercial movies and the Web show a clear improvement over the results of frame-based detection (in which the detector is applied to each frame of the video sequence).
A Functional and Putative Physiological Role of Calcitriol in Patched1/Smoothened Interaction (2015)

The Patched1 (Ptch)-mediated inhibition of Smoothened (Smo) is still an open question. However, a direct Ptch/Smo interaction has been excluded, Smo modulators were identified, but the endogenous signal transmitting molecule remains undiscovered. Here, we demonstrate that calcitriol, the hormonally active form of vitamin D3, is an excellent candidate for transmission of Ptch/Smo interaction. Our study reveals that Ptch expression is sufficient to release calcitriol from the cell and that calcitriol inhibits Smo action and ciliary translocation by acting on a site distinct from the 7-transmembrane domain or the cysteine-rich domain. Moreover calcitriol strongly synergizes with itraconazole (ITZ) in Smo inhibition, which did not result from elevated calcitriol bioavailability due to ITZ-mediated 24-hydroxylase inhibition but rather from a direct interaction of the compounds at the level of Smo. Together, we suggest that calcitriol represents a possible endogenous transmitter of Ptch/Smo interaction. Moreover calcitriol or calcitriol derivatives combined with ITZ might be a treatment option of Hedgehog-associated cancers.
Process Development of 1,2-Benzisothiazolin-3(2H)-one by Replacing of the Toxic Materials (2003)

1,2-Benzisothiazolin-3(2H)-one (2) was synthesized by 2,2′-dithiodibenzoic acid (1) with acetamide or urea in high yield via one-pot amidation-cyclization process.
Adrenergic innervation of rat sensory ganglia following proximal or distal painful sciatic neuropathy: distinct mechanisms revealed by anti‐NGF treatment (1999)

Sympathetic axons invade dorsal root ganglia (DRG) following nerve injury, and activity in the resulting pericellular axonal 'baskets' may underlie painful sympathetic-sensory coupling. Sympathetic sprouting into the DRG may be stimulated by nerve growth factor (NGF). To test this hypothesis, we investigated the effect of daily anti-NGF administration on pain and on sprouting in the DRG induced by chronic sciatic constriction injury (CCI) or L5 spinal nerve ligation (SNL). These models have been shown to differ subtly in the onset of pain behaviours and adrenergic sprouting, and we now demonstrate a fundamental difference in the way sympathetic axons invade the DRG: after CCI, perivascular noradrenergic collaterals sprouted into the DRG in a manner dependent upon peripherally derived NGF. In contrast, after SNL, regenerating sympathetic axons were diverted towards the DRG from the spinal nerve by the obstructing ligature, and this effect was only moderately impeded by anti-NGF. The differential dependence on anti-NGF suggests that adrenergic innervation of the DRG after SNL and CCI may reflect regenerative and collateral sprouting, respectively. Pain behaviour was similarly affected: anti-NGF completely prevented CCI-induced thermal hyperalgesia and mechanoallodynia, but the same treatment only partly relieved these symptoms following SNL. These differences emphasize that although CCI and SNL may result in similar behavioural abnormalities, the underlying mechanisms may be governed by distinct processes, differentially dependent on peripheral NGF. These mechanistic differences will have to be considered in the development of appropriate treatment strategies for neuropathic pain produced by different types of pathology.
Expression of human parathyroid hormone-(1-84) in Escherichia coli as a factor X-cleavable fusion protein. (1990)

Recombinant human parathyroid hormone (hPTH)-(1-84) was obtained from Escherichia coli using a cleavable fusion protein strategy. The fusion protein contains residues 1-138 of human growth hormone as the amino-terminal region and residues 1-84 of hPTH as the carboxyl-terminal region. A 7-residue linker containing the recognition/cleavage sequence of the site-specific blood coagulation protease activated factor X (factor Xa) joins the two regions. Intact hPTH-(1-84) is released from this fusion protein by cleavage in vitro with factor Xa. The fusion protein was produced at a high level and formed inclusion bodies which allowed it to be easily purified by low speed centrifugation, with a yield of approximately 50 mg/liter of culture. After factor Xa cleavage and high performance liquid chromatography purification, highly purified hPTH was obtained, with a final yield of 1.5-3 mg/liter. Physical and biological characterization of the purified hormone demonstrated that it was intact and active hPTH-(1-84).
Effects of unilateral stellate ganglion stimulation and ablation on electrophysiologic changes induced by acute myocardial ischemia in dogs. (1985)

We recorded direct-current extracellular electrograms simultaneously from 60 left ventricular epicardial sites in 38 alpha-chloralose-anesthetized dogs during repeated, 5 min coronary arterial occlusions. In each dog recordings made during control occlusions were compared with those made in occlusions after, or during, the following interventions on the sympathetic nervous system: left stellate ganglion stimulation, left stellectomy, right stellectomy, and clamping the abdominal aorta with intact sympathetic nerves to induce a rise of blood pressure equal to that present during left stellate stimulation. Heart rate was kept constant. Measurements included determination of TQ segment potentials and times of local activation. After 2 min of ischemia, the degree of TQ segment depression was increased by left stellate ganglion stimulation and was decreased by both left stellectomy and clamping the aorta. Also, the area showing negative TQ potentials, indicating decreased resting membrane potentials, was enlarged by both left stellate stimulation and right stellectomy and reduced by left stellectomy. No differences were found in the results of experiments in which the left anterior descending coronary artery was occluded and those in which the circumflex branch was occluded. Left stellate stimulation significantly improved conduction within the ischemic zone. No evidence was found to suggest that the arrhythmogenic effects of left stellate stimulation and of right stellectomy, confirmed in the present study, resulted from an increased likelihood for reentry in the subepicardium of the ischemic zone.
Core-shell structured titanium-nitrogen alloys with high strength, high thermal stability and good plasticity (2017)

Multifunctional materials with more than two good properties are widely required in modern industries. However, some properties are often trade-off with each other by single microstructural designation. For example, nanostructured materials have high strength, but low ductility and thermal stability. Here by means of spark plasma sintering (SPS) of nitrided Ti particles, we synthesized bulk core-shell structured Ti alloys with isolated soft coarse-grained Ti cores and hard Ti-N solid solution shells. The core-shell Ti alloys exhibit a high yield strength (~1.4 GPa) comparable to that of nanostructured states and high thermal stability (over 1100 °C, 0.71 of melting temperature), contributed by the hard Ti-N shells, as well as a good plasticity (fracture plasticity of 12%) due to the soft Ti cores. Our results demonstrate that this core-shell structure offers a design pathway towards an advanced material with enhancing strength-plasticity-thermal stability synergy.