gebhart/patrepeval huggingface dataset:
Transduction Peptides Within Naturally Occurring Proteins (2005)

First identified as peptides derived from the human immunodeficiency virus (HIV) transcriptional regulator Tat and the Drosophila transcription factor Antennapedia, transduction (or cell-penetrating) peptide sequences enable soluble proteins to cross biological membranes and interact with cytosolic and nuclear targets. Proteins containing such sequences have been found to function as transcription factors, to inhibit apoptosis, to play roles in axon guidance, or to transport viral mRNA between cells. The recent demonstration that dynorphins are able to act as transduction peptides suggests that these neuropeptides may have roles independent of opiate receptor activation.
A proteomics approach to characterizing human submandibular gland cell lines by fluorescent two-dimensional differential in-gel electrophoresis (2006)

The human salivary glands have a variety of histologic features such as intercalated duct cells, myoepithelial cells and acinar cells. A neoplastic human salivary intercalated duct cell line (HSG) and its derivatives, HSG with a myoepithelial cell phenotype (HSG-AZA1) and HSG with an acinar cell phenotype (HSG-AZA3) induced by 5-aza-2'-dC treatment of HSG cells, have been reported. To identify characterization of intercalated duct cells, myoepithelial cells and acinar cells in the salivary gland, we selected HSG, HSG-AZA1 and HSG-AZA3 cell lines to perform two-dimensional electrophoresis analysis. We used a fluorescent two-dimensional differential in-gel electrophoresis (2-D-DIGE) for comparative proteomics, which improved the reproducibility and reliability of differential protein expression analysis between the samples. Furthermore, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) peptide mass fingerprinting (PMF) was used to identify the proteins. These methods were combined to approach the protein profiles associated with characterization between HSG, HSG-AZA1 and HSG-AZA3 cells. Using these strategies, we identified seven HSG associated proteins, such as actin-beta, hydrocephalus inducing protein, L-plastin, KIAA0657 protein, septin 6 isoform A, lamin A/C isoform 2 and superoxide dismutase 2, three HSG-AZA1 associated proteins such as ubiquitin carboxyl-terminal esterase L1, myosin light chain 2 and muscle creatine kinase, and two HSG-AZA3 associated proteins, microtubule-associated protein 6 and Annexin A3. These results suggest that the proteins are associated with characterization of the salivary gland.
Dynamics of Persistent and Acute Deformed Wing Virus Infections in Honey Bees, Apis mellifera (2011)

The dynamics of viruses are critical to our understanding of disease pathogenesis. Using honey bee Deformed wing virus (DWV) as a model, we conducted field and laboratory studies to investigate the roles of abiotic and biotic stress factors as well as host health conditions in dynamics of virus replication in honey bees. The results showed that temperature decline could lead to not only significant decrease in the rate for pupae to emerge as adult bees, but also an increased severity of the virus infection in emerged bees, partly explaining the high levels of winter losses of managed honey bees, Apis mellifera, around the world. By experimentally exposing adult bees with variable levels of parasitic mite Varroa destructor, we showed that the severity of DWV infection was positively correlated with the density and time period of Varroa mite infestation, confirming the role of Varroa mites in virus transmission and activation in honey bees. Further, we showed that host conditions have a significant impact on the outcome of DWV infection as bees that originate from strong colonies resist DWV infection and replication significantly better than bee originating from weak colonies. The information obtained from this study has important implications for enhancing our understanding of host‑pathogen interactions and can be used to develop effective disease control strategies for honey bees.
Expression Level of Valosin-Containing Protein (p97) Is Associated with Prognosis of Esophageal Carcinoma (2004)

This study demonstrated the prognostic significance of VCP expression in ESCC.
PD-L1–Driven Tolerance Protects Neurogenin3-Induced Islet Neogenesis to Reverse Established Type 1 Diabetes in NOD Mice (2014)

A breakdown in self-tolerance underlies autoimmune destruction of β-cells and type 1 diabetes. A cure by restoring β-cell mass is limited by the availability of transplantable β-cells and the need for chronic immunosuppression. Evidence indicates that inhibiting costimulation through the PD-1/PD-L1 pathway is central to immune tolerance. We therefore tested whether induction of islet neogenesis in the liver, protected by PD-L1-driven tolerance, reverses diabetes in NOD mice. We demonstrated a robust induction of neo-islets in the liver of diabetic NOD mice by gene transfer of Neurogenin3, the islet-defining factor, along with betacellulin, an islet growth factor. These neo-islets expressed all the major pancreatic hormones and transcription factors. However, an enduring restoration of glucose-stimulated insulin secretion and euglycemia occurs only when tolerance is also induced by the targeted overexpression of PD-L1 in the neo-islets, which results in inhibition of proliferation and increased apoptosis of infiltrating CD4(+) T cells. Further analysis revealed an inhibition of cytokine production from lymphocytes isolated from the liver but not from the spleen of treated mice, indicating that treatment did not result in generalized immunosuppression. This treatment strategy leads to persistence of functional neo-islets that resist autoimmune destruction and consequently an enduring reversal of diabetes in NOD mice.
Selectivity: A Key to Synthetic Efficiency (1983)

The efficient synthesis of organic compounds requires the development of processes with enhanced selectivity. Selectivity is categorized according to chemical reactivity (chemoselectivity), orientation (regioselectivity), and spatial arrangement (diastereoselectivity and enantioselectivity). Recent developments in reduction-oxidation methods and C-C bond forming reactions illustrate some solutions to problems of selectivity. The design of selectivity-inducing groups and the increased role of main group and transition metals in enhancing selectivity are especially noted.
DROP-ON-DEMAND INKJET BIOPRINTING: A PRIMER (2011)

Engineering complex biological structures for regenerative medicine, in vitro tissue analysis, and pharmaceutical testing require new fabrication techniques that can place specific cells in specific target locations. Conventional cell seeding methods cannot achieve this level of spatial resolution. Biofabrication is a rapidly advancing field that uses a variety of delivery mechanisms to achieve the spatial resolution necessary to place cells, biomaterials, and bioactive macromolecules in specific target locations. One new technique within this field is bioprinting, which uses drop-on-demand delivery mechanisms to fabricate biological structures. This review focuses on drop-on-demand inkjet bioprinting and provides a primer for researchers seeking to enter the field.
FSS-1000: A 1000-Class Dataset for Few-Shot Segmentation (2020)

Over the past few years, we have witnessed the success of deep learning in image recognition thanks to the availability of large-scale human-annotated datasets such as PASCAL VOC, ImageNet, and COCO. Although these datasets have covered a wide range of object categories, there are still a significant number of objects that are not included. Can we perform the same task without a lot of human annotations? In this paper, we are interested in few-shot object segmentation where the number of annotated training examples are limited to 5 only. To evaluate and validate the performance of our approach, we have built a few-shot segmentation dataset, FSS-1000, which consists of 1000 object classes with pixelwise annotation of ground-truth segmentation. Unique in FSS-1000, our dataset contains significant number of objects that have never been seen or annotated in previous datasets, such as tiny daily objects, merchandise, cartoon characters, logos, etc. We build our baseline model using standard backbone networks such as VGG-16, ResNet-101, and Inception. To our surprise, we found that training our model from scratch using FSS-1000 achieves comparable and even better results than training with weights pre-trained by ImageNet which is more than 100 times larger than FSS-1000. Both our approach and dataset are simple, effective, and easily extensible to learn segmentation of new object classes given very few annotated training examples. Dataset is available at https://github.com/HKUSTCV/FSS-1000.
Visual Gaze Estimation by Joint Head and Eye Information (2010)

In this paper, we present an unconstrained visual gaze estimation system. The proposed method extracts the visual field of view of a person looking at a target scene in order to estimate the approximate location of interest (visual gaze). The novelty of the system is the joint use of head pose and eye location information to fine tune the visual gaze estimated by the head pose only, so that the system can be used in multiple scenarios. The improvements obtained by the proposed approach are validated using the Boston University head pose dataset, on which the standard deviation of the joint visual gaze estimation improved by 61:06% horizontally and 52:23% vertically with respect to the gaze estimation obtained by the head pose only. A user study shows the potential of the proposed system.
Protein Binding and Concentrations of Cephaloridine and Cefazolin in Serum and Interstitial Fluid of Dogs (1976)

Percentages of free and protein-bound cefazolin and cephaloridine in serum and interstitial fluid of dogs were determined by ultrafiltration and microbiologic assay. The percentages of cephaloridine and cefazolin bound to protein in serum were 10% and 80%, respectively. In interstitial fluid accumulating within tissue-embedded polypropylene capsules, 29% of cefazolin was bound to protein, and cephaloridine was unbound. Both antibiotics rapidly penetrated the interstitial fluid and attained measurable levels 5 min after intravenous administration. Levels of total cefazolin in the interstitial fluid were generally higher than those of cephaloridine; however, concentrations of free cephaloridine in the fluid exceeded the levels of free cefazolin after the first 15 min. Binding of anitbiotics by serum proteins does not restrict such agents to the intravascular space, since a highly protein-bound compound has been shown to penetrate interstitial fluid as readily as one that is minimally bound. It should be noted, however, that this penetration may be due primarily to the slow rate of binding of cefazolin to serum proteins.
ErbB3/HER3 intracellular domain is competent to bind ATP and catalyze autophosphorylation (2010)

ErbB3/HER3 is one of four members of the human epidermal growth factor receptor (EGFR/HER) or ErbB receptor tyrosine kinase family. ErbB3 binds neuregulins via its extracellular region and signals primarily by heterodimerizing with ErbB2/HER2/Neu. A recently appreciated role for ErbB3 in resistance of tumor cells to EGFR/ErbB2-targeted therapeutics has made it a focus of attention. However, efforts to inactivate ErbB3 therapeutically in parallel with other ErbB receptors are challenging because its intracellular kinase domain is thought to be an inactive pseudokinase that lacks several key conserved (and catalytically important) residues-including the catalytic base aspartate. We report here that, despite these sequence alterations, ErbB3 retains sufficient kinase activity to robustly trans-autophosphorylate its intracellular region--although it is substantially less active than EGFR and does not phosphorylate exogenous peptides. The ErbB3 kinase domain binds ATP with a K(d) of approximately 1.1 microM. We describe a crystal structure of ErbB3 kinase bound to an ATP analogue, which resembles the inactive EGFR and ErbB4 kinase domains (but with a shortened alphaC-helix). Whereas mutations that destabilize this configuration activate EGFR and ErbB4 (and promote EGFR-dependent lung cancers), a similar mutation conversely inactivates ErbB3. Using quantum mechanics/molecular mechanics simulations, we delineate a reaction pathway for ErbB3-catalyzed phosphoryl transfer that does not require the conserved catalytic base and can be catalyzed by the "inactive-like" configuration observed crystallographically. These findings suggest that ErbB3 kinase activity within receptor dimers may be crucial for signaling and could represent an important therapeutic target.
Nonphotic entrainment of the human circadian pacemaker (1998)

In organisms as diverse as single-celled algae and humans, light is the primary stimulus mediating entrainment of the circadian biological clock. Reports that some totally blind individuals appear entrained to the 24-h day have suggested that nonphotic stimuli may also be effective circadian synchronizers in humans, although the nonphotic stimuli are probably comparatively weak synchronizers, because the circadian rhythms of many totally blind individuals "free run" even when they maintain a 24-h activity-rest schedule. To investigate entrainment by nonphotic synchronizers, we studied the endogenous circadian melatonin and core body temperature rhythms of 15 totally blind subjects who lacked conscious light perception and exhibited no suppression of plasma melatonin in response to ocular bright-light exposure. Nine of these fifteen blind individuals were able to maintain synchronization to the 24-h day, albeit often at an atypical phase angle of entrainment. Nonphotic stimuli also synchronized the endogenous circadian rhythms of a totally blind individual to a non-24-h schedule while living in constant near darkness. We conclude that nonphotic stimuli can entrain the human circadian pacemaker in some individuals lacking ocular circadian photoreception.
Twice-Daily 0.2% Brimonidine–0.5% Timolol Fixed-Combination Therapy vs Monotherapy With Timolol or Brimonidine in Patients With Glaucoma or Ocular Hypertension (2006)

Fixed brimonidine-timolol is an effective and convenient IOP-lowering therapy.
Synthesis, X-ray Crystallographic, and NMR Characterizations of Platinum(II) and Platinum(IV) Pyrophosphato Complexes (2008)

A series of mononuclear cis-diamineplatinum(II) pyrophosphato complexes containing ammine (am), trans-1,2-cyclohexanediamine (dach), and 1,2-ethanediamine (en) as the amine ligands were synthesized and characterized by (31)P and (195)Pt NMR spectroscopy. Chemical shifts of (31)P NMR resonances of these completely deprotonated complexes appear at 2.12, 1.78, and 1.93 ppm, indicating a coordination chemical shift of at least 8 ppm. The (195)Pt NMR chemical shifts for the am and dach complexes were observed at -1503 and -1729 ppm. The complexes are highly stable at neutral pH; no aquation due to the release of either phosphate or amine ligands was observed within 48 h. Furthermore, no partial deligation of the pyrophosphate ligand was detected within several days at neutral pH. At lower pH, however, release of a pyrophosphate ion was observed with concomitant formation of a bridged pyrophosphatoplatinum(II) dinuclear complex. The extended crystal structure containing the dach ligand revealed a zigzag chain stacked in a head-to-tail fashion. Moreover, two zigzag chains are juxtaposed in a parallel fashion and supported by additional hydrogen bonds reminiscent of DNA structures where two strands of DNA bases are held by hydrogen bonds. Theoretical calculations support the notion that the two dinuclear units are held together primarily by hydrogen bonds between the amine and phosphate moieties. Platinum(II) pyrophosphato complexes were readily oxidized by hydrogen peroxide to yield cis-diamine-trans-dihydroxopyrophosphatoplatinum(IV) complexes. Two of these complexes, containing am and en, were characterized by X-ray crystallography. Notable structural features include Pt-O (phosphate) bond distances of 2.021-2.086 A and departures from 180 degrees in trans-HO-Pt-OH bond angles, >90 degrees in O-Pt-O, and >90 degrees in cis-N-Pt-N bond angles. The departure in the trans-HO-Pt-OH angle is more pronounced in the 1,2-ethanediamine complex compared to the dach analogue because of the existence of two molecules possessing enantiomeric conformations within the asymmetric unit. (31)P NMR spectra exhibited well-resolved (195)Pt satellites with coupling constants of 15.4 Hz for the ammine and 25.9 Hz for both the 1,2-ethanediamine and trans-1,2-cyclohexanediamine complexes. The (195)Pt NMR spectrum of the ammine complex clearly showed coupling with two equivalent N atoms.
Carrier Transport in Two-Dimensional Graphene Layers (2007)

Carrier transport in gated 2D graphene monolayers is considered in the presence of scattering by random charged impurity centers with density n(i). Excellent quantitative agreement is obtained (for carrier density n>10(12) cm(-2)) with existing experimental data. The conductivity scales linearly with n/n(i) in the theory. We explain the experimentally observed asymmetry between electron and hole conductivities, and the high-density saturation of conductivity for the highest mobility samples. We argue that the experimentally observed saturation of conductivity at low density arises from the charged impurity induced inhomogeneity in the graphene carrier density which becomes severe for n less, similarn(i) approximately 10(12) cm(-2).
Identification of the catalytic triad in the haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (1999)

The haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (LinB) is the enzyme involved in the gamma-hexachlorocyclohexane degradation. This enzyme hydrolyses a broad range of halogenated aliphatic compounds via an alkyl-enzyme intermediate. LinB is believed to belong to the family of alpha/beta-hydrolases which employ a catalytic triad, i.e. nucleophile-histidine-acid, during the catalytic reaction. The position of the catalytic triad within the sequence of LinB was probed by a site-directed mutagenesis. The catalytic triad residues of the haloalkane dehalogenase LinB are proposed to be D108, H272 and E132. The topological location of the catalytic acid (E132) is after the beta-strand six which corresponds to the location of catalytic acid in the pancreatic lipase, but not in the haloalkane dehalogenase of Xanthobacter autotrophicus GJ10 which contains the catalytic acid after the beta-strand seven.
Picogram quantities of anti-Ig antibodies coupled to dextran induce B cell proliferation. (1988)

To investigate the properties which enable type 2 Ag, as exemplified by dextran and Ficoll, to stimulate high levels of antibody responses in the relative absence of T cells, we conjugated anti-IgD and anti-IgM mAb to both dextran and Ficoll and examined their B cell-activating properties. Such conjugated anti-Ig antibodies stimulated both early and later stages of B cell activation at picogram concentrations, which are at least 1000-fold lower than that required for B cell stimulation by unconjugated anti-Ig antibodies, and the level of proliferation they stimulated was on average 10-fold greater. Furthermore, concentrations of anti-Ig dextran (100 pg/ml) which modulated little sIgD from the B cell surface were strong inducers of enhanced B cell expression of MHC class II molecules. Conjugation of Fab fragments of anti-IgD or nonmitogenic anti-IgM mAb to dextran rendered them as mitogenic as dextran conjugated to strongly stimulatory anti-IgD or anti-IgM antibodies. The ability of dextran and Ficoll to serve as effective carrier molecules for anti-IgD was not related solely to their large m.w., because anti-IgD coupled to polymerized BSA (m.w. 1.5 X 10(6), was only 10- to 50-fold more potent than unconjugated anti-IgD antibodies at stimulating B cell DNA synthesis. These results suggest, therefore, that the unique ability of picogram concentrations of haptenated type 2 Ag to stimulate Ig secretion in the absence of T cells may be a function of their ability to promote effective cross-linking without resulting in the modulation of sIg. This would enable such Ag to mediate repetitive B cell signaling, a situation that cannot be achieved by unconjugated anti-Ig antibodies which result in modulation of sIg at their mitogenic concentrations. These compounds therefore may be employed to study B cell activation stimulated by sIg cross-linking at concentrations that may more closely reflect those which are achieved under physiologic conditions by type 2 Ag.
Nucleoside transport sites in a cultured human retinal cell line established by SV-40 T antigen gene (1994)

Adenosine, an important neuromodulatory compound in the brain and retina, is a potent vasodilator in most vascular beds throughout the body. Its actions are potentiated by inhibitors of nucleoside transport into cells. Knowledge of the existence of specific adenosine uptake systems in mammalian retina and the inhibition of the uptake by nitrobenzylthioinosine (NBMPR), a potent inhibitor of nucleoside transport, raises the possibility that the associated nucleoside transport system may be of pharmacological importance in retinal function. We have characterized the binding of the nucleoside transporter probe, [3H]NBMPR, to a cultured human retinal cell line established by transfection of SV-40 T antigen plasmid-DNA. The binding was specific, saturable and reversible. Scatchard analysis of the saturation data revealed that NBMPR binds to a homogeneous population of high affinity binding sites (KD = 0.65 +/- 0.22 nM; Bmax = 466 +/- 157 fmol/mg protein) characteristically similar to the binding sites in human retinal tissue (KD = 0.32 +/- 0.01 nM; Bmax = 292 +/- 41 fmol/mg protein). Selected compounds inhibited the binding in the cell line and retinal tissue with the same rank order of potency, suggesting that the transporters in the cell line and retinal tissue are similar. The data showed that the cell line is a useful model for the study of nucleoside transporter function in human retina.
Research Challenges and Opportunities in Mobile Applications (2011)

tions, especially focusing on educational aspects and research problems, pointing out issues and opportunities for students in this area. Our goal is to explore challenges, possibilities, and approaches for enabling speech processing, as well as convenient and effective speech and multimodal user interfaces for mobile environments.