gebhart/patrepeval huggingface dataset:
Axonal regeneration into Schwann cell‐seeded guidance channels grafted into transected adult rat spinal cord (1995)

Schwann cells (SC) have been shown to promote regeneration in both the peripheral and central nervous systems. In this study we tested the ability of SC to enhance axonal regeneration in adult rat spinal cord by grafting SC-seeded guidance channels into transected cords. SC were purified in culture from adult inbred rat sciatic nerves, suspended in Matrigel, and seeded into semipermeable PAN/PVC channels (2.6 mm I.D. x 10 mm long) at a final density of 120 x 10(6) cells/ml. Channels filled with Matrigel alone served as controls. Adult isologous rat spinal cords were transected at the T8 level, and segments T9-T11 were removed. The rostral stump was inserted 1 mm into channels with capped distal ends. One month after grafting, a vascularized tissue cable was present within the channel in all animals. In SC-seeded channels (n = 14), a mean of 501 myelinated axons was found in the cable, and many axons extended 9-10 mm. Electron microscopy revealed typical SC ensheathment and myelination of axons with four times more unmyelinated than myelinated axons. Control channels (n = 8) contained fewer myelinated axons (mean = 71). When SC were prelabeled in culture with a nuclear dye, labeled nuclei were observed at 30 days, confirming SC survival. Astrocytes identified by glial fibrillary acidic protein staining did not migrate far into the cable, and prelabeled SC did not enter the cord. Lack of immunostaining for serotonin and dopamine beta-hydroxylase indicated that supraspinal axons did not regenerate into the cable. Fast Blue injections into the middle of the cable (n = 3) marked spinal cord interneurons (mean = 306) as far as nine segments rostral (25 mm, C7) extending axons into the graft; fewer dorsal root ganglion neurons were retrogradely labeled. In conclusion, purified populations of SC transplanted within channels promote both propriospinal and sensory axonal regeneration in the adult rat thoracic spinal cord.
Vismodegib (erivedge) for advanced Basal cell carcinoma. (2012)

Vismodegib (Erivedge) for advanced basal cell carcinoma.
Characterization of novel LPXTG-containing proteins of Staphylococcus aureus identified from genome sequences (2003)

Twenty-one genes encoding surface proteins belonging to the LPXTG family have been identified by in silico analysis of six Staphylococcus aureus genome sequences. Eleven genes encode previously described proteins, while 10 have not yet been characterized. Of these, eight contain the cell-wall sorting signal LPXTG responsible for covalently anchoring proteins to the cell-wall peptidoglycan. The remaining two, SasF and SasD, harbour a single residue variation in the fourth position of the LPXTG motif (LPXAG). Western blotting of lysostaphin-solubilized S. aureus cell-wall proteins demonstrated the release of SasF in the cell-wall fraction, indicating that proteins carrying LPXAG are sorted normally. Analysis of primary sequences of the Staphylococcus aureus surface (Sas) proteins indicated that several share a similar structural organization and a common signal sequence with previously characterized LPXTG proteins of S. aureus and other Gram-positive cocci. Protein SasG has 128 residue B repeats that are almost identical at the DNA level. PCR analysis indicated that recombinants with repeat length variations are present in the bacterial population whereas they are not detectable in the B-repeat-encoding region of sdrD. The sasG and sasH genes are significantly associated with invasive disease isolates compared to nasal carriage isolates. Several IgG samples purified from patients recovering from S. aureus infections had higher titres against Sas proteins than control IgG, suggesting that expression occurred during infection in some patients.
Association of Exaggerated HPA Axis Response to the Initial Injection of Interferon-Alpha With Development of Depression During Interferon-Alpha Therapy (2003)

The HPA axis response to the acute administration of IFN-alpha reveals a vulnerability to IFN-alpha-induced depression, possibly due to sensitization of corticotropin-releasing factor pathways.
Novel Insights into Interleukin 6 (IL-6) Cis- and Trans-signaling Pathways by Differentially Manipulating the Assembly of the IL-6 Signaling Complex (2015)

The IL-6 signaling complex is described as a hexamer, formed by the association of two IL-6·IL-6 receptor (IL-6R)·gp130 trimers, with gp130 being the signal transducer inducing cis- and trans-mediated signaling via a membrane-bound or soluble form of the IL-6R, respectively. 25F10 is an anti-mouse IL-6R mAb that binds to both membrane-bound IL-6R and soluble IL-6R with the unique property of specifically inhibiting trans-mediated signaling events. In this study, epitope mapping revealed that 25F10 interacts at site IIb of IL-6R but allows the binding of IL-6 to the IL-6R and the recruitment of gp130, forming a trimer complex. Binding of 25F10 to IL-6R prevented the formation of the hexameric complex obligate for trans-mediated signaling, suggesting that the cis- and trans-modes of IL-6 signaling adopt different mechanisms for receptor complex assembly. To study this phenomenon also in the human system, we developed NI-1201, a mAb that targets, in the human IL-6R sequence, the epitope recognized by 25F10 for mice. Interestingly, NI-1201, however, did not selectively inhibit human IL-6 trans-signaling, although both mAbs produced beneficial outcomes in conditions of exacerbated IL-6 as compared with a site I-directed mAb. These findings shed light on the complexity of IL-6 signaling. First, triggering cis- versus trans-mediated IL-6 signaling occurs via distinctive mechanisms for receptor complex assembly in mice. Second, the formation of the receptor complex leading to cis- and trans-signaling biology in mice and humans is different, and this should be taken into account when developing strategies to inhibit IL-6 clinically.
Differential loss of envelope glycoprotein gp120 from virions of human immunodeficiency virus type 1 isolates: effects on infectivity and neutralization (1991)

Several parameters which may affect the infectivity of human immunodeficiency virus type 1 in tissue culture were analyzed. In particular, we used gel exclusion chromatography to investigate how the loss of the surface glycoprotein gp120 from virions of the HTLV-IIIB (IIIB), HTLV-IIIRF (RF), and SF-2 isolates modulates infectivity. In IIIB and RF cultures, a high proportion of the total gp120 was virion bound initially but was gradually lost from the virions over time. In contrast, most of the gp120 (and p24) in SF-2-infected cultures was soluble and the few particles present had a fivefold-lower level of virus-bound gp120. However, this reduced level of virion-bound gp120 was more resistant to shedding. Loss of a major proportion of gp120 from IIIB and RF virions resulted in reduced infectivities, and in addition, the resulting accumulation of soluble gp120 in the cultures could competitively inhibit viral infection, especially with SF-2. Increased shedding of virion gp120 also affected the neutralization of IIIB and RF particles. However, the high sensitivity to human serum neutralization characteristic of SF-2 was unaffected by soluble gp120 in cultures, suggesting that the epitopes responsible are not present on soluble gp120.
Universal Inbox: providing extensible personal mobility and service mobility in an integrated communication network (2002)

Communication technology has been seeing rapid growth, characterized by new access networks (e.g. cellular, pager, wireless-IP) and end-devices (e.g. PDAs, two-way pagers, multi-model access devices). There have been several efforts at integrating services across such heterogeneity. However, little work has been done on identifying an underlying architecture for such an integration. We identify the requirements for this in the context of an integrated network with heterogeneous end-points. The Universal Inbox provides (a) generic data type transformation, (b) customizable redirection of incoming communication based on user preference profiles, and (c) device name mapping and translation. We present an architecture mapping these functionalities to reusable infrastructure components realized as Internet services. The unique feature of the architecture is its extensibility-it allows not only the integration of existing end-points but also extension in terms of the end-devices and novel services it can handle. We have implemented the Universal Inbox components in a test-bed setting, supporting a variety of devices and services: GSM cellular phones, voice-over-IP end-points, voice-mail, e-mail, instant messaging service, etc. With our architecture, building personal mobility and service mobility features and extending them to new end-points has been easy in concept and in implementation. The performance analyses with the initial implementation show that even the heavy-weight components can be scaled to accommodate a large user base.
Polyclonal and Monoclonal Antibodies in Clinic (2013)

Immunoglobulins (Ig) or antibodies are heavy plasma proteins, with sugar chains added to amino-acid residues by N-linked glycosylation and occasionally by O-linked glycosylation. The versatility of antibodies is demonstrated by the various functions that they mediate such as neutralization, agglutination, fixation with activation of complement and activation of effector cells. Naturally occurring antibodies protect the organism against harmful pathogens, viruses and infections. In addition, almost any organic chemical induces antibody production of antibodies that would bind specifically to the chemical. These antibodies are often produced from multiple B cell clones and referred to as polyclonal antibodies. In recent years, scientists have exploited the highly evolved machinery of the immune system to produce structurally and functionally complex molecules such as antibodies from a single B clone, heralding the era of monoclonal antibodies. Most of the antibodies currently in the clinic, target components of the immune system, are not curative and seek to alleviate symptoms rather than cure disease. Our group used a novel strategy to identify reparative human monoclonal antibodies distinct from conventional antibodies. In this chapter, we discuss the therapeutic relevance of both polyclonal and monoclonal antibodies in clinic.
Interleukin-12 and Host Defense against MurinePneumocystisPneumonia (2008)

Little is known about the role of the cytokine interleukin-12 (IL-12) in Pneumocystis pneumonia or its potential use as immunotherapy. We asked whether release of IL-12 is part of the normal host response to this infection and whether local treatment with IL-12 or gene transfer of IL-12 could accelerate clearance of infection. IL-12 was assayed by enzyme-linked immunosorbent assay in normal mice and in mice deficient in IL-12 after inoculation of Pneumocystis carinii. P. carinii-infected mice were treated with local instillation of IL-12 and gene transfer of the IL-12 gene. Inoculation of P. carinii into normal mice evoked a brisk release of IL-12 into lung tissue, and IL-12 P35-deficient mice showed delayed clearance of infection measured by PCR for P. carinii rRNA. In control mice, intranasal recombinant IL-12 accelerated clearance of infection, and this was associated with increased recruitment of inflammatory cells into lavage fluid and increased release of tumor necrosis factor alpha, IL-12, and gamma interferon. Similar results were observed in infected mice depleted of CD4+ lymphocytes by using in vivo transfer of the IL-12 gene in a replication-deficient adenoviral vector. IL-12 is part of the normal host response to infection with P. carinii. IL-12 therapy can enhance host resistance to infection in both normal mice and mice depleted of CD4+ T lymphocytes. A treatment effect of IL-12 is mediated through enhanced inflammatory cell recruitment into lung tissue and increased tissue concentrations of proinflammatory cytokines.
PICOSECOND-INDUCED NONLINEAR ABSORPTION IN LIQUID CRYSTAL MEDIA (1995)

The contributions to the nonlinear absorption of liquid crystal media in their isotropic phase are measured using a picosecond pump/probe technique at 587 nm. Good agreement between the experimental data and theory is obtained by assuming that two-photon absorption and excited state absorption dominate the nonlinear optical response. The important parameters are extracted from the experimental data and it is shown that the nonlinear absorption depends strongly on the molecular structure. The lifetime of the excited state is measured and found to compare well with the fluorescence lifetime.
cDNA cloning of murine interleukin-HP1: homology with human interleukin 6 (1988)

Interleukin-HP1 (HP1) is a murine T cell-derived lymphokine, originally described as a growth factor for B cell hybridomas and plasmacytomas, that was recently shown to stimulate growth and differentiation of normal B and T lymphocytes. Here, we describe a cDNA for HP1 that was isolated from a library prepared using mRNA of a murine helper T cell clone activated with a clonotypic antibody. The cDNA, which hybridizes with a mRNA of approximately 1300 bp, encodes a polypeptide consisting of 211 amino acids with a typical signal sequence of 24 residues followed by 187 amino acids, which form the mature protein (Mr = 21,710). No N-glycosylation site but several potential O-glycosylation sites were identified in the predicted sequence. Comparison of the cDNA sequence of HP1 with that of human interleukin 6 disclosed a homology of 65% at the DNA level and of 42% at the protein level with a maximum of 57% for the segment spanning residues 42-102 of mature HP1. Considering the functional homology that was previously established between these two proteins, we therefore propose that HP1 be renamed murine interleukin 6.
Acquisition of Desiccation Tolerance and Longevity in Seeds of Arabidopsis thaliana (A Comparative Study Using Abscisic Acid-Insensitive abi3 Mutants) (1993)

Two new abscisic acid (ABA)-insensitive mutants of Arabidopsis thaliana affected in the abi3 locus are described. These new mutants are severely ABA insensitive. Like the earlier described abi3-1 and the ABA-deficient and -insensitive double mutant aba,abi3, these new mutants vary in the extent of ABA-correlated physiological responses. Mutant seeds fail to degrade chlorophyll during maturation and show no dormancy, and desiccation tolerance and longevity are poorly developed. Carbohydrate accumulation as well as synthesis of LEA or RAB proteins are often suggested to be essential for acquisition of desiccation tolerance. In this work two points are demonstrated. (a) Accumulation of carbohydrates as such does not correlate with acquisition of desiccation tolerance or longevity. It is suggested that a low ratio of mono- to oligosac-charides rather than the absolute amount of carbohydrates controls seed longevity or stability to desiccation tolerance. (b) Synthesis of a few assorted proteins, which is responsive to ABA in the later part of seed maturation, is not correlated with desiccation tolerance or longevity.
Increased expression of the Mr 72,000 type IV collagenase in human colonic adenocarcinoma. (1991)

Proteolytic enzymes, such as type IV collagenase, play an important role in tumor invasion and metastasis. To examine Mr 72,000 type IV collagenase expression in human colon carcinoma, blot hybridization of total RNA from 19 primary colon tumors were performed. These filters were probed with complementary DNA probes encoding the Mr 72,000 type IV collagenase metalloenzyme. The results were expressed as the ratio of the messenger RNA (mRNA) levels in the tumor tissue to that in the adjacent normal mucosa (R). The level of the 3.1-kilobase type IV collagenase mRNA was higher in the primary tumor than in the normal adjacent colonic mucosa in 13 of 18 (72%) cases with a diagnosis of adenocarcinoma. These cases were divided into high expression (R, 4.50 to 29.34) and intermediate expression (R, 2.54 to 3.31) subgroups. Both groups showed statistically significant (P less than 0.05) elevations when compared with the five cases showing the lowest levels of Mr 72,000 type IV collagenase mRNA expression (low expression subgroup; R, 0.96 to 1.48). With this demonstrated elevation of Mr 72,000 type IV collagenase mRNA in colorectal adenocarcinoma we examined concomitant expression at the protein level using immunohistochemical techniques. Immunohistochemical examination of 70 cases of colon tumors, including 30 benign adenomas, using anti-Mr 72,000 type IV collagenase antibodies demonstrated a significant correlation with Duke's classification (P less than 0.001). Our results suggest that enhanced expression of the Mr 72,000 type IV collagenase enzyme may be a marker of human colorectal tumor invasiveness.
Loss of acute pilocarpine effect on outflow facility following surgical disinsertion and retrodisplacement of the ciliary muscle from the scleral spur in the cynomolgus monkey. (1976)

An ab-interno goniotomy-like operation for disinserting the ciliary muscle from the scleral spur in cynomolgus monkeys is described. Following postoperative miotic and corticosteroid treatment, the eyes did well clinically and the muscle reattached to the sclera posterior to the spur. Outflow facility and intraocular pressure were mildly reduced. There was drainage of aqueous humor via the conventional outflow routes, and blood flow to the ciliary body. The outflow facility increasing effect of intravenous and intracameral pilocarpine was nearly completely eliminated. These and other data suggest that: (1) the ciliary muscle was permanently disconnected, anatomically and functionally, from the trabecular meshwork; (2) the trabecular meshwork and Schlemm's canal remained relatively normal structurally and functionally; (3) monkey eyes with retrodisplaced ciliary muscles may prove valuable for testing the functional effects of drugs directly on the conventional outflow channels, independent of drug actions on the ciliary muscle.
Integrated multisensor chip (1986)

A multipurpose integrated-sensor chip has been fabricated for the simultaneous measurement of physical and chemical variables. The multipurpose chip which measures 8 × 9 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> contains conventional MOS devices for signal conditioning, array accessing, and output buffering along with the following on-chip sensors: a gas-flow sensor, an infrared-sensing array, a chemical-reaction sensor, cantilever-beam accelerometers, surface-acoustic-wave (SAW) vapor sensors, a tactile sensor array, and an infrared charge-coupled device imager. The multisensing functions of this chip utilize both the pyroelectdc and piezoelectric effects in ZnO thin films. Fabrication of the chip is carried out using a conventional 3-µm Si NMOS process combined with Si micromachining techniques. Compatible fabrication technology and sensor properties are described.
Plasmon enhanced colloidal nanocrystal composites incorporating Au nanoparticles in a repeating layered architecture (2009)

In summary, we presented plasmonic high-efficiency Au-CdTe nanocomposite films in a three-dimensional construction of repeating layers. These composites integrate Au nanoparticles at a fixed optimal dielectric spacing and plasmon-couple them with CdTe nanocrystal emitters for significantly enhanced emission. In the Au-CdTe nanocomposite film, we showed that the emission of CdTe NCs is increased by 4.37 fold and the quantum efficiency is increased by 43%, reaching a high level of 30% in film. This proof-of-concept demonstration of plasmonic AuCdTe nanocomposite films opens a new direction for the development of future NC-based optoelectronic devices.
Identifying Effective Enzyme Activity Targets for Recombinant Class I and Class II Collagenase for Successful Human Islet Isolation (2015)

A broader C1:C2 ratio can be used for human islet isolation than has been used in the past. Recombinant collagenase is an effective replacement for the natural enzyme and we have determined that high islet yield can be obtained even with low doses of rC1:rC2, which is beneficial for the survival of islets.
Comparative model building of interleukin‐7 using interleukin‐4 as a template: A structural hypothesis that displays atypical surface chemistry in helix D important for receptor activation (2000)

Using a combination of theoretical sequence structure recognition predictions and experimental disulfide bond assignments, a three-dimensional (3D) model of human interleukin-7 (hIL-7) was constructed that predicts atypical surface chemistry in helix D that is important for receptor activation. A 3D model of hIL-7 was built using the X-ray crystal structure of interleukin-4 (IL-4) as a template (Walter MR et al., 1992, J Mol Biol. 224:1075-1085; Walter MR et al., 1992, J Biol Chem 267:20371-20376). Core secondary structures were constructed from sequences of hIL-7 predicted to form helices. The model was constructed by superimposing IL-7 helices onto the IL-4 template and connecting them together in an up-up down-down topology. The model was finished by incorporating the disulfide bond assignments (Cys3, Cys142), (Cys35, Cys130), and (Cys48, Cys93), which were determined by MALDI mass spectroscopy and site-directed mutagenesis (Cosenza L, Sweeney E, Murphy JR, 1997, J Biol Chem 272:32995-33000). Quality analysis of the hIL-7 model identified poor structural features in the carboxyl terminus that, when further studied using hydrophobic moment analysis, detected an atypical structural property in helix D, which contains Cys 130 and Cys142. This analysis demonstrated that helix D had a hydrophobic surface exposed to bulk solvent that accounted for the poor quality of the model, but was suggestive of a region in IL-7 that maybe important for protein interactions. Alanine (Ala) substitution scanning mutagenesis was performed to test if the predicted atypical surface chemistry of helix D in the hIL-7 model is important for receptor activation. This analysis resulted in the construction, purification, and characterization of four hIL-7 variants, hIL-7(K121A), hIL-7(L136A), hIL-7(K140A), and hIL-7(W143A), that displayed reduced or abrogated ability to stimulate a murine IL-7 dependent pre-B cell proliferation. The mutant hIL-7(W143A), which is biologically inactive and displaces [125I]-hIL-7, is the first reported IL-7R system antagonist.
Performance of spread OFDM with LDPC coding in outdoor environments (2003)

The performance of OFDM systems that utilize coding and spreading is presented. The proposed systems operate in outdoor environments and achieve coding gains through the use of low-density parity-check (LDPC) encoding. It is shown that by introducing Hadamard-Walsh spreading in coded OFDM, additional gain in performance can be attained relative to uncoded as well as LDPC coded OFDM systems. Comparable systems using convolutional codes are shown to have similar performance, although the OFDM system require additional interleaving and deinterleaving.