gebhart/patrepeval huggingface dataset:
Use of a tuberculin purified protein derivative--Asn-Ala-Asn-Pro conjugate in bacillus Calmette-Guérin primed mice overcomes H-2 restriction of the antibody response and avoids the need for adjuvants. (1990)

Because of its immunodominancy, and because it is conserved in different geographical isolates of Plasmodium falciparum, the repetitive sequence of the circumsporozoite protein, (Asn-Ala-Asn-Pro)n [(NANP)n], has been envisaged for the development of an anti-falciparum malaria subunit vaccine. However, the murine immune response to (NANP)n peptides, either carrier-free or coupled to carrier proteins, was shown to be inducible only by using strong (e.g., Freund's) adjuvants. Furthermore, response to the carrier-free peptide, administered in adjuvant, is genetically restricted to I-Ab mice. In the present paper, we report that high titers of antibodies against the NANP repetitive epitope were obtained in responder C57BL/6 (H-2b) mice when they were primed with live BCG (bacillus Calmette-Guérin Mycobacterium tuberculosis var. bovis) and immunized once with the synthetic peptide (NANP)40 coupled to tuberculin purified protein derivative (PPD) without the use of any adjuvant. This approach also led to the production of high titers of anti-NANP antibodies in ASW (H-2s), B10.RIII (H-2r), BALB/c (H-2d), C3H/He (H-2k), and DBA/1 (H-2q) nonresponder mice after two injections of the conjugate. In both cases, BCG priming was obligatory for the induction of antibodies reacting with the synthetic peptide. The levels of anti-NANP antibodies in nonresponder BALB/c mice were demonstrated to be comparable to the levels induced after PPD-(NANP)40 immunization in Freund's complete or incomplete adjuvant. The antibodies induced were also capable of recognizing P. falciparum sporozoites in immunofluorescence assays and, furthermore, these antibodies inhibited the penetration of live sporozoites into human hepatocytes in vitro. This system functioned independently of the subjects' resistance or susceptibility to BCG infection. Given the widespread natural exposure to mycobacterial antigens and the extensive use of BCG and PPD in the human population, this approach might be envisaged for vaccination with malaria peptides.
<title>Novel design of semiconductor lasers for optical communication</title> (1995)

We propose a novel design of semiconductor lasers operating at 1.3 micrometers and 1.5 micrometers . A distinctive attribute of the proposed design is that the AlInGaAs active region is surrounded by an electron stopper layer on the p-side and a hole stopper layer on the n-side. The stopper layers do not impede the carrier injection into the active region and at the same time reduce the thermionic emission of carriers out of the active region. Utilization of stopper layers allows to increase the value of internal quantum efficiency and select the waveguide material corresponding to the optimum optical confinement factor value.
Very low threshold visible TS lasers (1981)

Fundamental transverse mode lasers with very low threshold currents have been realized by use of the modified terraced substrate (TS) geometry. The threshold currents of 250 μm cavity length lasers at room temperature are typically 20-30 mA for wavelengths around 750 nm. In the 710 nm laser, which is the shortest lasing wavelength in this work, the threshold is as low as 70 mA in CW operation. The 726 nm laser was operated for only 150 h, while a lifetime longer than 10 000 h is expected for TS lasers with a lasing wavelength longer than 750 nm.
Dde as a Protecting Group for Carbohydrate Synthesis. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Efficient recombinant adeno-associated virus production by a stable rep-cap HeLa cell line correlates with adenovirus-induced amplification of the integrated rep-cap genome (2000)

This study documents that stable rep-cap cells lines are severely hampered for rAAV assembly when a replicative adenovirus is substituted with an adenoviral plasmid. Furthermore, our results also suggest that the lack of amplification of the rep-cap genes, eventually combined with the altered distribution of the adenoviral proteins, E4orf6 and E1B-55kDa, is related to the low rAAV yields observed under these conditions.
Distinct Biology of Kaposi’s Sarcoma-Associated Herpesvirus from Primary Lesions and Body Cavity Lymphomas (1998)

The DNA sequence for Kaposi's sarcoma-associated herpesvirus was originally detected in Kaposi's sarcoma biopsy specimens. Since its discovery, it has been possible to detect virus in cell lines established from AIDS-associated body cavity-based B-cell lymphoma and to propagate virus from primary Kaposi's sarcoma lesions in a human renal embryonic cell line, 293. In this study, we analyzed the infectivity of Kaposi's sarcoma-associated herpesvirus produced from these two sources. Viral isolates from cultured cutaneous primary KS cells was transmitted to an Epstein-Barr virus-negative Burkitt's B-lymphoma cell line, Louckes, and compared to virus induced from a body cavity-based B-cell lymphoma cell line. While propagation of body cavity-based B-cell lymphoma-derived virus was not observed in 293 cell cultures, infection with viral isolates obtained from primary Kaposi's sarcoma lesions induced injury in 293 cells typical of herpesvirus infection and was associated with apoptotic cell death. Interestingly, transient overexpression of the Kaposi's sarcoma-associated herpesvirus v-Bcl-2 homolog delayed the process of apoptosis and prolonged the survival of infected 293 cells. In contrast, the broad-spectrum caspase inhibitors Z-VAD-fmk and Z-DEVD-fmk failed to protect infected cell cultures, suggesting that Kaposi's sarcoma-associated herpesvirus-induced apoptosis occurs through a Bcl-2-dependent pathway. Kaposi's sarcoma-associated herpesvirus isolates from primary Kaposi's sarcoma lesions and body cavity-based lymphomas therefore may differ and are likely to have distinct contributions to the pathophysiology of Kaposi's sarcoma.
Purification and partial biochemical characterization of IgE-binding factors secreted by a human B lymphoblastoid cell line. (1987)

IgE-binding factors (IgE-BFs) were purified from the culture supernatant of RPMI-8866 cells, a human lymphoblastoid B-cell line expressing IgE receptors. The material, purified by affinity-chromatography on immunoadsorbents coupled to IgE or to monoclonal antibody against IgE receptor, was comprised of two major components with apparent molecular weight (MW) of 25,000-27,000 and 12,000, as determined by SDS-PAGE and silver staining. Only the 25,000-27,000 MW molecules were identified as IgE-BFs, as demonstrated by their reactivity with MabER in the Western blot and the immunoprecipitation assays, and their ability to inhibit rosette formation of U937 cells with IgE- but not with IgG-coated erythrocytes. IgE-BFs were purified to homogeneity by combining affinity-chromatography and either DEAE-ion exchange or reverse-phase chromatography on an HPLC system. Chromatofocusing analysis demonstrated the microheterogeneity of IgE-BFs that were comprised of molecules with isoelectric points ranging from 5.0 to 4.4. IgE-BFs were sensitive to treatment with O-glycosidase but not with N-glycanase. These molecules were resistant to heat and to pH ranging from 2 to 9; their immunoreactivity was lost after treatment with trypsin and pepsin. Papain digestion of purified IgE-BFs generated 14,000-16,000 MW molecules that were still binding to IgE and to MabER.
Clinical Use of Mesenchymal Stromal Cells in the Treatment of Acute Graft-versus-Host Disease (2019)

Acute graft-versus-host disease (aGvHD) continues to impact morbidity and mortality after allogeneic stem cell transplantation (allo-SCT). First-line therapy for aGvHD still remains the use of high-dose corticosteroids. Unfortunately, 40-60% of patients with aGvHD exhibit steroid resistance, which is associated with a very poor prognosis. As no effective second-line therapy existed, in recent decades various treatment options were considered for the treatment of therapy-refractory GvHD. Based on their in vitro immunomodulatory properties, the use of mesenchymal stromal cells (MSCs) in the treatment of aGvHD has been introduced. However, most of the clinical data are generated from uncontrolled trials and case series, showing clinical responses to MSCs. Clinical results are more consistent in children despite the use of MSC preparations of various provenance and manufacturing protocols. While these data support the therapeutic principle, the great variability of outcomes strongly suggests that not all MSC preparations are equal and that the specific manufacturing protocols influence therapeutic success in vivo.
Communication-efficient Certificate Revocation Management for Advanced Metering Infrastructure and IoT (2019)

Advanced Metering Infrastructure forms a communication network for the collection of power data from smart meters in Smart Grid. As the communication between smart meters could be secured utilizing public-key cryptography, however, public-key cryptography still has certain challenges in terms of certificate revocation and management particularly related distribution and storage overhead of revoked certificates. To address this challenge, in this paper, we propose a novel revocation management approach by utilizing cryptographic accumulators which reduces the space requirements for revocation information significantly and thus enables efficient distribution of such information to all smart meters. We implemented the proposed approach on both ns-3 network simulator and a testbed. We demonstrated its superior performance with respect to traditional methods for revocation management.
Near-IR dye laser for diode-pumped operation (1995)

A dye laser pumped by AlGaInP laser diodes produced efficient, low threshold operation at wavelengths between 740 and 800 nm. Rhodamine 700, oxazine 750, DOTCI and oxazine 1 dyes were demonstrated. Optical conversion efficiencies approaching 50% and output power as high as 361 mW were obtained when pumping with a DCM-based dye laser. Parametric variations of the pump power and wavelength were performed over the range of 615 nm to 690 nm to provide a more complete characterization of the dye laser.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Heated Ascorbic/Citric Acid Solution as Browning Inhibitor for Pre‐Peeled Potatoes (1995)

ABSTRACT Treatment of pre‐peeled potatoes with heated ascorbic acid (AA)/citric acid (CA) solution to extend shelf‐life was investigated. Potatoes were abrasion or high pressure steam peeled, heated for 5–20 min in 1% AA + 2% CA at 45–55°C cooled, and then dipped for 5 min in browning inhibitor (BI) solution containing 4% AA +1% CA +1% sodium acid pyrophosphate. Combined treatment inhibited potato discoloration for 14 days at 4°C compared to 3–6 days with BI treatment alone. Raw material and treatment conditions were selected to minimize graying and textural abnormalities encountered with some treatments. Treatment with heated AA/CA may be an alternative to use of sulfites to control browning in pre‐peeled potatoes.
Near-Infrared Optical Imaging of Necrotic Cells by Photostable Lanthanide-Based Metallacrowns (2017)

Sensitive detection of cell necrosis is crucial for the determination of cell viability. Because of its high resolution at the cellular level and sensitivity, optical imaging is highly attractive for identifying cell necrosis. However, challenges associated with this technique remain present such as the rapid photobleaching of several types of organic fluorophores and/or the interference generated by biological autofluorescence. Herein, we synthesized novel biologically compatible Zn<sup>2+</sup>/Ln<sup>3+</sup> metallacrowns (MCs) that possess attractive near-infrared (NIR) emission and are highly photostable. In addition, these MCs have the ability to label differentially necrotic HeLa cells from living cells. This work is also the first demonstration of (i) the use of the NIR emission arising from a single lanthanide(III) cation for optical biological imaging of cells under single photon excitation, (ii) the first example of a lanthanide(III)-based NIR-emitting probe that can be targeted to a specific type of cell.
A reconfigurable built-in memory self-repair architecture for heterogeneous cores with embedded BIST datapath (2016)

Stringent test-time and yield targets together with increased embedded memory content has resulted in increased power and area of memory self-test and repair logic. It is common for high performance IP cores (CPU/DSP/GPU/etc.) to have embedded BIST datapath (DP) that is shared with functional logic to minimize the IP BIST area overhead and ease IP design-closure. However, different IP cores (from same/different vendors) have diverse embedded BIST DP implementations. While having a dedicated memory self-test and repair controller for each IP simplifies design implementation, it is area and power intensive. In this paper, we propose a reconfigurable centralized memory built-in self-repair (BISR) architecture that supports multiple IPs with diverse embedded BIST DP implementations while being area efficient. We also present a power and timing-aware BISR synthesis flow that enables test time reduction while satisfying timing and power constraints. Experimental results on 28nm designs indicate about 2.4X area reduction compared to native EDA solution. The proposed solution also helps achieve 4.9X reduction in test time.
<scp>HMGB</scp> 1 facilitates repair of mitochondrial <scp>DNA</scp> damage and extends the lifespan of mutant ataxin‐1 knock‐in mice (2014)

Mutant ataxin-1 (Atxn1), which causes spinocerebellar ataxia type 1 (SCA1), binds to and impairs the function of high-mobility group box 1 (HMGB1), a crucial nuclear protein that regulates DNA architectural changes essential for DNA damage repair and transcription. In this study, we established that transgenic or virus vector-mediated complementation with HMGB1 ameliorates motor dysfunction and prolongs lifespan in mutant Atxn1 knock-in (Atxn1-KI) mice. We identified mitochondrial DNA damage repair by HMGB1 as a novel molecular basis for this effect, in addition to the mechanisms already associated with HMGB1 function, such as nuclear DNA damage repair and nuclear transcription. The dysfunction and the improvement of mitochondrial DNA damage repair functions are tightly associated with the exacerbation and rescue, respectively, of symptoms, supporting the involvement of mitochondrial DNA quality control by HMGB1 in SCA1 pathology. Moreover, we show that the rescue of Purkinje cell dendrites and dendritic spines by HMGB1 could be downstream effects. Although extracellular HMGB1 triggers inflammation mediated by Toll-like receptor and receptor for advanced glycation end products, upregulation of intracellular HMGB1 does not induce such side effects. Thus, viral delivery of HMGB1 is a candidate approach by which to modify the disease progression of SCA1 even after the onset.
Rapid Regeneration of Vascularized Bone by Nanofabricated Amorphous Silicon Oxynitrophosphide (SiONP) Overlays (2019)

Fracture healing is a complex biological process. Severe bone loss and ischemia from traumatic fractures lead to inflammation and accumulation of damaging reactive oxygen species (ROS). Fixative devices that not only provide mechanical support but also stimulate antioxidants such as superoxide dismutase (SOD1) and influence signaling pathways for extracellular matrix (ECM) mineralization, are critical for normal healing of such fractures. In this study, we report a novel biomaterial, silicon oxynitrophosphide (SiONP) that provides sustained release of ionic silicon (Si<sup>+4</sup>) and phosphorous (P) over few weeks under physiological conditions. Anti-oxidant role of Si<sup>+4</sup> and augmented ECM mineralization by P ions lead to enhanced osteogenesis coupled with quick revascularization for rapid bone regeneration. Plasma enhanced chemical vapor deposition (PECVD) provided a conformal, well adherent and highly reproducible surface chemistry overlaid onto nanofabricated bioinspired surfaces. The Nitrogen to P and O content ratio was observed to change the dissolution rate and the release kinetics of the overlaid film. The SiONP films with optimal release kinetics promoted anti-oxidant expression via enhanced SOD1, which downstream upregulated other osteogenic markers with MC3T3-E1 cells. These surfaces also promoted angiogenesis evident by formation of thicker tubules by Human umbilical vein endothelial cells (HUVEC). <i>In-vivo</i> evaluation using a rat critical-sized calvarial defect model showed rapid bone-regeneration for these nanofabricated biomaterials as compared to control groups, and opens new horizon for future clinical trials of new antioxidant materials on biomedical devices that can reduce healing time, lower medical care cost, and increase the quality of newly formed bone in critical size defects.
Thick Acellular Heart Extracellular Matrix with Inherent Vasculature: A Potential Platform for Myocardial Tissue Regeneration (2012)

The decellularization of porcine heart tissue offers many opportunities for the production of physiologically relevant myocardial mimetic scaffolds. Earlier, we reported the successful isolation of a thin porcine cardiac extracellular matrix (pcECM) exhibiting relevant bio-mechanical properties for myocardial tissue engineering. Nevertheless, since native cardiac tissue is much thicker, such thin scaffolds may offer limited regeneration capacity. However, generation of thicker myocardial mimetic tissue constructs is hindered by diffusion limitations (~100 μm), and the lack of a proper vascular-like network within these constructs. In our present work, we focused on optimizing the decellularization procedure for thicker tissue slabs (10-15 mm), while retaining their inherent vasculature, and on characterizing the resulting pcECM. The trypsin/Triton-based perfusion procedure that resulted in a nonimmunogenic and cell-supportive pcECM was found to be more effective in cell removal and in the preservation of fiber morphology and structural characteristics than stirring, sonication, or sodium dodecyl sulfate/Triton-based procedures. Mass spectroscopy revealed that the pcECM is mainly composed of ECM proteins with no apparent cellular protein remains. Mechanical testing indicated that the obtained pcECM is viscoelastic in nature and possesses the typical stress-strain profile of biological materials. It is stiffer than native tissue yet exhibits matched mechanical properties in terms of energy dissipation, toughness, and ultimate stress behavior. Vascular network functionality was maintained to the first three-four branches from the main coronary vessels. Taken together, these results reaffirm the efficiency of the decellularization procedure reported herein for yielding thick nonimmunogenic cell-supportive pcECM scaffolds, preserving both native tissue ultra-structural properties and an inherent vascular network. When reseeded with the appropriate progenitor cells, these scaffolds can potentially serve as ex vivo screening platforms for new therapeutics, as models for human cardiac ECM, or as biomedical constructs for patch or transmural transplantation strategies.
Label Propagation Prediction of Drug-Drug Interactions Based on Clinical Side Effects (2015)

Drug-drug interaction (DDI) is an important topic for public health, and thus attracts attention from both academia and industry. Here we hypothesize that clinical side effects (SEs) provide a human phenotypic profile and can be translated into the development of computational models for predicting adverse DDIs. We propose an integrative label propagation framework to predict DDIs by integrating SEs extracted from package inserts of prescription drugs, SEs extracted from FDA Adverse Event Reporting System, and chemical structures from PubChem. Experimental results based on hold-out validation demonstrated the effectiveness of the proposed algorithm. In addition, the new algorithm also ranked drug information sources based on their contributions to the prediction, thus not only confirming that SEs are important features for DDI prediction but also paving the way for building more reliable DDI prediction models by prioritizing multiple data sources. By applying the proposed algorithm to 1,626 small-molecule drugs which have one or more SE profiles, we obtained 145,068 predicted DDIs. The predicted DDIs will help clinicians to avoid hazardous drug interactions in their prescriptions and will aid pharmaceutical companies to design large-scale clinical trial by assessing potentially hazardous drug combinations. All data sets and predicted DDIs are available at http://astro.temple.edu/~tua87106/ddi.html.
A Self‐Generating, Highly Active, and Recyclable‐Metathesis Catalyst. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Computing with faulty shared memory (1992)

This paper addresses problems which arise in the synchronization and coordination of distributed systems which employ unreliable shared memory. We present algorithms which solve the consensus problem, and which simulate reliable shared-memory objects, despite the fact that the available memory objects (e.g. read/write registers, test-and-set registers, read-modify-write registers) may be faulty.
Green-to-Red Photoconversion of GCaMP (2015)

Genetically encoded calcium indicators (GECIs) permit imaging intracellular calcium transients. Among GECIs, the GFP-based GCaMPs are the most widely used because of their high sensitivity and rapid response to changes in intracellular calcium concentrations. Here we report that the fluorescence of GCaMPs--including GCaMP3, GCaMP5 and GCaMP6--can be converted from green to red following exposure to blue-green light (450-500 nm). This photoconversion occurs in both insect and mammalian cells and is enhanced in a low oxygen environment. The red fluorescent GCaMPs retained calcium responsiveness, albeit with reduced sensitivity. We identified several amino acid residues in GCaMP important for photoconversion and generated a GCaMP variant with increased photoconversion efficiency in cell culture. This light-induced spectral shift allows the ready labeling of specific, targeted sets of GCaMP-expressing cells for functional imaging in the red channel. Together, these findings indicate the potential for greater utility of existing GCaMP reagents, including transgenic animals.