gebhart/patrepeval huggingface dataset:
Interferon‐inducible protein‐10 and lymphotactin induce the chemotaxis and mobilization of intracellular calcium in natural killer cells through pertussis toxin‐sensitive and ‐insensitive heterotrimeric G‐proteins (1997)

We show here that interferon-inducible protein-10 (IP-10), an ELR lacking CXC chemokine, and the C chemokine lymphotactin (Ltn) induce the chemotaxis and calcium mobilization in IL2-activated NK (IANK) and CC chemokine-activated NK (CHAK) cells. Cross-desensitization experiments show that IP-10 or Ltn use receptors not shared by other C, CC, or CXC chemokines. The chemotaxis induced by either IP-10 or Ltn for both cell types is inhibited upon pretreatment of these cells with pertussis toxin (PT). Also, Ltn-induced [Ca2+]i in IANK but not in CHAK cells is inhibited upon pretreatment with PT, whereas IP-10-induced [Ca2+]i in IANK and CHAK cells is inhibited upon pretreatment with this toxin. These results suggest important roles for PT-sensitive and -insensitive G-proteins in IP-10-induced and Ltn-induced chemotaxis and calcium fluxes in activated NK cells. This was further implicated after streptolysin O permeabilization of CHAK and IANK cells and after introduction of inhibitory antibodies to the PT-sensitive Gi and Go or the PT-insensitive Gq. Our results suggest that IP-10 and Ltn receptors are coupled to Gi, Go, and Gq in IANK cells and to Gi and Gq in CHAK cells, with a possible low coupling of IP-10, but not of Ltn, receptors to Go in these cells. Together, these results show that IP-10 and Ltn-dependent chemotaxis and calcium mobilization may differentiate at the level of receptor coupling to the heterotrimeric G-proteins.
Fabrication of large-area stamps, moulds, and conformable photomasks for soft lithography (2004)

Low-cost fabrication is essential to the successful introduction of organic electronics and reel-to-reel manufacturing processes. Here it is proposed that extending flexography into the micrometre-size resolution regime may provide an economical commercialization path for plastic devices. Flexography is a high-speed technique commonly used for printing onto very large-area flexible substrates. Although low resolution and poor registration are characteristics of today's flexographic process, it has many similarities with soft lithographic techniques. This work shows that large (12 in x 12 in), high-resolution printing plates appropriate for use on small tag and label flexographic presses can be prepared using simple and inexpensive flexographic-compatible processes. This paper illustrates the use of these plates for three representative soft lithographic processes: microcontact printing, replica moulding, and phase-shift lithography.
T-cell Repertoire and Thymus (1989)

The α/β T-cell repertoire in any given animal is known to be affected by four factors: the germ line genes available for receptor construction (Vα, Jα, Vβ, etc.), positive selection, self-tolerance, and exposure to foreign antigens. In this paper, we discuss two of these phenomena, namely, positive selection and tolerance due to clonal deletion in the thymus.
Early onset of phenotype and cell patterning in the embryonic zebrafish retina (1990)

The regular arrangement of retinal cone cells in a mosaic pattern is a common feature of teleosts. In the zebrafish, Brachydanio rerio, the retinal cone mosaic comprises parallel rows consisting of a repeating motif of four cone types. In order to elucidate the temporal and spatial aspects of the genesis of the cone mosaic in the developing retina, we generated a monoclonal antibody that specifically binds to the double cone photoreceptor of the adult. We first saw staining in the developing retina with this antibody, FRet 43, at 48 hours postfertilization, the time at which the first photoreceptor cells undergo their final mitotic division. We then injected embryonic fish with the thymidine analog, 5-bromo-2'-deoxyuridine (BrdU), confirming with a double-labeling experiment that the onset of FRet 43 antigenicity occurs within three hours of the cellular division that generates the double cone photoreceptors. Then we stained tangential sections of the 54-hour embryonic retina with FRet 43, further showing that cells devoid of staining alternate with stained pairs of cells in a pattern that is consistent with the arrangement of photoreceptors in the adult cone mosaic. These results indicate that a marker of the double cone phenotype is expressed at approximately the same time as cellular birthday and that the mosaic patterning is present within 6 hours of this expression.
VideoQ: a fully automated video retrieval system using motion sketches (2002)

The rapidity with which digital information, particularly video, is being generated, has necessitated the development of tools for efficient search of these media. Content based visual queries have been primarily focused on still image retrieval. In this paper we propose a novel interactive system on the Web, based on the visual paradigm, with spatio-temporal attributes playing a key role in video retrieval. The resulting system VideoQ, is the first on-line video search engine supporting automatic object based indexing and spatio-temporal queries.
Fluorescently-Labeled Ferrichrome Analogs as Probes for Receptor-Mediated, Microbial Iron Uptake (1996)

Biomimetic analogs 1 of the microbial siderophore (iron carrier) ferrichrome were labeled with a fluorescent marker at a site which does not interfere with iron binding or receptor recognition to provide iron(III) carriers 5 and 10 (Figure 1). These carriers were built from a tetrahedral carbon as an anchor which was symmetrically extended by three converging iron-binding chains and a single, exogenous anthracenyl residue. Carriers 5 varied in the nature of the amino acids (G = glycyl, A = alanyl and L = leucyl) linking the anchor with the iron-binding hydroxamate groups, while the alanyl derivative 10A differed from 5A in the spacer between the anthracenyl label and the anchor. Examination of these binders by 1H NMR confirmed that their conformations were analogous to those of the nonlabeled parent compounds. Titration experiments using UV/vis and fluorescence spectroscopy demonstrated the quenching of these compounds' fluorescence upon iron(III) loading and its recovery upon iron(III)'s release to a competing chelator. The quenching process fits the Perrin model for static quenching and was more efficient in derivatives 5, where the label could approach the iron-binding domain, than in derivative 10A, where the label's approach was prohibited. These data are in compliance with an intramolecular quenching process. In vivo examination of the labeled derivatives 5 with Pseudomonas putida as the indicator organism established that their behavior parallels that of the nonlabeled analogs 1, with the added benefit of signaling microbial activity by fluorescence emission. Thus incubation of P. putida with iron(III)-loaded (and therefore nonfluorescent) 5G caused buildup of the label's fluorescence in the culture medium. These observations provide direct evidence for a shuttle-mechanism of iron delivery where the fluorescent, iron-unloaded carrier is released to the medium. Inhibition of both phenomena by natural ferrichrome or NaN3 demonstrates the involvement of the microbial ferrichrome receptor and transport systems, respectively. On the other hand, 5A induced only modest iron(III) uptake by P. putida and failed to generate fluorescence in the culture medium, concurring with its action as an inhibitor. The fact that two strains of different Pseudomonas species did not respond to the ferrichrome analog 5G illustrates the specificity of these compounds. The performance of these carriers as structural and functional probes, paired with their high species specificity, encourage their consideration as diagnostic tools for the detection and identification of pathogenic bacteria and fungi.
Provisioning a Multi-tiered Data Staging Area for Extreme-Scale Machines (2011)

Massively parallel scientific applications, running on extreme-scale supercomputers, produce hundreds of terabytes of data per run, driving the need for storage solutions to improve their I/O performance. Traditional parallel file systems (PFS) in high performance computing (HPC) systems are unable to keep up with such high data rates, creating a storage wall. In this work, we present a novel multi-tiered storage architecture comprising hybrid node-local resources to construct a dynamic data staging area for extreme-scale machines. Such a staging ground serves as an impedance matching device between applications and the PFS. Our solution combines diverse resources (e.g., DRAM, SSD) in such a way as to approach the performance of the fastest component technology and the cost of the least expensive one. We have developed an automated provisioning algorithm that aids in meeting the check pointing performance requirement of HPC applications, by using a least-cost storage configuration. We evaluate our approach using both an implementation on a large scale cluster and a simulation driven by six-years worth of Jaguar supercomputer job-logs, and show that our approach, by choosing an appropriate storage configuration, achieves 41.5% cost savings with only negligible impact on performance.
Motor neuron derivation from human embryonic and induced pluripotent stem cells: experimental approaches and clinical perspectives (2014)

Motor neurons are cells located in specific areas of the central nervous system, such as brain cortex (upper motor neurons), brain stem, and spinal cord (lower motor neurons), which maintain control over voluntary actions. Motor neurons are affected primarily by a wide spectrum of neurological disorders, generally indicated as motor neuron diseases (MNDs): these disorders share symptoms related to muscular atrophy and paralysis leading to death. No effective treatments are currently available. Stem cell-derived motor neurons represent a promising research tool in disease modeling, drug screening, and development of therapeutic approaches for MNDs and spinal cord injuries. Directed differentiation of human pluripotent stem cells - human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs) - toward specific lineages is the first crucial step in order to extensively employ these cells in early human development investigation and potential clinical applications. Induced pluripotent stem cells (iPSCs) can be generated from patients' own somatic cells (for example, fibroblasts) by reprogramming them with specific factors. They can be considered embryonic stem cell-like cells, which express stem cell markers and have the ability to give rise to all three germ layers, bypassing the ethical concerns. Thus, hiPSCs constitute an appealing alternative source of motor neurons. These motor neurons might be a great research tool, creating a model for investigating the cellular and molecular interactions underlying early human brain development and pathologies during neurodegeneration. Patient-specific iPSCs may also provide the premises for autologous cell replacement therapies without related risks of immune rejection. Here, we review the most recent reported methods by which hESCs or iPSCs can be differentiated toward functional motor neurons with an overview on the potential clinical applications.
A Prospective Randomized Trial Comparing Percutaneous Local Ablative Therapy and Partial Hepatectomy for Small Hepatocellular Carcinoma (2006)

In Brief Objective: To compare the results of percutaneous local ablative therapy (PLAT) with surgical resection in the treatment of solitary and small hepatocellular carcinoma (HCC). Summary Background Data: PLAT is effective in small HCC. Whether it is as effective as surgical resection in the long-term survivals remains unknown. Methods: We conducted a prospective randomized trial on 180 patients with a solitary HCC ≦5 cm to receive either PLAT or surgical resection. The patients were regularly followed up after treatment with physical examination, blood, and radiologic tests. Results: Of the 90 patients who were randomized to PLAT, only 71 received PLAT because 19 withdrew their consent. Of the 90 patients who were randomized to surgical resection, a single Couinaud liver segment resection was carried out in 69 patients, 2 segments in 16 patients, and 3 or more segments in 3 patients. Ethanol injection was given during open surgery in 2 patients. Only 1 patient died after surgical resection within the same hospital admission. Posttreatment complications were more often and severe after surgery than PLAT. The 1-, 2-, 3-, and 4-year overall survival rates after PLAT and surgery were 95.8%, 82.1%, 71.4%, 67.9% and 93.3%, 82.3%, 73.4%, 64.0%, respectively. The corresponding disease-free survival rates were 85.9%, 69.3%, 64.1%, 46.4% and 86.6%, 76.8%, 69%, 51.6%, respectively. Statistically, there was no difference between these 2 treatments. Conclusion: PLAT was as effective as surgical resection in the treatment of solitary and small HCC. PLAT had the advantage over surgical resection in being less invasive. A prospective randomized trial on 180 patients with a solitary hepatocellular carcinoma ≦ 5 cm showed there was no significant difference in the long-term overall and disease-free survivals between treatment with percutaneous local ablative therapy or partial hepatectomy. Percutaneous local ablative therapy has the advantage over surgery in being less invasive.
Precision measurement for microsurgical instrument evaluation (2005)

An accurate three-dimensional optical sensing system to track the tip of a microsurgical instrument has been developed for laboratory use. The system is useful for evaluation of microsurgical instrument designs and devices for accuracy enhancement (both robotic devices and active hand-held instrument), as well as for assessment and training of microsurgeons. It can also be used as a high-precision input interface to micro-surgical simulators. Tracking is done by illuminating the workspace at an infrared wavelength and using optical sensors to find the position of a small reflective ball at the instrument tip. The RMS noise per coordinate is presently 1 micron. Sample results are presented.
Stochastic Optimization and Real-Time Scheduling in Cyber-Physical Systems (2012)

A principal goal of this dissertation is to study stochastic optimization and real-time scheduling in cyber-physical systems (CPSs) ranging from realtime wireless systems to energy systems to distributed control systems. Under this common theme, this dissertation can be broadly organized into three parts based on the system environments. The first part investigates stochastic optimization in real-time wireless systems, with the focus on the deadline-aware scheduling for real-time traffic. The optimal solution to such scheduling problems requires to explicitly taking into account the coupling in the deadline-aware transmissions and stochastic characteristics of the traffic, which involves a dynamic program that is traditionally known to be intractable or computationally expensive to implement. First, real-time scheduling with adaptive network coding over memoryless channels is studied, and a polynomial-time complexity algorithm is developed to characterize the optimal real-time scheduling. Then, real-time scheduling over Markovian channels is investigated, where channel conditions are timevarying and online channel learning is necessary, and the optimal scheduling policies in different traffic regimes are studied. The second part focuses on the stochastic optimization and real-time scheduling involved in energy systems. First, risk-aware scheduling and dispatch for plug-in electric vehicles (EVs) are studied, aiming to jointly optimize the EV charging cost and the risk of the load mismatch between the forecasted and the actual EV loads, due to the random driving activities of EVs. Then, the integration of wind generation at high penetration levels into bulk power grids is considered. Joint optimization of economic dispatch and interrupt-
Towards Polyoxometalate‐Integrated Nanosystems (2006)

Polyoxometalates represent a diverse range of molecular clusters with an almost unmatched range of physical properties and the ability to form structures that can bridge several length scales. The new building block principles that have been discovered are beginning to allow the design of complex clusters with desired properties and structures; several structural types and novel physical properties are examined herein. The overall message that is presented throughout is the possibility that polyoxometalate clusters could be excellent candidates to be exploited in the development of functional nanosystems or nanodevices. The concepts that underpin the development of nanoscale devices are discussed briefly, as are the considerable challenges that must be overcome to realise polyoxometalate-based functional nanosystems.
High Speed Networks Need Proactive Congestion Control (2015)

As datacenter speeds scale to 100 Gb/s and beyond, traditional congestion control algorithms like TCP and RCP converge slowly to steady sending rates, which leads to poorer and less predictable user performance. These reactive algorithms use congestion signals to perform gradient descent to approach ideal sending rates, causing poor convergence times. In this paper, we propose a proactive congestion control algorithm called PERC, which explicitly computes rates independently of congestion signals in a decentralized fashion. Inspired by message-passing algorithms with traction in other fields (e.g., modern Low Density Parity Check decoding algorithms), PERC improves convergence times by a factor of 7 compared to reactive explicit rate control protocols such as RCP. This fast convergence reduces tail flow completion time (FCT) significantly in high speed networks; for example, simulations of a realistic workloads in a 100 Gb/s network show that PERC achieves up to 4x lower 99th percentile FCT compared to RCP.
The role of alveolar macrophages in Pneumocystis carinii degradation and clearance from the lung. (1997)

Although studies indicate that alveolar macrophages participate in host defense against Pneumocystis carinii, their role in organism degradation and clearance from the lung has not yet been established. We, therefore, quantified the uptake and degradation of 35S-labeled P. carinii by cultured macrophages, demonstrating significant degradation of P. carinii over 6 h. We further evaluated the role of macrophages in elimination of P. carinii from the living host. Rats received either intratracheal PBS, liposomal PBS (L-PBS), or liposomal dichloromethylene diphosphonate (L-Cl2MDP), a preparation which leads to selective depletion of macrophages. Over 72 h, L-Cl2MDP-treated animals had loss of > 85% of their alveolar macrophages. In contrast, L-PBS-treated rats had cellular differentials identical to rats receiving PBS. Macrophage-depleted rats and controls were next inoculated with P. carinii and organism clearance was determined after 24 h. P. carinii elimination was evaluated with both cyst counts and an ELISA directed against glycoprotein A (gpA), the major antigen of P. carinii. Both assays indicated that macrophage-depleted rats had substantial inpairment of P. carinii clearance compared to L-PBS- or PBS-treated rats. These data provide the first direct evidence that macrophages mediate elimination of P. carinii from the living host.
Direct Binding of Apoptosis Signal-regulating Kinase 1 to Retinoblastoma Protein (2004)

The retinoblastoma protein Rb has antiproliferative and antiapoptotic functions. Our previous studies have shown that certain apoptotic signals can inactivate Rb via the p38 pathway. Here we show that Rb associates with the apoptosis signal-regulating kinase ASK1 in response to specific apoptotic signals. An LXCXE motif on ASK1 was required for Rb binding; this correlated with increased E2F1 transcriptional activity and up-regulation of the proapoptotic protein p73. Overexpression of Rb inhibited ASK1-induced apoptosis; in addition, an ASK1 mutant incapable of binding Rb could not induce apoptosis, indicating that ASK1 has to overcome the antiapoptotic properties of Rb to kill cells. Chromatin immunoprecipitation assays show that in asynchronous cells the p73P1 promoter is occupied predominantly by E2F3; upon tumor necrosis factor (TNF)-alpha stimulation, E2F3 is dissociated from the promoter and replaced by E2F1. At the same time, TNF-alpha stimulation causes Rb to dissociate from the p73P1 promoter. These are promoter-specific events because Rb binds to the mitogenic cdc25A promoter upon TNF-alpha stimulation. These studies suggest that Rb acts as a link between apoptotic and proliferative pathways by interacting with distinct kinases and occupying different promoters.
Geraniol Suppresses Angiogenesis by Downregulating Vascular Endothelial Growth Factor (VEGF)/VEGFR-2 Signaling (2015)

Geraniol exerts several direct pharmacological effects on tumor cells and, thus, has been suggested as a promising anti-cancer compound. Because vascularization is a major precondition for tumor growth, we analyzed in this study the anti-angiogenic action of geraniol. In vitro, geraniol reduced the migratory activity of endothelial-like eEND2 cells. Western blot analyses further revealed that geraniol downregulates proliferating cell nuclear antigen (PCNA) and upregulates cleaved caspase-3 (Casp-3) expression in eEND2 cells. Moreover, geraniol blocked vascular endothelial growth factor (VEGF)/VEGFR-2 signal transduction, resulting in a suppression of downstream AKT and ERK signaling pathways. In addition, geraniol significantly reduced vascular sprout formation in a rat aortic ring assay. In vivo, geraniol inhibited the vascularization of CT26 tumors in dorsal skinfold chambers of BALB/c mice, which was associated with a smaller tumor size when compared to vehicle-treated controls. Immunohistochemical analyses confirmed a decreased number of Ki67-positive cells and CD31-positive microvessels with reduced VEGFR-2 expression within geraniol-treated tumors. Taken together, these findings indicate that geraniol targets multiple angiogenic mechanisms and, therefore, is an attractive candidate for the anti-angiogenic treatment of tumors.
Herpes zoster and varicella infections in children with hodgkin's disease.An analysis of contributing factors (1978)

181 children with Hodgkin's disease were analyzed with respect to the occurrence of herpes zoster and varicella (HZ-V) infections, possible contributing factors, and prognostic significance. The overall frequency of HZ-V was 34.8%. The occurrence in stage I was significantly lower than in other stages. Previous splenectomy was not found to increase significantly the risk of infection. High-risk patients were those receiving extensive radiotherapy plus combination chemotherapy; 56% developed HZ-V infections in this group. The frequency with extensive field radiotherapy alone was 23.8%. 80% of infections occurred during the first year after completion of treatment. Their occurrence was not a poor prognostic sign in terms of relapse or fatality, even when occurring late. The high frequency of disseminated infection (27%) with its subsequent morbidity should lead toward a better understanding of the immunologic deficiencies in these patients and the possible role of prophylactic measures, in patients undergoing extensive radiotherapy in combination with multiagent chemotherapy.
Spectral-domain optical coherence phase and multiphoton microscopy (2007)

We describe simultaneous quantitative phase contrast and multiphoton fluorescence imaging by combined spectral-domain optical coherence phase and multiphoton microscopy. The instrument employs two light sources for efficient optical coherence microscopic and multiphoton imaging and can generate structural and functional images of transparent specimens in the epidirection. Phase contrast imaging exhibits spatial and temporal phase stability in the subnanometer range. We also demonstrate the visualization of actin filaments in a fixed cell specimen, which is confirmed by simultaneous multiphoton fluorescence imaging.