gebhart/patrepeval huggingface dataset:
Smallpox vaccines: targets of protective immunity (2010)

The eradication of smallpox, one of the great triumphs of medicine, was accomplished through the prophylactic administration of live vaccinia virus, a comparatively benign relative of variola virus, the causative agent of smallpox. Nevertheless, recent fears that variola virus may be used as a biological weapon together with the present susceptibility of unimmunized populations have spurred the development of new-generation vaccines that are safer than the original and can be produced by modern methods. Predicting the efficacy of such vaccines in the absence of human smallpox, however, depends on understanding the correlates of protection. This review outlines the biology of poxviruses with particular relevance to vaccine development, describes protein targets of humoral and cellular immunity, compares animal models of orthopoxvirus disease with human smallpox, and considers the status of second- and third-generation smallpox vaccines.
3D surface‐related multiple modeling, principles and results (2005)

Data‐driven SRME techniques do not require any a priori knowledge of the subsurface (reflectivity, structures and velocities). However, these methods require a shot location at each receiver location, wherein lies the main difficulty for their 3D implementation. Today solutions involve reconstruction of the missing data or reconstruction of the missing multiple contributions. In the following, we present a model‐based surface‐related multiple modeling technique (SRMM) free from any constraint relating to the shot position (including OBC) and distribution.
Role of natural and adaptive immunity in renal cell carcinoma response to VEGFR‐TKIs and mTOR inhibitor (2013)

Angiogenesis and immunosuppression work hand‐in‐hand in the renal cell carcinoma (RCC) microenvironment. Tumor growth is associated with impaired antitumor immune response in RCC, which involves T cells, natural killer cells, dendritic cells (DCs) and macrophages. Vascular endothelial growth factor receptor (VEGFR), such as sorafenib, sunitinib, pazopanib and axitinib, and mammalian target of rapamycin (mTOR) inhibitors, such as temsirolimus and everolimus, do exert both antiangiogenic and immunomodulatory functions. Indeed, these agents affect neutrophil migration, as well as T lymphocyte‐DC cross‐talk, DC maturation and immune cell metabolism and reactivity. In this review, we overview the essential role of innate and adaptive immune response in RCC proliferation, invasion and metastasis and the relationship between tumor‐associated immune cells and the response to targeted agents approved for the treatment of metastatic RCC.
Drug Delivery by Organ-Specific Immunoliposomes (1991)

Monoclonal antibodies highly specific to the mouse pulmonary endothelial cells were conjugated to liposomes. The resulting immunoliposomes showed high levels of lung accumulation when injected intravenously into mice. Optimal target binding and retention were achieved if the lipid composition included ganglioside (GM1) to reduce the uptake of immunoliposomes by the reticuloendothelial system. Details of the construction and optimization of these organ-specific immunoliposomes are reviewed. The drug delivery potential of this novel liposome system was demonstrated in an experimental pulmonary metastasis model. Immunoliposomes containing a lipophilic prodrug of deoxyfluorouridine effectively prolonged the survival time of the tumor-bearing mice. This and other therapeutic applications of the immunoliposomes are discussed.
Improved Non-chromatographic Purification of a Recombinant Protein by Cationic Elastin-like Polypeptides (2007)

This paper reports an improvement in the purification of thioredoxin (Trx) expressed from E. coli by inverse transition cycling (ITC) using cationic elastin-like polypeptides (ELPs). Two ELP libraries having 2% and 5% lysine residues and molecular weights ranging from 4 to 61.1 kDa showed greater salt sensitivity in their inverse transition behavior than purely aliphatic ELPs. Expression yield of Trx-ELP fusions was an unpredictable function of guest residue composition, but reducing the molecular weight of the ELP tag generally increased Trx yield. A cationic 4.3 kDa ELP is the shortest ELP used to purify any protein by ITC to date. A 15.9 kDa ELP with a guest residue composition of K:V:F of 1:7:1 was found to be the optimal cationic tag to purify Trx, as it provided 50% greater Trx yield and only required one-fifth the added NaCl for purification of Trx as compared to previously used aliphatic ELP tags.
A single-chain triplebody with specificity for CD19 and CD33 mediates effective lysis of mixed lineage leukemia cells by dual targeting (2011)

A single-chain triplebody (sctb) 33-ds16-ds19 comprising two distal single-chain Fv fragments (scFvs) specific for the lymphoid antigen CD19 and the myeloid antigen CD33 flanking a central scFv specific for CD16, which is the low affinity Fc-receptor (FcγRIII) present on natural killer cells and macrophages, was produced and its properties were investigated. CD33 and CD19 in combination are present on acute leukemiablasts with mixed lineage phenotype, but not on normal human hematopoietic cells. For comparison, two bispecific scFvs (bsscFvs), ds19-ds16 and 33-ds16, with monovalent binding to CD19 and CD33, respectively, were also studied. The sctb 33-ds16-ds19 specifically interacted with all 3 antigens. On the antigen double-positive cell line BV-173, the sctb bound with 2-fold greater avidity than bsscFv ds19-ds16 (KD = 21 vs. 42 nM) and with 1.4-fold greater avidity than bsscFv 33-ds16 (KD = 29 nM). All 3 fusion proteins had similar affinity for CD16 and sufficient thermic stability in human serum. In antibody-dependent cellular cytotoxicity (ADCC) reactions with human mononuclear cells as effectors, the sctb promoted lysis of BV-173 cells at 23-fold lower concentrations than bsscFv ds19-ds16 and at 1.4-fold lower concentrations than bsscFv 33-ds16. The sctb also mediated potent ADCC of the antigen double-positive mixed lineage leukemia cell line SEM, and the half-maximal concentration EC50 for BV-173 cells was 7 pM. Therefore, CD19 and CD33 are present on the surface of these leukemic cell lines such that they can be connected by a single sctb molecule, permitting the recruitment of NK cells via CD16 and tumor cell lysis.
Protein Kinase C β Inhibition Attenuates the Progression of Experimental Diabetic Nephropathy in the Presence of Continued Hypertension (2003)

In addition to hyperglycemia, hypertension and the renin-angiotensin system have been consistently implicated in the pathogenesis of diabetic nephropathy. Each of these pathogenetic factors may induce changes in cellular function by a common intracellular signaling pathway, the activation of protein kinase C (PKC) beta. The present study thus sought to determine the in vivo effect of PKC beta inhibition in experimental diabetic nephropathy in the setting of continued hyperglycemia, hypertension, and activation of the RAS. Studies were conducted in the (mRen-2)27 rat, a rodent that is transgenic for the entire mouse renin gene (Ren-2) and develops many of the structural, functional, and molecular characteristics of human diabetic nephropathy when experimental diabetes is induced with streptozotocin (STZ). Six-week-old female Ren-2 rats received an injection of STZ or vehicle and were maintained for 6 months. Within 24 h, diabetic rats were further randomized to receive treatment with the specific PKC beta inhibitor, LY333531, admixed in diet (10 mg x kg(-1) x d(-1)) or no treatment (n = 8/group). Diabetic rats developed albuminuria, glomerulosclerosis, and tubulointerstitial fibrosis with a concomitant increase in transforming growth factor-beta (TGF-beta). Western blot analysis demonstrated increased PKC beta in diabetic animals, localized by immunofluorescence to the glomerular mesangium. In vivo inhibition of PKC beta with LY333531 led to a reduction in albuminuria, structural injury, and TGF-beta expression, despite continued hypertension and hyperglycemia.
Homo-C-nucleosides. Synthesis of certain 6-substituted 4-pyrimidinones (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHomo-C-nucleosides. Synthesis of certain 6-substituted 4-pyrimidinonesJohn A. Secrist IIICite this: J. Org. Chem. 1978, 43, 14, 2925–2927Publication Date (Print):July 1, 1978Publication History Published online1 May 2002Published inissue 1 July 1978https://pubs.acs.org/doi/10.1021/jo00408a042https://doi.org/10.1021/jo00408a042research-articleACS PublicationsRequest reuse permissionsArticle Views157Altmetric-Citations19LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Adoptive T-cell therapy of prostate cancer targeting the cancer stem cell antigen EpCAM (2015)

Our data demonstrate that PBLs expressing with EpCAM-specific CARs have significant anti-tumor activity against prostate cancer. Therefore, the adoptive transfer of T cells targeting EpCAM could have great potential as a cancer treatment.
Basal tear turnover and topical timolol in glaucoma patients and healthy controls by fluorophotometry. (1992)

To assess the effect of glaucoma and timolol on tear secretion, basal tear turnover was measured with fluorophotometry in 13 open-angle glaucoma patients not using any ophthalmic medication, 24 patients using timolol medication daily, and 41 healthy control subjects. Basal tear turnover is defined as the tear turnover at the lowest level of reflex lacrimation possible under physiologic conditions. Tear turnover was calculated from the decay of the tear fluorescence after instillation of fluorescein. Minimal influence of reflex lacrimation was obtained by instilling 1 microliter of 2% fluorescein without touching the eye and by discarding measurements performed in the first 5 min. Minimization was confirmed by a monophasic decay of tear fluorescence. The values of patients who used timolol and those who did not use timolol were significantly lower than those of healthy control subjects (mean values in percent/minute +/- standard deviation: 10.1 +/- 3.2, 12.3 +/- 4.1, and 15.6 +/- 5.4, respectively; Student's t-test: P < 0.02). The values of patients who used timolol were significantly lower compared to those of patients who did not use timolol (P = 0.03). The tear film break up time values of patients who used timolol were significantly shorter than those of patients who did not use timolol and healthy control subjects (Fisher exact test: P < 0.03).(ABSTRACT TRUNCATED AT 250 WORDS)
Adrenergic Receptor Polymorphisms and Prevention of Ventricular Arrhythmias With Bucindolol in Patients With Chronic Heart Failure (2012)

Bucindolol prevents VT/VF in subjects with heart failure and reduced left ventricular ejection fractions, and this effect is modulated by β(1)389 Arg/Gly and α(2c)322-325 Wt/deletion adrenergic receptor polymorphisms.
SJ and TJ GaAs concentrator solar cells on Si virtual wafers (2005)

GaAs solar cells grown on Si wafers have been investigated for many years to find a way to reduce the solar cell cost, by replacing the expensive Ge substrates with a low cost material and less heavy. Both space and terrestrial applications are interested in the development of this type of technology. This paper is presenting the most recent results on this subject. The preparation of so called Si:Ge "virtual wafers" was carried out with a new approach for Ge deposition on Si wafers, originally developed for microelectronic. Both single junction and triple junction GaAs solar cells were manufactured and preliminary tested. Solar cells ranging from a size of 8 cm/sup 2/ down to 1 mm/sup 2/ were manufactured for terrestrial applications in concentrator systems.
Reliability of N-terminal pro-brain natriuretic peptide assay in diagnosis of heart failure: cohort study in representative and high risk community populations (2002)

This NT-proBNP assay seems to have value in the diagnosis of heart failure in the community. High negative predictive values indicate that the assay's chief use would be to rule out heart failure in patients with suspected heart failure with normal concentrations of NT-proBNP. Positive results may identify patients who need cardiac imaging.
Capacity-achieving decoding by guessing noise. (2018)

We introduce a new algorithm for realizing Maximum Likelihood (ML) decoding in channels with memory. The algorithm is based on the principle that the receiver rank orders noise sequences from most likely to least likely. Subtracting noise from the received signal in that order, the first instance that results in an element of the code-book is the ML decoding. 
For channels where the noise is independent of the input and determinable from the input and output, we establish that the algorithm is capacity-achieving with uniformly-at-random selected code-books. When the code-book rate is less than capacity, we identify error exponents as the block length becomes large. When the code-book rate is beyond capacity, we identify exponents for the probability that the ML decoding is the transmitted code-word. We determine properties of the complexity of the scheme in terms of the number of computations the receiver must perform. For code rates greater than capacity, this reveals thresholds for the number of guesses in which if an element of the code-book is identified, it is likely to be the transmitted code-word. A sufficient condition for this to occur is that the normalized code-book rate is less than one minus the min-entropy rate of the noise. 
Based on the analysis of this noise guessing approach to ML decoding, we introduce an Approximate ML decoding scheme (AML) where the receiver abandons the search for an element of the code-book after a fixed number of noise removal queries, giving an upper-bound on complexity. While not an ML decoder, we establish that AML is also capacity-achieving for an appropriate choice of abandonment threshold, and characterize its complexity, error and success exponents. Worked examples are presented for binary memoryless and Markovian noise. These indicate that the decoding scheme provides high rates for small block sizes with low complexity.
Overexpression of Gremlin�1 by sonic hedgehog signaling promotes pancreatic cancer progression (2018)

Sonic hedgehog (SHH) signaling is an important promotor of desmoplasia, a critical feature in pancreatic cancer stromal reactions involving the activation of pancreatic stellate cells (PSCs). Gremlin 1 is widely overexpressed in cancer-associated stromal cells, including activated PSCs. In embryonic development, SHH is a potent regulator of Gremlin 1 through an interaction network. This subtle mechanism in the cancer microenvironment remains to be fully elucidated. The present study investigated the association between Gremlin 1 and SHH, and the effect of Gremlin 1 in pancreatic cancer. The expression of Gremlin 1 in different specimens was measured using immunohistochemistry. The correlations among clinicopathological features and levels of Gremlin 1 were evaluated. Primary human PSCs and pancreatic cancer cell lines were exposed to SHH, cyclopamine, GLI family zinc finger-1 (Gli-1) small interfering RNA (siRNA), and Gremlin 1 siRNA to examine their associations and effects using an MTT assay, reverse transcription-quantitative polymerase chain reaction analysis, western blot analysis, and migration or invasion assays. The results revealed the overexpression of Gremlin 1 in pancreatic cancer tissues, mainly in the stroma. The levels of Gremlin 1 were significantly correlated with survival rate and pT status. In addition, following activation of the PSCs, the expression levels of Gremlin 1 increased substantially. SHH acts as a potent promoter of the expression of Gremlin 1, and cyclopamine and Gli-1 siRNA modulated this effect. In a screen of pancreatic cancer cell lines, AsPC-1 and BxPC-3 cells expressed high levels of Gremlin 1, but only AsPC-1 cells exhibited a high expression level of SHH. The results of the indirect co-culture experiment suggested that paracrine SHH from the AsPC-1 cells induced the expression of Gremlin 1 in the PSCs. Furthermore, Gremlin 1 siRNA negatively regulated the proliferation and migration of PSCs, and the proliferation, invasion and epithelial-mesenchymal transition of AsPC-1 and BxPC-3 cells. Based on the data from the present study, it was concluded that an abnormal expression level of Gremlin 1 in pancreatic cancer was induced by SHH signaling, and that the overexpression of Gremlin 1 enabled pancreatic cancer progression.
Scalable reader-writer synchronization for shared-memory multiprocessors (1991)

Reader-writer synchronization relaxes the constraints of mutual exclusion to permit more than one process to inspect a shared object concurrently, as long as none of them changes its value.
The role of gap junctions and ion channels in the modulation of electrical and chemical signals in human corpus cavernosum smooth muscle. (1993)

Intercellular communication through aqueous intercellular channels, known as gap junctions, has been postulated to provide an important mechanism for coordinating the rapid and synchronous responses of corporal smooth muscle during human penile erection and detumescence. Mathematical modeling analyses of drug diffusion were utilized to examine the potential physiological importance of the intercellular pathway to the regulation of smooth muscle tone in the human corpus cavernosum. In addition, patch clamp analyses and optical imaging studies were conducted to assess the ionic basis for cellular excitability and homeostasis in cultured corporal smooth muscle cells. In short, the computer modeling studies demonstrated that intercellular communication through gap junctions is likely to be the 'preferred' pathway for coordination of cellular activation and syncytial smooth muscle responses in this tissue. Moreover, the observed ion channel diversity reveals even further complexities to the modulation of corporal smooth muscle tone.
Heracles (2013)

This paper presents Heracles, an open-source, functional, parameterized, synthesizable multicore system toolkit. Such a multi/many-core design platform is a powerful and versatile research and teaching tool for architectural exploration and hardware-software co-design. The Heracles toolkit comprises the soft hardware (HDL) modules, application compiler, and graphical user interface. It is designed with a high degree of modularity to support fast exploration of future multicore processors of di erent topologies, routing schemes, processing elements (cores), and memory system organizations. It is a component-based framework with parameterized interfaces and strong emphasis on module reusability. The compiler toolchain is used to map C or C++ based applications onto the processing units. The GUI allows the user to quickly con gure and launch a system instance for easy factorial development and evaluation. Hardware modules are implemented in synthesizable Verilog and are FPGA platform independent. The Heracles tool is freely available under the open-source MIT license at: http://projects.csail.mit.edu/heracles
<title>In-vivo imaging of blood flow in human retinal vessels using color Doppler optical coherence tomography</title> (1999)

Quantification of retinal blood flow may lead to a better understanding of the progression and treatment of several ocular disorders, including diabetic retinopathy, age- related macular degeneration, and glaucoma. Current techniques, such as fluorescein angiography and laser Doppler velocimetry are limited, failing to provide sufficient information to the clinician. Color Doppler optical coherence tomography (CDOCT) is a novel technique using coherent heterodyne detection for simultaneous cross- sectional imaging of tissue microstructure and blood flow. This technique is capable of high spatial and velocity resolution imaging in highly scattering media. We implemented CDOCT for retinal blood flow mapping in human subjects. No dilation of the pupil was necessary. CDOCT is demonstrated for determining bidirectional flow in sub- 100micrometers diameter vessels in the retina. Additionally, we calculated Doppler broadening using the variance of depth- resolved spectra to identify regions with large velocity gradients within the Xenopus heart. This technique may be useful in quantifying local tissue perfusion in highly vascular retinal tissue.
Pathophysiology of bradykinesia in Parkinson's disease (2001)

Bradykinesia means slowness of movement and is one of the cardinal manifestations of Parkinson's disease. Weakness, tremor and rigidity may contribute to but do not fully explain bradykinesia. We argue that bradykinesia results from a failure of basal ganglia output to reinforce the cortical mechanisms that prepare and execute the commands to move. The cortical deficit is most apparent in midline motor areas. This leads to particular difficulty with self-paced movements, prolonged reaction times and abnormal pre-movement EEG activity. Movements are often performed with normally timed EMG bursts but the amount of EMG activity is underscaled relative to the desired movement parameters. There are also abnormalities in sensory scaling and sensorimotor integration. The brain appears to be able to compensate to some degree for the basal ganglia deficit. There is overactivity in the lateral premotor areas during task performance and movements can be speeded by giving sensory cues. Attention to movement is also beneficial. However, we propose that the engagement of compensatory processes may also lead to reduced performance in other tasks. For example, patients' problems in performing more than one task at the same time could result from lack of sufficient resources both to compensate for their basal ganglia deficit and to run two tasks simultaneously. Surgical therapies are unlikely to work solely by normalizing basal ganglia output to that seen in healthy individuals. It seems more plausible that surgery removes an interfering signal that allows more efficient compensation by other structures.