gebhart/patrepeval huggingface dataset:
Doing Real Work with FHE (2018)

We describe our recent experience, building a system that uses fully-homomorphic encryption (FHE) to approximate the coefficients of a logistic-regression model, built from genomic data. The aim of this project was to examine the feasibility of a solution that operates "deep within the bootstrapping regime,'' solving a problem that appears too hard to be addressed just with somewhat-homomorphic encryption. As part of this project, we implemented optimized versions of many bread and butter FHE tools. These tools include binary arithmetic, comparisons, partial sorting, and low-precision approximation of arbitrary functions (used for reciprocals, logarithms, etc.). Our solution can handle thousands of records and hundreds of fields, and it takes a few hours to run. To achieve this performance we had to be extremely frugal with expensive bootstrapping and data-movement operations. We believe that our experience in this project could serve as a guide for what is or is not currently feasible to do with fully-homomorphic encryption.
Surface Restructuring of Nanoparticles:  An Efficient Route for Ligand−Metal Oxide Crosstalk (2002)

Surface modification of nanocrystalline metal oxide particles with enediol ligands was found to result in altered optical properties of nanoparticles. The surface modification results in a red shift of the semiconductor absorption compared to unmodified nanocrystallites. The optical shift is correlated to the dipole moment of the Ti−ligand complexes at the particle surface and decreases with the ligand size. The binding was found to be exclusively characteristic of colloids in the nanocrystalline domain(<20 nm). X-ray near-edge structure measurements at Ti K edge indicate that in this size domain the surface Ti atoms adjust their coordination environment to form undercoordinated sites. These five-coordinated defect sites are the source of novel enhanced and selective reactivity of the nanoparticle toward bidentate ligand binding as observed using IR spectroscopy. Enediol ligands have the optimal geometry for chelating surface Ti atoms, resulting in a five-membered ring coordination complex and restored six-coordinated octahedral geometry of surface Ti atoms. The binding of enediol ligands is enhanced because of the stability gained from adsorption-induced restructuring of the nanoparticle surface. Consistent behavior was found for the three different nanocrystalline metal oxide systems: TiO2, Fe2O3, and ZrO2.
Overview and Classification of Some Regularization Techniques for the Gauss-Newton Inversion Method Applied to Inverse Scattering Problems (2009)

Different regularization techniques used in conjunction with the Gauss-Newton inversion method for electromagnetic inverse scattering problems are studied and classified into two main categories. The first category attempts to regularize the quadratic form of the nonlinear data misfit cost-functional at different iterations of the Gauss-Newton inversion method. This can be accomplished by utilizing penalty methods or projection methods. The second category tries to regularize the nonlinear data misfit cost-functional before applying the Gauss-Newton inversion method. This type of regularization may be applied via additive, multiplicative or additive-multiplicative terms. We show that these two regularization strategies can be viewed from a single consistent framework.
Organ Printing: Promises and Challenges (2007)

Organ printing or biomedical application of rapid prototyping, also defined as additive layer-by-layer biomanufacturing, is an emerging transforming technology that has potential for surpassing traditional solid scaffold-based tissue engineering. Organ printing has certain advantages: it is an automated approach that offers a pathway for scalable reproducible mass production of tissue engineered products; it allows a precised simultaneous 3D positioning of several cell types; it enables creation tissue with a high level of cell density; it can solve the problem of vascularization in thick tissue constructs; finally, organ printing can be done in situ. The ultimate goal of organ-printing technology is to fabricate 3D vascularized functional living human organs suitable for clinical implantation. The main practical outcomes of organ-printing technology are industrial scalable robotic biofabrication of complex human tissues and organs, automated tissue-based in vitro assays for clinical diagnostics, drug discovery and drug toxicity, and complex in vitro models of human diseases. This article describes conceptual framework and recent developments in organ-printing technology, outlines main technological barriers and challenges, and presents potential future practical applications.
Variation of the critical layer thickness with In content in strained InxGa1−xAs-GaAs quantum wells grown by molecular beam epitaxy (1987)

The critical width Lc for misfit dislocation generation has been determined for molecular beam epitaxy grown strained InxGa1−xAs (0.1&amp;lt;x≤1) quantum wells in a GaAs matrix by means of photoluminescence measurements. For the full alloy region the dependence Lc(x) is in good agreement with the theoretical expression proposed by J. W. Matthews and A. E. Blakeslee [J. Cryst. Growth 27, 118 (1974)].
Chinese Herbs With Common Foods: Recipes for Health and Healing (1998)

This text provides explanations of the effects of Chinese herbal formulas, how to prepare them and how their properties can be enhanced through combinations with everyday foods.
Circadian variation and triggers of onset of acute cardiovascular disease. (1989)

Information obtained during the past decade suggests the need to reexamine the possibility that the onset of myocardial infarction and sudden cardiac death is frequently triggered by daily activities. The importance of physical or mental stress in triggering onset of coronary thrombosis is supported by the findings that 1) the frequencies of onset of myocardial infarction, sudden cardiac death, and stroke show marked circadian variations with parallel increases in the period from 6:00 AM to noon, 2) transient myocardial ischemia shows a similar morning increase, and episodes are often preceded by mental or physical triggers, 3) a ruptured atherosclerotic plaque, often nonobstructive by itself, lies at the base of most coronary thrombi, 4) a number of physiologic processes that could lead to plaque rupture, a hypercoagulable state or coronary vasoconstriction, are accentuated in the morning, and 5) aspirin and beta-adrenergic blocking agents, which block certain of these processes, have been shown to prevent disease onset. The hypothesis is presented that occlusive coronary thrombosis occurs when 1) an atherosclerotic plaque becomes vulnerable to rupture, 2) mental or physical stress causes the plaque to rupture, and 3) increases in coagulability or vasoconstriction, triggered by daily activities, contribute to complete occlusion of the coronary artery lumen. Recognition of the circadian variation--and the possibility of frequent triggering--of onset of acute disease suggests the need for pharmacologic protection of patients during vulnerable periods, and provides clues to mechanism, the investigations of which may lead to improved methods of prevention.
Learning Deep Features for Scene Recognition using Places Database (2014)

Scene recognition is one of the hallmark tasks of computer vision, allowing defi-nition of a context for object recognition. Whereas the tremendous recent progress in object recognition tasks is due to the availability of large datasets like ImageNet and the rise of Convolutional Neural Networks (CNNs) for learning high-level fea-tures, performance at scene recognition has not attained the same level of success. This may be because current deep features trained from ImageNet are not competi-tive enough for such tasks. Here, we introduce a new scene-centric database called Places with over 7 million labeled pictures of scenes. We propose new methods to compare the density and diversity of image datasets and show that Places is as dense as other scene datasets and has more diversity. Using CNN, we learn deep features for scene recognition tasks, and establish new state-of-the-art results on several scene-centric datasets. A visualization of the CNN layers ’ responses al-lows us to show differences in the internal representations of object-centric and scene-centric networks. 1
Probing molecular interactions with homogeneous techniques based on rare earth cryptates and fluorescence energy transfer (1995)

A homogeneous assay method based on the long-lived fluorescence of rare earth cryptates and amplification by nonradiative energy transfer has been developed for immunoassays. The principles of the assay allow a double discrimination of the emitted signal through spectral and temporal selectivity. The cage structure of the complex, ion pairing around europium, as well as double-wavelength detection, fully shield the assay from perturbations of media. Events based on short-range interactions involving biomolecules are of tremendous importance in many domains of biology, either for analytical purposes or for molecular mechanism studies. Therefore, the principles and the reagents used to devise this homogeneous assay were adapted to various models representative of molecular and cellular processes and were chosen from the signaling pathways involved in cellular communication and expression: epidermal growth factor (EGF) receptor-ligand interaction, EGF receptor kinase activity, Jun/Fos protein-protein interaction, and DNA hybridization. Evaluation of the homogeneous assays yielded results compatible with those from comparison assays and demonstrates the versatility and wide range of applicability of this methodology.
Review of Detection of Brucella sp. by Polymerase Chain Reaction (2010)

Here we present a review of most of the currently used polymerase chain reaction (PCR)-based methods for identification of Brucella bacteria in biological samples. We focused in particular on methods using single-pair primers, multiplex primers, real-time PCRs, PCRs for marine Brucella, and PCRs for molecular biotyping. These methods are becoming very important tools for the identification of Brucella, at the species level and recently also at the biovar level. These techniques require minimum biological containment and can provide results in a very short time. In addition, genetic fingerprinting of isolates aid in epidemiological studies of the disease and its control. PCR-based methods are more useful and practical than conventional methods used to identify Brucella spp., and new methods for Brucella spp. identification and typing are still being developed. However, the sensitivity, specificity, and issues of quality control and quality assurance using these methods must be fully validated on clinical samples before PCR can be used in routine laboratory testing for brucellosis.
Kinetics of Antibody Response toEhrlichia canisImmunoreactive Proteins (2003)

Immunoreactive proteins of Ehrlichia canis and Ehrlichia chaffeensis that have been characterized include a family of 28-kDa major outer membrane proteins (p28) and two large antigenically divergent surface glycoprotein orthologs. We previously demonstrated that recombinant E. canis p28 and the 140- and 200-kDa glycoproteins gp140 and gp200, respectively, react strongly with serum antibodies from suspect canine ehrlichiosis cases that were positive for E. canis by immunofluorescent antibody test and in various phases of acute or chronic infection (J. Clin. Microbiol. 39:315-322, 2001). The kinetics of the antibody response to these potentially important vaccine and immunodiagnostic candidates is not known. Acute-phase serum antibody responses to whole-cell E. canis lysates and recombinant p28, gp140, and gp200 were monitored for 6 weeks in dogs experimentally infected with E. canis. Irrespective of the inoculation route, a T-helper 1-type response was elicited to E. canis antigens consisting of immunoglobulin G2 antibodies exclusively in both acute and convalescent phases in most dogs. Analysis of immuoreactive antigens for peak intensity and relative quantity identified major immunoreactive E. canis antigens recognized early in the infection as the 19-, 37-, 75-, and 140-kDa proteins. Later in infection, additional major immunoreactive E. canis proteins were identified, including the 28-, 47-, and 95-kDa proteins and the recently identified 200-kDa glycoprotein. All dogs had developed antibody against the recombinant gp140, gp200, and p28 in the convalescent phase. Immunoreactivity and antibody response kinetics suggest that major immunoreactive proteins identified are immunodominant, but early recognition suggests increased dominance by some antigens.
Phase III Trial of Carboplatin and Paclitaxel Compared With Cisplatin and Paclitaxel in Patients With Optimally Resected Stage III Ovarian Cancer: A Gynecologic Oncology Group Study (2003)

In patients with advanced ovarian cancer, a chemotherapy regimen consisting of carboplatin plus paclitaxel results in less toxicity, is easier to administer, and is not inferior, when compared with cisplatin plus paclitaxel.
Interferon-β gene therapy inhibits tumor formation and causes regression of established tumors in immune-deficient mice (1998)

Despite the potential of type 1 interferons (IFNs) for the treatment of cancer, clinical experience with IFN protein therapy of solid tumors has been disappointing. IFN-beta has potent antiproliferative activity against most human tumor cells in vitro in addition to its known immunomodulatory activities. The antiproliferative effect, however, relies on IFN-beta concentrations that cannot be achieved by parenteral protein administration because of rapid protein clearance and systemic toxicities. We demonstrate here that ex vivo IFN-beta gene transduction by a replication-defective adenovirus in as few as 1% of implanted cells blocked tumor formation. Direct in vivo IFN-beta gene delivery into established tumors generated high local concentrations of IFN-beta, inhibited tumor growth, and in many cases caused complete tumor regression. Because the mice were immune-deficient, it is likely that the anti-tumor effect was primarily through direct inhibition of tumor cell proliferation and survival. Based on these studies, we argue that local IFN-beta gene therapy with replication-defective adenoviral vectors might be an effective treatment for some solid tumors.
Data quality in context (1997)

In Context ATA-QUALITY (DQ) PROBLEMS ARE INCREASINGLY EVIdent, particularly in organizational databases. Indeed, 50% to 80% of computerized criminal records in the U.S. were found to be inaccurate, incomplete, or ambiguous. The social and economic impact of poor-quality data costs billions of dollars. [5-7, 10]. Organizational databases, however, reside in the larger context of information systems (IS). Within this larger context, data is collected from multiple data sources and stored in databases. From this stored data, useful information 1 is generated for organizational decision-making. A new study reveals businesses are defining data quality with the consumer in mind.
Early diagnosis of acute kidney injury in critically ill patients (2008)

Acute kidney injury (AKI) is a common and serious problem in critically ill patients. Tests currently used to detect AKI (i.e., serum creatinine, serum urea and various urinary indices) often result in delayed detection of injury--becoming abnormal at 48-72 h after the initial insult. This delayed detection translates into a potential missed opportunity for therapeutic interventions at a time when kidney damage may be limitable or reversible. This may also, in particular, account for the poor clinical outcomes commonly associated with AKI. The development of novel serum and urinary biomarkers capable of detecting AKI at an earlier phase of illness is therefore vital. This article will review the pitfalls of current conventional testing in kidney injury and discuss the emergence of novel biomarkers with the potential to revolutionize the field of critical care nephrology.
US trends in navigable digital map databases (2002)

Navigable digital map databases have long been recognized as a key element in a wide variety of applications in IVHS and related fields, ranging from in-vehicle navigation to demographic analysis and business planning. The traditional emphasis of navigable digital map database development in the US has been on in-vehicle route guidance products, among the earliest of the major IVHS applications to reach the market. As route guidance products start to reach a broad marketplace, and as other applications begin to get serious attention, there are several notable trends in the continuing development and management of navigable map databases in the US. This paper discusses some of these trends, including issues in database packaging, the need for a national field organization to maintain database currency and accuracy, data storage and retrieval, the emergence of new applications, and US government programs for data creation and transfer.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Pancreastatin, a Presumed Product of Chromogranin-A (Secretory Protein-I) Processing, Inhibits Secretion from Porcine Parathyroid Cells in Culture* (1989)

Chromogranin-A, also referred to as secretory protein-I, is a 50K protein found in and secreted by endocrine cells, in which it is costored with the native hormone. Porcine chromogranin-A contains a sequence identical to pancreastatin, a 49-amino acid, C-terminally amidated peptide that has been isolated from porcine pancreas, suggesting that chromogranin-A is the precursor of pancreastatin. Pancreastatin has been found to be a potent inhibitor of glucose-stimulated insulin release. As it is possible that pancreastatin inhibits secretion from other chromogranin-A-containing tissues in which it may be formed, we tested its action on dispersed porcine parathyroid cells in culture. Secretion of chromogranin-A and PTH was up to 6-fold greater at 0.5 mM Ca2+ than at 3.0 mM Ca2+. Pancreastatin (1 nM) reduced the secretion of both chromogranin-A and PTH at 0.5 mM Ca2+ to approximately the levels found at 3.0 mM Ca2+, but did not affect secretion at 3.0 mM Ca2+. Pancreastatin (0.01-1.0 nM) inhibited secretion of chromogranin-A in a dose-dependent fashion. Preincubation of the cells with pancreastatin was not required for inhibition. Transfer of inhibited cells to medium without pancreastatin led to restoration of secretion within 90 min. Phorbol myristate acetate (1.6 microM) stimulated secretion of PTH and chromogranin-A at 3.0 mM Ca2+, but not at 0.5 mM Ca2+. Pancreastatin reversed this stimulation, demonstrating that its inhibition was independent of Ca2+ concentration. These results are consonant with pancreastatin playing a physiological role in modulation of secretion by the parathyroid and, by extension, other endocrine tissues.
Raft mediated surface grafting of t‐butyl acrylate onto an ethylene–propylene copolymer initiated by gamma radiation (2007)

Abstract RAFT mediated grafting of poly( t ‐butyl acrylate) onto the surface of a commercial poly(ethylene‐ co ‐propylene), Elpro, has been carried out using initiation by 60 Co γ‐radiation at 298 and 273 K. The polymerizations were in bulk monomer and using the RAFT agent 1‐phenylethyl phenyldithioacetate. The rates of homopolymerization and grafting were found to decrease with increasing RAFT agent concentration, indicating that both polymerization processes involve participation of the RAFT agent. There was good agreement between the predicted and experimental molecular weights of the homopolymer that had a narrow polydispersity. The poly( t ‐butyl acrylate) grafts were hydrolyzed by trifluoroacetic acid to form poly(acrylic acid) grafts, which could either be further functionalized or used to control the surface polarity of the Elpro. ATR‐FTIR spectroscopy was used to characterize the grafts and Raman spectroscopy was used to assess the depth of the grafts. The water contact angle for the Elpro surface grafted with poly(acrylic acid) was found to be linearly dependent on the amount of the graft present. The living nature of the grafted chains was demonstrated by the addition of a second block of polystyrene. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 1074–1083, 2007
A coupled complex of T4 DNA replication helicase (gp41) and polymerase (gp43) can perform rapid and processive DNA strand-displacement synthesis (1996)

We have developed a coupled helicase-polymerase DNA unwinding assay and have used it to monitor the rate of double-stranded DNA unwinding catalyzed by the phage T4 DNA replication helicase (gp41). This procedure can be used to follow helicase activity in subpopulations in systems in which the unwinding-synthesis reaction is not synchronized on all the substrate-template molecules. We show that T4 replication helicase (gp41) and polymerase (gp43) can be assembled onto a loading site located near the end of a long double-stranded DNA template in the presence of a macro-molecular crowding agent, and that this coupled "two-protein" system can carry out ATP-dependent strand displacement DNA synthesis at physiological rates (400 to 500 bp per sec) and with high processivity in the absence of other T4 DNA replication proteins. These results suggest that a direct helicase-polymerase interaction may be central to fast and processive double-stranded DNA replication, and lead us to reconsider the roles of the other replication proteins in processivity control.
A randomized,double-blinded,controlled,multicenter clinical trial of linezolid versus vancomycin in the treatment of gram positive bacterial infection (2009)

Objective To evaluate the efficacy and safety of linezolid for injection in the treatment of gram positive bacterial infection.MethodsIn this randomized,double-blinded,controlled,multicenter clinical trial,patients with pneumonia or complicated skin and soft-tissue infections due to suspected or known gram-positive pathogens were randomized to receive either linezolid or vancomycin intravenously.ResultsA total of 144 patients were enrolled and 142 patients received study medication.The modified intention-to-treat(MITT)set was 141.The per-protocol(PP)set was 116.The safety set was 142.In the analysis with PP set,at follow-up,the clinical efficacy rates of linezolid group and vancomycin group were 86.9%(53/61)and 61.7%(37/60)respectively with statistically significant difference.In the population of pneumonia,the efficacy rates were 78.6%(22/28)and 52.9%(18/34).In the population of complicated skin and soft tissue infection,the efficacy rates were 78.6%(22/28)and 52.9%(18/34).the bacterial eradication rate was 79.2%(42/53)in linezolid group and 61.5%(32/52)in vancomycin group,with statistically significant difference.In the population of pneumonia,the bacterial eradication rates were 77.3%(17/22)and 53.6%(15/28);in the population of complicated skin and soft tissue infection,the bacterial eradication rates were 80.6%(25/31)and 70.8%%(17/24).In the analysis with safety set,the incidence of drug-related adverse event was 25.4%(18/71)in linezolid group,including 14.1%(10/71)clinical adverse reaction,such as fever,rash,dyspepsia,and 15.5%(11/71)laboratory abnormality,such as liver function abnormality,mild leukopenia,thrombocytopenia.The incidence of drug-related adverse event in vancomycin group was 16.9%(12/71),including 15.5%(11/71)clinical adverse reaction,such as fever,rash,red man syndrome,and 5.2%(3/71)laboratory abnormality,mainly liver function abnormality.Discontinuation rate due to adverse event(AE)was 5.6% in linezolid group and 11.3% in vancomycin group.Discontinuation rate due to drug-related adverse reaction was 1.4% and 5.6%,respectively.All the isolated pathogens were susceptible to linezolid and vancomycin.ConclusionsLinezolid for injection is well-tolerated and effective in the treatment of pneumonia and complicated skin and soft tissue infection caused by gram-positive pathogens.