gebhart/patrepeval huggingface dataset:
Genome plasticity of BCG and impact on vaccine efficacy (2007)

To understand the evolution, attenuation, and variable protective efficacy of bacillus Calmette-Guérin (BCG) vaccines, Mycobacterium bovis BCG Pasteur 1173P2 has been subjected to comparative genome and transcriptome analysis. The 4,374,522-bp genome contains 3,954 protein-coding genes, 58 of which are present in two copies as a result of two independent tandem duplications, DU1 and DU2. DU1 is restricted to BCG Pasteur, although four forms of DU2 exist; DU2-I is confined to early BCG vaccines, like BCG Japan, whereas DU2-III and DU2-IV occur in the late vaccines. The glycerol-3-phosphate dehydrogenase gene, glpD2, is one of only three genes common to all four DU2 variants, implying that BCG requires higher levels of this enzyme to grow on glycerol. Further amplification of the DU2 region is ongoing, even within vaccine preparations used to immunize humans. An evolutionary scheme for BCG vaccines was established by analyzing DU2 and other markers. Lesions in genes encoding sigma-factors and pleiotropic transcriptional regulators, like PhoR and Crp, were also uncovered in various BCG strains; together with gene amplification, these affect gene expression levels, immunogenicity, and, possibly, protection against tuberculosis. Furthermore, the combined findings suggest that early BCG vaccines may even be superior to the later ones that are more widely used.
Usefulness of fine‐needle aspiration in the diagnosis of thyroid carcinoma (2000)

BACKGROUND Nodular thyroid disease is a frequent occurrence in clinical practice. The numerous diagnostic procedures available make the diagnosis of thyroid carcinoma possible but, if not used rationally, may lead to an unjustified increase in cost with little practical gain. The aim of the current study was to evaluate the usefulness of fine-needle aspiration (FNA) of palpable thyroid nodules after functional evaluation by thyroid scintigraphy. METHODS The authors retrospectively evaluated 37,895 FNAs performed between 1980–1997. FNAs were performed on palpable thyroid nodules, except unambiguously autonomous (“hot”) nodules, at the time of thyroid scintigraphy. Cytologic and histologic diagnoses were compared in 4069 patients to estimate the accuracy of FNA. RESULTS The sensitivity of FNA was 91.8% and the specificity was 75.5%. A pretest probability of thyroid carcinoma of 4% was reduced to 0.4% in the patients with a cytologic diagnosis of benign nodular goiter, whereas it was increased to 90.7% in those patients with a positive cytologic diagnosis. Only in the case of a cytologic diagnosis of “follicular neoplasm” was the probability of malignancy not changed significantly and histologic evaluation of the nodule was necessary. CONCLUSIONS In the majority of cases, FNA of palpable thyroid nodules allows for the identification of thyroid carcinoma and the planning of subsequent appropriate therapy. This can be achieved by using simple and inexpensive procedures, if cooperation among clinicians, pathologists, and nuclear physicians is maximized. [See editorial on pages 325–329 and original article on pages 330–334, this issue.] Cancer (Cancer Cytopathol) 2000;90:357–363. © 2000 American Cancer Society.
Development of the Integrated Management System of the Control Points (2004)

Control stations managed by national and local governmes are associated with other survey work and constructing geography information and they are important assets in the national level as the positional standard of the country. Since these control points are managed as some type of register and the control points could not be easily updated due to the loss of control stations from construction work or urban development. Therefore, the users could not understand the present situation of the changed control stations. In this background, the aim of this study was to develop control station management system which the managers can use to efficiently maintain control points and to support the usage of the survey control points. For developing this system, we have designed input, update, network, analysis and statistic functions, and have constructed the system using Mapobject as main engine with other languages such as Visual C++ and Visual Basic. The graphic data used in this system are 1/5,000 digital map and digital cadastral map, and the attribute data of each control station are point name, map tile name, longitude and latitude coordinates, TM coordinates, surveying data with the format of year-month-day and control situation photos and so on. In the result of constructing this control station management system, we could achieve integrated management of graphic, attribute and positioning information of each control station.
Fast, inexpensive content-addressed storage in foundation (2008)

Foundation is a preservation system for users ’ personal, digital artifacts. Foundation preserves all of a user’s data and its dependencies—fonts, programs, plugins, kernel, and configuration state—by archiving nightly snapshots of the user’s entire hard disk. Users can browse through these images to view old data or recover accidentally deleted files. To access data that a user’s current environment can no longer interpret, Foundation boots the disk image in which that data resides under an emulator, allowing the user to view and modify the data with the same programs with which the user originally accessed it. This paper describes Foundation’s archival storage layer, which uses content-addressed storage (CAS) to retain nightly snapshots of users ’ disks indefinitely. Current state-of-the-art CAS systems, such as Venti [34], require multiple high-speed disks or other expensive hardware to achieve high performance. Foundation’s archival storage layer, in contrast, matches the storage efficiency of Venti using only a single USB hard drive. Foundation archives disk snapshots at an average throughput of 21 MB/s and restores them at an average of 14 MB/s, more than an order of magnitude improvement over Venti running on the same hardware. Unlike Venti, Foundation does not rely on the assumption that SHA-1 is collision-free. 1
Particle separation using virtual deterministic lateral displacement (vDLD) (2014)

We present a method for sensitive and tunable particle sorting that we term virtual deterministic lateral displacement (vDLD). The vDLD system is composed of a set of interdigital transducers (IDTs) within a microfluidic chamber that produce a force field at an angle to the flow direction. Particles above a critical diameter, a function of the force induced by viscous drag and the force field, are displaced laterally along the minimum force potential lines, while smaller particles continue in the direction of the fluid flow without substantial perturbations. We demonstrate the effective separation of particles in a continuous-flow system with size sensitivity comparable or better than other previously reported microfluidic separation techniques. Separation of 5.0 μm from 6.6 μm, 6.6 μm from 7.0 μm and 300 nm from 500 nm particles are all achieved using the same device architecture. With the high sensitivity and flexibility vDLD affords we expect to find application in a wide variety of microfluidic platforms.
Expression of a chimeric uidA gene indicates that polycistronic mRNAs are efficiently translated in tobacco plastids (1995)

Polycistronic mRNAs are the predominant form of plastid primary transcripts. To determine if there is internal initiation of translation of promoter-distal open reading frames, a promoterless uidA reporter gene was integrated into the tobacco plastid genome downstream of the rbcL gene. Monocistronic uidA mRNA does not accumulate from the promoterless uidA construct. However, due to inefficient rbcL transcription termination, a polycistronic transcription unit is created that contains the uidA gene as the second cistron. Numerous stop codons in all three reading frames between the rbcL and uidA coding regions ensure that translation of uidA initiates only from the correct start codon. The encoded reporter gene product, beta-glucuronidase (GUS) accumulates to high levels in the transplastomic plants indicating that promoter-distal cistrons can be efficiently translated in plastids.
Synthesis of Maleimide-Activated Carbohydrates as Chemoselective Tags for Site-Specific Glycosylation of Peptides and Proteins (2002)

An array of maleimide-activated mono- and oligosaccharides were synthesized to permit site-specific glycosylation of cysteine-containing peptides and proteins. Maleimide-activated monosaccharides, in which the native alpha- or beta-O-glycosidic linkages found for nonreducing terminal sugars of native glycoproteins are preserved, were prepared using 2'-aminoethyl glycosides as the key intermediates. In addition, a native high-mannose type oligosaccharide, Man(9)GlcNAc(2)Asn, was converted into its maleimide-activated form by taking advantage of the existing amino group in the Asn portion. The application of these maleimide-activated carbohydrates was exemplified by the site-specific glycosylation of a 36-mer HIV-1 gp41 peptide, T20, which is a potent inhibitor against HIV infection. The chemoselective ligation was found to be rapid, highly efficient, and essentially quantitative. Tagging the biologically active peptide with a mannose and/or oligomannose moiety will be useful for targeting the drug to macrophage and dendritic cells, which are primary targets for HIV-1 infection and are expressing mannose- and oligomanose-specific receptors on their surface. In combination with site-specific mutagenesis, the maleimide-activated carbohydrates can serve as generally applicable tags for site-specific glycosylation of proteins via the highly efficient maleimide-thiol ligation reaction.
[Surgical therapy of acute pancreatitis]. (1992)

In patients with proven acute pancreatitis which is not necrotizing conservative therapy leads to a rapid pain release; after sanitation of the basic disease, complete healing is achieved. In case of a biliary pancreatitis with incarcerated gallstones in the papilla an EPT with removal of the choledochal stones is carried out within the first 12 hours after onset of incarceration symptoms; after disappearance of the symptoms of acute pancreatitis an endoscopic or minilap.-cholecystectomy is performed. Conservative therapy leads to a complete cure in patients with minor necroses without any bacterial contamination and without extensive retroperitoneal fatty tissue necroses. Surgery is indicated if a surgical acute abdomen or a sepsis develops, if patients do not respond to maximum intensive care treatment over at least 72 hours, or if organ complications, such as pulmonary/renal insufficiency, cardiocirculatory dysfunction/shock and metabolic disorders grow worse under ICU treatment. The choice procedure against bacterially contaminated necrosis is their careful removal by necrosectomy or débridement. Resectional techniques should be avoided. A third of patients needs reoperation because of extensive inflammatory processes in the retroperitoneum and around the pancreas. Treatment centres report a hospital mortality rate of clearly below 20%.
Understanding bone responses in B-mode ultrasound images and automatic bone surface extraction using a Bayesian probabilistic framework (2004)

The registration of preoperative CT to intra-operative reality systems is a crucial step in Computer Assisted Orthopedic Surgery (CAOS). The intra-operative sensors include 3D digitizers, fiducials, X-rays and Ultrasound (US). Although US has many advantages over others, tracked US for Orthopedic Surgery has been researched by only a few authors. An important factor limiting the accuracy of tracked US to CT registration (1-3mm) has been the difficulty in determining the exact location of the bone surfaces in the US images (the response could range from 2-4mm). Thus it is crucial to localize the bone surface accurately from these images. Moreover conventional US imaging systems are known to have certain inherent inaccuracies, mainly due to the fact that the imaging model is assumed planar. This creates the need to develop a bone segmentation framework that can couple information from various post-processed spatially separated US images (of the bone) to enhance the localization of the bone surface. In this paper we discuss the various reasons that cause inherent uncertainties in the bone surface localization (in B-mode US images) and suggest methods to account for these. We also develop a method for automatic bone surface detection. To do so, we account objectively for the high-level understanding of the various bone surface features visible in typical US images. A combination of these features would finally decide the surface position. We use a Bayesian probabilistic framework, which strikes a fair balance between high level understanding from features in an image and the low level number crunching of standard image processing techniques. It also provides us with a mathematical approach that facilitates combining multiple images to augment the bone surface estimate.
Engineering picoliter droplets for ultra-high throughput microbial biotechnology: microfluidic strategies for culturing and screening the microverse and exploit its biosynthetic potential (2018)

From the microbiologists perspective, microfluidic droplets deliver a paradigm-changing experimental approach, providing a powerful platform in which the biochemical and physiological parameters of microbial samples can be explored with millions of droplets per experiment. The aim of this thesis was to develop technological and experimental enhancements to establish microfluidic droplet assays for the investigation and exploitation of microbial diversity. These developments include: A system for microbial cultivation in millions of picoliter enabling an enhanced and uniform oxygenation and control of pH for the microorganisms in all the droplets simultaneously. A method to take a single image of each droplet and linked the image acquisition to analysis and microfluidic actuation, enabling real-time image-based droplet sorting for the first time. With custom image analysis algorithms it was possible to detect and quantify microbes proliferating in droplets while also keeping quality descriptors monitored over the course of experimentation. A droplet population encoding strategy based on the encapsulation and detection of colored polymer microbeads was developed in order to test multiple conditions simultaneously. A strategy for facile production of multi-structured 3D microfluidic chips, making customized chip production accessible in non-specialized labs. An opto-electronic strategy to be able to simultaneously detect multiple fluorescent channels using a single sensor. A system enabling automated transfer and deposition of single sorted droplets onto Petri dishes or into wells of microplates; for the recovery of microorganisms isolated in single droplets. These developments and applications provide ground work for a broad application of droplet microfluidics in microbiology and biotechnology; contributing to further progress in the field, with both academic and industrial perspectives.
The Design and Analysis of Computer Algorithms (1974)

A text book for a first course in design and analysis of algorithms. The emphasis is on ideas and ease of understanding rather then on implementation details or programming tricks. It starts with formulating several models that include random access register machine, random access stored program machine and variants of these, so one can establish analytical results and at the same time accurately reflect on the salient features of real machines
Dynamic Measures of vergence Accommodation (1977)

Dynamic measures of vergence accommodation (VG-ACC) are necessary for complete analysis of the triadic near response but are difficult to obtain because eyeball rotation affects accommodative measures. A dynamic optometer that uses the third Purkinje image is shown to be insensitive to small eye rotations and permits dynamic measures of VG-ACC responses. Such measures are presented to demonstrate the feasibility of this method. Average latency measures of 260 msec for VG-ACC fall between the latency of 160 msec for disparity vergence and the latency of 380 msec for accommodation. Additional dynamic features of VG-ACC resemble those of other components of the near triad.
Transcription profiling during the cell cycle shows that a subset of Polycomb-targeted genes is upregulated during DNA replication (2013)

Genome-wide gene expression analyses of the human somatic cell cycle have indicated that the set of cycling genes differ between primary and cancer cells. By identifying genes that have cell cycle dependent expression in HaCaT human keratinocytes and comparing these with previously identified cell cycle genes, we have identified three distinct groups of cell cycle genes. First, housekeeping genes enriched for known cell cycle functions; second, cell type-specific genes enriched for HaCaT-specific functions; and third, Polycomb-regulated genes. These Polycomb-regulated genes are specifically upregulated during DNA replication, and consistent with being epigenetically silenced in other cell cycle phases, these genes have lower expression than other cell cycle genes. We also find similar patterns in foreskin fibroblasts, indicating that replication-dependent expression of Polycomb-silenced genes is a prevalent but unrecognized regulatory mechanism.
Scanned beam medical imager (2004)

We report on a conceptual design and feasibility demonstration for a scanned beam endoscope, with advantages over present CCD imaging technology in image resolution and quality, light source power, and package diameter. Theoretical calculations were made by optical modeling and finite element analysis of the performance projected for a design meeting size constraints. To verify the design target of 5 mm for the endoscope diameter, we conducted a design study of the deformation and resolution characteristics of a scan mirror small enough to fit within a 2.5 mm capsule within the endoscope. The results show that performance similar to the test system can be achieved. A functional prototype was then built and tested to validate the theory used. The test system consisted of a photonics module with red (635 nm), green (532 nm) and blue (473 nm) lasers, combined by dichroic mirrors and launched to a single mode fiber. The light emerging from the fiber is formed into a beam and reflected from a commercially available bi-axial MEMS scanner with a 1.56 mm square mirror, and a scan angle of 6 degrees zero to peak mechanical, at a frequency of 19.7 kHz. Scanned beam power from 1 to 3 mw impinges the test object at a range from 10 to 100 mm, and the scattered light is collected by several 3 mm diameter multimode fibers and conducted one-meter to detectors. The detected light was digitized and then reconstructed to form an image of the test object, with 800 by 600 output pixels. Several such images will be presented.
Generation of Neutralizing Activity against Human Immunodeficiency Virus Type 1 in Serum by Antibody Gene Transfer (2002)

Although several human immunodeficiency virus (HIV) vaccine approaches have elicited meaningful antigen-specific T-cell responses in animal models, no single vaccine candidate has engendered antibodies that broadly neutralize primary isolates of HIV type 1 (HIV-1). Thus, there remains a significant gap in the design of HIV vaccines. To address this issue, we exploited the existence of rare human monoclonal antibodies that have been isolated from HIV-infected individuals. Such antibodies neutralize a wide array of HIV-1 field isolates and have been shown to be effective in vivo. However, practical considerations preclude the use of antibody preparations as a prophylactic passive immunization strategy in large populations. Our concept calls for an antibody gene of choice to be transferred to muscle where the antibody molecule is synthesized and distributed to the circulatory system. In these experiments, we used a recombinant adeno-associated virus (rAAV) vector to deliver the gene for the human antibody IgG1b12 to mouse muscle. Significant levels of HIV-neutralizing activity were found in the sera of mice for over 6 months after a single intramuscular administration of the rAAV vector. This approach allows for predetermination of antibody affinity and specificity prior to "immunization" and avoids the need for an active humoral immune response against the HIV envelope protein.
Small interfering RNA targeting epidermal growth factor receptor enhances chemosensitivity to cisplatin, 5‐fluorouracil and docetaxel in head and neck squamous cell carcinoma (2006)

Overexpression of epidermal growth factor receptor (EGFR) has been found in various epithelial malignancies, including head and neck squamous cell carcinoma (HNSCC), and is associated with increased tumor growth, metastasis, resistance to chemotherapeutic agents and poor prognosis. As such, EGFR is a potential target for antitumor therapy and several EGFR inhibitors have been investigated in preclinical or clinical settings. In the present study, we used small interfering RNA (siRNA) to downregulate EGFR expression while evaluating the effect of EGFR siRNA on cell proliferation, and the combined effects with cisplatin, 5-fluorouracil (5-FU) and docetaxel in HNSCC. Furthermore, HNSCC xenografts were treated with EGFR siRNA alone or in combination with cisplatin, and tumor growth was examined. EGFR expression, proliferation, angiogenesis and apoptosis index were evaluated by immunohistochemistry. The results showed that EGFR siRNA efficiently downregulated EGFR expression and inhibited cell growth of HNSCC. Treatment with EGFR siRNA in combination with cisplatin, 5-FU and docetaxel enhanced chemosensitivity with a significant increase in apoptosis. EGFR siRNA delivered by atelocollagen enhanced the antitumor effect of cisplatin in the HNSCC xenograft model. These cumulative results suggest that EGFR siRNA combined with cisplatin, 5-FU and docetaxel may be a feasible strategy to enhance the effects of chemotherapy in patients with HNSCC.
Prostaglandin E2deficiency causes a phenotype of aspirin sensitivity that depends on platelets and cysteinyl leukotrienes (2013)

Aspirin-exacerbated respiratory disease (AERD) is characterized by asthma, tissue eosinophilia, overproduction of cysteinyl leukotrienes (cysLTs), and respiratory reactions to nonselective cyclooxygenase (COX) inhibitors. Ex vivo studies suggest that functional abnormalities of the COX-2/microsomal prostaglandin (PG)E2 synthase-1 system may underlie AERD. We demonstrate that microsomal PGE2 synthase-1 null mice develop a remarkably AERD-like phenotype in a model of eosinophilic pulmonary inflammation. Lysine aspirin (Lys-ASA)-challenged PGE2 synthase-1 null mice exhibit sustained increases in airway resistance, along with lung mast cell (MC) activation and cysLT overproduction. A stable PGE2 analog and a selective E prostanoid (EP)2 receptor agonist blocked the responses to Lys-ASA by ∼90%; EP3 and EP4 agonists were also active. The increases in airway resistance and MC products were blocked by antagonists of the type 1 cysLT receptor or 5-lipoxygenase, implying that bronchoconstriction and MC activation were both cysLT dependent. Lys-ASA-induced cysLT generation and MC activation depended on platelet-adherent granulocytes and T-prostanoid (TP) receptors. Thus, lesions that impair the inducible generation of PGE2 remove control of platelet/granulocyte interactions and TP-receptor-dependent cysLT production, permitting MC activation in response to COX-1 inhibition. The findings suggest applications of antiplatelet drugs or TP receptor antagonists for the treatment of AERD.