gebhart/patrepeval huggingface dataset:
Clinical applications of maternal plasma fetal DNA analysis: translating the fruits of 15 years of research (2012)

The collection of fetal genetic materials is required for the prenatal diagnosis of fetal genetic diseases. The conventional methods for sampling fetal genetic materials, such as amniocentesis and chorionic villus sampling, are invasive in nature and are associated with a risk of fetal miscarriage. For decades, scientists had been pursuing studies with goals to develop non-invasive methods for prenatal diagnosis. In 1997, the existence of fetal derived cell-free DNA molecules in plasma of pregnant women was first demonstrated. This finding provided a new source of fetal genetic material that could be obtained safely through the collection of a maternal blood sample and provided a new avenue for the development of non-invasive prenatal diagnostic tests. Now 15 years later, the diagnostic potential of circulating fetal DNA analysis has been realized. Fruitful research efforts have resulted in the clinical implementation of a number of non-invasive prenatal tests based on maternal plasma DNA analysis and included tests for fetal sex assessment, fetal rhesus D blood group genotyping and fetal chromosomal aneuploidy detection. Most recently, research groups have succeeded in decoding the entire fetal genome from maternal plasma DNA analysis which paved the way for the achievement of non-invasive prenatal diagnosis of many single gene diseases. A paradigm shift in the practice of prenatal diagnosis has begun.
Critical area computation—a new approach (1998)

In this paper we present a new approach for computing the critical area for shorts in a circuit layout. The critical area calculation is the main computational problem in VLSI yield prediction. The method is based on the concept of Voronoi diagrams and computes the critical area for shorts (for all possible defect radii, assuming square defects) accurately in O(n log n) time, where n is the size of the input. The method is presented for rectilinear layouts but it is extendible to general layouts. As a byproduct we briefly sketch how to speed up the grid method of Wagner and Koren [16].
Integrating structural and functional imaging for computer assisted detection of prostate cancer on multi-protocol in vivo 3 Tesla MRI (2009)

Screening and detection of prostate cancer (CaP) currently lacks an image-based protocol which is reflected in the high false negative rates currently associated with blinded sextant biopsies. Multi-protocol magnetic resonance imaging (MRI) offers high resolution functional and structural data about internal body structures (such as the prostate). In this paper we present a novel comprehensive computer-aided scheme for CaP detection from high resolution <i>in vivo</i> multi-protocol MRI by integrating functional and structural information obtained via dynamic-contrast enhanced (DCE) and T2-weighted (T2-w) MRI, respectively. Our scheme is fully-automated and comprises (a) prostate segmentation, (b) multimodal image registration, and (c) data representation and multi-classifier modules for information fusion. Following prostate boundary segmentation via an improved active shape model, the DCE/T2-w protocols and the T2-w/<i>ex vivo</i> histological prostatectomy specimens are brought into alignment via a deformable, multi-attribute registration scheme. T2-w/histology alignment allows for the mapping of true CaP extent onto the <i>in vivo</i> MRI, which is used for training and evaluation of a multi-protocol MRI CaP classifier. The meta-classifier used is a random forest constructed by bagging multiple decision tree classifiers, each trained individually on T2-w structural, textural and DCE functional attributes. 3-fold classifier cross validation was performed using a set of 18 images derived from 6 patient datasets on a per-pixel basis. Our results show that the results of CaP detection obtained from integration of T2-w structural textural data and DCE functional data (area under the ROC curve of 0.815) significantly outperforms detection based on either of the individual modalities (0.704 (T2-w) and 0.682 (DCE)). It was also found that a meta-classifier trained directly on integrated T2-w and DCE data (data-level integration) significantly outperformed a decision-level meta-classifier, constructed by combining the classifier outputs from the individual T2-w and DCE channels.
Secure and Low Cost Selective Encryption for JPEG2000 (2008)

Selective encryption is a new trend in content protection. It aims at reducing the amount of data to encrypt while achieving a sufficient and inexpensive security. This approach is particularly desirable in constrained communication (real time networking with delay constraints, mobile communication with limited computational power...). In this paper we introduce selective encryption from information theory point of view. We define a set of evaluation criteria for selective encryption algorithms and propose a novel selective encryption algorithm for JPEG2000 compressed images satisfying all these criteria. The main contribution of this proposal consists of reaching the minimum amount of data to encrypt regarding a given level of security and target application requirements. For this purpose, we exploit the R-D optimization performed by JPEG2000 EBCOT algorithm.
Relative concentrations of serum neutralizing antibody to VP3 and VP7 proteins in adults infected with a human rotavirus (1988)

Two outer capsid rotavirus proteins, VP3 and VP7, have been found to elicit neutralizing-antibody production, but the immunogenicity of these proteins during human rotavirus infection has not been determined. The relative amounts of serum neutralizing antibody against the VP3 and VP7 proteins of the CJN strain of human rotavirus were, therefore, determined in adult subjects before and after infection with this virus. Reassortant strains of rotavirus that contained the CJN gene segment for only one of these two neutralization proteins were isolated and used for this study. The geometric mean titer of serum neutralizing antibody to a reassortant virus (CJN-M) that contained VP7 of CJN and VP3 of another human rotavirus was 12.7 times less than that of antibody to CJN before infection and 20.3 times less after infection. This indicated that most neutralizing antibody was against the VP3 rather than the VP7 protein of CJN. This result was confirmed with other reassortants between CJN and animal rotavirus strains (EDIM and rhesus rotavirus). These findings suggest that VP3 is the primary immunogen that stimulates neutralizing antibody during at least some rotavirus infections of humans.
THE SEPARATION OF ACETONE-METHANOL MIXTURE BY EXTRACTIVE DISTILLATION (1988)

Abstract Acetone and methanol can not be readily separated by ordinary distillation because of the presence of the minimum boiling azeotrope. Either acetone or methanol can be the overhead product when an appropriate agent is applied in extractive distillation. An unusual phenomenon, “temperature inversion”, was observed when ketones were used as the extractive distillation agents. The dissolving of the vapors into the liquid phase could be the cause for the overhead at a temperature higher than that of the stillpot.
Superlattice quantum cascade lasers operating at very long wavelengths (λ≅17 μm) (2003)

Summary form only given. Quantum cascade (QC) lasers operating on intersubband transitions between conduction band states in InGaAs/AlInAs heterostructures have proven so far to be extremely versatile, covering the range of wavelengths of the two atmospheric windows (3.4 /spl mu/m-13 /spl mu/m). Their extension to even longer wavelengths is, however, problematic, due to the increasingly smaller radiative efficiency of intersubband transitions and to the optical losses from intraband free-carrier absorption, which are roughly proportional to /spl lambda/. We present the realization of a QC laser employing these so-called "chirped" superlattices and operating at /spl lambda//spl sim/17 /spl mu/m which represents the first demonstration of a semiconductor injection laser based on intra-band transitions at wavelengths beyond the atmospheric windows. A schematic band diagram of the structure, which has been grown by molecular beam epitaxy (MBE) in the InGaAs/InA1As material system lattice matched to InP substrate is presented.
Comparison of PF4/Heparin ELISA Assay With the<sup>14</sup>C-Serotonin Release Assay in the Diagnosis of Heparin-induced Thrombocytopenia (1995)

The diagnosis of heparin-induced thrombocytopenia (HIT) may be affirmed by demonstrating heparin-dependent anti-platelet antibodies using the 14C-serotonin release assay (SRA). In this study, results of the SRA was compared with the recently described platelet factor 4 (PF4)/heparin enzyme-linked immunosorbent assay (ELISA). Compared with the SRA, the sensitivity and specificity of a PF4/heparin ELISA was 87% and 92%, respectively, using an assay developed in our laboratory; and 90% and 98%, respectively, using a commercially developed kit (Diagnostica Stago, Asnieres, France). However, antibodies to PF4/heparin were also detected in up to 8% of patients whose plasma was negative by SRA, and 23% of patients receiving heparin who were not thrombocytopenic. These data indicate that results obtained with the PF4/heparin ELISA and the SRA are generally in accord in patients with a clinical diagnosis of HIT. However, discrepant results occur in approximately 20% of cases because of the greater sensitivity of ELISA and the possible involvement of other heparin-binding proteins. The fact that each assay contributes independent information in some cases must be considered in the sequence of test performance and in providing consultation to the practicing hematologist.
Multi-scale iterative reconstruction (2011)

Zoomed ROI reconstruction is a natural challenge for iterative reconstruction (IR), since the reprojection step requires knowledge of the entire object attenuating the x-ray beam. In contrast, analytic FBP can reconstruct images within the zoomed ROI without the need of the full FOV reconstruction, provided projection data is not truncated. To overcome this challenge in IR, the following approaches have been suggested: 1) Remove the part of the projection data corresponding to the outside-of-ROI part of the image volume. 2) Use two volume grids, one for full FOV and one for desired ROI. In the case when the size of desired ROI becomes very small, resolution of the fine grid becomes dominated by the coarse grid, and small features cannot be resolved. Our approach is inspired by multi-resolution framework. Image reconstruction is done in several steps. At each step we reduce the size of reconstruction FOV, for example by half, thus refining the scale, since matrix size remains constant. The proposed approach provides the following advantages compared to the standard 2-grid approach 1) Spatial resolution is preserved in zoomed ROI reconstructions. 2) Computational burden and computer memory requirement are reduced. 3) Parameter optimization is simplified, since only one volume is reconstructed at each iteration.
Main Magnetic Focus Ion Source: II. The first investigations at 10 keV (2015)

The basic principles of design for the compact ion source of new generation are presented. The device uses the local ion trap created by the axial electron beam rippled in a thick magnetic lens. In accordance with this feature, the ion source is given the name main magnetic focus ion source. The experimental evidences for the production of Ir$^{59+}$, Xe$^{44+}$, and Ar$^{16+}$ ions are obtained. The control over depth of the local ion trap is shown to be feasible.
Production of moth sex pheromones for pest control by yeast fermentation (2020)

Abstract The use of insect sex pheromones is an alternative technology for pest control in agriculture and forestry, which, in contrast to insecticides, does not have adverse effects on human health or environment and is efficient also against insecticide-resistant insect populations. 1,2 Due to the high cost of chemically synthesized pheromones, mating disruption applications are currently primarily targeting higher value crops, such as fruits. 3 Here we demonstrate a biotechnological method for the production of pheromones of economically important moth pests using engineered yeast cell factories. Biosynthetic pathways towards several pheromones or their precursors were reconstructed in the oleaginous yeast Yarrowia lipolytica , which was further metabolically engineered for improved pheromone biosynthesis by decreasing fatty alcohol degradation and downregulating storage lipid accumulation. The sex pheromone of the cotton bollworm Helicoverpa armigera was produced by oxidation of fermented fatty alcohols into corresponding aldehydes. The resulting pheromone was just as efficient and specific for trapping of H. armigera male moths in cotton fields in Greece as a synthetic pheromone mixture. We further demonstrated the production of the main pheromone component of the fall armyworm Spodoptera frugiperda . Our work describes a biotech platform for the production of commercially relevant titres of moth pheromones for pest control by yeast fermentation. Significance statement Agriculture largely relies on insecticides and genetically modified crops for pest control, however alternative solutions are required due to emerging resistance, toxicity and regulatory issues, and consumer preferences. Mating disruption with sex pheromones that act by preventing insect reproduction is considered the most promising and scalable alternative to insecticides. This method is highly efficient and safe for human health and environment. The likelihood of insect resistance development is very low and can be handled by adjusting the pheromone composition. The high cost of chemically synthesized pheromones is the major barrier for the wider adoption of pheromones. A novel method based on yeast fermentation enables the production of insect sex pheromones as a lower cost from renewable feedstocks.
New structures of polyphase claw-pole machines (2003)

New structures of motor magnetic circuit can be realized by use of the soft magnetic composites (SMC). This paper presents new claw-pole motors with a polyphase winding and a standard cylindrical rotor which are using these isotropic materials. A division of the stator magnetic circuit in 3 parts and the use of a centralized winding with a small number of coils simplify the production process, the mechanical assembly and the winding realization. With these special stator geometries, the electromagnetic, mechanical and thermal functions are integrated in the same stator parts. This integration is much better than in a classical 2D structure using a laminated material. There is no end-winding and the copper volume can be minimized. The size of the additional parts which are necessary for the bearing housings and the mechanical fixation of the rotor are reduced. These structures can be equipped with an integrated cooling system, with efficient air convection or water circulation. This paper describes the design approach of these original structures. It demonstrates that such 3D structures can be derived from their equivalent 2D structures with a concentrated winding. The concept and the design approach are validated by the realization and the comparative experimental tests of two prototypes with a 3D and its equivalent 2D structure.
Recent Developments in the Zymomonas Process for Ethanol Production (1983)

The bacterium Zymomonas mobilis, which is used in the tropics to make pulque and alcoholic palm wines, appears to have considerable potential for industrial alcohol fermentations. Some of the advantages of the Zymomonas process reported in studies from our laboratory1-24 are1. There are significantly higher specific rates of sugar uptake and ethanol production compared to those found for yeasts.2. Considerably higher volumetric ethanol productivities found in continuous cell recycle systems (up to 120 to 200 g/hr).3. There are higher ethanol yields and lower biomass production than for yeasts. The lower biomass concentrations would seem to be a consequence of the lower metabolic energy available for growth. Zymomonas metabolize glucose via the Entner-Doudoroff pathway while yeasts convert glucose to ethanol via glycolysis.4. Zymomonas cultures grow anaerobically and, unlike yeasts, do not require the controlled addition of oxygen to maintain viability at high cell concentrations.5. The ethanol tolerance of some selected strains of Zymomonas is comparable if not higher than strains of Saccharomyces cerevisiae. Ethanol concentrations of 85 g/(up to 11% v/v) have been achieved in continuous culture and up to 130 g/(16% v/v) in batch culture.
Low‐Thermal‐Expansion Polycrystalline Zirconyl Phosphate Ceramic (1985)

The synthesis of thermal‐shock‐resistant material from zirconyl phosphate, 2ZrO 2 P 2 O 5 , was investigated. Modifications of the compound were examined; only the a phase appears to be thermodynamically stable. Sintering of a‐phase powder to a dense ceramic was promoted by adding a metal oxide. Crystalline zirconyl phosphate has a low average thermal expansion coefficient. The relation of microcracking to grain size and strength was studied using specimens sintered under varied conditions. A strong low‐thermal‐expansion polycrystalline ceramic was obtained by controlling grain growth.
BIOAVAILABILITY OF IRON FROM SPINACH USING AN IN VITRO/HUMAN CACO-2 CELL BIOASSAY MODEL (2004)

Spinach (Spinacia oleracea) cv Whitney was tested for iron bioavailabilty using an in vitro human intestinal cell culture ferritin bioassay technique previously developed. Spinach was cultured in a growth chamber for 33 days, harvested, and freeze-dried. Total iron in the samples was an average of 71 micrograms/g dry weight. Spinach was digested in vitro (pepsin and 0.1 M HCl followed by pancreatin and 0.1 M NaHCO3) with and without the addition of supplemental ascorbic acid. Caco-2 cell cultures were used to determine iron bioavailability from the spinach mixtures. Production of the iron-binding protein ferritin in the Caco-2 cells showed the supplemental ascorbic acid doubled bioavailability of iron from spinach. The data show fresh spinach is a poor source of iron, and emphasize the importance of evaluation of whole meals rather than single food items. The data support the usefulness of the in vitro/Caco-2 cell ferritin bioassay model for prescreening of space flight diets for bioavailable iron.
Saw filters based on diamond (1995)

The surface acoustic wave (SAW) devices using a ZnO/diamond structure was summarized in this paper including late result on high frequency filter of 3.5GHz by 0.75{mu}m in interdigital transducers on diamond. This technology is applied to 1.5GHz narrow bandwidth filter by resonator type filter. Theoretical studies with new material systems were also performed. Zero temperature coefficient filter can be expected by additional amorphous SiO{sub 2} deposition. By LiNbO{sub 3}/diamond structure, high electromechanical coefficient can be expected with high SAW velocity. The varieties of material systems on SAW and advanced devices based on diamond will find broad applications on high frequency devices in future communication systems.
Evaluation of Surgical Tissue From Patients with Crohnʼs Disease for the Presence of Mycobacterium avium Subspecies paratuberculosis DNA by In Situ Hybridization and Nested Polymerase Chain Reaction (2005)

Crohn's disease (CD) is a chronic inflammatory bowel disease (IBD) with tissue granuloma and histopathological alteration that resembles aspects in tuberculosis, leprosy, and paratuberculosis. Mycobacterium avium subsp paratuberculosis (MAP) is the causative agent of paratuberculosis, with a suspected role in the etiology of CD. We investigated the presence of MAP DNA in 31 surgical tissue samples from 20 subjects using fluorescence in situ hybridization (FISH) with the aid of confocal scanning laser microscopy and nested polymerase chain reaction (PCR) using the IS900 sequence unique to MAP. MAP DNA was detected by PCR in tissue from 10 of 12 (83%) patients with CD: 7/12 (58%) in inflamed, 6/11 (55%) in noninflamed and in 10 (83%) of either tissue and by FISH in 8 of 12 (67%) patients with CD: 7 of 12 (58%) in inflamed, 4 of 11 (36%) in noninflamed, and in 8(67%) of either tissue. In non-IBD subjects, MAP DNA was detected in the tissue of only 1 of 6 patients (17%) by PCR and 0 of 6 patients (0%) by FISH. MAP DNA was identified by PCR in inflamed tissue from 2 of 2 patients with ulcerative colitis. The detection of MAP DNA by either technique in tissue from subjects with CD is significant compared with non-IBD subjects (P < 0.005). Identification of MAP DNA in both inflamed and noninflamed tissue by both techniques suggests that MAP infection in patients with CD may be systemic. The data add more evidence toward a possible association of MAP in the pathogenesis of CD.
Treatment of out-of-hospital cardiac arrest with a low-energy impedance-compensating biphasic waveform automatic external defibrillator. The LIFE Investigators. (1999)

Few victims of sudden cardiac arrest survive. A new generation of automatic external defibrillators (AEDs), smaller, lighter, easier to use, and less costly, makes the goal of widespread AED deployment and early defibrillation feasible. A low-energy impedance-compensating biphasic waveform allows AED device characteristics more suitable to the goal of early defibrillation than high-energy waveforms. This study observed the performance of such a biphasic waveform in the out-of-hospital setting on 100 consecutive victims of sudden cardiac arrest treated by a wide range of first-responders. AEDs incorporating 150-J impedance-compensating biphasic waveforms were placed into service of 34 EMS systems. Data were obtained from the AED PC data card-recording system. The first endpoint was to determine the effectiveness of this waveform in terminating ventricular fibrillation (VF). The second endpoint was to determine whether or not the use of such an AED culminated in an organized rhythm at the time of patient transfer to an advanced life support (ALS) team or emergency department (ED). The third endpoint was to assess the efficiency of the human-factors design of the AED by measuring user time intervals. The 34 sites provided data from 286 consecutive AED uses, 100 from SCA victims with VF as their initial rhythm upon attachment of the AED. All 286 patients were correctly identified by the AED as requiring a shock (100% sensitivity for the 100 VF patients) or not (100% specificity to the 186 patients not presenting in VF). Times from emergency call to first shock delivery averaged 9.1 +/- 7.3 minutes. A single 150-J biphasic shock defibrillated the initial VF episode in 86% of patients. For all 450 episodes of VF in these 100 patients, an average of 86% +/- 24% of VF episodes were terminated with a single biphasic shock. Of the 449 VF episodes that received up to three shocks, 97% +/- 11% were terminated with three shocks or fewer. The average number of shocks per VF episode was 1.3 +/- 0.7. The average time from AED power-on and pads attached to first defibrillation was 25 +/- 23 sec. At the time of patient transfer, an organized rhythm was present in 65% of the VF patients; asystole was the result in 25%, and VF was in progress in 10%. It is concluded that low-energy impedance-compensating biphasic waveforms terminate long-duration VF at high rates in out-of-hospital cardiac arrest and provide defibrillation rates exceeding those previously achieved with high-energy shocks. Use of this waveform allows AED device characteristics consistent with widespread AED deployment and early defibrillation.