Miracle-dz/UniFAR-FTUs huggingface dataset:
Hematopoietic cancers and Nup98 fusions: determining common mechanisms of malignancy

Chromosomal aberrations are very frequent in leukemias and several recurring mutations capable of malignant transformation have been described. These mutations usually occur in hematopoietic stem cells (HSC), transforming them into leukemia stem cells. NUP98 gene translocations are an example of such chromosomal aberrations; these translocations produce a fusion protein containing the N-terminal portion of Nup98 and the C-terminal of a fusion partner. Over 75% of Nup98 fusions can interact with chromatin, and lead to changes in gene expression. Therefore, I hypothesize that nup98 fusions act as rogue transcriptional regulators in the cell. Collecting previously published gene expression data (microarray) from HSCs expressing Nup98 fusions, we can generate data to corroborate this hypothesis. Several different fusions affect the expression of similar genes; these are involved in a few biological processes in the cell: embryonic development, immune system formation and chromatin organization. Deregulated genes also present similar transcription factor binding sites in their regulatory regions. These putative regulatory transcription factors are highly interconnected through protein-protein interactions and transcriptional regulation among themselves, and they have important roles in cell cycle regulation, embryonic development, hematopoiesis, apoptosis and chromatin modifica - tion.
Multiparty privacy protection for electronic health records

Recently, the amount of personal medical information online is increasing exponentially, opening up new avenues for hackers to expose personal data that, unlike financial information, can result in a permanent violation of privacy. To protect the privacy of patient data, such as electronic health records (EHRs), access control was used before and attributed-based encryption is used recently. These techniques can effectively prevent from the outside attacks, but are hard to withstand the inside attacks, where the database administrator or the key manager is an attacker. In this paper, we provide a solution to protect the privacy of patient data (EHRs) under the multi-party framework where all EHRs are encrypted with the common public key and an encrypted EHR can be decrypted only by the cooperation of all parties. Based on the ElGamal threshold public key encryption scheme, we propose several EHR access control protocols where multiple parties cooperate to control clinicians' access to EHRs without actually knowing EHRs. Our solution can protect the patient data against the inside attacks as long as at least one party can be trusted. Because our solution is built on Public Key Infrastructure (PKI), it facilitates the clinician registration and revocation.
Effect of Upper Body Position on Arterial Stiffness: Influence of Hydrostatic Pressure and Autonomic Function

Conventional markers of arterial stiffness, such as carotid beta‐stiffness index, are traditionally obtained in the supine position. In the seated position, it is not known if correcting for hydrostatic pressure is an adequate adjustment for estimation of beta‐stiffness index or if other factors need to be considered, such as autonomic modulation.
The DISC Predictive Scales (DPS): efficiently screening for diagnoses.

OBJECTIVE To derive and test a series of brief diagnosis-specific scales to identify subjects who are at high probability of meeting diagnostic criteria and those who may safely be spared more extensive diagnostic inquiry. METHOD Secondary data analysis of a large epidemiological data set (n = 1,286) produced a series of gate and contingent items for each diagnosis. Findings were replicated in a second retrospective analysis from a residential care sample (n = 884). The DISC Predictive Scales (DPS) were then used prospectively as a self-report questionnaire in two studies, in which parents (n = 128) and/or adolescents (n = 208) had subsequent diagnostic interviewing with the Diagnostic Interview Schedule for Children or the Schedule for Affective Disorders and Schizophrenia for School-Age Children. RESULTS All analyses showed that gate item selection was valid and that any missed cases were due solely to inconsistent reports on the same questions. Screening performance of the full scales was shown to be good, and substantial reductions in scale length were not associated with significant changes in discriminatory power. CONCLUSIONS The DPS can accurately determine subjects who can safely be spared further diagnostic inquiry in any diagnostic area. This has the potential to speed up structured diagnostic interviewing considerably. The full DPS can be used to screen accurately for cases of specific DSM-III-R disorders.
Posters, metadata, description schemas

The number of electronic archives holding image documents such as posters is increasing besides traditional, textual materials. It is definitely true for the digitized poster collections that the use of metadata is essential for their operation as with the help of metadata electronic documents can be efficiently sorted and retrieved. This study shows an example how it is possible to store the metadata of posters efficiently.
A Resource of Mapped Dissociation Launch Pads for Targeted Insertional Mutagenesis in the Arabidopsis Genome1

We describe a new resource for targeted insertional mutagenesis in Arabidopsis using a maize (Zea mays) Activator/Dissociation (Ds) two-element system. The two components of the system, T-DNA vectors carrying a Ds launch pad and a stable Activator transposase source, were designed to simplify selection of transposition events and maximize their usefulness. Because Ds elements preferentially transpose to nearby genomic sites, they can be used in targeted mutagenesis of linked genes. To efficiently target all genes throughout the genome, we generated a large population of transgenic Arabidopsis plants containing the Ds launch pad construct, identified lines containing single Ds launch pad inserts, and mapped the positions of Ds launch pads in 89 lines. The integration sites of the Ds launch pads were relatively evenly distributed on all five chromosomes, except for a region of chromosomes 2 and 4 and the centromeric regions. This resource therefore provides access to the majority of the Arabidopsis genome for targeted tagging.
Protection against Streptococcus pneumoniae Elicited by Immunization with Pneumolysin and CbpA

ABSTRACT The need for the development of cheap and effective vaccines against pneumococcal disease has necessitated the evaluation of common virulence-associated proteins of Streptococcus pneumoniae as potential vaccine antigens. In this study, we examined the capacity of active immunization with a genetic toxoid derivative of pneumolysin (PdB) and/or a fragment of choline binding protein A (CbpA; also known as PspC, Hic, and SpsA) to protect mice from intraperitoneal challenge with medium to very high doses of a highly virulent capsular type 2 pneumococcal strain, D39. The median survival times for mice immunized with the individual protein antigens in different adjuvant combinations were significantly longer than those for mice that received the respective adjuvants alone. Mice immunized with CbpA alone were significantly better protected than mice immunized with PdB alone. Correspondingly, the median survival times for mice that were immunized with a combination of PdB and CbpA were significantly longer than those for mice that received PdB alone but not significantly different from those that received CbpA alone. Mice immunized with the protein antigens in a mixture of monophospholipid A (MPL) and aluminium phosphate (AlPO4) adjuvants had higher antibody titers than mice that received the antigens in AlPO4 alone. Mice immunized with PdB in MPL plus AlPO4 were also significantly better protected than mice that received PdB in AlPO4 alone.
A New Perspective on the Cylindrical Antenna Theory

This paper presents a new perspective on the analysis of the cylindrical antenna theory. It applies the cylindrical surface waves on an infinitely long cylindrical conductor, which are similar to the Sommerfeld axial cylindrical surface waves, to describe the conventional postulate of applying a sinusoidal current distribution on a cylindrical dipole antenna. This treatment leads to the derivation of simple expression for the current on a cylindrical dipole antenna of finite conductivity, which is in good agreement with the current obtained from the three-term approximations. Also, it proposes an expression for the current on an infinitely long cylindrical dipole antenna of finite conductivity, which is also in good agreement to the current found from applying the Fourier transform technique. Moreover, this paper shows that the complex propagation constant used in the three-term approximation is similar to the complex propagation constant of the principal Sommerfeld wave on the surface of an infinitely long cylindrical conductor. Therefore, a more accurate representation of the current near the feeding point is proposed based on the complex propagation constants of multiple Sommerfeld waves.
Bispectral EEG Index during Nitrous Oxide Administration

Background Nitrous oxide (N2 O) is a commonly used sedative for painful diagnostic procedures and dental work. The authors sought to characterize the effects of N2 O on quantitative electroencephalographic (EEG) variables including the bispectral index (BIS), a quantitative parameter developed to correlate with the level of sedation induced by a variety of agents. Methods Healthy young adult volunteers (n = 13) were given a randomized sequence of N2 O/O2 combinations via face mask. Five concentrations of N2 O (10, 20, 30, 40, and 50% atm) were administered for 15 min (20 min for the first step). EEG was recorded from bilateral frontal poles continuously. At the end of each exposure, level of sedation was assessed using primarily the Observer Assessment of Alertness/Sedation (OAA/S) scale. Results One subject withdrew from the study because of emesis at 50% N (2) O. N2 O (50%) increased theta, beta, 40 - 50 Hz, and 70 - 110 Hz band powers. BIS and spectral edge frequency during 50% N2 O/O2 did not differ significantly from baseline values. Abrupt decreases from higher to lower concentrations frequently evoked a profound, transient slowing of activity. No significant change in OAA/S was detected during the study. Conclusions Although the spectral content of the EEG changed during N (2) O administration, reflecting some pharmacologic effect, the subjects remained cooperative and responsive throughout, and therefore N2 O can only be considered a weak sedative at the tested concentrations. Despite changes in the lower and higher frequency ranges of EEG activity, the BIS did not change, which is consistent with its design objective as a specific measure of hypnosis.
Hyperthermia of large superficial tumor with a flat LHM lens

Flat left-handed metamaterial (LHM) lens shows great potentials for superficial tumor hyperthermia. In clinic, superficial tumor may occur in a considerably large area, and take different shapes. For such superficial tumors, joint heating by using multiple sources are desired for effective hyperthermia. In this paper, it is demonstrated by numerical simulations that by properly arranging the positions of the sources, the heat region in tissue characterized by heating temperature above 42°C can be enlarged properly.
Surface modification and size dependence in particle translocation during early embryonic development

Since the mid-1990s, the number of studies linking air pollutants to preterm and low birth weight, as well as to cardiac birth defects, has grown steadily each year. The critical period in the development of mouse embryos begins with the commencement of gastrulation at day 7.5 of gestation. Our aim is to examine the role of particles size and surface modification in particle translocation during this early embryonic development. Fluorescent polystyrene particles (PS) were employed because they offer an efficient and safe tracking method. Pregnant female mice were sacrificed at 7.5 days of gestation. After cutting open the deciduas, the parietal endoderm was carefully separated and removed. Different sizes of amine- and carboxyl-modified PS beads were injected via the extraembryonic tissue. The embryos were incubated for 12 h, and were investigated under fluorescent microscopy, confocal microscopy, and mesoscopic fluorescence tomography. The results show that 20-nm carboxylic PS distribute in the embryonic and extraembryonic germ layers of ectoderm, mesoderm, and endoderm. Moreover, when the particles are bigger than 100 nm, PS accumulate in extraembryonic tissue, but nevertheless 200-nm amine-modified particles can pass into the embryos. Interestingly, a growth inhibition was observed in the embryos containing nanoparticles. Finally, the stronger translocation effect is associated with amine- modified PS beads (200 nm) instead of the smaller (20 nm, 100 nm) carboxyl ones.
Laser ultrasonic assessment of the effects of oxidation and microcracking on the elastic moduli of nuclear graphites

Structure-property relationships in bulk materials can be important in establishing sensing methods to assess the state of material microstructure. This is particularly true for nuclear graphites since these materials can display anisotropy and can become oxidized under service conditions. Both anisotropy and oxidation-induced porosity can influence structural integrity and this must be confirmed during the lifetime of the material. In this work, laser ultrasonic methods were used to measure the elastic response of various graphite grades with a focus on NBG-18, NBG-25 and IG-110. Results of laser ultrasonic measurements in oxidized graphites show that the moduli decrease with increasing porosity. This variation can be interpreted successfully using effective medium models if the characteristics of graphite porosity are taken into account. Results of laser ultrasonic shear wave birefringence measurements can be used to assess elastic anisotropy. This anisotropy can be expressed in terms of the orientation distribution coefficients W400 and W200. Interpretation of results requires the use of appropriate property-averaging schemes.
A CMOS-compatible process for fabricating electrical through-vias in silicon

In the past, traditional CMOS scaling has been one of the principal levers to achieve increased system-level performance. Today, scaling is becoming increasingly difficult and less effective, and a range of new two- and three-dimensional silicon integration technologies are needed to support next-generation systems. A silicon-carrier system-on-package (SOP) is an advanced packaging solution, enabling interconnection between ICs and other devices at densities far beyond those of current first-level packaging. Silicon-carrier employs fine pitch Cu damascene wiring, high-density solder pads/joins and high-yielding electrical through-vias. A novel approach to fabricating robust though-vias in silicon is described. The key design feature enabling large-area, uniform arrays to be produced with high yield is the annular via shape. As compared to a standard cylindrical via shape, the annular via is easier to integrate into a standard CMOS copper back-end-of-the-line (BEOL) process flow. Two process flows are compared: the first having the conductor metal within the gap of the insulated annulus itself, the second having a conducting metal core enclosed within the inner wall of the annulus. For the first process flow, two annular conductors, plated copper and CVD tungsten, are compared in terms of ease of integration, yield and susceptibility to failure during thermal stressing. Large area (45 times 48 mm) silicon carrier modules containing more than 51,000 electrically measurable through-vias are used to compare overall yield and robustness of each process. Results on deep thermal cycling, current carrying capacity and thermomechanical modeling are discussed. Wafer-level via testing is used to statistically distinguish between via chain opens caused by bond and assembly issues versus failures in the vias or integrated wiring structures. Through-via resistances on the order of ~10 mOmega are typical, and through-via yields of 99.98% at module level have been demonstrated
Mucinous cystadenomas and intraductal papillary mucinous tumors of the pancreas in magnetic resonance cholangiopancreatography.

BACKGROUND AND STUDY AIMS In mucin-producing tumors of the pancreas, diagnosis using endoscopic retrograde cholangiopancreatography (ERCP) is limited to cystic formations that communicate with the main pancreatic duct. Magnetic resonance cholangiopancreatography (MRCP) is a new, sophisticated method which is currently under evaluation. The authors describe the usefulness of MRCP in diagnosis of mucin-producing tumors. PATIENTS AND METHODS Six patients with mucin-producing tumors were investigated using MRCP and ERCP. Imaging was compared with surgery and histopathological examinations. RESULTS Three patients were found to have mucinous cystadenomas (MC), two patients had intraductal papillary mucinous tumors (IPMT) and one patient had a cystadenocarcinoma. MRCP demonstrated the cystic formations in all patients. Magnetic resonance imaging (MRI) showed contrast-mediated enhancement of the cystic wall in patients with MC, and visualized the pancreatic ducts completely in patients with IPMT. ERCP failed to visualize the cystic lesion in one patient with MC of the pancreatic tail. Furthermore, ERCP showed evidence of IPMT in dilated main ducts with multiple filling defects but did not visualize the ducts completely. CONCLUSIONS MRCP provides visualization of pancreatic ducts, extraductal variations, and cystic formations more completely than ERCP does. It avoids complications seen in ERCP. MRCP may replace ERCP in the evaluation of mucin-producing tumors of the pancreas.
Ferredoxin-activated fructose diphosphatase of spinach chloroplasts. Resolution of the system, properties of the alkaline fructose diphosphatase component, and physiological significance of the ferredoxin-linked activation.

Abstract The hydrolytic cleavage of Pi from fructose diphosphate by the fructose diphosphatase (FDPase) system of spinach chloroplasts was found to require (a) an alkaline FDPase component insensitive to inhibition by AMP or fructose diphosphate; (b) reduced ferredoxin; (c) a protein factor; and (d) Mg++. Reduced spinach ferredoxin could be replaced by reduced methyl viologen or dithiothreitol but not by reduced bacterial ferredoxin. Activation of the alkaline FDPase component by the nonphysiological substitutes required the protein factor. The alkaline FDPase component in isolated intact chloroplasts was also activated by light. The protein factor component of the FDPase system has been partly purified and found to have a molecular weight of 40,000. The alkaline FDPase component, purified to homogeneity, had a molecular weight of 145,000 and contained 2% carbohydrate. Except for a remarkably high half-cystine content (16% by weight as compared to 2% for mammalian FDPases) which reflects an apparent abundance of cystine, the amino acid composition of the chloroplast alkaline FDPase component resembled that of the mammalian FDPases. In the absence of reduced ferredoxin and protein factor, the chloroplast alkaline FDPase component can be activated by high concentrations of Mg++. Like liver alkaline FDPase, the chloroplast enzyme component is also activated by cystamine or 5,5'-dithiobis(2-nitrobenozic acid) (DTNB). Ferredoxin-activated FDPase was inhibited completely by 5 x 10-4 m EDTA but was insensitive to KCN, cuprizone, and diethyldithiocarbamate (all at 1 x 10-3 m). The activity of chloroplast FDPase during photosynthesis appears to be controlled photochemically through reduced ferredoxin. What, if any, physiological role can be ascribed to the activation of the enzyme by high concentrations of Mg++ and disulfide reagents, independently of reduced ferredoxin, is not clear.
The association between DRD2/ANKK1 and genetically informed measures of alcohol use and problems

In 1990, Blum and colleagues first reported an association between DRD2 and alcoholism. While there have been subsequent replications of this genetic association, there have also been numerous studies that failed to detect an association between DRD2 and alcohol dependence. We propose that one aspect contributing to this inconsistency is the variation in alcohol phenotype used across studies. Within the population‐based Finnish twin sample, FinnTwin16, we previously performed multivariate twin analyses to extract latent genetic factors, which account for the variation across seven measures of alcohol consumption (frequency of drinking, frequency × quantity, frequency of heavy drinking, frequency of intoxication and maximum drinks in a 24‐hour period) and problems (the Rutgers Alcohol Problem Index—RAPI and the Mälmö‐modified Michigan Alcohol Screen Test—MmMAST) in 3065 twins. In the present study, we examined the association between 31 DRD2/ANKK1 single‐nucleotide polymorphisms (SNPs) and the genetic factor scores generated by twin analyses in a subset of FinnTwin16 (n = 602). We focus on two of the genetic factors: a general alcohol consumption and problems factor score, which represents shared genetic variance across alcohol measures, and a alcohol problems genetic factor score, which loads onto the two indices of problematic drinking (MAST and RAPI). After correction for multiple testing across SNPs and phenotypes, of the 31 SNPs genotyped across DRD2/ANKK1, one SNP (rs10891549) showed significant association with the general alcohol consumption and problems factor score (P = 0.004), and four SNPs (rs10891549, rs1554929, rs6275, rs6279), representing two independent signals after accounting for linkage disequilibrium, showed significant association with the alcohol problems genetic factor score (P = 0.005, P = 0.005, P = 0.003, P = 0.003). In this study, we provide additional positive evidence for the association between DRD2/ANKK1 and alcohol outcomes, including frequency of drinking and drinking problems. Additionally, post hoc analyses indicate stronger association signals using genetic factor scores than individual measures, which suggest that accounting for the genetic architecture of the alcohol measures reduces genetic heterogeneity in alcohol dependence outcomes in this sample and enhances the ability to detect association.
GlYFF: A framework for global yield and floorplan aware design optimization

Diminishing yields for modern CMOS and emerging technologies have become a major growing concern for IC manufacturers due to its direct impact on revenue. To this end, “Design for Yield (DFY)” have been proposed to proactively address manufacturing yield issues in the system design stage. While many DFY approaches have been developed for caches, GPUs and CPUs, they remain decoupled from each other, which is not ideal for modern microprocessors or MPSoCs that integrate multiple components onto a single die. In this paper we introduce “Global Yield and Floorplan Aware Design Optimization Framework (GlYFF)”, a holistic computer-aided DFY framework that unifies redundancy based yield-centric design optimizations and floorplanning for MP-SoCs. GlYFF recognizes the different yield enhancement strategies for different on-die components, and is able to output detailed floorplans for accurate area/performance measurements. We demonstrate that compared to a segregated DFY methodology, GlYFF can achieve ~20% improvement in yield-per-area, a metric strongly correlated to revenue.