gebhart/patrepeval huggingface dataset:
Countering Gattaca: Efficient and Secure Testing of Fully-Sequenced Human Genomes (Full Version) (2011)

Recent advances in DNA sequencing technologies have put ubiquitous availability of fully sequenced human genomes within reach. It is no longer hard to imagine the day when everyone will have the means to obtain and store one's own DNA sequence. Widespread and affordable availability of fully sequenced genomes immediately opens up important opportunities in a number of health-related fields. In particular, common genomic applications and tests performed in vitro today will soon be conducted computationally, using digitized genomes. New applications will be developed as genome-enabled medicine becomes increasingly preventive and personalized. However, this progress also prompts significant privacy challenges associated with potential loss, theft, or misuse of genomic data. In this paper, we begin to address genomic privacy by focusing on three important applications: Paternity Tests, Personalized Medicine, and Genetic Compatibility Tests. After carefully analyzing these applications and their privacy requirements, we propose a set of efficient techniques based on private set operations. This allows us to implement in in silico some operations that are currently performed via in vitro methods, in a secure fashion. Experimental results demonstrate that proposed techniques are both feasible and practical today.
THE ROLE OF CYSTEINE PROTEASES IN (2000)

Autodigestion by proteolytic enzymes is thought to represent the critical mechanism by which acute pancreatitis is initiated. Where and why pancreatic proteases, which are physiologically stored and secreted as inactive precursor zymogens, are activated within the pancreas has remained controversial. Here we present data which indicate that: the lysosomal protease cathepsin B can activate trypsinogen in vitro in a manner that is similar to trypsinogen activation by enterokinase; that cathepsin B colocalizes with trypsinogen in the secretory compartment of the rat pancreas and of the human pancreas; that trypsinogen activation begins in a secretory compartment that is distinct from mature zymogen granules; and that the inhibition of cathepsin B can either increase or decrease premature trypsinogen activation depending on the concentration of the inhibitor, its specificity and its site of action in the pancreatic acinar cell. These observations elucidate some of the complex relations between cysteine and serine proteases in the pancreas with respect to their mechanisms of activation, their subcellular sites of action, and their possible role in the onset of pancreatitis.
Cell Surface Delivery of TRAIL Strongly Augments the Tumoricidal Activity of T Cells (2011)

Targeted delivery of TRAIL to cell surface antigens of T cells potently enhances the tumoricidal activity of T cells. This approach may be generally applicable to enhance the efficacy of adoptive T-cell therapy.
Thermal Stability of Portable Micro-Tubular Solid Oxide Fuel Cell and Stack (2008)

Rapid start-up times are a big challenge for high temperature fuel cells such as solid oxide fuel cells (SOFCs), especially large-sized stacks with high power outputs. This paper presents the development of tubular and micro-tubular anode-supported SOFCs and the design and testing of the thermal stability of such single cells and stacks. It was demonstrated that single cells with various sizes have very good thermal shock resistance. Preliminary results also showed that stacks can be started up within minutes and withstand more than 50 thermal cycles and temperature changes of 550oC/min. Several factors that affect the thermal stability are discussed.
Joining of ribooligonucleotides with T4 RNA ligase and identification of the oligonucleotide-adenylate intermediate. (1976)

T4 RNA ligase was found to join A-A-A-A-A-A and 32pU-U-U-U in the presence of ATP as cofactor. In this reaction the pyrophosphate of pU-U-U-U and pA was isolated by chromatography on a RPC-5 column, besides the joined product and the starting materials. This pyrophosphate was shown to be an intermediate in the joining reaction because of the fact that coupling with A-A-A-A-A-A to give the decanucleotide could be performed in the absence of ATP. The structure of the oligonucleotide-adenylate was determined by enzymatic digestion with base-nonspecific nuclease and venom phosphodiesterase. Futher evidence for the proposed structure was obtained by isolation of the intermediate obtained by using pU-U-U-U and [alpha-32p]ATP. This pyrophosphate gave pA and pU by treatment with venom phosphodiesterase. Several other joining reactions between various purine- and pyrimidine ribooligonucleotides to 5'-phosphorylated ribooligonucleotides are discussed.
Diffusion Barriers of Tripartite Sporopollenin Microcapsules Prepared from Pine Pollen (2003)

Tripartite sporopollenin microcapsules prepared from pine pollen (Pinus sylvestris L. and Pinus nigra Arnold) were analysed with respect to the permeability of the different strata of the exine which surround the gametophyte and form the sacci. The sexine at the surface of the sacci is highly permeable for polymer molecules and latex particles with a diameter of up to 200 nm, whereas the nexine covering the gametophyte is impermeable for dextran molecules, with a Stokes' radius > or =4 nm (Dextran T 70), and for the tetravalent anionic dye Evans Blue (Stokes' radius = 1.3 nm). The central capsules obtained by dissolution of the sporoplasts showed strictly membrane-controlled exchange of non-electrolytes, with half-equilibration times in the range of minutes (monosaccharides, oligosaccharides) to hours (dextran molecules with Stokes' radii up to 2.5 nm). The dependence of the permeability coefficients of the nexine for non-electrolytes on Stokes' radius or molecular weight shows that the aqueous pores through the nexine are inhomogeneous with respect to their size, and that most pores are too narrow for free diffusion of sugar molecules. To explain the barrier function of the nexine for Evans Blue, it is assumed that at least the larger pores, which enable slow permeation of dextran molecules, contain negative charges.
Mayhem in the Push Clouds (2014)

Push messaging is among the most important mobile-cloud services, offering critical supports to a wide spectrum of mobile apps. This service needs to coordinate complicated interactions between developer servers and their apps in a large scale, making it error prone. With its importance, little has been done, however, to understand the security risks of the service. In this paper, we report the first security analysis on those push-messaging services, which reveals the pervasiveness of subtle yet significant security flaws in them, affecting billions of mobile users. Through even the most reputable services like Google Cloud Messaging (GCM) and Amazon Device Messaging (ADM), the adversary running carefully-crafted exploits can steal sensitive messages from a target device, stealthily install or uninstall any apps on it, remotely lock out its legitimate user or even completely wipe out her data. This is made possible by the vulnerabilities in those services' protection of device-to-cloud interactions and the communication between their clients and subscriber apps on the same devices. Our study further brings to light questionable practices in those services, including weak cloud-side access control and extensive use of PendingIntent, as well as the impacts of the problems, which cause popular apps or system services like Android Device Manager, Facebook, Google+, Skype, PayPal etc. to leak out sensitive user data or unwittingly act on the adversary's command. To mitigate this threat, we developed a technique that helps the app developers establish end-to-end protection of the communication with their apps, over the vulnerable messaging services they use.
The Prevalence of Diabetic Retinopathy Among Adult Type1 Diabetic Persons in the United States (2004)

Retinopathy due to type 1 DM is an important public health problem in the United States, affecting 1 per 300 persons 18 years and older, and 1 per 600 persons with advanced, vision-threatening retinopathy.
Near optimum tree-search detection schemes for bit-synchronous multiuser CDMA systems over Gaussian and two-path Rayleigh-fading channels (1997)

Simple reduced tree-search detection schemes of the breadth-first type are applied to suboptimal joint multiuser detection in bit-synchronous code-division multiple access (CDMA) systems over both Gaussian and two-path Rayleigh-fading channels. It is pointed out that in contrast to the case of the optimal multiuser detector, the choice of the receiver filter severely influences the performance of suboptimal multiuser detectors. Simulation results supported by analysis show that breadth-first tree-search algorithms using a decorrelating noise whitening receiver filter perform better than similar receivers, which solely use a matched filter (MF) for virtually all nonsingular spreading code sets studied. Most of the code sets are randomly generated. The M- and T-algorithm detectors based on decorrelating noise whitening filter (WF) outputs can achieve near optimum performance at a very low complexity compared to the optimal detector, although the proposed detectors are more complex than some known suboptimum detectors. Furthermore, the use of combining techniques is considered for a two-path Rayleigh-fading channel, and a semi-synchronous CDMA structure is proposed. It is shown that if maximum ratio combining (MRC) is employed, the decorrelating noise WF still exists. The corresponding suboptimal combining detector with a decorrelating noise WF outperforms a similar noncombining detector.
MDM2 Antagonist Nutlin-3 Displays Antiproliferative and Proapoptotic Activity in Mantle Cell Lymphoma (2009)

These findings suggest that the MDM2 antagonist Nutlin-3 may be an effective agent in the treatment of MCL with or without wt-TP53.
PackMerger: A 3D Print Volume Optimizer (2014)

Abstract We propose an optimization framework for 3D printing that seeks to save printing time and the support material required to print 3D shapes. Three‐dimensional printing technology is rapidly maturing and may revolutionize how we manufacture objects. The total cost of printing, however, is governed by numerous factors which include not only the price of the printer but also the amount of material and time to fabricate the shape. Our PackMerger framework converts the input 3D watertight mesh into a shell by hollowing its inner parts. The shell is then divided into segments. The location of splits is controlled based on several parameters, including the size of the connection areas or volume of each segment. The pieces are then tightly packed using optimization. The optimization attempts to minimize the amount of support material and the bounding box volume of the packed segments while keeping the number of segments minimal. The final packed configuration can be printed with substantial time and material savings, while also allowing printing of objects that would not fit into the printer volume. We have tested our system on three different printers and it shows a reduction of 5–30% of the printing time while simultaneously saving 15–65% of the support material. The optimization time was approximately 1 min. Once the segments are printed, they need to be assembled.
Current and emerging bladder cancer biomarkers with an emphasis on urine biomarkers (2019)

<b>Introduction</b>: Bladder cancer detection typically requires unpleasant and costly cystoscopy, a procedure potentially harmful and often accompanied by variable adverse effects. The use of urine analysis as a noninvasive method is of great scientific interest since it is enriched in tumor-related proteins, DNA and RNA which can provide a molecular landscape with multiple alterations identified in bladder cancer.<b>Areas covered</b>: Current sensitivity, specificity and diagnostic accuracy of FDA approved urine-based assays are still suboptimal with none of them routinely used by clinics. The recent introduction of RNA/DNA based bladder cancer tests, some of them commercially available, establishes a promising new horizon of clinical applicability.<b>Expert opinion</b>: There is growing evidence toward the use of minimally invasive 'liquid biopsies' to identify biomarkers in urothelial malignancy. Urine has been identified as an optimal noninvasive source of proteins, DNA and RNA; therefore, it has been identified as a type of liquid biopsy likely to soon be routine clinical practice. Cell-free proteins and peptides, exosomes, cell-free DNA, methylated DNA and DNA mutations, circulating tumor cells, miRNA, lncRNA, rtRNA and mRNAs, have been assessed in urine specimens. However, lack of well-designed multicenter clinical studies remain as important limitation, and therefore, precludes their use in clinical practice.
Time-domain model for injection locking in nonharmonic oscillators (2008)

Time-domain delay-based modeling of injection locking is used to describe injection-locking phenomena in nonharmonic oscillators. The model is used to predict the locking bandwidth, and the locking dynamics of the locked oscillator. The model predictions are verified against simulations and measurements of a four-stage differential ring oscillator. The model is further used to predict the injection-locking behavior of a single-ended CMOS inverter based ring oscillator.
FROST AND SORPTION EFFECTS IN ARGILLACEOUS ROCKS (1972)

AS A RESULT OF RESEARCH ON AGGREGATE MATERIALS, IT SEEMED POSSIBLE THAT THE FORMATION OF ICE IN SOME MINERAL AGGREGATES MIGHT BE A MUCH LESS IMPORTANT PROCESS OF DESTRUCTION THAN WETTING AND DRYING. DIFFERENTIAL THERMAL ANALYSIS IN THE RANGE OF ABOUT-20 C TO AS LOW AS -40 C DISCLOSED THAT CARBONATE ROCKS THAT WERE CONSIDERED TO BE UNSOUND AS A RESULT OF STANDARD NEW YORK STATE ENGINEERING TESTS (MAGNESIUM SULFATE AND FREEZE-THAW) TENDED TO CONTAIN RELATIVELY LITTLE OR NO WATER THAT WAS FREEZABLE IN THE TEMPERATURE RANGES USED. CONVERSELY, IN THE SOUND ROCKS WATER FROZE READILY AND RAPIDLY IN ALL CASES. THE NATURE OF THE CONTAINED WATER WAS FOUND BY DETERMINING THE AMOUNT OF WATER ADSORBED IN 72 HOURS AT 100 PERCENT RELATIVE HUMIDITY AT 30 C, THE AMOUNT OF WATER ADDED ON IMMERSION FOR 24 HOURS UNDER AMBIENT T AND P, AND THE AMOUNT OF WATER ADDED AFTER 6 HOURS IN VACUUM SATURATED AT AMBIENT T. THE ROCKS THAT ADSORBED THE MOST WATER HAD THE LEAST FREEZABLE WATER; I.E., THE WATER THAT COULD NOT BE DETECTED AS FREEZING WAS MOSTLY THE ADSORBED COMPONENT. IT IS CONCLUDED THAT SORPTIVE INTERACTIONS WITH WATER VAPOR OR LIQUID WATER ARE FAR MORE DESTRUCTIVE OF SHALES, SILTSTONES, AND ARGILLACEOUS CARBONATE ROCKS THAN IS FREEZING AND THAWING. IT IS FURTHER CONCLUDED THAT DESTRUCTION OF ROCKS (EXCLUDING FROST WEDGING) IN NEW YORK STATE BY THE FORMATION OF INTERGRANULAR ICE MAY BE A RELATIVELY RARE PHENOMENON, AT LEAST DURING INITIAL STAGES OF DETERIORATION. DETERIORATION OF CONCRETE OR OTHER HIGHLY HETEROGENEOUS SYSTEMS IS BELIEVED TO BE CAUSED BY BOTH THE FORMATION OF ICE AND BY SORPTIVE FORCES, THE INFLUENCE OF EACH DEPENDING ON MANY VARIABLES. SODIUM CHLORIDE IN WATER APPARENTLY ENHANCES THE EFFICIENCY OF THE SORPTIVE FORCES IN ROCK AND MAY ALSO DO SO IN CONCRETE. /AUTHOR/
ChemInform Abstract: DIAMINOPHOSPHENIUM IONS IN MASS SPECTRA OF 2,3‐DIHYDRO‐1H‐1,3,2‐BENZODIAZAPHOSPHOLES (1976)

Abstract Durch Umsetzung des Tetraäthyldiamids der Phenylphosphonigsäure(II) mit N‐substituierten o‐Phenylendiaminen (I) entstehen die Benzo‐diazaphosphole (III).Ohne diese Substanzen zu isolieren, kann man das Reaktionsgemisch sofort mit Schwefel behandeln und erhält so die Sulfide (IV).
Modeling Low-Platinum-Loading Effects in Fuel-Cell Catalyst Layers (2011)

The cathode catalyst layer within a proton-exchange-membrane fuel cell is the most complex and critical, yet least understood, layer within the cell. The exact method and equations for modeling this layer are still being revised and will be discussed in this paper, including a 0.8 reaction order, existence of Pt oxides, possible non-isopotential agglomerates, and the impact of a film resistance towards oxygen transport. While the former assumptions are relatively straightforward to understand and implement, the latter film resistance is shown to be critically important in explaining increased mass-transport limitations with low Pt-loading catalyst layers. Model results demonstrate agreement with experimental data that the increased oxygen flux and/or diffusion pathway through the film can substantially decrease performance. Also, some scale-up concepts from the agglomerate scale to the more macroscopic porous-electrode scale are discussed and the resulting optimization scenarios investigated.
Small Intestinal Submucosa as an Intra-Articular Ligamentous Graft Material: A Pilot Study in Dogs (1994)

Summary This pilot study was performed to determine the potential for using small intestinal submucosa (SIS) xenografts for intra-articular ligament reconstruction. Porcine SIS was used to replace the excised cranial cruciate ligament (CCL) in five normal dogs. Grafts were evaluated histologically at 10, 12, 16, and 26 weeks after implantation. Two grafts were evaluated biomechanically at 26 weeks. All of the SIS neoligaments appeared macroscopically as white fibrous bands. The histological appearance progressed, with time, from disorganized immature connective tissue to large bundles of organized connective tissue, covered by a synovial membrane, that resembled the native CCL. There was no histological evidence of immune-mediated nor any foreign body reaction to the xenogeneic SIS graft material. The neoligaments 26 weeks after implantation had a maximum force to failure that was 16.2 and 21.4 times greater than the original SIS graft material and were 7.6 and 11.1 percent as strong as the contralateral control CCLs. We conclude that porcine SIS, used as an intra-articular graft material to replace the normal CCL in dogs, supported host tissue ingrowth, remodelled to form a ligamentous structure, and is worthy of further investigation. Small intestinal submucosa was used to replace the excised cranial cruciate ligament (CCL) in five normal dogs. The histo-logical appearance of the grafts progressively changed, with time, from disorganized immature connective tissue to large bundles of organized connective tissue that resembled the native CCL. Graft strength increased between implantation and 26 weeks after the operation, however remained weaker than controls.
Reaction of Carboxylic Acids and Isonitriles in Small Spaces (2008)

Reversible encapsulation complexes are applied to the reaction of isonitriles with carboxylic acids. Encapsulation facilitates these reactions by amplifying the concentration of reactants, arranging the acid and isonitrile in the appropriate orientations, isolating intermediates from bulk solution, and providing an organized solvent cage.
Polymorphism of Ganglioside-Water Systems: a New Class of Micellar Cubic Phases. Freeze-Fracture Electron Microscopy and X-Ray Scattering Studies (1995)

The (T, c)-dependent phase diagrams of two gangliosides, GM1 and GM1(acetyl), have been explored, in spite of the frequent occurrence of metastable states. In GM1 two lamellar, one hexagonal and two cubic (aspects # 5 and 13) phases were identified, in addition to the isotropic micellar solution. In GM1(acetyl) two of the phases are cubic (aspects # 8 and 13), one is the fluid isotropic solution. The structure of the lamellar and the hexagonal phases are trivial. The structure of the cubic phases was determined using a combination of freeze-fracture electron microscope and X-ray scattering experiments. The three cubic phases consist of lipid micelles of type I (oil-in-water); in two of the phases (Q225 and Q229) the micelles are all identical and of quasi-spherical shape. Phase Q223 was previously known to contain two types of micelles, one quasi-spherical, the other slightly flattened. The radii of the micelles determined from the dimensions of the electron density troughs were consistent with the chemical data. In keeping with what is known of the micellar solutions, the size of the micelles of the cubic phases of GM1(acetyl) is compatible with a spherical shape, whereas the micelles of GM1 seem to be somewhat too large to be compatible with the length of the molecules and with a spherical shape. Such a wealth of micellar cubic phases is unusual in lipid-water systems.
‘A Hidden Side to the Story’: Reading Rape in Recent South African Literature (2002)

Sexual violence has had an uneasy relationship with literary representation in South Africa. Portrayals of rape have ambivalent potential, and the stakes are high where rape stories have served the interests of colonialism and apartheid. While it cannot be denied that representations of sexual violation have consolidated certain master narratives in South Africa, it is also true that narratives have been suppressed where these challenge power. Beth Goldblatt and Sheila Meintjes, reporting in the aftermath of the Truth and Reconciliation Commission, claim that violence against women remains ‘one of the hidden sides to the story of our past’ (Goldblatt and Meintjes 7).
Major histocompatibility complex haplotypes and complement C4 alleles in systemic lupus erythematosus. Results of a multicenter study. (1992)

In a multicenter study more than 300 central European systemic lupus erythematosus (SLE) patients were examined for HLA-B, HLA-DR, and complement C4 phenotypes. For 174 SLE patients MHC haplotypes were determined by family segregation analysis, and for 155 patients C4 gene deletions were determined by TaqI restriction fragment length polymorphism. Two haplotypes, B8-C4AQ0-C4B1-DR3 and B7-C4A3-C4B1-DR2, were identified as risk factors for SLE. These findings were confirmed by applying the haplotype frequency difference (HFD) method, which uses nontransmitted haplotypes from the family study as internal controls. Furthermore, only HLA-DR2, but not DR3, B7, or B8, was significantly increased in SLE patients independently of the two risk haplotypes. C4A gene deletions, but not silent C4AQ0 alleles, were increased in SLE patients and neither C4BQ0 alleles nor C4B gene deletions were increased. The observed frequencies of homozygosity and heterozygosity for the two haplotypes and the frequencies of homozygotes for C4AQ0 and C4A deletions did not differ from the expected values, indicating that the risk for SLE is conveyed by single allele effects. In conclusion, there are two MHC-linked susceptibility factors for Caucasian SLE patients carried by the haplotypes B7-DR2 and B8-DR3. The results argue against C4Q0 alleles being the decisive factors increasing susceptibility to SLE.
DNA Replication-Current Advances (2011)

The study of DNA advanced human knowledge in a way comparable to the major theories in physics, surpassed only by discoveries such as fire or the number zero. However, it also created conceptual shortcuts, beliefs and misunderstandings that obscure the natural phenomena, hindering its better understanding. The deep conviction that no human knowledge is perfect, but only perfectible, should function as a fair safeguard against scientific dogmatism and enable open discussion. With this aim, this book will offer to its readers 30 chapters on current trends in the field of DNA replication. As several contributions in this book show, the study of DNA will continue for a while to be a leading front of scientific activities.