gebhart/patrepeval huggingface dataset:
Computer-Assisted Structure Identification (CASI)—An Automated Platform for High-Throughput Identification of Small Molecules by Two-Dimensional Gas Chromatography Coupled to Mass Spectrometry (2013)

Compound identification is widely recognized as a major bottleneck for modern metabolomic approaches and high-throughput nontargeted characterization of complex matrices. To tackle this challenge, an automated platform entitled computer-assisted structure identification (CASI) was designed and developed in order to accelerate and standardize the identification of compound structures. In the first step of the process, CASI automatically searches mass spectral libraries for matches using a NIST MS Search algorithm, which proposes structural candidates for experimental spectra from two-dimensional gas chromatography with time-of-flight mass spectrometry (GC × GC-TOF-MS) measurements, each with an associated match factor. Next, quantitative structure-property relationship (QSPR) models implemented in CASI predict three specific parameters to enhance the confidence for correct compound identification, which were Kovats Index (KI) for the first dimension (1D) separation, relative retention time for the second dimension separation (2DrelRT) and boiling point (BP). In order to reduce the impact of chromatographic variability on the second dimension retention time, a concept based upon hypothetical reference points from linear regressions of a deuterated n-alkanes reference system was introduced, providing a more stable relative retention time measurement. Predicted values for KI and 2DrelRT were calculated and matched with experimentally derived values. Boiling points derived from 1D separations were matched with predicted boiling points, calculated from the chemical structures of the candidates. As a last step, CASI combines the NIST MS Search match factors (NIST MF) with up to three predicted parameter matches from the QSPR models to generate a combined CASI Score representing the measure of confidence for the identification. Threshold values were applied to the CASI Scores assigned to proposed structures, which improved the accuracy for the classification of true/false positives and true/false negatives. Results for the identification of compounds have been validated, and it has been demonstrated that identification using CASI is more accurate than using NIST MS Search alone. CASI is an easily accessible web-interfaced software platform which represents an innovative, high-throughput system that allows fast and accurate identification of constituents in complex matrices, such as those requiring 2D separation techniques.
A quantitative histological study of early clinical and preclinical Alzheimer's disease (1990)

Brains from 70 unselected general hospital necropsy cases aged 60-95 years were surveyed histologically for changes of Alzheimer's disease using Congo Red-Gallocyanin preparations. Counts were made of neurofibrillary tangles in two areas of the neocortex, the hippocampal formation and the substantia innominata. Neurons were counted in the subiculum of the hippocampus, the substantia innominata and the locus coeruleus. In addition, a retrospective enquiry was made concerning the mental health of the patients in the study; cognitive performance was graded on the Global Deterioration Scale (GDS 1-7). Four cases (5.7%) had clinical and pathological changes amounting to early Alzheimer's disease. Tangles were very numerous in all areas and there was a 30% deficit or more of neurons in at least two of the structures counted. Although the diagnosis of Alzheimer's disease was not recorded during life, all had shown signs of early cognitive decline (GDS grades 3-6). A further six cases (8.6%) showed excessive tangle accumulation which may represent preclinical Alzheimer's disease. Tangles were present in the temporal neocortex (Brodmann area 22), whereas they were absent in the remainder of the survey. Tangle density in the hippocampal formation (greater than 50 tangles in a 10 microns section) was also above the baseline level of the majority of cases. However, neuron loss was not widespread in these cases and none had shown evidence of cognitive impairment. The findings confirm that the early stages of Alzheimer's disease commonly occur amongst general hospital necropsies. The emergence of clinical signs of dementia appears to be related to the loss of a critical volume of neurons and not to tangle accumulation alone.
Choosing Haplotype-Tagging SNPS Based on Unphased Genotype Data Using a Preliminary Sample of Unrelated Subjects with an Example from the Multiethnic Cohort Study (2003)

We describe an approach for picking haplotype-tagging single nucleotide polymorphisms (htSNPs) that is presently being taken in two large nested case-control studies within a multiethnic cohort (MEC), which are engaged in a search for associations between risk of prostate and breast cancer and common genetic variations in candidate genes. Based on a preliminary sample of 70 control subjects chosen at random from each of the 5 ethnic groups in the MEC we estimate haplotype frequencies using a variant of the Excoffier-Slatkin E-M algorithm after genotyping a high density of SNPs selected every 3-5 kb in and surrounding a candidate gene. In order to evaluate the performance of a candidate set of htSNPS (which will be genotyped in the much larger case-control sample) we treat the haplotype frequencies estimate above as known, and carry out a formal calculation of the uncertainty of the number of copies of common haplotypes carried by an individual, summarizing this calculation as a coefficient of determination, R2h. A candidate set of htSNPS of a given size is chosen so as to maximize the minimum value of R2h over the common haplotypes, h.
Identification, Synthesis, and Biological Evaluation of Metabolites of the Experimental Cancer Treatment Drugs Indotecan (LMP400) and Indimitecan (LMP776) and Investigation of Isomerically Hydroxylated Indenoisoquinoline Analogues as Topoisomerase I Poisons (2012)

Hydroxylated analogues of the anticancer topoisomerase I (Top1) inhibitors indotecan (LMP400) and indimitecan (LMP776) have been prepared because (1) a variety of potent Top1 poisons are known that contain strategically placed hydroxyl groups, which provides a clear rationale for incorporating them in the present case, and (2) the hydroxylated compounds could conceivably serve as synthetic standards for the identification of metabolites. Indeed, incubating LMP400 and LMP776 with human liver microsomes resulted in two major metabolites of each drug, which had HPLC retention times and mass fragmentation patterns identical to those of the synthetic standards. The hydroxylated indotecan and indimitecan metabolites and analogues were tested as Top1 poisons and for antiproliferative activity in a variety of human cancer cell cultures and in general were found to be very potent. Differences in activity resulting from the placement of the hydroxyl group are explained by molecular modeling analyses.
Clinical and pathological characteristics of oral lichen planus in hepatitis C-positive and -negative patients (2002)

The reported prevalence rate of anti-hepatitis C virus (HCV) antibodies in patients with oral lichen planus shows wide geographical variation and ranges from 0 to 65%. Certain characteristic clinical features have been attributed to oral lichen planus associated to HCV infection. The purpose of this investigation has been to assess hypothetical clinical differences, as well as differences in the intensity of the subepithelial inflammatory infiltrate between oral lichen planus-HCV +ve patients and oral lichen planus-HCV -ve patients. A total of sixty-two patients entered the study. Their mean age was 63.5 +/- 14.49 years, and 48.4% of them were men and 51.6% women. Patients were classified according to their serum HCV positivity. Age, sex, clinical presentation (reticular or atrophic-erosive), extension of the lesions, location of the lesions, number of locations affected, intensity of the inflammatory infiltrate and Candida albicans colonization were recorded for each patient. Reticular lichen planus was the most frequent clinical presentation in both HCV +ve (57.1%) and HCV -ve patients (63.6%). C. albicans colonization ranged from 42.8% in HCV +ve and 41.7% in HCV -ve patients. HCV + ve patients showed certain oral locations more frequently affected than HCV -ve ones: lip mucosa, 28.6% versus 7.3%; tongue, 57.1% versus 29.1%; and gingiva, 71.4% versus 23.6%. The number of affected intraoral locations was higher in HCV +ve patients (71.4%) than among HCV -ve ones (20.4%; chi2 = 8.34; P < 0.011). No statistically significant differences could be established in terms of density of subepithelial inflammatory infiltrate between the groups. Our results reinforce the need for liver examination in all patients with oral lichen planus, particularly those showing lesions on the gingiva with multiple intraoral locations affected, as no pathological differences could be identified between HCV + ve and HCV -ve patients.
Cardiac segmentation in MR cine data using inverse consistent deformable registration (2010)

This paper proposes a registration-based segmentation technique to fully automatically segment the left ventricle in cardiac cine magnetic resonance studies. We propose an inverse consistent deformable registration algorithm to recover one set of forward and backward deformation fields that allow us to access the deformation from any frame to any other frame in the cardiac sequence. Cardiac phases are segmented using a shortest path algorithm and time consistency is enforced through the deformation fields. We demonstrate on 52 datasets with expert outlined ground truth that the algorithm produces accurate (1.39 pixels median error, 2.10 pixels RMS error, 0.88 Dice coefficient) and fast (0.3 s/image) results.
Modeling and system development for the FLAG L-band phased array feed for large-dish astronomical observations (2015)

Wide-field phased array feeds (PAFs) are part of the next generation of receivers for astronomical observatories. Groups around the world are developing array feeds for medium to large size dish antennas. The Brigham Young University (BYU) radio astronomy group is focusing its efforts on modeling and developing new high performance PAF systems for the Green Bank Telescope (GBT) with 100-meter reflector, which is the largest fully steerable radio telescope in the world.
Recent Progress in Living Cationic Polymerization of Vinyl Ethers (2010)

Abstract Recent advancements in living cationic polymerization of vinyl ethers are reviewed, especially focusing on newly developed initiating systems using various Lewis acid catalysts. In concert with the diversification of efficient metal halide catalysts, several types of initiators (cationogens) have been shown to mediate living polymerization, in which the nature of the central metals is responsible for the polymerization behavior. Other types of initiating systems, e.g., living cationic polymerization using metal oxides as solid catalysts and Lewis acid-free systems, are also summarized, as well as the applications of the polymerization for the synthesis of functional poly(vinyl ether)s.
The Chemistry of Formation of Some Secondary Arsenate Minerals of Cu(II), Zn(II) and Pb(II) (1988)

Abstract Solution studies have been carried out on natural and synthetic arsenate minerals, which are often found in the oxide zones of base metal orebodies. Solubility products and free energy of formation data have been derived for the minerals olivenite, cornubite, clinoclase, adamite, legrandite, euchroite, duftite, conichalcite, austinite, bayldonite, and schultenite at 298.2 K (25 °C). The data have been used in turn to construct stability field diagrams illustrating the chemical conditions under which the various species may crystallize from aqueous solution. This equilibrium model is then compared with several natural occurrences of the arsenate suites and it is demonstrated that it can be used to explain a number of observed paragenetic sequences. Descriptions of solution conditions which describe the stabilities of the arsenate minerals with respect to more commonly found secondary minerals of Pb(II), Cu(II), and Zn(II) involve more complex calculations and estimates of the likely levels of various dissolved species, but it is shown how these may be taken into account in the development of a more complex equilibrium model.
Return to the Zombie Gadgets: Undermining Destructive Code Reads via Code Inference Attacks (2016)

The concept of destructive code reads is a new defensive strategy that prevents code reuse attacks by coupling fine-grained address space layout randomization with a mitigation for online knowledge gathering that destroys potentially useful gadgets as they are disclosed by an adversary. The intuition is that by destroying code as it is read, an adversary is left with no usable gadgets to reuse in a control-flow hijacking attack. In this paper, we examine the security of this new mitigation. We show that while the concept initially appeared promising, there are several unforeseen attack tactics that render destructive code reads ineffective in practice. Specifically, we introduce techniques for leveraging constructive reloads, wherein multiple copies of native code are loaded into a process' address space (either side-by-side or one-after-another). Constructive reloads allow the adversary to disclose one code copy, destroying it in the process, then use another code copy for their code reuse payload. For situations where constructive reloads are not viable, we show that an alternative, and equally powerful, strategy exists: leveraging code association via implicit reads, which allows an adversary to undo in-place code randomization by inferring the layout of code that follows already disclosed bytes. As a result, the implicitly learned code is not destroyed, and can be used in the adversary's code reuse attack. We demonstrate the effectiveness of our techniques with concrete instantiations of these attacks against popular applications. In light of our successes, we argue that the code inference strategies presented herein paint a cautionary tale for defensive approaches whose security blindly rests on the perceived inability to undo the application of in-place randomization.
Palladin promotes assembly of non-contractile dorsal stress fibers through VASP recruitment (2014)

Stress fibers are major contractile actin structures in non-muscle cells where they have an important role in adhesion, morphogenesis and mechanotransduction. Palladin is a multidomain protein, which associates with stress fibers in a variety of cell types. However, the exact role of palladin in stress fiber assembly and maintenance has remained obscure, and whether it functions as an actin filament crosslinker or scaffolding protein was unknown. We demonstrate that palladin is specifically required for the assembly of non-contractile dorsal stress fibers, and is, consequently, essential for the generation of stress fiber networks and the regulation of cell morphogenesis in osteosarcoma cells migrating in a three-dimensional collagen matrix. Importantly, we reveal that palladin is necessary for the recruitment of vasodilator stimulated phosphoprotein (VASP) to dorsal stress fibers and that it promotes stress fiber assembly through VASP. Both palladin and VASP display similar rapid dynamics at dorsal stress fibers, suggesting that they associate with stress fibers as a complex. Thus, palladin functions as a dynamic scaffolding protein that promotes the assembly of dorsal stress fibers by recruiting VASP to these structures.
Preparation of Biopex-Supported Gold Nanoparticles as Potential Fiducial Markers for Image-Guided Radiation Therapy (2022)

Image-guided radiation therapy (IGRT) has emerged as a promising technique for cancer treatment to improve radiation precision and accuracy, thereby reducing the treatment toxicity and optimizing therapeutic efficacy. In IGRT, fiducial markers are required to be inserted near the tumor to get the spatial information of the tumor. Currently used metal fiducial markers with large sizes would be highly invasive; therefore, it is critical to develop minimally invasive alternatives to these markers. In this work, an injectable marker based on Biopex-supported Au NPs with adequate radio-opacity for X-ray visualization was developed. Biopex can function as a substrate for the growth of Au NPs and avoid excessive reaction-induced aggregation and precipitation. The self-curing property of Biopex prevents the leakage and elimination of isolated Au NPs, enabling long-term X-ray observation and radiotherapy. The effect of Biopex amount, gold precursor concentration, and reaction time were evaluated. The visibility of samples prepared by the optimized formula was also examined. The developed Biopex-Au NPs could be injected through a 21 G needle and exhibit great visibility in the X-ray visualization test, showing great potential as a fiducial marker for image-guided radiation therapy.
A vibratory sensor for locating parts (1992)

SUMMARY A vibratory sensor capable of locating parts by measuring their inertial properties is described in this paper. The sensor is designed to be fitted to the wrist of a robot and used to acquire parts from a stack or a tray. The initial coordinates of the parts need only be approximately known (say to ±25 mm and ±45°). The robot is thus said to operate in a “semi-ordered” environment which can be realised inexpensively as accurate pallets, fixtures or other parts presentation equipment are not required. Furthermore, the absence of complete disorder, as would exist with a “bin-picking” approach where parts are allowed to lie at random in a bin, reduces the degree of sophistication demanded of the sensor system. Consequently, the cost of the latter can also be kept low. The proposed sensor has a circular platform mounted on the shaft of a motor such that the shaft is normal to the platform. The part whose location is to be determined is held on the platform by magnetic or other means. The assembly consisting of the part, platform and motor is constrained to vibrate about an axis parallel to the platform. Two methods for computing the location of the part relative to the platform are described. Both methods require the natural frequencies of vibration of the part-platform-motor assembly for various angular positions of the platform. A simulation study to examine the effect of various design and operational parameters (inertias of the platform and part, stiffness of the spring restraining the movements of the vibrating assembly, location of part on platform, accuracy of frequency measurements) on the accuracy of the location computed is presented. The simulation results clearly demonstrate the feasibility of the sensor.
Influence of the storage conditions on prestressing steel relaxation losses (2012)

Stress relaxation losses on active reinforcement have significant impact on prestressed concrete structures. This is why relaxation tests are carried out on prestressing steel wires and strands after being manufactured. Then, these materials are coiled and stored for a long-term period, sometimes in excess of one year. The influence of these operations, carried out after manufacturing, is usually neglected. Nevertheless, some manufacturers and contractors have noticed that, sometimes, when relaxation tests are carried out after a long-term storage, the relaxation losses found are higher than those measured immediately after manufacturing. In this work, lab tests are performed to check the influence of the coiling radius and the period of storage on the relaxation test. In addition to this, an analytical model is presented to predict the results of a relaxation test carried out on a wire coiled and stored for a long-term period. This model explains the evolution on the cross-sectional stress profile along the coiling-storing-uncoiling process, as well as the influence of the residual stresses on it.
Quantum theory of all-optical switching in nonlinear Sagnac interferometers (2012)

Recently, our group has demonstrated an ultrafast, low-loss, fiber-loop switch based on a nonlinear Sagnac-interferometer design, using which entangled photons were shown to be routed without any measurable degradation in their entanglement fidelity [Hall {\it et al.}, Phys. Rev. Lett. {\bf 106}, 053901 (2011)]. Such a device represents an enabling technology for a rich variety of networked quantum applications. In this paper we develop a comprehensive quantum theory for such switches in general, i.e., those based on nonlinear Sagnac interferometers, where the in-coupling of quantum noise is carefully modeled. Applying to the fiber-loop switch, the theory shows good agreement with the experimental results without using any fitting parameter. This theory can serve as an important guiding tool for configuring switches of this kind for future quantum networking applications.
INVESTIGATING THE CRITICAL SITUATION IN HYPERTENSION MANAGEMENT: PHYSICIAN PERCEPTION AND USE OF THE ESH–ESC TREATMENT GUIDELINES (SHARE SURVEY): PP.20.306 (2010)

Objectives: To assess i) the influence of treatment guidelines on prescribing habits, ii) physician familiarity with the ESH–ESC guidelines, and iii) physicians’ opinions on the ESH–ESC guideline-recommended blood pressure (BP) targets and on getting patients to targets in practice. Design and Methods: 2629 physicians from across Europe and from a range of specialities (including primary and secondary care) completed the interactive Supporting Hypertension Awareness and Research Europe-wide (SHARE) survey. This survey aimed to investigate the current situation in hypertension management. T-tests and Chi-Square tests were used to compare responses from office- versus hospital-based physicians. Results: Physicians acknowledge that clinical guidelines and healthcare literature should influence treatment choices more than they currently do, while factors such as hospital and economic directives should influence treatment choices less than at present. In general, hospital-based physicians were most familiar with and rated most highly the ESH-ESC guidelines, whereas office-based physicians were most familiar with their national guidelines (Figure). The majority of physicians (76%) thought that BP targets recommended in the ESH–ESC guidelines were ‘about right’, however a higher number of office- versus hospital-based physicians thought targets were ‘too tight and not achievable’ (24% versus 8%, respectively; p < 0.0001). In total 77% of all physicians found it challenging to get patients to ESH–ESC BP targets, with more office-based than hospital-based physicians finding it a challenge (82% versus 63%, respectively; p < 0.0001). On average physicians said that only 52.6% of their patients achieved BP targets. Conclusions: The ESH–ESC guidelines are respected as a good source of information and play an important role in treatment choices. However, with half of office-based and a third of hospital-based physicians not being familiar with these guidelines it is important to raise awareness about these guidelines in the healthcare community. In general, physicians think that the BP targets recommended by the ESH–ESC guidelines are correct, but find it challenging to get their patients to these targets in practice.