gebhart/patrepeval huggingface dataset:
Role of neutral transport in aspect ratio dependent plasma etching of three-dimensional features (2017)

Fabrication of semiconductor devices having three-dimensional (3D) structures places unprecedented demands on plasma etching processes. Among these demands is the frequent need to simultaneously etch features with a wide variety of aspect ratios (AR) on the same wafer. Many plasma etching processes exhibit aspect ratio dependent etching (ARDE)—different etch rates for features that have different aspect ratios, usually slower for larger AR. Processes subject to ARDE require over-etch to clear the larger AR features, which increases the need for high selectivity and low damage. Despite these issues, the physical processes which contribute to ARDE are not well understood. In this paper, results are discussed from a computational investigation on the root causes of ARDE during Ar/Cl2 plasma etching of Si, and, in particular, the role which neutral transport plays in this process. Parametric studies were performed varying neutral-to-ion flux ratios, surface recombination rates of atomic Cl, and neutral and ion angular distributions to determine their influence on neutral transport of Cl to the etch front and ARDE. It was found that each parameter has a significant influence on neutral transport to the etch front (with the exception of the ion angular distribution). Methods for increasing neutral flux (for a given set of ion fluxes) to the etch front were found to push the system toward a neutral saturated, ion starved regime which alleviates ARDE for some range of AR. Increased neutral flux is also correlated with more tapered features, which tend to exhibit more significant ARDE. This coupling of neutral transport with feature profiles makes it difficult to alleviate all ARDE in this system. However, it is possible to optimize parameters in such a way to postpone the onset of ARDE to fairly large AR (&amp;gt;8).
Corticobasal degeneration and progressive supranuclear palsy share a common tau haplotype (2001)

The CBD tau association described here suggests that PSP and CBD share a similar cause, although the pathogenic mechanism behind the two diseases leads to a different clinical and pathologic phenotype.
Quasi-Cyclic LDPC Codes for the Magnetic Recording Channel: Code Design and VLSI Implementation (2007)

By implementing a field-programmable gate array (FPGA)-based simulator, we investigate the performance of randomly constructed high-rate quasi-cyclic (QC) low-density parity-check (LDPC) codes for the magnetic recording channel at very low block sector error rates. On the basis of extensive simulations, we conjecture guidelines for designing randomly constructed high-rate regular QC-LDPC codes with low error floor for the magnetic recording channel. Experimental results show that our high-rate regular QC-LDPC codes do not suffer from error floor, at least at block error rates of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-9</sup> , and can realize significant coding gains over Reed-Solomon codes that are used in current practice. Furthermore, we develop a QC-LDPC decoder hardware architecture that is well suited to achieving high decoding throughput. Finally, to evaluate the implementation feasibility of LDPC codes for the magnetic recording channel, using 0.13 mum standard cell and memory libraries, we designed a read channel signal processing datapath consisting of a parallel max-log-MAP detector and a QC-LDPC decoder, which can achieve a throughput up to 1.8 Gb/s
Cognitive‐Performance Recovery of Alzheimer's Disease Model Mice by Modulation of Early Soluble Amyloidal Assemblies (2008)

A rationally designed oligomerization inhibitor interacts with early intermediate assemblies of amyloid-beta polypeptide (Abeta) through the aromatic elements and inhibits their assembly into the toxic oligomers that cause Alzheimer's disease by a unique C(alpha)-methylation beta-breakage strategy. The electrostatic potential of the low-energy conformation of the dipeptide inhibitor bound to Abeta is shown.
Working equations for piezoelectric actuators and sensors (1999)

A new solution to the force, displacements, and charges developed in piezoelectric beams is derived. Differing from previous solutions, this development determines the neutral axis where the bending strains are zero and results in a closed form solution (without matrix inversion). With the closed form, simplifications become evident which increase understanding and facilitate calculations. These equations are than expanded to account for axial, built-in strains in the beam. A design example where axial forces exerted by the piezoelectric layer are important is presented.
Cold preserved nerve allografts: Changes in basement membrane, viability, immunogenicity, and regeneration (1998)

Rat sciatic nerve graft segments were harvested and pretreated by either placement in the University of Wisconsin Cold Storage Solution at 5 degrees C and storage from 1 to 26 weeks, or repeatedly freezing (-40 degrees C) and thawing (20 degrees C). Following pretreatment, grafts were transplanted as either syngeneic or allogeneic nerve grafts. Storage and freeze-thawing did not affect the Schwann cell basal lamina or laminin distribution of the peripheral nerve. Graft cell viability decreased with increasing time of storage, with some viable cells detectable even after 3 weeks of storage. Freeze-thawed grafts were not viable. Increasing time of storage led to decreasing immune response and graft rejection, but improved regeneration. Freeze-thawed and 26-week stored allografts were nonimmunogenic and rejection was not seen, but regeneration was delayed compared to autografts. Graft storage may become a useful adjunct to clinical nerve allografting to permit elective scheduling of surgery, provide greater time for preoperative tissue testing, and possibly blunt the immune response.
Biological Macromolecule Crystallization Database, Version 3.0: new features, data and the NASA archive for protein crystal growth data (1994)

Version 3.0 of the NIST/NASA/CARB Biological Macromolecule Crystallization Database (BMCD) includes crystal and crystallization data on all forms of biological macromolecules which have produced crystals suitable for X-ray diffraction studies. The data include summary information on each of the macromolecules, crystal data, crystallization conditions and comments about the crystallization procedure if it varies from the traditional methods employed for crystal growth. The database-management software maintains continuity with previous versions providing similar search procedures and displays. Version 3.0 of the BMCD includes protocols and results of crystallization experiments undertaken in space. These new data are comprised of both the NASA Protein Crystal Growth Archive, which includes information on all NASA-sponsored protein crystal growth experiments, and data describing other internationally sponsored microgravity macromolecule crystallization studies. The entries for the space growth crystallization experiments contain the crystallization protocols, apparatus descriptions, flight summary data, indication of success or failure of the experiments, references, etc. Other new features of the BMCD include the addition of crystallization procedures for small peptides and cross references to other structural biology databases.
Ribosomally Synthesized Antibacterial Peptides in Gram Positive Bacteria (2002)

The emergence of multidrug-resistant pathogens that has caused a serious problem in hospitals worldwide, has intensified the search for novel drugs, in order to replace or to be used in complement with the existing antibiotics. In this connection much interest has been focused on a group of antimicrobial peptides, so-called bacteriocins. These antagonising peptides, which are gene-encoded in contrast to those made by multi-enzyme-complexes, share some common physico-chemical properties, such as being small, cationic, amphiphilic and often being membrane active. However, they differ greatly from each other in their primary sequence and exhibit an impressively large inhibitory spectrum which covers almost all bacterial genera, including many important pathogens and food-spoilage bacteria. Many of these peptides are produced by lactic acid bacteria, organisms which have been used by man from ancient time in diverse fermentation processes, to improve and/or prolong self-life of many food and feed products. Numerous bacteriocins have been purified and characterised in great detail, both at biochemical and genetic levels. Still, novel bacteriocins with new properties are reported in an increasing number in recent years. In this review we will give a brief status quo of the present knowledge on bacteriocin research; thus different aspects such as their diversity in nature, biochemical properties, modes of action, biosynthesis and genetics will be treated.
Increased atherosclerosis in LDL receptor–null mice lacking ACAT1 in macrophages (2001)

During atherogenesis, circulating macrophages migrate into the subendothelial space, internalize cholesterol-rich lipoproteins, and become foam cells by progressively accumulating cholesterol esters. The inhibition of macrophage acyl coenzyme A:cholesterol acyltransferase (ACAT), which catalyzes the formation of cholesterol esters, has been proposed as a strategy to reduce foam cell formation and to treat atherosclerosis. We show here, however, that hypercholesterolemic LDL receptor-deficient (LDLR(-/-)) mice reconstituted with ACAT1-deficient macrophages unexpectedly develop larger atherosclerotic lesions than control LDLR(-/-) mice. The ACAT1-deficient lesions have reduced macrophage immunostaining and more free cholesterol than control lesions. Our findings suggest that selective inhibition of ACAT1 in lesion macrophages in the setting of hyperlipidemia can lead to the accumulation of free cholesterol in the artery wall, and that this promotes, rather than inhibits, lesion development.
Self-Steering Antenna Arrays for Distributed Picosatellite Networks (2003)

The potential for using self-steering arrays for secure crosslinks in picosatellite networks is investigated. The principle of operation and methods of characterization of these so-called retrodirective arrays is reviewed, and examples developed by our group are presented. New challenges for the space environment are identified, specifically the development of two-dimensional, circularly polarized retrodirective arrays optimized for size and power consumption.
Dietary Intakes of Female and Male Combat Support Hospital Personnel Subsisting on Meal-Focused or Standard Versions of the Meal, Ready-to-Eat (2002)

This study investigated gender differences in nutrient intake and energy expenditure of combat support hospital personnel during a field training exercise, as well as evaluated a test ration which was slightly higher in carbohydrate and lower in fat than standard MREs and included items being considered for future MREs. Women consumed less energy than men (p&lt;0.01) from both the Concept ration (mean +/- SD: 2092 +/- 570 kcal/d vs. 2678 +/- 516 kcal/d for women and men, respectively) and MRE XVII (1818 +/- 492 kcal/d vs. 2396 +/- 678 kcal/d, respectively). Energy expenditures of the female and male volunteers measured by doubly-labeled water were 2745 +/- 87 kcal/d and 3956 +/- 243 kcal/d (mean +/- SE), respectively, suggesting a significant energy deficit. However, there were no gender difference in energy intakes (31 +/- 9 kcal/kg for women vs. 31 +/- 10 kcal/kg for men) or energy expenditures (44.9 +/- 1.5 kcal/kg for women vs. 45.5 +/- 2.3 kcal/kg for men) when normalized for body weight. When intakes of nutrients were normalized for energy intake or body size, there were very few gender differences. Primarily because women consumed less energy than men, greater proportions of women than men (p&lt;0.01) failed to meet intake criteria for folate, vitamins B6 and B12, calcium, iron, magnesium, and zinc. The Concept ration did enhance energy and carbohydrate intakes; however, protein intakes in the Concept group were marginally adequate. Thus, the nutrient densities of the field rations tested are not adequate at the levels of energy intake observed in these women (and some men), suggesting that supplementation or further fortification of ration components should be investigated. Efforts to enhance carbohydrate intakes in operational settings will need to ensure that protein intakes are not compromised.
Accuracy of pulse oximeters in estimating heart rate at rest and during exercise. (1991)

Pulse oximeters are being widely used for non-invasive, simultaneous assessment of haemoglobin oxygen saturation. They are reliable, accurate, relatively inexpensive and portable. Pulse oximeters are often used for estimating heart rate at rest and during exercise. However, at present the data available to validate their use as heart rate monitors are not sufficient. We evaluated the accuracy of two oximeters (Radiometer, ear and finger probe; Ohmeda 3700, ear probe) in monitoring heart rate during incremental exercise by comparing the pulse oximeters with simultaneous ECG readings. Data were collected on eight men (713 heart rate readings) during graded cycle ergometer and treadmill exercise to volitional fatigue. Analysis by linear regression revealed that general oximeter readings significantly correlated with those of ECG (r = 0.91, P less than 0.0001). However, comparison of heart rate at each level of work showed that oximeter readings significantly (P less than 0.05) under-estimated rates above 155 beats/min. These results indicate that the use of pulse oximeters as heart rate monitors during strenuous exercise is questionable. This inaccuracy may well originate from the instability of the probes, sweating, other artefacts during exercise, and measurement of different components in the cardiovascular cycle.
The leuX-encoded tRNA5Leu but not the pathogenicity islands I and II influence the survival of the uropathogenic Escherichia coli strain 536 in CD-1 mouse bladder mucus in the stationary phase (1998)

The uropathogenic Escherichia coli strain 536 carries two pathogenicity islands, each of which is associated with either of the tRNA genes selC or leuX, respectively. Growth competition in CD-1 mouse mucus between the wild-type strain E. coli 536, its leuX mutant 536Δ102 and its mutant 536R3, lacking both pathogenicity islands but expressing a functional tRNA5Leu, revealed a major impact of leuX on E. coli survival in bladder mucus. The impaired survival in CD-1 mouse mucus observed upon deletion of the leuX gene was abolished after complementation with the leuX gene. The survival of bacteria in bladder mucus was not influenced by the presence of pathogenicity islands I and II.
[Changes of nuclear matrix proteins during differentiation of human osteosarcoma MG-63 cells induced by HMBA]. (2006)

Human osteosarcoma MG-63 cells were induced into differentiation by hexamethylene bisacetamide (HMBA). Its nuclear matrix proteins were selectively extracted, and subjected to two dimensional gel electrophoresis analysis. The resulted protein patterns were analyzed by Melanie software. There were 12 spots changed remarkably during the differentiation induced by HMBA, nine of which were identified. The up-regulated proteins were identified as MHC class II antigen, interferon-stimulated gene factor 3d, hypothetical protein DKFZp434M2221.1,8-hydroxy-guanine glycosylase homolog ogg1, and vimentin. The down-regulated ones were hnRNP A2/B1 and actin; and two newly expressed proteins under induction were 60S ribosomal protein L21 and ST2 protein. This study suggests that the induced differentiation of carcinoma cells is accompanied with changes of nuclear matrix proteins, and confirms the presence of some specific nuclear matrix proteins associated with carcinoma cell growth and differentiation. The changed nuclear matrix proteins are potential markers for cancer diagnosis or targets for cancer therapy.
Coupling mammalian cell surface display with somatic hypermutation for the discovery and maturation of human antibodies (2011)

A novel approach has been developed for the isolation and maturation of human antibodies that replicates key features of the adaptive immune system by coupling in vitro somatic hypermutation (SHM) with mammalian cell display. SHM is dependent on the action of the B cell specific enzyme, activation-induced cytidine deaminase (AID), and can be replicated in non-B cells through expression of recombinant AID. A library of human antibodies, based on germline V-gene segments with recombined human regions was used to isolate low-affinity antibodies to human β nerve growth factor (hβNGF). These antibodies, initially naïve to SHM, were subjected to AID-directed SHM in vitro and selected using the same mammalian cell display system, as illustrated by the maturation of one of the antibodies to low pM K(D). This approach overcomes many of the previous limitations of mammalian cell display, enabling direct selection and maturation of antibodies as full-length, glycosylated IgGs.
Integrated Electroanatomic Mapping With Three-Dimensional Computed Tomographic Images for Real-Time Guided Ablations (2006)

Image integration with high-resolution 3D CT allows accurate placement of anatomically guided ablation lesions and can facilitate complex ablation strategies. This may provide significant advantages for anatomically based procedures such as ablation of atrial fibrillation and nonidiopathic ventricular tachycardia.
The potential of proteasome inhibitors in cancer therapy (2008)

Bortezomib as first-in-class proteasome inhibitor has proven to be highly effective in some hematological malignancies, overcomes conventional chemoresistance, directly induces cell cycle arrest and apoptosis, and also targets the tumor microenvironment. It has been granted approval by the FDA for relapsed multiple myeloma, and recently for relapsed mantle cell lymphoma. Combination chemotherapy regimens have been developed providing high remission rates and remission quality in frontline treatment or in the relapsed setting in multiple myeloma. The combination of proteasome inhibition with novel targeted therapies is an emerging field in oncology. Moreover, novel proteasome inhibitors, such as NPI-0052 and carfilzomib, have been developed. This review summarizes our knowledge of the ubiquitin-proteasome system and recent data from cancer clinical trials.
Antimicrobial susceptibility of bifidobacteria (2004)

With regard to a general concern about the safety of probiotics, such as potential transferability of resistance determinants, bifidobacteria, with their low natural and acquired resistance to 30 antibiotics, appear risk-free.
Synthesis, characterization, and immunological properties in mice of conjugates composed of detoxified lipopolysaccharide of Salmonella paratyphi A bound to tetanus toxoid with emphasis on the role of O acetyls (1996)

Salmonella paratyphi A, the second most common cause of enteric fever in Southeast Asia, is a habitant of and a pathogen for humans only. Lipopolysaccharides (LPS) are both essential virulence factors and protective antigens for systemic infections caused by groups A, B, C, and D nontyphoidal salmonellae. The O-specific polysaccharide of S. paratyphi A is composed of a trisaccharide, -->2-alpha-D)-Manp-(1-->4)-alpha-L-Rhap-(1-->3)-alpha-D-Galp -(1-->, with a branch of D-paratose from the C-3 of alpha-D-mannose, and the C-3 of beta-L-rhamnose is partially O acetylated (C. G. Hellerqvist, B. Lindberg, K. Samuelsson, and A. A. Lindberg, Acta Chem. Scand. 25:955-961, 1971). On the basis of data from our investigational vaccines for enteric bacterial pathogens, including group B salmonellae (D. C. Watson, J. B. Robbins, and S. C. Szu, Infect. Immun. 60:4679-4686, 1992), conjugates composed of the detoxified LPS of S. paratyphi A bound to tetanus toxoid (TT) were prepared by several schemes. LPS was detoxified with acetic acid or with hydrazine; the latter removed O acetyls from the O-specific polysaccharide. The detoxified polysaccharides were activated with cyanogen bromide (CNBr) or with 1-cyano-4-dimethylaminopyridinium tetratfluoroborate (CDAP) and bound to TT with or without a spacer. Solutions of 2.5 microgram of saccharide, alone or as a conjugate, were injected subcutaneously into young mice, and LPS and TT antibodies were measured by enzyme-linked immunosorbent assaying. A conjugate synthesized with higher-molecular-weight O-SP elicited the highest anti-LPS levels. Only conjugates with O acetyls elicited serum immunoglobulin G anti-LPS with bactericidal activity. There were no statistically significant differences between LPS antibody levels elicited by conjugates synthesized with or without a spacer. The conjugate with O-specific polysaccharide activated by CDAP and bound to TT without a spacer elicited the highest level of TT antibodies. Clinical evaluation (if S. paratyphi A conjugates is planned.
The variation of the specific heat ratio and the speed of sound in air with temperature, pressure, humidity, and CO2 concentration (1993)

This paper describes a precise numerical calculation of the specific heat ratio and speed of sound in air as a function of temperature, pressure, humidity, and CO2 concentration. The above parameters are calculated utilizing classical thermodynamic relationships and a real gas equation of state over the temperature range 0 °C–30 °C. The shortcomings of previous determinations are also discussed. For both parameters, the coefficients of an interpolating equation are given, which are suitable for use in applications requiring high precision. The overall uncertainty in the specific heat ratio is estimated to be less than 320 ppm and the uncertainty in the speed of sound is similarly estimated to be less than 300 ppm.
Inactivation of factor Xa by the synthetic inhibitor DX-9065a causes strong anticoagulant and antiplatelet actions in human blood (1999)

In an in vitro study, anticoagulant and antiplatelet effects of the synthetic, direct factor Xa inhibitor DX-9065a, (+)-2S-2-[4-[[(3S)-1-acetimidoyl-3-pyrrolidinyl]oxy]phenyl]-3-[7-a midino-2-naphthyl]propanoic acid hydrochloride pentahydrate, which shows a high affinity and selectivity towards the enzyme, were investigated. Anticoagulant actions of DX-9065a were studied in human plasma using global clotting assays [prothrombin time (PT), activated partial thromboplastin time (APTT), thrombin time (TT) and Heptest]. The effect on thrombin generation was measured in whole blood by determining the plasma concentration of prothrombin fragment F1.2. The influence on agonist-induced platelet activation in whole blood was studied using flow cytometric analysis. DX-9065a caused a concentration-dependent prolongation of clotting times in the PT and APTT assay, whereas Heptest was less affected and TT was not influenced. Furthermore, DX-9065a strongly inhibited the generation of thrombin without and after coagulation activation. The factor Xa inhibitor did not affect platelet activation mediated by either thrombin receptor activating peptide, arachidonic acid or y-thrombin, but prevented tissue factor- and factor Xa-induced activation of platelets in a concentration-dependent manner. Inactivation of factor Xa by a highly effective and selective inhibitor, and the resulting inhibition of thrombin generation leads to strong anticoagulant and antiplatelet actions. The interference with the coagulation system at the early level of factor Xa is expected to be an effective approach for a successful anticoagulant/antithrombotic therapy.