gebhart/patrepeval huggingface dataset:
Angle-resolved environmental X-ray photoelectron spectroscopy: A new laboratory setup for photoemission studies at pressures up to 0.4 Torr (2012)

The paper presents the development and demonstrates the capabilities of a new laboratory-based environmental X-ray photoelectron spectroscopy system incorporating an electrostatic lens and able to acquire spectra up to 0.4 Torr. The incorporation of a two-dimensional detector provides imaging capabilities and allows the acquisition of angle-resolved data in parallel mode over an angular range of 14° without tilting the sample. The sensitivity and energy resolution of the spectrometer have been investigated by analyzing a standard Ag foil both under high vacuum (10(-8) Torr) conditions and at elevated pressures of N(2) (0.4 Torr). The possibility of acquiring angle-resolved data at different pressures has been demonstrated by analyzing a silicon/silicon dioxide (Si/SiO(2)) sample. The collected angle-resolved spectra could be effectively used for the determination of the thickness of the native silicon oxide layer.
Characterization of RNase HII substrate recognition using RNase HII–argonaute chimaeric enzymes from <i>Pyrococcus furiosus</i> (2010)

RNase H (ribonuclease H) is an endonuclease that cleaves the RNA strand of RNA-DNA duplexes. It has been reported that the three-dimensional structure of RNase H is similar to that of the PIWI domain of the Pyrococcus furiosus Ago (argonaute) protein, although the two enzymes share almost no similarity in their amino acid sequences. Eukaryotic Ago proteins are key components of the RNA-induced silencing complex and are involved in microRNA or siRNA (small interfering RNA) recognition. In contrast, prokaryotic Ago proteins show greater affinity for RNA-DNA hybrids than for RNA-RNA hybrids. Interestingly, we found that wild-type Pf-RNase HII (P. furiosus, RNase HII) digests RNA-RNA duplexes in the presence of Mn2+ ions. To characterize the substrate specificity of Pf-RNase HII, we aligned the amino acid sequences of Pf-RNase HII and Pf-Ago, based on their protein secondary structures. We found that one of the conserved secondary structural regions (the fourth beta-sheet and the fifth alpha-helix of Pf-RNase HII) contains family-specific amino acid residues. Using a series of Pf-RNase HII-Pf-Ago chimaeric mutants of the region, we discovered that residues Asp110, Arg113 and Phe114 are responsible for the dsRNA (double-stranded RNA) digestion activity of Pf-RNase HII. On the basis of the reported three-dimensional structure of Ph-RNase HII from Pyrococcus horikoshii, we built a three-dimensional structural model of RNase HII complexed with its substrate, which suggests that these amino acids are located in the region that discriminates DNA from RNA in the non-substrate strand of the duplexes.
Update on photoprotection (2007)

Photoprotection is an effective method for preventing damaging effects from ultraviolet radiation (UVR). Photoprotection is accomplished through the use of sunscreens, protective clothing, and safe sun practices. Sunscreens are composed of various UV filters, including inorganic/physical blockers and organic/chemical sunscreen agents. New technologies are emerging in sunscreen development and may soon be available to U.S. consumers. General guidelines for sunscreen use should be reinforced to improve patient compliance and sunscreen efficacy. Habitual use of sunscreen is recommended with UV exposure, and concerns for vitamin D deficiency with sunscreen use should not supersede proper photoprotective behavior.
Polymers with tunable side-chain amphiphilicity as non-hemolytic antibacterial agents (2013)

Quaternized polymers mimicking the antimicrobial peptides were created by tuning the side-chain amphiphilicity using a first-time approach of post-functionalization. They displayed excellent efficacy against pathogenic bacteria even in human plasma and membrane disruptive mode of action. The optimized polymers and degraded products were non-hemolytic.
Electrooptic Effect in Homeotropically Aligned Ferroelectric Liquid Crystal (1991)

New types of electrooptic effects in a homeotropically aligned cell of ferroelectric liquid crystal have been proposed, and their characteristics have been studied. Especially, in the oblique incident type of the homeotropic cell, a new electrooptic effect with a sharp threshold, very fast response and a hysteresis loop is observed.
Task decomposition and analysis of robotic assembly task plans using Petri nets (1994)

This paper describes a framework for robotic task sequence planning which decomposes tasks into operations sequences for a generic robotic workcell. The approach provides robust execution of tasks through properties of: traceability-implicit mapping operations representation, and viability-retaining multiple execution. Given the descriptions of the objects in the system and all feasible geometric configurations and relationships among these objects, an AND/OR net which describes the relationships of all feasible geometric states and associated feasibility criteria for net transitions is generated. This AND/OR net is mapped into a Petri net which incorporates all feasible sequences of high level operations. The resulting Petri net is then decomposed in a stepwise manner into lower level Petri nets of which each transition can be directly implemented by control commands or command sequences based on devices and objects in the system, or, by lower level planning transitions corresponding to path planning, grasp planning, fine motion planning, etc. The property analysis for different levels of decomposition is also presented, and the inheritance of properties between levels is defined. All possible task sequences could be found using a search algorithm based on feasible system states. The shortest sequence may be chosen from the lowest level decomposition and is guaranteed to be the optimal output of the hierarchical planning system to efficiently implement the desired tasks.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Continuous affinity-based selection: rapid screening and simultaneous amplification of bacterial surface-display libraries (2001)

A new method for continuous biopanning has been developed. We have combined the power of affinity chromatography with the fecundity of bacteria in a unique process that mimics clonal selection. Mixed populations of bacteria were applied to a fermenter containing the immobilized ligand of interest. Bacteria retained in this affinity fermenter were allowed to grow under continuous washout conditions, such that weakly bound organisms were selectively lost. Those initially rare founder bacteria expressing a receptor for the immobilized ligand (R+ve) were thus enriched and amplified simultaneously. From an initial culture containing 1 x 10(10) R-ve cells spiked with fewer than 30 R+ve bacteria (<1 in 10(8)), final ratios of R+ve/R-ve bacteria as high as 1 in 12 were observed, representing an enrichment factor of 55 million-fold. This technology has considerable potential for rapid screening of bacterial surface-display libraries and in facilitating directed-evolution studies.
SYNTHESIS AND BIOLOGICAL ACTIVITY OF 4′-<i>C</i>-HYDROXYMETHYL-2′-FLUORO- D-ARABINOFURANOSYLPURINE NUCLEOSIDES (2001)

A series of 4'-C-hydroxymethyl-2'-fluoro-D-arabinofuranosylpurine nucleosides was prepared and evaluated for cytotoxicity. The details of a convenient synthesis of the carbohydrate precursor 4-C-hydroxymethyl-3,5-di-O-benzoyl-2-fluoro-alpha-D-arabinofuranosyl bromide (13) are presented. Proof of the structure and configuration at all chiral centers of the sugars and the nucleosides were obtained by proton NMR. All five target nucleosides were evaluated for cytotoxicity in human tumor cell lines. The 4'-C-hydroxymethyl clofarabine analogue (16beta) showed slight cytotoxicity in CCRF-CEM leukemia cells.
Improved performance of optical phased arrays assisted by transparent graphene nanoheaters and air trenches (2018)

In this paper, high-performance optical phased arrays (OPAs) assisted by transparent graphene nanoheaters and air trenches have been designed and simulated. By directly locating graphene nanoheaters on silicon waveguides, heating efficiency is enhanced by 62.96% compared to conventional structures with 1 μm SiO<sub>2</sub> overlays, and is further enhanced by a factor of 200% by the presence of air trenches. Thanks to the high thermal conductivity of graphene, a record-high operation speed on the order of 200 kHz is realized. Power consumption for π phase shift is 4.65 mW, approximately half of that of the state-of-the-art OPAs. By introducing air trenches, thermal crosstalk is significantly reduced, resulting in an enlarged fill factor. In addition, a novel beam steering scheme in the <i>θ</i> direction is proposed. By applying a 30 mW heating power, a temperature gradient along antennas is generated and beam steering of 2.3° is achieved, satisfying applications such as long-range collision avoidance for autonomous driving.
Reversible Data Hiding in Encrypted JPEG Bitstream (2014)

This correspondence proposes a framework of reversible data hiding (RDH) in an encrypted JPEG bitstream. Unlike existing RDH methods for encrypted spatial-domain images, the proposed method aims at encrypting a JPEG bitstream into a properly organized structure, and embedding a secret message into the encrypted bitstream by slightly modifying the JPEG stream. We identify usable bits suitable for data hiding so that the encrypted bitstream carrying secret data can be correctly decoded. The secret message bits are encoded with error correction codes to achieve a perfect data extraction and image recovery. The encryption and embedding are controlled by encryption and embedding keys respectively. If a receiver has both keys, the secret bits can be extracted by analyzing the blocking artifacts of the neighboring blocks, and the original bitstream perfectly recovered. In case the receiver only has the encryption key, he/she can still decode the bitstream to obtain the image with good quality without extracting the hidden data.
Activation of hageman factor by collagen (1968)

Purified acid-soluble and insoluble human collagen accelerated the clotting of plateletpoor plasma in silicone-treated tubes. The clot-promoting effect did not appear to be due to thromboplastic activity since the collagen preparations did not activate factor X in the presence of factor VII and calcium. Instead, collagen appeared to accelerate clotting by activating Hageman factor (factor XII) on the basis of the following findings: collagen increased the clot-promoting activity of partially purified Hageman factor but exerted no further effect in the presence of kaolin, a known activator of Hageman factor; clot-promoting eluates were obtained from collagen exposed to normal, hemophilic, or PTC-deficient plasma but not from collagen exposed to Hageman or PTA-deficient plasma. The collagen molecule itself appeared to be required for the clot-promoting activity since digestion with collagenase or thermal denaturation at pH 2.5 (about 35 degrees C) resulted in very marked reduction in clot-promoting activity. Since thermal denaturation is associated with transformation of collagen structure from triple helical to random coil form, it is suggested that the native form of collagen is essential for the ability to activate Hageman factor. Blockage of the free amino groups by treatment with nitrous acid or dinitrofluorobenzene only slightly reduced the clot-promoting activity of collagen. In contrast, since addition of cationic proteins to collagen markedly reduced pro-coagulant activity it is suggested that negatively charged sites on the collagen molecule are critical for Hageman factor activation. This suggestion is supported by the finding that pepsin treatment of collagen, which removes the predominantly negatively charged telopeptides, results in significant decrease in coagulant activity. Esterification of collagen, which neutralizes 80-90% of the free carboxyl groups, reduced coagulant activity by over 90% and it is suggested that the free carboxyl groups of glutamic and aspartic acids provide the negatively charged sites critical for Hageman factor activation.
Hydroxylapatite Ossicular Replacement Prostheses: A Four‐Year Experience (1992)

Between 1987 and 1991, I have used 215 hydroxylapatite middle ear implants, in various styles, for hearing reconstruction. The first such implants were composed entirely of hydroxylapatite. Because of intraoperative difficulties in shaping and trimming these prostheses, hybrid prostheses using Plasti-Pore were developed. For each of four implant designs (incus, incus-stapes, PORP, and TORP), the head is constructed from hydroxylapatite and the shaft from Plasti-Pore. Extrusion rate for the hybrid prostheses is low (4.3%). Hearing results from 47 patients with the hybrid hydroxylapatite prostheses, 140 patients with total hydroxylapatite prostheses, and 75 control group patients with homograft bone or Plasti-Pore prostheses were compared. A "successful" hearing result was achieved in 51.1%, 51.4%, and 60.0% of the three groups, respectively. Surgical technique for use of the new hybrid hydroxylapatite prostheses is described.
First Precise Spaceborne Sea Surface Altimetry With GNSS Reflected Signals (2019)

The precision of sea surface altimetry using bistatically reflected signals of the Global Navigation Satellite System (GNSS) is typically one to two orders of magnitude worse than dedicated radar altimeters. However, when the scattering is coherent, the electromagnetic phase of the carrier signal can be tracked, providing precise ranging measurements. Under grazing angle (GA) geometries, the conditions for coherent scattering are maximized, enabling carrier phase-delay altimetric techniques over sea waters. This work presents the first implementation of GA carrier phase sea surface altimetry using data acquired from a spaceborne platform (NASA Cyclone GNSS mission) and transmitted from both GPS and Galileo constellations. The altimetric results show that the measurement system precision is 3/4.1 cm (median/mean) at 20 Hz sampling, cm level at 1 Hz, comparable to dedicated radar altimeters. The combined precision, including systematic errors, is 16/20 cm (median/mean) precision at 50 ms integration (a few cm level at 1 Hz). The wind and wave requirements to enable coherent scattering at GA geometries appear to be below 6 m/s wind and 1.5 m significant wave height, although only 33% of tracks under these conditions present sufficient coherence. Given that this technique could be implemented by firmware updates of existing GNSS radio occultation missions, and given the large number of such missions, the study indicates that the resulting precision and spatio-temporal resolution would contribute to resolving some submesoscale ocean signals.
Microbial degradation of validamycin A by Flavobacterium saccharophilum. Enzymatic cleavage of C-N linkage in validoxylamine A. (1984)

The enzymatic cleavage of C-N linkage in the degradation of validamycin A by Flavobacterium saccharophilum was examined using N-p-nitrophenyl derivatives of validamine and valienamine as synthetic model substrates for validoxylamine A. Incubation of N-p-nitrophenylvalidamine with the membrane fraction from the organism led to formation of N-p-nitrophenyl-3-ketovalidamine, and succeeding cleavage of C-N linkage. As the products of the cleavage step, one was identified as p-nitroaniline and another keto compound could not be purified enough because of its instability. However, on the basis of its hydrogenation products, the structure of the keto compound could be established as 5D-(5/6)-5-C-(hydroxy-methyl)-2,6-dihydroxy-2-cyclohexen-1-one. The same experiment was carried out with N-p-nitrophenylvalienamine. In this case, N-p-nitrophenyl-3-ketovalienamine could be isolated as an intermediate but the desired keto compound from the cleavage step could not be isolated because of its instability. The participation of two enzymes, that is, a dehydrogenase and a C-N lyase on the cleavage of C-N linkage was assured, and moreover, the analysis of its products, together with those of the previous studies allow us to propose a degradation pathway of validamycin A by Flavobacterium saccharophilum.
Single-cell sequencing of neonatal uterus reveals an Misr2+ endometrial progenitor indispensable for fertility (2019)

The Mullerian ducts are the anlagen of the female reproductive tract, which regress in the male fetus in response to MIS. This process is driven by subluminal mesenchymal cells expressing Misr2, which trigger the regression of the adjacent Mullerian ductal epithelium. In females, these Misr2+ cells are retained, yet their contribution to the development of the uterus remains unknown. Here, we report that subluminal Misr2+ cells persist postnatally in the uterus of rodents, but recede by week 37 of gestation in humans. Using single-cell RNA sequencing, we demonstrate that ectopic postnatal MIS administration inhibits these cells and prevents the formation of endometrial stroma in rodents, suggesting a progenitor function. Exposure to MIS during the first six days of life, by inhibiting specification of the stroma, dysregulates paracrine signals necessary for uterine development, eventually resulting in apoptosis of the Misr2+ cells, uterine hypoplasia, and complete infertility in the adult female.
Ventriculoperitoneal Shunt Flow Dependency on the Number of Patent Holes in a Ventricular Catheter (2000)

Minimally invasive recanalization of obstructed ventricular catheters is a new treatment modality currently under investigation. It has been shown that blocked ventricular catheters can be at least partly reopened with ultrasonic cavitation, fiberoptic delivery of laser energy and electrocautery. It is not known, however, how many of the holes must be reopened in order to establish acceptable pressure-flow characteristics. In this study, the pressure-flow relationship of partially obstructed ventricular catheters was determined using experimental and electrical circuit/computer models. It has been demonstrated in all cases that an additional pressure of no more than 0.5 cm of water is generated when only a single 500-microm-diameter hole in the ventricular catheter permits flow. Partial recanalization of a ventricular catheter provides acceptable CSF hydrodynamics.
Phenotypic alterations and component analysis of seed yield in transgenic <i>Brassica napus</i> plants expressing the <i>tzs</i> gene (1998)

Cytokinins play an important role in plant development. We investigated the possibility that the nopaline Ti plasmid gene ( tzs ) from Agrobacterium tumefaciens could encode a protein able to participate in plant cytokinin production and lead to alterations in plant phenotype as a result of the expression of endogenous tzs . tzs was placed under the control of a heat‐inducible promoter from the Zea mays hsp70 gene. The expression of this fused gene was examined in transgenic Brassica napus plants. The tzs gene, which encodes the enzyme dimethylallyl transferase, was used as a cytokinin biosynthetic gene. The expression of the tzs gene was monitored by RNA hybridization and analysis of cytokinin content. Overproduction of cytokinin was observed even when the plants had not been heat‐shocked, and the plants displayed a reduced root system, increased height and branching, and delayed flowering. In addition, a significant increase in seed yield was observed in the transgenic plants, accounted for by increased number of seeds per silique and seed weight. The results suggest that increased levels of cytokinins, through the expression of tzs , are correlated with growth rather than with differentiation processes.
Secretory immune responses in human kidneys. (1986)

The secretory immune system has been well studied in the intestinal, bronchial, and biliary systems and breast. Tissue studies of secretory immunoglobulins in the kidney are scanty, mostly related to nephropathies with IgA. Renal tissues from 37 autopsies selected for any history of renal dysfunction were processed for immunohistologic studies on frozen sections with several antisera, including a purified rabbit anti-human secretory component (SC). By immunohistology, gel diffusion, and immunoblotting, the anti-SC antibody reacted appropriately with purified human SC, saliva, intestinal epithelium, and breast milk and did not cross-react with immunoglobulin heavy or light chains, lactoferrin, and other tissue proteins. IgA and SC were seen in tubular casts in 70% of patients, whereas less impressive staining with IgM, IgG, and albumin was seen, respectively, in 24%, 13%, and 22% of the patients. SC was present in the cytoplasm of distal tubule and Henle's loop cells in 78% of specimens. A control group of 10 healthy individuals who died suddenly showed minimal staining of casts and tubules in 2 specimens. Renal pathology in the group with IgA-SC+ casts included acute tubular necrosis (54%), severe chronic renal disease (61%), and mild chronic renal injury (38%). The group with negative IgA-SC casts included acute tubular necrosis (64%), infectious interstitial nephritis (36%), and negligible renal disease (36%). This study suggests that discrete distal segments of the nephron may have the capability of secreting SC, which is probably coupled with serum-derived IgA and incorporated into luminal tubular secretions. The low level of immunosecretions in kidneys which are normal or minimally damaged suggests that this system may need to be turned on by unknown, probably pathogenic stimulating factors.
Guidelines for the Use of Extensible Markup Language (XML) within IETF Protocols (2003)

The Extensible Markup Language (XML) is a framework for structuring data. While it evolved from Standard Generalized Markup Language (SGML) -- a markup language primarily focused on structuring documents -- XML has evolved to be a widely-used mechanism for representing structured data.
Designing Physics Game to Support Inquiry Learning and to Promote Retrieval Practice (2014)

Abstract: Instruction in physics aims at achieving two goals: the acquisition of body of knowledge and problem solving skills in physics. This requires students to connect physical phenomena, physics principles, and physics sym-bols. Computer simulation provides students with graphical model that unites phenomenon and principles in physics. However, such minimally guided approach may harm learning since it overburdens the working mem-ory. Also, simulation is inadequate in promoting problem solving skills since students need to exercise with a variety of physics problems. Intelligent tutoring systems (ITS), in contrast, train students in solving physics problems. In this paper, we designed an online puzzle game in physics that combines simulation and pseudo-tutor (namely QTut). We addressed three challenges: extensibility, scalability, and reusability in designing our game. We conducted usability tests with 10 participants on the game prototype to study the user performances and perceptions for improvement. The results indicate the game as educative and moderately entertaining. The use of scaffolding in the game positively contributed to the game learning experience. Moreover, the game GUI expressed information well that made the game understandable, even with little instructions. 1