gebhart/patrepeval huggingface dataset:
Metal-binding proteins for the detection of heavy metals in aquatic organisms (1988)

This presentation will focus on the potential in aquatic organisms for metal-binding proteins and peptides (BP), which are analogous to metallothionein, to serve as biomarkers. The discussion will focus on research from the authors laboratories on the presence, nature, and chemical and biological properties of Cd, Zn, and Cu-binding molecules which illustrate some of the issues involved in their use as sentinals of environmental heavy metal contamination. Freshwater fishes have very large concentrations of Zn, Cu-BPs, which, presumably, are involved in the normal metabolism of these metals. As with metallothionein, an integrated functional understanding of the role of BP in cellular activities is lacking. It is in this setting that exposure to heavy metals will be considered.
Non-transferrin-bound iron in plasma or serum from patients with idiopathic hemochromatosis (1989)

The nature of non-transferrin-bound iron in the plasma or serum of iron-overloaded hemochromatosis patients was studied by high performance liquid chromatography (HPLC) and high resolution nuclear magnetic resonance (NMR). 500-MHz proton Hahn spin-echo NMR spectra of plasma or serum, combined with the use of the iron chelator desferrioxamine, suggests complexation of iron ions with citrate and a possible involvement of acetate. Addition of FeCl3 to hemochromatosis samples broadened the NMR signals from citrate. HPLC analysis rigorously confirmed the presence of an iron-citrate complex in ultrafiltrates of plasma or serum studies with added FeCl3 or desferrioxamine supported this conclusion. It is proposed that non-transferrin-bound iron in the plasma of iron-overloaded patients exists largely as complexes with citrate and possibly also as ternary iron-citrate-acetate complexes. The presence of such complexes would account for the ability of non-transferrin-bound iron to be measurable by the bleomycin assay and for its rapid clearance from the circulation by the liver.
TIM1 (HAVCR1) Is Not Essential for Cellular Entry of Either Quasi-enveloped or Naked Hepatitis A Virions (2020)

ABSTRACT Receptor molecules play key roles in the cellular entry of picornaviruses, and TIM1 (HAVCR1) is widely accepted to be the receptor for hepatitis A virus (HAV), an unusual, hepatotropic human picornavirus. However, its identification as the hepatovirus receptor predated the discovery that hepatoviruses undergo nonlytic release from infected cells as membrane-cloaked, quasi-enveloped HAV (eHAV) virions that enter cells via a pathway distinct from naked, nonenveloped virions. We thus revisited the role of TIM1 in hepatovirus entry, examining both adherence and infection/replication in cells with clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-engineered TIM1 knockout. Cell culture-derived, gradient-purified eHAV bound Huh-7.5 human hepatoma cells less efficiently than naked HAV at 4°C, but eliminating TIM1 expression caused no difference in adherence of either form of HAV, nor any impact on infection and replication in these cells. In contrast, TIM1-deficient Vero cells showed a modest reduction in quasi-enveloped eHAV (but not naked HAV) attachment and replication. Thus, TIM1 facilitates quasi-enveloped eHAV entry in Vero cells, most likely by binding phosphatidylserine (PtdSer) residues on the eHAV membrane. Both Tim1 −/− Ifnar1 −/− and Tim4 −/− Ifnar1 −/− double-knockout mice were susceptible to infection upon intravenous challenge with infected liver homogenate, with fecal HAV shedding and serum alanine aminotransferase (ALT) elevations similar to those in Ifnar1 −/− mice. However, intrahepatic HAV RNA and ALT elevations were modestly reduced in Tim1 −/− Ifnar1 −/− mice compared to Ifnar1 −/− mice challenged with a lower titer of gradient-purified HAV or eHAV. We conclude that TIM1 is not an essential hepatovirus entry factor, although its PtdSer-binding activity may contribute to the spread of quasi-enveloped virus and liver injury in mice. IMPORTANCE T cell immunoglobulin and mucin-containing domain protein 1 (TIM1) was reported more than 2 decades ago to be an essential cellular receptor for hepatitis A virus (HAV), a picornavirus in the Hepatovirus genus, resulting in its designation as “hepatitis A virus cellular receptor 1” (HAVCR1) by the Human Genome Organization Gene Nomenclature Committee. However, recent studies have shown that HAV exists in nature as both naked, nonenveloped (HAV) virions and membrane-cloaked, quasi-enveloped infectious virus (eHAV), prompting us to revisit the role of TIM1 in viral entry. We show here that TIM1 (HAVCR1) is not an essential cellular receptor for HAV entry into cultured cells or required for viral replication and pathogenesis in permissive strains of mice, although it may facilitate early stages of infection by binding phosphatidylserine on the eHAV surface. This work thus corrects the published record and sets the stage for future efforts to identify specific hepatovirus entry factors.
Pulsed field gradients: a new tool for routine NMR (1998)

A complete review of 1D and 2D gradient-based NMR experiments published since 1990 is provided. The ease of implementation and the excellent and reproducible results obtained from such experiments offer a powerful tool for the study of molecular structures and dynamics. Thus, when sufficient sample concentration is available, ultra-clean spectra are obtained in very short acquisition times, making the experiments suitable for automated data acquisition. For these reasons, the concept of routine NMR work for chemists has been dramatically changed in the last few years and, with the correct choice of the experiments to be performed, a large number of chemical questions can be resolved in considerably reduced times. However, sensitivity and resolution are dependent on where the PFGs are incorporated into the pulse sequences and, therefore, these two important factors need to be considered in highly demanding applications. Illustrative examples of the most interesting applications to typical organic compounds are given. ©1998 John Wiley & Sons, Ltd.
Bifunctional RuII‐Complex‐Catalysed Tandem C−C Bond Formation: Efficient and Atom Economical Strategy for the Utilisation of Alcohols as Alkylating Agents (2016)

Catalytic activities of a series of functional bipyridine-based Ru<sup>II</sup> complexes in β-alkylation of secondary alcohols using primary alcohols were investigated. Bifunctional Ru<sup>II</sup> complex (3 a) bearing 6,6'-dihydroxy-2,2'-bipyridine (6DHBP) ligand exhibited the highest catalytic activity for this reaction. Using significantly lower catalyst loading (0.1 mol %) dehydrogenative carbon-carbon bond formation between numerous aromatic, aliphatic and heteroatom substituted alcohols were achieved with high selectivity. Notably, for the synthesis of β-alkylated secondary alcohols this protocol is a rare one-pot strategy using a metal-ligand cooperative Ru<sup>II</sup> system. Remarkably, complex 3 a demonstrated the highest reactivity compared to all the reported transition metal complexes in this reaction.
Investigations of Oil Combustion in the Race Way of the Blast Furnace (1974)

I n order to clarify the phenomenological challges in the blast furnace accollljlanied wilh the iruection of heavy oil through the tz!yeres, the reaction gas in th e race way was sampled by the li se of a hori~ontal jJl"obe and analysed. i n the case withollt oil irUection, the CO 2 content gradually increased with decreasing content of ox)'gen along Ihe inward direction, and the COli tents of co and H 2 increased in the region passed through the maximum point of CO 2 ' A s the injection rate of heavy oil increased, this trend was more intensified and it was accomplished in a shorter range.
Sessile Serrated Adenomas (2008)

Purpose: Hyperplastic polyps (HP) have usually been regarded as lesions with no malignant potential. However, a variant of HP with malignant potential called “sessile serrated polyp/adenoma (SSA)” is increasingly being recognized. Clinical characteristics of these polyps are not well known and there is no published practice guidelines regarding management of these polyps. We aimed to study demographic, clinical and endoscopic characteristics of patients with SSA. Methods: Patients with SSA were identified by review of the pathology data base of Mayo Clinic Arizona from 2005 to 2007. Patient charts were reviewed for data on demographics and colonoscopies. Data on endoscopic characteristics of polyps, polypectomy methods used, synchronous adenomatous polyps or cancers, complications from polypectomy were collected and analyzed. Results: Among patients undergoing colonoscopy, a total of 5991 patients were found to have polyps. Of these 171 (2.9%) patients had a total of 226 SSAs. Patients with SSAs were mostly white (164, 96%) with mean (SE) age of 65.9 (0.8) years. Ninety one patients were men (53%). The mean size of the SSAs were 8.1 (0.4) mm (range 2–40 mm); 42% were 5 mm or less in size and 69% were 9 mm or less in size. Fifty-one per cent of SSAs were located in the cecum or ascending colon. All SSAs were sessile or flat in appearance. The mean (SE) number of polyps per patient was 3 (range 1–24). Approximately half (87, 51%) of the patients had synchronous polyps of other histological types. The commonest type of associated pathology in these synchronous polyps were tubular adenoma in 62 (49%) polyps, tubulovillous adenoma in 13 (10%) polyps and hyperplastic polyps were present in 50 (40%) polyps. Interestingly, synchronous adenocarcinoma was present in 7 (4%) cases and all these cancers were present in the cecum or ascending colon. Ninety seven percent of polyps were removed by colonoscopy and 2.7% required surgical excision. There was no complication associated with endoscopic resection of these polyps. The histopathology was consistent with typical SSA in 184 polyps (81%); 6.6 and 12% polyps were reported to have mixed features with adenomatous or hyperplastic components, respectively. Conclusion: Among patients with colon polyps, 2.9% of patients found to have SSAs in our study population. Most of SSAs were located in the right side of the colon and were safely managed by colonoscopy. Synchronous lesions including adenomas and right sided colon cancers were not uncommon. Forty two percent of SSAs were less than 5 mm and 69% of SSAs were less than 9 mm in our study, and these polyps may not be detected or reported by CT colography.
A simple and sensitive method for determining reducing sugars in plant tissues. Application to quantify the sugar content in quinoa (Chenopodium quinoa Willd.) seedlings (1998)

A simple and sensitive method for the colorimetric determination of reducing sugars in plant materials is proposed. The procedure is based on reduction under alkaline conditions of potassium ferricyanide by the reducing groups of the carbohydrates, followed by colour development as the o-phenanthroline complex. All sugars tested produced an equal colour yield. The method proved to be reproducible and precise with a high degree of sensitivity which makes it possible to use with small sample quantities. The method is quick, easy and cheap, hence permiting its use in routine analysis. © 1998 John Wiley & Sons, Ltd.
Magnetic Field Orientation of Liquid Crystalline Epoxy Thermosets (1998)

The effect of magnetic fields on the orientation and properties of 4,4'-bis(2,3-epoxypropoxy)-alpha-methylstilbene cured with sulfanilamide has been studied. This epoxy system is initially isotropic and forms a smectic A phase upon curing. A magnetic field was applied during the cure reaction, resulting in alignment of the molecules along the direction of the applied field. Measurement of the orientation parameter of the fully cured material by wide-angle X-ray scattering (WAXS) showed that orientation improved with an increase in field strength. The orientation parameters of the smectic layer normals calculated from the inner reflection of the WAXS pattern attained a maximum level of approximately 0.8 at a field strength of approximately 12 T. The orientation parameters calculated from the outer reflection of the WAXS pattern were considerably lower, possibly due to the presence of amorphous regions associated with domain boundaries or the loss of molecular alignment within the smectic layers due to topological restrictions of the cross-linking sites. Orientation resulted in an anisotropic linear thermal expansion coefficient after curing, although the overall volumetric expansion was constant. The elastic tensile modulus increased with the square of the orientation parameter, attaining a maximum value of 8.1 GPa, compared to 3.1 GPa for the unoriented material. The change in modulus with orientation could be fit with a simple model for the modulus of anisotropic materials.
Two‐Photon Polymerization — A Versatile Microfabrication Tool (2016)

Abstract With additive manufacturing entering the consumer market and exciting the stock market, “3D printing” has become fashionable in society. Freedom in design as well as easy workflows are positive attributes associated with this umbrella terminology for a variety of fabrication techniques. 3D printing, or additive manufacturing, gives designers previously unknown flexibilities and eliminates one of the most cost‐, time‐ and labour‐intensive stages of the product development process in industrial manufacturing, the production of tools. 3D printing is more precise, faster and mostly less expensive than traditional forms of manufacturing, especially in respect of rapid prototyping of individual parts. 3D objects of almost any shape can be printed from a virtual model in a variety of materials.
Lightweight object specification with typestates (2005)

Previous work has proven typestates to be useful for modeling protocols in object-oriented languages. We build on this work by addressing substitutability of subtypes as well as improving precision and conciseness of specifications. We propose a specification technique for objects based on abstract states that incorporates state refinement, method refinement, and orthogonal state dimensions. Union and intersection types form the underlying semantics of method specifications. The approach guarantees substitutability and behavioral subtyping. We designed a dynamic analysis to check existing object-oriented software for protocol conformance and validated our approach by specifying two standard Java libraries. We provide preliminary evidence for the usefulness of our approach.
A TWT grid modulator for MTI radar transmitters (2002)

The design of HV (high-voltage) pulse circuitry using series connected HV MOSFETs is traced from the development of the basic switching module through integration into a TWT (traveling wave tube) modulator. The modulator deck floats at the -45.5 kV TWT cathode potential and supplies filament power and control grid pulses directly to dual TWTs. Prime power is 115 VAC, 70 Hz, single phase. Control signals, start and stop pulses and fault signals are transmitted via a multichannel fiber optic link. RF stability measurements made on the transmitter have confirmed the adequacy of the modulator design.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A METHOD TO IMPROVE THE SPATIAL RESOLUTION OF PHOTOSYNTHETIC RATES OBTAINED BY OXYGEN MICROSENSORS (1998)

To determine gross photosynthesis in benthic microalgal communities, oxygen microelectrodes were used to measure the rate of decrease within the first 4 s after extinction of light. Photosynthetic rates calculated from third‐order polynomial fits to the curve of decreasing O 2 concentration were compared to the rates obtained by the traditional method, where rates were estimated from linear regression. When photosynthesis was calculated for the fitted initial rates of O 2 decrease, maximum rates in microbial mats were up to 32% higher, and the depth‐integrated gross photosynthesis was 5%–10% higher than the rates determined by the traditional method. The determinations from fitted initial rates also resulted in a more detailed profile of photosynthetic rate than that normally obtained. Computer simulation based on diffusion models, where the estimated initial rates of O 2 decrease were assumed to represent actual photosynthesis rates, verified the validity of the curve‐fitting procedure for obtaining high‐resolution photosynthesis profiles.
A Software Implementation for a Hybrid Firewall Using Linux Netfilter (2010)

We are developing an embedded hybrid firewall prototype which combines an embedded CPU (MPC8260) with a specifically designed FPGA-based packet classification coprocessor. The packet header matching between the input packets and a pre-defined rule set is fully achieved by the hardware coprocessor on-line. The embedded CPU under Linux operation system takes charge of the remaining data-path processing and the management of the firewall, including receiving input packets, sending them to the coprocessor, forwarding the packet according to the classifying results from the coprocessor, and the rule set updating and management. After a brief introduction to our hybrid firewall, we will focus on the software implementation of the firewall. The Linux-2.4.4 has been ported into out system. By modifying the Linux kernel to utilize the hook functions of Linux net filter, input packets are intercepted and their headers are sent to the coprocessor meanwhile the packets are queued in a buffer until the classifying results come out from the coprocessor. A daemon process running at the embedded CPU was designed for updating the filter rule sets so that a remote computer as a client can visit the firewall and manipulate the running of the firewall. A simple demo program running on a PC (under windows OS) was also designed to demonstrate the proper operations of the firewall.
Carbon dioxide capture from flue gas using regenerable sodium-based sorbents (2003)

The overall objective of this project is to develop a simple and inexpensive process to separate carbon dioxide (CO2) as an essentially pure stream from a fossil fuel combustion gases using a regenerable sodium-based sorbent. This objective of this phase of the project is to evaluate CO2 capture using sodium-based sorbents in single-cycle and multicycle tests as a function of calcination and carbonation conditions. The sorbent precursors investigated were sodium bicarbonates supplied by Church and Dwight, Inc., and natural trona supplied by Solvay. All precursors were first calcined to sodium carbonate and then converted to sodium bicarbonate (NaHCO3) or Wegscheider’s salt (Na2CO3?NaHCO3) through reaction with carbon dioxide and water vapor. Both sodium bicarbonate and Wegscheider’s salt are regenerated to sodium carbonate when heated, producing a nearly pure CO2 stream after condensation of water vapor. An electrobalance reactor (thermogravimetric analyzer) and a fixed-bed reactor system were used to study the reaction rate and achievable sorbent capacity as a function of carbonation temperature, carbonation gas composition, and calcination temperature and atmosphere. Sorbent reproducibility and durability were studied in multi-cycle tests. Electrobalance tests show that sodium bicarbonate (SBC) samples had better performance than Trona samples. Lower carbonation temperature (60oC) and higher CO2/H2O concentrations resulted in faster reaction rate and larger sorbent capacity. More severe calcination conditions had a more significant negative effect on Trona than SBC sorbents. In addition, a small amount SO2 (<0.1%) resulted in a cumulative decrease in CO2 removal capacity with increasing carbonation cycle number. Results from 1.5-cycle fixed-bed reactor tests indicate that better CO2 removal efficiency for SBC-3 was achieved at a lower carbonation temperature of 60oC, where average prebreakthrough concentrations corresponded to approximately 75% CO2 removal. There was no obvious deterioration with cycle number. Instead, improved performance between cycle 1 and the remaining cycles was clear for SBC Grades 1 and 3 under the reaction conditions investigated. Prebreakthrough CO2 removal (at the third carbonation sample) increased from 63% in cycle 1 to about 90% for the remaining cycles at 60oC carbonation.
THE OPTICAL SPECTRUM OF THIOZONE S$_3$ AND OTHER SULFUR RICH SYSTEMS (2009)

J. R. Spencer, K. L. Jessup, M. A. McGrath, G. E. Ballester and R. Yelle, \textit{ScienceA. Mollet, E. Lellouch, R. Moreno, M. A. Gurwell and C. Moore, \textit{A\&amp;AP. Geissler, A. McEwen, C. Porco, D. Strobel, J. Saur, J. Ajello and R. West, \textit{Icarus
Impact of Early Feeding: Metagenomics Analysis of the Infant Gut Microbiome (2022)

Fecal samples analyzed from BF and FF infants demonstrated differences in microbiota genera. The BF cohort includes greater presence of beneficial genus <i>Bifidobacterium.</i> Several genes were identified as present at different abundances between cohorts indicating differences in functional pathways such as cellular defense mechanisms and carbohydrate metabolism influenced by feeding. Confirmation of gene level NGS data <i>via</i> PCR and electrophoresis analysis revealed distinct differences in gene abundances associated with important biologic pathways.
EVALUATION OF BONE GRAFT SUBSTITUTES FOR FEMORAL IMPACTION ALLOGRAFTING IN AN OVINE HEMIARTHROPLASTY MODEL (2005)

Introduction and Aims: The usefulness of bone graft substitutes and growth factors to promote bone graft incorporation and prosthesis fixation in hip replacement should be examined in a loaded model, as results from cortical defect models may not apply. This paper reviews the results of femoral impaction grafting using these materials in an ovine hip replacement model. Method: At cemented hemiarthroplasty, sheep femurs were impacted with allograft bone (control group n=23) or with allograft mixed with: 1) corglaes bioglass (n=12); 2) a synthetic hydroxyapatite (HA) (n=6) or the bone morpohogenetic protein OP-1 (n=6) (study groups) and implanted with a cemented double taper femoral stem. Sheep were sacrificed at between six and 26 weeks. The primary outcome was femoral stem subsidence, as determined more recently by the development of clinical radiostereometric analysis (RSA) in this model. Femoral fixation, as assessed by ex-vivo mechanical testing, and bone graft incorporation, as assessed by histological review and histoquantitation, were also key outcomes. Results: In the control groups, there was a consistent response with bone graft incorporation by new bone advancing proximal to distally in the femur and advancing from the endocortex towards the cement mantle. Mineralised bone apposition occurred by six weeks and this was preceeded by partial resorption of the graft. Complete graft incorporation, with subsequent remodelling of bone, was evident proximally by 26 weeks. Bone graft incorporation in femurs impacted with a 1:1 allograft: bioglass mix was minimal and there was often partial or complete resorption of the graft with replacement by fibrous tissue, resorption of endocortical bone and instability of the femoral prosthesis. Supplementation of allograft with OP-1 promotes initial graft resorption, thus hastening bone graft incorporation and remodelling but one case of stem subsidence, that may have been associated with early resorption seen in the OP-1 group, reinforces the need for further studies examining dose response. There was excellent incorporation of the allograft and HA, with new woven bone directly apposing the HA surface and integrated into the larger porous spaces of the HA. There was no adverse response to the HA and there was minimal to no subsidence of the stem at the cement-bone interface, as determined by RSA. Conclusion: This model is extremely valuable for investigating new biological approaches to reconstruction of major bone deficiency at revision hip replacement and demonstrates clear differences between materials used to supplement allograft, with HA and OP-1 giving encouraging results. RSA is an essential outcomes tool for this model.