gebhart/patrepeval huggingface dataset:
Micromachining Microcarrier-Based Biomolecular Encoding for Miniaturized and Multiplexed Immunoassay (2003)

Micromachining techniques, which originated in the microelectronics industry, have been employed to manufacture microparticles bearing an engraved dot-type signature for biomolecular encoding. These metallic microstructures are photolithographically defined and manufactured in a highly reproducible manner. In addition, the code introduced on the particle face is a straightforward visible feature that is easily recognizable with the use of optical microscopy. The number of distinct codes theoretically could be many thousands, depending on the coding element numbers. Such microparticles are, thus, with appropriate surface organic functionalizations, ideal for encoding biomolecular libraries and serving as a platform for developing high-throughput multiplexed bioassay schemes based on suspension array technology. As proof of this statement, we demonstrated that encoded microparticles tagged with antibodies to human immunoglobulin classes are capable, using imaging detection as the interrogating approach, of high sensitivity and high specificity, as well as multiplexed detection of the respective antigens in a microliter-sample volume.
The efficacy and safety of fasciectomy and fasciotomy for Dupuytren’s contracture in European patients: a structured review of published studies (2011)

A structured review of published papers was done to assess the efficacy and safety of fasciectomy and fasciotomy in European patients with Dupuytren's contracture. The outcomes varied across 48 studies. For fasciectomy, outcomes and results were as follows: the proportions of patients with a 100% correction in contracture angle ranged from 61 to 97%, the mean improvement in contracture angle ranged from 58 to 79%, and cases judged excellent/good ranged from 63 to 90%. Fasciotomy had similar outcomes, with a mean improvement in contracture angle ranging from 46 to 88%. Immediate failures upon recovery were reported for both procedures. The average recurrence rates were 39% after a fasciectomy and 62% after a fasciotomy at a median time of about 4 years. Overall, about 20% of fasciectomy and fasciotomy patients experienced an adverse event. In summary, postoperative outcomes were successful, but surgical complications were common and recurrence of a contracture was likely within a few years.
An Attempt to Make Platelet Rich Fibrin from Bone Marrow Aspirate (2017)

PRF can be made from bone marrow aspirate by adding anti-coagulant in aspiration and reversed with calcium chloride just before centrifugation.
A Lazy Concurrent List-Based Set Algorithm (2007)

We present a novel “lazy” list-based implementation of a concurrent set object. It is based on an optimistic locking scheme for inserts and removes and includes a simple wait-free membership test. Our algorithm improves on the performance of all previous such algorithms.
Fluorescein-labeled Tyramide Strongly Enhances the Detection of Low Bromodeoxyuridine Incorporation Levels (1997)

Immunocytochemical detection of bromodeoxyuridine (BrdU) labeling can be hampered by low BrdU incorporation levels. We describe here an amplification method for weak BrdU immunosignals. The tyramide signal amplification method based on catalyzed reporter deposition (CARD) uses fluorescein-labeled tyramide as a substrate for horseradish peroxidase. The enzyme catalyzes the formation of highly reactive tyramide radicals with a very short half-life, resulting in the binding of fluorescein-conjugated tyramide only at the site of the enzymatic reaction. MCF-7 cells were grown in vitro in medium containing charcoal-stripped fetal bovine serum supplemented by growth factors. Under these culture conditions, the BrdU immunosignal was hard to detect but could be enhanced specifically by the tyramide signal amplification system, resulting in clear-cut differences between BrdU-negative and BrdU-positive cells. This enabled rapid and objective quantification of the BrdU labeling index without the risk of underestimating the number of cells in S-phase. Therefore, this amplification of BrdU immunosignals might also prove valuable for in vivo cancer prognosis, cell kinetics studies, and computer-assisted image analyses.
Total variation image restoration: numerical methods and extensions (2002)

We describe some numerical techniques for the total variation image restoration method, namely a primal-dual linearization for the Euler-Lagrange equations and some preconditioning issues. We also highlight extension of this technique to color images, blind deconvolution and the staircasing effect.
Nonconstrained total elbow arthroplasty. (1983)

Thirty capitellocondylar unhinged implant arthroplasties were performed on 27 patients during the period from October 1976 through June 1981. The average patient age was 59.4 years, with a preoperative diagnosis of rheumatoid arthritis in 28 elbows and osteoarthritis in two elbows. Follow-up periods averaged 39.9 months (range, 10-62 months). The indication for elbow arthroplasty were intractable pain, joint instability, failed synovectomy, or bilateral limitation of motion. Ranged of motion evaluations showed moderate increases in flexion, pronation and supination after operation, although there was no significant improvement in extension. Ewald functional evaluation scores improved significantly from the mean of eight points prior to operation to the postoperative mean of 85 points. The significant complications occurring were deep wound infections, necessitating removal of the prosthesis (6.6%), and subluxation (13.2%), which responded to conservative treatment by long-arm casting. One patient required reconstruction of the medial collateral ligament for subluxation. Ulnar nerve paresthesia developed in 10% of the patients. One patient required neurolysis and transposition of the nerve for relief of symptoms. The posterolateral approach was adopted to reduce the incidence of ulnar nerve complications.
Metal–semiconductor junctions on <i>p</i>-type strained Si1−<i>x</i>Ge<i>x</i> layers (1996)

The electrical properties of Schottky junctions on high-quality p-type strained Si1−xGex layers have been studied for Ge fractions 0≤x≤0.24. A multicrystal high-resolution x-ray diffractometer was used to investigate the sample’s quality and the strain state and to accurately determine the Ge fraction in the fabricated devices. Several different metals, having a wide range of barrier heights, were used to reach conclusions on the variation of barrier height with the Ge content in the grown strained Si1−xGex layers. It has been found that the Schottky barrier height decreases with increasing Ge fraction in the Si1−xGex layer for the different metals investigated. The change in the barrier height with x has been found to be directly correlated to the valence band discontinuity in the Si/Si1−xGex heterojunction.
High-power diode-laser-pumped CW solid-state lasers using stable-unstable resonators (1997)

We present a novel design for an efficient, high power (>100 W), continuous-wave (CW) Nd:YAG laser with diffraction-limited performance. It uses side-pumped, sidecooled, zigzag slab which is incorporated in a stable-unstable resonator that has a variable reflectivity output coupler. A geometric magnification of at least 1.3 in the unstable direction can be achieved. Modeled performance characteristics are presented.
Mg doping of InP and InGaAs grown by metalorganic molecular beam epitaxy using bis-cyclopentadienyl magnesium (1993)

We have investigated the feasibility of Mg doping using bis-cyclopentadienyl magnesium (Cp2Mg) during growth of InP and InGaAs by metalorganic molecular beam epitaxy. In InP, hole concentrations between 5×1016 and 4×1018 cm−3 were readily attained without degradation of the surface morphology. Comparison with secondary ion mass spectrometry analysis shows good electrical activation for concentrations ≤2×1018 cm−3 though compensation at low doping levels was observed due to compensation from carbon and oxygen impurities which were present at levels of 9×1016 and 5×1016 cm−3, respectively. Mg profiles in InGaAs tended to be more abrupt than those in InP and hole concentrations up to 1019 cm−3 were achieved. p-InGaAs/n-InP structures annealed at 600 °C for 10 s showed no evidence of Mg diffusion.
Stabilization of Metal−Organic Frameworks with High Surface Areas by the Incorporation of Mesocavities with Microwindows (2009)

Reactions between two novel hexatopic carboxylate ligands and copper salts give rise to two isostructural metal-organic frameworks (MOFs) with a (3,24)-connected network topology containing both micro- and mesocavities with sizes of up to 3 nm. Both frameworks retain their porosity after guest-molecule removal, leading to high surface areas. Constructing MOFs containing mesocavities with microwindows may serve as a general approach toward stable MOFs with high surface areas.
A criterion for vortex breakdown (1987)

A criterion for the onset of vortex breakdown over a wide range of the Reynolds number is proposed. Based upon previous experimental, theoretical, and numerical studies, as well as a new numerical study, an appropriately defined local Rossby number is used to delineate the region where breakdown occurs. Comparisons are made with previously suggested criticality parameters and the unique features of the proposed Rossby number parameter are shown. A number of previous theoretical studies concentrating on inviscid standing-wave analyses for trailing wing-tip vortices are reviewed and reinterpreted, along with the previous numerical and experimental studies, in terms of the Rossby number parameter. For the case of trailing wing-tip-type vortices, it is shown that previous numerical studies were performed at lower Reynolds numbers than the corresponding laboratory experiments. Utilizing a consistently defined Reynolds number, Rossby number–Reynolds number plots of these previous vortex breakdown studies, for both trailing wing-tip and leading-edge vortices, are obtained. A criticality condition is identified for both types of vortices.
Low-Temperature Hot Corrosion in the Refining Industry (2011)

Abstract Hot corrosion is an accelerated degradation (oxidation and/or sulfidation) of metals and alloys in the presence of liquid melts of salts and/or oxides. It’s generally divided into two forms: Type I and Type II. Type I hot corrosion usually occurs at 850- 950 °C (1550-1750 °F), and it is also known as high-temperature hot corrosion. Type II hot corrosion occurs at 600-800 °C (1112-1472 °F). Type II hot corrosion is also called low-temperature hot corrosion. It may take the form of fuel-ash or oil-ash corrosion in refinery heater fire side tube surfaces as the result of fuel impurities. Another potential location for Type II hot corrosion is FCCU regenerators, where the operating temperatures are normally in the range of 650 to 788 °C (1200 to 1450 °F). The mechanisms and characteristics of Type II hot corrosion will be presented. The analytical methods and mitigation strategies for Type II hot corrosion will also be discussed.
Performance Comparison of Downlink Multiuser MIMO-OFDMA and MIMO-MC-CDMA with Transmit Side Information - Multi-Cell Analysis (2007)

Orthogonal frequency division multiple access (OFDMA) and multicarrier code division multiple access (MC-CDMA) have recently drawn much attention for being potential candidates of future generation cellular systems. In single-cell scenario, while MC-CDMA is good at achieving frequency diversity when there is no channel state information available at the transmit side (CSIT), OFDMA achieves higher capacity than MC-CDMA due to its finer resolution in exploiting multiuser diversity with CSIT. Whether multiple-input-multiple-output (MIMO) MC-CDMA or OFDMA is a better option in multi-cell system remains unjustified in the literature. In this paper, we study the ergodic capacity and the goodput of MIMO-MC-CDMA and MIMO-OFDMA downlink systems with CSIT in multi-cell scenario assuming that the base station has the knowledge of the average inter-cell interference level only. Several types of users modeling different interference patterns are considered: (I) high data rate delay-insensitive users, (II) high data rate delay-sensitive .users, and (III) voice users (low data rate and bursty). Optimal resource allocation algorithms are used to compute the capacities of the systems, while a simple heuristic is used to obtain the achievable goodputs for both systems. The effects of path loss, number of antennas and different user types are studied and insightful results are obtained. We find that OFDMA has a higher system goodput for both Type I and Type II high data rate users, while MC-CDMA has a higher goodput for Type III users. Compared to MC-CDMA, the goodput of an OFDMA system is more sensitive to the activity factor of the voice users and suffers from noticeable loss. This demonstrates the superiority of the two systems in different practical situations.
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences (2006)

In 2001 and 2002, we published two papers (Bioinformatics, 17, 282-283, Bioinformatics, 18, 77-82) describing an ultrafast protein sequence clustering program called cd-hit. This program can efficiently cluster a huge protein database with millions of sequences. However, the applications of the underlying algorithm are not limited to only protein sequences clustering, here we present several new programs using the same algorithm including cd-hit-2d, cd-hit-est and cd-hit-est-2d. Cd-hit-2d compares two protein datasets and reports similar matches between them; cd-hit-est clusters a DNA/RNA sequence database and cd-hit-est-2d compares two nucleotide datasets. All these programs can handle huge datasets with millions of sequences and can be hundreds of times faster than methods based on the popular sequence comparison and database search tools, such as BLAST.
<title>Efficient interactive image retrieval with multiple seed images</title> (1998)

An interactive image query system based on multiple seed images is proposed in this work. With this proposed system, the query can be refined so that the meaning of similarity becomes clear along the query process. A particular way to achieve interactive query is implemented, i.e. adaptive filtering with multiple low-level indexing features based on user's feedback. The proposed query system consists of the following building blocks. First, browsing, image sketching and feature editing are employed for query formation input. The combination of the three methods provides high flexibility for users to get desired query images. In the system, images can also be selected from the candidate image set. By using a query set composed of multiple seed images instead of a single image, we can improve the query performance with more accurate similarity information. Two key procedures, initial guess and further refinement, are utilized to achieve high efficient query. At the initial stage, we try to expand the candidate image set to include as many features as possible. In the refinement process, users are able to initiate a more complex filtering strategy by using the feedback. The relative weighting of different features is further decided. Extensive examples are used to illustrate the proposed interactive query process and the corresponding retrieval performance.
Hepatic Accumulation and Intracellular Binding of Conjugated Bilirubin (1978)

A B S T R A C T After the intravenous injection of un- conjugated [3H]bilirubin into normal Sprague-Dawley and Wistar R rats, radiolabeled bile pigments rapidly accumulated in the liver. By 1.5 min after injection, an average of 36% of the injected isotope was present in liver homogenates. Between 3 and 15 min, 37-64%
Activity of nucleic acid polymers in rodent models of HBV infection (2017)

Nucleic acid polymers (NAPs) block the release of HBsAg from infected hepatocytes. These compounds have been previously shown to have the unique ability to eliminate serum surface antigen in DHBV-infected Pekin ducks and achieve multilog reduction of HBsAg or HBsAg loss in patients with chronic HBV infection and HBV/HDV coinfection. In ducks and humans, the blockage of HBsAg release by NAPs occurs by the selective targeting of the assembly and/or secretion of subviral particles (SVPs). The clinically active NAP species REP 2055 and REP 2139 were investigated in other relevant animal models of HBV infection including woodchucks chronically infected with WHV, HBV transgenic mice and HBV infected SCID-Hu mice. The liver accumulation of REP 2139 in woodchucks following subcutaneous administration was examined and was found to be similar to that observed in mice and ducks. However, in woodchucks, NAP treatment was associated with only mild (36-79% relative to baseline) reductions in WHsAg (4/10 animals) after 3-5 weeks of treatment without changes in serum WHV DNA. In HBV infected SCID-Hu mice, REP 2055 treatment was not associated with any reduction of HBsAg, HBeAg or HBV DNA in the serum after 28 days of treatment. In HBV transgenic mice, no reductions in serum HBsAg were observed with REP 2139 with up to 12 weeks of treatment. In conclusion, the antiviral effects of NAPs in DHBV infected ducks and patients with chronic HBV infection were weak or absent in woodchuck and mouse models despite similar liver accumulation of NAPs in all these species, suggesting that the mechanisms of SVP assembly and or secretion present in rodent models differs from that in DHBV and chronic HBV infections.
Meat Quality Attributes of broilers supplemented with Herbal Toxin binder Product (2009)

Raw and cooked meat quality is of immense consideration to consumers in present scenario. A study was conducted in 50 unsexed day old broiler chicks with an aim to assess effect of herbal toxin binder product on meat quality attributes. Chicks were randomly divided into two groups. Group I was untreated control (G1), while G2 was given treatment with herbal toxin binder (Toxiroak) @1.5 Kg / tonne of feed (supplied by Ayurvet Ltd. Baddi, India). Carcass quality traits, raw and cooked meat quality attributes, organoleptic characteristics of cooked meat and proximate analysis of raw and cooked meat were studies at the end of 6 week experimental trial by slaughtering the birds of both the groups. Supplementation of herbal toxin binder product in basal diet is efficacious in improving overall meat quality attributes such as carcass yield, dressing %, giblet yield, fillet and tender yield, sensory raw meat characteristics, organoleptic cooked meat parameters, overall palatability and acceptability of meat. The product doesn't have any residual or adverse effect on raw, eating and cooking quality of meat & hence is safe for usage.
Identification and Quantification of Toxic Chemicals by Use of <i>Escherichia coli</i> Carrying <i>lux</i> Genes Fused to Stress Promoters (1998)

The luxCDABE bioluminescence genes of the Vibrio fischeri lux system have been used as a reporter system for different stress and regulatory promoters of Escherichia coli. Selected E. coli strains carrying lux genes fused to different promoters were exposed to various toxic chemicals, and the recorded luminescence was used for the characterization of the biologic signature of each compound. Analysis of these data with the aid of a proper algorithm allowed quantitative and qualitative assessment of toxic chemicals. Of the 25 tested chemicals, 23 were identified by this novel strategy in a 3-h procedure. This system can also be adapted for the identification of simple mixtures of toxic agents when the biologic signatures of the individual compounds are known. This biologic recognition strategy also provides a tool for evaluating the degree of similarity between the modes of action of different toxic agents.
A Continuum of Cell States Spans Pluripotency and Lineage Commitment in Human Embryonic Stem Cells (2009)

These findings on gene expression in single embryonic stem cells are in concert with recent studies of early mammalian development, which reveal molecular heterogeneity and a stochasticity of gene expression in blastomeres. Our work indicates that only a small fraction of the population resides at the top of the hierarchy, that lineage priming (co-expression of stem cell and lineage specific genes) characterizes pluripotent stem cell populations, and that extrinsic signaling pathways are upstream of transcription factor networks that control pluripotency.
Thermally induced Zr incorporation into Si from zirconium silicate thin films (2001)

Monochromatic x-ray photoelectron spectroscopy, time-of-flight secondary ion mass spectrometry, and Rutherford backscattering spectrometry are used to study the outdiffusion of Zr from the alternate gate dielectric candidate ZrSixOy thin films deposited on Si(100). We find that Zr incorporation into Si from ZrSixOy appears to occur at annealing temperatures higher than 1000 °C. Incorporation of Zr to depths of up to 23 nm into the silicon substrate is observed. A diffusion coefficient of D0∼2×10−15 cm2/s is estimated from the associated depth profiles.
Purification and some properties of soybean saponin hydrolase from Aspergillus oryzae KO-2. (1991)

We had investigated the enzymatic hydrolysis of soybean saponins and selected soybean saponin hydrolase from Aspergillus oryzae KO-2. We attempted purification of this enzyme for further characterization. This enzyme was purified 1500-fold using ammonium sulfate fractionation and Sephadex G-200 gel filtrations. The enzyme was electrophoretically homogeneous and a glycoprotein by PAS staining. By gel filtration, the molecular weight of enzyme was 158, 000 and SDS-PAGE showed the enzyme to have a tetrameric structure composed of heterogeneous subunits of 35, 000 and 45, 000. The enzyme activity was stable at temperatures below 40°C and stable from pH 5.0 to 8.0. The optimum pH was pH 4.5 to 5.0 and the optimum temperature was 50°C. The Km and Vmax for soyasaponin I were 0.48 mM and 9.8 μmol/hr mg protein, respectively. After hydrolysis with the enzyme, soyasapogenol B and α-L-rhamnopyranosyl (1→2)-β-D-galactopyranosyl (l→2)-D-glucuronopyranoside were released from soyasaponin I.