gebhart/patrepeval huggingface dataset:
Genetic Identification of a Common Collagen Disease in Puerto Ricans via Identity-by-Descent Mapping in a Health System (2017)

Abstract Achieving confidence in the causality of a disease locus is a complex task that often requires supporting data from both statistical genetics and clinical genomics. Here we describe a combined approach to identify and characterize a genetic disorder that leverages distantly related patients in a health system and population-scale mapping. We utilize genomic data to uncover components of distant pedigrees, in the absence of recorded pedigree information, in the multi-ethnic Bio Me biobank in New York City. By linking to medical records, we discover a locus associated with genetic relatedness that also underlies extreme short stature. We link the gene, COL27A1 , with a little-known genetic disease, previously thought to be rare and recessive. We demonstrate that disease manifests in both heterozygotes and homozygotes, indicating a common collagen disorder impacting up to 2% of individuals of Puerto Rican ancestry, leading to a better understanding of the continuum of complex and Mendelian disease.
LC/MS-Based Global Metabolomic Identification of Serum Biomarkers Differentiating Hepatocellular Carcinoma from Chronic Hepatitis B and Liver Cirrhosis (2021)

Chronic hepatitis B virus (CHB) infection is one of the primary risk factors associated with the development of hepatocellular carcinoma (HCC). Despite having been extensively studied, diagnosing early-stage HCC remains challenging, and diagnosed patients have a poor (3-5%) survival rate. Identifying new approaches to detect changes in the serum metabolic profiles of patients with CHB and liver cirrhosis (LC) may provide a valuable approach to better detect HCC at an early stage when it is still amenable to treatment, thereby improving patient prognosis and survival. In the present study, we, therefore, employed a liquid chromatography-mass spectrometry (LC-MS)-based approach to evaluate the serum metabolic profiles of 30 CHB patients, 29 LC patients, and 30 HCC patients. We then employed appropriate statistical methods to identify those metabolites that were best able to distinguish HCC cases from LC and CHB controls. A mass-based database was then used to putatively identify these metabolites. We then confirmed the identities of a subset of these metabolites through comparisons with the MS/MS fragmentation patterns and retention times of reference standards. The serum samples were then reanalyzed to quantify the levels of these selected metabolites and of other metabolites that have previously been identified as potential HCC biomarkers. Through this approach, we observed clear differences in the metabolite profiles of the CHB, LC, and HCC patient groups in both positive- and negative-ion modes. We found that the levels of taurodeoxy cholic acid (TCA) and 1,2-diacyl-3-β-d-galactosyl-<i>sn</i>-glycerol rose with the progression from CHB to LC to HCC, whereas levels of 5-hydroxy-6<i>E</i>,8<i>Z</i>,11<i>Z</i>,14<i>Z</i>,17<i>Z</i>-eicosapentaenoic acid, and glycyrrhizic acid were gradually reduced with liver disease progression in these groups. The ROC analysis showed that taurodeoxy cholic acid (TCA), 1,2-diacyl-3-β-d-galactosyl-<i>sn</i>-glycerol, 5-hydroxy-6<i>E</i>,8<i>Z</i>,11<i>Z</i>,14<i>Z</i>,17<i>Z</i>-eicosapentaenoic acid, and glycyrrhizic acid had a diagnosis performance with liver disease progression. These four metabolites have a significant correlation with alpha fetal protein (AFP) level and age. Our results highlight novel metabolic biomarkers that have the potential to be used for differentiating between CHB, LC, and HCC patients, thereby facilitating the identification and treatment of patients with early-stage HCC.
Magnetoluminescent Light Switches – Dual Modality in DNA Detection (2013)

The synthesis and properties of two responsive magnetoluminescent iron oxide nanoparticles for dual detection of DNA by MRI and luminescence spectroscopy are presented. These magnetoluminescent agents consist of iron oxide nanoparticles conjugated with metallointercalators via a polyethylene glycol linker. Two metallointercalators were investigated: Ru(bpy')(phen)(dppz), which turns on upon DNA intercalation, and Eu-DOTA-Phen, which turns off. The characteristic light-switch responses of the metallointercalators are not affected by the iron oxide nanoparticles; upon binding to DNA the luminescence of the ruthenium complexes increases by ca. 20-fold, whereas that of the europium complex is >95% quenched. Additionally, the 17-20 nm magnetite cores, having permeable PEG coatings and stable dopamide anchors, render the two constructs efficient responsive contrast agents for MRI with unbound longitudinal and transverse relaxivities of 12.4-9.2 and 135-128 mM(-1)(Fe)s(-1), respectively. Intercalation of the metal complexes in DNA results in the formation of large clusters of nanoparticles with a resultant decrease of both r1 and r2 by 32-63% and 24-38%, respectively. The potential application of these responsive magnetoluminescent assemblies and their reversible catch-and-release properties for the purification of DNA is presented.
Deconvolution and enhancement of optical coherence tomograms (1997)

Subsurface images of biological tissue obtained by optical coherence tomography (OCT) lack of contrast and are corrupted by coherent noise. In this study we investigated model-based deconvolution methods designed for improving the quality of optical-coherence tomograms of living skin. The methods incorporate a priori information about the point-spread function of the imaging optics, as well as optical properties of the tissue. Deconvolution of the aberrated point-spread function was carried out by using CLEAN, an iterative point reconstruction method. A modification of the standard CLEAN algorithm based on a Wiener filter was made to reduce corrugation artifacts in images of densely packed clusters of scatterers. The algorithms were evaluated first on simulated one-dimensional data arrays and then applied to two- dimensional optical coherence tomograms of skin. Our results suggest that significant improvement in image contrast and resolution can be achieved with the deconvolution algorithm.© (1997) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
DeepWalking Backwards: From Embeddings Back to Graphs (2021)

Low-dimensional node embeddings play a key role in analyzing graph datasets. However, little work studies exactly what information is encoded by popular embedding methods, and how this information correlates with performance in downstream machine learning tasks. We tackle this question by studying whether embeddings can be inverted to (approximately) recover the graph used to generate them. Focusing on a variant of the popular DeepWalk method (Perozzi et al., 2014; Qiu et al., 2018), we present algorithms for accurate embedding inversion - i.e., from the low-dimensional embedding of a graph G, we can find a graph H with a very similar embedding. We perform numerous experiments on real-world networks, observing that significant information about G, such as specific edges and bulk properties like triangle density, is often lost in H. However, community structure is often preserved or even enhanced. Our findings are a step towards a more rigorous understanding of exactly what information embeddings encode about the input graph, and why this information is useful for learning tasks.
A Comprehensive Comparative Study on Inductive and Ultrasonic Wireless Power Transmission to Biomedical Implants (2018)

This paper presents a comprehensive comparison between inductive coupling and ultrasound for wireless power transmission (WPT) to biomedical implants. Several sets of inductive and ultrasonic links for different powering distances (<i>d</i> <sub>12</sub>) and receiver dimensions have been optimized, and their key parameters, including power transmission efficiency (PTE) and power delivered to the load (PDL) within safety constraints, have been compared to find out which method is optimal for any given condition. Two design procedures have been presented for maximizing the PTE of inductive and ultrasonic links by finding the optimal geometry for the transmitter (Tx) and receiver (Rx) coils and ultrasonic transducers as well as the optimal operation frequency (<i>f<sub>p</sub></i> ). Our simulation and measurement results showed that the ultrasonic link transcends the inductive link in PTE and somewhat in PDL for a small Rx of 1.1 mm<sup>3</sup> (diameter of 1.2 mm), particularly when the Rx was deeply implanted inside the tissue (<i>d</i> <sub>12</sub> ≥ 10 mm). However, for a larger 20 mm<sup>3</sup> Rx (diameter of 5 mm), the inductive link achieved higher PTE and PDL, particularly at shorter distances (<i>d</i> <sub>12</sub> < 30 mm). The optimal loading condition is shown to be quite different in inductive and ultrasonic links. Despite higher performance for small Rx and large <i>d</i> <sub>12</sub>, the ultrasonic link is more sensitive to Rx misalignments and orientations. This led us to propose a new design procedure based on the worst-case misalignment scenario. The simulation results have been validated by measurements. The inductive and ultrasonic links, operating at 30 MHz and 1.1 MHz, achieved measured PTEs of 0.05% and 0.65% for the 1.1 mm<sup>3</sup> Rx located 30 mm inside tissue and oil environments with optimal load resistances of 295 Ω and 3.8 kΩ, respectively.
A Micro Triggered Spark Gap Switch with Three Electrodes (2011)

A planar micro triggered spark gap switch with three electrodes was designed and fabricated based on non-silicon surface micromachining technology. It consists of two main electrodes, the shape of which is semicircle, and a triggering electrode which is a thin strip. The gap distance between two main electrodes is 800μm. Benefitting from MEMS technology, the switch is integratable and its cost has the potential to be reduced. The designed switch has been optimized and tested. It gives out a pulse current with peak of 5165.21A and 129.6ns rise time. The test data has an agreement with the simulation results.
Increase in crystallinity in poly(vinylidene fluoride) by electron beam radiation (1987)

Abstract We examine the influence of high‐energy radiation and subsequent aging and orientation on the degree of crystallinity of poly(vinylidene fluoride) (PVDF) films. In particular, PVDF films were exposed to electron beam radiation (doses up to 50 Mrad) and aged at room temperature for varying lengths of time followed by uniaxial orientation. The degree of crystallinity of these films was found to increase significantly with increasing radiation dose. In addition, a further substantial increase in the degree of crystallinity was observed upon subsequent aging of irradiated films at room temperature. Upon orientation, in addition to a further rise in the degree of crystallinity, the crystallites were observed to undergo the α form → β form transformation, the latter phase being the polar phase effective for piezo‐electric/pyroelectric activity.
Transtracheal Ventilation (1975)

Effective percutaneous oxygenation and ventilation can be achieved through the use of transtracheal catheters. A graphic study of pressure-flow requirements through different-sized catheters can serve as a guide for the caliber and driving pressure requirement to obtain optimal oxygen flow.
Acetyl coenzyme A carbosylase. Circular dichroism studies of Escherichia coli biotin carboxyl carrier protein. (1976)

The biotin carboxyl carrier protein (BCCP) component of Escherichia coli acetyl coenzyme A carboxylase and three peptides derived from BCCP by proteolytic digestion have been examined by circular dichroism spectroscopy. BCCP, which has a peptide molecular weight of 22,500, has a spectrum typical of globular proteins with negative extrema at 222 nm and 208 nm. The two smallest peptides, BCCP(SC) and BCCP(9,100), with molecular weights of 8,900 and 9,100, respectively, exhibit unusual positive CD bands centered at 237 nm and 220 nm. BCCP(10,400), with a molecular weight of 10,400, has a CD spectrum intermediate between BCCP and that of the smallest peptides. Since d-biotin exhibits a positive CD band at 233 nm, it was suspected that the biotin prosthetic group might be the chromophore responsible for the 237 nm CD band seen in BCCP(SC) and BCCP(9,100). Enzymatic carboxylation of BCCP(SC) to form CO2-BCCP(SC) caused the CD spectrum to change with a shift of the 237 nm band to 232 nm. The positive CD band at 220 nm was unaffected by carboxylation of the biotin prosthetic group. These date suggest that the 237 nm signal may be due either to the biotin which acts as a chromophore directly or to a chromophore that is perturbed by the carboxylation of biotin. A spectropolarimetric titration was carried out to investigate the possible contribution of the single tyrosine residue of BCCP(SC) to the CD spectrum of this peptide. At pH values over 9 the CD spetrum changed with the disappearance of the 237 nm band, suggesting that tyrosine might contribute to this CD band. Denaturation of BCCP(SC) or BCCP(9,100) with 8 M urea of 6 M guanidine HCl abolished the positive CD bands and resulted in spectra typical of a random coil, whereas treatment of BCCP(SC) with 1% sodium dodecyl sulfate abolished the positive bands and left a spectrum exhibiting a shoulder at 222 nm and a negative band at 205 nm, suggestive of a high degree of ordered structure. It is concluded that the CD band at 237 nm in BCCP(SC) and BCCP(9,100) is prabably due to a noncovalent interaction of biotin with an amino acid residue(s) of the protein. It is suggested that the biotin prosthetic group is partially buried in the surface of the protein, rather than swinging free at the end of the lysine side chain through which it is covalently linked to the protein, to permit this interaction to occur.
Dose modification proximity effect correction scheme with inherent forward scattering corrections (1997)

A new approach to dose modification proximity effect correction (PEC) has been proposed that accounts for both short range and long range scatter in advanced direct-write electron beam lithography systems. This scheme can be applied to device writing and to optical mask making where critical dimension (CD) control is of increasing importance. This technique is unique because detailed knowledge of the short range scatter dose distribution is unnecessary; by correcting only for long range scatter, both short and long range compensation is obtained. The new approach is based on the fact that if the characteristic distance of short range scatter is about one third or less of the smallest feature, and if each feature is at least five addressable pixels in the beam writer, then the feature can be printed at its coded dimension if the resist clearing or threshold dose is at the midpoint of the dose profile. Si wafers coated with a positive tone e-beam resist were exposed to a test pattern using no PEC, conventional dose modification PEC and the new scheme. Results show that CD control is maintained over a larger pattern density variation and over a larger exposure dose range by the new technique when compared to the older method and to the uncorrected patterns.
Immunomodulatory activities ofPetiveria alliacea L. (1997)

The hexane extract of Petiveria alliacea increased the phagocytotic index of human granulocytes from 4.0 to 6.2, while a cyclohexane–methanol fraction gave a maximum value of 5.6 at 0.5 mg/mL. These values were not significantly different (p <0.05) from the modified immunostimulatory dipeptide: N-formyl-methionyl-phenylalanine at the same dose. Mature mice treated intraperitoneally with the hexane extract at a dose of 23.0 mg/kg/day gave a differential cell count (DCC) value of 8.66%±0.9% while its medium polar counterpart gave 6.26%±0.9%. The control value was 3.18%±0.85%. One of the active immunomodulatory compounds present in the extract is dibenzyltrisulphide. Both extracts and compound caused an increase in the weight of the thymus and Peyer's patches, however the splenic mass was not significantly altered. © 1997 John Wiley & Sons, Ltd.
Bioadhesive and biodissolvable hydrogels consisting of water‐swellable poly(acrylic acid)/poly(vinylpyrrolidone) complexes (2019)

Films that can form bioadhesive hydrogels on wet biotissues absorbing blood or body fluids are useful for medical devices such as hemostats, adhesion barriers, wound dressings, and drug release devices. We focused on a hydrogen-bonding polymer complex consisting of poly(acrylic acid) (PAA) and poly(vinylpyrrolidone) (PVP). PAA is known as a tissue-adhesive polymer. However, simple mixing of aqueous PAA and PVP solutions resulted in the formation of an insoluble nonadhesive precipitate. We developed a novel solid/solution interface complexation method to afford a PAA/PVP complex that forms a strongly bioadhesive hydrogel with low cytotoxicity. The complex hydrogel can be slowly dissociated and dissolved in the body. The formation of the complexes as well as their swelling and degradation behavior depended strongly on the molecular weights and cross-linking densities of the component polymers. When the complex film was applied to a clipped incised jugular vein of a rat, it immediately formed a hydrogel and closed the incision. After removal of the clip, blood flowed through the vessel without any leakage. Application of the complex film to the surface of an incised mouse liver resulted in firm adhesion and the hemorrhage was effectively stopped. Such bioadhesive and biodissolvable materials consisting of low-toxicity synthetic polymers have high potential for implantable medical devices.
Purification and characterization of cloned alkaline protease gene of Geobacillus stearothermophilus (2014)

Thermostable alkaline serine protease gene of Geobacillus stearothermophilus B-1172 was cloned and expressed in Escherichia coli BL21 (DE3) using pET-22b(+), as an expression vector. The growth conditions were optimized for maximal production of the protease using variable fermentation parameters, i.e., pH, temperature, and addition of an inducer. Protease, thus produced, was purified by ammonium sulfate precipitation followed by ion exchange chromatography with 13.7-fold purification, with specific activity of 97.5 U mg(-1) , and a recovery of 23.6%. Molecular weight of the purified protease, 39 kDa, was determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The enzyme was stable at 90 °C at pH 9. The enzyme activity was steady in the presence of EDTA indicating that the protease was not a metalloprotease. No significant change in the activity of protease after addition of various metal ions further strengthened this fact. However, an addition of 1% Triton X-100 or SDS surfactants constrained the enzyme specific activity to 34 and 19%, respectively. Among organic solvents, an addition of 1-butanol (20%) augmented the enzyme activity by 29% of the original activity. With casein as a substrate, the enzyme activity under optimized conditions was found to be 73.8 U mg(-1) . The effect of protease expression on the host cells growth was also studied and found to negatively affect E. coli cells to certain extent. Catalytic domains of serine proteases from eight important thermostable organisms were analyzed through WebLogo and found to be conserved in all serine protease sequences suggesting that protease of G. stearothermophilus could be beneficially used as a biocontrol agent and in many industries including detergent industry.
Impact of nanosecond laser energy density on the C40-TiSi2 formation and C54-TiSi2 transformation temperature (2020)

The formation of Ti based contacts in new image sensor complementary metal–oxide–semiconductor technologies is limited by the requirement of a low thermal budget. The objectives of these new 3D-technologies are to promote ohmic, low resistance, repeatable, and reliable contacts by keeping the process temperature as low as possible. In this work, ultraviolet-nanosecond laser annealing was performed before classical rapid thermal annealing (RTA) to promote the formation at lower RTA temperatures of the low resistivity C54-TiSi2 phase. The laser energy density was varied from 0.30 to 1.00 J/cm² with three pulses in order to form the C40-TiSi2 phase and finally to obtain the C54-TiSi2 phase by a subsequent RTA at low temperatures. The formed Ti-silicides were characterized by four-point probe measurements, x-ray diffraction, transmission electron microscopy, and atom probe tomography. A threshold in the laser energy density for the formation of the C40-TiSi2 is observed at an energy density of 0.85 J/cm² for the targeted TiN/Ti stack on blanket wafers. The C40-TiSi2 formation by laser annealing prior to RTA enables to reduce the formation temperature of the C54-TiSi2 phase by 150 °C in comparison to a single RTA applied after the Ti/TiN deposition. This specific phase sequence is only observed for a laser energy density close to 0.85 J/cm². At higher energy densities, the presence of C49-TiSi2 or a mixture of C49-TiSi2 and C54-TiSi2 is observed. The underlying mechanisms of the phase sequence and formation are discussed in detail.
Plasma‐assisted molecular beam epitaxy of strain‐compensated a‐plane InGaN/AlGaN superlattices (2015)

Abstract Strain‐compensated InGaN/AlGaN structures can enable the growth of thick layers of InGaN epitaxial films far beyond the critical thickness for InGaN grown pseudomorphically to GaN. In this paper, we demonstrate the epitaxial growth of high‐quality strain‐compensated a‐plane In 0.12 Ga 0.88 N/Al 0.19 Ga 0.81 N superlattices up to 5 times thicker than the critical thickness on free‐standing a‐plane GaN substrates by plasma‐assisted molecular beam epitaxy (PA‐MBE). The superlattices consist of 50 to 200 periods of 10 nm thick In 0.12 Ga 0.88 N and 6 nm thick Al 0.19 Ga 0.81 N layers. The structures are characterized using a double crystal X‐ray diffractometer, asymmetric reciprocal space mapping, and atomic force microscopy. We use X‐ray diffraction to determine the strain, composition, degree of relaxation, and superlattice period of our samples. The structural characteristics of periodic structures containing from 50 to 200 periods are compared to single layer, uncompensated In 0.12 Ga 0.88 N films. A 100 period structure exhibited only 15% relaxation compared to 69% relaxation for the bulk In 0.12 Ga 0.88 N film grown with the same total InGaN thickness but without strain‐compensating layers. (© 2015 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Fluoride-Selective Binding in a New Deep Cavity Calix[4]pyrrole:  Experiment and Theory (2002)

A new "super-extended cavity" tetraacetylcalix[4]pyrrole derivative was synthesized and characterized, and X-ray crystal structures of complexes bound to fluoride and acetonitrile were obtained. The binding behavior of this receptor was investigated by NMR titration, and the complex was found to exclusively bind fluoride ions in DMSO-d(6). This unusual binding behavior was investigated by Monte Carlo free energy perturbation simulations and Poisson calculations, and the ion specificity was seen to result from the favorable electrostatic interactions that the fluoride gains by sitting lower in the phenolic cavity of the receptor. The effect of water present in the DMSO on the calculated free energies of binding was also investigated. Owing to the use of a saturated ion solution, the effect of contaminating water is small in this case; however, it has the potential to be very significant at lower ion concentrations. Finally, the adaptive umbrella WHAM protocol was investigated and optimized for use in binding free energy calculations, and its efficiency was compared to that of the free energy perturbation calculations; adaptive umbrella WHAM was found to be approximately two times more efficient. In addition, structural evidence demonstrates that the protocol explores a wider conformational range than free energy perturbation and should therefore be the method of choice. This paper represents the first complete application of this methodology to "alchemical" changes.