gebhart/patrepeval huggingface dataset:
UniProt Knowledgebase: a hub of integrated protein data (2011)

The UniProt Knowledgebase (UniProtKB) acts as a central hub of protein knowledge by providing a unified view of protein sequence and functional information. Manual and automatic annotation procedures are used to add data directly to the database while extensive cross-referencing to more than 120 external databases provides access to additional relevant information in more specialized data collections. UniProtKB also integrates a range of data from other resources. All information is attributed to its original source, allowing users to trace the provenance of all data. The UniProt Consortium is committed to using and promoting common data exchange formats and technologies, and UniProtKB data is made freely available in a range of formats to facilitate integration with other databases. Database URL: http://www.uniprot.org/
A study of the geometrical and mechanical properties of a self‐expanding metallic stent—theory and experiment (1993)

Stents are tubular devices that are used in cylindrical passages of the body following trauma or disease in order to keep the cross section of these passages open. A mathematical model of a self-expanding metallic stent has been developed with the aim of predicting various geometrical and mechanical properties of the stent. The model was developed with the main assumptions that the stent acts as a combination of a number of independent open-coiled helical springs with ends fixed against rotation, and that the springs undergo elastic deformations only. A series of experiments has been carried out in order to assess the validity of the model. The experimental results show good agreement with theory for the tests involving stent diameter and longitudinal force as a function of stent length and fair agreement, limited by frictional effects, for the tests involving radial pressure as a function of stent diameter.
Size-Dependent Energy Transfer Pathways in CdSe Quantum Dot–Squaraine Light-Harvesting Assemblies: Förster versus Dexter (2014)

Energy transfer coupled with electron transfer is a convenient approach to mimic photosynthesis in light energy conversion. Better understanding of mechanistic details of energy transfer processes is important to enhance the performance of dye or quantum dot-sensitized solar cells. Energy transfer through both long-range dipole-based Förster resonance energy transfer (FRET) and short-range Dexter energy transfer (DET) mechanisms have been identified to occur between CdSe quantum dots (QDs) linked to a red-infrared-absorbing squaraine dye through a short thiol functional group (SQSH). Solutions of SQSH linked to CdSe were investigated through steady-state and time-resolved spectroscopy experiments to explore both mechanisms. Photoluminescence studies revealed that smaller QDs had higher energy transfer efficiencies than predicted by FRET, and femtosecond transient absorption experiments revealed faster energy transfer rates in smaller donor QD sizes. These findings supported a DET process dominating at small donor sizes. The presence of both processes illustrates multiple strategies for utilizing energy transfer in light-harvesting assemblies and the required considerations in device design to maximize energy transfer gains through either mechanism.
Molecular cloning and functional characterization of the pig analogue of CD59: relevance to xenotransplantation. (1998)

In this work, we report the cloning of the cDNA for the porcine analogue of human CD59. Degenerate primers, derived from the N-terminal sequence of pig erythrocyte CD59, were used to obtain the corresponding cDNA sequence. From this sequence, gene-specific primers were designed and used to amplify the 3' and 5' ends of the cDNA using the rapid amplification of cDNA ends (RACE) method. The complete 768-bp cDNA so obtained consisted of a 84-bp 5' untranslated region, a 26-amino-acid NH2-signal peptide, a 98-amino-acid coding region, including putative N-glycosylation sites and a glycosylphosphatidylinositol-anchoring signal, and a 312-bp 3' untranslated region. The mature protein sequence was 48% identical to human CD59 at the amino acid level. Northern blot analysis revealed several distinct CD59 transcripts, and a variability in expression levels of the different transcripts in the panel of tissues screened. Stable expression of pig CD59 in a CD59-negative human cell line conferred protection against lysis by complement from pig and several other species. Separate expression of pig and human CD59 at similar levels in the same cell line allowed a direct functional comparison between these two analogues. Pig CD59 and human CD59 showed similar activity in inhibiting lysis by complement from all species tested; in particular, expressed pig CD59 efficiently inhibited lysis by human complement. The relevance of these data to current work in the engineering of pig organs for xenotransplantation is discussed.
Maleimidophenylmethacrylates and their Derivatives as Polystyrene Thermal Stabilizers (2008)

Effects of maleimidophenylmethacrylates on thermal stability of polystyrene have been examined by dynamic thermogravimetric analysis in air conditions. The maleimidophenylmethacrylates with substitutes of various molecular architecture in imide cycle have been built in polystyrene macromolecular chains (as much as 1 mol %) by means of copolymerization reaction. The thermal stabilizing effects depend on the structure features of the used compounds. Some of the additives show the inhibiting effect only whereas other ones show combined inhibiting and retarding effects. The last ones revealed as very effective stabilizers of polystyrene against thermal oxidative degradation.
N -Glycolylneuraminic Acid Deficiency in Mice: Implications for Human Biology and Evolution (2007)

Humans and chimpanzees share >99% identity in most proteins. One rare difference is a human-specific inactivating deletion in the CMAH gene, which determines biosynthesis of the sialic acid N-glycolylneuraminic acid (Neu5Gc). Since Neu5Gc is prominent on most chimpanzee cell surfaces, this mutation could have affected multiple systems. However, Neu5Gc is found in human cancers and fetuses and in trace amounts in normal human tissues, suggesting an alternate biosynthetic pathway. We inactivated the mouse Cmah gene and studied the in vivo consequences. There was no evidence for an alternate pathway in normal, fetal, or malignant tissue. Rather, null fetuses accumulated Neu5Gc from heterozygous mothers and dietary Neu5Gc was incorporated into oncogene-induced tumors. As with humans, there were accumulation of the precursor N-acetylneuraminic acid and increases in sialic acid O acetylation. Null mice showed other abnormalities reminiscent of the human condition. Adult mice showed a diminished acoustic startle response and required higher acoustic stimuli to increase responses above the baseline level. In this regard, histological abnormalities of the inner ear occurred in older mice, which had impaired hearing. Adult animals also showed delayed skin wound healing. Loss of Neu5Gc in hominid ancestors approximately 2 to 3 million years ago likely had immediate and long-term consequences for human biology.
Example-based synthesis of stylized facial animations (2017)

We introduce a novel approach to example-based stylization of portrait videos that preserves both the subject's identity and the visual richness of the input style exemplar. Unlike the current state-of-the-art based on neural style transfer [Selim et al. 2016], our method performs non-parametric texture synthesis that retains more of the local textural details of the artistic exemplar and does not suffer from image warping artifacts caused by aligning the style exemplar with the target face. Our method allows the creation of videos with less than full temporal coherence [Ruder et al. 2016]. By introducing a controllable amount of temporal dynamics, it more closely approximates the appearance of real hand-painted animation in which every frame was created independently. We demonstrate the practical utility of the proposed solution on a variety of style exemplars and target videos.
αChanneling in a Rotating Plasma (2008)

The wave-particle alpha-channeling effect is generalized to include rotating plasma. Specifically, radio frequency waves can resonate with alpha particles in a mirror machine with ExB rotation to diffuse the alpha particles along constrained paths in phase space. Of major interest is that the alpha-particle energy, in addition to amplifying the rf waves, can directly enhance the rotation energy which in turn provides additional plasma confinement in centrifugal fusion reactors. An ancillary benefit is the rapid removal of alpha particles, which increases the fusion reactivity.
Increased binding of synovial T lymphocytes from rheumatoid arthritis to endothelial-leukocyte adhesion molecule-1 (ELAM-1) and vascular cell adhesion molecule-1 (VCAM-1). (1992)

The infiltration of the synovial membrane (SM) by mononuclear cells, mostly T cells, is a typical histopathological feature associated with rheumatoid arthritis (RA). The entry of T lymphocytes into the SM is believed to be mediated by a number of molecules in the endothelium that are induced in response to a series of inflammatory mediators. In this study, we have investigated the adhesion of synovial T cells from RA patients to two endothelial ligands: endothelial-leukocyte adhesion molecule-1 (ELAM-1), the only selectin known to function as a vascular addressin for T cells, and vascular cell adhesion molecule-1 (VCAM-1), the cellular ligand of VLA-4. Our results clearly demonstrate that synovial T cells isolated from both SM and synovial fluid (SF), bearing an activated and memory phenotype, displayed an enhanced capacity to interact with these two endothelial molecules as compared with T cells from peripheral blood (PB) either of the same RA patients or healthy donors. A further enhancement of VLA-4-mediated T cell binding to VCAM-1 and fibronectin could be observed when already in vivo-activated synovial T cells were stimulated in vitro with phorbol esters, suggesting the existence of several cellular affinity levels for both very late activation-4 (VLA-4) ligands. Moreover, both PB and synovial T cells from RA patients exhibited strong proliferative responses when they were cultured with either fibronectin or VCAM-1 in combination with submitogenic doses of anti-CD3 mAb. This increased endothelial binding ability of synovial T lymphocytes together with their proliferation in response to the interaction with VCAM-1 and fibronectin may represent important mechanisms in the regulation of T cell penetration and persistence in the chronically inflamed SM of RA.
Assessment of glycosaminoglycan distribution in human lumbar intervertebral discs using chemical exchange saturation transfer at 3 T: feasibility and initial experience (2011)

Recent studies have proposed that glycosaminoglycan chemical exchange saturation transfer (gagCEST) is associated with a loss of glycosaminoglycans (GAGs), which may be an initiating factor in intervertebral disc (IVD) degeneration. Despite its promising potential, this application has not been reported in human in vivo IVD studies because of the challenges of B(0) magnetic field inhomogeneity in gagCEST. This study aimed to evaluate the feasibility of quantifying CEST values in IVDs of healthy volunteers using a clinical 3 T scanner. A single-slice turbo spin echo sequence was used to quantify the CEST effect in various GAG phantoms and in IVDs of 12 volunteers. The phantom results indicated high correlation between gagCEST and GAG concentrations (R(2) = 0.95). With optimal B(0) inhomogeneity correction, in vivo CEST maps of IVDs showed robust contrast between the nucleus pulposus (NP) and the annulus fibrosus (AF) (p < 0.01), as well as higher signal in the central relative to the peripheral NP. In addition, a trend of decreasing CEST values from upper to lower disc levels was evident in NP. Our results demonstrate that in vivo gagCEST quantification in human lumbar IVDs is feasible at 3 T in combination with successful B(0) inhomogeneity correction, but without significant hardware modifications. Our initial findings suggest that it would be worthwhile to perform direct correlation studies between CEST and GAGs using cadaver samples, and to extend this novel technique to studies on patients with degenerative discs to better understand its distinct imaging features relative to conventional techniques.
Studies on Metal Chelate Compounds of Phenazine Derivatives. I. Spectrophotometric Studies on Copper Chelate Compounds of 1-Hydroxyphenazine and its Di-N-oxide. (1958)

The properties of copper chelate compound of 1-hydroxyphenazine, which possesses one oxine-like functional group to form a chelate, as well as the composition of the chelate in solution and its dissociation constant were studied by the spectrophotometric method. 1-Hydroxyphenazine-copper chelate forms a five-membered ring compound in a neutral medium. 1-Hydroxyphenazine di-N-oxide also has a chelating functional group which seems to be a little different from the former compound, and the properties and composition of copper chelate were also investigated. The copper chelate of its di-N-oxide forms a six-membered chelate ring.
Substituted Salicylanilides as Inhibitors of Two-Component Regulatory Systems in Bacteria (1998)

A new class of inhibitors of the two-component regulatory systems (TCS) of bacteria was discovered based on the salicylanilide screening hits, closantel (1) and tetrachlorosalicylanilide (9). A systematic SAR study versus a model TCS, KinA/Spo0F, demonstrated the importance of electron-attracting substituents in the salicyloyl ring and hydrophobic groups in the anilide moiety for optimal activity. In addition, derivatives 8 and 16, containing the 2, 3-dihydroxybenzanilide structural motif, were potent inhibitors of the autophosphorylation of the KinA kinase, with IC50s of 2.8 and 6. 3 &microM, respectively. Compound 8 also inhibited the TCS mediating vancomycin resistance (VanS/VanR) in a genetically engineered Enterococcus faecalis cell line at concentrations subinhibitory for growth. Closantel (1), tetrachlorosalicylanilide (9), and several related derivatives (2, 7, 10, 11, 20) had antibacterial activity against the drug-resistant organisms, methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecium (VREF).
NK cells in childhood obesity are activated, metabolically stressed, and functionally deficient (2017)

Childhood obesity is a major global concern, with over 50 million children now classified as obese. Obesity has been linked to the development of numerous chronic inflammatory diseases, including type 2 diabetes and multiple cancers. NK cells are a subset of innate effector cells, which play an important role in the regulation of adipose tissue and antitumor immunity. NK cells can spontaneously kill transformed cells and coordinate subsequent immune responses through their production of cytokines. We investigated the effect of obesity on NK cells in a cohort of obese children, compared to children with a healthy weight. We demonstrated a reduction in peripheral NK cell frequencies in childhood obesity and inverse correlations with body mass index and insulin resistance. Compared with NK cells from children with normal weight, we show increased NK cell activation and metabolism in obese children (PD-1, mTOR activation, ECAR, and mitochondrial ROS), along with a reduced capacity to respond to stimulus, ultimately leading to loss of function (proliferation and tumor lysis). Collectively we show that NK cells from obese children are activated, metabolically stressed, and losing the ability to perform their basic duties. Paired with the reduction in NK cell frequencies in childhood obesity, this suggests that the negative effect on antitumor immunity is present early in the life course of obesity and certainly many years before the development of overt malignancies.
Spinal Cord Stimulation for Chronic Reflex Sympathetic Dystrophy — Five-Year Follow-up (2006)

To the Editor: Reflex sympathetic dystrophy is a painful, disabling disorder of unknown pathophysiological origin that usually commences after trauma to or surgery on a limb. In chronic cases, the syndrome leads to extreme pain, disability, and an inability to work, symptoms that dramatically change the lives of both patients and their families.1,2 We undertook the present trial to determine whether treatment of chronic reflex sympathetic dystrophy with spinal cord stimulation and physical therapy is more effective than treatment with physical therapy alone. In spinal cord stimulation, an electrode is positioned in the epidural space on the dorsal aspect . . .
DEFINING PROSTATE SPECIFIC ANTIGEN PROGRESSION AFTER RADICAL PROSTATECTOMY: WHAT IS THE MOST APPROPRIATE CUT POINT? (2001)

Biochemical, PSA progression rates vary markedly depending on the method used to define PSA failure. Methods that require multiple increasing PSA values, for example the ASTRO definition, give misleading results, especially if the event time is backdated. Standards for defining PSA progression would allow more consistent and comparable progression estimates after radical prostatectomy. PSA 0.4 ng./ml. or greater may be the most appropriate cut point to use since a significant number of patients with lower PSA do not have a continued increase in it.
Human ribosomal RNA gene: nucleotide sequence of the transcription initiation region and comparison of three mammalian genes. (1982)

The transcription initiation site of the human ribosomal RNA gene (rDNA) was located by using the single-strand specific nuclease protection method and by determining the first nucleotide of the in vitro capped 45S preribosomal RNA. The sequence of 1,211 nucleotides surrounding the initiation site was determined. The sequenced region was found to consist of 75% G and C and to contain a number of short direct and inverted repeats and palindromes. By comparison of the corresponding initiation regions of three mammalian species, several conserved sequences were found upstream and downstream from the transcription starting point. Two short A + T-rich sequences are present on human, mouse, and rat ribosomal RNA genes between the initiation site and 40 nucleotides upstream, and a C + T cluster is located at a position around -60. At and downstream from the initiation site, a common sequence, T-AG-C-T-G-A-C-A-C-G-C-T-G-T-C-C-T-CT-T, was found in the three genes from position -1 through +18. The strong conservation of these sequences suggests their functional significance in rDNA. The S1 nuclease protection experiments with cloned rDNA fragments indicated the presence in human 45S RNA of molecules several hundred nucleotides shorter than the supposed primary transcript. The first 19 nucleotides of these molecules appear identical--except for one mismatch--to the nucleotide sequence of the 5' end of a supposed early processing product of the mouse 45S RNA.
HEAX: An Architecture for Computing on Encrypted Data (2019)

With the rapid increase in cloud computing, concerns surrounding data privacy, security, and confidentiality also have been increased significantly. Not only cloud providers are susceptible to internal and external hacks, but also in some scenarios, data owners cannot outsource the computation due to privacy laws such as GDPR, HIPAA, or CCPA. Fully Homomorphic Encryption (FHE) is a groundbreaking invention in cryptography that, unlike traditional cryptosystems, enables computation on encrypted data without ever decrypting it. However, the most critical obstacle in deploying FHE at large-scale is the enormous computation overhead. In this paper, we present HEAX, a novel hardware architecture for FHE that achieves unprecedented performance improvement. HEAX leverages multiple levels of parallelism, ranging from ciphertext-level to fine-grained modular arithmetic level. Our first contribution is a new highly-parallelizable architecture for number-theoretic transform (NTT) which can be of independent interest as NTT is frequently used in many lattice-based cryptography systems. Building on top of NTT engine, we design a novel architecture for computation on homomorphically encrypted data. We also introduce several techniques to enable an end-to-end, fully pipelined design as well as reducing on-chip memory consumption. Our implementation on reconfigurable hardware demonstrates 164-268x performance improvement for a wide range of FHE parameters.
Loss of heterozygosity on chromosome 16 in hepatocellular carcinoma (1992)

In order to understand the molecular genetics of human hepatocellular carcinoma (HCC) a common chromosomal abnormality in HCC was examined using restriction fragment length polymorphism (RFLP) analysis. Sixty-eight HCC specimens were examined for loss of heterozygosity at 11 different chromosomal arms including 1p, 5p, 11p, 11q, 13q, 14q, 15q, 16p, 16q, 18q, and 19q. Losses were not detected on chromosome 1, 5, 14, 15 or 19, and the frequencies of losses were low (11-19%) for chromosomes 11, 13 and 18. In contrast, loss of heterozygosity was frequently observed for three different loci on chromosome 16, the HBA locus at 16p13.3 (22%), the MT2 locus at 16q21-22.1 (15%) and the HP locus at 16q22.1-22.2 (39%). There was no remarkable difference in the frequencies of loss of heterozygosity at these loci among HBV related HCC, HCV related HCC and neither virus (NBNC) related HCC. Thus, the results indicate that at least three different genetic abnormalities in chromosome 16 are commonly observed in various HCC, and that this chromosome may have some important role(s) in recessive genetic changes which generate this tumour.
Deposition and Properties of Low‐Pressure Chemical‐Vapor Deposited Polycrystalline Silicon‐Germanium Films (1994)

The deposition of undoped polycrystalline silicon‐germanium alloy films onto by the pyrolysis of and in a low‐pressure chemical vapor deposition system is described. The deposited films are compatible with standard wet‐cleaning baths, and their formation and patterning are very controllable processes; therefore, their application should not introduce significant process complexity into silicon‐based technologies. Depending upon their Ge content, films can be deposited in polycrystalline form at temperatures as low as ∼400°C, because the transition temperature between polycrystalline and amorphous film deposition decreases with increasing Ge content. grains are columnar in structure and have a relatively low density of microtwins, and their average size is larger than that of grains in poly‐Si films deposited at the same temperature. These properties of make it a promising material for thin film transistor applications in three‐dimensionally integrated circuits and large‐area electronics technologies, which have limited thermal process budget requirements.