gebhart/patrepeval huggingface dataset:
The Infant Skull: A Vault of Information (2004)

The art of interpreting skull radiographs is slowly being lost as trainees in radiology see fewer plain radiographs and depend more heavily on computed tomography and magnetic resonance imaging. Nevertheless, skull radiographs still provide significant information that is helpful in finding pathologic conditions and appreciating their extents. Abnormalities in the skull may be reflected as variations in the density, size, and shape of the skull, as well as skull defects. Skeletal dysplasias may manifest as a generalized decrease in calvarial density (hypophosphatasia, osteogenesis imperfecta), a generalized increase in calvarial density (osteopetrosis), or a focal increase in density (frontometaphyseal dysplasia). Diffusely decreased or increased calvarial density is usually associated with a process that affects the entire skeleton. Therefore, correct differentiation among these dysplasias depends on other concurrent features. Decreased size of the cranial vault at birth generally implies an underlying insult to the brain, including fetal alcohol syndrome and the so-called TORCH infections (toxoplasmosis, rubella, cytomegalovirus infection, herpes simplex). Macrocephaly may result from skeletal dysplasia or an increase in the intracranial volume (eg, due to underlying anomalies of the brain such as hydrocephalus).
Identification and Molecular Characterization of the β-Ketoacyl-[Acyl Carrier Protein] Synthase Component of the Arabidopsis Mitochondrial Fatty Acid Synthase (2004)

Substrate specificity of condensing enzymes is a predominant factor determining the nature of fatty acyl chains synthesized by type II fatty acid synthase (FAS) enzyme complexes composed of discrete enzymes. The gene (mtKAS) encoding the condensing enzyme, beta-ketoacyl-[acyl carrier protein] (ACP) synthase (KAS), constituent of the mitochondrial FAS was cloned from Arabidopsis thaliana, and its product was purified and characterized. The mtKAS cDNA complemented the KAS II defect in the E. coli CY244 strain mutated in both fabB and fabF encoding KAS I and KAS II, respectively, demonstrating its ability to catalyze the condensation reaction in fatty acid synthesis. In vitro assays using extracts of CY244 containing all E. coli FAS components, except that KAS I and II were replaced by mtKAS, gave C(4)-C(18) fatty acids exhibiting a bimodal distribution with peaks at C(8) and C(14)-C(16). Previously observed bimodal distributions obtained using mitochondrial extracts appear attributable to the mtKAS enzyme in the extracts. Although the mtKAS sequence is most similar to that of bacterial KAS IIs, sensitivity of mtKAS to the antibiotic cerulenin resembles that of E. coli KAS I. In the first or priming condensation reaction of de novo fatty acid synthesis, purified His-tagged mtKAS efficiently utilized malonyl-ACP, but not acetyl-CoA as primer substrate. Intracellular targeting using green fluorescent protein, Western blot, and deletion analyses identified an N-terminal signal conveying mtKAS into mitochondria. Thus, mtKAS with its broad chain length specificity accomplishes all condensation steps in mitochondrial fatty acid synthesis, whereas in plastids three KAS enzymes are required.
Interference Management via Sliding-Window Coded Modulation for 5G Cellular Networks (2016)

SWCM aims to mitigate the adverse effects of interference at the physical layer by tracking the optimal maximum likelihood decoding performance with low-complexity decoding and minimal coordination overhead. This article reviews the basic structure of the SWCM scheme built on the principles of network information theory, and discusses how it can be extended and implemented in practical wireless communication systems. Using a representative implementation based on LTE OFDM MIMO systems, extensive link-level and system-level performance simulations are carried out, which demonstrate that SWCM offers significant gains for all users over conventional interference-aware communication schemes. Network operating prerequisites for SWCM are also discussed to facilitate the standardization effort for its adoption in the fifth generation cellular network.
Effects of modulators of protein kinases on taxol-induced apoptosis of human leukemic cells possessing disparate levels of p26BCL-2 protein. (1995)

Taxol-induced polymerization of tubulin into stable microtubules and cell cycle metaphase arrest have been demonstrated to result in internucleosomal DNA fragmentation and morphological features of apoptosis in human leukemia cells. Recent studies have also shown that Taxol-induced apoptosis, but not Taxol-induced microtubular bundling or mitotic arrest, is significantly inhibited in cells that overexpress the bcl-2 gene product p26BCL-2. In the present studies we examined the effects of several modulators of activities of protein kinases on Taxol-induced DNA fragmentation and apoptosis in human pre-B leukemia 697 cells transfected with the cDNA of the bcl-2 gene and expressing high intracellular levels of p26BCL-2 (697/BCL-2 cells). Treatment with 0.1-1.0 microM MTaxol for 24 h produced prolonged mitotic arrest of control 697/neo cells, which had been transfected with the neomycin resistance gene. This resulted in apoptosis-associated large DNA fragments ranging between 5 and 200 kb and internucleosomal DNA fragmentation. Cotreatment with the phorbol ester phorbol dibutyrate (PdBU) significantly reduced Taxol-induced internucleosomal and large DNA fragmentation and inhibited apoptosis of 697/neo cells. In contrast, a combined exposure to Taxol and staurosporine (ST; 5 or 50 ng/ml), a potent inhibitor of protein kinase C and other kinases, significantly increased DNA fragmentation and apoptosis of 697/neo cells. Additionally, in 697/BCL-2 cells, ST partially overcame the suppressive effects of high p26BCL-2 levels on Taxol-induced apoptosis. Cotreatment with the tyrosine kinase inhibitor Genistein (30 microM) markedly inhibited Taxol-induced DNA fragmentation and apoptosis of 697/neo cells. However, it is noteworthy that the modulations of Taxol-induced DNA fragmentation and apoptosis by PdBU, ST, and Genistein occurred without significant effects on Taxol-mediated mitotic arrest of 697/neo cells. These agents also did not affect intracellular p26BCL-2 levels in 697/neo or 697/BCL-2 cells. These findings indicate that Taxol-induced apoptosis can be modulated by agents that affect the activities of protein kinases, and these effects are not mediated by modulations of Taxol-induced mitotic arrest or by alterations of intracellular p26BCL-2 levels.
Cloning and Expression of the cDNA Encoding the Human Homologue of the DNA Repair Enzyme, Escherichia coli Endonuclease III (1997)

We previously purified a bovine pyrimidine hydrate-thymine glycol DNA glycosylase/AP lyase. The amino acid sequence of tryptic bovine peptides was homologous to Escherichia coli endonuclease III, theoretical proteins of Saccharomyces cerevisiae and Caenorhabditis elegans, and the translated sequences of rat and human 3'-expressed sequence tags (3'-ESTs) (Hilbert, T. P., Boorstein, R. J., Kung, H. C., Bolton, P. H., Xing, D., Cunningham, R. P., Teebor, G. W. (1996) Biochemistry 35, 2505-2511). Now the human 3'-EST was used to isolate the cDNA clone encoding the human enzyme, which, when expressed as a GST-fusion protein, demonstrated thymine glycol-DNA glycosylase activity and, after incubation with NaCNBH3, became irreversibly cross-linked to a thymine glycol-containing oligodeoxynucleotide, a reaction characteristic of DNA glycosylase/AP lyases. Amino acids within the active site, DNA binding domains, and [4Fe-4S] cluster of endonuclease III are conserved in the human enzyme. The gene for the human enzyme was localized to chromosome 16p13.2-.3. Genomic sequences encoding putative endonuclease III homologues are present in bacteria, archeons, and eukaryotes. The ubiquitous distribution of endonuclease III-like proteins suggests that the 5,6-double bond of pyrimidines is subject to oxidation, reduction, and/or hydration in the DNA of organisms of all biologic domains and that the resulting modified pyrimidines are deleterious to the organism.
The Determination of Brønsted Acid Sites in Zeolite ERS-7 by Neutron and X-ray Powder Diffraction (2001)

The deuterated acid form of zeolite ERS-7 (Si/Al = 8.4) has been prepared by repeated cycles of D2O exposure and calcination. 27Al NMR data show that the relative proportions of tetrahedral and octahedral Al in the resulting material are 70 and 30%, respectively. Three Brønsted sites were identified by a combined Rietveld refinement that simultaneously employed synchrotron X-ray powder diffraction data and neutron powder diffraction data. Final lattice parameters were a = 9.7843(1) Å, b = 12.3676(1) Å, and c = 22.8336(2) Å, the combined Rwp factor was 6.3%, and χ2(reduced) was 1.48. Acid deuterons were located approximately 1 Å from oxygens O3, O5, and O7, with occupancy factors of 0.16(2), 0.16(3), and 0.18(2), respectively. These correpsond to 1.28(16), 0.64(12), and 1.44(16) deuterons per unit cell, respectively, for a total of 3.36(26) acid sites per unit cell, which is consistent with the tetrahedral Al content. Only deuteron D5 lies on a special position. T−O bond lengths suggest a site preference for Al at T4, T1, and possibly T2, each of which is bonded to at least one of the observed acid-site oxygens. A bridging framework oxygen site was identified in both the PND and PXD difference Fourier maps that appears to be disordered over at least two distinct sites; this corresponds to different local arrangements of Al at the neighboring T-sites. The out-of-plane framework hydroxyl tilt angles at each acid site were comparable to those of H+ SSZ-13 and D+ RHO. Acid site D7 demonstrated a significant in-plane hydroxyl tilt angle (7.5°), consistent with ab initio quantum mechanical calculations. This tilt clearly indicates an Al preference for site T4 over T6.
Mutations in multicopy Tn10 tet plasmids that confer resistance to inhibitory effects of inducers of tet gene expression (1983)

Escherichia coli K-12 strains that carry the Tn10 tetracycline resistance determinant (tet) on multicopy plasmids are hypersensitive to 5a,6-anhydrotetracycline and heated chlortetracycline, two tetracycline derivatives that are relatively more effective as inducers of tet gene expression than as inhibitors of bacterial growth. Twenty spontaneous mutations that confer resistance to anhydrotetracycline (Atr) and resistance to heated chlortetracycline (Ctr) were isolated and characterized. All of these Atr mutations are located in the Tn10 tet region; the majority (18 of 20) have no effect on tetR repressor function. Atr mutations can increase, reduce, or eliminate the phenotypic expression of plasmid tetracycline resistance (Tcr). IS insertions that result in an Atr Tcs phenotype are clustered in a 150-base-pair promoter-proximal region of the tetA resistance gene. Some Atr mutations reduce expression of the tetA gene by altering either the tetR repressor or the tetA promoter. In addition, it appears that E. coli cannot tolerate constitutive expression of the wild-type tetA gene from a multicopy plasmid containing a tetR deletion. These observations support the proposal that high level expression of the 36-kilodalton tetA gene product inhibits the growth of E. coli. We speculate that this inhibition is related to the interaction of the tetA gene product with the cytoplasmic membrane.
An In Vitro Human Cell-Based Assay to Rank the Relative Immunogenicity of Proteins (2003)

A method to rank proteins based on their relative immunogenicity has been devised. A statistical analysis of peptide-specific responses in large human donor pools provides a structure index value metric that ranked four industrial enzymes in the order determined by both mouse and guinea pig exposure models. The ranking method also compared favorably with human sensitization rates measured in occupationally exposed workers. Structure index values for other proteins known to cause immune responses in humans were also determined and found to be higher than the value determined for human beta2-microglobulin. Using values from known immunogenic and putative nonimmunogenic proteins, a cut-off value was established. The structure index value calculation provides a comparative method to predict subsequent immunogenicity on a human population basis without the need to use animal models. Information provided by this assay can be used in the early development of protein therapies and other protein-based applications to select or create reduced immunogenicity variants.
Conversion of Cetuximab and Trastuzumab into T cell-engaging BiTE antibodies creates novel drug candidates with superior anti-tumor activity (2008)

2402 Monoclonal IgG1 antibodies cetuximab and trastuzumab have become standard of care for the treatment of patients with advanced colon and breast cancer, respectively. Mode of action of these antibodies includes inhibition of signalling and antibody-dependent cellular cytotoxicity (ADCC). Numerous efforts are ongoing to increase the anti-tumor activity of therapeutic antibodies, which typically require weekly doses of 2-8 mg/kg and show only limited efficacy as monotherapy in metastatic disease. Conventional antibodies such as cetuximab and trastuzumab cannot directly engage T cells, which are considered the most potent cytotoxic cells in the organism. This is because T cells lack antibody-binding Fcγ receptors. We have developed so called BiTE antibodies that can redirect T cells --irrespective of T cell receptor specificity and peptide antigen presentation-- to tumor cells expressing a particular surface antigen.  Here, we have converted both cetuximab and trastuzumab into T cell-engaging BiTE antibodies. Respective single-chain antibodies were crafted from the variable domains of cetuximab and trastuzumab and genetically linked to anti-CD3 single-chain antibodies that confer the particular T cell-engaging properties of BiTE antibodies. The resulting EGFR- and HER-2-specific BiTE antibodies were stable 55 kDa proteins with binding specificity to EGFR and HER-2 on tumor cells, respectively, and to CD3 on T cells. Both showed potent redirected lysis of EGFR- and HER-2-expressing target cell lines by peripheral human T cells at half maximal concentrations of 0.1-0.2 ng/ml (ca. 2-4 picomolar). Redirected lysis was highly specific for target antigens. Concomitant T cell activation was only observed in the presence of target cells but not when cetuximab- and trastuzumab-based BiTE antibodies were incubated with T cells alone.  The anti-tumor activity of cetuximab and trastuzumab was directly compared with that of the corresponding BiTE antibodies in cytotoxicity assays using identical assay conditions and the same donors as source for peripheral mononuclear effector cells (PBMC). BiTE antibodies consistently showed a higher activity than the conventional antibodies. In contrast to the IgG1 antibodies, the BiTE antibodies led to a complete lysis of target cells during the assay period. Data from animal models will be presented that compare the efficacy of cetuximab and trastuzumab side-by-side with that of respective BiTE antibodies.  Our data show that established therapeutic monoclonal antibodies can be successfully converted into BiTE antibodies, with the potential to engage T cells for highly potent and strictly target-dependent tumor cell elimination.
ORIGINAL RESEARCH—BASIC SCIENCE: Acute and Repeated Flibanserin Administration in Female Rats Modulates Monoamines Differentially Across Brain Areas: A Microdialysis Study (2010)

Systemic administration of flibanserin to female rats differentially affects the monoamine systems of the brain. This may be the mechanistic underpinning of flibanserin's therapeutic efficacy in HSDD, as sexual behavior is controlled by an intricate interplay between stimulatory (catecholaminergic) and inhibitory (serotonergic) systems.
Envelope Glycoprotein Determinants of Neutralization Resistance in a Simian-Human Immunodeficiency Virus (SHIV-HXBc2P 3.2) Derived by Passage in Monkeys (2001)

The simian-human immunodeficiency virus SHIV-HXBc2 contains the envelope glycoproteins of a laboratory-adapted, neutralization-sensitive human immunodeficiency virus type 1 variant, HXBc2. Serial in vivo passage of the nonpathogenic SHIV-HXBc2 generated SHIV KU-1, which causes rapid CD4(+) T-cell depletion and an AIDS-like illness in monkeys. A molecularly cloned pathogenic SHIV, SHIV-HXBc2P 3.2, was derived from the SHIV KU-1 isolate and differs from the parental SHIV-HXBc2 by only 12 envelope glycoprotein amino acid residues. Relative to SHIV-HXBc2, SHIV-HXBc2P 3.2 was resistant to neutralization by all of the antibodies tested with the exception of the 2G12 antibody. The sequence changes responsible for neutralization resistance were located in variable regions of the gp120 exterior envelope glycoprotein and in the gp41 transmembrane envelope glycoprotein. The 2G12 antibody, which neutralized SHIV-HXBc2 and SHIV-HXBc2P 3.2 equally, bound the HXBc2 and HXBc2P 3.2 envelope glycoproteins on the cell surface comparably. The ability of the other tested antibodies to achieve saturation was less for the HXBc2P 3.2 envelope glycoproteins than for the HXBc2 envelope glycoproteins, even though the affinity of the antibodies for the two envelope glycoproteins was similar. Thus, a highly neutralization-sensitive SHIV, by modifying both gp120 and gp41 glycoproteins, apparently achieves a neutralization-resistant state by decreasing the saturability of its envelope glycoproteins by antibodies.
A human testis-specific mRNA for phosphoribosylpyrophosphate synthetase that initiates from a non-AUG codon. (1990)

Two highly homologous subunits for phosphoribosylpyrophosphate synthetase are encoded by human X-linked genes, PRPS1 and PRPS2 (Taira, M., Kudoh, J., Minoshima, S., Iizasa, T., Shimada, H., Shimizu, Y., Tatibana, M., and Shimizu, N. (1989b) Somat. Cell Mol. Genet. 15, 29-37). These genes are expressed in most tissues, whereas an additional unique mRNA (1.4 kilobases) is present in the testes of rats as well as mice and humans (Taira, M., Iizasa, T., Yamada, K., Shimada, H., and Tatibana, M. (1989a) Biochim. Biophys. Acta 1007, 203-208). In this paper, cDNA cloning revealed that the human testis-specific mRNA was encoded by an autosomal gene, termed PRPS3. RNA blot analysis showed that the expression of this gene began at 4 weeks of age in rats, coinciding with the reported appearance of primary spermatocytes. A cDNA clone of PRPS3 was sequenced and found to encode a predicted product of 317 amino acids which was highly homologous to those of PRPS1 and PRPS2 (94.3% and 91.2% identities, respectively). However, the PRPS3 cDNAs lacked an ATG initiator for translation at the expected position, and instead contained an ACG triplet. In vitro transcription/translation studies, combined with in vitro site-directed mutagenesis experiments, suggested that the ACG codon at this position did serve as a start codon. Analysis of amino-terminal sequence of the radiolabeled PRPS3 product, prepared by in vitro translation, supported the predicted sequence starting with Pro-1, and, in addition, this product was labeled with N-formyl[35S]methionyl-tRNAi. These results suggested that the synthesis of the nascent polypeptide could initiate with methionine at the position corresponding to the ACG codon.
High-resolution characterization of sequence signatures due to non-random cleavage of cell-free DNA (2015)

These background signals in cell-free DNA sequencing data stem from the non-random biological cleavage of these fragments. This sequence structure can be harnessed to improve bioinformatics algorithms, in particular for CNV and structural variant detection. Descriptive measures for cell-free DNA features developed here could also be used in biomarker analysis to monitor the changes that occur during different pathological conditions.
Wavefront image sensor chip (2010)

We report the implementation of an image sensor chip, termed wavefront image sensor chip (WIS), that can measure both intensity/amplitude and phase front variations of a light wave separately and quantitatively. By monitoring the tightly confined transmitted light spots through a circular aperture grid in a high Fresnel number regime, we can measure both intensity and phase front variations with a high sampling density (11 microm) and high sensitivity (the sensitivity of normalized phase gradient measurement is 0.1 mrad under the typical working condition). By using WIS in a standard microscope, we can collect both bright-field (transmitted light intensity) and normalized phase gradient images. Our experiments further demonstrate that the normalized phase gradient images of polystyrene microspheres, unstained and stained starfish embryos, and strongly birefringent potato starch granules are improved versions of their corresponding differential interference contrast (DIC) microscope images in that they are artifact-free and quantitative. Besides phase microscopy, WIS can benefit machine recognition, object ranging, and texture assessment for a variety of applications.
Mutations within a human IgG2 antibody form distinct and homogeneous disulfide isomers but do not affect Fc gamma receptor or C1q binding (2010)

Human IgG2 antibodies may exist in at least three distinct structural isomers due to disulfide shuffling within the upper hinge region. Antibody interactions with Fc gamma receptors and the complement component C1q contribute to immune effector functions. These interactions could be impacted by the accessibility and structure of the hinge region. To examine the role structural isomers may have on effector functions, a series of cysteine to serine mutations were made on a human IgG2 backbone. We observed structural homogeneity with these mutants and mapped the locations of their disulfide bonds. Importantly, there was no observed difference in binding to any of the Fc gamma receptors or C1q between the mutants and the wild-type IgG2. However, differences were seen in the apparent binding affinity of these antibodies that were dependent on the selection of the secondary detection antibody used.
Highly efficient color filter array using resonant Si_3N_4 gratings (2013)

We demonstrate the design and fabrication of a highly efficient guided-mode resonant color filter array. The device is designed using numerical methods based on rigorous coupled-wave analysis and is patterned using UV-laser interferometric lithography. It consists of a 60-nm-thick subwavelength silicon nitride grating along with a 105-nm-thick homogeneous silicon nitride waveguide on a glass substrate. The fabricated device exhibits blue, green, and red color response for grating periods of 274, 327, and 369 nm, respectively. The pixels have a spectral bandwidth of ~12 nm with efficiencies of 94%, 96%, and 99% at the center wavelength of blue, green, and red color filter, respectively. These are higher efficiencies than reported in the literature previously.