gebhart/patrepeval huggingface dataset:
Situs inversus and embryonic ciliary morphogenesis defects in mouse mutants lacking the KIF3A subunit of kinesin-II (1999)

The embryonic cellular events that set the asymmetry of the genetic control circuit controlling left-right (L-R) axis determination in mammals are poorly understood. New insight into this problem was obtained by analyzing mouse mutants lacking the KIF3A motor subunit of the kinesin-II motor complex. Embryos lacking KIF3A die at 10 days postcoitum, exhibit randomized establishment of L-R asymmetry, and display numerous structural abnormalities. The earliest detectable abnormality in KIF3A mutant embryos is found at day 7.5, where scanning electron microscopy reveals loss of cilia ordinarily present on cells of the wild-type embryonic node, which is thought to play an important role in setting the initial L-R asymmetry. This cellular phenotype is observed before the earliest reported time of asymmetric expression of markers of the L-R signaling pathway. These observations demonstrate that the kinesin-based transport pathway needed for flagellar and ciliary morphogenesis is conserved from Chlamydomonas to mammals and support the view that embryonic cilia play a role in the earliest cellular determinative events establishing L-R asymmetry.
Effects of pentoxifylline on circulating cytokine concentrations and hemodynamics in patients with septic shock (1996)

Pentoxifylline is able to decrease serum TNF but not IL-6 or IL-8 serum concentrations during septic shock. Pentoxifylline was well tolerated by all eight patients with no adverse effect. Further studies are needed to determine if pentoxifylline's ability to lower circulating TNF concentration without altering hemodynamics will improve outcome in septic shock.
Punycode: A Bootstring encoding of Unicode for Internationalized Domain Names in Applications (IDNA) (2003)

Punycode is a simple and efficient transfer encoding syntax designed for use with Internationalized Domain Names in Applications (IDNA).It uniquely and reversibly transforms a Unicode string into an ASCII string.ASCII characters in the Unicode string are represented literally, and non-ASCII characters are represented by ASCII characters that are allowed in host name labels (letters, digits, and hyphens).This document defines a general algorithm called Bootstring that allows a string of basic code points to uniquely represent any string of code points drawn from a larger set.Punycode is an instance of Bootstring that uses particular parameter values specified by this document, appropriate for IDNA.
Renal ischemia reperfusion inhibits VEGF expression and induces ADAMTS-1, a novel VEGF inhibitor (2008)

Reductions in vascular density occur following acute ischemia-reperfusion (I/R) injury that may predispose the development of chronic kidney disease. The mechanisms mediating vascular loss are not clear but may relate to the lack of effective vascular repair responses. To determine the regulation of the VEGF/VEGFR pathway following I/R injury, male Sprague-Dawley rats were subjected to bilateral renal ischemia (45 min) and allowed to recover for 1, 3, 7, and 35 days. VEGF mRNA expression was repressed by greater than 50% of control values up to 3 days postischemia, while VEGF protein was repressed for up to 7 days postischemia. The renal mRNA expression of receptors was not altered postischemia; however, VEGFR1 (flt-1) protein was transiently reduced in kidney while soluble flt-1 was elevated in plasma at 7 days following injury. Microarray analysis of angiogenesis-related genes identified the enhanced expression of a number of genes, among these was ADAMTS-1 (a disintegrin and metalloproteinase with thrombospondin motif-1), a secreted VEGF inhibitor. The altered expression of ADAMTS-1 was confirmed using RT-PCR and Western blot analysis; immunofluorescence localized its expression to proximal tubules following I/R injury. Other genes identified using microarray included aminopeptidase N, Smad-1, and Id-3 and their localization was also examined using immunohistochemistry. In summary, the data indicate no clear pattern of anti-angiogenic gene expression following renal I/R injury. However, the studies do suggest an overall inhibition of the VEGF pathway during the early injury and repair phase of renal ischemia that may contribute to an overall reduction in renal microvascular density.
Purification of the human O6‐methylguanine‐DNA methyltransferase and uracil‐DNA glycosylase, the latter to apparent homogeneity (1988)

Uracil-DNA glycosylase, the enzyme that catalyzes the release of free uracil from single-stranded and double-stranded DNA, has been purified 26,600-fold from HeLa S3 cell extracts. The enzyme preparation was essentially homogeneous as judged by sodium dodecyl sulfate/polyacrylamide gel electrophoresis. The native enzyme is a small monomeric protein of molecular mass 29 kDa. A minor uracil-DNA glycosylase preparation was also obtained in the final chromatographic step. This preparation is homogeneous with a molecular mass of 29 kDa and may represent the mitochondrial enzyme. This report also presents a 700-fold purification of HeLa S3 cell O6-methylguanine-DNA methyltransferase. The glycosylase and methyltransferase showed very similar chromatographic properties. The report indicates that the lability of the methyltransferase upon purification may be a consequence of the total separation of the two DNA repair enzymes or of the possibility that some other stabilizing factor is involved.
Drug delivery to the retina: challenges and opportunities (2003)

Retinal drug delivery is a challenging area in the field of ophthalmic drug delivery. An ideal drug delivery system for the retina and vitreous humor has not yet been found, despite extensive research. Drug delivery to retinal tissue and vitreous via systemic administration is constrained due to the presence of a blood-retinal barrier (BRB) which regulates permeation of substances from blood to the retina. Although intravitreal administration overcomes this barrier, it is associated with several other problems. In recent years, transporter targeted drug delivery has become a clinically significant drug delivery approach for enhancing the bioavailabilities of drug molecules with poor membrane permeability characteristics. Various nutrient transporters, which include peptide, amino acid, folate, monocarboxylic acid transporters and so on, have been reported to be expressed on the retina and BRB. Prodrug derivatisation of drug molecules which target these transporters could result in enhanced ocular bioavailability. Highlighted in this review are various strategies currently employed for drug delivery to the posterior chamber, and novel opportunities that can be exploited to enhance ocular bioavailability of drugs.
Folding of HIV‐1 Envelope glycoprotein involves extensive isomerization of disulfide bonds and conformation‐dependent leader peptide cleavage (2003)

Human immunodeficiency virus binds and enters cells via the Envelope glycoprotein gp160 at its surface. In infected cells, gp160 is found not only on the plasma membrane but also in the endoplasmic reticulum (ER). Our aim was to establish rate-determining steps in the maturation process of gp160, using a radioactive pulse-chase approach. We found that gp160 has an intricate folding process: disulfide bonds start to form during synthesis but undergo extensive isomerization until the correct native conformation is reached. Removal of the leader peptide critically depends on formation of at least some disulfide bonds in subunit gp120 during folding. Envelope folds extremely slowly and therefore resides in the ER longer than other proteins, but the yield of properly folded molecules is high and degradation is undetectable. The large quantity of gp160 in the ER hence is a result of its slow transit through this compartment. We show here that newly synthesized HIV-1 Envelope glycoprotein apparently follows a slow but high-yield folding path in which co- and post-translational formation of disulfide bonds in gp120, disulfide isomerization and conformation dependent removal of the leader sequence are determining and intertwined events.
T-cell responses against CD19+ pediatric acute lymphoblastic leukemia mediated by bispecific T-cell engager (BiTE) are regulated contrarily by PD-L1 and CD80/CD86 on leukemic blasts (2016)

T-cell immunotherapies are promising options in relapsed/refractory B-precursor acute lymphoblastic leukemia (ALL). We investigated the effect of co-signaling molecules on T-cell attack against leukemia mediated by CD19/CD3-bispecific T-cell engager. Primary CD19+ ALL blasts (n≥10) and physiologic CD19+CD10+ bone marrow precursors were screened for 20 co-signaling molecules. PD-L1, PD-1, LAG-3, CD40, CD86, CD27, CD70 and HVEM revealed different stimulatory and inhibitory profiles of pediatric ALL compared to physiologic cells, with PD-L1 and CD86 as most prominent inhibitory and stimulatory markers. PD-L1 was increased in relapsed ALL patients (n=11) and in ALLs refractory to Blinatumomab (n=5). Exhaustion markers (PD-1, TIM-3) were significantly higher on patients' T cells compared to physiologic controls. T-cell proliferation and effector function was target-cell dependent and correlated to expression of co-signaling molecules. Blockade of inhibitory PD-1-PD-L and CTLA-4-CD80/86 pathways enhanced T-cell function whereas blockade of co-stimulatory CD28-CD80/86 interaction significantly reduced T-cell function. Combination of Blinatumomab and anti-PD-1 antibody was feasible and induced an anti-leukemic in vivo response in a 12-year-old patient with refractory ALL. In conclusion, ALL cells actively regulate T-cell function by expression of co-signaling molecules and modify efficacy of therapeutic T-cell attack against ALL. Inhibitory interactions of leukemia-induced checkpoint molecules can guide future T-cell therapies.
Structural Requirements for TFPI-Mediated Inhibition of Neointimal Thickening After Balloon Injury in the Rat (1999)

The intimal thickening that follows vascular injury is inhibited by periprocedural tissue factor pathway inhibitor (TFPI) treatment in animal models. TFPI is a multivalent Kunitz-type protease inhibitor that inhibits factor Xa via its second Kunitz domain and the factor VIIa/tissue factor (TF) complex via its first Kunitz domain. The basic C-terminus of TFPI is required for the binding of TFPI to cell surfaces and cell-bound TFPI mediates the internalization and degradation of factor X and the down regulation of surface factor VIIa/TF activity. The C-terminus of TFPI is also required for its reported direct inhibition of smooth muscle cell proliferation in vitro. To examine the structural requirements for the inhibition of neointimal formation by TFPI, several TFPI-related proteins were tested in the rat carotid angioplasty model: 1) XK(1), a hybrid protein containing the N-terminal portion of factor X and the first Kunitz domain of TFPI that directly inhibits factor VIIa/TF; 2) TFPI(WT), the full-length TFPI molecule that inhibits factor Xa and factor VIIa/TF and binds cell surfaces; 3) TFPI(K36I), an altered form of TFPI that inhibits factor Xa, but not factor VIIa/TF, and binds cell surfaces; 4) TFPI(13-161), a truncated form of TFPI that inhibits factor VIIa/TF but interacts with factor Xa poorly and does not bind to cell surfaces. Seven day infusions of XK(1), TFPI(WT), and high levels of TFPI(K36I) begun the day before balloon-induced vascular injury produced a significant reduction in the intimal hyperplasia measured 28 days after angioplasty. The infusion of high concentrations of TFPI(13-161) was ineffective in this model. These in vivo results directly mirror the ability of each TFPI-related protein to inhibit tissue thromboplastin-induced coagulation in rat plasma: XK(1) approximately TFPI(WT)>TFPI(K36I)>>TFPI(13-161). The studies confirm the important role of TF-mediated coagulation in the smooth muscle proliferation and neointimal thickening that follows vascular injury and suggest that the anticoagulant effect alone of TFPI and TFPI-related proteins is sufficient to explain their therapeutic action.
MIPS: a database for protein sequences and complete genomes (1998)

The MIPS group [Munich Information Center for Protein Sequences of the German National Center for Environment and Health (GSF)] at the Max-Planck-Institute for Biochemistry, Martinsried near Munich, Germany, is involved in a number of data collection activities, including a comprehensive database of the yeast genome, a database reflecting the progress in sequencing the Arabidopsis thaliana genome, the systematic analysis of other small genomes and the collection of protein sequence data within the framework of the PIR-International Protein Sequence Database (described elsewhere in this volume). Through its WWW server (http://www.mips.biochem.mpg.de ) MIPS provides access to a variety of generic databases, including a database of protein families as well as automatically generated data by the systematic application of sequence analysis algorithms. The yeast genome sequence and its related information was also compiled on CD-ROM to provide dynamic interactive access to the 16 chromosomes of the first eukaryotic genome unraveled.
Endometrial VEGF induces placental sFLT1 and leads to pregnancy complications (2014)

There is strong evidence that overproduction of soluble fms-like tyrosine kinase-1 (sFLT1) in the placenta is a major cause of vascular dysfunction in preeclampsia through sFLT1-dependent antagonism of VEGF. However, the cause of placental sFLT1 upregulation is not known. Here we demonstrated that in women with preeclampsia, sFLT1 is upregulated in placental trophoblasts, while VEGF is upregulated in adjacent maternal decidual cells. In response to VEGF, expression of sFlt1 mRNA, but not full-length Flt1 mRNA, increased in cultured murine trophoblast stem cells. We developed a method for transgene expression specifically in mouse endometrium and found that endometrial-specific VEGF overexpression induced placental sFLT1 production and elevated sFLT1 levels in maternal serum. This led to pregnancy losses, placental vascular defects, and preeclampsia-like symptoms, including hypertension, proteinuria, and glomerular endotheliosis in the mother. Knockdown of placental sFlt1 with a trophoblast-specific transgene caused placental vascular changes that were consistent with excess VEGF activity. Moreover, sFlt1 knockdown in VEGF-overexpressing animals enhanced symptoms produced by VEGF overexpression alone. These findings indicate that sFLT1 plays an essential role in maintaining vascular integrity in the placenta by sequestering excess maternal VEGF and suggest that a local increase in VEGF can trigger placental overexpression of sFLT1, potentially contributing to the development of preeclampsia and other pregnancy complications.
Schottky barrier engineering in III–V nitrides via the piezoelectric effect (1998)

A method for enhancing effective Schottky barrier heights in III–V nitride heterostructures based on the piezoelectric effect is proposed, demonstrated, and analyzed. Two-layer GaN/AlxGa1−xN barriers within heterostructure field-effect transistor epitaxial layer structures are shown to possess significantly larger effective barrier heights than those for AlxGa1−xN, and the influence of composition, doping, and layer thicknesses is assessed. A GaN/Al0.25Ga0.75N barrier structure optimized for heterojunction field-effect transistors is shown to yield a barrier height enhancement of 0.37 V over that for Al0.25Ga0.75N. Corresponding reductions in forward-bias current and reverse-bias leakage are observed in current–voltage measurements performed on Schottky diodes.
Normal Colonic Wall Thickness at CT and Its Relation to Colonic Distension (2002)

The normal colonic wall thickness at CT should be regarded as a dynamic value that stays in clear relation to the local colonic distension. In contracted colonic segments, a colonic wall thickness of 6-8 mm may still be normal. On the other hand, a colonic wall measuring 5 and 3 mm should be regarded as thickened if found in colonic segments with a luminal width of >2 and 4 cm, respectively.
Characterization of the human ω‐oxidation pathway for ω‐hydroxy‐very‐long‐chain fatty acids (2008)

Very-long-chain fatty acids (VLCFAs) have long been known to be degraded exclusively in peroxisomes via beta-oxidation. A defect in peroxisomal beta-oxidation results in elevated levels of VLCFAs and is associated with the most frequent inherited disorder of the central nervous system white matter, X-linked adrenoleukodystrophy. Recently, we demonstrated that VLCFAs can also undergo omega-oxidation, which may provide an alternative route for the breakdown of VLCFAs. The omega-oxidation of VLCFA is initiated by CYP4F2 and CYP4F3B, which produce omega-hydroxy-VLCFAs. In this article, we characterized the enzymes involved in the formation of very-long-chain dicarboxylic acids from omega-hydroxy-VLCFAs. We demonstrate that very-long-chain dicarboxylic acids are produced via two independent pathways. The first is mediated by an as yet unidentified, microsomal NAD(+)-dependent alcohol dehydrogenase and fatty aldehyde dehydrogenase, which is encoded by the ALDH3A2 gene and is deficient in patients with Sjögren-Larsson syndrome. The second pathway involves the NADPH-dependent hydroxylation of omega-hydroxy-VLCFAs by CYP4F2, CYP4F3B, or CYP4F3A. Enzyme kinetic studies show that oxidation of omega-hydroxy-VLCFAs occurs predominantly via the NAD(+)-dependent route. Overall, our data demonstrate that in humans all enzymes are present for the complete conversion of VLCFAs to their corresponding very-long-chain dicarboxylic acids.
Complexity of expression of antigenic determinants, recognized by monoclonal antibodies HMFG-1 and HMFG-2, in normal and malignant human mammary epithelial cells. (1983)

Abstract The monoclonal antibodies HMFG-1 and HMFG-21 are produced by hybridomas derived by fusing spleen cells of mice immunized with delipidated preparations of the human milk fat globule. Enzyme-linked immunosorbent (ELISA) assays of Western blots prepared from gels separating components of the milk fat globule showed that both antibodies recognize determinants fouinn dh igh molecular weight components (&amp;gt;400K). Lectin-blocking experiments indicated that both antibodies recognizeo ligosaccharide sequences containing galactose, N-acetyl glucosamine, and, possibly, N-acetyl galactosamine. However, the determinant recognized by HMFG-1 is different from the determinant recognbizye dH MFG-2,w hich may contain or be adjacent to a nonterminal sialic acid residue. The expression of these antigenic determinants by normal mammary epithelial cells cultured from milk (HumE) and by a breast cancer cell line (T47D), was studied. In a live cell, radioimmune assay lower levels of HMFG-1 than HMFG-2 were required for effective binding to HumE cells, whereas HMFG-2 bound to T47D cells at lower concentrations than HMFG-1. Kinetic experiments using 125I-Iabeled antibodies showed that high affinity binding sites for both antibodies are present on HumE cells, but the number of sites binding HMFG-1 is greater than the number of sites binding HMFG-2. Thkei netics of dissociation of labeled antibodies from T47D cells sug gested the presenceo f several sites with different affinities for each antibody. Only in the case of HMFG-2 did some of these sites show a high affinity for the antibody. Western blots of gel-separated components of cell lysates when reacted in an ELISA assay showed that HMFG- 1r eacted with high molecular weight compoinn eHnutms E cells similar to those seen in the HMFG preparation. In contrast, high affinity sites for HMFG-2 were expressed by HumE and T47D on several components of lower molecular weight. All other breast carcinoma lines examined and metastatic cells from two breast cancer patients expressed high affinity binding sites for HMFG-2 on components of varying size (80K to &amp;gt;400K). Only two of five cell lines and cancer cells from one of the two patients expressed high affinity sites for HMFG-1 and these were found on high molecular weight glycoprotein(s3 00-400K). The results are consistent with the interpretation that the HMFG-1 determinant is present in large glycoprotein molecules with complex carbohydrate side chains, and the HMFG-2 determinant is more commonly found in smaller molecules where glycosylation may be incomplete and sialic acid residues more exposed. The preferential binding of HMFG-2 to some breast cancers may therefore reflect a changed glycosylation patteirnn these cells.
Inhibition of HIV-1 infection of primary CD4+ T-cells by gene editing of CCR5 using adenovirus-delivered CRISPR/Cas9 (2015)

CCR5 serves as an essential coreceptor for human immunodeficiency virus type 1 (HIV-1) entry, and individuals with a CCR5(Δ32) variant appear to be healthy, making CCR5 an attractive target for control of HIV-1 infection. The CRISPR/Cas9, which functions as a naturally existing adaptive immune system in prokaryotes, has been recently harnessed as a novel nuclease system for genome editing in mammalian cells. Although CRISPR/Cas9 can be readily delivered into cell lines, due to the large size of the Cas9 protein, efficient delivery of CCR5-targeting CRISPR/Cas9 components into primary cells, including CD4(+) T-cells, the primary target for HIV-1 infection in vivo, remains a challenge. In the current study, following design of a panel of top-ranked single-guided RNAs (sgRNAs) targeting the ORF of CCR5, we demonstrate that CRISPR/Cas9 can efficiently mediate the editing of the CCR5 locus in cell lines, resulting in the knockout of CCR5 expression on the cell surface. Next-generation sequencing revealed that various mutations were introduced around the predicted cleavage site of CCR5. For each of the three most effective sgRNAs that we analysed, no significant off-target effects were detected at the 15 top-scoring potential sites. More importantly, by constructing chimeric Ad5F35 adenoviruses carrying CRISPR/Cas9 components, we efficiently transduced primary CD4(+) T-lymphocytes and disrupted CCR5 expression, and the positively transduced cells were conferred with HIV-1 resistance. To our knowledge, this is the first study establishing HIV-1 resistance in primary CD4(+) T-cells utilizing adenovirus-delivered CRISPR/Cas9.