gebhart/patrepeval huggingface dataset:
A melanocyte-specific gene, Pmel 17, maps near the silver coat color locus on mouse chromosome 10 and is in a syntenic region on human chromosome 12. (1991)

Melanocytes preferentially express an mRNA species, Pmel 17, whose protein product cross-reacts with anti-tyrosinase antibodies and whose expression correlates with the melanin content. We have now analyzed the deduced protein structure and mapped its chromosomal location in mouse and human. The amino acid sequence deduced from the nucleotide sequence of the Pmel 17 cDNA showed that the protein is composed of 645 amino acids with a molecular weight of 68,600. The Pmel 17 protein contains a putative leader sequence and a potential membrane anchor segment, which indicates that this may be a membrane-associated protein in melanocytes. The deduced protein contains five potential N-glycosylation sites and relatively high levels of serine and threonine. Three repeats of a 26-amino acid motif appear in the middle of the molecule. The human Pmel 17 gene, designated D12S53E, maps to chromosome 12, region 12pter-q21; and the mouse homologue, designated D12S53Eh, maps to the distal region of mouse chromosome 10, a region also known to carry the coat color locus si (silver).
A Simple and Efficient Procedure for Generating Random Point Mutations and for Codon Replacements Using Mixed Oligodeoxynucleotides (1988)

A very simple and highly efficient procedure for the generation of single and multiple substitutions in segments of DNA is described which has no requirements for conveniently placed restriction sites, and allows all DNA sequences to be equally accessible. A mixed pool of oligodeoxynucleotides is synthesized by contaminating the monomeric nucleotides with low levels of the other three nucleotides such that the full-length oligonucleotide contains on the average one to two changes per molecule. This pool is used in priming in vitro synthesis of the complementary strand of cloned DNA fragments in M13 or pEMBL vectors which have previously been passed through a dut-, ung- Escherichia coli host. Strong selection for the newly synthesized strand is provided by transforming the heteroduplex into a dut+, ung+ host. Single and multiple substitutions in the carboxy-terminal coding region of the MATa1 gene of Saccharomyces cerevisiae are introduced at high efficiency (25-55%) and the changes are identified by direct sequencing alone. The same principle can be used to generate multiple sets of changes at any specified codon.
Prevalence of Home Parenteral and Enteral Nutrition in the United States (2017)

Compared with results from 1992, the prevalence of HEN has increased dramatically, while the prevalence of HPN has declined.
Improved elongation factor-1 alpha-based vectors for stable high-level expression of heterologous proteins in Chinese hamster ovary cells (2014)

The p1.1 vector was very effective for stable transfection of CHO cells and capable of rapid MTX-driven target gene amplification, while p1.2-Hygro achieved similar eGFP expression levels as p1.1. The set of vectors we have developed should speed-up the process of generating highly productive clonal cell lines while substantially decreasing the associated experimental effort.
A Genetic Modifier of the Gut Microbiome Influences the Risk of Graft-versus-Host Disease and Bacteremia After Hematopoietic Stem Cell Transplantation (2015)

The human gut microbiome is involved in vital biological functions, such as maintenance of immune homeostasis and modulation of intestinal development and enhanced metabolic capabilities. Disturbances of the intestinal microbiota have been associated with development and progression of inflammatory conditions, including graft-versus-host disease (GVHD). The fucosyltransferase 2 (FUT2) gene produces an enzyme that is responsible for the synthesis of the H antigen in body fluids and on the intestinal mucosa. FUT2 genotype has been shown to modify the gut microbiome. We hypothesized that FUT2 genotype influences risk of GVHD and bacterial translocation after allogeneic hematopoietic stem cell transplantation (HSCT). FUT2 genotype was determined in 150 consecutive patients receiving allogeneic HSCT at our center. We abstracted clinical characteristics and outcomes from the transplantation database. Cumulative risk of any acute GVHD varied by FUT2 genotype, with decreased risk in those with A/A genotype and increased risk in those with G/G genotype. In contrast, the cumulative incidence of bacteremia was increased in those with A/A genotype. We conclude that the FUT2 genotype influences risk of acute GVHD and bacteremia after HSCT. We hypothesize that the mechanisms involve altered intestinal surface glycosylation and microbial composition but this requires additional study.
Synthetic, implantable polymers for local delivery of IUdR to experimental human malignant glioma (1998)

Synthetic, implantable biodegradable polymers provide the local, controlled release of IUdR and result in the high, local delivery of IUdR to experimental intracranial human malignant glioma. This technique holds promise for the local delivery of IUdR for radiosensitization of human brain tumors.
Determination of the Site-specific O-Glycosylation Pattern of the Porcine Submaxillary Mucin Tandem Repeat Glycopeptide (1997)

The heterogeneously glycosylated 81-residue tryptic tandem repeat glycopeptide from porcine submaxillary mucin (PSM) has been isolated and its glycosylation pattern determined by amino acid sequencing. Key to these studies is the ability to trim the structurally heterogeneous PSM oligosaccharide side chains to homogeneous GalNAc monosaccharide side chains by mild trifluoromethanesulfonic acid treatment. Trypsin treatment of trifluoromethanesulfonic acid-treated PSM releases the 81-residue tandem repeat as an ensemble of 81-residue glycopeptides with different glycosylation patterns. Automated amino acid sequencing using Edman degradative chemistry of the repeat was used to determine the extent of glycosylation of nearly every Ser and Thr residue. The Thr residues are all highly glycosylated within the range of 73-90%, giving an average Thr glycosylation of 83%. In contrast, the Ser residues display a wide range of glycosylations, ranging between 33 and 95%, giving an average Ser glycosylation of 74%. These data are consistent with the known elevated glycosylation of Thr peptides over Ser peptides for the porcine UDP-N-acetylgalactosamine:polypeptide N-acetylgalactosaminyltransferase. It is also observed that the extent of glycosylation of the repeat correlates poorly with published predictive methods. An examination of the sequences surrounding the glycosylation sites reveals that nearly all of the highly glycosylated sites have a penultimate Gly residue, whereas those that are less highly glycosylated have medium to large side chain penultimate residues. As observed by others, glycosylation also appears to be modulated by the presence of Pro residues. On the basis of these findings we suggest that the acceptor peptide binds the transferase in a beta-like conformation and that penultimate residue side chain steric interactions may play a role in determining extent that a given Ser or Thr is glycosylated. A model for the GalNAc transferase peptide binding site is proposed.
Engineering enzymes for improved catalytic efficiency: a computational study of site mutagenesis in epothilone-B hydroxylase (2009)

Epothilone F, 21-hydroxyl-epothilone B, is an intermediate in the synthesis of BMS-310705, an antitumor compound that has been evaluated in Phase I clinical trials. A bioconversion process utilizing the Gram-positive bacterium Amycolatopsis orientalis was used to prepare epothilone F from epothilone B. In order to improve the yield of epothilone F, a mutagenesis program was performed with the goal of engineering the epothilone-B hydroxylase (EBH) enzyme to improve the yield of epothilone F through oxidative biotransformation. The mutations in EBH increased the yield of epothilone F from 21% in the recombinant expression system to higher than 80% utilizing the best EBH mutants. The studies described here show how a homology model of EBH was used to obtain an understanding of the possible mechanism that led to improved yield of epothilone F in the mutated enzymes. A novel aspect of this study is that it provides some insight into how mutations distant from the binding site can affect enzyme activity.
Read/write performance and reliability of a flying optical head using a monolithically integrated LD–PD (1991)

A flying head using the switching characteristics of an optically switched laser diode is shown to have an excellent read/write performance and head-disk interface. This head consists of an aluminum nitride slider and a 1.3-microm wavelength InGaAsP laser diode monolithically integrated with a photodetector (LD-PD). A ridged waveguide is fabricated on top of the LD facet to converge the light beam. The lensless flying head has a minimum power of 18 mW for writing information (at 1 MHz) at a medium velocity of 7 m/s. The disk has a SiN protective layer over a SbTeGe phase-change recording medium. The head signal remains good after more than 5 x 10(4) contact start/stop cycles and 4.4 x 10(8) passes in an experimental room environment.
Characterization of and modulation by a beta-subunit of a human maxi KCa channel cloned from myometrium. (1995)

cDNAs encoding functional maxi KCa channel alpha-subunits (hslo) were cloned from human myometrium. Northern blot analysis revealed a high abundance of mRNA in human uterine smooth muscle. Calcium- and voltage-activated K+ currents were recorded from Xenopus laevis oocytes injected with hslo cRNA and compared with currents after reconstitution of oocyte membranes expressing cloned maxi KCa channels. The expressed channels displayed characteristics of native maxi KCa channels, including large conductance (280 pS in symmetrical 110 mM K+), calcium sensitivity, kinetics and pharmacology. Currents were activated by niflumic acid; blocked by tetraethylammonium, charybdotoxin and iberiotoxin; and were insensitive to lemakalim, pinacidil, apamin and 4-aminopyridine. Coexpression with the beta-subunit, cloned from bovine trachea smooth muscle, dramatically increased the apparent calcium sensitivity as evident from a leftward shift of the voltage-activation curves. Half maximal activation (V1/2), measured in 10 microM Ca2+, was 12 +/- 18 mV (+/- SD, n = 62) for the alpha-subunit alone and -87 +/- 10 mV (+/- SD, n = 39) in presence of the beta-subunit.
Delivery of Adeno-Associated Virus Vectors to the Fetal Retina: Impact of Viral Capsid Proteins on Retinal Neuronal Progenitor Transduction (2003)

The development of fetal ocular gene transfer may be useful as a therapeutic tool for the prevention of retinal genetic disorders with congenital or early clinical manifestations. In this study we explored the neural progenitor transduction patterns of adeno-associated virus (AAV) vectors following delivery to the developing retina. Recombinant vectors with the same genome carrying the enhanced green fluorescent protein (EGFP) transgene packaged in capsids of differing serotypes (serotypes 1, 2, and 5, termed AAV2/1, AAV2/2, and AAV2/5, respectively) were created. Delivery of the AAV vectors during early retinal development resulted in efficient and stable transduction of retinal progenitors. Vector surface proteins and the developmental status of the retina profoundly affected viral tropism and transgene distribution. The procedure is not detrimental to retinal development and function and therefore provides a safe delivery vehicle for potential therapeutic applications and a means of assessing the mechanisms of retina development and disease.
Detection of cell free placental DNA in maternal plasma: direct evidence from three cases of confined placental mosaicism (2004)

Fetal cells are consistently found in the maternal circulation, and polymerase chain reaction based studies have led to the identification of cell free fetal DNA (fetal DNA) in maternal blood. Approximately 1.2 nucleated fetal cells/ml of whole blood from women carrying a male fetus were detectable,1 and relative enrichment of fetal DNA was detected in the maternal plasma and serum.2 The amount of fetal DNA in the maternal blood increases with progression of pregnancy, and 3.4–6.2% of the total maternal plasma DNA during pregnancy was of fetal origin.3 Therefore, cell free fetal DNA in pregnant women’s plasma is useful for non-invasive prenatal diagnosis, especially for detection of fetal sex,3,4 RhD blood type,5–7 and gene mutations of paternal origin.8–10 Previous studies indicated that pregnant women with pre-eclampsia,11 placenta previa12 and fetal chromosome abnormalities13 tend to have elevated levels of fetal DNA in their plasma. Since functional or structural abnormalities of the placenta and destruction of the trophoblast may be associated with these diseases,14 it is suggested that cell free fetal DNA is of placental origin. This implies that quantitative analysis of fetal DNA may be valuable to screen for placental dysfunction. Ng et al15 recently reported that placental mRNA is present in the maternal circulation, and suggested that the same might occur for placental DNA,16 However, no direct evidence has been given for placenta derived cell free fetal DNA in the maternal blood, although its clinical use is growing.17

Confined placental mosaicism, which is defined by the presence of abnormal karyotypes only in the placenta while the fetus itself is usually diploid,18 may occur through a loss of the extra chromosome in a trisomic zygote during an early mitotic cell division in only the …
One-pot synthesis of nanostructured carbon materials from carbon dioxide via electrolysis in molten carbonate salts (2016)

As the primary culprit of greenhouse effect, carbon dioxide has garnered global attention, and the technologies currently being developed to reduce the emission of CO2 vary widely. In this study, CO2 was electrochemically reduced in various molten mixtures of LiNaK carbonates to carbon nanomaterials. By regulating the electrolysis current density, electrolyte, and electrolytic temperature, the carbon products had different morphologies of honeycomb-like and nanotubular structures. A transition from a honeycomb/platelet to nanomaterial carbon morphology was observed to occur at ∼600 °C with increase in temperature. The observation of nanostructures is consistent with a higher diversity of structures possible with enhanced rearrangement kinetics that can occur at higher temperature. A high yield of a carbon nanotube (CNT) was not observed from a LiNaK electrolyte, no CNTs are formed from a NaK carbonate electrolyte, but a high yield is observed from pure Li, or mixed LiNa or mixed LiBa carbonate electrolytes, and the carbon nanotube product diameter is observed to increase with increasing electrolysis time.
Interaction between Mycobacterium avium subsp. paratuberculosis and environmental protozoa (2006)

This study demonstrated that ingestion of Map by and survival and multiplication of Map within Acanthamoeba spp. is possible, and that Map cells ingested by amoebae are more resistant to inactivation by chlorine than free Map cells. These findings have implications with respect to the efficacy of chlorination applied to Map infected surface waters.
ERECTA family genes regulate development of cotyledons during embryogenesis (2014)

Receptor-like kinases are important regulators of plant growth. Often a single receptor is involved in regulation of multiple developmental processes in a variety of tissues. ERECTA family (ERf) receptors have previously been linked with stomata development, above-ground organ elongation, shoot apical meristem function, flower differentiation and biotic/abiotic stresses. Here we explore the role of these genes during embryogenesis. ERfs are expressed in the developing embryo, where their expression is progressively limited to the upper half of the embryo. During embryogenesis ERfs redundantly stimulate the growth of cotyledons by promoting cell proliferation and inhibiting premature stomata differentiation.
Biosimilar, biobetter and next generation therapeutic antibodies (2011)

On November 18, 2010, the European Medicine Agency (EMA) released a draft guideline on similar medicinal products containing monoclonal antibodies (mAbs), following a workshop organized by the agen...
Development of a Highly Efficient Gene Targeting System Induced by Transient Repression of YKU80 Expression in Candida glabrata (2007)

In the pathogenic yeast Candida glabrata, gene targeting to generate knockouts and "knockins" is a potentially powerful method for the analysis of gene function. Its importance increased after the C. glabrata genome sequence project, but progress in the field is hampered by inefficient mechanisms for gene targeting. With the use of 40-bp homologous flanking DNA, no gene targeting was identified. To address this issue, YKU80 was disrupted, leading to an increase in targeting efficiency of 5.1% using 40-bp flanking homologous DNA. To harness the beneficial effects of YKU80 inactivation on gene targeting frequency without incurring any negative effects, such as synthetic sickness or lethality, we developed a new system whereby the expression of YKU80 was restored following a transient knockdown of expression during transformation. Strains used for this new system carried a SAT1 flipper in the YKU80 promoter region, which was used to repress expression during transformation but was spontaneously excised from the locus after the transformation. By using this strain, DNA damage induced by methyl methane sulfonate, H(2)O(2), UV irradiation, and hydroxyurea before and during gene targeting was evaluated and the mutation rate of URA3 was determined. No significant effects of the SAT1 flipper on these processes have been identified. After the SAT1 flipper is excised, a 34-bp FLP recombination target sequence is left in the promoter region. However, the levels of mRNA transcription were restored and no difference in the survival ratio in vivo compared to that with the YKU80 wild-type strain was identified.
Targeting Perlecan in Human Keratinocytes Reveals Novel Roles for Perlecan in Epidermal Formation (2005)

Heparin-binding growth factors are crucial for the formation of human epidermis, but little is known about the role of heparan sulfate proteoglycans in this process. Here we investigated the role of the heparan sulfate proteoglycan, perlecan, in the formation of human epidermis, by utilizing in vitro engineered human skin. By disrupting perlecan expression either in the dermis or the epidermis, we found that epidermally derived perlecan is essential for epidermal formation. Perlecan-deficient keratinocytes formed a strikingly thin and poorly organized epidermis because of premature apoptosis and failure to complete their stratification program. Exogenous perlecan fully restored epidermal formation. Perlecan deposition in the basement membrane zone correlated with formation of multilayered epidermis. Perlecan deficiency, however, had no effect on the lining and deposition of major basement membrane components as was evident by a continuous linear staining of laminin and collagen IV. Similarly, perlecan deficiency did not affect the distribution of beta1 integrin. Addition of the perlecan ligand, fibroblast growth factor 7, protected perlecan-deficient keratinocytes from cell death and improved the thickness of the epidermis. Taken together, our results revealed novel roles for perlecan in epidermal formation. Perlecan regulates both the survival and terminal differentiation steps of keratinocytes. Our results suggested a model whereby perlecan regulates these processes via controlling the bioavailability of perlecan-binding soluble factors involved in epidermal morphogenesis.
Split tolerance of Thl and Th2 cells in tolerance to Theiler's murine encephalomyelitis virus (1993)

Theiler's murine encephalomyelitis virus (TMEV) produces a chronic, inflammatory demyelinating disease in susceptible mouse strains that is used as a model for multiple sclerosis. Because disease susceptibility correlates temporally with the development of virus-specific delayed-type hypersensitivity (DTH) responses, we studied methods and mechanisms by which virus-specific DTH could be specifically inhibited. The intravenous injection of UV-inactivated TMEV coupled to syngeneic splenocytes via a carbodiimide linkage (TMEV-SP), prior to immunization, induced a significant degree of tolerance in virus-specific helper (Th) cells as determined by decreased DTH and T cell proliferative responses, and decreased interleukin (IL)-2 and interferon (IFN)-gamma protein and mRNA levels. In contrast to the reduced levels of Th1-specific lymphokine mRNA levels, IL-4-specific mRNA levels in response to virus stimulation were not affected in tolerant mice. Surprisingly, the total anti-TMEV antibody response in DTH tolerant mice was enhanced 20-100-fold over sham-tolerized controls and was composed of reduced levels of anti-virus IgG2a, but dramatically increased levels of anti-virus IgG1. The "split-tolerance" was antigen specific, dependent on the concentrations of TMEV and carbodiimide used in the coupling procedure, and varied with the number of coupled syngeneic splenocytes administered. The fixative effects of carbodiimide on antigen-presenting function were necessary for the induction of DTH tolerance with TMEV-SP, since intravenous administration of virus coupled to splenocytes via a biotin-avidin linkage led to enhanced virus-specific antibody responses, but was unable to inhibit DTH unless concomitantly fixed with carbodiimide. Collectively, the data indicate that Th1 cells (mediating DTH, IL-2 and IFN-gamma production, and helper function for IgG2a production) were specifically anergized, with concomitant stimulation of Th2 cells (producing IL-4 and mediating helper function for IgG1 antibody production).
Engineering an endomorphin-2 gene for use in neuropathic pain therapy (2007)

Endomorphin-2 (EM-2) is a carboxy-amidated tetrapeptide that binds the mu-opioid receptor with high affinity and is analgesic in several animal models of pain. Endomorphin peptides have been isolated from bovine and human brain, but no DNA sequences corresponding to a potential preproendomorphin gene have been identified in human genome sequence databases. In this study we designed a tripartite synthetic gene to direct production, cleavage, and amidation of EM-2, and placed the endomorphin gene expression cassette in a replication defective Herpes simplex virus (HSV) vector (vEM2). Biosynthesis of amidated endomorphin-2 peptide was quantified by radioimmunoassay and the identity confirmed by mass spectroscopy following vEM2 transduction of cultured primary dorsal root ganglion neurons. Subcutaneous inoculation of vEM2 resulted in vector delivery to dorsal root ganglion where expression of EM-2 peptide from the engineered gene was confirmed by ELISA. vEM2 delivery provided an analgesic effect in the spinal nerve ligation model of neuropathic pain measured by reduction of mechanical allodynia and thermal hyperalgesia. The analgesic effect of vEM2 was blocked by intrathecal delivery of the mu-receptor antagonist CTOP. The gene construct design described represents a broadly useful platform for biosynthesis and delivery of carboxy-amidated peptides for therapeutic and experimental purposes, and the results demonstrate that HSV-gene transfer to sensory neurons provides an effective means to achieve local biosynthesis of endomorphin peptides for the treatment of chronic pain.
Reconstruction of an object from the modulus of its Fourier transform (1978)

We present a digital method for solving the phase-retrieval problem of optical-coherence theory: the reconstruction of a general object from the modulus of its Fourier transform. This technique should be useful for obtaining high-resolution imagery from interferometer data.