gebhart/patrepeval huggingface dataset:
Synthesis of Glycopeptide-conjugates via Ring-opening Polymerization of Sugar-substituted .ALPHA.-Amino Acid N-Carboxyanhydrides (GlycoNCAs). (1997)

This article briefly reviews our recent investigation on the synthesis and biological functions of artificial glycopeptide-conjugates via ring-opening polymerization of D-glucose- or N-acetyl-D-glucosamine-substituted L-serine N-carboxyanhydrides (glycoNCAs). Primary amine-initiated polymerization of glycoNCAs proceeded without side reactions to give linear glycopeptide-conjugates of controlled chain lengths. A variety of block copolymers and graft copolymers containing glycopeptide segments were synthesized by utilizing the living nature of the ring-opening polymerization of glycoNCAs. Reaction of primary amine-terminated poly(amido amine) dendrimers of different generations with a slight excess of glycoNCAs at -30°C gave a new type of dendrimers whose surfaces were modified with the corresponding mono(glycopeptide) moieties. Oligomerization of glycoNCAs with poly(amido amine) dendrimer as a multifunctional macroinitiator at 27°C provided globular macromolecules coated with oligo(glycopeptide) chains. Molecular recognition abilities of these linear and globular glycopeptide-conjugate macromolecules were evaluated by the hemagglutination inhibition assay.
Neurogenic potential of progenitors derived from human circulating CD14+ monocytes (2006)

We previously reported a primitive cell fraction derived from human circulating CD14+ monocytes, named monocyte-derived multipotential cells (MOMC), that can differentiate along mesenchymal lineages, including bone, cartilage, fat, skeletal muscle and cardiac muscle. In this study, we investigated whether MOMC can differentiate into the neuronal lineage. MOMC were fluorescently labelled and cocultivated with a primary culture of rat neurons for up to 4 weeks. The protein and gene expressions of neuron-specific markers in the human MOMC were evaluated over time using immunohistochemistry, in situ hybridization and reverse transcription followed by PCR. Shortly after cocultivation with rat neurons, nearly all the MOMC expressed early neuroectodermal markers, Mash1, Neurogenin2 and NeuroD, together with nestin, an intermediate filament expressed in neurogenesis. After 14 days of coculture, a subpopulation of MOMC displayed a multipolar morphology with elongated neurites and expressed mature neuron-specific markers, including neurofilament, microtubule-associated protein type 2, beta3-tubulin, NeuN and Hu. Transdifferentiation of monocytes into the neuroectodermal lineage was shown by the simultaneous expression of proneural markers and CD45/CD14 early in the differentiation process. The cocultivated MOMC retained their proliferative capacity for at least 16 days. Finally, the neuronal differentiation of MOMC was observed when they were cultured with neurons without cell-to-cell contact. The capacity of MOMC to differentiate into both mesodermal and neuroectodermal lineages suggests that circulating CD14+ monocytes are more multipotential than previously thought.
Fbx15 Is a Novel Target of Oct3/4 but Is Dispensable for Embryonic Stem Cell Self-Renewal and Mouse Development (2003)

Embryonic stem (ES) cells are immortal and pluripotent cells derived from early mammalian embryos. Transcription factor Oct3/4 is essential for self-renewal of ES cells and early mouse development. However, only a few Oct3/4 target genes have been identified. In this study, we found that F-box-containing protein Fbx15 was expressed predominantly in mouse undifferentiated ES cells. Inactivation of Oct3/4 in ES cells led to rapid extinction of Fbx15 expression. Reporter gene analyses demonstrated that this ES cell-specific expression required an 18-bp enhancer element located approximately 500 nucleotides upstream from the transcription initiation site. The enhancer contained an octamer-like motif and an adjacent Sox-binding motif. Deletion or point mutation of either motif abolished the enhancer activity. The 18-bp fragment became active in NIH 3T3 cells when Oct3/4 and Sox2 were coexpressed. A gel mobility shift assay demonstrated cooperative binding of Oct3/4 and Sox2 to the enhancer sequence. In mice having a beta-galactosidase gene knocked into the Fbx15 locus, 5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside staining was detected in ES cells, early embryos (two-cell to blastocyst stages), and testis tissue. Despite such specific expression of Fbx15, homozygous mutant mice showed no gross developmental defects and were fertile. Fbx15-null ES cells were normal in morphology, proliferation, and differentiation. These data demonstrate that Fbx15 is a novel target of Oct3/4 but is dispensable for ES cell self-renewal, development, and fertility.
Use of Bacteriophage λ Recombination Functions To Promote Gene Replacement in Escherichia coli (1998)

Replacement of Escherichia coli's RecBCD function with phage lambda's Red function generates a strain whose chromosome recombines with short linear DNA fragments at a greatly elevated rate. The rate is at least 70-fold higher than that exhibited by a recBC sbcBC or recD strain. The value of the system is highlighted by gene replacement with a PCR-generated DNA fragment. The deltarecBCD::Plac-red kan replacement allele can be P1 transduced to other E. coli strains, making the hyper-Rec phenotype easily transferable.
A Multiparameter Wearable Physiologic Monitoring System for Space and Terrestrial Applications (2005)

A novel, unobtrusive and wearable, multiparameter ambulatory physiologic monitoring system for space and terrestrial applications, termed LifeGuard, is presented. The core element is a wearable monitor, the crew physiologic observation device (CPOD), that provides the capability to continuously record two standard electrocardiogram leads, respiration rate via impedance plethysmography, heart rate, hemoglobin oxygen saturation, ambient or body temperature, three axes of acceleration, and blood pressure. These parameters can be digitally recorded with high fidelity over a 9-h period with precise time stamps and user-defined event markers. Data can be continuously streamed to a base station using a built-in Bluetooth RF link or stored in 32 MB of on-board flash memory and downloaded to a personal computer using a serial port. The device is powered by two AAA batteries. The design, laboratory, and field testing of the wearable monitors are described.
Recent innovations in the structural analysis of heparin (2016)

Heparin, the widely used anticoagulant drug, is unusual among major pharmaceutical agents being neither single chemical entity nor a defined mixture of compounds. Its composition, while conforming to approximate average disaccharide composition or sulfation levels, exhibits heterogeneity and variability depending on the source, as well as its geographical origin. Furthermore, individual polysaccharide chains, whose physico-chemical properties are extremely similar, cannot be separated with current state-of-the-art techniques, presenting a challenge to those interested in the quality control of heparin, in ensuring its provenance and safety, and those with an interest in investigating the relationships between its structure and biological activity. The review consists of two main sections: The first is the Introduction, comprising (i) The History, Occurrence and Use of Heparin and (ii) Approaches to Structure-Activity Relationships. The second section is Improved Techniques for Structural Analysis, comprising; (i) Separation and Identification, (ii) Spectroscopic Methods, (iii) Enzymatic Approaches and (iv) Other Physico-Chemical Approaches. The ~60 references cover recent technological advances in the study of heparin structural analysis, largely since 2010.
A visual software process language (1992)

essential element of the nextgeneration Integrated Project Support Environments (IPSEs) is expected to be the ability to create an internal, customized model of the software development process being used, written in a Process Programming Language (PPL). Information from this model would be used by the IPSE to automate some portions of the process, guide others, and remove administrative burden from the users. Any PPL must be flexible to model all potential processes, yet detailed enough to be of real use to the IPSE. Such an IPSE, while supporting initial development, will also be essential for the long-term maintenance of software.
The Development of an Aza‐C‐Glycoside Library Based on a Tandem Staudinger/Aza‐Wittig/Ugi Three‐Component Reaction (2012)

Abstract We report the tandem Staudinger/aza‐Wittig/Ugi three‐component reaction mediated synthesis of a 64‐member compound library of aza‐C‐glycosides. The library is composed of four pyrrolidine and three piperidine scaffolds, onto which a number of functional groups is grafted to form seven sublibraries. Variation in the library is achieved by transformation of two pentoses and a hexose into the corresponding 4‐azidopentanal and 5‐azidohexanal derivatives as precursors for the Staudinger/aza‐Wittig process. Further variation is achieved by using different isocyanides as well as protective‐ and functional‐group manipulations on the fully protected Ugi‐3CR intermediates. Preliminary biological evaluation of the compound library revealed several low micromolar inhibitors of human acid glucosylceramidase.
Response and resilience of soil biocrust bacterial communities to chronic physical disturbance in arid shrublands (2011)

The impact of 10 years of annual foot trampling on soil biocrusts was examined in replicated field experiments at three cold desert sites of the Colorado Plateau, USA. Trampling detrimentally impacted lichens and mosses, and the keystone cyanobacterium, Microcoleus vaginatus, resulting in increased soil erosion and reduced C and N concentrations in surface soils. Trampled biocrusts contained approximately half as much extractable DNA and 20-52% less chlorophyll a when compared with intact biocrusts at each site. Two of the three sites also showed a decline in scytonemin-containing, diazotrophic cyanobacteria in trampled biocrusts. 16S rRNA gene sequence and terminal restriction fragment length polymorphism (T-RFLP) analyses of soil bacteria from untrampled and trampled biocrusts demonstrated a reduced proportion (23-65% reduction) of M. vaginatus and other Cyanobacteria in trampled plots. In parallel, other soil bacterial species that are natural residents of biocrusts, specifically members of the Actinobacteria, Chloroflexi and Bacteroidetes, became more readily detected in trampled than in untrampled biocrusts. Replicate 16S rRNA T-RFLP profiles from trampled biocrusts at all three sites contained significantly more fragments (n = 17) than those of untrampled biocrusts (n≤6) and exhibited much higher variability among field replicates, indicating transition to an unstable disturbed state. Despite the dramatic negative impacts of trampling on biocrust physical structure and composition, M. vaginatus could still be detected in surface soils after 10 years of annual trampling, suggesting the potential for biocrust re-formation over time. Physical damage of biocrusts, in concert with changing temperature and precipitation patterns, has potential to alter performance of dryland ecosystems for decades.
MEEF as a matrix (2002)

Mask error enhancement factor (MEEF) depends on the two groups of factors. The first group is process-related, and includes parameters such as illumination settings and exposure dose. The second group is mask-related and includes feature sizes, feature shapes, and proximity interactions between features. Factors from the second group have not been studied to the same depth as factors of the first group. Only simple shapes like dense lines, isolated lines, and contact holes, each with only one degree of the distortion freedom, have been addressed by the traditional MEEF theory. We present here a comprehensive MEEF theory for arbitrary 2D mask shapes, with multiple degrees of the distortion freedom. This theory provides a rigorous formal framework for studying impact of the complex mask errors. We introduce mask error enhancement matrix (MEEM) to capture self- and cross-enhancement effects when neighboring mask distortions collectively contribute into the wafer errors. The norm of this matrix is called a generalized MEEF, an important characteristic of the pattern transfer process. The Singular Value Decomposition of MEEM naturally groups edges of the mask shapes into the proximity-related sets, each with a distinct G-MEEF value. Ranking mask areas by this value helps to identify difficult-to-print regions and to design MEEF-sensitive test patterns. An application of matrix MEEF theory is shown to be iterative feedback techniques for model-based OPC.
The Treatment Outcomes in 9 Cases with Meniscal Cyst and Literature Review (2004)

We present 9 cases of meniscal cyst diagnosed at the Chinese Medical University Hospital from 1999 to 2003. We summarize the symptoms/signs, the duration of symptoms, image findings and treatment of these 9 cases. Four women and five men comprised the study group. Patient age ranged from 18 to 51 years (average 33.4 years). Five of the cysts were in the right knee and four were in the left knee. Eight cysts were in lateral side and one cyst in the medial side. History of trauma was documented in three patients. All cases received MRI examination of affected knees before surgical treatment. The follow-up period ranged from 12 to 22 months (average 18 months). Pain in the joint line of the affected knees was the most important symptoms in all the patients. The physical examination revealed a palpable mass and local swelling in the affected knee joint in all patients. Yet the Pisani sign was not noted in these patients. There was no obvious bony erosion in all these cases on radiographic examination. All magnetic resonance imaging studies revealed decreased and homogenous signal intensity in T1WI and increased signal intensity in T2WI in the cystic lesions. The MRI also revealed eight meniscal cysts contact with anterior horn or mid-body of the lateral menisus. There was associated injury of the knees in three patients. The average diameter of the cysts was 3.4cm. All our cases were successfully treated with arthroscopy and open excision of the cyst. The mensical cysts in our series located more in the lateral side than in the medical side. Most cysts were located in the anterior and mid-body of the lateral meniscus. Only three meniscal cysts were associated with lateral meniscal tear. There was no recurrence noted at outpatient clinic follow-up. All the cases were able to return to full activities without limitation
STIMULATION OF (PRO-)INSULIN BIOSYNTHESIS AND RELEASE BY GASTRIC INHIBITORY POLYPEPTIDE IN ISOLATED ISLETS OF RAT PANCREAS (1979)

(Pro-)Insulin biosynthesis ([3H]leucine incorporation) and insulin secretion were studied in collagenase-isolated rat islets incubated for 3 hours at 1 and 2 mg/ml glucose in the presence of gastric inhibitory polypeptide (GIP). GIP augmented [3H]leucine incorporation and release of insulin at both glucose concentrations. In a second series of experiments it was found that an amino acid mixture was without influence on the insulotrophic action of GIP. Combined stimulation of insulin release by GIP and glucagon did not result in higher insulin output than observed in the presence of each substance alone. Thus GIP, in constrast to many other gastrointestinal peptides, however similar to glucagon, enhances not only release but also biosynthesis of insulin. This insulinotrophic action can be observed already at a glucose concentration of 1 mg/ml. The results underline the outstanding role which GIP appears to play in the regulation of beta-cell function.
Human Factor IX Transgenic Sheep Produced by Transfer of Nuclei from Transfected Fetal Fibroblasts (1997)

Ovine primary fetal fibroblasts were cotransfected with a neomycin resistance marker gene (neo) and a human coagulation factor IX genomic construct designed for expression of the encoded protein in sheep milk. Two cloned transfectants and a population of neomycin (G418)-resistant cells were used as donors for nuclear transfer to enucleated oocytes. Six transgenic lambs were liveborn: Three produced from cloned cells contained factor IX and neo transgenes, whereas three produced from the uncloned population contained the marker gene only. Somatic cells can therefore be subjected to genetic manipulation in vitro and produce viable animals by nuclear transfer. Production of transgenic sheep by nuclear transfer requires fewer than half the animals needed for pronuclear microinjection.
Killing of non‐Hodgkin lymphoma cells by autologous CD19 engineered T cells (2005)

Adoptive immunotherapy with tumour-specific T cells is an emerging technology that may be applicable to a broad range of cancers. However, tumours can avoid T cell-mediated attack through multiple mechanisms including downregulation of major histocompatability complex (MHC). Consequently, engineering T cells to target intact protein antigen directly, thus bypassing the need for MHC presentation, can facilitate T cell targeting of tumour cells. Peripheral blood lymphocytes from nine of nine patients with non-Hodgkin lymphoma (NHL) were successfully gene-modified to express a receptor consisting of a CD19 single chain variable fragment (scFv) fused to the T cell CD3zeta signalling molecule. These T cells were functionally active against the CD19(+) Raji Burkitt's lymphoma cell line. Importantly, engineered T cells from seven of nine NHL patients efficiently lysed autologous lymph node tumour biopsy cells. There was a clear correlation between levels of CD19 expression on the tumour and effective killing by the engineered T cells. For two patients with a low or absent CD19(+) cells within the biopsy, no significant killing was observed. These results demonstrate that patients with CD19(+) NHL would be suitable candidates for this form of therapy in the setting of a phase I clinical trial.
Spontaneous Intermolecular Amide Bond Formation between Side Chains for Irreversible Peptide Targeting (2010)

Peptides and synthetic peptide-like molecules are powerful tools for analysis and control of biological function. One major limitation of peptides is the instability of their interactions with biomolecules, because of the limited accessible surface area for noncovalent interactions and the intrinsic flexibility of peptides. Peptide tags are nonetheless fundamental for protein detection and purification, because their small size minimizes the perturbation to protein function. Here we have designed a 16 amino acid peptide that spontaneously forms an amide bond to a protein partner, via reaction between lysine and asparagine side chains. This depended upon splitting a pilin subunit from a human pathogen, Streptococcus pyogenes, which usually undergoes intramolecular amide bond formation to impart mechanical and proteolytic stability to pili. Reaction of the protein partner was able to proceed to 98% conversion. The amide bond formation was independent of redox state and occurred at pH 5-8. The reaction was efficient in phosphate buffered saline and a wide range of biological buffers. Surprisingly, amide bond formation occurred at a similar rate at 4 and 37 degrees C. Both peptide and protein partners are composed of the regular 20 amino acids and reconstituted efficiently inside living E. coli. Labeling also showed high specificity on the surface of mammalian cells. Irreversible targeting of a peptide tag may have application in bioassembly, in cellular imaging, and to lock together proteins subject to high biological forces.
Chromatin Architecture near a Potential 3′ End of the Igh Locus Involves Modular Regulation of Histone Modifications during B-Cell Development and In Vivo Occupancy at CTCF Sites (2005)

The murine Igh locus has a 3' regulatory region (3' RR) containing four enhancers (hs3A, hs1,2, hs3B, and hs4) at DNase I-hypersensitive sites. The 3' RR exerts long-range effects on class switch recombination (CSR) to several isotypes through its control of germ line transcription. By measuring levels of acetylated histones H3 and H4 and of dimethylated H3 (K4) with chromatin immunoprecipitation assays, we found that early in B-cell development, chromatin encompassing the enhancers of the 3' RR began to attain stepwise modifications typical of an open conformation. The hs4 enhancer was associated with active chromatin initially in pro- and pre-B cells and then together with hs3A, hs1,2, and hs3B in B and plasma cells. Histone modifications were similar in resting splenic B cells and in splenic B cells induced by lipopolysaccharide to undergo CSR. From the pro-B-cell stage onward, the approximately 11-kb region immediately downstream of hs4 displayed H3 and H4 modifications indicative of open chromatin. This region contained newly identified DNase I-hypersensitive sites and several CTCF target sites, some of which were occupied in vivo in a developmentally regulated manner. The open chromatin environment of the extended 3' RR in mature B cells was flanked by regions associated with dimethylated K9 of histone H3. Together, these data suggest that 3' RR elements are located within a specific chromatin subdomain that contains CTCF binding sites and developmentally regulated modules.
A New Weapon for Attacking Tumor Blood Vessels (2008)

The vascular endothelial growth factor is the target of the antiangiogenic drug bevacizumab. Another protein, placental growth factor, also represents a promising target for countering tumor angiogenesis.
Human bone marrow osteoprogenitors express estrogen receptor‐alpha and bone morphogenetic proteins 2 and 4 mRNA during osteoblastic differentiation (1999)

Understanding the mechanisms that control the proliferation and commitment of human stem cells into cells of the osteogenic lineage for the preservation of skeletal structure is of basic importance in bone physiology. This study examines some aspects of the differentiation in vitro of human bone marrow fibroblastic cells cultured in the absence (basal media) or presence of 1nM dexamethasone and 50 μg/ml ascorbate for 6, 10, 14, and 21 days. Northern blot analysis and in situ hybridisation with digoxygenin-labelled riboprobes for Type I collagen, osteocalcin, bone morphogenetic proteins 2 (BMP-2), and 4 (BMP-4) and the estrogen receptor alpha (ERα), together with immunocytochemical analysis of ERα expression and histochemical staining of alkaline phosphatase was performed. In basal media, alkaline phosphatase activity and collagen expressions were detected at day 6, ERα from day 10 and osteocalcin from day 10. In the presence of dexamethasone and ascorbate, cell proliferation and alkaline phosphatase were markedly stimulated over 10 to 14 days with a dramatic increase in the temporal expression of Type I collagen, ERα, and osteocalcin mRNAs in these cultures. Northern blot analysis showed cells cultured in basal media, expressed the highest levels of the mRNA for each marker protein at day 14, whereas in the presence of ascorbate and dexamethasone, the highest levels for alkaline phosphatase, ERα, osteocalcin, BMP-2, and BMP-4 were observed at day 21. ERα, BMP-2, and BMP-4 expression were found to correlate temporally with induction of the osteoblast phenotype as determined by alkaline phosphatase, collagen, and osteocalcin expression. These results give additional information on the development of the osteoblast phenotype from early fibroblastic stem cells and on the biological factors involved in this process. These studies suggest a role for estrogen and BMP-2 and -4 in the differentiation of osteoprogenitor cells. J. Cell. Biochem. 75:382–392, 1999. © 1999 Wiley-Liss, Inc.