gebhart/patrepeval huggingface dataset:
Site-Specific Mapping of Sialic Acid Linkage Isomers by Ion Mobility Spectrometry (2016)

Detailed structural elucidation of protein glycosylation is a tedious process often involving several techniques. Glycomics and glycoproteomics approaches with mass spectrometry offer a rapid platform for glycan profiling but are limited by the inability to resolve isobaric species such as linkage and positional isomers. Recently, ion mobility spectrometry (IMS) has been shown to effectively resolve isobaric oligosaccharides, but the utility of IMS to obtain glycan structural information on a site-specific level with proteomic analyses has yet to be investigated. Here, we report that the addition of IMS to conventional glycoproteomics platforms adds additional information regarding glycan structure and is particularly useful for differentiation of sialic acid linkage isomers on both N- and O-linked glycopeptides. With further development IMS may hold the potential for rapid and complete structural elucidation of glycan chains at a site-specific level.
学科间交叉的障碍:科学、技术与社会(STS)研究的含义 (1992)

学科间的交叉性研究工作是件棘手的难事,因为在不同的领域里,对知识的探求需要不同的兴趣,因而也会有不同的价值观;而有关不同学科知识的各种可能性,也将导致不同的认识论。这样,在属于不同学科的学者之间的差异,也就是十分普遍的了。这种差异被确切地称之为文化差异,而学科间交叉性研究则需要超越无意识的思维习惯。对这些无意识思维习惯阐释得越清晰,我们就越是可以更多地理解,为什么属于各种知识文化的不相干的特点,必然与不同的兴趣、价值观和认识论联系在一起,而学科间交叉研究的更大可行性也就是超越思维习惯的目标。有两种学科间交叉的努力看上去似乎是成功的:有些群体解决了特定的、边界明确的难题,在这些群体中,事实上是多学科的而不是学科间交叉的研究工作;其次,在已有学科的交叉部分涌现出了许多新的学科。这两种模式与STS都不相符。那么,STS是否是有生命力的呢?
Zebrafish TrkC1 and TrkC2 Receptors Define Two Different Cell Populations in the Nervous System during the Period of Axonogenesis (1998)

We identified previously five distinct trk genes in the zebrafish. The structures of two of these, TrkC1 and TrkC2, are most similar to mammalian TrkC. Detailed sequence comparisons reported here indicate that although the similarities to TrkC are greatest in those regions of the extracellular domain implicated in ligand binding, the two sequences also differ significantly in these regions. Whole-mount in situ hybridization experiments in the early embryo revealed full-length trkC1 but no trkC2 transcripts in the cranial ganglia and in a subset of Rohon-Beard neurons. At the same time, full-length trkC2 but no trkC1 transcripts were detected laterally in the spinal cord, in the caudal hindbrain, in reticulospinal neurons of rhombomeres 4, 5, and 6, and in the midbrain. Both types of transcripts were expressed in clusters of cells in the dorsal telencephalon and the nucleus of the tract of the postoptic commissure. These results suggest distinct functions of trkC1 and trkC2 in nervous system development. The expression patterns define two different neuronal populations in the zebrafish.
Structural adaptation in young neocortical networks modeled by spatially coupled oscillators (2007)

The spontaneous synchronous activity in neocortical networks during early development is considered to be a requisite for the maturation of the networks. To analyze the structural adaptation of synaptic connections in large scale area, we simulate the network activity by distributed population models (complex oscillators). In this way we get a spatial distribution of parameters and activity and are able to study effects of local external stimulation and propagation of excitation waves in large network areas. Considering a small world connection strategy most connections are local but there are a number of long range connections, which work as shortcuts and help to synchronize the whole network activity. These long range connections can be used to adapt the network architecture by a Hebbian learning mechanism depending on the intrinsic wavelike network activity and external stimulation.
Scalable lithography from Natural DNA Patterns via polyacrylamide gel (2015)

A facile strategy for fabricating scalable stamps has been developed using cross-linked polyacrylamide gel (PAMG) that controllably and precisely shrinks and swells with water content. Aligned patterns of natural DNA molecules were prepared by evaporative self-assembly on a PMMA substrate, and were transferred to unsaturated polyester resin (UPR) to form a negative replica. The negative was used to pattern the linear structures onto the surface of water-swollen PAMG, and the pattern sizes on the PAMG stamp were customized by adjusting the water content of the PAMG. As a result, consistent reproduction of DNA patterns could be achieved with feature sizes that can be controlled over the range of 40%-200% of the original pattern dimensions. This methodology is novel and may pave a new avenue for manufacturing stamp-based functional nanostructures in a simple and cost-effective manner on a large scale.
Mesenchymal stromal cells and interferon α (IFNα) in cancer immunotherapy (2016)

In the past decade, there has been particular excitement for the inclusion of immunotherapy approaches for the treatment of cancer, beyond conventional chemotherapy, radiotherapy and targeted therapies (1). Immunotherapy approaches are now designed mainly to overcome tumor immune evasion mechanisms and allow targeting of neoplastic cells by antitumor immune responses (1). The importance of both innate and adaptive immune responses against tumor growth has been supported by evidence from spontaneous and carcinogen-induced tumorigenesis in vivo models (2).
Inhibition of nitric oxide synthase (NOS) aggravates <i>Staphylococcus aureus</i> septicaemia and septic arthritis (1997)

The aim of this study was to assess the role of NO and its metabolites in bacterial arthritis. The murine model of haematogenously acquired septic arthritis was used. Swiss mice treated with NOS inhibitors (N(G)-monomethyl-L-arginine or N(omega)-nitro-L-arginine methyl ester) were injected intravenously with toxic shock syndrome toxin-1 (TSST-1) producing Staphylococcus aureus LS-1. Arthritis was evaluated clinically and histopathologically. Serum cytokine levels, bacterial isolates and intracellular capacity of macrophages to kill bacteria were also analysed. The frequency of arthritis in mice treated with NOS inhibitors was three to four-fold higher than that in non-treated controls (75% versus 20%). The severity of arthritis, expressed as mean arthritic index, was 1.4 and 0.4, respectively. Cartilage and/or bone destruction occurred in 63% of NOS inhibitor-treated mice, but only in 10% of controls. Also, the cumulative septicaemia-induced mortality was clearly higher in mice treated with NOS inhibitors compared with non-treated controls. Intracellular killing capacity of the peritoneal macrophages, treated in vitro with NOS inhibitors, was decreased. Thus, 24 h after bacterial inoculation peritoneal macrophages pretreated with NOS inhibitors killed more than 10 times less bacteria than the control ones (P<0.01). We conclude that NOS inhibitors aggravate S. aureus arthritis, possibly by inducing impairment of the intracellular killing capacity of macrophages.
Inorganic speciation of dissolved elements in seawater: the influence of pH on concentration ratios (2002)

Assessments of inorganic elemental speciation in seawater span the past four decades. Experimentation, compilation and critical review of equilibrium data over the past forty years have, in particular, considerably improved our understanding of cation hydrolysis and the complexation of cations by carbonate ions in solution. Through experimental investigations and critical evaluation it is now known that more than forty elements have seawater speciation schemes that are strongly influenced by pH. In the present work, the speciation of the elements in seawater is summarized in a manner that highlights the significance of pH variations. For elements that have pH-dependent species concentration ratios, this work summarizes equilibrium data (<i>S</i> = 35, <i>t</i> = 25°C) that can be used to assess regions of dominance and relative species concentrations. Concentration ratios of complex species are expressed in the form log[A]/[B] = pH - <i>C</i> where brackets denote species concentrations in solution, A and B are species important at higher (A) and lower (B) solution pH, and <i>C</i> is a constant dependent on salinity, temperature and pressure. In the case of equilibria involving complex oxy-anions (MO <sub><i>x</i></sub> (OH) <sub><i>y</i></sub> ) or hydroxy complexes (M(OH) <sub><i>n</i></sub> ), <i>C</i> is written as p<i>K</i> <sub><i>n</i> </sub> = -log <i>K</i> <sub><i>n</i> </sub> or p<i>K</i> <sub><i>n</i></sub> * = -log <i>K</i> <sub><i>n</i></sub> * respectively, where <i>K</i> <sub><i>n</i> </sub> and <i>K</i> <sub><i>n</i></sub> * are equilibrium constants. For equilibria involving carbonate complexation, the constant <i>C</i> is written as p<i>Q</i> = -log(<i>K</i> <sub>2</sub> <sup><i>l</i></sup> <i>K</i> <sub><i>n</i> </sub> [HCO<sub>3</sub> <sup>-</sup>]) where <i>K</i> <sub>2</sub> <sup><i>l</i> </sup> is the HCO<sub>3</sub> <sup>-</sup> dissociation constant, <i>K</i> <sub><i>n</i> </sub> is a cation complexation constant and [HCO<sub>3</sub> <sup>-</sup>] is approximated as 1.9 × 10<sup>-3</sup> molar. Equilibrium data expressed in this manner clearly show dominant species transitions, ranges of dominance, and relative concentrations at any pH.
An Albino Puffin (1932)

Brfin•ich's Murre in Southern New Jersey.--OnJanuary 23, 1932, E. B. Rohrer and the writer saw a Bri•nnich's Murre (Uria lomvia lomvia) at the end of the breakwater above Cape May City.The bird was seen clearly with good glasses at very close range and its distinguishing characteristics carefully noted.The flesh-colored stripe on the mandible near the gape as well as the dark band across the breast showed plainly that it was a mature bird in winter plumage.The bird remained near us for several minutes, diving constantly and giving us exceptionally fine views.Then it departed under water and we did not see it again.--W.S?umR?CR•M•R, •,01 E. Ki• Street, Lancaster, Pa.An Albino Pufttn.--During the past s•mrner, while stationed near .Cape Whittle on the North Shore of the Gulf of St. Lawrence, a specimen of a partial albino Puffin (Fraterc•la ar•tica arctica) was presented to me by Mr. Ruben Jones of Wolf Bay who collected and preserved it fourteen years ago.The skin is well made up accordlag to the style which Mr. Jones learned from M. Abbott Frazar when he worked on that par• of the coast in 1884 and had been taken at Wolf Bay
Diagnosis of Deep Venous Thrombosis by Use of Soluble Necrosis Factor Receptor (1998)

The purpose of this clinical study was to find a relationship between soluble tumor necrosis factor (TNF) receptor, deep venous thrombosis (DVT), and pulmonary emboli (PE). Clinical diagnosis of deep venous thrombosis and pulmonary emboli is a major dilemma for the clinician. Most existing tests are technician dependent, are expensive, or require sophisticated equipment. Advances in molecular biology will permit investigation of the value of TNF receptor as a test for screening, diagnosis, and evolution of DVT and PE. Forty patients with diagnosis of DVT, documented by real-time ultrasound imaging, were the subject of this clinical study. Five cc of plasma from each patient was studied by enzyme-linked immunosorbent assay (Elisa) for measurement of soluble TNF receptor. Significantly increased concentration of plasma-soluble TNF receptor was present in patients with DVT as opposed to normal individuals. There was a close relationship between plasma concentration of soluble TNF receptor and evaluation of the disease. In this preliminary clinical study, it appears that plasma measurement of soluble TNF receptor could be used as a clinical test for diagnosis of DVT and PE.
Subpressor Doses of Angiotensin II Increase Plasma F <sub>2</sub> -Isoprostanes in Rats (2000)

The present study was performed to determine whether physiologically relevant doses of angiotensin II (Ang II), which do not affect renal hemodynamics but do cause slow response hypertension, result in oxidative stress as measured by production of vasoconstrictor F(2)-isoprostane, a prostaglandin-like non-cyclooxygenase-produced arachidonic acid metabolite that is the end product of lipid peroxidation. Rats were instrumented with abdominal aortic and left femoral venous catheters, and before and throughout Ang II (or saline) infusion, all rats received enalapril (250 mg/L). Four days after the initiation of enalapril, rats were infused with Ang II (10 ng. kg(-1). min(-1), n=6) or saline (n=6) for 14 days. Mean arterial pressure was measured 24 hours per day, and on day 12, glomerular filtration rate and renal plasma flow were measured. Mean arterial pressure in control rats averaged 85+/-1 mm Hg, and with Ang II infusion, mean arterial pressure increased slowly and reached a plateau on day 3, averaging 117+/-2 mm Hg (P<0.0001 compared with enalapril alone). Glomerular filtration rate and renal plasma flow were not affected by Ang II. Free F(2)-isoprostanes in plasma increased by 54% with Ang II (P<0.01), and the production of F(2)-isoprostanes esterified in plasma lipids tended to be higher with Ang II also but did not reach significance (P=0.1). These studies suggest that low doses of Ang II are capable of producing oxidative stress in animals. Whether oxidative stress plays a causative role in Ang II-mediated slow-response hypertension or is secondary to the hypertension is not clear from these data and will require further study.
Multipotent hair follicle stem cells promote repair of spinal cord injury and recovery of walking function (2008)

The mouse hair follicle is an easily accessible source of actively growing, pluripotent adult stem cells. C57BL transgenic mice, labeled with the fluorescent protein GFP, afforded follicle stem cells whose fate could be followed when transferred to recipient animals. These cells appear to be relatively undifferentiated since they are positive for the stem cell markers nestin and CD34 but negative for the keratinocyte marker keratin 15. These hair follicle stem cells can differentiate into neurons, glia, keratinocytes, smooth muscle cells and melanocytes in vitro. Implanting hair follicle stem cells into the gap region of severed sciatic or tibial nerves greatly enhanced the rate of nerve regeneration and restoration of nerve function. The transplanted follicle cells transdifferentiated mostly into Schwann cells, which are known to support neuron regrowth. The treated mice regained the ability to walk essentially normally. In the present study, we severed the thoracic spinal chord of C57BL/6 immunocompetent mice and transplanted GFP-expressing hair follicle stem cells to the injury site. Most of the transplanted cells also differentiated into Schwann cells that apparently facilitated repair of the severed spinal cord. The rejoined spinal cord reestablished extensive hind-limb locomotor performance. These results suggest that hair follicle stem cells can promote the recovery of spinal cord injury. Thus, hair follicle stem cells provide an effective accessible, autologous source of stem cells for the promising treatment of peripheral nerve and spinal cord injury.
Loxiglumide protects against experimental pancreatitis. (1987)

Loxiglumide (D,L-4-(3,4-dichloro-benzoylamino)- 5-(N-3-methoxypropyl-pentylamino)-5-oxo-pentanoic acid, CR 1505) is a derivative of pentanoic acid and belongs to a newly discovered class of agents with cholecystokinin antagonistic activities. Loxiglumide has preventive effects on different types of experimental pancreatitis, induced e.g. by ceruletide (i.p. ED50 ca. 9 mumol/kg), by intrapancreatic taurocholate (i.p. ED50 ca. 80 mumol/kg) or by choline-deficient ethionine-supplemented diet (i.p. ED50 ca. 45 mumol/kg). Loxiglumide has a simple, non-polypeptidic chemical structure and may be a candidate for clinical investigations in man, e.g. for pancreatitis.
Rapid identification of "very virulent" strains of infectious bursal disease virus by reverse transcription-polymerase chain reaction combined with restriction enzyme analysis (2001)

A reverse transcription-polymerase chain reaction (RT-PCR) combined with restriction enzyme analysis (REA) was developed for differentiation of classical virulent (cv) and very virulent (vv) strains of infectious bursal disease virus (IBDV). The VP2 gene was used for primer annealing to amplify the hypervariable region. An amplification product was obtained with serotype 1 and serotype 2 strains of IBDV.The restriction enzymes SacI and BspMI were used to identify and to differentiate the serotype 1 strains: SacI only cleaved cvIBDV RT-PCR products, whereas products obtained with vvIBDV strains were only cleaved with BspMI; serotype 2 strain products were not cleaved by either of these restriction enzymes. RT-PCR combined with REA as described in this study is thus suitable to detect IBDV of both serotypes and to distinguish rapidly between cvIBDV,vvIBDV and serotype 2 IBDV.Our investigation of a total of 11 different IBDV isolates and available nucleotide sequence data of other isolates indicate that the application of this protocol might be a useful tool for the rapid identification of vvIBDV isolates, a prerequisite for the effective control of this economically important virus infection of commercial poultry.
Isolation and characterization of porcine circovirus type 2 from pigs showing signs of post‐weaning multisystemic wasting syndrome in the Netherlands (2000)

Pigs with wasting syndrome were examined for macroscopic and histopathological lesions, and for porcine circovirus (PCV). Histopathological lesions were comparable to those previously documented for post-weaning multisystemic wasting syndrome (PMWS). In addition, in seven out of ten examined PMWS-affected pigs focal-to-slight mononuclear meningitis and focal cerebral mononuclear infiltrates (4 out of 10) were observed. A virus was isolated from organs and sera from pigs showing wasting syndrome. An immunoperoxidase monolayer assay and an indirect immunofluorescence assay were performed on the infected PK-15 and Dulac cell cultures, respectively, and both assays indicated the presence of PCV type 2 (PCV2). The nested-polymerase chain reaction (nPCR) technique, based on the use of PCV2 specific oligonucleotides, revealed specific amplified products of 481 bp. Nucleotide sequence analysis of the entire genome of the Dutch PCV isolate 24657 NL showed a homology with known nucleotide sequences of porcine PCV type 1 (PCV1) and PCV2 isolates of 77.1% and >96%, respectively. This is the first report of the isolation and characterization of PCV2 in PMWS-affected pigs in the Netherlands.
Short Communication: HTLV-I/HTLV-II Coinfection in an AIDS Patient from São Paulo, Brazil (2000)

A serological survey for HTLV infection identified an AIDS patient with HTLV-I/HTLV-II dual seroreactivity. Two further sequential blood samples were collected (samples A and B) for PCR, restriction fragment length polymorphism (RFLP), and sequence analyses of HTLV-I and HTLV-II strains. PCR analyses confirmed dual infection in both samples. Restriction digests of the env region amplified from sample A showed the presence of an HTLV-IIa subtype; the HTLV-II provirus was found to be defective in the pol and env regions in the second sample from this patient. RFLP analysis of the HTLV-II LTR region of both samples confirmed this finding and identified an a5/bzl restriction type. Nucleotide sequence analyses revealed full homology in the HTLV-I env and LTR regions and in the HTLV-II LTR region between the two samples. These findings document the first case of an HTLV-I/HTLV-II coinfection that was fully confirmed and characterized by means of molecular analyses.
Crystallographic and Enzymic Investigations on the Role of Ser558, His610, and Asn614 in the Catalytic Mechanism of Azotobacter vinelandii Dihydrolipoamide Acetyltransferase (E2p) (1995)

Dihydrolipoamide acetyltransferase (E2p) is the structural and catalytic core of the pyruvate dehydrogenase multienzyme complex. In Azotobacter vinelandii E2p, residues Ser558, His610', and Asn614' are potentially involved in transition state stabilization, proton transfer, and activation of proton transfer, respectively. Three active site mutants, S558A, H610C, and N614D, of the catalytic domain of A. vinelandii E2p were prepared by site-directed mutagenesis and enzymatically characterized. The crystal structures of the three mutants have been determined at 2.7, 2.5, and 2.6 A resolution, respectively. The S558A and H610C mutants exhibit a strongly (200-fold and 500-fold, respectively) reduced enzymatic activity whereas the substitution of Asn614' by aspartate results in a moderate (9-fold) reduced activity. The decrease in enzymatic activity of the S558A and H610C mutants is solely due to the absence of the hydroxyl and imidazole side chains, respectively, and not due to major conformational rearrangements of the protein. Furthermore the sulfhydryl group of Cys610' is reoriented, resulting in a completely buried side chain which is quite different from the solvent-exposed imidazole group of His610' in the wild-type enzyme. The presence of Asn614' in A. vinelandii E2p is exceptional since all other 18 known dihydrolipoamide acyltransferase sequences contain an aspartate in this position. We observe no difference in conformation of Asp614' in the N614D mutant structure compared with the conformation of Asn614' in the wild-type enzyme. Detailed analysis of all available structures and sequences suggests two classes of acetyltransferases: one class with a catalytically essential His-Asn pair and one with a His-Asp-Arg triad as present in chloramphenicol acetyltransferase [Leslie, A. G. W. (1990) J. Mol. Biol. 213, 167-186] and in the proposed active site models of Escherichia coli and yeast E2p.
A 44 GHz 0.18&#x003BC;m CMOS Superharmonic Frequency Divider (2007)

This paper presents a low power 44 GHz 0.18 μm CMOS superharmonic frequency divider. The superharmonic locking technique is proposed to perform direct divide-by-four operation. The integrated circuit was implemented in the commercial 0.18 μm CMOS technology. Operated at 1.2 V, the frequency divider consumes only 1.8 mW of power. The measured locking range of the frequency divider is 200 MHz. By applying varactor tuning, the operating range of the divider can be extended to 2.14 GHz. The chip occupied 0.77 mm × 0.8 mm of silicon area including the testing pads.