gebhart/patrepeval huggingface dataset:
Network analysis of human Y microsatellite haplotypes (1996)

To investigate the utility of Y chromosome microsatellites for studying human male-lineage evolution, we typed samples from three populations for five tetranucleotide repeats and an Alu insertion polymorphism. We found very high levels of haplotype diversity and evidence that most mutations involve the gain or loss of only one repeat unit, implying that any given microsatellite haplotype may have arisen independently on two or more Y-chromosome lineages. Together, these factors suggest that interpretation of small sample sizes (< 30) will be problematic. By typing a large sample of individuals (n = 174) from one population, East Anglia, we were able to construct a haplotype network. The network exhibits a well-connected core structure of commoner haplotypes. Computer simulations based on this network estimate the convergence time for African and Caucasian groups may be between 1.4 and 1.8 times as long as the convergence of the East Anglian population. Based on our comparison between large and small sample sizes, we suggest that large sample sizes are necessary in order to interpret Y-microsatellite haplotypes, and that a network analysis of the type we describe may prove informative in future studies.
Parameters-based speech packet recovery of adaptive CVSD for wireless PCN applications (2003)

Continuous variable slope delta (CVSD) modulation speech coder is a simple and robust speech coding algorithm with good speech coding quality at medium to high data rates. In this paper, the packet loss issue of adaptive CVSD is addressed for wireless personal communication network (PCN) applications. To solve the problem of packet loss, we propose a parameters-based packet recovery algorithm, which utilizes the parameters derived from 16 kb/s adaptive CVSD. A series of computer simulation is conducted and the results are compared with previously proposed algorithms. It is shown that our proposed packet recovery algorithm is robust in radio channel and is a suitable choice for wireless PCN applications.
Generation, Expansion, and Differentiation of Human Induced Pluripotent Stem Cells (hiPSCs) Derived From the Umbilical Cords of Newborns (2014)

The umbilical cord is tissue that is normally discarded after the delivery of the infant, but it has been shown to be a rich source of stem cells from the cord blood, Wharton's jelly, and umbilical endothelial cells. Patient-specific human induced pluripotent stem cells (hiPSCs) reprogrammed from patient specific human umbilical vein endothelial cells in the neonatal intensive care unit (NICU) population (specifically, premature neonates) have not been shown in the literature. This unit describes a protocol for the generation and expansion of hiPSCs originating from umbilical cords collected from patients in the NICU.
A rapid colorimetric LAMP assay for detection of Rhizoctonia solani AG-1 IA causing sheath blight of rice (2020)

Rhizoctonia solani is one of the most devastating pathogens. R. solani AG-1 IA causes sheath blight in rice, maize, and other Gramineous plants. Accurate identification is essential for the effective management of this pathogen. In the present study, a set of four primers were designed viz. RSPG1, RSPG2, RSPG4, and RSPG5 for polygalacturonase (PG) gene, an important virulence factor in phytopathogenic fungi. All four primer sets showed specific amplification of 300 bp (RSPG1F/R), 375 bp (RSPG2F/R), 500 bp (RSPG4F/R) and 336 bp (RSPG5F/R) amplicons. q-PCR detection using each primer sets could detect up to 10 pg of DNA. We also designed six primers (RS_pg_F3_1/RS_pg_B3_1, RS_pg_FIP_1.1/RS-pg_BIP_1.1, and RS_pg_LF_1/RS_pg_LB_1) for PG gene. Further, a colorimetric LAMP assay developed yielded visual confirmation of the pathogen within 45 min of sample collection when coupled with rapid high throughput template preparation method (rHTTP) from infected samples. The sensitivity of the LAMP assay was as low as 1.65 fg/µl of template DNA and could effectively detect R. solani AG-1 IA from diseased plant tissues and soil samples. The LAMP assay was highly specific for R. solani as it did not show any amplification with other AG groups of R. solani and closely related fungal and bacterial outgroups. This study will help in designing an effective point of care diagnostic method for early monitoring of R. solani and thereby planning timely preventive measures against the pathogen.
Purkinje neuron degeneration in nervous ( <i>nr</i> ) mutant mice is mediated by a metabolic pathway involving excess tissue plasminogen activator (2006)

Purkinje neurons (PNs), the central cells in cerebellar circuitry and function, constitute a vulnerable population in many human genetic, malignant, hypoxic, and toxic diseases. In the nervous (nr) mutant mouse, the majority of PNs die in the fourth to fifth postnatal weeks, but the responsible molecules are unknown. We first disclose a remarkable increase in mRNA expression and protein concentration in the nr cerebellum of tissue plasminogen activator (tPA), a gene closely linked to the mapped but as-yet-uncloned nr locus. Evidence that excessive tPA triggers nr PN death was obtained with organotypic slice cultures expressing the nr PN phenotype, in which an inhibitor of tPA led to increased nr PN survival. An antagonist of protein kinase C, a downstream component in the tPA pathway, also increased nr PN survival. Additional downstream targets in the tPA pathway (the mitochondrial voltage-dependent anion channel, brain-derived neurotrophic factor, and neurotrophin 3) were also abnormal, in parallel with the alterations in PN mitochondrial morphology, dendritic growth, and synaptogenesis that culminate in nr PN death and motor incoordination. We thus propose a molecular pathway by which the excessive tPA in nr cerebellum mediates PN degeneration.
A Solvent-Dyeing Process for Aramid Fibers (1979)

A solvent-dyeing process for aramid fibers is described which is capable of producing fiber and fabrics having excellent depth of shades. The brightness of the fibers and fabrics is quite high when the undyed fibers are bright. When properly selected basic dyes are used, and when heavy shades are developed on the fabrics, good dyed lightfastness values are ob tained. Carpet samples of Nomex® dyed via the solvent-dyeing process described are considerably brighter, cleaner, and deeper in shades than commercial carpet samples of Nomex dyed using the producer-recommended dyeing process. More over, the dyed lightfastness values (Gray Scale) are considerably higher for these solvent-dyed carpet samples. Thus. ratings as poor as 2 and 1 after, respectively, 20 and 40 hours in the Fade-Ometer were obtained on the commercial carpet samples, whereas certain of the test samples rated 2—3 even after 320 hours. In addition to the improvement in dyeing obtained with the solvent-dyeing process, it was observed that the aramid fibers based on poly- m-phenyleneisophthalamide (MPD-I) and the polyisophthalamide of 4,4'-methylenedianiline (MDA-I) apparently undergo a certain degree of relaxation. For example, on blank dyeing in pyridine the tenacity of the wet-spun MDA-I fiber decreased only slightly, while the initially somewhat low elongation-to-break value increased significantly. For Nomex 10 dpf staple the average elongation-to-break value increased slightly, but the range of this value narrowed considerably. Two rigid, rod-like, wholly aromatic fibers, the DuPont Company's Kevlar® aramid fiber, and the Monsanto Company's experimental X-500 polyamide-hydrazide fiber, do not show the same type relaxation effects exhibited by either MDA-I or MPD-I ( i.e. Nomex). Thus, the tenacity of the Kevlar increased somewhat, and the initial modulus values for both rod-like fibers increased moderately.
Herpes Virus Genome, The Pressure Is On (2013)

Herpes simplex virus type 1 (HSV-1) packages its micrometers-long double-stranded DNA genome into a nanometer-scale protein shell, termed the capsid. Upon confinement within the capsid, neighboring DNA strands experience repulsive electrostatic and hydration forces as well as bending stress associated with the tight curvature required of packaged DNA. By osmotically suppressing DNA release from HSV-1 capsids, we provide the first experimental evidence of a high internal pressure of tens of atmospheres within a eukaryotic human virus, resulting from the confined genome. Furthermore, the ejection is progressively suppressed by increasing external osmotic pressures, which reveals that internal pressure is capable of powering ejection of the entire genome from the viral capsid. Despite billions of years of evolution separating eukaryotic viruses and bacteriophages, pressure-driven DNA ejection has been conserved. This suggests it is a key mechanism for viral infection and thus presents a new target for antiviral therapies.
Characterization and dynamics of O-linked glycosylation of human cytokeratin 8 and 18. (1992)

The glycosylation of human cytokeratin (CK) 8 and 18 was studied after metabolic labeling of HT29 colonic cells with [3H]glucosamine. Labeling of CK8/18 was not inhibited by tunicamycin, suggesting that glycosylation was not N-linked. Acid hydrolysis of CK8 and CK18, purified from [3H]glucosamine-labeled cells, generated free glucosamine. In the presence of UDP-[3H]galactose, galactosyltransferase catalyzed the labeling of cytokeratin 8 and 18. beta-Elimination of the [3H]galactose- labeled CK8/18 generated the disaccharide N-acetyllactosaminitol, indicating that cytokeratin 8 and 18 contain single O-linked N-acetylglucosamine residues. Using chemical analysis, the stoichiometry of glycosylation was found to be 1.5 and 2 molecules of N-acetylglucosamine/protein molecule of CK8 and CK18, respectively. Peptide maps of [3H]glucosamine-labeled CK8/18 showed that multiple peptides were labeled with the amino sugar. The biosynthetic and degradation rates of the carbohydrate moiety were faster than the protein core as determined by metabolic radiolabeling or pulse-chase experiments, respectively. Our results show that CK8 and 18 are glycosylated at multiple sites with a single O-linked N-acetylglucosamine. Furthermore, CK8/18 glycosylation is a dynamic process which is likely to have functional relevance.
Colonic stem cell data are consistent with the immortal model of stem cell division under non‐random strand segregation (2009)

Allowing for preferential strand segregation considerably alters previously published conclusions relating to stem cell numbers and turnover mechanisms. Evidence in favour of the stochastic model may not be as strong as previously thought.
IL-12 and IL-27 Sequential Gene Therapy via Intramuscular Electroporation Delivery for Eliminating Distal Aggressive Tumors (2010)

Eradication of residual malignancies and metastatic tumors via a systemic approach is the key for successfully treating cancer and increasing cancer patient survival. Systemic administration of IL-12 protein in an acute large dose is effective but toxic. Systemic administration of IL-12 gene by persistently expressing a low level of IL-12 protein may reduce the systemic toxicity but only eradicates IL-12-sensitive tumors. In this study, we discovered that sequential administration of IL-12- and IL-27-encoding DNA, referred to as sequential IL-12-->IL-27 (IL-12 administration followed by IL-27 administration 10 d after) gene therapy, not only eradicated IL-12-sensitive CT26 tumors from 100% of mice but also eradicated the highly malignant 4T1 tumors from 33% of treated mice in multiple independent experiments. This IL-12-->IL-27 sequential gene therapy is not only superior to IL-12-encoding plasmid DNA given a total of two times at a 10-d interval sequential gene therapy for eliminating tumors but also for inducing CTL activity, increasing T cell infiltration into tumors, and yielding a large number of tumor-specific IFN-gamma-positive CD8 T cells. Notably, depletion of either T or NK cells during the IL-27 treatment phase reverses tumor eradication, suggesting an NK cell requirement for this sequential gene therapy-mediated tumor eradication. Both reversal of the administration sequence and coadministration of IL-12 and IL-27 impaired tumor eradication in 4T1 tumor-bearing mice. This IL-12-->IL-27 sequential gene therapy, via sequential administration of IL-12- and IL-27-encoding plasmid DNA into tumor-bearing mice through i.m. electroporation, provides a simple but effective approach for eliminating inaccessible residual tumors.
Type I cAMP-dependent Protein Kinase Delays Apoptosis in Human Neutrophils at a Site Upstream of Caspase-3 (1998)

Current data suggest that apoptosis controls neutrophil numbers in tissues. We analyzed roles for and the sites of action for the cAMP-dependent protein kinases (cAPKs) in apoptosis induced in human neutrophils by in vitro storage, cycloheximide (CHX) exposure, and anti-Fas exposure. Treatment with 8-chlorophenylthio-cAMP (8-CPT-cAMP) prolonged the time required for 50% of the cells to exhibit apoptotic morphology (t50) from 16.3 to 41.8 h (in vitro culture), from 2.4 to 7.8 h (CHX), and from 4.8 to 6.5 h (anti-Fas). CHX +/- 8-CPT-cAMP did not significantly alter resting intracellular calcium levels and H-89, a selective inhibitor of cAPK, had no effect on apoptosis in the absence of the analogue. In contrast, site-selective cAMP analogues that specifically activated the type I cAPK, but not type II cAPK, synergistically attenuated apoptosis. Exposure to 8-CPT-cAMP delayed, in parallel, the activity of caspase-3 (CPP-32beta), whereas mitogen-activated protein kinase kinase (MAPKK) inhibitor, PD98059, had no effect on CHX-induced apoptosis +/- 8-CPT-cAMP. Together these results indicate that type I cAPK activation is necessary and sufficient to mediate cAMP-induced delay in human neutrophil apoptosis induced by several mechanisms and suggest that one of the major sites of cAPK action is upstream of caspase-3 (CPP-32beta) activation.
Myoblast‐mediated gene transfer to the joint (1997)

Several genetic and acquired pathologic conditions of the musculoskeletal system, such as arthritis and damage to ligament, cartilage, and meniscus, may be amenable to gene therapy. Even though ex vivo gene transfer with synovial cells has been shown to deliver genes encoding for anti-arthritic proteins into the rabbit knee joint, its success has been limited by a transient transgene expression. In this study, data were investigated regarding the use of muscle cells as an alternative gene-delivery vehicle to the joint in newborn rabbit and adult severe combined immunodeficiency mice. We demonstrated that myoblasts were transduced more efficiently than synovial cells with use of the same adenoviral preparation in vitro. After intra-articular injection, the engineered muscle cells adhered to several structures in the joint, including the ligament, capsule, and synovium. In addition, myoblasts fused to form many post-mitotic myotubes and myofibers at different locations of the joint of the newborn rabbit 5 days after the injection. In the knee of the adult mouse, myoblasts fused and expressed the reporter gene for at least 35 days after the injection. The presence of post-mitotic myofibers in the knee joint raises the possibility of long-term expression of the secreted protein. Currently, numerous tissues in the joint (ligament, meniscus, and cartilage) have poor intrinsic healing capacity and frequently need surgical corrections. A stable gene-delivery vehicle to the joint producing proteins that ameliorate these different musculoskeletal conditions may change the clinical implications of these pathologies.
Omnidirectional absolute band gaps in two-dimensional photonic crystals (2001)

A plane-wave expansion method has been developed to investigate the off-plane propagation of electromagnetic waves in a two-dimensional (2D) photonic crystal. Photonic band-structure calculations indicate that some 2D crystal structures can support a common band gap for both polarizations and for all off-plane angles from $0\ifmmode^\circ\else\textdegree\fi{}$ up to $90\ifmmode^\circ\else\textdegree\fi{}.$ The presence of such an omnidirectional absolute band gap implies that a 2D photonic crystal can exhibit some of the functionalities of a three-dimensional crystal with a complete band gap.
Ablation of Solids under Femtosecond Laser Pulses (2002)

We study the basic mechanisms leading to ablation by femtosecond laser pulses using molecular dynamics and a simple two-dimensional Lennard-Jones model. We demonstrate that the ablation process involves three different mechanisms as a function of deposited energy. In particular, it can result from mechanical fragmentation, which does not require the system to cross any metastability or instability line. The relevance of homogeneous nucleation and vaporization for the description of ablation in this regime is also established.
T cell receptor gamma/delta+ lymphocyte subsets during HIV infection. (1989)

The gamma/delta T cell receptor is expressed on 1-15% of normal human peripheral blood lymphocytes (PBL). This subpopulation is recognized by anti-TcR-delta 1 MoAb which is functionally defined as a pan-delta MoAb. Two other antibodies, anti-Ti-gamma A and anti-delta-TcS1 are directed at variable determinants of either the gamma or the delta chain, respectively. In normal individuals anti-Ti-gamma A characterizes two thirds of the TcR-delta 1+ subpopulation whereas anti-delta TcS1 reacts with most of the delta-TcR1+, Ti-gamma A- cells. In the present study, we have used these three MoAbs to characterize the TcR gamma/delta+ peripheral lymphocytes during HIV infection. Fifty patients at three distinct clinical stages (SPC/PGL, ARC, AIDS) of the infection have been studied. The Ti-gamma A+ subset in the whole group accounted for 3.45% of PBL and did not differ from controls; it was also unchanged when the three groups were analysed separately. The Ti-gamma A+ circulating cells were in a resting state as assessed by the absence of surface-expressed activation markers. In contrast, in some patients the proportion of circulating TcR-delta 1+, Ti-gamma A-, delta TcS1+ cells was increased (4.75%) leading to an inversion of the Ti-gamma A/delta-TcS1 ratio. Altogether, those data suggest a conservation of the Ti-gamma A+ subset during HIV infection, contrasting with an increase of the delta-TcS1+, Ti-gamma A- fraction in some cases.
[Report of a case of allergic granulomatous vasculitis (Churg-Strauss syndrome)]. (1989)

A 35 year female with a previous history of asthma came to our observation about 10 months ago. She was dyspneic, showed small nodules (2 to 5 mm) in arms, hands and legs and had radiological evidence of pulmonary granulomatosis and pleural effusion. Diagnosis was made by means of cutaneous biopsy showing a necrotic granulomatous vasculitic lesions with eosinophilic infiltration and giant cells, consistent with allergic granulomatosis of Churg-Strauss syndrome. Steroid therapy alone (prednisone 1 mg/kg/die) led to a rapid and complete clinical and humoral remission. The patient is still doing an alternate day prednisone therapy (15 mg) and is well after a 10 months follow-up.
A Study of Factors Influencing the Costs of Funding as a Function of Research Area and Financial Institutions (2013)

Purpose: In this paper, we analyzed the factors that affect research grants using linear regression analysis in order to increase the effectiveness of investments in national research projects. Methods: We collected 15,454 pieces of data on research projects that finished between 2008 and 2010. Data preprocessing and visualization were done to derive statistically significant results. We identified factors that affected funding by using linear regression, and estimated increasing or decreasing tendencies based on those factors. Results: We identified the relative importance of the factors in awarding research grants. Strategies were suggested for the reasonable estimation of R&D budgets for investment purposes. Conclusion: This study will assist the decision-making process of governments in estimating funds required for R&D projects.
Lysosomal enzyme pattern in lung lymph and blood during E. coli sepsis in sheep (1987)

AbstractSystemic release of lysosomal enzymes and local release in the pulmonary microcirculation from sequestrated and activated leucocytes could be an important factor in the development of the lung microvascular injury seen after septicaemia. The maximal activities of 11 lysosomal acid hydrolases (acid phosphatase, α- and β-glucosidase, α- and β-galactosidase, α-mannosidase, β-acetylglucosaminidase, β-glucuronidase, arylamidase and cathepsins B and C) were measured in serum and lung lymph from seven sheep before and after infusion of live E. coli bacteria. In the early phase of septicaemia (the first hour) the activities of eight enzymes were increased in serum and/or lung lymph (1.1 to 2× pre-infusion values). In the late phase, 3–4 h after sepsis, there were significantly elevated serum activities of β-glucosidase (5.4×), α- and β-galactosidases (2.7×, 1.5×), β-acetylglucosaminidase (2.0×) arylamidase (1.2×) and cathepsin B (1.7×). In lymph acid phosphatase (1.7×), α- and β-glucosidases (1.6×, 6.4×), α- and β-galactosidases (2.1×, 1.7×). β-acetylglucosaminidase (2.6×), and β-glucuronidase (4.0× pre-infusion) were elevated. The findings of a heterogenicity of changes in serum and lymph activities, as well as the large molecular sizes of some of the enzymes with changed activities indicated to us that permeability changes were not major causes of increased lymph enzyme activities. The results could indicate a local release of enzymes either from sequestrated leucocytes or lung tissue due to local reactions in the lung or lung microvessels. The heterogenous changes in activities for the various lysosomal enzymes as found in the present study indicated that measurement of only one enzyme could be misleading. Furthermore, in order to obtain an over all view of lysosomal enzyme involvement in septicaemia, both local and systemic enzyme activities ought to be studied.Key words: acid hydrolaseslung injurymicrovascular permeabilitypulmonary pathophysiology
Nanoporous gold electrocatalysis for ethylene monitoring and control (2008)

Summary Maintaining the quality and freshness of fruit and vegetables during transportation and storage is an important role for most postharvest industries. One way to control freshness is by carefully monitoring and regulating exposure to ethylene. By limiting exposure to ethylene the natural aging process of fresh produce is slowed down, thus prolonging its shelf life. This is especially important for organic produce where the use of chemicals for decay control is not practiced. In this paper, the performance characteristics and method of use of a new sensing approach for postharvest ethylene measurements is introduced. In this sensor, ETH-1010, oxidation of ethylene on a gold electrocatalyst produces a highly detectable and measurable amperometric signal. ETH-1010 has been packaged into a complete field portable unit. It continuously samples the air at a set flow rate, (commonly between 200 and 500 ml min -1 ), and reports the ethylene concentration in air at a user-specified time interval. The direct contact between the ethylene molecules in air and electrocatalytic surface renders this process more sensitive and responsive than conventional diffusion-type electrochemical cells. This approach has been shown to be quite effective for continuous monitoring of cold storage rooms, where detection of lower than 10 ppm down to 10 ppb is desirable. This configuration was also used to examine the applicability of electrocatalysis for scrubbing ethylene. Results for ethylene removal have been presented in this paper where the surface reactivity on the electrocatalyst is typically between 0.1 and 0.2 µmol h -1 cm -2 . In the sensor, the high reaction rate provides high sensitivity and response time, while making it feasible to consider using electrocatalysis in a scrubbing mode for future applications.