gebhart/patrepeval huggingface dataset:
Increased Sensitivity to Complement and a Decreased Red Blood Cell Life Span in Mice Mosaic for a Nonfunctional Piga Gene (1999)

The gene PIGA encodes one of the protein subunits of the 1-6-N acetylglucosaminyltransferase complex, which catalyses an early step in the biosynthesis of glycosyl phosphatidylinositol (GPI) anchors. PIGA is somatically mutated in blood cells from patients with paroxysmal nocturnal hemoglobinuria (PNH), leading to deficiency of GPI-linked proteins on the cell surface. To investigate in detail how inactivating mutations of the PIGA gene affect hematopoiesis, we generated a mouse line, in whichloxP-mediated excision of part of exon 2 occurs on the expression of Cre. After crossbreeding with EIIa-cre transgenic mice, recombination occurs early in embryonic life. Mice that are mosaics for the recombined Piga gene are viable and lack GPI-linked proteins on a proportion of circulating blood cells. This resembles the coexistence of normal cells and PNH cells in patients with an established PNH clone. PIGA(−) blood cells in mosaic mice have biologic features characteristic of those classically seen in patients with PNH, including an increased sensitivity toward complement mediated lysis and a decreased life span in circulation. However, during the 12-month follow-up, the PIGA(−) cell population did not increase, clearly showing that a Piga gene mutation is not sufficient to cause the human disease, PNH.
Soil protist function varies with elevation in the Swiss Alps (2021)

Protists are abundant and play key trophic functions in soil. Documenting how their trophic contributions vary across large environmental gradients is essential to understand and predict how biogeochemical cycles will be impacted by global changes. Here, using amplicon sequencing of environmental DNA in open habitat soil from 161 locations spanning 2600 m of elevation in the Swiss Alps (from 400 to 3000 m), we found that, over the whole study area, soils are dominated by consumers, followed by parasites and phototrophs. In contrast, the proportion of these groups in local communities shows large variations in relation to elevation. While there is, on average, three times more consumers than parasites at low elevation (400-1000 m), this ratio increases to 12 at high elevation (2000-3000 m). This suggests that the decrease in protist host biomass and diversity toward mountains tops impact protist functional composition. Furthermore, the taxonomic composition of protists that infect animals was related to elevation while that of protists that infect plants or of protist consumers was related to soil pH. This study provides a first step to document and understand how soil protist functions vary along the elevational gradient.
Magnetically controlled nano-composite based 3D printed cell scaffolds as targeted drug delivery systems for cancer therapy (2015)

Scaffolds are salient materials used in tissue engineering. Nanocomposite scaffolds act as potential drug carriers in the treatment of a variety of cancer. 3D printing allows scaffolds to be contrived with custom design thus eliminating the risks of suitable pore size for bioactivity and custom designing. This paper projects the potentiality of producing 3D printed nanostructured scaffolds using graphene oxide and polymer nanocomposite (Poly-Caprolactone) that could deliver drugs to cancer cells, effectively reducing neovascularizations. We present an effective technique for remotely controlling the scaffold by magnetic field to deliver the drugs to specific cancer sites. Nanostructured graphene polymer composite act as reinforcing agents to fabricate mechanically strong biodegradable scaffolds that could carry drugs to targeted cancer cells. Graphene has the ability to improve the biological properties and its ability to promote adhesion, proliferation proves it to be an effective material for scaffold designing. 3D Printing is useful for the direct fabrication of scaffolds with tailored porosity from a CAD file. The 3D-Bioplotter System is a suitable 3D Bioprinter for scaffold fabrication. Graphic Software such as NetFab, supplied with the device, would allow easy transfer of 3D model from CAD applications to G code. G code is recorded on an SD card and the device reads the data and then creates a model of the scaffold in a relatively short time depending on its complexity.
Plasmonic multiple exciton generation (2019)

We show that biexciton formation can be highly efficient in a solar cell whose semiconductor absorber is filled with an array of metallic nanoparticles having plasmonic resonances tuned to the semiconductor gap energy. This process can be viewed as a plasmon-enhanced multiple exciton generation, with the resulting cell efficiency exceeding the Shockley-Queisser limit. We demonstrate via theory and simulations that the efficiency of the process increases with decreasing semiconductor gap size, and illustrate such by considering in detail three systems with gradually decreasing gap size: GaAs, Si, and Ge.
Marker assisted selection in rice. (2010)

A rising global population requires increased crop production and some research suggests that the rate of increase in crop yields is currently declining and traits related to yield, stability and sustainability should be a major focus of plant breeding efforts. These traits include durable disease resistance, abiotic stress tolerance and nutrient and water use efficiency. The use of DNA markers in plant breeding is called marker assisted selection (MAS). So far, about 40 major blast genes have been identified, about 30 genes have been mapped on different rice chromosomes, and tightly linked DNA markers have been developed. Eight blast resistance genes have been cloned and the genes have been used for their selective introgression into susceptible rice cultivars. Recently Genetic and physical mapping of blast resistance gene Pi-42(t) located on the short arm of rice chromosome 12 in a resistant genotype ‘DHR9’ has been achieved. The PCR-based allele specific and in Del marker sets are available for nine blast resistance genes and they provide an efficient marker system for MAS for blast resistance breeding. Recently a novel resistance gene Pi40 derived from wild Oryza species ( O. australiensis ), have been located on chromosomes 6 and it shows promise for broad spectrum resistance. Tetep, the likely donor of Pi5(t) confers broad-spectrum resistance to Magnaporthe grisea . Additionally, several blast resistance genes could be combined using MAS in a single genetic background to develop rice cultivars with broad-spectrum durable resistance to blast. In future combination of conventional and marker assisted selection approach will provide opportunities for breeders to develop high yielding, stress tolerant and better quality rice cultivars. No doubt the cost of using DNA markers is expensive but it is worth the investment. Key words: Rice, Molecular markers, Polymorphism, Foreground and background selection Sabina Akhtar et al. Marker Assisted Selection in Rice. J Phytol 2/10 (2010) 66-81
Compton Camera Imaging of a Gamma‐Ray Glow From a Thunderstorm (2022)

Abstract Gamma‐ray glows associated with thunderclouds have been observed since the 1980s, however it remains unclear how, and at which thunderstorms gamma‐ray glows are generated in dense atmospheres. In this study, we report the first Compton camera imaging of a gamma‐ray glow from a winter thundercloud. On 14 January 2022, using two identical Bi 4 Ge 3 O 12 scintillators in energy range of 0.05–5 MeV, we detected two gamma‐ray glows lasting ∼4 min in a mountain area 25 km from the Japan Sea and 410 m above sea level. The same events were also observed by the Compton camera, where the first glow we observed suggested statistically significant (4.0 and 5.9 σ level) signals of two enhanced concentrations in gamma‐ray photon images in a range of 0.15–1.5 MeV. These concentrations were most clearly observed in a time window of Δ t = 50 s around the peak intensity of the gamma‐ray glow.
Towards Selective Syntheses of Octadienylethers from the Butadiene Palladium‐catalyzed Telomerization with Polyols in Aqueous Biphasic Medium (2019)

Abstract The palladium catalyzed telomerization of butadiene with polyols has been efficiently performed under aqueous and biphasic medium leading to the corresponding octadienylethers. Depending on the choice of the organic co‐solvent and nature of the catalyst employed to promote the reaction, mono‐ to fully substituted ethers could be obtained with high selectivities and yields. Particularly, pentaerythritol was telomerized for the first time allowing the selective synthesis of the corresponding monotelomers by using methylethylketone as organic co‐solvent and the water soluble ligand TPPTS associated to a simple palladium precursor. Polyethers of sorbitol could be efficiently obtained by using a mixture of TPPTS and PPh 3 ligands.
Functional Analysis of the Melanin-Associated Gene CmMR1 in Coniothyrium minitans (2018)

<i>Coniothyrium minitans</i> is a sclerotial parasite, which has been investigated for commercial control of crop diseases caused by <i>Sclerotinia sclerotiorum</i>. Previously, we obtained a T-DNA insertional mutant, ZS-1TN24363, which did not produce melanin during conidiation. To understand the function of melanin in <i>C. minitans</i>, we cloned the gene that was disrupted by the T-DNA insertion, and found that this gene, called <i>CmMR1</i>, encoded a putative protein of 1,011 amino acids, which is a homolog of the transcription factor MR. Full-length <i>CmMR1</i> contains 3,167 bp, with three exons and two introns. To confirm that the disrupted gene is responsible for the melanin-deficiency of the mutant, <i>CmMR1</i> was disrupted and three targeted knockout mutants were obtained. Biological assays showed that the phenotype of the targeted knockout mutants was similar to that of the T-DNA insertional mutant. Furthermore, gene complementation confirmed that <i>CmMR1</i> is responsible for the mutant phenotype. <i>CmMR1</i> disruption did not affect hyphal growth, conidiation, and parasitization of <i>C. minitans</i>, however, the ROS accumulation increased and tolerance to UV light decreased significantly in the mutants. Our result may enhance the understanding of melanin in the ecology of <i>C. minitans</i> on molecular level.
COX‐1, COX‐2 and articular joint disease: A role for chondroprotective agents (2002)

It is widely accepted that whilst exhibiting clinically useful anti-inflammatory and analgesic activity, the application of non-steroidal anti-inflammatory drugs (NSAIDs) does not affect the underlying pathogenesis of articular diseases such as rheumatoid arthritis. The demonstration of a role for COX-2 in the resolution of inflammation may partly underly the lack of disease modifying activity seen with NSAIDs in long term use in these inflammatory joint diseases. This has led to the suggestion that the anti-arthritic efficacy of these agents may be improved by altering prescribing practice such that they are not given during periods of disease remission, which may be difficult to achieve in the clinic. Alternatively, they may benefit from concomitant administration of chondroprotective agents, such as diacetylrhein, which may protect against the deleterious effects of traditional NSAIDs on cartilage degradation and, further, inhibit additional pathways such as cytokine elaboration which are important in joint destruction.
Small non‐coding RNAs in Caulobacter crescentus (2008)

Small non-coding RNAs (sRNAs) are active in many bacterial cell functions, including regulation of the cell's response to environmental challenges. We describe the identification of 27 novel Caulobacter crescentus sRNAs by analysis of RNA expression levels assayed using a tiled Caulobacter microarray and a protocol optimized for detection of sRNAs. The principal analysis method involved identification of sets of adjacent probes with unusually high correlation between the individual intergenic probes within the set, suggesting presence of a sRNA. Among the validated sRNAs, two are candidate transposase gene antisense RNAs. The expression of 10 of the sRNAs is regulated by either entry into stationary phase, carbon starvation, or rich versus minimal media. The expression of four of the novel sRNAs changes as the cell cycle progresses. One of these shares a promoter motif with several genes expressed at the swarmer-to-stalked cell transition; while another appears to be controlled by the CtrA global transcriptional regulator. The probe correlation analysis approach reported here is of general use for large-scale sRNA identification for any sequenced microbial genome.
Learning Rankings via Convex Hull Separation (2005)

We propose efficient algorithms for learning ranking functions from order constraints between sets—i.e. classes—of training samples. Our algorithms may be used for maximizing the generalized Wilcoxon Mann Whitney statistic that accounts for the partial ordering of the classes: special cases include maximizing the area under the ROC curve for binary classification and its generalization for ordinal regression. Experiments on public benchmarks indicate that: (a) the proposed algorithm is at least as accurate as the current state-of-the-art; (b) computationally, it is several orders of magnitude faster and—unlike current methods—it is easily able to handle even large datasets with over 20,000 samples. 1
Urine pH and Citrate as Predictors of Calcium Phosphate Stone Formation (2023)

Key Points The occurrence of calcium phosphate stones has increased over the past five decades, and this is most notable in female stone formers. High urine pH and hypocitraturia are the most discriminatory urine parameters between calcium phosphate and calcium oxalate stone formers. High urine pH in calcium phosphate stone formers is independent of the effect of dietary alkali and acid. Background Urinary parameters, including urine pH and citrate, are recognized as critical in the pathophysiology of calcium-based stones. The factors contributing to variation in these parameters between calcium oxalate (CaOx) and calcium phosphate (CaP) stone formers (SFs) are, however, not well-understood. In this study, using readily available laboratory data, we explore these differences to delineate the odds of forming CaP versus CaOx stones. Methods In this single-center retrospective study, we compared serum and urinary parameters between adult CaP SFs, CaOx SFs, and non–stone formers. Results Urine pH was higher and urine citrate lower in CaP SFs compared with same-sex CaOx SFs and non–stone formers. In CaP SFs, higher urine pH and lower citrate were independent of markers of dietary acid intake and gastrointestinal alkali absorption, suggesting abnormal renal citrate handling and urinary alkali excretion. In a multivariable model, urine pH and urine citrate were most discriminatory between CaP SFs and CaOx SFs (receiver-operating characteristic area under the curve of 0.73 and 0.65, respectively). An increase in urine pH by 0.35, a decrease in urine citrate by 220 mg/d, a doubling of urine calcium, and female sex all independently doubled the risk of CaP stone formation compared with CaOx stones. Conclusions High urine pH and hypocitraturia are two clinical parameters that distinguish the urine phenotype of CaP SFs from CaOx SFs. Alkalinuria is due to intrinsic differences in the kidney independent of intestinal alkali absorption and is accentuated in the female sex.
LPS binding protein and CD14 in the LPS dependent activation of cells. (1994)

Editors Jack Levin University of California School of Medicine and Veterans Administration Medical Center San Francisco, California Sander J.H. van Deventer Center for Hemostasis, Thrombosis, and Atherosclerosis Research Academic Medical Center University of Amsterdam Amsterdam, The Netherlands Tom van der Poll Laboratory of Surgical Metabolism Cornell Medical Center New York Hospital New York Augueste Sturk Department of Clinical Chemistry Academic Medical Hospital Leiden Leiden, The Netherlands
Introduction (1977)

The climate in which I first thought of trying to answer some of my own questions about pre-school children and television was full of talk about education in the impressionable years, what we call, strangely enough, 'nursery education'. How big a part did television play in the lives of children under five whose parents were demanding such education? What did they remember of what they viewed? Were they confused by the oblong screen that at one moment found room for an aeroplane and the next for a fist holding a revolver? Did violence make them violent? Were they frightened by television? How many hours a day did they spend in front of a set? How many could they spend without damage to their physical and mental development? Did they miss the television when they first came to school? A compelling subject since educated children are the essential ingredient of a continuing civilised society. But how, if necessary, protect children from an established, almost nationwide, part of daily living? Or, if television showed itself to be as valuable a teaching tool as I have found it in a primary school, how discover the best way to use it to supplement the thin provision of education outside their own homes for three- and four-year-olds in this country? In 1971 that provision was for five per cent of three-year-olds and thirty-five per cent of four-year-olds.
Rapid activation of C-Raf-1 after stimulation of the T-cell receptor or the muscarinic receptor type 1 in resting T cells. (1993)

The c-Raf-1 serine/threonine kinase is an important component of signal transduction pathways mediating the effects of a variety of growth factors. In activated T cells, IL-2 has been shown to induce activation of c-Raf-1, but c-Raf-1 has not previously been shown to be activated through the T-cell receptor (TCR) in resting G0 T cells. Using a sensitive immune complex kinase reaction, we show that cross-linking of the stimulatory and costimulatory receptors CD3, CD4, or CD28 induces c-Raf-1 activation in highly purified resting peripheral blood human T cells. In contrast, cross-linking the nonstimulatory receptor CD45 did not induce c-Raf-1. Surprisingly, although earlier studies had shown delayed kinetics in response to Thy-1 stimulation in murine cells, c-Raf-1 activation in response to CD3 cross-linking was one of the earliest measurable events. In spite of its early kinetics, c-Raf-1 activation was found to be downstream of several other early signal transduction events, including activation of a tyrosine kinase and a tyrosine phosphatase. Several lines of evidence suggest that activation of c-Raf-1 in response to TCR stimulation may be PKC-dependent: first, phorbol esters are extremely potent activators of c-Raf-1 in human T cells; second, the kinetics of accumulation of products of phosphatidylinositol hydrolysis coincides with the kinetics of c-Raf-1 activation; and third, physiologic activation of the PLC/PKC pathway through a transfected, G-protein-coupled receptor HM1 induced similar levels of c-Raf-1 activation with a similar time course. We conclude that c-Raf-1 activation is tightly coupled to TCR stimulation and may participate in signal transduction pathways in resting, G0 T cells. The observation that the HM1 receptor can also activate c-Raf-1 suggests that T cells have the capability to utilize both tyrosine kinase-dependent and tyrosine kinase-independent mechanisms of c-Raf-1 activation.
Agile software development in large organizations (2004)

The need to see compelling evidence before adopting new methods looms greater in large organizations because of their complexity and the need to integrate new technologies and processes with existing ones. To further evaluate agile methods and their underlying software development practices, several Software Experience Center (SEC) member companies initiated a series of activities to discover if agile practices match their organizations' needs. Although each organization evaluated agile methods according to its specific needs, here we attempt to generalize their findings by analyzing some of their common experiences in the particular context of large organizations with well-established structures and processes. We base this analysis on experience collected and shared among four SEC members namely ABB, DaimlerChrysler, Motorola, and Nokia.
Corneal Endothelial Cells Are Protected from Apoptosis by Gene Therapy (2010)

Corneal grafting is the most prevalent form of transplantation. Corneal endothelial cells (ECs), which form a monolayer of the cornea with minimal proliferative potential, are pivotal for maintenance of corneal clarity. Loss of EC viability and apoptosis leads to graft failure posttransplantation and reduces the quality of donor corneas in storage, such that up to 30% do not meet selection criteria and must be discarded. The current study investigates antiapoptotic effects of transduced mammalian Bcl-x(L) and baculoviral p35 on human ECs. Multiple apoptotic cell features are observed while inducing apoptosis either via the extrinsic (death receptor) or intrinsic (mitochondrial) apoptotic pathway. Human ECs were studied under three experimental conditions: (1) as an immortalized cell line, (2) as primary cells, and (3) in an intact cornea. Interestingly, in primary EC suspensions, Bcl-x(L) was protective against apoptosis mediated via both pathways. However, p35 was significantly more protective against apoptosis mediated via the intrinsic pathway compared with Bcl-x(L). Our results provide critical insight into the role of apoptotic pathways in the maintenance of EC viability and the efficacy with which these protective proteins exert their effect. These observations could form the basis for future applications of antiapoptotic gene therapy to corneal preservation aiming to reduce both graft failure after transplantation as well as donor corneal damage during storage.