gebhart/patrepeval huggingface dataset:
Mitochondrial fission‐fusion as an emerging key regulator of cell proliferation and differentiation (2013)

Mitochondrial shape change, brought about by molecules that promote either fission or fusion between individual mitochondria, has been documented in several model systems. However, the deeper significance of mitochondrial shape change has only recently begun to emerge: among others, it appears to play a role in the regulation of cell proliferation. Here, I review the emerging interplay between mitochondrial fission-fusion components with cell cycle regulatory machineries and how that may impact cell differentiation. Regulation of mitochondrial shape may modulate mitochondrial metabolism and/or energetics to promote crosstalk between signaling components and the cell cycle machinery. Focused research in this area will reveal the exact role of mitochondria in development and disease, specifically in stem cell regulation and tumorigenesis. Such research may also reveal whether and how the endosymbiotic event that gave rise to the mitochondrion was crucial for the evolution of cell cycle regulatory mechanisms in eukaryotes that are absent in prokaryotes.
Application-Specific Integrated Circuits (1997)

Addressing the trend in industry away from fully custom chip design to semi-custom technology, this book provides the first comprehensive introduction to Application Specific Integrated Circuits (ASICs).
Measurements of negative ion densities in 13.56-MHz rf plasmas of CF4, C2F6, CHF3, and C3F8 using microwave resonance and the photodetachment effect (1991)

The high-power density of a frequency quadrupled pulsed Nd-YAG laser has been used to photodetach electrons from negative ions in rf plasmas generated within a microwave cavity. Negative ion densities have been determined by measuring the frequency shift of the resonance transmission, the shift being caused by the photoelectrons created by irradiating the plasma with the laser pulse. By measurement of the shape of the resonance curve as a function of time and of microwave frequency, and consecutive fitting of a parabola to the top of the resonance curve, the negative ion density has been determined as a function of gas pressure, rf power, and position in the plasma. Measurements were performed in plasmas of CF4, C2F6, CHF3, and C3F8. The results indicate that the negative ion densities are about one order of magnitude larger than the electron density, which is in good agreement with a fluid model calculation. The pressure and power dependence of the electron density and of the negative ion density gives insight in the relation between the electron temperature and the macroscopic plasma parameters. Measurements as a function of the laser wavelength, using a pulsed dye laser, show that in CF4 the negative ions mainly consist of F−, whereas in C2F6 significant densities of other negative ions may occur.
Protein-Protein Fusion Catalyzed by Sortase A (2011)

Chimeric proteins boast widespread use in areas ranging from cell biology to drug delivery. Post-translational protein fusion using the bacterial transpeptidase sortase A provides an attractive alternative when traditional gene fusion fails. We describe use of this enzyme for in vitro protein ligation and report the successful fusion of 10 pairs of protein domains with preserved functionality--demonstrating the robust and facile nature of this reaction.
Plasma Prealbumin in Women with Epithelial Ovarian Carcinoma (1994)

Prealbumin is studied in women with epithelial ovarian carcinoma prior to and during chemotherapy, and is found to vary inversely with changes in tumor volume.
Re‐Establishing Immune Tolerance in Type 1 Diabetes via Regulatory T Cells (2008)

Type 1 diabetes (T1D) is a disease in which tolerance to self-antigens, such as insulin, is broken leading to expansion of autoreactive T cells that attack pancreatic beta cells with consequent loss of insulin production. Regulatory T cells (Tregs) represent a specific T cell subset that plays a key role in inducing and maintaining immunological tolerance to self and non-self antigens. The naturally occurring CD4+CD25+ Tregs (nTregs) originate from the thymus, constitutively express the transcription factor FOXP3, and suppress immune responses mainly via cell-cell contact. Depletion of nTregs results in systemic autoimmune diseases in mice and, vice versa, transfer of nTregs prevents development of autoimmune diseases. Regulatory T type 1 (Tr1) cells are inducible Tregs generated in the periphery by chronic exposure to antigens in the presence of interleukin (IL)10. Tr1 cells are defined by their unique cytokine production profile (i.e. IL10++, IL5+, TGFbeta+, IL4-, IL2(low), IFNgamma(low). Tr1 cells are induced by a specialized subset of tolerogenic dendritic cells and suppress undesired immune responses mainly through production of IL10 and TGFbeta. Interestingly,Trl cells modulate responses to self-antigens such as insulin- and islet-derived peptides. In vitro expansion/induction of Tregs can be therefore envisaged as a therapeutic tool for re-establishing self-tolerance in T1D subjects.
Peripheral and Central Interactions between the Renin‐Angiotensin System and the Renal Sympathetic Nerves in Control of Renal Function (2001)

Increases in renal sympathetic nerve activity (RSNA) regulate the functions of the nephron, the vasculature, and the renin-containing juxtaglomerular granular cells. As increased activity of the renin-angiotensin system can also influence nephron and vascular function, it is important to understand the interactions between RSNA and the renin-angiotensin system in the control of renal function. These interactions can be intrarenal, that is, the direct (via specific innervation) and indirect (via angiotensin II) contributions of increased RSNA to the regulation of renal function. The effects of increased RSNA on renal function are attenuated when the activity of the renin-angiotensin system is suppressed or antagonized with angiotensin-converting enzyme inhibitors or angiotensin II-type AT1 receptor antagonists. The effects of intrarenal administration of angiotensin II are attenuated following renal denervation. These interactions can also be extrarenal, that is, in the central nervous system, wherein RSNA and its arterial baroreflex control are modulated by changes in activity of the renin-angiotensin system. In addition to the circumventricular organs, the permeable blood-brain barrier of which permits interactions with circulating angiotensin II, there are interactions at sites behind the blood-brain barrier that depend on the influence of local angiotensin II. The responses to central administration of angiotensin II type AT1 receptor antagonists, into the ventricular system or microinjected into the rostral ventrolateral medulla, are modulated by changes in activity of the renin-angiotensin system produced by physiological changes in dietary sodium intake. Similar modulation is observed in pathophysiological models wherein activity of both the renin-angiotensin and sympathetic nervous systems is increased (e.g., congestive heart failure). Thus, both renal and extrarenal sites of interaction between the renin-angiotensin system and RSNA are involved in influencing the neural control of renal function.
Organization of genes required for gellan polysaccharide biosynthesis in Sphingomonas elodea ATCC 31461 (2004)

Sphingomonas elodea ATCC 31461 produces gellan, a capsular polysaccharide that is useful as a gelling agent for food and microbiological media. Complementation of nonmucoid S. elodea mutants with a gene library resulted in identification of genes essential for gellan biosynthesis. A cluster of 18 genes spanning 21 kb was isolated. These 18 genes are homologous to genes for synthesis of sphingan polysaccharide S-88 from Sphingomonas sp. ATCC 31554, with predicted amino acid identities varying from 61% to 98%. Both polysaccharides have the same tetrasaccharide repeat unit, comprised of [-->4)-alpha- l-rhamnose-(1-->3)-beta- d-glucose-(1-->4)-beta- d-glucuronic acid-(1-->4)-beta- d-glucose-(1-->]. Polysaccharide S-88, however, has mannose or rhamnose in the fourth position and has a rhamnosyl side chain, while gellan has no sugar side chain but is modified by glyceryl and acetyl substituents. Genes for synthesis of the precursor dTDP- l-rhamnose were highly conserved. The least conserved genes in this cluster encode putative glycosyl transferases III and IV and a gene of unknown function, gelF. Three genes ( gelI, gelM, and gelN) affected the amount and rheology of gellan produced. Four additional genes present in the S-88 sphingan biosynthetic gene cluster did not have homologs in the gene cluster for gellan biosynthesis. Three of these gene homologs, gelR, gelS, and gelG, were found in an operon unlinked to the main gellan biosynthetic gene cluster. In a third region, a gene possibly involved in positive regulation of gellan biosynthesis was identified.
Evaluation of Vaccinia Viral Lysates as Therapeutic Vaccines in the Treatment of Melanomaa (1993)

Patients who develop metastases from melanoma in regional lymph nodes are known to be at high risk of developing further recurrences after surgical removal of the lymph node metastases. This study examines whether immunization over a two-year period with a vaccine made from vaccinia viral lysates of an allogeneic melanoma cell (VMCL), following surgical removal of lymph node metastases, would help prevent the development of distant metastases and improve survival from the disease. Eighty patients treated with VMCL alone and followed for a minimum of 5.5 years had improved survival compared with that of a historical control group of 151 patients and a concurrent nonrandomized group of 55 patients. Similarly, survival of 102 patients treated with VMCL plus low dose cyclophosphamide for a minimum of 3.5 years was superior to that of the historical control group but not to that of the group treated with VMCL alone. Improvement in survival measured from the date of removal of the primary tumor was still evident. Analysis of subsets of patients showed that VMCL treatment appeared to benefit patients irrespective of the number of lymph nodes involved and whether surgery was carried out near to (synchronous metastases) or some time after removal of the primary (delayed metastases). Analysis of two additional aspects provided further evidence for a biologic effect of the vaccine. One was an apparent alteration in distribution of metastases with a lower incidence of cutaneous metastases relative to visceral metastases in VMCL-treated patients. The second was a change in time to development of recurrences with a higher proportion of metastases occurring after 2 years in the treated patients. Of a projected 400 patients, 384 were entered into a randomized control (phase III) study to further evaluate this treatment. An interim analysis gave no reason for premature closure of the trial. This next analysis is scheduled for 9 months after closure of the trial.
Clem Christesen and His Legacy (2004)

This is a task I have been dodging for a long time, I realise as I sit down to write.Clem Christesen was a complex and contradictory individual, and his life-work even more so.The two are hard to separate: for more than three decades, from 1940 until 1974, Clem's name was synonymous with that of Meanjin, but his contribution to Australian cultural life extends far beyond the magazine's pages.In many ways he was a larger-than-life figure who defies any neat summation.As an individual, Clem was the most quixotic person I have ever known.He was irascible and charming by turns, a great hater who remained intensely loyal to those who were willing to weather his storms.To give a small example from my own experience, at one point we fell out over my editing of Judith Armstrong's The Christesen Romance, and he sent me to Coventry for two years.Then, late one afternoon, I picked up the phone to hear a familiar gravelly voice saying 'Jenny?It's your old mate from Eltham.' (I'm sure he'd rehearsed that line.)And our friendship resumed more or less where it had left off, with some new silences.Clem was quixotic in another sense: in the political arena, he was constitutionally incapable of not tilting at windmills.(St Clement, the patron saint of lost causes?)He was a committed democrat, sympathetic to socialism -the archetypal fellow-traveller in Cold War terms.But what made his political stance distinctive was his visceral rebellion against Australian insularity.He often recalled the shock he had experienced in 1939, when he left the intellectual and political ferment of Europe on the brink of war and returned to Brisbane, only to find the town mired in inward-looking complacency.This sense of being out of place at home had much to do with his determination to set up a literary magazine.His editorial endeavours were driven by a fierce desire to connect Australians with the wider world and prod them out of the 'stomach-and-pocket view of life', as he called it in
A survey of best practices for RNA-seq data analysis (2016)

RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping. We highlight the challenges associated with each step. We discuss the analysis of small RNAs and the integration of RNA-seq with other functional genomics techniques. Finally, we discuss the outlook for novel technologies that are changing the state of the art in transcriptomics.
A mixed frequency-time approach for finding the steady-state solution of clocked analog circuits (2003)

Performing detailed simulation of clocked analog circuits (e.g. switched-capacitor filters and switching power supplies) with circuit simulation programs like SPICE is computationally very expensive. The authors present a more efficient method for computing the detailed steady-state solution of clocked analog circuits. The method exploits the property of such circuits that the waveforms in each clock cycle are similar but not exact duplicates of the proceeding or following cycles. Therefore, by computing accurately a few selected cycles, the entire steady-state solution can be constructed efficiently.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Reversal of Autocrine and Paracrine Effects of Interleukin 1 (IL-1) in Human Arthritis by Type II IL-1 Decoy Receptor (2000)

Interleukin 1 (IL-1), produced by both synovial cells and chondrocytes, plays a pivotal role in the pathogenesis of cartilage destruction in osteoarthritis (OA). We examined the specific expression and function of IL-1 receptor family-related genes in human joint tissues. Gene array analysis of human normal and OA-affected cartilage showed mRNA expression of IL-1 receptor accessory protein (IL-1RAcp) and IL-1 type I receptor (IL-1RI), but not IL-1 antagonist (IL-1ra) and IL-1 type II decoy receptor (IL-1RII). Similarly, human synovial and epithelial cells showed an absence of IL-1RII mRNA. Functional genomic analyses showed that soluble (s) IL-1RII, at picomolar concentrations, but not soluble TNF receptor:Fc, significantly inhibited IL-1beta-induced nitric oxide (NO) and/or prostaglandin E(2) production in chondrocytes, synovial and epithelial cells. In OA-affected cartilage, the IC(50) for inhibition of NO production by sIL-1RII was 2 log orders lower than that for sIL-1RI. Human chondrocytes that overexpressed IL-1RII were resistant to IL-1-induced IL-1beta mRNA accumulation and inhibition of proteoglycan synthesis. In osteoarthritis, deficient expression by chondrocytes of innate regulators or antagonists of IL-1 such as IL-1ra and IL-1RII (soluble or membrane form) may allow the catabolic effects of IL-1 to proceed unopposed. The sensitivity of IL-1 action to inhibition by sIL-1RII has therapeutic implications that could be directed toward correcting this unfavorable tissue(s) dependent imbalance.
Wafer-scale Reduced Graphene Oxide Films for Nanomechanical Devices (2008)

We report a process to form large-area, few-monolayer graphene oxide films and then recover the outstanding mechanical properties found in graphene to fabricate high Young's modulus (<E> =185 GPa), low-density nanomechanical resonators. Wafer-scale films as thin as 4 nm are sufficiently robust that they can be delaminated intact and resuspended on a bed of pillars or field of holes. From these films, we demonstrate radio frequency resonators with quality factors (up to 4000) and figures of merit ( f x Q>10(11)) well exceeding those of pure graphene resonators reported to date. These films' ability to withstand high in-plane tension (up to 5 N/m) as well as their high Q-values reveals that film integrity is enhanced by platelet-platelet bonding unavailable in pure graphite.
A taxonomy and evaluation of dense two-frame stereo correspondence algorithms (2002)

Stereo matching is one of the most active research areas in computer vision. While a large number of algorithms for stereo correspondence have been developed, relatively little work has been done on characterizing their performance. In this paper, we present a taxonomy of dense, two-frame stereo methods designed to assess the different components and design decisions made in individual stereo algorithms. Using this taxonomy, we compare existing stereo methods and present experiments evaluating the performance of many different variants. In order to establish a common software platform and a collection of data sets for easy evaluation, we have designed a stand-alone, flexible C++ implementation that enables the evaluation of individual components and that can be easily extended to include new algorithms. We have also produced several new multiframe stereo data sets with ground truth, and are making both the code and data sets available on the Web.
PET genes of Saccharomyces cerevisiae (1990)

We describe a collection of nuclear respiratory-defective mutants (pet mutants) of Saccharomyces cerevisiae consisting of 215 complementation groups. This set of mutants probably represents a substantial fraction of the total genetic information of the nucleus required for the maintenance of functional mitochondria in S. cerevisiae. The biochemical lesions of mutants in approximately 50 complementation groups have been related to single enzymes or biosynthetic pathways, and the corresponding wild-type genes have been cloned and their structures have been determined. The genes defined by an additional 20 complementation groups were identified by allelism tests with mutants characterized in other laboratories. Mutants representative of the remaining complementation groups have been assigned to one of the following five phenotypic classes: (i) deficiency in cytochrome oxidase, (ii) deficiency in coenzyme QH2-cytochrome c reductase, (iii) deficiency in mitochondrial ATPase, (iv) absence of mitochondrial protein synthesis, and (v) normal composition of respiratory-chain complexes and of oligomycin-sensitive ATPase. In addition to the genes identified through biochemical and genetic analyses of the pet mutants, we have cataloged PET genes not matched to complementation groups in the mutant collection and other genes whose products function in the mitochondria but are not necessary for respiration. Together, this information provides an up-to-date list of the known genes coding for mitochondrial constituents and for proteins whose expression is vital for the respiratory competence of S. cerevisiae.
Context-aware clustering of DNS query traffic (2008)

The Domain Name System (DNS) is a one of the most widely used services in the Internet. In this paper, we consider the question of how DNS traffic monitoring can provide an important and useful perspective on network traffic in an enterprise. We approach this problem by considering three classes of DNS traffic: canonical (i.e., RFC-intended behaviors), overloaded (e.g.,black-list services), and unwanted (i.e., queries that will never succeed). We describe a context-aware clustering methodology that is applied to DNS query-responses to generate the desired aggregates. Our method enables the analysis to be scaled to expose the desired level of detail of each traffic type, and to expose their time varying characteristics. We implement our method in a tool we call TreeTop, which can be used to analyze and visualize DNS traffic in real-time. We demonstrate the capabilities of our methodology and the utility of TreeTop using a set of DNS traces that we collected from our campus network over a period of three months. Our evaluation highlights both the coarse and fine level of detail that can be revealed by our method. Finally, we show preliminary results on how DNS analysis can be coupled with general network traffic monitoring to provide a useful perspective for network management and operations.
The Role of Chelating Diamine Ligands in the Goldberg Reaction:  A Kinetic Study on the Copper-Catalyzed Amidation of Aryl Iodides (2005)

The mechanistic details of the Cu-catalyzed amidation of aryl iodides are presented. The kinetic data suggest that the diamine ligand prevents multiple ligation of the amide. The formation of an amidocuprate species external to the catalytic cycle helped to rationalize the dependence on diamine concentration and the inverse dependence on amide concentration at low diamine concentrations. The intermediacy of a Cu(I) amidate was established through both its chemical and kinetic competency.
Antibodies and Genetically Engineered Related Molecules: Production and Purification (2004)

Antibodies and antibody derivatives constitute 20 % of biopharmaceutical products currently in development, and despite early failures of murine products, chimeric and humanized monoclonal antibodies are now viable therapeutics. A number of genetically engineered antibody constructions have emerged, including molecular hybrids or chimeras that can deliver a powerful toxin to a target such as a tumor cell. However, the general use in clinical practice of antibody therapeutics is dependent not only on the availability of products with required efficacy but also on the costs of therapy. As a rule, a significant percentage (50-80%) of the total manufacturing cost of a therapeutic antibody is incurred during downstream processing. The critical challenges posed by the production of novel antibody therapeutics include improving process economics and efficiency, to reduce costs, and fulfilling increasingly demanding quality criteria for Food and Drug Administration (FDA) approval. It is anticipated that novel affinity-based separations will emerge from the development of synthetic ligands tailored to specific biotechnological needs. These synthetic affinity ligands include peptides obtained by synthesis and screening of peptide combinatorial libraries and artificial non-peptidic ligands generated by a de novo process design and synthesis. The exceptional stability, improved selectivity, and low cost of these ligands can lead to more efficient, less expensive, and safer procedures for antibody purification at manufacturing scales. This review aims to highlight the current trends in the design and construction of genetically engineered antibodies and related molecules, the recombinant systems used for their production, and the development of novel affinity-based strategies for antibody recovery and purification.