gebhart/patrepeval huggingface dataset:
Metadata logging in an NFS server (1995)

Over the last few years, there have been several efforts to use logging to improve performance, reliability, and recovery times of file systems. The two major techniques are metadata logging, where the log records metadata changes and is a supplement to the on-disk file system, and logstructured file systems, whose log is their only ondisk representation. When the file system is mainly or wholly accessed through the Network File System (NFS) protocol, it adds new considerations to the suitability of the logging technique. NFS requires that all operations be updated to stable storage before returning. As a result, file system implementations that were effective for local access may perform poorly on an NFS server. This paper analyzes the issues regarding the use of logging on an NFS server, and describes an implementation of a BSD Fast File System (FFS) with metadata logging that performs effectively for a dedicated NFS server. 1.
Intravenous Iron Administration and Hypophosphatemia in Clinical Practice (2015)

Introduction. Parenteral iron formulations are frequently used to correct iron deficiency anemia (IDA) and iron deficiency (ID). Intravenous formulation efficacy on ferritin and hemoglobin level improvement is greater than that of oral formulations while they are associated with lower gastrointestinal side effects. Ferric carboxymaltose- (FCM-) related hypophosphatemia is frequent and appears without clinical significance. The aim of this study was to assess the prevalence, duration, and potential consequences of hypophosphatemia after iron injection. Patients and Methods. The medical records of all patients who underwent parenteral iron injection between 2012 and 2014 were retrospectively reviewed. Pre- and postinjection hemoglobin, ferritin, plasma phosphate, creatinine, and vitamin D levels were assessed. Patients who developed moderate (range: 0.32-0.80 mmol/L) or severe (<0.32 mmol/L) hypophosphatemia were questioned for symptoms. Results. During the study period, 234 patients received iron preparations but 104 were excluded because of missing data. Among the 130 patients included, 52 received iron sucrose (FS) and 78 FCM formulations. Among FS-treated patients, 22% developed hypophosphatemia versus 51% of FCM-treated patients, including 13% who developed profound hypophosphatemia. Hypophosphatemia severity correlated with the dose of FCM (p = 0.04) but not with the initial ferritin, hemoglobin, or vitamin D level. Mean hypophosphatemia duration was 6 months. No immediate clinical consequence was found except for persistent fatigue despite anemia correction in some patients. Conclusions. Hypophosphatemia is frequent after parenteral FCM injection and may have clinical consequences, including persistent fatigue. Further studies of chronic hypophosphatemia long-term consequences, especially bone assessments, are needed.
Design of an Amphiphilic Polymer for Nanoparticle Coating and Functionalization (2008)

Amphiphilic polymer-coating for nanoparticles: The facile one-pot synthesis of a comblike polymer can be tailored in order to vary its hydrophobic side-chains or to directly incorporate functional molecules without the need for crosslinkers. This leads to a general and robust method of phase-transfer of hydrophobic nanoparticles to aqueous solution, as well as to their modification with functional molecules. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2296/2008/z700654_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
New Efficient Synthesis of 4-Amino-3-arylphenols (1995)

Treatment in an alkaline medium of the cycloadducts obtained from the Diels-Alder cycloaddition of Danishefsky’s diene with different oxazol-5(4H)-ones constitutes an efficient method for the aromatisation of the cyclohexene ring, allowing the synthesis of 3-substituted 4-aminophenols, by previous hydrolysis of the benzamide group.
Tau protein level in cerebrospinal fluid is increased in patients with early multiple sclerosis (2005)

Axonal damage has been proposed as the major substrate of permanent clinical disability in multiple sclerosis. Tau protein, a microtubule-associated protein localised in neuronal axons, may serve as a biochemical surrogate marker to evaluate axonal damage in vivo. We intended to determine the extent of axonal damage in different stages and clinical subtypes of MS by investigating cerebrospinal fluid tau concentrations. Tau was measured using an immunoassay in 35 patients with relapsing-remitting MS, eight patients with secondary progressive MS, nine patients with primary progressive MS, 50 patients with clinically isolated syndrome suggestive of early MS and 46 normal controls. Cerebrospinal fluid tau was significantly elevated in MS compared with normal controls (median 206.0 pg/mL versus 152.0 pg/mL; P = 0.002). No significant difference among different subtypes of MS could be detected, although highest levels were found in very early disease stages. There was a significant elevation of CSF tau among patients with gadolinium-enhancing brain lesions in magnetic resonance imaging (P = 0.02) and a tendency towards higher CSF tau levels in patients with pronounced intrathecal IgG synthesis, supporting the notion that axonal damage is influenced by inflammatory activity.
Catalysis of serine and tyrosine autophosphorylation by the human insulin receptor. (1992)

The protein kinase activity of human insulin receptors purified from Sf9 insect cells after infection with a recombinant baculovirus was evaluated. The following experimental observations led to the unexpected conclusion that this receptor protein catalyzes both serine and tyrosine autophosphorylation at significant stoichiometries. (i) Phosphorylation of lectin-purified insulin receptors with [gamma-32P]ATP resulted in rapid receptor tyrosine phosphorylation (7 mol of P per high-affinity binding site) and the delayed onset of insulin-stimulated receptor serine phosphorylation (about 7% of total phosphorylation). The tyrosine kinase inhibitor (hydroxy-2-naphthalenylmethyl)phosphonic acid (HNMPA), which has no effect on protein kinase C or cyclic AMP-dependent protein kinase activities, inhibited both the receptor serine and tyrosine phosphorylation. (ii) Phosphorylation of a synthetic peptide substrate composed of insulin receptor residues 1290-1319 on serines-1305/1306 by partially purified insulin receptors was also inhibited by HNMPA. (iii) Insulin receptors sequentially affinity-purified on immobilized wheat germ agglutinin and immobilized insulin showed no apparent contaminant proteins on silver-stained SDS/polyacrylamide gels yet catalyzed autophosphorylation on receptor serine and tyrosine residues when incubated with [gamma-32P]ATP. These results suggest that the catalytic site of the insulin receptor tyrosine kinase also recognizes receptor serine residues as substrates for the phosphotransfer reaction. Furthermore, insulin-stimulated receptor serine phosphorylation in intact cells may occur in part by an autophosphorylation mechanism subsequent to tyrosine phosphorylation of the insulin receptor.
Zinc Finger Nucleases: A new era for transgenic animals (2011)

The rational engineering of eukaryotic genomes would facilitate the study of heritable changes in gene expression and offer enormous potential across basic research, drug-discovery, bioproduction and therapeutic development. A significant advancement toward this objective was achieved with the advent of a novel technology that enables high-frequency and high-fidelity genome editing via the application of custom designed zinc finger nucleases (ZFNs). A ZFN is a chimeric protein that consists of the non-specific endonuclease domain of FokI fused to a DNA-binding domain composed of an engineered zinc-finger motif. Within these chimeric proteins, the DNA binding specificity of the zinc finger protein determines the site of nuclease action. Once the engineered ZFNs recognize and bind to their specified locus, it leads to the dimerization of the two nuclease domains on the ZFNs to evoke a double-strand break (DSB) in the targeted DNA. The cell then employs the natural DNA repair processes of either non-homologous end joining (NHEJ) or homology-directed repair (HDR) to repair the targeted break. Due to the imperfect fidelity of NHEJ, a proportion of DSBs within a ZFN-treated cellular population will be misrepaired, leading to cells in which variable heterogeneous genetic insertions or deletions have been made at the target site. Alternatively, the HDR repair pathway enables precise insertion of a transgene or other defined alterations into the targeted region. By this approach, a donor template containing the transgene flanked by sequences that are homologous to the regions either side of the cleavage site is co-delivered into the cell along with the ZFNs. By creating a specific DSB, these cellular repair mechanisms are harnessed to generate precisely targeted genomic edits resulting in both cell lines and animal models with targeted gene deletions, integrations, or modifications. This review will discuss the development, mechanism of action, and applications of ZFN technology to genome engineering and the creation of animal models.
A hybrid approach for named entity and sub-type tagging (2000)

This paper presents a hybrid approach for named entity (NE) tagging which combines Maximum Entropy Model (MaxEnt), Hidden Markov Model (HMM) and handcrafted grammatical rules. Each has innate strengths and weaknesses; the combination results in a very high precision tagger. MaxEnt includes external gazetteers in the system. Sub-category generation is also discussed.
Short‐term effect of latanoprost and timolol eye drops on tear fluid and the ocular surface in patients with primary open‐angle glaucoma and ocular hypertension (2000)

Regarding ocular surface effects, no clinically important differences between latanoprost and timolol were observed as all the effects remained in the normal range.
Biodistribution and Pharmacokinetic Studies of Bone-Targeting N-(2-Hydroxypropyl)methacrylamide Copolymer−Alendronate Conjugates (2008)

The biodistribution and pharmacokinetics of bone-targeting N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer-alendronate conjugates were evaluated following intravenous administration of radioiodinated conjugates to young healthy BALB/c mice. The synthesis of a polymerizable and cathepsin K cleavable alendronate derivative, N-methacryloylglycylglycylprolylnorleucylalendronate, enabled the preparation of HPMA copolymer-alendronate conjugates with varying composition. Using the RAFT (reversible addition-fragmentation chain transfer) polymerization technique, four conjugates with different molecular weight and alendronate content and two control HPMA copolymers (without alendronate) with different molecular weight were prepared. The results of biodistribution studies in mice demonstrated a strong binding capacity of alendronate-targeted HPMA copolymer conjugates to bone. Conjugates with low (1.5 mol%) alendronate content exhibited a similar bone deposition capacity as conjugates containing 8.5 mol % of alendronate. The molecular weight was an important factor in the biodistribution of the HPMA copolymer conjugates. More conjugate structures need to be evaluated, but the data suggest that medium molecular weights (50-100 kDa) might be effective drug carriers for bone delivery.
Induction and Prevention of Severe Hyperammonemia in the spfash Mouse Model of Ornithine Transcarbamylase Deficiency Using shRNA and rAAV-mediated Gene Delivery (2011)

Urea cycle defects presenting early in life with hyperammonemia remain difficult to treat and commonly necessitate liver transplantation. Gene therapy has the potential to prevent hyperammonemic episodes while awaiting liver transplantation, and possibly also to avert the need for transplantation altogether. Ornithine transcarbamylase (OTC) deficiency, the most prevalent urea cycle disorder, provides an ideal model for the development of liver-targeted gene therapy. While we and others have successfully cured the spf(ash) mouse model of OTC deficiency using adeno-associated virus (AAV) vectors, a major limitation of this model is the presence of residual OTC enzymatic activity which confers a mild phenotype without clinically significant hyperammonemia. To better model severe disease we devised a strategy involving AAV2/8-mediated delivery of a short hairpin RNA (shRNA) to specifically knockdown residual endogenous OTC messenger RNA (mRNA). This strategy proved highly successful with vector-treated mice developing severe hyperammonemia and associated neurological impairment. Using this system, we showed that the dose of an AAV rescue construct encoding the murine OTC (mOTC) cDNA required to prevent hyperammonemia is fivefold lower than that required to control orotic aciduria. This result is favorable for clinical translation as it indicates that the threshold for therapeutic benefit is likely to be lower than indicated by earlier studies.
Connectional networks within the orbital and medial prefrontal cortex of macaque monkeys (1996)

The intrinsic cortico-cortical connections within the orbital and medial prefrontal cortex (OMPFC) were demonstrated with retrograde and anterograde tracers injected into each of the architectonic areas that constitute this region. Although many of the connections linked neighboring areas, others selectively connected relatively distant areas. Most, but not all, of the connections were reciprocal. Altogether, the connections formed at least two distinct networks within the OMPFC. The "orbital" prefrontal network linked most of the areas within the orbital cortex, with very few connections to medial prefrontal areas. Areas Iam, Iapm, Ial, 12l, 12m, and 12r in the caudal and lateral parts of the orbital cortex (which received inputs from several sensory modalities) had convergent connections with areas 13l, 13m, and 13b in the central orbital cortex, with further connections to the rostral orbital area 11l. For the connections between areas Iapm, Iam, Ial, 13m, 13l, and 11l, rostrally directed fibers arose mainly in layer V, whereas caudally directed fibers originated mainly in layer III. The "medial" prefrontal network selectively involved medial areas 14r, 14c, 24, 25, 32, and 10m, rostral orbital areas 10o and 11m, and agranular insular area Iai in the posterior orbital cortex. Two orbital areas, 13a and 12o, had substantial connections to both networks and may serve as points of interaction between them; otherwise there were relatively few interconnections. The two networks also had distinct connections with other cortical regions, with limbic structures, and with the mediodorsal thalamic nucleus. Their role in guidance of affective behaviour is discussed.
Antibody‐induced growth inhibition is mediated through immunochemically and functionally distinct epitopes on the extracellular domain of the c‐erbb‐2 (her‐2/neu) gene product p185 (1993)

Over-expression of the c-erbB-2 (HER-2/neu) gene product p185 occurs in 30% of breast and ovarian cancers. The p185 protein might serve as a target for serotherapy in that antibodies against different epitopes on the extracellular domain of p185 can inhibit growth of tumor cells in the absence of cellular or humoral effector mechanisms. To define epitopes of functional relevance, 11 monoclonal antibodies (MAbs) were evaluated for their ability to bind to the extracellular domain of p185. Results of competition studies with 125I-labeled and non-labeled antibodies indicated that 10 of 11 epitopes were grouped in a linear array. Antibodies against 7 epitopes inhibited anchorage-independent growth and antibodies against 2 of these epitopes also inhibited anchorage-dependent growth of SKBr3 breast-cancer cells that over-expressed p185. Treatment with antibodies exerted cytotoxic rather than cytostatic effects. When antibodies were used in combination, additive or supra-additive inhibition of anchorage-independent and anchorage-dependent growth was observed between pairs of antibodies. Growth inhibition did not relate to the affinity of the antibody or its isotype. Two antibodies that inhibited both anchorage-dependent and anchorage-independent growth also blocked binding of the HER-2/neu ligand, whereas 5 antibodies that inhibited only anchorage-independent growth had no effect on ligand binding. Inhibition of cell growth did not correlate with internalization of p185 or down-regulation of p185 on the cell surface. Fab fragments of active antibodies could also inhibit anchorage-independent growth of SKBr3. Thus, murine MAbs and their fragments recognized both immunochemically distinct and functionally distinct epitopes on the p185 molecule. Whereas inhibition of anchorage-dependent growth correlated with the ability of antibodies to block ligand binding, inhibition of anchorage-independent growth did not correlate with effects on ligand binding, internalization, cell-surface expression or cross-linking of p185.
Clusterin promotes amyloid plaque formation and is critical for neuritic toxicity in a mouse model of Alzheimer's disease (2002)

Studies have shown that clusterin (also called apolipoprotein J) can influence the structure and toxicity of amyloid-beta (Abeta) in vitro. To determine whether endogenous clusterin plays a role in influencing Abeta deposition, structure, and toxicity in vivo, we bred PDAPP mice, a transgenic mouse model of Alzheimer's disease, to clusterin(-/-) mice. By 12 months of age, PDAPP, clusterin(-/-) mice had similar levels of brain Abeta deposition as did PDAPP, clusterin(+/+) mice. Although Abeta deposition was similar, PDAPP, clusterin(-/-) mice had significantly fewer fibrillar Abeta (amyloid) deposits than PDAPP mice expressing clusterin. In the absence of clusterin, neuritic dystrophy associated with the deposited amyloid was markedly reduced, resulting in a dissociation between fibrillar amyloid formation and neuritic dystrophy. These findings demonstrate that clusterin markedly influences Abeta structure and neuritic toxicity in vivo and is likely to play an important role in Alzheimer's disease pathogenesis.
Gaze-directed volume rendering (1990)

We direct our gaze at an object by rotating our eyes or head until the object's projection falls on the fovea, a small region of enhanced spatial acuity near the center of the retina. In this paper, we explore methods for encorporating gaze direction into rendering algorithms. This approach permits generation of images exhibiting continuously varying resolution, and allows these images to be displayed on conventional television monitors. Specifically, we describe a ray tracer for volume data in which the number of rays cast per unit area on the image plane and the number of samples drawn per unit length along each ray are functions of local retinal acuity. We also describe an implementation using 2D and 3D mip maps, an eye tracker, and the Pixel-Planes 5 massively parallel raster display system. Pending completion of Pixel-Planes 5 in the spring of 1990, we have written a simulator on a Stellar graphics supercomputer. Preliminary results indicate that while users are aware of the variable-resolution structure of the image, the high-resolution sweet spot follows their gaze well and promises to be useful in practice.
Virion Incorporation of Human Immunodeficiency Virus Type-1 Vif Is Determined by Intracellular Expression Level and May Not Be Necessary for Function (1998)

The viral infectivity factor (Vif) of human immunodeficiency virus type-1 (HIV-1) functions at a late stage of the viral life cycle to confer infectivity on progeny virions. Although Vif is present in HIV-1 particles, both the relevance of incorporation for function and the mechanism that underlies incorporation remain unresolved. Using matched T cell systems that express high or low levels of Vif, we demonstrate that the extent of Vif incorporation into virions varies in relation to cellular expression levels. Because viral infectivity is not affected by these variations, we suggest that the packaging of Vif is neither specific nor necessary for function.
Forms of Power (1995)

The various constituents of power are always bound together in some form or another to make up concrete power. What binds them together are the rights possessed by certain groups. The rights possessed by such groups unite the various constituents of power and form the concrete powers of these groups. However, there are various aspects to these rights, and it would be difficult to deal with them all exhaustively here. I shall therefore cite only the most typical of them. What I shall explain here are the concrete forms of power in the sense that I indicated previously. This concreteness resides chiefly in the persons to whom power belongs, and is therefore determined by the rights they enjoy. So, then, how are we to consider some of the typical rights of representative groups?
Odorant-odorant metabolic interaction, a novel actor in olfactory perception and behavioral responsiveness (2017)

In the nasal olfactory epithelium, olfactory metabolic enzymes ensure odorant clearance from the olfactory receptor environment. This biotransformation of odorants into deactivated polar metabolites is critical to maintaining peripheral sensitivity and perception. Olfactory stimuli consist of complex mixtures of odorants, so binding interactions likely occur at the enzyme level and may impact odor processing. Here, we used the well-described model of mammary pheromone-induced sucking-related behavior in rabbit neonates. It allowed to demonstrate how the presence of different aldehydic odorants efficiently affects the olfactory metabolism of this pheromone (an aldehyde too: 2-methylbut-2-enal). Indeed, according to in vitro and ex vivo measures, this metabolic interaction enhances the pheromone availability in the epithelium. Furthermore, in vivo presentation of the mammary pheromone at subthreshold concentrations efficiently triggers behavioral responsiveness in neonates when the pheromone is in mixture with a metabolic challenger odorant. These findings reveal that the periphery of the olfactory system is the place of metabolic interaction between odorants that may lead, in the context of odor mixture processing, to pertinent signal detection and corresponding behavioral effect.
Total synthesis of porcine cholecystokinin-33 (CCK-33) (1987)

Porcine cholecystokinin-pancreozymin (CCK), which is a 33 amino acid peptide having a sulphated tyrosyl residue at position 27, was synthesized by the classical solution procedure applying our maximum protection strategy, for which the phenoxyacetyl group was used for the first time for protection of Ser residues.