gebhart/patrepeval huggingface dataset:
TGF-? receptor function in the endothelium (2004)

Genetic studies in mice and humans have revealed the pivotal role of transforming growth factor-beta (TGF-beta) signaling during angiogenesis. Mice deficient for various TGF-beta signaling components present an embryonic lethality due to vascular defects. In patients, mutations in the TGF-beta type I receptor ALK1 or in the accessory TGF-beta receptor endoglin are linked to an autosomal dominant disorder of vascular dysplasia termed Hereditary Haemorrhagic Telangiectasia (HHT). It has puzzled researchers for years to explain the effects of TGF-beta being a stimulator and an inhibitor of angiogenesis in vitro and in vivo. Recently, a model has been proposed in which TGF-beta by binding to the TGF-beta type II receptor can activate two distinct type I receptors in endothelial cells (ECs), i.e., the EC-restricted ALK1 and the broadly expressed ALK-5, which have opposite effects on ECs behavior. ALK1 via Smad1/5 transcription factors stimulates EC proliferation and migration, whereas ALK5 via Smad2/3 inhibits EC proliferation and migration. Here, the new findings are presented concerning the molecular mechanisms that take place in ECs to precisely regulate and even switch between TGF-beta-induced biological responses. In particular, the role of the accessory TGF-beta receptor endoglin in the regulation of EC behavior is addressed and new insights are discussed concerning the possible mechanisms that are implicated in the development of HHT.
Synthesis of Indolo and benzimidazoquinazolines and benzodiazepines (1973)

Abstract Indolo[1,2‐ c ] quinazolines, indolo[1,2‐ d ] [1,4]benzodiazepines, indolo [1,2‐ d ] [1,4]benzodi‐azepin‐6‐ones and benzimidazo[1,2‐ d ] [1,4] benzodiazepin‐6‐ones were synthesized. In an acid medium, the indoloquinazolines were produced from 2‐(o‐aminophenyl)indole and acyl halides. However, in the presence of sodium acetate, the acylated amine was obtained and was cyclized to the indolobenzodiazepinones using sodium hydride. The syntheses are described in detail and characterization data are given.
Promoter hypermethylation patterns of p16, O6-methylguanine-DNA-methyltransferase, and death-associated protein kinase in tumors and saliva of head and neck cancer patients. (2001)

Aberrant promoter hypermethylation is common in head and neck cancer and may be useful as a marker for cancer cells. We examined whether cells with tumor-specific aberrant DNA-methylation might be found in the saliva of affected patients. We tested 30 patients with primary head and neck tumors using methylation-specific PCR searching for promoter hypermethylation of the tumor suppressor gene p16 (CDKN2A), the DNA repair gene O6-methylguanine-DNA-methyltransferase (MGMT) and the putative metastasis suppressor gene death-associated protein kinase (DAP-K). Aberrant methylation of at least one of these genes was detected in 17 (56%) of 30 head and neck primary tumors; 14 (47%) of 30 at p16, 10 (33%) of 30 at Dap-K and 7 (23%) of 30 at MGMT. In 11 (65%) of 17 methylated primary tumors abnormal methylated DNA was detected in the matched saliva samples. Abnormal promoter methylation in saliva DNA was found in all tumor stages and more frequently in tumors located in the oral cavity. Moreover, none of the saliva from patients with methylation-negative tumors displayed methylation of any marker. Of 30 saliva samples from healthy control subjects (15 smokers and 15 nonsmokers), only one sample from a smoking patient was positive for DNA methylation at two target genes. Detection of aberrant promoter hypermethylation patterns of cancer-related genes in saliva of head and cancer patients is feasible and may be potentially useful for detecting and monitoring disease recurrence. Long-term longitudinal studies are needed to evaluate this approach for early detection of head and neck cancer in at-risk populations.
Fast exact summation using small and large superaccumulators (2015)

I present two new methods for exactly summing a set of floating-point numbers, and then correctly rounding to the nearest floating-point number. Higher accuracy than simple summation (rounding after each addition) is important in many applications, such as finding the sample mean of data. Exact summation also guarantees identical results with parallel and serial implementations, since the exact sum is independent of order. The new methods use variations on the concept of a "superaccumulator" - a large fixed-point number that can exactly represent the sum of any reasonable number of floating-point values. One method uses a "small" superaccumulator with sixty-seven 64-bit chunks, each with 32-bit overlap with the next chunk, allowing carry propagation to be done infrequently. The small superaccumulator is used alone when summing a small number of terms. For big summations, a "large" superaccumulator is used as well. It consists of 4096 64-bit chunks, one for every possible combination of exponent bits and sign bit, plus counts of when each chunk needs to be transferred to the small superaccumulator. To add a term to the large superaccumulator, only a single chunk and its associated count need to be updated, which takes very few instructions if carefully implemented. On modern 64-bit processors, exactly summing a large array using this combination of large and small superaccumulators takes less than twice the time of simple, inexact, ordered summation, with a serial implementation. A parallel implementation using a small number of processor cores can be expected to perform exact summation of large arrays at a speed that reaches the limit imposed by memory bandwidth. Some common methods that attempt to improve accuracy without being exact may therefore be pointless, at least for large summations, since they are slower than computing the sum exactly.
Dense arrays of well-aligned carbon nanotubes completely filled with single crystalline titanium carbide wires on titanium substrates (1999)

We report the synthesis of dense and uniform arrays of well-aligned carbon nanotubes on titanium substrates over large areas, in which all the tubes are simultaneously and completely filled with single crystals of titanium carbide. The carbon nanotubes were synthesized by thermal chemical vapor deposition of ethylene on iron-coated substrates, while the titanium carbide was simultaneously formed inside the nanotubes through a simultaneous solid state reaction. We propose a base dissolution and precipitation mechanism for the growth of titanium carbide filled carbon nanotubes. The same method can be used to fabricate oriented nanotube arrays filled with other carbides on a variety of substrates over large scale. Such well-aligned and densely packed uniform carbon nanotubes, completely filled with nanowires on conducting substrates, will have great potential in many applications.
E2F-1 Blocks Terminal Differentiation and Causes Proliferation in Transgenic Megakaryocytes (1996)

The transcription factor E2F-1 plays a central role in the cell cycle through its ability to activate genes involved in cell division. E2F-1 activity is regulated by a number of proteins, including the retinoblastoma susceptibility gene product, cyclin-dependent kinases, and their inhibitors, proteins that have been implicated in the control of certain developmental processes. To investigate a potential role of E2F-1 in differentiation, we assayed the ability of megakaryocytes to form platelets in an in vivo transgenic model. E2F-1 expression in megakaryocytes blocked differentiation during maturation, resulting in severe thrombocytopenia. Ultrastructural analysis of megakaryocytes revealed abnormal development characterized by hyperdemarcation of cytoplasmic membranes and reduced numbers of alpha granules. Administration of megakaryocyte growth and development factor or interleukin 6 could not overcome the differentiation block. Additionally, E2F-1 caused massive megakaryocyte accumulation in both normal and ectopic sites, first evident in E15 embryonic liver. Furthermore, significant apoptosis was observed in transgenic megakaryocytes. These data indicate that E2F-1 can prevent terminal differentiation, probably through its cell cycle-stimulatory activity.
The Development of Classically and Alternatively Activated Macrophages Has Different Effects on The Varied Stages of Radiation-induced Pulmonary Injury in Mice (2011)

The classical and alternative activation of macrophages has been proposed to play a role in radiation-induced pneumonitis and fibrosis, respectively. To test this hypothesis, the thoraces of C57BL/6 mice were irradiated with 12 Gy X-rays, and irradiated and control mice were euthanized at 1, 8, 12, 24 and 72 hours, and 2, 4, 8, 16 and 24 weeks after irradiation. The expression of inducible nitric oxide synthase (iNOS) and arginase type 1 (Arg-1) was evaluated at the mRNA and protein levels at different stages post-irradiation. We demonstrated that the enhanced mRNA and protein expression of iNOS occurred within the pneumonic stage, whereas the high levels of Arg-1 expression occurred within the fibrotic phase. Immunohistochemistry revealed that iNOS and Arg-1 were mainly expressed in macrophages. The expression of iNOS and Arg-1 may be associated with acute radiation pneumonitis and the development of radiation fibrosis, respectively. Although the function of macrophages cannot explain the whole process of radiation-induced pulmonary injury development, it may play an important regulatory role during this process.
The accuracy of diagnosis of parkinsonian syndromes in a specialist movement disorder service (2002)

We have reviewed the clinical and pathological diagnoses of 143 cases of parkinsonism seen by neurologists associated with the movement disorders service at The National Hospital for Neurology and Neurosurgery in London who came to neuropathological examination at the United Kingdom Parkinson's Disease Society Brain Research Centre, over a 10-year period between 1990 and the end of 1999. Seventy-three (47 male, 26 female) cases were diagnosed as having idiopathic Parkinson's disease (IPD) and 70 (42 male, 28 female) as having another parkinsonian syndrome. The positive predictive value of the clinical diagnosis for the whole group was 85.3%, with 122 cases correctly clinically diagnosed. The positive predictive value of the clinical diagnosis of IPD was extremely high, at 98.6% (72 out of 73), while for the other parkinsonian syndromes it was 71.4% (50 out of 70). The positive predictive values of a clinical diagnosis of multiple system atrophy (MSA) and progressive supranuclear palsy (PSP) were 85.7 (30 out of 35) and 80% (16 out of 20), respectively. The sensitivity for IPD was 91.1%, due to seven false-negative cases, with 72 of the 79 pathologically established cases being diagnosed in life. For MSA, the sensitivity was 88.2% (30 out of 34), and for PSP it was 84.2% (16 out of 19). The diagnostic accuracy for IPD, MSA and PSP was higher than most previous prospective clinicopathological series and studies using the retrospective application of clinical diagnostic criteria. The seven false-negative cases of IPD suggest a broader clinical picture of disease than previously thought acceptable. This study implies that neurologists with particular expertise in the field of movement disorders may be using a method of pattern recognition for diagnosis which goes beyond that inherent in any formal set of diagnostic criteria.
A Report on the 2017 Native Language Identification Shared Task (2017)

Shervin Malmasi, Keelan Evanini, Aoife Cahill, Joel Tetreault, Robert Pugh, Christopher Hamill, Diane Napolitano, Yao Qian. Proceedings of the 12th Workshop on Innovative Use of NLP for Building Educational Applications. 2017.
Increases in α4* but not α3*/α6* nicotinic receptor sites and function in the primate striatum following chronic oral nicotine treatment (2006)

Knowledge of the effects of chronic nicotine is critical considering its widespread use in tobacco products and smoking cessation therapies. Although nicotine is well known to up-regulate alpha4* nAChR sites and function in the cortex, its actions in the striatum are uncertain because of the presence of multiple subtypes with potentially opposing effects. We therefore investigated the effect of long-term nicotine treatment on nAChR sites and function in the primate striatum, which offers the advantage of similar proportions of alpha3*/alpha6* and alpha4* nAChRs. Nicotine was given in drinking water, which resembles smoking in its intermittent but chronic delivery. Plasma nicotine and cotinine levels were similar to smokers. Chronic nicotine treatment (> 6 months) enhanced alpha4* nAChR-evoked [(3)H]dopamine release in striatal subregions, with an overall pattern of increase throughout the striatum when normalized to uptake. This increase correlated with elevated striatal alpha4* nAChRs. Under the same conditions, striatal alpha3*/alpha6* nAChR sites and function were decreased or unchanged. These divergent actions of chronic nicotine treatment on alpha4* versus alpha6* nAChRs, as well as effects on dopamine uptake, allow for a complex control of striatal activity to maintain dopaminergic function. Such knowledge is important for understanding nicotine dependence and the consequences of nicotine administration for the treatment of neurological disorders.
Contraction-induced Changes in Acetyl-CoA Carboxylase and 5′-AMP-activated Kinase in Skeletal Muscle (1997)

The concentration of malonyl-CoA, a negative regulator of fatty acid oxidation, diminishes acutely in contracting skeletal muscle. To determine how this occurs, the activity and properties of acetyl-CoA carboxylase beta (ACC-beta), the skeletal muscle isozyme that catalyzes malonyl-CoA formation, were examined in rat gastrocnemius-soleus muscles at rest and during contractions induced by electrical stimulation of the sciatic nerve. To avoid the problem of contamination of the muscle extract by mitochondrial carboxylases, an assay was developed in which ACC-beta was first purified by immunoprecipitation with a monoclonal antibody. ACC-beta was quantitatively recovered in the immunopellet and exhibited a high sensitivity to citrate (12-fold activation) and a Km for acetyl-CoA (120 microM) similar to that reported for ACC-beta purified by other means. After 5 min of contraction, ACC-beta activity was decreased by 90% despite an apparent increase in the cytosolic concentration of citrate, a positive regulator of ACC. SDS-polyacrylamide gel electrophoresis of both homogenates and immunopellets from these muscles showed a decrease in the electrophoretic mobility of ACC, suggesting that phosphorylation could account for the decrease in ACC activity. In keeping with this notion, citrate activation of ACC purified from contracting muscle was markedly depressed. In addition, homogenization of the muscles in a buffer free of phosphatase inhibitors and containing the phosphatase activators glutamate and MgCl2 or treatment of immunoprecipitated ACC-beta with purified protein phosphatase 2A abolished the decreases in both ACC-beta activity and electrophoretic mobility caused by contraction. The rapid decrease in ACC-beta activity after the onset of contractions (50% by 20 s) and its slow restoration to initial values during recovery (60-90 min) were paralleled temporally by reciprocal changes in the activity of the alpha2 but not the alpha1 isoform of 5'-AMP-activated protein kinase (AMPK). In conclusion, the results suggest that the decrease in ACC activity during muscle contraction is caused by an increase in its phosphorylation, most probably due, at least in part, to activation of the alpha2 isoform of AMPK. They also suggest a dual mechanism for ACC regulation in muscle in which inhibition by phosphorylation takes precedence over activation by citrate. These alterations in ACC and AMPK activity, by diminishing the concentration of malonyl-CoA, could be responsible for the increase in fatty acid oxidation observed in skeletal muscle during exercise.
SPHINGOLIPID FUNCTIONS INSACCHAROMYCES CEREVISIAE: Comparison to Mammals (1998)

Many roles for sphingolipids have been identified in mammals. Available data suggest that sphingolipids and their intermediates also have diverse roles in Saccharomyces cerevisiae. These roles include signal transduction during the heat stress response, regulation of calcium homeostasis or components in calcium-mediated signaling pathways, regulation of the cell cycle, and functions as components in trafficking of secretory vesicles from the endoplasmic reticulum to the Golgi apparatus and as the lipid moiety in many glycosylphosphatidylinositol-anchored proteins. S. cerevisiae is likely to be the first organism in which all genes involved in sphingolipid metabolism are identified. This information will provide an unprecedented opportunity to determine, for the first time in any organism, how sphingolipid synthesis is regulated. Through the use of both genetic and biochemical techniques, the identification of the complete array of processes regulated by sphingolipid signals is likely to be possible, as is the quantification of the physiological contribution of each.
Excitatory amino acids and neurotoxicity. (1994)

In the past three decades evidence indicating a role for excitatory amino acids in determining certain neurological disorders has been accumulated. Although the mechanisms underlying the neuronal damage induced by glutamate are not yet fully understood, many intracellular processes are thought to contribute to the development of excitotoxic injury, acting in combination to determine cell death. In this article we report the leading hypotheses in the understanding of excitatory amino acid-induced toxicity, which focus on the role of Ca2+ and Ca(2+)-activated processes, for example the activation of Ca(2+)-dependent enzymes such as kinases, lipases and proteases and the formation of the messenger molecule nitric oxide for the production of free radicals, in the development of neuronal damage. The possible implications for excitotoxicity of second messenger systems generated by glutamate acting on the metabotropic receptor subtypes will also be discussed.
Disease-modifying agents in multiple sclerosis (2009)

Since 1993, six disease-modifying therapies for multiple sclerosis (MS) have been proven to be of benefit in rigorous phase III clinical trials. Other agents are also available and are used to treat MS, but definitive data on their efficacy is lacking. Currently, disease-modifying therapy is used for relapsing forms of MS. This includes clinically isolated syndrome/first-attack high-risk patients, relapsing patients, secondary progressive patients who are still experiencing relapses, and progressive relapsing patients. The choice of agent depends upon drug factors (including affordability, availability, convenience, efficacy, and side effects), disease factors (including clinical and neuroimaging prognostic indicators), and patient factors (including comorbidities, lifestyle, and personal preference). This review will discuss the disease-modifying agents used currently in MS, as well as available alternative agents.
The cellular composition of induced sputum in chronic obstructive pulmonary disease (1999)

Asthma and chronic obstructive pulmonary disease are characterized by airway inflammation, which can be assessed by bronchoscopic techniques as well as by the analysis of induced sputum. A method to induce sputum with inhaled hypertonic saline was adapted for use in 21 chronic obstructive pulmonary disease (COPD) patients (mean baseline forced expiratory volume in one second (FEV1) 1.60 L, or 54% predicted) and in 16 healthy volunteers. The success rate and safety of the method, were investigated along with the reproducibility of cell counts and differences in cell counts between both groups. All subjects produced adequate samples and the procedure did not alter spirometric values. A marked sputum neutrophilia was noted in patients with COPD (74.9+/-4.7%), whereas mainly macrophages were seen in healthy volunteers (74.0+/-4.0%). Reliability of the cell counts was high, both within investigators (r=0.99 neutrophils, r=0.99 macrophages) and between investigators (r=0.95 neutrophils, r=0.77 macrophages). In patients with COPD, an inverse correlation was noted between percentage of neutrophils and FEV1 (r(s)=-0.48, p<0.05). Immunostaining revealed a large proportion of activated macrophages in both groups. It was concluded that induction of sputum is a safe and reproducible method to study the composition of airway secretions in patients with chronic obstructive pulmonary disease.
Partition functions of unit-copy plasmids can stabilize the maintenance of plasmid pBR322 at low copy number (1986)

The maintenance of plasmid pBR322 is highly unstable in a polA12 strain of Escherichia coli at 29 degrees C due to severely reduced copy number. Under these conditions, introduction of the par (partition) locus of plasmid P1 or the par (sop) region of F into pBR322 stabilizes it. A region with similar activity was detected in the P7 plasmid. The activity of the P1 par locus was dependent on the P1 parA gene product and was sensitive to par-specified incompatibility.
Long-Term Dosing of AMG 531 Is Effective and Well Tolerated in Thrombocytopenic Patients with Immune Thrombocytopenic Purpura. (2005)

Abstract AMG 531 is a novel platelet-stimulating peptibody that targets the TPO receptor, resulting in increased production of platelets. This ongoing, open-label study assessed the safety and efficacy of long-term AMG 531 dosing in ITP patients. Eligible patients have completed a previous AMG 531 study in ITP, are ≥18 years of age, have a baseline platelet count ≤50 x 109/L, with no recent significant change in medical history. The AMG 531 starting dose is 1μg/kg by SC injection with dose adjustment to an original maximum of 30μg/kg, since reduced to 15μg/kg. Patients are treated weekly unless the platelet count is &gt;400x109/L. Concurrent corticosteroids can be tapered when the platelet count is ≥50x109/L. Preliminary data are available for 26 patients treated for up to 24 weeks: 17 women and 9 men; mean age, 48.4±11.6 (SD) years; mean baseline platelet count, 18.5±12.3 (SD) x109/L. Twenty-one patients (80.8%) had undergone a splenectomy before study entry; 6 (23.1%) were receiving concurrent corticosteroids for ITP. Twenty-one of 26 patients (80.8%) had a protocol-defined platelet response to AMG 531 (doubling of the baseline platelet count and ≥50x109/L). The mean AMG 531 dose at the first response was 3.7±2.7 (SD) μg/kg (at median 5 weeks); the mean dose at week 24 was 7.2±4.2 (SD) μg/kg. Twelve of 26 patients (46.2%) had a durable platelet response (doubling of the baseline count and ≥50x109/L at 6 or more of weeks 17–24). Twenty patients (76.9%) had a platelet count ≥100x109/L at least once; 7 (26.9%) had a platelet count ≥400x109/L. Of 6 patients on concurrent corticosteroids, 3 discontinued treatment and 2 had a ≥25% dose reduction. At least 1 serious adverse event was reported in 4 patients: anal fistula (unrelated to treatment), adverse drug reaction (unrelated), multiple sclerosis relapse (unrelated), bone pain (related), and diffuse reticulin formation in the bone marrow reported as myelofibrosis (related). Reticulin formation is hypothesized as due to excessive accumulation of megakaryocytes in the bone marrow. AMG 531 was discontinued, and a bone marrow 3 months later showed improvement. One patient experienced adverse events (musculoskeletal pain and headache) resulting in withdrawal from the study. No neutralizing antibodies have been detected to date. In summary, repeated exposure to AMG 531 has been generally well tolerated in this ongoing study. A total 80.8% of patients achieved a platelet response, defined as doubling of the baseline count and ≥50x109/L. Individualized weekly doses of AMG 531 may provide a therapeutic option in ITP, potentially enabling patients to taper off long-term corticosteroid therapy.