gebhart/patrepeval huggingface dataset:
One-pot production of 2,5-dimethylfuran from fructose over Ru/C and a Lewis–Brønsted acid mixture in N,N-dimethylformamide (2016)

A one-pot process for the production of 2,5-dimethylfuran from fructose by using Ru/C and a Lewis–Brønsted acid mixture as catalysts.
Sequence of contactin, a 130-kD glycoprotein concentrated in areas of interneuronal contact, defines a new member of the immunoglobulin supergene family in the nervous system (1988)

The primary amino acid sequence of contactin, a neuronal cell surface glycoprotein of 130 kD that is isolated in association with components of the cytoskeleton (Ranscht, B., D. J. Moss, and C. Thomas. 1984. J. Cell Biol. 99:1803-1813), was deduced from the nucleotide sequence of cDNA clones and is reported here. The cDNA sequence contains an open reading frame for a 1,071-amino acid transmembrane protein with 962 extracellular and 89 cytoplasmic amino acids. In its extracellular portion, the polypeptide features six type 1 and two type 2 repeats. The six amino-terminal type 1 repeats (I-VI) each consist of 81-99 amino acids and contain two cysteine residues that are in the right context to form globular domains as described for molecules with immunoglobulin structure. Within the proposed globular region, contactin shares 31% identical amino acids with the neural cell adhesion molecule NCAM. The two type 2 repeats (I-II) are each composed of 100 amino acids and lack cysteine residues. They are 20-31% identical to fibronectin type III repeats. Both the structural similarity of contactin to molecules of the immunoglobulin supergene family, in particular the amino acid sequence resemblance to NCAM, and its relationship to fibronectin indicate that contactin could be involved in some aspect of cellular adhesion. This suggestion is further strengthened by its localization in neuropil containing axon fascicles and synapses.
Chemistry of Protein Stabilization by Trehalose (1994)

Carbohydrates are widely used to stabilise dried protein and peptide drugs. Several sugars can prevent damage to proteins during drying, but the products often have a short shelf life at ambient temperatures. There is increasing evidence to suggest that this is due to a progressive chemical reaction between the reducing carbonyl groups of the sugars and the amino groups of proteins, the so-called Maillard reaction. The rational choice of an excipient for pharmaceutical use must thus consider not only the avoidance of desiccation damage but also subsequent degradative chemistries on storage. We present data from comparative studies on the long term stability of a variety of proteins, including enzymes and therapeutic peptides, dried using various carbohydrate excipients, which establish the superiority of the simple disaccharide trehalose as a stabilising excipient. These observations illustrate the chemical stability of trehalose and document the protein degradation observed in samples dried using other carbohydrates.
Effect of particle size on mechanical properties of core shell polymers prepared by microemulsion polymerization (2005)

Society of Plastics Engineers Annual Technical Conference 2005, ANTEC 2005, 1 May 2005 through 5 May 2005.
The European internet-based patient and research database for primary immunodeficiencies: update 2011 (2011)

In order to build a common data pool and estimate the disease burden of primary immunodeficiencies (PID) in Europe, the European Society for Immunodeficiencies (ESID) has developed an internet-based database for clinical and research data on patients with PID. This database is a platform for epidemiological analyses as well as the development of new diagnostic and therapeutic strategies and the identification of novel disease-associated genes. Since its start in 2004, 13,708 patients from 41 countries have been documented in the ESID database. Common variable immunodeficiency (CVID) represents the most common entity with 2880 patients or 21% of all entries, followed by selective immunoglobulin A (sIgA) deficiency (1424 patients, 10·4%). The total documented prevalence of PID is highest in France, with five patients per 100,000 inhabitants. The highest documented prevalence for a single disease is 1·3 per 100,000 inhabitants for sIgA deficiency in Hungary. The highest reported incidence of PID per 100,000 live births was 16·2 for the period 1999-2002 in France. The highest reported incidence rate for a single disease was 6·7 for sIgA deficiency in Spain for the period 1999-2002. The genetic cause was known in 36·2% of all registered patients. Consanguinity was reported in 8·8%, and 18·5% of patients were reported to be familial cases; 27·9% of patients were diagnosed after the age of 16. We did not observe a significant decrease in the diagnostic delay for most diseases between 1987 and 2010. The most frequently reported long-term medication is immunoglobulin replacement.
Recovery of left ventricular function following in vivo reexpression of cardiac myosin binding protein C (2018)

The loss of cardiac myosin binding protein C (cMyBP-C) results in left ventricular dilation, cardiac hypertrophy, and impaired ventricular function in both constitutive and conditional cMyBP-C knockout (<i>MYBPC3</i> null) mice. It remains unclear whether the structural and functional phenotypes expressed in the <i>MYBPC3</i> null mouse are reversible, which is an important question, since reduced expression of cMyBP-C is an important cause of hypertrophic cardiomyopathy in humans. To investigate this question, we generated a cardiac-specific transgenic mouse model using a Tet-Off inducible system to permit the controlled expression of WT cMyBP-C on the <i>MYBPC3</i> null background. Functional Tet-Off mice expressing WT cMyBP-C (FT-WT) were generated by crossing tetracycline transactivator mice with responder mice carrying the WT cMyBP-C transgene. Prior to dietary doxycycline administration, cMyBP-C was expressed at normal levels in FT-WT myocardium, which exhibited similar levels of steady-state force and in vivo left ventricular function as WT mice. Introduction of dietary doxycycline for four weeks resulted in a partial knockdown of cMyBP-C expression and commensurate impairment of systolic and diastolic function to levels approaching those observed in <i>MYBPC 3</i> null mice. Subsequent withdrawal of doxycycline from the diet resulted in the reexpression of cMyBP-C to levels comparable to those observed in WT mice, along with near-complete recovery of in vivo ventricular function. These results show that the cardiac phenotypes associated with <i>MYBPC3</i> null mice are reversible. Our work also validates the use of the Tet-Off inducible system as a means to study the mechanisms underlying hypertrophic cardiomyopathy.
Alzheimer's Disease (2010)

This review of Alzheimer's disease assembles a variety of findings relevant to the mechanism of the disease and ties them together using the current understanding of the basis of the loss of cognition: the accumulation of misfolded proteins, which cause oxidative and inflammatory damage to the brain and, ultimately, synaptic dysfunction.
Comparison of dimethyl dioctadecyl ammonium bromide, Freund's complete adjuvant and mineral oil for induction of humoral antibodies, cellular immunity and resistance to Newcastle disease virus in chickens (1993)

Dimethyl dioctadecyl ammonium bromide (DDA), a lipophilic quaternary amine, was evaluated in adult chickens for potentiation of immunological responses to subcutaneously administered inactivated Newcastle disease virus (NDV) vaccines. DDA enhanced humoral and cell-mediated immune (CMI) responses to levels which were significantly higher than those induced by the vaccine alone The haemagglutination inhibition antibody titers induced by DDA were slightly lower than those induced by mineral oil although neutralizing antibody titers seemed to be higher. DDA induced strong CMI (DTH and lymphocyte proliferation) responses, more than those induced by Freund's complete adjuvant and mineral oil. Both DDA and mineral oil induced comparable high levels of protection to challenge doses of 200,000 LD50 per chicken. No toxic effects or local tissue damage were observed in any of the inoculated chickens.
Modular Three-Component Solid-Phase Synthesis of Unsymmetrical Guanidines via Resin Capture of Carbodiimides (2003)

Because of their basicity and hydrogen-bonding properties, guanidines are an important functional group in many biologically active compounds of natural or synthetic origin. Consequently, methodologies for the parallel synthesis of guanidines have attracted much attention from both academia and industry. Numerous solid-phase routes have been reported, and the vast majority of these involve either urea or thiourea precursors or guanidine synthesis from pseudoureas or similarly activated amidines.
INTENTION-BASED CORRECTIVE FEEDBACK GENERATION USING CONTEXT-AWARE MODEL (2010)

In order to facilitate language acquisition, when language learners speak incomprehensible utterances, a Dialog-based Computer Assisted Language Learning (DB-CALL) system should provide matching fluent utterances by inferring the actual learner’s intention both from the utterance itself and from the dialog context as human tutors do. We propose a hybrid inference model that allows a practical and principled way of separating the utterance model and the dialog context model so that only the utterance model needs to be adjusted for each fluency level. Also, we propose a feedback generation method that provides native-like utterances by searching Example Expression Database using the inferred intention. In experiments, our hybrid model outperformed the utterance only model. Also, from the increased dialog completion rate, we can conclude that our method is suitable to produce appropriate feedback even when the learner's utterances are highly incomprehensible. This is because the dialog context model effectively confines candidate intentions within the given context.
Targeting the Glutamatergic System for the Treatment of HIV-Associated Neurocognitive Disorders (2013)

The accumulation of excess glutamate in the extracellular space as a consequence of CNS trauma, neurodegenerative diseases, infection, or deregulation of glutamate clearance results in neuronal damage by excessive excitatory neurotransmission. Glutamate excitotoxicity is thought to be one of several mechanisms by which HIV exerts neurotoxicity that culminates in HIV-associated neurocognitive disorders (HAND). Excess glutamate is released upon HIV infection of macrophage/microglial cells and has been associated with neurotoxicity mediated by gp120, transactivator of transcription (Tat) and other HIV proteins. Several strategies have been used over the years to try to prevent glutamate excitotoxicity. Since the main toxic effects of excess glutamate are thought to be due to excitotoxicity from over activation of glutamate receptors, antagonists of these receptors have been popular therapeutic targets. Early work to ameliorate the effects of excess extracellular glutamate focused on NMDA receptor antagonism, but unfortunately, potent blockade of this receptor has been fraught with side effects. One alternative to direct receptor blockade has been the inhibition of enzymes responsible for the production of glutamate such as glutaminase and glutamate carboxypeptidase II. Another approach has been to regulate the transporters responsible for modulation of extracellular glutamate such as excitatory amino acid transporters and the glutamate-cystine antiporter. There is preliminary experimental evidence that these approaches have potential therapeutic utility for the treatment of HAND. These efforts however, are at an early stage where the next steps are dependent on the identification of drug-like inhibitors as well as the development of predictive neuroAIDS animal models.
The origin of Barkhausen noise in small permalloy magnetoresistive sensors (1981)

The magnetoresistive (MR) response of permalloy sensors is increasingly plagued by jumps or noise of a magnetic origin (so-called Barkhausen noise) as their sizes are reduced to tens of microns. The origin of this noise is not presently understood. In previous work (1) we reported a study of the Barkhausen noise by separately measuring the MR response and the domain processes involved, but detailed correlation between the two was still lacking. In this work, therefore, we performed simultaneous measurements of both the MR response and domain patterns on small MR elements of typically 12μm×24μm, enabling us to analyze the domain processes affecting the MR output. We have identified two classes of domain processes primarily responsible for noise in the MR output, namely, abrupt domain wall population reductions during early stages of demagnetization, and wall state transitions involving nucleation and expansion of N− wall segments around zero field. Additional insight into the N+→N− transitions has been obtained through consideration of the energetics of formation of the N− segment, and the response of such a segment to applied fields.
TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies (2004)

In order to understand gene regulation, accurate and comprehensive knowledge of transcriptional regulatory elements is essential. Here, we report our efforts in building a mammalian Transcriptional Regulatory Element Database (TRED) with associated data analysis functions. It collects cis- and trans-regulatory elements and is dedicated to easy data access and analysis for both single-gene-based and genome-scale studies. Distinguishing features of TRED include: (i) relatively complete genome-wide promoter annotation for human, mouse and rat; (ii) availability of gene transcriptional regulation information including transcription factor binding sites and experimental evidence; (iii) data accuracy is ensured by hand curation; (iv) efficient user interface for easy and flexible data retrieval; and (v) implementation of on-the-fly sequence analysis tools. TRED can provide good training datasets for further genome-wide cis-regulatory element prediction and annotation, assist detailed functional studies and facilitate the decipher of gene regulatory networks (http://rulai.cshl.edu/TRED).
Carboxyl Methylation of Ras-Related Proteins During Signal Transduction in Neutrophils (1993)

In human neutrophils, as in other cell types, Ras-related guanosine triphosphate-binding proteins are directed toward their regulatory targets in membranes by a series of posttranslational modifications that include methyl esterification of a carboxyl-terminal prenylcysteine residue. In intact cells and in a reconstituted in vitro system, the amount of carboxyl methylation of Ras-related proteins increased in response to the chemoattractant N-formyl-methionyl-leucyl-phenylalanine (FMLP). Activation of Ras-related proteins by guanosine-5'-O-(3-thiotriphosphate) had a similar effect and induced translocation of p22rac2 from cytosol to plasma membrane. Inhibitors of prenylcysteine carboxyl methylation effectively blocked neutrophil responses to FMLP. These findings suggest a direct link between receptor-mediated signal transduction and the carboxyl methylation of Ras-related proteins.
Increased Risk of Cardiovascular Disease with Erythropoietin in Chronic Dialysis Patients (1996)

Recombinant human erythropoietin is widely used in chronic dialysis patients. However, the long-term effect, especially on the incidence of cardiovascular disease, has not been critically evaluated. We observed the annual incidence of stroke and acute myocardial infarction from April 1988 through March 1993 in Okinawa, Japan. Until April 1990, erythropoietin was not generally used. Therefore, we have two periods: pre-erythropoietin, April 1988 through March 1990, and post-erythropoietin, April 1990 through March 1993. Two thousand one hundred and sixteen patients (1,219 males and 897 females) were on chronic dialysis during the study period by March 31, 1993. Every case of stroke and acute myocardial infarction during the study period was registered. The odds ratio was calculated using the data of the general population in each sex and age class obtained in the same area. A total of 86 cases of stroke and 15 cases of acute myocardial infarction were registered during the study period. The annual incidence, per 1,000 patient-years, of stroke was 12.5 (1988), 10.5 (1989), 12.7 (1990), 14.0 (1991), and 17.5 (1992). The incidence of stroke was increased in the post-erythropoietin period compared to the pre-erythropoietin period, odds ratio 1.22 and 95% confidence interval (95% CI 1.06-1.41, p < 0.01). The annual incidence of acute myocardial infarction was 1.0 (1988), 1.8 (1989), 0.8 (1990), 2.9 (1991) and 4.7 (1992). The incidence of acute myocardial infarction was increased significantly in the post-erythropoietin period compared to the pre-erythropoietin period, odds ratio 1.87 (95% CI 1.66-2.10, p < 0.01). The odds ratio of stroke to the general population was 4.25 (95% CI 3.10-5.82) in the pre-erythropoietin and 4.58 (95% CI 2.14-9.80) in the post-erythropoietin period. In acute myocardial infarction, it was 2.98 (95% CI 2.84-3.12) and 3.81 (95% CI 3.18-4.56). The odds ratio of acute myocardial infarction was significantly increased (p < 0.01). The introduction of erythropoietin was associated with an increased risk of cardiovascular disease, especially acute myocardial infarction. Erythropoietin may unmask the sclerotic lesion in chronic dialysis patients.
Experimental mechanical and histologic evaluation of the Kennedy ligament augmentation device. (1985)

Reconstruction of the knee with a chronic injury to the anterior cruciate ligament is an unsolved problem. Biologic graft substitutes have failed to maintain knee stability in the longer postreconstruction intervals. In an attempt to overcome the limitations in graft performance, synthetic materials have been proposed to augment the biologic tissue. In this study, a 6-mm polypropylene braid Ligament Augmentation Device (LAD) possessing a tensile strength of 1500 N and excellent fatigue and creep properties was investigated as an adjunct to the MacIntosh/Marshall Over-the-Top repair. A two-year animal study of 54 adult goats was conducted in which experimental ACL defects were created and reconstructed with a transplant consisting of a portion of the rectus femoris tendon, prepatellar tissue, and the central one-third of the patellar tendon. The goats were equally divided between nonaugmented and LAD-augmented groups and sacrificed at three, six, 12, and 24 months after surgery. Mechanically, the augmented transplants were substantially stronger at the time of initial implantation (364N versus 26N) and again at two years (841N versus 528N). Intermediate times did not demonstrate a difference in strength. Histologically, the augmented transplants consisted of a loosely organized fibrous capsule surrounding the LAD. At 24 months, "insertion fibers" were noted to provide continuity between the fibrous tissue and bone on both the tibia and femur.
Liposome Bupivacaine Femoral Nerve Block for Postsurgical Analgesia after Total Knee Arthroplasty (2016)

FNB with liposome bupivacaine (266 mg) resulted in modestly lower pain scores and reduced opioid requirements after surgery, with an adverse event profile similar to placebo.
Experimental demonstration of OBS/WSON multi-layer optical switched networks with an OpenFlow-based unified control plane (2012)

In the current IP/optical multi-layer networks, the control approaches for IP and optical domains are separated, which is inconvenient for the end-to-end service provisioning. Therefore, the investigation of a unified control plane for multi-layer networks is a very important issue for network carriers, since it can simplify the network manageability, improve the network agility and reduce the operational expenditure (OPEX) and capital expenditure (CAPEX). The OpenFlow protocol, which has been proposed recently, provides a potential solution to address such an issue. On the other hand, the multi-layer optical burst switching (OBS)/wavelength switched optical network (WSON) has been proposed as one of the promising paradigms for future optical Internet, and the respective control plane for OBS and WSON layers under an overlay model has been intensively investigated in our previous works. In light of this, in this paper, we experimentally present an OpenFlow-based unified control plane for OBS/WSON multi-layer optical switched networks. The protocol extensions and design details of the OpenFlow-controlled OBS/WSON are discussed. By using two different signaling approaches (with and without confirmation mechanism during the lightpath provisioning period), we successfully demonstrate the overall feasibility of a unified control plane for OBS/WSON networks, and the performance of two signaling solutions is quantitatively evaluated in terms of end-to-end signaling latency and packet loss rate.
Preparation and characterization of STM tips for electrochemical studies (1989)

We report on a fabrication technique for scanning tunneling microscopy (STM) tips for in situ electrochemical investigations. Unwanted Faradaic currents were minimized by insulating the STM tips with Apiezon wax. Cyclic voltammetry showed Apiezon wax to be inert in various electrolytes.
Sirpent: a high-performance internetworking approach (1989)

A clear target for computer communication technology is to support a high-performance global internetwork. Current internetworking approaches use either concatenated virtual circuits, as in X.75, or a “universal” internetwork datagram, as in the DoD Internet IP protocol and the ISO connectionless network protocol (CLNP). Both approaches have significant disadvantages. This paper describes Sirpent™ (Source Internetwork Routing Protocol with Extended Network Transfer) 1 , a new approach to an internetwork architecture that makes source routing the basis for interconnection, rather than an option as in IP. Its benefits include simple switching with low per-packet processing and delay, support for accounting and congestion control, and scalability to a global internetwork. It also supports flexible, user-controlled routing such as required for security, policy-based routing and realtime applications. We also propose a specific internetwork protocol, called VIPER™ 2 , as a realization of the Sirpent approach.
Characterizing the expression of the human olfactory receptor gene family using a novel DNA microarray (2007)

While our results corroborate the functional annotation of the majority of predicted human odorant receptors, we find that a large number of putative human OR genes are expressed in non-olfactory tissues, sometimes exclusively so. Our evolutionary analysis of ectopically expressed human OR genes does not lend support to the hypothesis that these genes have alternative functions.