gebhart/patrepeval huggingface dataset:
Newborn infants detect the beat in music (2009)

To shed light on how humans can learn to understand music, we need to discover what the perceptual capabilities with which infants are born. Beat induction, the detection of a regular pulse in an auditory signal, is considered a fundamental human trait that, arguably, played a decisive role in the origin of music. Theorists are divided on the issue whether this ability is innate or learned. We show that newborn infants develop expectation for the onset of rhythmic cycles (the downbeat), even when it is not marked by stress or other distinguishing spectral features. Omitting the downbeat elicits brain activity associated with violating sensory expectations. Thus, our results strongly support the view that beat perception is innate.
Conference Summary: Novel HIV Therapies—From Discovery to Clinical Proof of Concept (1996)

In this report we have highlighted only a few examples of the extensive efforts underway to better understand the process of HIV pathogenesis, to develop new therapeutic agents to inhibit virus replication, and to identify strategies to restore damage done to the immune system during HIV disease progression. It is expected that progress in these areas will continue to advance, and that development of more effective therapies will lead to comprehensive multifaceted, multipronged treatment regimens.
Influence of Salmonella enterica Serovar Typhimurium Infection on Intestinal Goblet Cells and Villous Morphology in Broiler Chicks (2010)

Live broiler chickens are important in the transmission of Salmonella to humans. Reducing Salmonella levels in the intestine of broiler chickens, in part, requires understanding of the interactions between Salmonella and the intestinal barriers that represent the first line of defense. Such barriers include the mucus layer (composed of mucins secreted by goblet cells) and the underlying epithelium. Two experiments were conducted to evaluate the effect of Salmonella Typhimurium infection on intestinal goblet cell dynamics (density and size) and villous morphology in broiler chicks. In Experiment 1, broiler chicks were either challenged with sterile media (control treatment) or orally given 7.4 x 10(7) colony-forming units (CFU) at 3 days of age (termed the CST treatment). Treatments were similar in Experiment 2, except that chicks in the CST treatment were challenged with 7.8 x 10(6) CFU at 4 days of age. Duration of each experiment was 14 days. At 7 days postchallenge (PC) in Experiment 1, jejunal tissue sections were collected, formalin-fixed, and routinely processed for histologic measurement of villous morphometric indices. In Experiment 2, at 10 days PC, jejunal tissue sections were collected and processed for histologic determination of goblet cell numbers and size, in addition to villous measurements. Results showed that Salmonella Typhimurium infection increased goblet cell density, reduced villous surface area, increased the incidence of epithelial exfoliation, and increased the incidence of heterophil influx into the lamina propria (P < 0.05). It was concluded that Salmonella Typhimurium infection impacts goblet cell biology and exerts morphopathologic changes in the jejunum of broiler chicks.
Use of Lidocaine Patch 5% for Chronic Low Back Pain: A Report of Four Cases (2002)

Based on our experience with the four cases presented here and with other patients in our clinic, we believe that addition of the lidocaine patch 5% to the analgesic regimen in chronic low back pain may be beneficial. Prospective, controlled clinical trials are planned to further evaluate the efficacy and safety of the lidocaine patch for treatment of chronic low back pain with or without a neuropathic component.
Long-Term Outcomes of Surgical and Nonsurgical Management of Lumbar Spinal Stenosis: 8 to 10 Year Results from the Maine Lumbar Spine Study (2005)

Among patients with lumbar spinal stenosis completing 8- to 10-year follow-up, low back pain relief, predominant symptom improvement, and satisfaction with the current state were similar in patients initially treated surgically or nonsurgically. However, leg pain relief and greater back-related functional status continued to favor those initially receiving surgical treatment. These results support a shared decision-making approach among physicians and patients when considering treatment options for lumbar spinal stenosis.
Effects of Electrolyte and Potential on the in Situ Structure of Alkanethiol Self-Assembled Monolayers on Silver (1998)

Surface Raman spectroscopy using an emersion approach has been utilized to study the effects of electrolyte and applied potential on the in situ structure and conformational order of self-assembled monolayers (SAMs) formed from n-alkanethiols on smooth Ag surfaces. Vibrational information in the ν(C−S), ν(C−C), δ(C−H), and ν(C−H) regions is particularly useful in elucidating the degree of order and presence of defects in the monolayer before and after exposure of the SAM to electrolyte and potential. Spectral results from these studies suggest that aqueous 0.1 M electrolytes (NaF, NaCl, NaSCN, NaOH, H2SO4) and potential have different effects on the order of the SAMs studied. The order of short chain alkanethiol SAMs is more easily affected by electrolyte and potential than that of the longer chain SAMs.
The synthesis and characterization of novel carboxyl telechelic microspheres (1998)

A series of novel carboxyl telechelic microspheres (CTMs) with different length of oligo-caprolactone telechelic chains are readily prepared via a three-step approach involving: (1) the hydrolytic oligomerization of ε-caprolactone, (2) the esterification of oligo-caprolactone with maleic anhydride, and (3) the suspension polymerization of maleic acid polycaprolactone ester acid (MAPCLA) with divinylbenzene. The CTMs, which are water swellable, spherical, and porous, contain carboxyl functionalities of 1.0 to 4.2 mEq/g (dry), which are found to be lower swelling change (during conversion of ionic form) and higher exchange efficiencies than those of the Emerk. IV resin. The intermediate products, oligo-caprolacton, and MAPCLA are characterized by the acid–base titration, hydroxyl value titration, and infrared and 1H nuclear magnetic resonance analysis, respectively. The morphology and porous of CTMs are also tested by scanning electron microscopy and Brunauer-Emett-Teller technology. The effects of the length of the telechelic chains and the degree of crosslinking (divinylbenzene), as well as the amount of porogen (toluene), on the physical and chemical parameters of the CTMs are also described. © 1998 John Wiley & Sons, Inc. J Appl Polym Sci 68:205–216, 1998
Short-Term Serum-Free Culture Reveals that Inhibition of Gsk3β Induces the Tumor-Like Growth of Mouse Embryonic Stem Cells (2011)

Here, we present evidence that the tumor-like growth of mouse embryonic stem cells (mESCs) is suppressed by short-term serum-free culture, which is reversed by pharmacological inhibition of Gsk3β. Mouse ESCs maintained under standard conditions using fetal bovine serum (FBS) were cultured in a uniquely formulated chemically-defined serum-free (CDSF) medium, namely ESF7, for three passages before being subcutaneously transplanted into immunocompromised mice. Surprisingly, the mESCs failed to produce teratomas for up to six months, whereas mESCs maintained under standard conditions generated well-developed teratomas in five weeks. Mouse ESCs cultured under CDSF conditions maintained the expression of Oct3/4, Nanog, Sox2 and SSEA1, and differentiated into germ cells in vivo. In addition, when mESCs were cultured under CDSF conditions supplemented with FBS, or when the cells were cultured under CDSF conditions followed by standard culture conditions, they consistently developed into teratomas. Thus, these results validate that the pluripotency of mESCs was not compromised by CDSF conditions. Mouse ESCs cultured under CDSF conditions proliferated significantly more slowly than mESCs cultured under standard conditions, and were reminiscent of Eras-null mESCs. In fact, their slower proliferation was accompanied by the downregulation of Eras and c-Myc, which regulate the tumor-like growth of mESCs. Remarkably, when mESCs were cultured under CDSF conditions supplemented with a pharmacological inhibitor of Gsk3β, they efficiently proliferated and developed into teratomas without upregulation of Eras and c-Myc, whereas mESCs cultured under standard conditions expressed Eras and c-Myc. Although the role of Gsk3β in the self-renewal of ESCs has been established, it is suggested with these data that Gsk3β governs the tumor-like growth of mESCs by means of a mechanism different from the one to support the pluripotency of ESCs.
Vaccine Protection against a Heterologous, Non-Syncytium-Inducing, Primary Human Immunodeficiency Virus (1998)

Vaccine-induced protection of chimpanzees against laboratory-adapted and syncytium-inducing, multiply passaged primary human immunodeficiency virus type 1 (HIV-1) isolates, but not against non-syncytium-inducing, minimally passaged ones, has been demonstrated. Following challenge with such an isolate, HIV-15016, we obtained complete protection in one of three chimpanzees previously protected against low- and high-dose HIV-1SF2 exposures after immunization with an adenovirus-HIV-1MN gp160 priming-HIV-1SF2 gp120 boosting regimen. At challenge, the protected chimpanzee exhibited broad humoral immunity, including neutralizing antibody activity. These results demonstrate the potential of this combination vaccine strategy and suggest that vaccine protection against an HIV isolate relevant to infection of people is feasible.
Targeted Delivery of Peptides, Proteins, and Genes by Receptor-Mediated Endocytosis (1997)

Receptor-mediated endocytosis (RME) is one type of delivery system by which therapeutic agents can be specifically transported to their target. Although many successful studies have been performed at a preclinical level, its clinical application is restricted by a number of factors, including the low targeting efficiency that stems from the characteristics of RME. One important approach to overcome this is to improve the drug delivery system by a series of chemical modifications and evaluate the drug targeting efficiency from a kinetic point of view.
Mutations in the epidermal growth factor receptor (EGFR) gene in triple negative breast cancer: possible implications for targeted therapy (2011)

This study is among the first to document the presence and estimate the prevalence of EGFR mutations in triple negative breast cancer. These findings have potential implications for the design of clinical trials involving anti-EGFR directed therapy which currently do not select for patients based on presence of activating EGFR mutations, which may hence be underpowered to detect significant benefit in unselected populations. More complete sampling of EGFR mutation status in triple negative breast cancer is needed to determine the true mutation rate.
Monocyte chemoattractant protein-1-induced CCR2B receptor desensitization mediated by the G protein-coupled receptor kinase 2 (1998)

Monocyte chemoattractant protein 1 (MCP-1) is a member of the chemokine cytokine family, whose physiological function is mediated by binding to the CCR2 and CCR4 receptors, which are members of the G protein-coupled receptor family. MCP-1 plays a critical role in both activation and migration of leukocytes. Rapid chemokine receptor desensitization is very likely essential for accurate chemotaxis. In this report, we show that MCP-1 binding to the CCR2 receptor in Mono Mac 1 cells promotes the rapid desensitization of MCP-1-induced calcium flux responses. This desensitization correlates with the Ser/Thr phosphorylation of the receptor and with the transient translocation of the G protein-coupled receptor kinase 2 (GRK2, also called beta-adrenergic kinase 1 or betaARK1) to the membrane. We also demonstrate that GRK2 and the uncoupling protein beta-arrestin associate with the receptor, forming a macromolecular complex shortly after MCP-1 binding. Calcium flux responses to MCP-1 in HEK293 cells expressing the CCR2B receptor were also markedly reduced upon cotransfection with GRK2 or the homologous kinase GRK3. Nevertheless, expression of the GRK2 dominant-negative mutant betaARK-K220R did not affect the initial calcium response, but favored receptor response to a subsequent challenge by agonists. The modulation of the CCR2B receptor by GRK2 suggests an important role for this kinase in the regulation of monocyte and lymphocyte response to chemokines.
Transfected Aequorin in the Measurement of Cytosolic Ca2+ Concentration ([Ca2+]c) (1995)

Targeted recombinant aequorins represent to date the most specific means of monitoring [Ca2+] in subcellular organelles (Rizzuto, R., Simpson, A. W. M., Brini, M., and Pozzan, T. (1992) Nature 358, 325-328; Brini, M., Murgia, M., Pasti, L., Picard, D., Pozzan, T., and Rizzuto, R. (1993) EMBO J. 12, 4813-4819; Kendall, J. M., Dormer, R. L., and Campbell, A. K. (1992) Biochem. Biophys. Res. Commun. 189, 1008-1016). Up until now, however, only limited attention has been paid to the use of recombinant photoproteins for measuring, in mammalian cells, the [Ca2+] in the cytoplasm, a compartment for which effective Ca2+ probes are already available. Here we describe this approach in detail, highlighting the advantages, under various experimental conditions, of using recombinant cytosolic aequorin (cytAEQ) instead of classical fluorescent indicators. We demonstrate that cytAEQ is expressed recombinantly at high levels in transiently transfected cell lines and primary cultures as well as in stably transfected clones, and we describe a simple algorithm for converting aequorin luminescence data into [Ca2+] values. We show that although fluorescent indicators at the usual intracellular concentrations (50-100 microM) are associated with a significant buffering of the [Ca2+]c transients, this problem is negligible with recombinantly expressed aequorin. The large dynamic range of the photoprotein also allows an accurate estimate of the large [Ca2+]c increases that are observed in some cell types such as neurons. Finally, cytAEQ appears to be an invaluable tool for measuring [Ca2+]c in cotransfection experiments. In particular, we show that when cotransfected with an alpha 1-adrenergic receptor (coupled to inositol 1,4,5-trisphosphate generation), cytAEQ faithfully monitors the subpopulation of cells expressing the receptor, whereas the signal of fura-2, at the population level, is dominated largely by that of the untransfected cells.
The Development of Microsystems and New Applications of Electrochemistry (2001)

Brief introduction to microsystems 2 Discussions on the developments of microsystem technologies 3 Applications of electrochemistry in microsystem 3.1 Confined Etchant Layer Technique (CELT) for the complex 3D-pattern micromachining 3.2 Focusing Electrophoresis and the application of microsystem in (bio) chemistry (μTAS or Lab on A Chip) 3.3 Smart Electro-Osmosis pump——a reasonable choosing for microfluidic network 4 Concluding remark
Antimicrobial Peptides: Multifunctional Drugs for Different Applications (2012)

Antimicrobial peptides (APs) are an important part of the innate immune system in epithelial and non-epithelial surfaces. So far, many different antimicrobial peptides from various families have been discovered in non-vertebrates and vertebrates. They are characterized by antibiotic, antifungal and antiviral activities against a variety of microorganisms. In addition to their role as endogenous antimicrobials, APs participate in multiple aspects of immunity. They are involved in septic and non-septic inflammation, wound repair, angiogenesis, regulation of the adaptive immune system and in maintaining homeostasis. Due to those characteristics AP could play an important role in many practical applications. Limited therapeutic efficiency of current antimicrobial agents and the emerging resistance of pathogens require alternate antimicrobial drugs. The purpose of this review is to highlight recent literature on functions and mechanisms of APs. It also shows their current practical applications as peptide therapeutics and bioactive polymers and discusses the possibilities of future clinical developments.
Genomic analyses of the evolution of LGR genes. (2006)

Recent completion of the sequencing of genomes from several mammals, teleosts and invertebrates has shown that G protein-coupled receptors (GPCRs) are one of the conserved groups of cell surface receptors with an ancient origin. GPCRs play important roles in diverse physiological functions and are the most important targets for pharmaceutical discoveries. Recent work based on the search for gene with structural similarity to LH, FSH and thyroid-stimulating hormone (TSH) receptors in diverse genomes has led to the identification of a group of GPCRs called Leucine-rich repeat-containing, G protein-coupled Receptor (LGR). We present the genomic analyses of the evolution of LGR genes in the literature.
The mechanical memory of lung myofibroblasts (2012)

Fibroblasts differentiate into the highly synthetic and contractile myofibroblast phenotype when exposed to substrates with an elastic modulus corresponding to pathologically stiff fibrotic tissue. Cellular responses to changes in substrate stiffness are typically analyzed after hours or days, which does not enable the monitoring of myofibroblast persistence, a hallmark of fibrosis. To determine long-lasting effects on the fibrotic behavior of lung fibroblasts, we followed a novel approach of explanting and repeatedly passaging fibroblasts on silicone substrates with stiffness representing various states of lung health. Fibrotic activity was determined by assaying for myofibroblast proliferation, cell contractility, expression of α-smooth muscle actin, extracellular matrix and active TGFβ1. As predicted, myofibroblast activity was low on healthy soft substrates and increased with increasing substrate stiffness. However, explanting and mechanically priming lung fibroblasts for 3 weeks on pathologically stiff substrates resulted in sustained myofibroblast activity even after the cells were returned to healthy soft cultures for 2 weeks. Such primed cells retained higher fibrotic activity than cells that had been exclusively cultured on soft substrates, and were not statistically different from cells continuously passaged on stiff surfaces. Inversely, priming lung fibroblasts for 3 weeks on soft substrates partially protected from myofibroblast activation after the shift to stiff substrates. Hence, mechano-sensed information relating to physical conditions of the local cellular environment could permanently induce fibrotic behavior of lung fibroblasts. This priming effect has important implications for the progression and persistence of aggressive fibrotic diseases such as idiopathic pulmonary fibrosis.
Effect on Glycemic Control of Exenatide (Synthetic Exendin-4) Additive to Existing Metformin and/or Sulfonylurea Treatment in Patients With Type 2 Diabetes (2003)

AC2993 is a promising therapeutic for patients with type 2 diabetes. In this study, it had significant effects on HbA(1c) levels in patients not currently achieving optimal glucose control with diet and/or OAAs.
Design and initial characterization of a circular permuted variant of the potent HIV‐inactivating protein cyanovirin‐N (2001)

A circular permuted variant of the potent human immunodeficiency virus (HIV)-inactivating protein cyanovirin-N (CV-N) was constructed. New N- and C-termini were introduced into an exposed helical loop, and the original termini were linked using residues of the original loop. Since the three-dimensional structure of wild-type cyanovirin-N is a pseudodimer, the mutant essentially exhibits a swap between the two pseudo-symmetrically related halves. The expressed protein, which accumulates in the insoluble fraction, was purified, and conditions for in vitro refolding were established. During refolding, a transient dimeric species is also formed that converts to a monomer. Similar to the wild-type CV-N, the monomeric circular permuted protein exhibits reversible thermal unfolding and urea denaturation. The mutant is moderately less stable than the wild-type protein, but it displays significantly reduced anti-HIV activity. Using nuclear magnetic resonance spectroscopy, we demonstrate that this circular permuted monomeric molecule adopts the same fold as the wild-type protein. Characterization of these two architecturally very similar molecules allows us to embark, for the first time, on a structure guided focused mutational study, aimed at delineating crucial features for the extraordinary difference in the activity of these molecules.
Memory coloring: a compiler approach for scratchpad memory management (2005)

Scratchpad memory (SPM), a fast software-managed on-chip SRAM, is now widely used in modern embedded processors. Compared to hardware-managed cache, it is more efficient in performance, power and area cost, and has the added advantage of better time predictability. This paper introduces a general-purpose compiler approach, called memory coloring, to efficiently allocating the arrays in a program to an SPM. The novelty of our approach lies in partitioning an SPM into a "register file", splitting the live ranges of arrays to create potential data transfer statements between the SPM and off-chip memory, and finally, adapting an existing graph-colouring algorithm for register allocation to assign the arrays in the program into the register file. Our approach is efficient due to the practical efficiency of graph-colouring algorithms. We have implemented this work in SUIF and machSUIF. Preliminary results over benchmarks show that our approach represents a promising solution to automatic SPM management.
Epidemiology of myelodysplastic syndromes and chronic myeloproliferative disorders in the United States, 2001-2004, using data from the NAACCR and SEER programs (2008)

Reporting of myelodysplastic syndromes (MDSs) and chronic myeloproliferative disorders (CMDs) to population-based cancer registries in the United States was initiated in 2001. In this first analysis of data from the North American Association of Central Cancer Registries (NAACCR), encompassing 82% of the US population, we evaluated trends in MDS and CMD incidence, estimated case numbers for the entire United States, and assessed trends in diagnostic recognition and reporting. Based on more than 40 000 observations, average annual age-adjusted incidence rates of MDS and CMD for 2001 through 2003 were 3.3 and 2.1 per 100,000, respectively. Incidence rates increased with age for both MDS and CMD (P < .05) and were highest among whites and non-Hispanics. Based on follow-up data through 2004 from the Surveillance, Epidemiology, and End Results (SEER) Program, overall relative 3-year survival rates for MDS and CMD were 45% and 80%, respectively, with males experiencing poorer survival than females. Applying the observed age-specific incidence rates to US Census population estimates, approximately 9700 patients with MDS and 6300 patients with CMD were estimated for the entire United States in 2004. MDS incidence rates significantly increased with calendar year in 2001 through 2004, and only 4% of patients were reported to registries by physicians' offices. Thus, MDS disease burden in the United States may be underestimated.