gebhart/patrepeval huggingface dataset:
Extending the treatment of backbone energetics in protein force fields: Limitations of gas‐phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations (2004)

Computational studies of proteins based on empirical force fields represent a powerful tool to obtain structure-function relationships at an atomic level, and are central in current efforts to solve the protein folding problem. The results from studies applying these tools are, however, dependent on the quality of the force fields used. In particular, accurate treatment of the peptide backbone is crucial to achieve representative conformational distributions in simulation studies. To improve the treatment of the peptide backbone, quantum mechanical (QM) and molecular mechanical (MM) calculations were undertaken on the alanine, glycine, and proline dipeptides, and the results from these calculations were combined with molecular dynamics (MD) simulations of proteins in crystal and aqueous environments. QM potential energy maps of the alanine and glycine dipeptides at the LMP2/cc-pVxZ//MP2/6-31G* levels, where x = D, T, and Q, were determined, and are compared to available QM studies on these molecules. The LMP2/cc-pVQZ//MP2/6-31G* energy surfaces for all three dipeptides were then used to improve the MM treatment of the dipeptides. These improvements included additional parameter optimization via Monte Carlo simulated annealing and extension of the potential energy function to contain peptide backbone phi, psi dihedral crossterms or a phi, psi grid-based energy correction term. Simultaneously, MD simulations of up to seven proteins in their crystalline environments were used to validate the force field enhancements. Comparison with QM and crystallographic data showed that an additional optimization of the phi, psi dihedral parameters along with the grid-based energy correction were required to yield significant improvements over the CHARMM22 force field. However, systematic deviations in the treatment of phi and psi in the helical and sheet regions were evident. Accordingly, empirical adjustments were made to the grid-based energy correction for alanine and glycine to account for these systematic differences. These adjustments lead to greater deviations from QM data for the two dipeptides but also yielded improved agreement with experimental crystallographic data. These improvements enhance the quality of the CHARMM force field in treating proteins. This extension of the potential energy function is anticipated to facilitate improved treatment of biological macromolecules via MM approaches in general.
Safety and efficacy of imatinib cessation for CML patients with stable undetectable minimal residual disease: results from the TWISTER study (2013)

Most patients with chronic myeloid leukemia (CML) treated with imatinib will relapse if treatment is withdrawn. We conducted a prospective clinical trial of imatinib withdrawal in 40 chronic-phase CML patients who had sustained undetectable minimal residual disease (UMRD) by conventional quantitative polymerase chain reaction (PCR) on imatinib for at least 2 years. Patients stopped imatinib and were monitored frequently for molecular relapse. At 24 months, the actuarial estimate of stable treatment-free remission was 47.1%. Most relapses occurred within 4 months of stopping imatinib, and no relapses beyond 27 months were seen. In the 21 patients treated with interferon before imatinib, a shorter duration of interferon treatment before imatinib was significantly associated with relapse risk, as was slower achievement of UMRD after switching to imatinib. Highly sensitive patient-specific BCR-ABL DNA PCR showed persistence of the original CML clone in all patients with stable UMRD, even several years after imatinib withdrawal. No patients with molecular relapse after discontinuation have progressed or developed BCR-ABL mutations (median follow-up, 42 months). All patients who relapsed remained sensitive to imatinib re-treatment. These results confirm the safety and efficacy of a trial of imatinib withdrawal in stable UMRD with frequent, sensitive molecular monitoring and early rescue of molecular relapse.
ChainReaction (2013)

This paper proposes a Geo-distributed key-value datastore, named ChainReaction, that offers causal+ consistency, with high performance, fault-tolerance, and scalability. ChainReaction enforces causal+ consistency which is stronger than eventual consistency by leveraging on a new variant of chain replication. We have experimentally evaluated the benefits of our approach by running the Yahoo! Cloud Serving Benchmark. Experimental results show that ChainReaction has better performance in read intensive workloads while offering competitive performance for other workloads. Also we show that our solution requires less metadata when compared with previous work.
Nicotinic Cholinergic Receptor Expression in the Human Nasal Mucosa (2003)

Twenty-four nasal mucosa specimens were obtained from the inferior or middle turbinates of 6 normal subjects and 18 patients with chronic sinusitis, inflammatory polyp formation, or sinus allergies. Reverse transcription-polymerase chain reaction analysis was used to identify the non-neuronal nicotinic cholinergic receptor (nAChR) subunits that were expressed in the nasal mucosa. Collectively, transcripts for alpha (alpha1, alpha2, alpha3, alpha4, alpha6, alpha7) and beta (beta2, beta3, beta4) nAChR subunit genes were detected in the respiratory mucosa. The alpha3, alpha7, and beta2 subunits were expressed in 92%, 88%, and 75% of the subjects, respectively. There was a high degree of interindividual variation in nAChR subunit gene expression among subjects. A significant univariate association was found between tissue type and beta4 expression and between gender and beta3 expression. These data suggest that cells in the nasal mucosa express the necessary messenger RNAs (mRNAs) for numerous nAChR combinations. Moreover, our identification of nAChR subunit mRNAs in the nasal mucosa extends the findings of other functional studies of nAChRs in nasal epithelial cells and implies that nicotine from tobacco products such as cigarette smoke and nicotine nasal spray may have direct cellular effects on nasal mucosa cells through activation of homogeneous or heterogeneous nAChRs. A significant number of patients receiving nicotine nasal spray have reported nasal irritation, and there are reports of transient irritation of the throat and trachea with the use of smoke-free nicotine cigarettes. These adverse respiratory effects may be due to activation of nAChRs in epithelial cells of the nose and trachea.
Novel piezo motor enables positive displacement microfluidic pump (2007)

We present the world’s smallest linear motor and its use in tiny syringe and reciprocating piston pumps for microfluidic applications. SQUIGGLE ® motors create direct displacement pumps that achieve nanoliter precision yet the pump assembly is the size of a pen cap. Linear motion directly moves a piston or bellows. The output pressure and flow are easily scaled by adjusting the piston diameter. SQUIGGLE motor pumps can miniaturize a variety of instruments including lab-on-a-chip systems, drug delivery devices, micro fuel cells, cooled computer chips, lubrication systems, spacecraft thrusters and liquid optics. A reference pump design is presented that achieves output pressure of 255 kPa, flow of 0.24 ml per minute at an oscillation frequency of 0.8 Hz and flow precision of 0.8 nl. In contrast, commercial oscillating membrane pumps are much larger, generate a 20 Hz or higher pulse frequency and produce much lower output pressure and accuracy.
Secondary spectrum access networks (2009)

The radio spectrum is a precious resource that underpins various wireless services. It is traditionally regulated by a fixed frequency assignment policy, which allocates frequency bands to license holders for exclusive use. Dynamic spectrum access has been proposed as a promising approach to improve spectrum utilization by allowing new wireless systems to dynamically access or share the licensed band on a negotiated or an opportunistic basis.
Plasma Klotho and Mortality Risk in Older Community-Dwelling Adults (2011)

In older community-dwelling adults, plasma klotho is an independent predictor of all-cause mortality. Further studies are needed to elucidate the potential biological mechanisms by which circulating klotho could affect longevity in humans.
Requirement for Anticoagulant Heparan Sulfate in the Fibroblast Growth Factor Receptor Complex (1999)

A divalent cation-dependent association between heparin or heparan sulfate and the ectodomain of the fibroblast growth factor (FGF) receptor kinase (FGFR) restricts FGF-independent trans-phosphorylation between self-associated FGFR and determines specificity for and mediates binding of activating FGF. Here we show that only the fraction of commercial heparin or rat liver heparan sulfate which binds to immobilized antithrombin formed an FGF-binding binary complex with the ectodomain of the FGFR kinase. Conversely, only the fraction of heparin that binds to immobilized FGFR inhibited Factor Xa in the presence of antithrombin. Only the antithrombin-bound fraction of heparin competed with (3)H-heparin bound to FGFR in absence of FGF, whereas both antithrombin-bound and unretained fractions competed with radiolabeled heparin bound independently to FGF-1 and FGF-2. The antithrombin-bound fraction of heparin was required to support the heparin-dependent stimulation of DNA synthesis of endothelial cells by FGF-1. The requirement for divalent cations and the antithrombin-binding motif distinguish the role of heparan sulfate as an integral subunit of the FGFR complex from the wider range of effects of heparan sulfates and homologues on FGF signaling through FGFR-independent interactions with FGF.
A familial form of conduction defect related to a mutation in the PRKAG2 gene (2007)

We describe four members of the same family with a very similar ECG pattern characterized by conduction defects (right bundle branch block, frequent left anterior hemiblock, atrial hypertrophy, and sometimes severe nodal dysfunction) contrasting with a short PR interval. Significant clinical events were reported only after 60 years of age. A mutation in the gamma2 subunit of the AMP activated protein kinase gene (PRKAG2) was identified in the four members of the family, with an autosomal dominant inheritance. The phenotype observed in this family appears different from that previously described as associated with this gene as neither left ventricular hypertrophy nor Wolff-Parkinson-White syndrome was present. These findings extend the phenotype associated with the PRKAG2 gene and emphasize an additional cause of familial conduction defect.
Schizophrenia and Nicotinic Receptors (1994)

Patients with schizophrenia often cannot respond to important features of their environment and filter out irrelevant stimuli. This dysfunction could be related to an underlying defect in inhibition--i.e., the brain's ability to alter its sensitivity to repeated stimuli. One of the neuronal mechanisms responsible for such inhibitory gating involves the activation of cholinergic nicotinic receptors in the hippocampus. These receptors are diminished in many specimens of hippocampal brain tissue obtained postmortem from schizophrenic patients. In living schizophrenic patients, stimulation of cholinergic receptors by nicotine transiently restores inhibitory gating of evoked responses to sensory stimuli. Many people with schizophrenia are heavy smokers, but the properties of the nicotinic receptor favor only short-term activation, which may explain why cigarette smoking is only a transient symptomatic remedy. This paper reviews the clinical phenomenology of inhibitory gating deficits in people with schizophrenia, the neurobiology of such gating mechanisms, and the evidence that some individuals with the disorder may have a heritable deficit in the nicotinic cholinergic receptors involved in this neurobiological function. Inhibitory gating deficits are only partly normalized by neuroleptic drugs and are thus a target for new therapeutic strategies for schizophrenia.
Understanding the impact of pulmonary arterial hypertension on patients' and carers' lives (2013)

Pulmonary arterial hypertension (PAH) is a rare, debilitating and rapidly progressive disease. Although there have been important medical advances in PAH management, the search for a cure continues. Despite an increased understanding of the disease, data on the wider effect of PAH on patients and carers, beyond the clinical symptoms, are still limited. In order to explore this, a large-scale international survey investigated four key areas affected by PAH (physical and practical, emotional, social, and information needs) and provides new insight into patients' and carers' experiences of living with the disease. The results from the survey highlight not only the limited ability of patients to carry out everyday tasks, but also the financial impact and social isolation experienced by both patients and carers. The study confirmed that a decline in a patient's World Health Organization functional class, which indicates an increase in clinical severity of the disease, is associated with greater limitations. Results from the survey demonstrate the need for multidisciplinary PAH management and a comprehensive standard of care to assess and improve all aspects of well-being for both patients and carers. In addition, they underline the need for updated PAH guidelines that address these needs.
Structure-function studies of amphiphilic antibacterial peptides (1993)

The synthesis of 11 peptides, ranging in composition from 9 to 17 amino acid residues, by solid-phase methodology was accomplished with the purpose of studying how the amphiphilic and hydrophobic character, the size of the molecule, and the charge distribution modulate the antibacterial activity. It was found that peptides composed of 16 and 17 amino acid residues, with high hydrophobic (mainly due to Trp or Phe) and hydrophilic (due to Lys) character distributed along opposite amphiphilic faces, showed considerable antibacterial activity against clinically isolated bacteria together with Gram positive and Gram negative ATCC bacterial strains. However, the hemolytic capacity of the peptides was also significant. Decreasing the hydrophobic character of the molecule by replacing Trp or Phe with Leu residues while maintaining the basic contribution of Lys drastically reduced the hemolytic activity and only slightly decreased the bioactivity. Peptides composed of 9-10 amino acid residues with high hydrophobic and basic nature possess antibacterial activity but, in general, are less active than the larger counterpart peptides. By replacing all Trp residues of a short peptide by Leu residues, the activity was considerably reduced. Circular dichroism studies and antibacterial assays showed that shorter peptides with very low helical content, and thus deprived of amphiphilic character, still have appreciable bioactivity. This observation, coupled with the fact that due to their small size they cannot span the bacterial outer lipid bilayer, may suggest different mechanisms of action for long-chain vis-a-vis short-chain peptides.
Chronic estrogen-induced cervical and vaginal squamous carcinogenesis in human papillomavirus type 16 transgenic mice. (1996)

High-risk human papillomaviruses (HPVs), including type 16, have been identified as factors in cervical carcinogenesis. However, the presence and expression of the virus per se appear to be insufficient for carcinogenesis. Rather, cofactors most likely are necessary in addition to viral gene expression to initiate neoplasia. One candidate cofactor is prolonged exposure to sex hormones. To examine the possible effects of estrogen on HPV-associated neoplasia, we treated transgenic mice expressing the oncogenes of HPV16 under control of the human keratin-14 promoter (K14-HPV16 transgenic mice) and nontransgenic control mice with slow release pellets of 17beta-estradiol. Squamous carcinomas developed in a multistage pathway exclusively in the vagina and cervix of K14-HPV16 transgenic mice. Estrogen-induced carcinogenesis was accompanied by an incremental increase in the incidence and distribution of proliferating cells solely within the cervical and vaginal squamous epithelium of K14-HPV16 mice. Expression of the HPV transgenes in untreated transgenic mice was detectable only during estrus; estrogen treatment resulted in transgene expression that was persistent but not further upregulated, remaining at low levels at all stages of carcinogenesis. The data demonstrate a novel mechanism of synergistic cooperation between chronic estrogen exposure and the oncogenes of HPV16 that coordinates squamous carcinogenesis in the female reproductive tract of K14-HPV16 transgenic mice.
An asymmetric synthesis of 2,4-dimethylvalerolactone and mevalonolactone using chiral binaphtyldiamine derivatives (1984)

Axially dissymmetric binaphthyldiamine derivatives formed by asymmetric ring opening of the cyclic anhydrides (3) and (4) ring close on hydrolysis to give (–)-trans-2,4-dimethylvalerolactone with 74% e.e.
Long-Term Correction of Phagocyte NADPH Oxidase Activity by Retroviral-Mediated Gene Transfer in Murine X-Linked Chronic Granulomatous Disease (1999)

Chronic granulomatous disease (CGD) is an inherited deficiency of the superoxide-generating phagocyte nicotinamide adenine dinucleotide phosphate (NADPH) oxidase, resulting in recurrent, severe bacterial and fungal infections. The X-linked form of this disorder (X-CGD) results from mutations in the X-linked gene for gp91(phox), the larger subunit of the oxidase flavocytochrome b(558). In this study, we used a murine model of X-CGD to examine the long-term function of retroviral vectors for expression of gp91(phox) based on the murine stem cell virus (MSCV) backbone. NADPH oxidase activity was reconstituted in neutrophils and macrophages for up to 18 to 24 months posttransplantation of transduced X-CGD bone marrow into lethally irradiated syngeneic X-CGD mice. Southern blot analysis and secondary transplant data showed proviral integration in multilineage repopulating cells. Although relatively small amounts of recombinant gp91(phox) (approximately 5% to 10% of wild-type levels) were detected in neutrophils after retroviral-mediated gene transfer, superoxide-generating activity was approximately 20% to 25% of wild-type mouse neutrophils. Expression of gp91(phox) is normally restricted to mature phagocytes. No obvious toxicity was observed in other hematopoietic lineages in transplant recipients, and provirus-marked cells were capable of reconstituting secondary transplant recipients, who also exhibited NADPH oxidase-positive neutrophils. MSCV-based vectors for long-term expression of gp91(phox) may be useful for gene therapy of human CGD targeted at hematopoietic stem cells.
Glucagon-like peptide-1, a gastrointestinal hormone with a pharmaceutical potential. (1999)

Glucagon-like peptide-1 (GLP-1) is an insulinotropic hormone secreted from endocrine cells in the gut mucosa in response to meal ingestion. It is an important incretin hormone; mice with a null mutation in the GLP-1 receptor gene develop glucose intolerance. In addition, it inhibits gastrointestinal secretion and motility and is thought to be part of the "ileal brake" mechanism. Perhaps because of the latter actions it inhibits food intake, but intracerebral injection of GLP-1 also inhibits food intake. The insulinotropic effect is preserved in patients with type 2 diabetes mellitus, in whom also glucagon secretion is inhibited. Thus upon i.v. GLP-1 infusion blood glucose may be completely normalised. Because its actions are glucose-dependent hypoglycaemia does not develop. However, GLP-1 is metabolised extremely rapidly in vivo, initially by a mechanism that involves the enzyme dipeptidyl peptidase-IV. It is currently being investigated how GLP-1 or analogues thereof can be employed in practical diabetes therapy. Promising solutions include the development of stable analogues and inhibitors of the degrading enzyme.
Artificial Molecular-Level Machines:  Which Energy To Make Them Work? (2001)

The concept of machine can be extended to the molecular level by designing and synthesizing (supra)molecular species capable of performing mechanical movements. The energy needed to make a machine work can be supplied as chemical energy, electrical energy, or light. When a chemical "fuel" is used, waste products are formed, whereas this is not the case when suitable photochemical or electrochemical energy inputs are employed. A number of elementary functions performed by molecular-level machines are illustrated, and more complex ones are foreseen.
TWIST1 associates with NF-κB subunit RELA via carboxyl-terminal WR domain to promote cell autonomous invasion through IL8 production (2012)

Our data demonstrate that the TWIST1 WR domain plays a critical role in TWIST1-induced IL8 expression through interactions with and activation of NF-κB. The produced IL8 signals through an autocrine loop and promotes extracellular matrix degradation to enable cell invasion across the basement membrane.
Development of a lipopeptide-based therapeutic vaccine to treat chronic HBV infection. I. Induction of a primary cytotoxic T lymphocyte response in humans. (1995)

Our goal is to use peptide epitopes that are recognized by cytotoxic T lymphocytes (CTL) as immunogens for the development of prophylactic and therapeutic vaccines with chronic hepatitis B virus (HBV) infection being our first therapeutic target. Because most CTL peptide epitopes are poor immunogens, we specifically modified them by covalently attaching two additional components: a T helper peptide epitope and two lipid molecules. Using the murine influenza virus CTL epitope NP 147-155 as a model system, we found this construct to be highly immunogenic, and a single injection resulted in memory CTL induction that persisted for > 1 yr. Based on the animal studies, a vaccine was designed and tested for both safety and its ability to induce a primary CTL response in normal subjects. The three vaccine components included HBV core antigen peptide 18-27 as the CTL epitope, tetanus toxoid peptide 830-843 as the T helper peptide, and two palmitic acid molecules as the lipids. A dose escalation trial (5, 50, and 500 micrograms) carried out in 26 normal subjects showed that the vaccine was safe and able to induce a primary HBV-specific CTL response. A dose-response curve was observed and five out of five subjects responded to the 500-micrograms dose.
Developmental change in fetal response to repeated low‐intensity sound (2007)

The aim of this study was to investigate developmental changes in heart rate response to repeated low-intensity (85 dB) sound stimulation in fetuses between 32 and 37 weeks of gestation. We measured amplitude changes in heart rate as our index of fetal response. At 35 to 37 weeks of gestation, the majority of fetuses showed a deceleratory response at the first trial. Amplitude decreased with further trials using the same stimulus before recovering when exposed to another type of stimulation. In contrast, responses in fetuses at 32 to 34 weeks of gestation were variable across trials and there was no recovery with exposure to another type of stimulation. Our results suggest that fetal habituation of cardiac response changes with developmental age.
Optimization of electrostatic binding free energy (1997)

An analytic result is derived that defines the charge distribution of the tightest-binding ligand given a receptor charge distribution and spherical geometries. Using the framework of continuum electrostatics, the optimal distribution is expressed as a set of multipoles determined by minimizing the electrostatic free energy of binding. Results for two simple receptor systems are presented to illustrate applications of the theory.