gebhart/patrepeval huggingface dataset:
Hydrodynamic Radii of Native and Denatured Proteins Measured by Pulse Field Gradient NMR Techniques (1999)

Pulse field gradient NMR methods have been used to determine the effective hydrodynamic radii of a range of native and nonnative protein conformations. From these experimental data, empirical relationships between the measured hydrodynamic radius (R(h)) and the number of residues in the polypeptide chain (N) have been established; for native folded proteins R(h) = 4.75N (0.29)A and for highly denatured states R(h) = 2.21N (0.57)A. Predictions from these equations agree well with experimental data from dynamic light scattering and small-angle X-ray or neutron scattering studies reported in the literature for proteins ranging in size from 58 to 760 amino acid residues. The predicted values of the hydrodynamic radii provide a framework that can be used to analyze the conformational properties of a range of nonnative states of proteins. Several examples are given here to illustrate this approach including data for partially structured molten globule states and for proteins that are unfolded but biologically active under physiological conditions. These reveal evidence for significant coupling between local and global features of the conformational ensembles adopted in such states. In particular, the effective dimensions of the polypeptide chain are found to depend significantly on the level of persistence of regions of secondary structure or features such as hydrophobic clusters within a conformational ensemble.
From sentencing to execution – the processes of apoptosis (2010)

Abstract Objectives Cell proliferation and apoptosis play a major role in maintaining homeostasis and as such any disruption within these processes can lead to disease states. Apoptosis occurs in three non-distinct phases – induction, effector and degradation – and can be executed through both the extrinsic and intrinsic pathways in addition to recognised sub-pathways such as the p53 and lysosomal pathways. This review article highlights these pathways, incorporating an overview of the molecular regulators of apoptosis. Key findings These regulators include the prominent apoptotic players ‘the caspases’ in addition to the main regulators of the Bcl-2 family. Increased understanding of the physiological processes of apoptosis at the molecular level not only offers an insight in disease pathogenesis but, in addition, allows for the development of diagnostic, prognostic and therapeutic tools. Summary While apoptosis remains the key player in cellular death, other processes cannot be dismissed. Many other proteins, in addition to caspases, within apoptotic pathways have been identified. Research continues into establishing the precise aspects of their molecular mechanisms of action and inter-relationships. Inappropriate apoptosis due to dysregulation of cell death pathways provides a plethora of molecular checkpoints that can be targeted and modulated as part of therapeutic intervention. Increased research into these areas will prove useful for the design of novel chemotherapeutic drugs, an area that is particularly important due to increased risk of chemoresistance.
Amyotrophic Lateral Sclerosis: Molecular Mechanisms to Diagnostics (2004)

Amyotrophic lateral sclerosis (ALS) is a relentlessly progressive and fatal motor neuron disease, characterized by loss of motor neurons in the cortex, brainstem and spinal cord. Clinical management is plagued by a lack of biomarkers and effective treatment. In spite of numerous scientific advancements, molecular mechanisms involved in its initiation and progression remain an enigma. At the mechanistic level, ALS is considered multifactorial. Extracellular signals may modulate nuclear events with a possible consequence being the reactivation of cell cycle-related genes and protein alterations in the terminally differentiated motor neurons. In the first specific aim, we hypothesized that re-entry of post-mitotic motor neurons into the cell cycle, concurrent with altered activity or distribution of transcription factors will result in apoptosis of motor neurons during ALS. To address this hypothesis, we utilized archived human autopsy material from the cortical and spinal cord regions of ALS and age-matched control cases. We conclude that surviving ALS motor neurons in these regions exhibited increased levels of G1 to S phase regulators (Cyclin D1, CDK4, hyperphosphorylated -pRb and E2F-1). It also revealed two intriguing results: (i) E2F-1, a transcription factor, was cytoplasmic and (ii) increased nuclear p53 was noted in spinal motor neurons but absent in neurons of the motor cortex. In addition there was increased protein levels of apoptotic death markers (BAX, FAS, Caspases) and DNA fragmentation. Therefore we have identified a potential role for cell cycle proteins in an apoptotic mode of motor neuron death in ALS. In the second specific aim we hypothesized that a mass spectrometry-based proteomics approach will identify diagnostic biomarkers and molecular targets for drug discoveries. We used cerebrospinal fluid (CSF) from ALS and control subjects to identify and validate a biomarker panel specific to ALS. Furthermore, utilizing peptide map fingerprinting and tandem mass-spectrometry, we have identified three of the protein peaks to be a carboxyl-terminal fragment of neurosecretory chaperone protein 7B2 (3.44kDa), Cystatin C (13.3kDa) and monomer of transthyretin (13.78kDa).Taken together, this body of work furthers the understanding of both the mechanisms leading to selective motor neuron loss in ALS and paves the way for diagnostics and therapeutics.
Characterization of molecular orientation in polyethylene by Raman spectroscopy (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCharacterization of molecular orientation in polyethylene by Raman spectroscopyMarie Pigeon, Robert E. Prud'homme, and Michel PezoletCite this: Macromolecules 1991, 24, 20, 5687–5694Publication Date (Print):September 1, 1991Publication History Published online1 May 2002Published inissue 1 September 1991https://pubs.acs.org/doi/10.1021/ma00020a032https://doi.org/10.1021/ma00020a032research-articleACS PublicationsRequest reuse permissionsArticle Views1503Altmetric-Citations141LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
The Abilities of Babies: A Study in Mental Measurement (1955)

This book aims to demonstrate a method for studying the mental abilities of babies from 2 weeks to 2 years of age. As a result of observations of the growth and development of babies, the author has devised a comprehensive measuring instrument to cover the following five areas: locomotive, personal and social, hearing and speech, hand and eye, and performance. These areas were selected on the basis of various investigations and were assumed to reflect the general intelligence of a baby, which, after two years, could be comparable to the usual battery of intelligence tests. Such comparison has yet to be made. In 1953 the intelligence scale was standardized on about 600 babies in London; 370 boys and girls were tested in infant welfare centers, 113 in day nurseries, 14 in residential nurseries, 44 in their own homes or in private offices, and 30 in outpatient departments of hospitals (not
Atherosclerotic Plaque Destabilization (2014)

Understanding the pathophysiology of atherogenesis and the progression of atherosclerosis have been major goals of cardiovascular research during the previous decades. However, the complex molecular and cellular mechanisms underlying plaque destabilization remain largely obscure. Here, we review how lesional cells undergo cell death and how failed clearance exacerbates necrotic core formation. Advanced atherosclerotic lesions are further weakened by the pronounced local activity of matrix-degrading proteases as well as immature neovessels sprouting into the lesion. To stimulate translation of the current knowledge of molecular mechanisms of plaque destabilization into clinical studies, we further summarize available animal models of plaque destabilization. Based on the molecular mechanisms leading to plaque instability, we outline the current status of clinical and preclinical trials to induce plaque stability with a focus on induction of dead cell clearance, inhibition of protease activity, and dampening of inflammatory cell recruitment.
Safety, tolerability, and efficacy of fluoxetine as an antiviral for acute flaccid myelitis (2018)

This study provides Class IV evidence that for patients with EV-D68-associated AFM, fluoxetine is well-tolerated and not associated with improved neurologic outcomes.
Handbook of chemical vapor deposition (CVD) : principles, technology, and applications (1999)

Handbook of Chemical Vapor Deposition: Principles, Technology and Applications provides information pertinent to the fundamental aspects of chemical vapor deposition. This book discusses the applications of chemical vapor deposition, which is a relatively flexible technology that can accommodate many variations. Organized into 12 chapters, this book begins with an overview of the theoretical examination of the chemical vapor deposition process. This text then describes the major chemical reactions and reviews the chemical vapor deposition systems and equipment used in research and production. Other chapters consider the materials deposited by chemical vapor deposition. This book discusses as well the potential applications of chemical vapor deposition in semiconductors and electronics. The final chapter deals with ion implantation as a major process in the fabrication of semiconductors. This book is a valuable resource for scientists, engineers, and students. Production and marketing managers and suppliers of equipment, materials, and services will also find this book useful.
What is an Art Deco fireplace (2002)

The interwar period saw greater domestic use of newer forms of heating, including electric radiant heaters, hot water radiators and kerosene heaters, as well as gas fires.
A revival of parabiosis in biomedical research (2014)

Modern medicine wields the power to treat large numbers of diseases and injuries most of us would have died from just a hundred years ago, yet many of the most devastating diseases of our time are still untreatable. Chronic conditions of age such as cardiovascular disease, diabetes, osteoarthritis or Alzheimer's disease turn out to be of a complexity that may require transformative ideas and paradigms to understand and treat them. Parabiosis, which is characterised by a shared blood supply between two surgically connected animals, may just provide such a transformative experimental paradigm. Although forgotten and shunned now in many countries, it has contributed to major breakthroughs in tumour biology, endocrinology and transplantation research in the past century. Interestingly, recent studies from the United States and Britain are reporting stunning advances in stem cell biology and tissue regeneration using parabiosis between young and old mice, indicating a possible revival of this paradigm. We review here briefly the history of parabiosis and discuss its utility to study physiological and pathophysiological processes. We argue that parabiosis is a technique that should enjoy wider acceptance and application, and that policies should be revisited to allow its use in biomedical research.
<title>Variable-focus microlenses as a potential technology for endoscopy</title> (2000)

Using a new device which contains an array of microlenses whose focal lengths can be electrically varied, we have been able to control the input from one microlens to a single mode fibre using an applied voltage. For such a microlens array many closely-spaced focal spots can be generated in parallel, and electrically switched to address, potentially, an array of receiver fibres. We show how the particular switching characteristics of the device, whereby the lenses switch from diverging to converging, serves in turn to disperse light and to focus it into the fibre.
Interleukin-1 receptor antagonist and tumor necrosis factor binding protein decrease osteoclast formation and bone resorption in ovariectomized mice. (1994)

To investigate the contribution of IL-1, IL-6, and TNF to the increased osteoclastogenesis induced by estrogen deficiency, ovariectomized (ovx) mice were treated with either IL-1 receptor antagonist (IL-1ra), a competitive inhibitor of IL-1, TNF binding protein (TNFbp), an inhibitor of TNF, or the anti-IL-6 antibody (Ab) 20F3 for the first 2 wk after surgery. ovx increased the bone marrow cells secretion of IL-1 and TNF, but not IL-6, and the formation of TRAP-positive osteoclast-like multinucleated cells (MNCs) in bone marrow cultures treated with 1,25(OH)2D3. The increase in MNC formation induced by ovx was prevented by in vivo treatment with either 17 beta estradiol, IL-1ra, TNFbp, or anti-IL-6 Ab. However, the percent change in MNC formation induced by the anti-IL-6 Ab was similar in ovx and sham-operated animals, whereas IL-1ra and TNFbp were effective only in ovx mice. MNC formation was also decreased by in vitro treatment of bone marrow cultures with IL-1ra and TNFbp, but not with anti-IL-6 Ab. Ovx also increased bone resorption in vivo and in vitro, as assessed by the urinary excretion of pyridinoline cross links and the formation of resorption pits, respectively. IL-1ra, TNFbp and estrogen decreased bone resorption in vivo and in vitro whereas the anti-IL-6 Ab inhibited bone resorption in vitro but not in vivo. In conclusion, these data indicate that IL-1 and TNF play a direct role in mediating the effects of ovx on osteoclastogenesis and bone resorption. The data also suggest that IL-6 is not essential for increasing bone resorption in the early postovariectomy period.
Cloning of cDNAs for human aldehyde dehydrogenases 1 and 2. (1985)

Partial cDNA clones encoding human cytosolic aldehyde dehydrogenase (ALDH1) and mitochondrial aldehyde dehydrogenase (ALDH2) were isolated from a human liver cDNA library constructed in phage lambda gt11. The expression library was screened by using rabbit antibodies against ALDH1 and ALDH2. Positive clones thus obtained were subsequently screened with mixed synthetic oligonucleotides compatible with peptide sequences of ALDH1 and ALDH2. One of the positive clones for ALDH1 contained an insertion of 1.6 kilobase pairs (kbp). The insert encoded 340 amino acid residues and had a 3' noncoding region of 538 bp and a poly(A) segment. The amino acid sequence deduced from the cDNA sequence coincided with the reported amino acid sequence of human ALDH1 [Hempel, J., von Bahr-Lindström, H. & Jörnvall, H. (1984) Eur. J. Biochem. 141, 21-35], except that valine at position 161 in the previous amino acid sequence study was found to be isoleucine in the deduced sequence. Since the amino acid sequence of ALDH2 was unknown, 33 tryptic peptides of human ALDH2 were isolated and sequenced. Based on the amino acid sequence data thus obtained, a mixed oligonucleotide probe was prepared. Two positive clones, lambda ALDH2-21 and lambda ALDH2-36, contained the same insert of 1.2 kbp. Another clone, lambda ALDH2-22, contained an insert of 1.3 kbp. These two inserts contained an overlap region of 0.9 kbp. The combined cDNA contained a sequence that encodes 399 amino acid residues, a chain-termination codon, a 3' untranslated region of 403 bp, and a poly(A) segment. The deduced amino acid sequence was compatible with the amino acid sequences of the tryptic peptides. The degree of homology between human ALDH1 and ALDH2 is 66% for the coding regions of their cDNAs and 69% at the protein level. No significant homology was found in their 3' untranslated regions.
Inflammation and Coronary Artery Disease (1994)

Recent research suggests that focal inflammation in the coronary arteries may be involved in the genesis of unstable coronary syndromes. In this issue of the Journal, Liuzzo et al.1 report that the acute-phase reactants, C-reactive protein and serum amyloid A protein, were elevated in most of their patients with a diagnosis of unstable angina (based on the initial absence of elevated cardiac-enzyme levels), including those who subsequently proved to have had a myocardial infarction. The patients with elevated levels of acute-phase reactants, which reflect the stimulation of hepatic production by circulating inflammatory mediators such as cytokines, had a less favorable . . .
Postmenopausal Osteoporosis (2005)

A 63-year-old woman presents with a history of acute low back pain. She had menopause at 44 years of age but never received postmenopausal hormone-replacement therapy. She reports a Colles' fracture at the age of 60. Her mother had a hip fracture at 70. Lumbar-spine films reveal a new vertebral fracture. Dual-energy x-ray absorptiometry of the hip shows a bone mineral density T score of –1.3. How should her case be managed?
Correlation Between Sweat Glucose and Blood Glucose in Subjects with Diabetes (2012)

Sweat glucose, when properly harvested to prevent contamination from other sources on the skin's surface, can accurately reflect blood glucose levels.
Antigen/Antibody Immunocomplex from CdTe Nanoparticle Bioconjugates (2002)

Complementary bioconjugates based on antibody−antigen interactions were synthesized from luminescent CdTe nanoparticles (NPs). Antigen (bovine serum albumin) was conjugated to red-emitting CdTe NPs, while green-emitting NPs were attached to the corresponding anti-BSA antibody (IgG). The NP bioconjugates were characterized by native and SDS−PAGE electrophoresis, gel-permeation HPLC, and circular dichroism. Antigen−antibody binding affinity was evaluated by enzyme-linked immunosorbent assay (ELISA). The formation of BSA−IgG immunocomplex resulted in the Förster resonance energy transfer (FRET) between the two different NPs: the luminescence of green-emitting NPs was quenched whereas the emission of the red-emitting NPs was enhanced. The luminescence recovered when the immunocomplex was exposed to an unlabeled antigen. The immunocomplexes can be considered as a prototype of NP superstructures based on biospecific ligands, while the competitive FRET inhibition can be used in an immunoassay protocol.
Recombinant Newcastle Disease virus Expressing IL15 Demonstrates Promising Antitumor Efficiency in Melanoma Model (2014)

Recombinant Newcastle Disease Virus (rNDV) has shown oncolytic therapeutic effect in preclinical studies. Previous data indicate that rNDV carrying IL2 has shown promise in cancer therapy. Due to the significant side effects of IL2, IL15 has been introduced into cancer therapy. A number of studies have suggested that IL15 efficiently enhances the activities of CTL and NK cells and inhibits the tumor recurrence and metastasis. Furthermore, IL15 is less toxic than IL2. Therefore, we hypothesize that a recombinant NDV expressing IL15 would be a promising agent for the treatment of malignant tumors. The human IL15 gene or IL2 gene was incorporated into the genome of lentogenic LaSota strain at the position between the HN and L genes (namely rNDV-IL15 or rNDV-IL2). The two viruses efficiently infected tumor cells and expressed IL15 or IL2 protein. Melanoma tumor-bearing mice were treated by intra-tumoral (i.t.) injection of rNDV-IL15 or rNDV-IL2. Both rNDV-IL15 and rNDV-IL2 effectively suppressed tumor growth compared with rNDV. The 120-day survival rate of rNDV-IL15- treated group was 12.5% higher than that of rNDV-IL2 group, although the difference was not statistically significant, both recombinant viruses had strong abilities to induce CD41 T cell and CTL cell responses. However, rNDV-IL15 significantly induced more IFN-γ release and stimulated more CD81 T cells infiltration in the tumor sites compared with rNDV-IL2. In the tumor re-challenged experiment, the survival rates of rNDV-IL15 group and rNDV-IL2 group were statistically higher than that of PBS group. The survival rate of rNDV-IL15 group was 26.67% higher than that of rNDV-IL2 group although the difference was not statistically significant. In conclusion, rNDV-IL15 is a promising antitumor agent against melanoma.
CheriABI (2019)

The CHERI architecture allows pointers to be implemented as capabilities (rather than integer virtual addresses) in a manner that is compatible with, and strengthens, the semantics of the C language. In addition to the spatial protections offered by conventional fat pointers, CHERI capabilities offer strong integrity, enforced provenance validity, and access monotonicity. The stronger guarantees of these architectural capabilities must be reconciled with the real-world behavior of operating systems, run-time environments, and applications. When the process model, user-kernel interactions, dynamic linking, and memory management are all considered, we observe that simple derivation of architectural capabilities is insufficient to describe appropriate access to memory. We bridge this conceptual gap with a notional abstract capability that describes the accesses that should be allowed at a given point in execution, whether in the kernel or userspace. To investigate this notion at scale, we describe the first adaptation of a full C-language operating system (FreeBSD) with an enterprise database (PostgreSQL) for complete spatial and referential memory safety. We show that awareness of abstract capabilities, coupled with CHERI architectural capabilities, can provide more complete protection, strong compatibility, and acceptable performance overhead compared with the pre-CHERI baseline and software-only approaches. Our observations also have potentially significant implications for other mitigation techniques.
High performance SOI RF switches for wireless applications (2010)

This paper describes 0.18um CMOS silicon-on-insulator (SOI) technology and design techniques for SOI RF switch designs for wireless applications. The measured results of SP4T (single pole four throw) and SP8T (single pole eight throw) switch reference designs are presented. It has been demonstrated that SOI RF switch performance, in terms of power handling, linearity, insertion loss and isolation, is very competitive with those utilizing GaAs pHEMT and silicon-on-sapphire (SOS) technologies, while maintaining a cost and manufacturing advantage.