gebhart/patrepeval huggingface dataset:
Imaging and ‘omic’ methods for the molecular diagnosis of cancer (2010)

Molecular imaging methods can noninvasively detect specific biological processes that are aberrant in cancer, including upregulated glycolytic metabolism, increased cellular proliferation and altered receptor expression. PET using the glucose analogue 18F-fluoro-2-deoxyglucose, which detects the increased glucose uptake that is a characteristic of tumor cells, has been widely used in the clinic to detect tumors and their responses to treatment; however, there are many new PET tracers being developed for a wide range of biological targets. Magnetic resonance spectroscopy (MRS), which can be used to detect cellular metabolites, can also provide prognostic information, particularly in brain, breast and prostate cancers. An emerging technique, which by hyperpolarizing 13C-labeled cell substrates dramatically enhances their sensitivity to detection, could further extend the use of MRS in molecular imaging in the clinic. Molecular diagnostics applied to serum samples or tumor samples obtained by biopsy, can measure changes at the individual cell level and the underlying changes in gene or protein expression. DNA microarrays enable high-throughput gene-expression profiling, while mass spectrometry can detect thousands of proteins that may be used in the future as biomarkers of cancer. Probing molecular changes will aid not only cancer diagnosis, but also provide tumor grading, based on gene-expression analysis and imaging measurements of cell proliferation and changes in metabolism; staging, based on imaging of metastatic spread and elevation of protein biomarkers; and the detection of therapeutic response, using serial molecular imaging measurements or monitoring of serum markers. The present article provides a summary of the molecular diagnostic methods that are currently being trialed in the clinic.
One-step formation of methyl acetate with methanol used as the sole source and catalysis by RuII–SnIIcluster complexes (1990)

S. Shinoda and T. Yamakawa, J. Chem. Soc., Chem. Commun., 1990, 1511 DOI: 10.1039/C39900001511
Diversity and applications ofBacillusbacteriocins (2010)

Members of the genus Bacillus are known to produce a wide arsenal of antimicrobial substances, including peptide and lipopeptide antibiotics, and bacteriocins. Many of the Bacillus bacteriocins belong to the lantibiotics, a category of post-translationally modified peptides widely disseminated among different bacterial clades. Lantibiotics are among the best-characterized antimicrobial peptides at the levels of peptide structure, genetic determinants and biosynthesis mechanisms. Members of the genus Bacillus also produce many other nonmodified bacteriocins, some of which resemble the pediocin-like bacteriocins of the lactic acid bacteria (LAB), while others show completely novel peptide sequences. Bacillus bacteriocins are increasingly becoming more important due to their sometimes broader spectra of inhibition (as compared with most LAB bacteriocins), which may include Gram-negative bacteria, yeasts or fungi, in addition to Gram-positive species, some of which are known to be pathogenic to humans and/or animals. The present review provides a general overview of Bacillus bacteriocins, including primary structure, biochemical and genetic characterization, classification and potential applications in food preservation as natural preservatives and in human and animal health as alternatives to conventional antibiotics. Furthermore, it addresses their environmental applications, such as bioprotection against the pre- and post-harvest decay of vegetables, or as plant growth promoters.
THE MANAGEMENT OF INJURIES –A REVIEW OF DEATHS IN HOSPITAL (1988)

A prospective review was undertaken of the management of 111 consecutive patients who died in hospital after admission for treatment of injuries. A standard set of data relating to each patient was reviewed by each member of a trauma death audit committee and then by the whole committee. Autopsy reports were available on all patients. Conclusions were drawn concerning defective aspects of patient management and possible avoidance of each death. Injury severity was assessed using the Trauma Score (TS) and Injury Severity Score (ISS). The possibly avoidable death (PAD) rate was 17%. The most common defects in management were related to inadequate fluid resuscitation and delays in definitive management. The greatest contributions to the PAD rate were from inadequate fluid resuscitation, delays and inadequate perception of the severity of injuries or significance of clinical deterioration. Increasing age was related to a higher frequency of PAD. PAD rate in the presence of severe head injury was 8%, but was 63% in the absence of a severe head injury. It is concluded that review of all trauma deaths is an achievable, beneficial and essential part of a hospital-based integrated trauma service. TS and ISS are not sufficiently sensitive to justify their use in selecting deaths for review. Improved blood volume replacement, earlier and more direct management and supervision by senior specialist staff, and elimination of causes of delay in patient management should all decrease the death rate from injuries particularly in patients without severe head injury.
Serine Phosphorylation of Insulin Receptor Substrate 1 by Inhibitor κB Kinase Complex (2002)

Insulin resistance contributes importantly to the pathophysiology of type 2 diabetes mellitus. One mechanism mediating insulin resistance may involve the phosphorylation of serine residues in insulin receptor substrate-1 (IRS-1), leading to impairment in the ability of IRS-1 to activate downstream phosphatidylinositol 3-kinase-dependent pathways. Insulin-resistant states and serine phosphorylation of IRS-1 are associated with the activation of the inhibitor kappaB kinase (IKK) complex. However, the precise molecular mechanisms by which IKK may contribute to the development of insulin resistance are not well understood. In this study, using phosphospecific antibodies against rat IRS-1 phosphorylated at Ser(307) (equivalent to Ser(312) in human IRS-1), we observed serine phosphorylation of IRS-1 in response to TNF-alpha or calyculin A treatment that paralleled surrogate markers for IKK activation. The phosphorylation of human IRS-1 at Ser(312) in response to tumor necrosis factor-alpha was significantly reduced in cells pretreated with the IKK inhibitor 15 deoxy-prostaglandin J(2) as well as in cells derived from IKK knock-out mice. We observed interactions between endogenous IRS-1 and IKK in intact cells using a co-immunoprecipitation approach. Moreover, this interaction between IRS-1 and IKK in the basal state was reduced upon IKK activation and increased serine phosphorylation of IRS-1. Data from in vitro kinase assays using recombinant IRS-1 as a substrate were consistent with the ability of IRS-1 to function as a direct substrate for IKK with multiple serine phosphorylation sites in addition to Ser(312). Taken together, our data suggest that IRS-1 is a novel direct substrate for IKK and that phosphorylation of IRS-1 at Ser(312) (and other sites) by IKK may contribute to the insulin resistance mediated by activation of inflammatory pathways.
Metabolic Syndrome and Carotid Intima-Media Thickness in Young Adults: Roles of Apolipoprotein B, Apolipoprotein A-I, C-Reactive Protein, and Secretory Phospholipase A2: The Cardiovascular Risk in Young Finns Study (2010)

High levels of apoB, C-reactive protein, and type II secretory phospholipase A2 and low levels of apoA-I associate with MetS in young adults. The atherogenicity of MetS in this population assessed by incident high carotid intima-media thickness appears to be substantially mediated by elevated apoB but not inflammatory markers.
Ultrasound assessment of response to intra-articular therapy in osteoarthritis of the knee (2015)

Ultrasonography can detect short-term synovial response in knee OA. In particular, power Doppler score may be both responsive to and associated with pain, warranting further investigation.
3D position, attitude and shape input using video tracking of hands and lips (1994)

Recent developments in video-tracking allow the outlines of moving, natural objects in a video-camera input stream to be tracked live, at full video-rate. Previous systems have been available to do this for specially illuminated objects or for naturally illuminated but polyhedral objects. Other systems have been able to track nonpolyhedral objects in motion, in some cases from live video, but following only centroids or key-points rather than tracking whole curves. The system described here can track accurately the curved silhouettes of moving non-polyhedral objects at frame-rate, for example hands, lips, legs, vehicles, fruit, and without any special hardware beyond a desktop workstation and a video-camera and framestore.
Time-resolved immunofluorometric assay of human prostate-specific antigen. (1990)

Assay of human serum prostate-specific antigen (PSA) is gaining importance in diagnosis and follow-up of prostatic cancer. In this time-resolved immunofluorometric assay of PSA, strip-wells were coated with a polyclonal antibody against PSA. To prepare the label, a monoclonal antibody displaying high affinity towards PSA was purified and derivatized with diethylenetriaminepentaacetic acid. With use of this derivative, seven to eight Eu atoms could be combined with one antibody molecule with no decrease in immunoreactivity. The minimum detectable concentration of PSA was 0.12 microgram/L. In 60 of 63 women studied, the PSA concentration in serum was less than 0.2 microgram/L. The increase in PSA in serum of asymptomatic men 51 years old or older, as compared with that for younger subjects, was possibly a result of "occult" prostatic hyperplasia. Most of the patients with prostatic hyperplasia or prostatic cancer had higher PSA concentrations than did subjects of ages less than 50 years or asymptomatic age-matched healthy subjects. Results compared favorably with those by an established technique relying on the use of radioactive label. Our method for measuring PSA in human serum is convenient, inexpensive, and well compatible with present clinical practice.
An experimental investigation of hypervigilance for threat in children and adolescents with post-traumatic stress disorder (2001)

The results of the study are interpreted as a consolidation and extension of previous research on attentional bias and emotional disorder in younger participants.
OpenMP task scheduling strategies for multicore NUMA systems (2012)

The recent addition of task parallelism to the OpenMP shared memory API allows programmers to express concurrency at a high level of abstraction and places the burden of scheduling parallel execution on the OpenMP run-time system. Efficient scheduling of tasks on modern multi-socket multicore shared memory systems requires careful consideration of an increasingly complex memory hierarchy, including shared caches and non-uniform memory access (NUMA) characteristics. In order to evaluate scheduling strategies, we extended the open source Qthreads threading library to implement different scheduler designs, accepting OpenMP programs through the ROSE compiler. Our comprehensive performance study of diverse OpenMP task-parallel benchmarks compares seven different task-parallel run-time scheduler implementations on an Intel Nehalem multi-socket multicore system: our proposed hierarchical work-stealing scheduler, a per-core work-stealing scheduler, a centralized scheduler, and LIFO and FIFO versions of the Qthreads round-robin scheduler. In addition, we compare our results against the Intel and GNU OpenMP implementations. Our hierarchical scheduling strategy leverages different scheduling methods at different levels of the hierarchy. By allowing one thread to steal work on behalf of all of the threads within a single chip that share a cache, the scheduler limits the number of costly remote steals. For cores on the same chip, a shared LIFO queue allows exploitation of cache locality between sibling tasks as well as between a parent task and its newly created child tasks. In the performance evaluation, our Qthreads hierarchical scheduler is competitive on all benchmarks tested. On five of the seven benchmarks, it demonstrates speedup and absolute performance superior to both the Intel and GNU OpenMP run-time systems. Our run-time also demonstrates similar performance benefits on AMD Magny Cours and SGI Altix systems, enabling several benchmarks to successfully scale to 192 CPUs of an SGI Altix.
Investigation of protein refolding using a fractional factorial screen: A study of reagent effects and interactions (2005)

A recurring obstacle for structural genomics is the expression of insoluble, aggregated proteins. In these cases, the use of alternative salvage strategies, like in vitro refolding, is hindered by the lack of a universal refolding method. To overcome this obstacle, fractional factorial screens have been introduced as a systematic and rapid method to identify refolding conditions. However, methodical analyses of the effectiveness of refolding reagents on large sets of proteins remain limited. In this study, we address this void by designing a fractional factorial screen to rapidly explore the effect of 14 different reagents on the refolding of 33 structurally and functionally diverse proteins. The refolding data was analyzed using statistical methods to determine the effect of each refolding additive. The screen has been miniaturized for automation resulting in reduced protein requirements and increased throughput. Our results show that the choice of pH and reducing agent had the largest impact on protein refolding. Bis-mercaptoacetamide cyclohexane (BMC) and tris (2-carboxyethylphosphine) (TCEP) were superior reductants when compared to others in the screen. BMC was particularly effective in refolding disulfide-containing proteins, while TCEP was better for nondisulfide-containing proteins. From the screen, we successfully identified a positive synergistic interaction between nondetergent sulfobetaine 201 (NDSB 201) and BMC on Cdc25A refolding. The soluble protein resulting from this interaction crystallized and yielded a 2.2 Angstroms structure. Our method, which combines a fractional factorial screen with statistical analysis of the data, provides a powerful approach for the identification of optimal refolding reagents in a general refolding screen.
Differential sensitivity to fibrinogen inhibition of SP-C- vs. SP-B-based surfactants (1992)

Inhibition of surfactant function by plasma-derived proteins is assumed to occur under conditions of alveolar protein leakage. We investigated surface properties and sensitivity to the inhibitory capacity of fibrinogen (Fbg) of artificial surfactants in a pulsating-bubble surfactometer. Phospholipid-fatty acid mixtures (PLM) with or without hydrophobic apoproteins [natural bovine surfactant proteins (SP) B and C, recombinant human SP-C] were used. Without Fbg, all apoprotein-based surfactants exhibited rapid absorption facilities and reduced surface tension to near zero values under dynamic compression. Fbg caused a dose-dependent reduction of adsorption kinetics and dynamic surface tension-lowering properties of all surfactant preparations, but there was a marked rank order of "Fbg sensitivity": PLM without apoprotein being the most sensitive and SP-B-based PLM the least. Fbg sensitivity of recombinant SP-C-based PLM could be lowered dose dependently by adding small amounts of SP-B. For further support of a putative role of SP-B in resistance to Fbg inhibition, calf lung surfactant extract was incubated with monoclonal antibody against SP-B. Without Fbg, anti-SP-B had little influence. However, sensitivity to the inhibitory effect of Fbg was markedly and dose dependently increased by anti-SP-B but not by control immunoglobulin. We conclude that SP-B-based surfactant preparations display markedly lower susceptibility to Fbg inhibition than SP-C combinants.
Thrombosis in Patients with the Lupus Anticoagulant (1980)

A retrospective study was carried out to determine the frequency of thrombosis in patients with the lupus anticoagulant. Thirty-five patients fulfilled laboratory criteria for the diagnosis of the lupus anticoagulant. Eight of these patients had evidence of clinically significant thrombosis while their plasma showed a prolonged partial thromboplastin time due to the anticoagulant. Four of the patients wity thrombosis had concurrent autoimmune disease and three other patients were receiving phenothiazine medication. Moderate thrombocytopenia was noted in four patients with thrombosis. None of the patients with the lupus anticoagulant bled abnormally. This study suggests that patients with the lupus anticoagulant may be at increased risk of thrombosis.
LINGCOD MUSCLE PURINE NUCLEOSIDE PHOSPHORYLASE (1958)

A purine nucleoside phosphorylase enzyme preparation, which catalyzed the general reaction ribose (deoxyribose) [Formula: see text] nucleoside (deoxynucleoside)+orthophosphate, was isolated from muscles of the lingcod (Ophiodon elongatus). The reaction was found to be about 85% in favor of nucleoside synthesis with 10 μM./ml. concentrations of reactants in the hypoxanthine–inosine system. With similar concentrations of reactants in the guanine–guanosine system the equilibrium was about 75% in favor of nucleoside synthesis, and with considerably higher concentrations of reactants in this system this percentage decreased markedly. Purified preparations were stable for over a year at −20 °C., contained two major protein components (zone electrophoresis and ultracentrifuge data), were rather heat labile, and possessed a maximum activity corresponding to liberation of 32 μM. orthophosphate/mg. protein N/hour. Evidence is given in support of the view that a single enzyme is responsible for the above reaction and that it possesses strict specificity for α-D-ribofuranose 1-phosphate and deoxyribose 1-phosphate. Of a large number of substituted purines investigated, only the following were active: hypoxanthine, xanthine, 6-mercaptopurine, 6-methylpurine, 8-azaguanine, guanine, adenine, and 2, 6-diaminopurine. Methods are given for the preparation, in good yield, of analytically pure dicyclohexylammonium salts of ribose 1-phosphate and deoxyribose 1-phosphate.
The Burden of Influenza B: A Structured Literature Review (2013)

We reviewed the epidemiology, clinical characteristics, disease severity, and economic burden of influenza B as reported in the peer-reviewed published literature. We used MEDLINE to perform a systematic literature review of peer-reviewed, English-language literature published between 1995 and 2010. Widely variable frequency data were reported. Clinical presentation of influenza B was similar to that of influenza A, although we observed conflicting reports. Influenza B-specific data on hospitalization rates, length of stay, and economic outcomes were limited but demonstrated that the burden of influenza B can be significant. The medical literature demonstrates that influenza B can pose a significant burden to the global population. The comprehensiveness and quality of reporting on influenza B, however, could be substantially improved. Few articles described complications. Additional data regarding the incidence, clinical burden, and economic impact of influenza B would augment our understanding of the disease and assist in vaccine development.
Machine Learning, a Probabilistic Perspective (2014)

Kevin P. MurphyHardcover: 1104 pagesYear: 2012Publisher: The MIT PressISBN-13: 978-0262018029I have to admit the rather embarrassing fact that Machine Learning, a Probabilistic Perspective is the f...
Stoichiometry of Envelope Glycoprotein Trimers in the Entry of Human Immunodeficiency Virus Type 1 (2005)

The human immunodeficiency virus type 1 (HIV-1) envelope glycoproteins (Envs) function as a trimer, mediating virus entry by promoting the fusion of the viral and target cell membranes. HIV-1 Env trimers induce membrane fusion through a pH-independent pathway driven by the interaction between an Env trimer and its cellular receptors, CD4 and CCR5/CXCR4. We studied viruses with mixed heterotrimers of wild-type and dominant-negative Envs to determine the number (T) of Env trimers required for HIV-1 entry. To our surprise, we found that a single Env trimer is capable of supporting HIV-1 entry; i.e., T = 1. A similar approach was applied to investigate the entry stoichiometry of envelope glycoproteins from amphotropic murine leukemia virus (A-MLV), avian sarcoma/leukosis virus type A (ASLV-A), and influenza A virus. When pseudotyped on HIV-1 virions, the A-MLV and ASLV-A Envs also exhibit a T = 1 entry stoichiometry. In contrast, eight to nine influenza A virus hemagglutinin trimers function cooperatively to achieve membrane fusion and virus entry, using a pH-dependent pathway. The different entry requirements for cooperativity among Env trimers for retroviruses and influenza A virus may influence viral strategies for replication and evasion of the immune system.
A Brief Review of Chelators for Radiolabeling Oligomers (2010)

The chemical modification of oligomers such as DNA, PNA, MORF, LNA to attach radionuclides for nuclear imaging and radiotherapy applications has become a field rich in innovation as older methods are improved and new methods are introduced. This review intends to provide a brief overview of several chelators currently in use for the labeling of oligomers with metallic radionuclides such as 99mTc, 111In and 188Re. While DNA and its analogs have been radiolabeled with important radionuclides of nonmetals such as 32P, 35S, 14C, 18F and 125I, the labeling methods for these isotopes involve covalent chemistry that is quite distinct from the coordinate-covalent chelation chemistry described herein. In this review, we provide a summary of the several chelators that have been covalently conjugated to oligomers for the purpose of radiolabeling with metallic radionuclides by chelation and including details on the conjugation, the choice of radionuclides and labeling methods.
Light‐responsive elements of the tobacco PSI‐D gene are located both upstream and within the transcribed region (1997)

psaDb is a nuclear gene encoding the ferredoxin-binding subunit of photosystem I in Nicotiana sylvestris. The organization of the light-responsive cis-elements of psaDb was studied using transgenic tobacco plants. Three types of psaDb chimeric constructs were created: (1) a 5' upstream fragment of psaDb transcriptionally fused with the beta-glucuronidase (GUS) gene, and a series of its 5' deletion derivatives, (2) the transcribed region of psaDb driven by the cauliflower mosaic virus (CaMV) 35S promoter, and (3) the 5' terminal 35 bases (the entire leader, +1 to +23, and the initiation codon context, +24 to +35) of the psaDb mRNA translationally fused with a GUS reporter gene under the operation of the CaMV 35S promoter. Light-responsiveness of these fusions in transgenic plants was examined by GUS assay and primer extension analysis. The results indicate that the light-responsive elements (LRE) of psaDb are located both upstream (-170 to +24) and within (+1 to +861) the transcribed region. The internal LRE is utilized in etiolated seedings but not in green leaves. The leader and initiation codon context construct (+1 to +35) did not show any light-response under the conditions tested. Therefore, it is likely that a combination of the upstream and internal LREs generates the complex light-responsive and tissue-specific regulation of this gene. This study also revealed that psaDb has adjacent activator (-267 to -254) and repressor (-253 to -234) regions for basal transcriptional activity; the former contains the ACGT binding motif recognized by many plant bZIP proteins, and the latter has the R3 decamer motif found in several photosystem I-related genes.