gebhart/patrepeval huggingface dataset:
Correction for the metabolic exchange of 14C for 12C atoms in the pathway of gluconeogenesis in vivo. (1982)

Methods designed for estimation of the synthesis of plasma glucose are based on the transfer of 14C atoms from a selected precursor (substrate) such as lactate or alanine. This approach was shown to lead to an underestimation of the true synthesis of glucose because of the metabolic exchange of 14C atoms for 12C atoms in the hepatic oxaloacetate pool. From the incorporation of 14C atoms from intravenously infused [2-14C]acetate into plasma glucose, the extent of the metabolic exchange has been estimated. In normal dogs, metabolic exchange leads to an underestimation of plasma glucose synthesis from plasma lactate or alanine by a factor of 2.2 +/- 0.07, i.e., by 55%. In insulin-deprived diabetic dogs, the factor was found to be 1.8 +/- 0.05. In long-term fasted dogs, the factor may be higher than in the postabsorptive state, whereas treatment with methylprednisolone has no effect. The assumptions and sources of possible errors in the estimation of the extent of metabolic exchange are reviewed.
Clinical Features of 85 Fatal Cases of COVID-19 from Wuhan. A Retrospective Observational Study (2020)

<b>Rationale:</b> The global death toll from coronavirus disease (COVID-19) virus as of May 12, 2020, exceeds 286,000. The risk factors for death were attributed to advanced age and comorbidities but have not been accurately defined.<b>Objectives:</b> To report the clinical features of 85 fatal cases of COVID-19 in two hospitals in Wuhan.<b>Methods:</b> Medical records were collected of 85 fatal cases of COVID-19 between January 9, 2020, and February 15, 2020. Information recorded included medical history, exposure history, comorbidities, symptoms, signs, laboratory findings, computed tomographic scans, and clinical management.<b>Measurements and Main Results:</b> The median age of the patients was 65.8 years, and 72.9% were male. Common symptoms were fever (78 [91.8%]), shortness of breath (50 [58.8%]), fatigue (50 [58.8%]), and dyspnea (60 [70.6%]). Hypertension, diabetes, and coronary heart disease were the most common comorbidities. Notably, 81.2% of patients had very low eosinophil counts on admission. Complications included respiratory failure (80 [94.1%]), shock (69 [81.2%]), acute respiratory distress syndrome (63 [74.1%]), and arrhythmia (51 [60%]), among others. Most patients received antibiotic (77 [90.6%]), antiviral (78 [91.8%]), and glucocorticoid (65 [76.5%]) treatments. A total of 38 (44.7%) and 33 (38.8%) patients received intravenous immunoglobulin and IFN-α2b, respectively.<b>Conclusions:</b> In this depictive study of 85 fatal cases of COVID-19, most cases were males aged over 50 years with noncommunicable chronic diseases. The majority of the patients died of multiple organ failure. Early onset of shortness of breath may be used as an observational symptom for COVID-19 exacerbations. Eosinophilopenia may indicate a poor prognosis. A combination of antimicrobial drugs did not offer considerable benefit to the outcome of this group of patients.
Bioprinted Amniotic Fluid-Derived Stem Cells Accelerate Healing of Large Skin Wounds (2012)

Stem cells obtained from amniotic fluid show high proliferative capacity in culture and multilineage differentiation potential. Because of the lack of significant immunogenicity and the ability of the amniotic fluid-derived stem (AFS) cells to modulate the inflammatory response, we investigated whether they could augment wound healing in a mouse model of skin regeneration. We used bioprinting technology to treat full-thickness skin wounds in nu/nu mice. AFS cells and bone marrow-derived mesenchymal stem cells (MSCs) were resuspended in fibrin-collagen gel and "printed" over the wound site. At days 0, 7, and 14, AFS cell- and MSC-driven wound closure and re-epithelialization were significantly greater than closure and re-epithelialization in wounds treated by fibrin-collagen gel only. Histological examination showed increased microvessel density and capillary diameters in the AFS cell-treated wounds compared with the MSC-treated wounds, whereas the skin treated only with gel showed the lowest amount of microvessels. However, tracking of fluorescently labeled AFS cells and MSCs revealed that the cells remained transiently and did not permanently integrate in the tissue. These observations suggest that the increased wound closure rates and angiogenesis may be due to delivery of secreted trophic factors, rather than direct cell-cell interactions. Accordingly, we performed proteomic analysis, which showed that AFS cells secreted a number of growth factors at concentrations higher than those of MSCs. In parallel, we showed that AFS cell-conditioned media induced endothelial cell migration in vitro. Taken together, our results indicate that bioprinting AFS cells could be an effective treatment for large-scale wounds and burns.
Kinetic model‐based factor analysis of dynamic sequences for 82‐rubidium cardiac positron emission tomography (2010)

Kinetic model-based factor analysis can be used to provide physiologically accurate decomposition of (82)Rb dynamic PET images, and may improve the precision of MBF quantification.
Fabrication of InAs quantum dots in AlAs∕GaAs DBR pillar microcavities for single photon sources (2005)

We report the molecular beam epitaxy growth of low-density strain-induced InAs quantum dots (QD) embedded in an AlAs∕GaAs distributed Bragg reflector structure for a triggered photon source. By optimal selection of growth temperature, InAs deposited thickness and other experimental parameters, it is possible to grow low density (10∕μm2) InAs quantum dots with a suitable emission wavelength for a triggered photon source. The empirical formulas for the refractive indices of AlAs and GaAs materials at high temperature over a wide wavelength range are constructed by combining high resolution x-ray diffraction, dynamic optical reflectivity, and optical reflectivity spectrum techniques. Utilizing the electron-beam lithography and electron-cyclotron-resonance plasma etching techniques, a micropost microcavity with the top diameter of 0.6μm and the post height of 4.2μm has been fabricated. Narrow, spectrally limited single QD emission embedded in a micropost microcavity is observed in the photoluminescence.
[Differentiation of mesenchymal stem cells into cardio myogenic cells under the induction of myocardial cell lysate]. (2005)

Myocardial cell lysate is an ideal inducer to differentiate MSCs into myocardial-like cells in vitro. The differentiation promoting effect of myocardial cell lysate is more predominant than that of 5-aza.
Cross‐linking of galectin 3, a galactose‐binding protein of mammalian cells, by tissue‐type transglutaminase (1995)

The 30 kDa beta-galactoside-binding protein of baby hamster kidney (BHK) cells [Mehul et al. (1994), J. Biol. Chem. 269, 18250-18258] homologous to galectin 3, a widely distributed mammalian lectin, has been found to be a substrate for tissue type transglutaminase, as shown by the incorporation in a calcium- and time-dependent manner of 5-(biotinamido) pentylamine in the presence of guinea pig liver transglutaminase. The amino-terminal domain of hamster galectin 3, which is a repetitive sequence rich in glutamine, tyrosine, glycine and proline, is also an excellent substrate. A single lysine residue in the N-terminal domain is an essential requirement for transglutaminase-mediated oligomerization, and two equivalent glutamine residues present in identical sequence repeats within this domain appear to be involved as amine acceptors in cross-linking reactions. Transglutaminase-mediated cross-linking of galectin 3 to itself or to matrix components may be one mechanism for stabilisation of a multivalent binding form of the lectin in cell secretions or in extracellular matrices.
Sortase‐Catalyzed Initiator Attachment Enables High Yield Growth of a Stealth Polymer from the C Terminus of a Protein (2013)

Conventional methods for synthesizing protein/peptide-polymer conjugates, as a means to improve the pharmacological properties of therapeutic biomolecules, typically have drawbacks including low yield, non-trivial separation of conjugates from reactants, and lack of site- specificity, which results in heterogeneous products with significantly compromised bioactivity. To address these limitations, the use of sortase A from Staphylococcus aureus is demonstrated to site-specifically attach an initiator solely at the C-terminus of green fluorescent protein (GFP), followed by in situ growth of a stealth polymer, poly(oligo(ethylene glycol) methyl ether methacrylate) by atom transfer radical polymerization (ATRP). Sortase-catalyzed initiator attachment proceeds with high specificity and near-complete (≈95%) product conversion. Subsequent in situ ATRP in aqueous buffer produces 1:1 stoichiometric conjugates with >90% yield, low dispersity, and no denaturation of the protein. This approach introduces a simple and useful method for high yield synthesis of protein/peptide-polymer conjugates.
Distinct Mutants of Retrograde Intraflagellar Transport (IFT) Share Similar Morphological and Molecular Defects (1998)

A microtubule-based transport of protein complexes, which is bidirectional and occurs between the space surrounding the basal bodies and the distal part of Chlamydomonas flagella, is referred to as intraflagellar transport (IFT). The IFT involves molecular motors and particles that consist of 17S protein complexes. To identify the function of different components of the IFT machinery, we isolated and characterized four temperature-sensitive (ts) mutants of flagellar assembly that represent the loci FLA15, FLA16, and FLA17. These mutants were selected among other ts mutants of flagellar assembly because they displayed a characteristic bulge of the flagellar membrane as a nonconditional phenotype. Each of these mutants was significantly defective for the retrograde velocity of particles and the frequency of bidirectional transport but not for the anterograde velocity of particles, as revealed by a novel method of analysis of IFT that allows tracking of single particles in a sequence of video images. Furthermore, each mutant was defective for the same four subunits of a 17S complex that was identified earlier as the IFT complex A. The occurrence of the same set of phenotypes, as the result of a mutation in any one of three loci, suggests the hypothesis that complex A is a portion of the IFT particles specifically involved in retrograde intraflagellar movement.
Protein Protocols Handbook, The (2002)

The Protein Protocols Handbook, Second Edition aims to provide a cross-section of analytical techniques commonly used for proteins and peptides, thus providing a benchtop manual and guide for those wh
Lactobacillus vaginalis sp. nov. from the Human Vagina (1989)

Biochemical, chemical, and nucleic acid analyses were carried out on some lactobacilli isolated from the vaginas of patients suffering from trichomoniasis. Phenotypically the strains resembled Lactobacillus fermentum and L. reuteri. Nucleic acid studies, however, showed that the vaginal strains were distinct from these and all other lactobacilli examined and therefore warrant a new species. The name Lactobacillus vaginalis sp. nov. is proposed. The type strain of L. vaginalis is NCTC 12197.
Gevokizumab, an anti-IL-1β mAb for the potential treatment of type 1 and 2 diabetes, rheumatoid arthritis and cardiovascular disease. (2010)

The inflammatory cytokine IL-1β has an essential role in the innate immune response. High levels of IL-1β have been implicated in the development of many diseases, including type 1 and 2 diabetes (T1D and T2D), rheumatoid arthritis (RA) and cardiovascular disease. XOMA is developing gevokizumab (XOMA-052), an IgG2 humanized mAb against human IL-1β, for the potential treatment of these diseases. Gevokizumab has a high affinity for IL-1β and a long t1/2, which would allow for once-monthly dosing and offer a considerable advantage for patients over agents requiring more frequent dosing. Data from preclinical studies and clinical trials suggest that gevokizumab is a potentially effective and well-tolerated treatment for the indicated diseases. At the time of publication, phase II clinical trials were ongoing in patients with T1D, T2D and RA, with the T2D trials assessing key cardiovascular markers. Following promising data from a recent pilot trial, XOMA was also planning a phase I/II trial of gevokizumab for the potential treatment of uveitis in patients with the vasculitic inflammatory disorder Behçet's disease and the autoinflammatory conditions familial cold autoinflammatory syndrome and Muckle-Wells syndrome.
Regional calpain and caspase-3 proteolysis of α-spectrin after traumatic brain injury (1998)

Activity of calpains and caspase-3 inferred from proteolysis of the cytoskeletal protein alpha-spectrin into signature spectrin breakdown products (SBDPs) was used to provide the first systematic and simultaneous comparison of changes in activity of these two families of cysteine proteases after traumatic brain injury (TBI) in rats. Distinct regional and temporal patterns of calpain/caspase-3 processing of alpha-spectrin were observed in brain regions ipsilateral to the site of injury after TBI, including large increases of 145 kDa calpain-mediated SBDP in cortex (up to 30-fold), and enduring increases (up to 2 weeks) of 145 kDa SBDP in hippocampus and thalamus. By contrast, 120 kDa caspase-3-mediated SBDP was absent in cortex and showed up to a 2-fold increase in hippocampus and striatum at early (hours) after TBI. Future studies will clarify the pathological significance of large regional differences in activation of calpain and caspase-3 proteases after TBI.
Crystal Structure of LacI Member, PurR, Bound to DNA: Minor Groove Binding by α Helices (1994)

The three-dimensional structure of a ternary complex of the purine repressor, PurR, bound to both its corepressor, hypoxanthine, and the 16-base pair purF operator site has been solved at 2.7 A resolution by x-ray crystallography. The bipartite structure of PurR consists of an amino-terminal DNA-binding domain and a larger carboxyl-terminal corepressor binding and dimerization domain that is similar to that of the bacterial periplasmic binding proteins. The DNA-binding domain contains a helix-turn-helix motif that makes base-specific contacts in the major groove of the DNA. Base contacts are also made by residues of symmetry-related alpha helices, the "hinge" helices, which bind deeply in the minor groove. Critical to hinge helix-minor groove binding is the intercalation of the side chains of Leu54 and its symmetry-related mate, Leu54', into the central CpG-base pair step. These residues thereby act as "leucine levers" to pry open the minor groove and kink the purF operator by 45 degrees.
Behavioural facilitation following brain stimulation: Implications for neurorehabilitation (2011)

Studies showing facilitation of behavioural performance by transcranial magnetic stimulation (TMS), and transcranial direct current stimulation (tDCS) in sensory and perceptual domains, spatial attention, working memory, and executive and emotional tasks are reviewed. In these domains the performance of neurologically unimpaired participants may be modulated, with behavioural facilitation or interference, by TMS, and by tDCS. The mapping of the frequency-dependent effects of TMS, and of the polarity-dependent effects of tDCS on behaviour does not systematically and mechanistically result in an increase or decrease of behavioural performance. Factors such as the parameters of the cerebral stimulation (localisation, duration, intensity), and the features of the task (complexity, phase of training) contribute to determine the final net effect on the participants' performance. Non-invasive brain stimulation (NIBS), which modulates learning, and appears to have, under some conditions, long lasting effects, is a promising tool to be used in the rehabilitation of a variety of neurological and cognitive disorders, that typically involve repeated behavioural training sessions.
Harmful effects of transfusion of older stored red blood cells: iron and inflammation (2011)

Retrospective studies suggest that the transfusion of older, stored red blood cells (RBCs) may be associated with increases in mortality, serious infections, multiorgan failure, thrombosis, and hospital length of stay. Our research is based on the overarching hypothesis that the adverse effects associated with transfusion of older, stored RBCs result from the acute delivery of hemoglobin iron to the monocyte-macrophage system. To test this "iron hypothesis," we are recruiting healthy human volunteers to donate double, leukoreduced, RBC units. We then transfuse them with one autologous fresh unit (i.e., after 3-7 days of storage) and one older, stored unit (i.e., at 40-42 days of storage). The primary study outcome will compare laboratory iron measures and proinflammatory cytokines after transfusion of fresh or older, stored RBCs. Similar studies using allogeneic RBC transfusions will be performed in chronically transfused patients with either sickle cell disease or β-thalassemia. Although prospective, randomized studies will ultimately determine the existence of adverse effects from transfusing older, stored RBCs, our goal is to determine the mechanism(s) for this potential effect.
Salt Doping in PEO-Containing Block Copolymers: Counterion and Concentration Effects (2009)

The phase behavior of lithium salt-doped poly(styrene-b-ethylene oxide) (PS−PEO) was studied as a function of salt concentration, lithium (Li) counterion (X), and annealing temperature. Three LiX salts were employed in this work: LiClO4, LiCF3SO3, and LiAsF6. Increasing the salt doping ratio ([EO]:[Li]) from 48:1 to 3:1 led to morphological changes from hexagonally packed cylinders to lamellar morphologies; however, comparison between the small-angle X-ray scattering (SAXS) and transmission electron microscopy (TEM) results shows that the location of these morphological changes are altered by the different counterions. We interpret our SAXS, TEM, and differential scanning calorimetry data using strong segregation theory to estimate an effective interaction parameter (χeff) for our salt-doped copolymers. This χeff varies linearly with salt concentration for a single PS-PEO:LiX material; however, the slope for each χeff,PS−PEO:LiX is influenced by the nature of the counterion. We rationalize these effects by examining the Lewis acidity of each anion.
Optimally profiling and tracing programs (1992)

This paper presents algorithms for inserting monitoring code to profile and trace programs. These algorithms greatly reduce the cost of measuring programs. Profiling counts the number of times each basic block in a program executes and has a variety of applications. Instruction traces are the basis for trace-driven simulation and analysis, and are also used in trace-driven debugging. The profiling algorithm chooses a placement of counters that is optimized—and frequently optimal—with respect to the expected or measured execution frequency of each basic block and branch in the program. The tracing algorithm instruments a program to obtain a subsequence of the basic block trace—whose length is optimized with respect to the program's execution—from which the entire trace can be efficiently regenerated. Both algorithms have been implemented and produce a substantial improvement over previous approaches. The profiling algorithm reduces the number of counters by a factor of two and the number of counter increments by up to a factor of four. The tracing algorithm reduces the file size and overhead of an already highly optimized tracing system by 20-40%.
Molecular Modeling Suggests Conformational Scaffolds Specifically Targeting Five Subtypes of Somatostatin Receptors (2007)

Several analogs of somatostatin with conformational constraints in their peptide backbones have been modeled to determine energetically feasible conformations. Comparison of low-energy backbone structures of these peptides suggested unique conformations of the central Phe/Ala(i)-D-Trp(i+1)-Lys(i+2)-Thr(i+3) fragment characteristic for specific interactions of somatostatin with each of the five distinct subtypes of somatostatin receptors (SSTRs). The conformations obtained were in good agreement with experimental data obtained earlier by NMR measurements and/or X-ray crystallography. The results help rationalize experimental observations on the specificity of binding of various somatostatin analogs with different subtypes of the SSTRs. They also serve as templates for the design of conformationally constrained non-peptide scaffolds that effectively and selectively interact with different subtypes of SSTRs. Such scaffolds can be convenient carriers of radiolabels and near-infrared labels in specific agents for imaging tumors expressing different SSTR subtypes.
Using Cohort-Scheduling to Enhance Server Performance (2002)

A server application is commonly organized as a collection of concurrent threads, each of which executes the code necessary to process a request. This software architecture, which causes frequent control transfers between unrelated pieces of code, decreases instruction and data locality, and consequently reduces the effectiveness of hardware mechanisms such as caches, TLBs, and branch predictors. Numerous measurements demonstrate this effect in server applications, which often utilize only a fraction of a modern processorâs computational throughput. This paper addresses this problem through cohort scheduling, a new policy that increases code and data locality by batching the execution of similar operations arising in different server requests. Effective implementation of the policy relies on a new programming abstraction, staged computation, which replaces threads. The StagedServer library provides an efficient implementation of cohort scheduling and staged computation. Measurements of two server applications written with this library show that cohort scheduling can improve server throughput by as much as 20%, by reducing the processor cycles per instruction by 30% and L2 cache misses by 50%.
Improved confidence estimators for the multivariate normal confidence set (2000)

Traditionally, the constant coverage probability estimator, confidence coefficient, is used to report the confidence of a multivariate normal confidence set. Robinson (1979), Lu and Berger (1989) and Robert and Casella (1994) all showed that there are certain estimators better than the confidence coefficient when the number of unknown parameters is greater than 4. In this paper some other better estimators are provided.