gebhart/patrepeval huggingface dataset:
Roles of metal ions in the maintenance of the tertiary and quaternary structure of arginase from Saccharomyces cerevisiae. (1991)

Arginase from Saccharomyces cerevisiae has long been known to be a metal ion-requiring enzyme as it requires heating at 45 degrees C in the presence of 10 mM Mn2+ for catalytic activation. Metals are also thought to play a structural role in the enzyme, but the identity of the structural metal and its precise structural role have not been defined. Analysis of the metal ions that bind to yeast arginase by atomic absorption spectroscopy reveals that there is a weakly associated Mn2+ that binds to the trimeric enzyme with a stoichiometry of 1.04 +/- 0.05 mol of Mn2+ bound per subunit and an apparent K'D value of 26 microM at pH 7.0 and 4 degrees C. A more tightly associated Zn2+ ion can only be removed by dialysis against chelating agents. In occasional preparations, this site contained some Mn2+; however, Zn2+ and Mn2+ together bind to high affinity sites with a stoichiometry of 1.14 +/- 0.25/mol of subunit. Both the loosely associated catalytic Mn2+ ion and the more tightly associated structural Zn2+ ion confer stability to the enzyme. Removal of the weakly bound Mn2+ ion results in a 3 degree C decrease in the midpoint of the thermal transition (T 1/2) (from 57 by 54 degrees C) as monitored by UV difference absorption spectroscopy. Removal of the tightly bound Zn2+ ion produces a 19 degrees C decrease in T 1/2 (to 38 degrees C). Similar results are obtained by circular dichroism measurements. When the Zn2+ ion is removed, the steady-state fluorescence intensity increases 100% as compared to the holoenzyme, with a shift in the emission maximum from 337 to 352 nm. This suggests that in the folded trimeric metalloenzyme, the tryptophan fluorescence is quenched and that upon removal of the structural metal, the quenching is relieved as tryptophan residues become exposed to more polar environments. Equilibrium sedimentation experiments performed after dialysis of the enzyme against EDTA demonstrate that arginase exists in a reversible monomer-trimer equilibrium, in the absence of metal ions, with a KD value of 5.05 x 10(-11) M2. In contrast, the native enzyme exists as a trimer with no evidence of dissociation when Mn2+ and Zn2+ are present (Eisenstein, E., Duong, L.T., Ornberg, R. L., Osborne, J.C., Jr., and Hensley, P. (1986) J. Biol. Chem. 261, 12814-12819). In summary, the study presented here demonstrates that binding of a weakly bound Mn2+ ion confers catalytic activity. In contrast, binding of a more tightly associated Zn2+ ion confers substantial stability to the tertiary and quaternary structure of the enzyme.
The Sickness Impact Profile: Conceptual Formulation and Methodology for the Development of a Health Status Measure (1976)

The development of a health status measure, the Sickness Impact Profile (SIP), is described in terms of both its conceptualization and methodology. The need for a health status measure that is sensitive and appropriate, based on sickness-related behavior, and culturally unbiased, is discussed. A model of sickness behavior is presented as a guide for methodological development. The description of the initial developmental stage of the SIP includeds detailed discussion and documentation of the collection, sorting and grouping of items that comprise the SIP, scaling of the items, scoring of the instrument, and testing and revision of the prototype instrument. Results of preliminary tests of reliability, validity, and administrative feasibility are presented. Subsequent steps in revision and finalization, now under way, are outlined.
Ovarian cancer screening: are we making any progress? (2001)

Given the burden of suffering associated with the development of ovarian cancer and the clear survival gradient related to the stage of disease at diagnosis, there is much enthusiasm for the development of effective screening strategies aimed at early detection. To date, no evidence exists to justify mass population screening; however, emphasis on subpopulation screening, identification of novel serologic markers, and multimodality screening designs have provided hope that these refinements may eventually translate into a reduction in ovarian cancer mortality.
Visualization components for persistent conversations (2001)

An appropriately designed interface to persistent, threaded conversations could reinforce socially beneficial behavior by prominently featuring how frequently and to what degree each user exhibits such behaviors. Based on the data generated by the Netscan data-mining project [9], we have developed a set of tools for illustrating the structure of discussion threads like those found in Usenet newsgroups and the patterns of participation within the discussions. We describe the benefits and challenges of integrating these tools into a multi-faceted dashboard for navigating and reading discussions in social cyberspaces like Usenet and related interaction media. Visualizations of the structure of online discussions have applications for research into the sociology of online groups as well as possible interface designs for their members.
Protein Interaction Mapping in C. elegans Using Proteins Involved in Vulval Development (2000)

Protein interaction mapping using large-scale two-hybrid analysis has been proposed as a way to functionally annotate large numbers of uncharacterized proteins predicted by complete genome sequences. This approach was examined in Caenorhabditis elegans, starting with 27 proteins involved in vulval development. The resulting map reveals both known and new potential interactions and provides a functional annotation for approximately 100 uncharacterized gene products. A protein interaction mapping project is now feasible for C. elegans on a genome-wide scale and should contribute to the understanding of molecular mechanisms in this organism and in human diseases.
Cross-Linked Network Polymer Electrolytes Based on a Polysiloxane Backbone with Oligo(oxyethylene) Side Chains:  Synthesis and Conductivity (2003)

A novel cross-linked siloxane-based solid polymer network has been synthesized by the hydrosilylation of polymethylhydrosiloxane (PMHS) partly substituted with oligo(ethylene glycol) methyl ether side groups and a α,ω-diallyl poly(ethylene glycol) cross-linking reagent. The ionic conductivities of the networks doped with LiTFSI are high at ambient temperature (σ = 1.33 × 10-4 S cm-1 at the optimum LiTFSI concentration EO/Li+ = 20:1). The temperature dependence of the conductivity followed the VTF form, indicating that polymer segmental motion assists the ion transport in the solid networks.
ABA Triblock Brush Polymers: Synthesis, Self-Assembly, Conductivity, and Rheological Properties (2015)

The synthesis, self-assembly, conductivity, and rheological properties of ABA triblock brush polymers (BBCPs) with grafted polystyrene (A block, NPS = 21) and poly(ethylene oxide) (B block, NPEO = 45) side chains are reported. Two backbone molecular weights (NA:NB:NA = 11:78:11 and 15:119:15) were investigated with lithium bis(trifluoromethane)sulfonimide (LiTFSI) doping ratios 2 ≤ [EO]:[Li+] ≤ 20. Blends with 2 ≤ [EO]:[Li+] ≤ 10 suppress PEO crystallization and self-assemble into hexagonally packed cylinders of the minority gPS component. Conductivity is on the order of 10–3 S/cm at 105 °C with a corresponding elastic modulus ca. 104 Pa. The optimum conductivity occurs at a blend ratio near 10:1 [EO]:[Li+], similar to that reported for linear block copolymer analogues.
Povidone-iodine solution as SARS-CoV-2 prophylaxis for procedures of the upper aerodigestive tract a theoretical framework (2020)

Such an approach represents a low-cost, low-morbidity measure that may reduce the risks associated with aerosol-generating procedures performed commonly in otorhinolaryngology operating rooms.
WNT/β-catenin mediates radiation resistance of mouse mammary progenitor cells (2007)

Recent studies have identified a subpopulation of highly tumorigenic cells with stem/progenitor cell properties from human breast cancers, and it has been suggested that stem/progenitor cells, which remain after breast cancer therapy, may give rise to recurrent disease. We hypothesized that progenitor cells are resistant to radiation, a component of conventional breast cancer therapy, and that that resistance is mediated at least in part by Wnt signaling, which has been implicated in stem cell survival. To test this hypothesis, we investigated radioresistance by treating primary BALB/c mouse mammary epithelial cells with clinically relevant doses of radiation and found enrichment in normal progenitor cells (stem cell antigen 1-positive and side population progenitors). Radiation selectively enriched for progenitors in mammary epithelial cells isolated from transgenic mice with activated Wnt/beta-catenin signaling but not for background-matched controls, and irradiated stem cell antigen 1-positive cells had a selective increase in active beta-catenin and survivin expression compared with stem cell antigen 1-negative cells. In clonogenic assays, colony formation in the stem cell antigen 1-positive progenitors was unaffected by clinically relevant doses of radiation. Radiation also induced enrichment of side population progenitors in the human breast cancer cell line MCF-7. These data demonstrate that, compared with differentiated cells, progenitor cells have different cell survival properties that may facilitate the development of targeted antiprogenitor cell therapies.
Deletion analysis of dengue virus type 4 nonstructural protein NS2B: identification of a domain required for NS2B-NS3 protease activity (1993)

Most proteolytic cleavages in the nonstructural protein (NS) region of the flavivirus polyprotein are effected by a virus-encoded protease composed of two viral proteins, NS2B and NS3. The N-terminal 180-amino-acid-region of NS3 includes sequences with homology to the active sites of serine proteases, and there is evidence that this portion of NS3 can mediate proteolytic cleavages. In contrast, nothing is known about required sequences in NS2B. We constructed a series of deletion mutations in the NS2B portion of plasmid pTM/NS2B-30% NS3, which expresses dengue virus type 4 (DEN4) cDNA encoding NS2B and the N-terminal 184 residues of NS3 from the T7 RNA polymerase promoter. Mutant or wild-type plasmids were transfected into cells that had been infected with a recombinant vaccinia virus expressing T7 RNA polymerase, and the protease activities of the expressed polyproteins were assayed by examining the extent of self-cleavage at the NS2B-NS3 junction. The results identify a 40-amino-acid segment of NS2B (DEN4 amino acids 1396 to 1435) essential for protease activity. A hydrophobicity profile of DEN4 NS2B predicts this segment constitutes a hydrophilic domain surrounded by hydrophobic regions. Hydrophobicity profiles of the NS2B proteins of other flaviviruses show similar patterns. Amino acid sequence alignment of this domain of DEN4 NS2B with comparable regions of other proteins of flaviviruses indicates significant sequence conservation, especially at the N-terminal end. These observations suggest that the central hydrophilic domain of NS2B of these other flaviviruses will also prove to be essential for protease activity.
Model recommendation for action recognition (2012)

Simply choosing one model out of a large set of possibilities for a given vision task is a surprisingly difficult problem, especially if there is limited evaluation data with which to distinguish among models, such as when choosing the best “walk” action classifier from a large pool of classifiers tuned for different viewing angles, lighting conditions, and background clutter. In this paper we suggest that this problem of selecting a good model can be recast as a recommendation problem, where the goal is to recommend a good model for a particular task based on how well a limited probe set of models appears to perform. Through this conceptual remapping, we can bring to bear all the collaborative filtering techniques developed for consumer recommender systems (e.g., Netflix, Amazon.com). We test this hypothesis on action recognition, and find that even when every model has been directly rated on a training set, recommendation finds better selections for the corresponding test set than the best performers on the training set.
Ionic Conduction in Lithium Ion Battery Composite Electrode Governs Cross-sectional Reaction Distribution (2016)

Composite electrodes containing active materials, carbon and binder are widely used in lithium-ion batteries. Since the electrode reaction occurs preferentially in regions with lower resistance, reaction distribution can be happened within composite electrodes. We investigate the relationship between the reaction distribution with depth direction and electronic/ionic conductivity in composite electrodes with changing electrode porosities. Two dimensional X-ray absorption spectroscopy shows that the reaction distribution is happened in lower porosity electrodes. Our developed 6-probe method can measure electronic/ionic conductivity in composite electrodes. The ionic conductivity is decreased for lower porosity electrodes, which governs the reaction distribution of composite electrodes and their performances.
Insig-2, a second endoplasmic reticulum protein that binds SCAP and blocks export of sterol regulatory element-binding proteins (2002)

This paper describes insig-2, a second protein of the endoplasmic reticulum that blocks the processing of sterol regulatory element-binding proteins (SREBPs) by binding to SCAP (SREBP cleavage-activating protein) in a sterol-regulated fashion, thus preventing it from escorting SREBPs to the Golgi. By blocking this movement, insig-2, like the previously described insig-1, prevents the proteolytic processing of SREBPs by Golgi enzymes, thereby blocking cholesterol synthesis. The sequences of human insig-1 and -2 are 59% identical. Both proteins are predicted to contain six transmembrane helices. The proteins differ functionally in two respects: (i) production of insig-1, but not insig-2, in cultured mammalian cells requires nuclear SREBPs; and (ii) at high levels of expression, insig-1, but not insig-2, can block SCAP movement in the absence of exogenous sterols. The combined actions of insig-1 and -2 permit feedback regulation of cholesterol synthesis over a wide range of sterol concentrations.
Identification of differentially expressed mRNAs in human fetal liver across gestation (1999)

Differential gene expression, with its precise start and stop times, is believed to be critical for the programmed development of new cells and tissues. Within the developing fetus, one tissue of particular interest is fetal liver. This organ undergoes rapid changes in the pathway toward liver development in utero since it is also the major site of hematopoiesis, until bone marrow hematopoiesis predominates. Believing that patterns would emerge from the bi-weekly large-scale inspection of expressed genes in the fetal liver, we employed differential display reverse transcription-polymerase chain reaction (DDRT-PCR) as ourprimary inspection tool. Using DDRT-PCR, we isolated cDNAs differentially expressed throughout fetal liver development and in adult liver. We displayed approximately 25 000 cDNAs from 10 and 24 week fetal liver and adult liver. From this initial screen, we determined that approximately 0.1-1% of the mRNA population undergoes expression changes. We extracted, purified and sequenced 25 differentially displayed cDNA bands. Fourteen cDNAs had similarities to known genes, while 11 cDNAs were not similar to any characterized gene. The differentially expressed cDNAs from known genes present in fetal liver include alpha-fetoprotein, stem cell factor, erythroid alpha-spectrin, 2,3-bisphosphoglycerate mutase, insulin-like growth factor-2, porphobilinogen deaminase and Mac30. The differentially expressed cDNAs present in adult liver but not in 10 week fetal liver were nicotinamide deaminase, human fibrinogen-related protein and alpha-acid glycoprotein. The majority of differentially expressed genes found during this effort appear to be turned on during organogenesis, however, some genes were found that are apparently turned off completely.
A Gift from Knowledge Distillation: Fast Optimization, Network Minimization and Transfer Learning (2017)

We introduce a novel technique for knowledge transfer, where knowledge from a pretrained deep neural network (DNN) is distilled and transferred to another DNN. As the DNN performs a mapping from the input space to the output space through many layers sequentially, we define the distilled knowledge to be transferred in terms of flow between layers, which is calculated by computing the inner product between features from two layers. When we compare the student DNN and the original network with the same size as the student DNN but trained without a teacher network, the proposed method of transferring the distilled knowledge as the flow between two layers exhibits three important phenomena: (1) the student DNN that learns the distilled knowledge is optimized much faster than the original model, (2) the student DNN outperforms the original DNN, and (3) the student DNN can learn the distilled knowledge from a teacher DNN that is trained at a different task, and the student DNN outperforms the original DNN that is trained from scratch.
Modernism and the sense of history (2016)

Modernism in the arts and literature is conventionally thought of as anti-traditional and therefore as anti-historical, in spite of the insistence by Eliot, Greenberg, Pound, and others of their of their interest in both archaic traditions and the redemption of what was best in ‘the past.’ Modern historiographical theory distinguishes between ‘the past’ and that ‘history’ which is only a part of it. This essay exploits this distinction by seeking to identify the extent to which the first generation of modernist writers rejected ‘history’ as an impediment to a knowledge of ‘a past’ on which to base a reformation of a Western culture grown stagnant and desiccated as a result of ‘modernization.’
The gut: a central organ after surgical stress. (1988)

The intestinal tract plays a central role in the protein catabolic response after injury and infection. The mucosa utilizes glutamine and thus spares glucose--presumably sparing this essential fuel source for tissues with an obligate glucose requirement. With inadequate nutritional support or prolonged stress, glutamine levels decrease in both the plasma and the tissue pools, which suggests that glutamine deficiency occurs. This is associated in time with atrophy of the gastrointestinal mucosa. This provision of dietary glutamine results in correction of the abnormally low glutamine concentrations and increased cellularity of the gut mucosa. The derangements in the intestinal mucosa associated with starvation, injury, infection, immunosuppression, chemotherapy, lack of enteral feedings, and other stresses are associated with a breakdown in the barrier function of the gut. Both bacteria and their toxins may enter the host from the intestinal lumen. Through interaction with the reticuloendothelial system, cytokines are produced, which stimulate the pituitary-adrenal axis and thus contribute to the stress response. The elaboration of glucocorticoids facilitates proteolysis, thus increasing glutamine release from skeletal muscle for gut repair. Although this homeostatic mechanism appears to aid mucosal repair and support immunologic responses, severe injury or prolonged glutamine deficits do not adequately support intestinal recovery and allow this cycle to become self-perpetuating (Fig 3). Adequate enteral feedings initiated early in the course of a disease appear to maintain adequate gut barrier function. In the frequent circumstance when feeding by this route is inadequate or impossible, glutamine-containing parenteral feedings offer an appropriate alternative therapy for bowel and immunologic support. Glutamine-containing parenteral feedings are associated with increased mucosal cellularity and improved survival after gut injury. Specific hormones also stimulate mucosal growth, and it is anticipated that a combination of hormones and specific nutrients will provide optimal support of the gut mucosa in the severely ill patient.
Conserved epitopes on the hemagglutinin-neuraminidase proteins of human and bovine parainfluenza type 3 viruses: nucleotide sequence analysis of variants selected with monoclonal antibodies (1986)

We have previously identified 11 epitopes located in two topologically nonoverlapping antigenic sites (A and B) and a third bridging site (C) on the human type 3 parainfluenza virus (PIV3) hemagglutinin-neuraminidase (HN) glycoprotein by using monoclonal antibodies (MAbs) which inhibit hemagglutination and virus infectivity (K. L. Coelingh, C. C. Winter, and B. R. Murphy, Virology 143:569-582, 1985). We have identified three additional antigenic sites (D, E, and F) on the HN molecule by competitive-binding assays of anti-HN MAbs which have no known biological activity. Epitopes in sites A, D, and F are conserved on the bovine PIV3 HN glycoprotein and also among a wide range of human isolates. The dideoxy method was used to identify nucleotide substitutions in the HN genes of antigenic variants selected with neutralizing MAbs representing epitopes in site A which are shared by human and bovine PIV3. The deduced amino acid substitutions in the variants were located in separate hydrophilic stretches of HN residues which are conserved in the primary structures of the HN proteins of both human and bovine PIV3 strains.
SPECT in Dementia (2003)

Single photon emission computerized tomography (SPECT) is a relatively cheap and widely available instrument for the examination of brain perfusion, cerebral blood flow and activity of neurotransmitter systems. The European project “SPECT in dementia” sets out to overcome some of the factors holding back the development of clinical neuroimaging.
Shaping the Borrelia burgdorferi genome: crystal structure and binding properties of the DNA‐bending protein Hbb (2007)

The genome of the Lyme disease-causing spirochete Borrelia burgdorferi encodes only a single polypeptide from the integration host factor (IHF)/HU or 'DNABII' family of nucleoid-associated proteins - Hbb. DNABII proteins induce large bends in DNA and serve as architectural factors in a variety of prokaryotic cellular processes. We have solved the crystal structure of an Hbb-DNA complex in which the DNA is bent by over 180 degrees . We find that like IHF, Hbb relies exclusively on indirect readout to recognize its cognate site. Additional binding studies show that the sequence preferences of Hbb are related to, yet distinct from those of IHF. Defining these binding characteristics may help to uncover additional roles for Hbb in Borrelia DNA metabolism as well as further our understanding of the mechanism of indirect readout.