gebhart/patrepeval huggingface dataset:
Identification of the altered pyrrole in the isomeric sulfmyoglobins: hyperfine shift patterns as indicators of ring saturation in ferric chlorins (1988)

Analysis of the 1H NMR hyperfine shift patterns of isomeric sulfmyoglobins is carried out in the met-aquo and met-cyano states to determine the site of saturation in each protein. The utility of the patterns for structure elucidation is established by specific deuterium labeling of the heme methyls of the terminal base product. On the basis of the known saturation of ring B in this isomer [Chatfield, M.J., La Mar, G.N., Lecomte, J.T.J., Balch, A.L., Smith, K.M., & Langry, K.C. (1986) J. Am. Chem. Soc. 108, 7108-7110], the methyl resonance of the saturated ring is found to have strongly attenuated contact shift. Thus, the heme methyl contact shift pattern is diagnostic for the saturated pyrrole in the high-spin state. This rationale is then applied to analyze the assigned NMR spectra of the initial and terminal acid sulfmyoglobin products, revealing that the same ring B is saturated in each isomer. In contrast, the heme methyl contact shift pattern in low-spin ferric complexes reveals that the methyls both on the affected pyrrole and on the trans pyrrole are influenced similarly on sulfmyoglobin formation, precluding the use of this methyl shift pattern as a unique indicator of the site of saturation. Identification of exchangeable proximal histidine resonances for met-aquo sulfmyoglobin complexes with shifts similar to that in native myoglobin dictates inconsequential axial alterations in the sulfmyoglobins, while location of downfield meso proton resonances analogous to those of the native protein demonstrates the retention of the coordinate water in the active site of met-sulfmyoglobin.
Mitral valve leaflet remodelling during pregnancy: insights into cell-mediated recovery of tissue homeostasis (2016)

Little is known about how valvular tissues grow and remodel in response to altered loading. In this work, we used the pregnancy state to represent a non-pathological cardiac volume overload that distends the mitral valve (MV), using both extant and new experimental data and a modified form of our MV structural constitutive model. We determined that there was an initial period of permanent set-like deformation where no remodelling occurs, followed by a remodelling phase that resulted in near-complete restoration of homeostatic tissue-level behaviour. In addition, we observed that changes in the underlying MV interstitial cell (MVIC) geometry closely paralleled the tissue-level remodelling events, undergoing an initial passive perturbation followed by a gradual recovery to the pre-pregnant state. Collectively, these results suggest that valvular remodelling is actively mediated by average MVIC deformations (i.e. not cycle to cycle, but over a period of weeks). Moreover, tissue-level remodelling is likely to be accomplished by serial and parallel additions of fibrillar material to restore the mean homeostatic fibre stress and MVIC geometries. This finding has significant implications in efforts to understand and predict MV growth and remodelling following such events as myocardial infarction and surgical repair, which also place the valve under altered loading conditions.
<title>Extension of SALS to transmural quantitative structural analysis of planar tissues</title> (1999)

Planar fibrous connective tissues are composed of a dense extra-cellular network of collagen and elastin fibers embedded in a ground matrix. Thus, quantification of fiber architecture an important step in developing an understanding of the mechanics of planar tissues. We have extensively used small angle light scattering (SALS) to map the gross fiber orientation of several soft membrane connective tissues using a custom built high speed mapping instrument. However, the current technique is limited to total through-thickness tissue structural analysis. The current study was undertaken to determine the feasibility of obtaining transmural tissue structural information from 2D SALS data. Methods: The basic approach is to utilize precisely aligned serial histological sections cut en-face through a tissue block and obtain 2D fiber structure from each section using SALS. Transumural fiber structure information is then derived by integration of 2D data to form a single data set containing the complete transmural fiber structure. To demonstrate the feasibility of the method, both explanted bioprosthetic heart valve (BHV) and native bovine pericardium (BP) tissues were evaluated. Results: The transmural SALS technique revealed for explanted BHV preferential damage in the fibrosa layer, while for BP variations in transmural fiber architecture were found consistent with optical histology. Conclusions: The transmural SALS technique successfully demonstrated quantitative transmural variations in fiber architecture in two dense collagenous tissues in a rapid, cost-effective approach.
Supplementary Figure 5 from STC1 Expression By Cancer-Associated Fibroblasts Drives Metastasis of Colorectal Cancer (2023)

&lt;p&gt;PDF file - 938K, Analyses of relationship between size of primary tumor and metastases.&lt;/p&gt;
SIMULATION OF GREENHOUSE CUCUMBER LEAF AREA BASED ON RADIATION AND THERMAL EFFECTIVENESS (2006)

Background and Aims Leaf area index (LAI) is one of the most important crop parameters in photosynthesis driven crop growth simulation models. Temperature and radiation are important climate factors affecting crop leaf growth. The aim of this study is to quantitatively investigate the effects of both temperature and photosynthetically active radiation (PAR) on the leaf growth of greenhouse cucumber (Cucumis sativus). Methods Experiments with different cultivars and sowing dates were conducted in greenhouses of Shanghai Academy of Agricultural Sciences during August,2003 and July,2004. We used the following quantitative relationships based on experimental data to model the relationship between the product of thermal effectiveness and PAR (TEP): accumulated TEP to the number of unfolding leaves per plant and the number of old leaves removed per plant,leaf position relative to the rate of increase in leaf length and the maximum leaf length; and the ratio of leaf area to leaf length. Based on these quantitative relationships,a leaf area simulation model for greenhouse cucumber was developed. Independent experimental data were used to validate the model. The simulated results of the model developed in this study were compared with those of the traditional GDD based model (which predict leaf area based on growing degree days) and SLA based model (which predict leaf area based on the specific leaf area and leaf dry weight). Key Results The coefficient of determination (R2) and the root mean squared error (RMSE) between the simulated and the measured leaf area index (LAI) based on the 1∶1 line are 0.879 2 and 0.398 0,respectively. The prediction accuracy of this model is 37% and 74% higher,respectively,than that of the traditional GDD and SLA based models. Conclusions The model developed in this study can predict LAI satisfactorily using air temperature,radiation,date of the first leaf unfolding and planting density. The simple model input makes the model user friendly and more applicable in greenhouse crop and climate management practices.
Autologous haematopoietic stem-cell transplantation versus bortezomib–melphalan–prednisone, with or without bortezomib–lenalidomide–dexamethasone consolidation therapy, and lenalidomide maintenance for newly diagnosed multiple myeloma (EMN02/HO95): a multicentre, randomised, open-label, phase 3 study (2020)

Janssen and Celgene.
3-Amido-3-aryl-piperidines: A Novel Class of Potent, Selective, and Orally Active GlyT1 Inhibitors (2014)

3-Amido-3-aryl-piperidines were discovered as a novel structural class of GlyT1 inhibitors. The structure-activity relationship, which was developed, led to the identification of highly potent compounds exhibiting excellent selectivity against the GlyT2 isoform, drug-like properties, and in vivo activity after oral administration.
Periodic stripe domains and hybrid-alignment regime in nematic liquid crystals: Threshold analysis (1994)

Recently we investigated the occurrence of static periodic stripes in a hybrid aligned nematic cell. Assuming that the tilt anchoring was stronger at the planar wall than at the homeotropic wall, we have found the critical thickness of the cell for the transition from planar to periodic alignment as a function of the surface energy in the presence of a magnetic field. Here we study, for the same kind of cell, the critical thickness between the periodic and the aperiodic deformed structure by means of an appropriate numerical technique. As expected, such a threshold was found to be greater than the asymptotic threshold between planar and aperiodic structures. We performed an experiment, which allowed us to give an estimate of the surfacelike elastic constant ${\mathit{K}}_{24}$.
Heterogeneous Alterations in Human Alloimmunity Associated with Immunization (2005)

Background. The presence of alloantibodies and/or alloreactive T cells in a patient prior to a transplant can impact graft outcome. Environmental factors, including therapeutic vaccinations, may influence the strength and/or specificity of alloimmunity. Methods. To address this issue, we prospectively evaluated the effects of two different immunization protocols in human subjects on cellular alloimmunity using an IFNγ ELISPOT assay and on alloantibody reactivity by flow cytometric analysis of HLA-coated beads. Results. Vaccination/immunization was associated with augmentation of cellular and/or humoral alloimmune reactivity in >50% of the test subjects. The effects were heterogeneous in that some detected increases were transient, peaking 30-60 days postimmunization, whereas others persisted for the length of the study. Antibodies reactive to the immunizing agent did not cross react with the detected alloantibodies, suggesting that the augmentation of alloimmune reactivity was most likely due to a nonspecific adjuvant effect from the vaccine. Conclusions. Therapeutic vaccinations can alter the strength of cellular and humoral alloimmunity in humans. The results suggest that serial immune monitoring of alloreactivity might be beneficial when immunizations are administered to potential transplant recipients.
Control of Sequence Distribution of Ethylene Copolymers:  Influence of Comonomer Sequence on the Melting Behavior of Ethylene Copolymers (2003)

New unbridged mixed-ligand zirconocenes were synthesized, characterized, and studied in the copolymerizations of ethylene−propylene (EP) and ethylene−1-hexene (EH). The MAO-activated metallocene [1-benzyl-2-(3‘,5‘-di-tert-butyl)phenylindenyl][2-phenylindenyl]zirconium dichloride (8) catalyzed EP and EH copolymerizations with products of reactivity ratios greater than one (rerp = 2.4, rerh = 2.2) to give rubbery, semicrystalline, high-melting polymers. Crystallinity was detected by differential scanning calorimetry (DSC) in both EP and EH copolymers containing only 50 mol % ethylene. Solvent fractionation of high ethylene content EH copolymers revealed that these copolymers were composed of a small ether-soluble fraction and heptane-soluble and heptane-insoluble fractions whose compositions and sequence distributions matched closely with those of the unfractionated polymer. Collectively, the reactivity ratios, DSC, and fractionation results gave evidence that these copolymers contained long crystallizable ethylene sequences. A comparison of the melting point behavior of a series of ethylene−1-hexene copolymers with 80 mol % ethylene revealed a sensitive dependence of the melting transition to the comonomer sequence distribution.
P4‐177: MCI Trial Enrichment Using MRI Hippocampus Texture (2016)

Magnetic resonance imaging (MRI) hippocampal volume has been qualified by the European Medicines Agency (EMA) as an enrichment biomarker for mild cognitive impairment (MCI) trials [[1]]. We tested the potential of adding MRI hippocampal texture [[2]] for further enrichment of MCI trials. The MCI subjects from the “complete annual year 2 visit” 1.5T standardized Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset [[3]] that had an associated cerebrospinal fluid (CSF) measurement available from the Center for Neurodegenerative Disease Research, University of Pennsylvania School of Medicine, Philadelphia [[4]] were identified (127 subjects, age 74.5±7.4, 30.7% female, mini-mental state examination [MMSE] 26.9±1.8, Alzheimer’s Disease Assessment Scale-cognitive subscale [ADAS-Cog] 18.6±6.2).Two T1-weighted MRI biomarkers were computed: hippocampal volume divided by intra-cranial volume (cross-sectional FreeSurfer v.5.1.0, default parameters), and hippocampal texture (in house software). In addition, we used log(total tau / Aβ 1 to 42 peptide) as CSF biomarker. Biomarkers were combined using linear regression with change in cognitive score over two years as dependent variable. Costs were computed based on sample size estimates and using the same price for MRI and CSF assessment. Effect size and corresponding cost were monitored as a function of number of subjects selected for both MMSE and ADAS-cog (see Figure). Texture generally demonstrated larger effect size while at the same time maintaining a lower cost across the range of selected subjects compared to volume. Combining MRI and CSF was generally beneficial.
The Excitation Processes of Sensitized Luminescence in YAl3(BO3)4:Eu3+, Gd3+Phosphors (2003)

The photoluminescence of YAl3(BO3)4:Eu3+ phosphor is sensitized by the codoping of Gd3+ ions under ultraviolet excitation from 130 nm to 160 nm. The Gd3+ ions sensitize the emission of Eu3+ ions by a two-step energy transfer from the host to Gd3+ and then to Eu3+ ions.
<title>Warping time-frequency and time-scale representations to match signals</title> (1995)

Warping similarity transformations provide a powerful vehicle for generating new classes of joint distributions based on concepts different from time, frequency, and scale. These new signal representations focus on the critical characteristics of large classes of signals, and hence, prove useful for representing and processing signals that are not well matched by current techniques. Interestingly, all distributions that have been used to illustrate more complicated generalized distribution design techniques can be generated using the warping method.
Revealing the Interfacial Self-Assembly Pathway of Large-Scale, Highly-Ordered, Nanoparticle/Polymer Monolayer Arrays at an Air/Water Interface (2013)

The pathway of interfacial self-assembly of large-scale, highly ordered 2D nanoparticle/polymer monolayer or bilayer arrays from a toluene solution at an air/water interface was investigated using grazing-incidence small-angle scattering at a synchrotron source. Interfacial-assembly of the ordered nanoparticle/polymer array was found to occur through two stages: formation of an incipient randomly close-packed interfacial monolayer followed by compression of the monolayer to form a close-packed lattice driven by solvent evaporation from the polymer. Because the nanoparticles are hydrophobic, they localize exclusively to the polymer-air interface during self-assembly, creating a through thickness asymmetric film as confirmed by X-ray reflectivity. The interfacial self-assembly approach can be extended to form binary NP/polymer arrays. It is anticipated that by understanding the interfacial self-assembly pathway, this simple evaporative procedure could be conducted as a continuous process amenable to large area nanoparticle-based manufacturing needed for emerging energy technologies.
Comprehensive Biomarker Analysis and Final Efficacy Results of Sorafenib in the BATTLE Trial (2013)

Sorafenib demonstrates clinical activity in NSCLC, especially with wild-type EGFR. SSS was associated with improved PFS. These data identify subgroups that may derive clinical benefit from sorafenib and merit investigation in future trials.
Reducing Unnecessary Conservativeness in Access Rights Analysis with String Analysis (2007)

The Java <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">TM</sup> 2 runtime system has a security mechanism which guarantees the code under execution has appropriate access permissions to a certain system resource. Use of this security mechanism requires access control policies to specify what operations are permitted on each such resource at each program point. Previous work proposed a program analysis algorithm to statically infer a semi-optimal policy set from given program text. However the proposed method cannot calculate the optimal policy when the target resource is determined by string values at run-time, since it does not keep track of all potential string values generated through built-in or user-defined methods. This results in generating excessive access policies where actually unnecessary resource accesses are permitted. To overcome such limitations, we apply static string analysis to program variables relevant to access control policies. This paper shows that unnecessary permissions can be reduced with string analysis by applying it to analyzing open-source libraries.
Common genetic variation and the control of HIV-1 in humans (2009)

To extend the understanding of host genetic determinants of HIV-1 control, we performed a genome-wide association study in a cohort of 2,554 infected Caucasian subjects. The study was powered to detect common genetic variants explaining down to 1.3% of the variability in viral load at set point. We provide overwhelming confirmation of three associations previously reported in a genome-wide study and show further independent effects of both common and rare variants in the Major Histocompatibility Complex region (MHC). We also examined the polymorphisms reported in previous candidate gene studies and fail to support a role for any variant outside of the MHC or the chemokine receptor cluster on chromosome 3. In addition, we evaluated functional variants, copy-number polymorphisms, epistatic interactions, and biological pathways. This study thus represents a comprehensive assessment of common human genetic variation in HIV-1 control in Caucasians.
Genetic characterization and regulation of the nadB locus of Salmonella typhimurium (1987)

The nadB locus encodes the first enzyme of NAD synthesis. It has been reported that this gene and nadA are regulated by a positive regulatory protein encoded in the nadB region. In pursuing this regulatory mechanism, we constructed a fine-structure genetic map of the nadB gene. The region appears to include a single complementation group; no evidence for a positive regulatory element was found. Several mutations causing resistance to the analog 6-aminonicotinamide mapped within the structural gene and probably cause resistance to feedback inhibition. Regulatory mutations for nadB were isolated. These mutants mapped far from nadB near the pnuA gene, which encodes a function required for nicotinamide mononucleotide transport. The regulatory mutations appear to affect a distinct function encoded in the same operon as pnuA.
DNA-Functionalized, Bivalent Proteins* (2020)

Bivalent\nDNA conjugates of β-galactosidase (βGal),\nhaving pairs of oligonucleotides positioned closely on opposing faces\nof the protein, have been synthesized and characterized. These structures,\ndue to their directional bonding characteristics, allow for the programmable\naccess of one-dimensional protein materials. When conjugates functionalized\nwith complementary oligonucleotides are combined under conditions\nthat support DNA hybridization, periodic wire-type superstructures\nconsisting of aligned proteins form. These structures have been characterized\nby gel electrophoresis, cryo-transmission electron microscopy, and\nnegative-stain transmission electron microscopy. Significantly, melting\nexperiments of complementary building blocks display narrowed and\nelevated melting transitions compared to the free duplex DNA, further\nsupporting the formation of the designed binding mode, and unambiguously\ncharacterizing their association as DNA-mediated. These novel structures\nillustrate, for the first time, that directional DNA bonding can be\nrealized with only a pair of DNA modifications, which will allow one\nto engineer directional interactions and realize new classes of superstructures\nnot possible simply through shape control or isotropically functionalized\nmaterials.
Autologous Muscle-Derived Cells as a Therapy for Stress Urinary Incontinence: a Randomized, Blinded, Multi-dose Study (2009)

Chemosensory neurons of the vomeronasal organ (VNO) are supposed to detect pheromones controlling social and reproductive behavior in most terrestrial vertebrates. Recent studies indicate that pheromone signaling in VNO neurons is mediated via phospholipase C (PLC) activation generating the two second messengers inositol-1,4,5-trisphosphate (IP3) and diacylglycerol (DAG). Since Gαi and Gαo predominantly expressed in VNO neurons are usually not involved in activating PLC, it was explored if PLC activation may be mediated by Gβγ subunits. It was found that a scavenger for βγ dimers reduced the urine-induced IP3 formation in VNO preparations in a dose-dependent manner indicating a role for Gβγ complexes. Towards an identification of the relevant Gβ and Gγ subunit(s), PCR approaches as well as immunohistochemical experiments were performed. It was found that out of the five known Gβ subtypes, only Gβ2 was expressed in both Gαi as well as Gαo neurons. Experimental approaches focusing on the spatial expression profile of identified Gγ subtypes revealed that Gγ8-positive neurons are preferentially localized to the basal region of the vomeronasal epithelium, whereas Gγ2-reactive cells are restricted to the apical Gαi-positive layer of the sensory epithelium. As IP3 formation induced upon stimulation with volatile urinary compounds was selectively blocked by Gγ2-specific antibodies whereas second messenger formation elicited upon stimulation with α2u globulin was inhibited by antibodies recognizing Gγ8, it is conceivable that PLC activation in the two populations of chemosensory VNO neurons is mediated by different Gβγ complexes.
Budget-aware Index Tuning with Reinforcement Learning (2022)

Index tuning aims to find the optimal index configuration for an input workload. It is a resource-intensive task since it requires making multiple expensive "what-if" calls to the query optimizer to estimate the cost of a query given an index configuration without actually building the indexes. In this paper, we study the problem of budget-aware index tuning where the number of what-if calls allowed when searching for the optimal configuration during tuning is constrained. This problem is challenging as it requires addressing the trade-off between investing what-if calls on exploring new configurations versus exploiting a known promising configuration. We formulate budget-aware index tuning as a Markov decision process, and propose a solution based on Monte Carlo tree search, a classic reinforcement learning technology. Experimental evaluation on both standard industry benchmarks and real workloads shows that our solution can significantly outperform alternative budget-aware solutions in terms of the quality of the index configuration.