gebhart/patrepeval huggingface dataset:
Charge‐Assisted Chalcogen Bonds: CSD and DFT Analyses and Biological Implication in Glucosidase Inhibitors (2020)

This study reports a combined Cambridge Structural Database and theoretical DFT study of charge assisted chalcogen bonds involving sulfonium, selenonium, and telluronium cations. The chalcogen bond has been recently defined by IUPAC as the net attractive interaction between an electrophilic region associated with a chalcogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. Divalent chalcogen atoms typically have up to two σ-holes and forms up to two ChBs; the same holds for tetravalent chalcogens which adopt a seesaw arrangement. In sulfonium, selenonium, and telluronium salts chalcogen atoms form three covalent bonds, three σ-holes are located opposite to these bonds, and up to three charge assisted ChBs can be formed between these holes and the counterions. The covalent bond arrangement around these chalcogen atoms is similar to trivalent pnictogen atoms and translates into a similar pattern of noncovalent interactions. We have found and studied this type of charge-assisted chalcogen bonds in various sulfonium ion-containing inhibitors of glucosidase, for example, salacinol and kotalanol.
Accurate Determination of Interlayer Resistivity of 2-D Layered Systems: Graphene Case Study (2020)

In this article, we provide an accurate method to determine the interlayer resistivity of 2-D layered systems by directly measuring the resistance at a mono- to bi-layer step and feeding the measurement to a distributed resistance model. We take CVD-grown few-layer graphene (up to four layers) with different twist angles ranging from AB-stacked to totally decoupled graphene as an example. Our results show that the interlayer resistivity of AB-stacked CVD grown bilayer graphene (BLG) is in the range of 50-140 Ω.m, which is two to five orders of magnitude greater than the previously reported values for AB-stacked graphite. On the other hand, twisted BLG shows an interlayer resistivity as low as 6 Ω.m and it decreases monotonically with increasing the twist angle, suggesting that interlayer conduction is not limited by phonon scattering, as previously reported. Furthermore, the total resistance of twisted BLG was found to be about one order of magnitude lower than its AB-stacked counterpart, which might lead to lower delay and energy-delay product in twisted graphene interconnects. In addition to that, the universality of our approach allows for accurate determination of interlayer resistivity of other 2-D layered systems such as metal dichalcogenides.
COMPARISON OF STRUCTURAL REPAIR FOLLOWING CHARACTERIZED CHONDROCYTE IMPLANTATION OR MICROFRACTURE FOR THE TREATMENT OF SYMPTOMATIC CARTILAGE DEFECTS OF THE KNEE (2009)

Purpose: This study compared the efficacy and safety of Characterized Chondrocyte Implantation (CCI) to microfracture in the repair of symptomatic cartilage defects of the femoral condyle. Methods: CCI (n=51) was compared to microfracture (n=61) in patients with grade III–IV symptomatic cartilage defects of the femoral condyles in a prospective, multicenter, randomized, controlled trial. Structural repair was assessed at 1 year by histopathologists blinded to the treatment using computerized histomorphometry and an overall histology assessment. Clinical outcome was measured using the Knee Injury and Osteoarthritis Outcome Score (KOOS). Safety was recorded throughout the study. Results: CCI resulted in better structural repair than microfracture at 1 year post-treatment, as assessed by histomorphometry (p=0.003) and overall histology (p=0.012). Structural repair parameters relating to chondrocyte phenotype and tissue structure were also superior with CCI. Noninferiority of CCI was demonstrated for clinical outcome at 12–18 months, and both treatments were generally well tolerated. Conclusion: At 1 year post-treatment, CCI resulted in superior tissue repair compared to microfracture. Short-term clinical outcome after 12–18 months was similar for both treatments, as was the safety profile. The superior structural repair achieved with CCI may lead to improved long-term clinical benefits.
The Plant Golgi Apparatus: Structure, Functional Organization and Trafficking Mechanisms (1995)

262 INTRODUCTION 262 THE OOLGI APPARATUS, TON AND PCR 263 The Plant Golgi Apparatus Consists of a Set of Dispersed, Functionally Independent Golgi Stack-TGN Units 263 A Goigi Matrix Encompasses E a c h Golgi Stack and its Trans-Golgi Network ... 264 Cryofixed Golgi Stacks: Differences in Cisternae and Stack Architecture ..... 266 TON vs PCR: Two Functional Domains of the Same Organelle? 268 The Biosynthesis of N-Glycans Involves Enzymes in ER and Golgi Compartments ... ........ 270 a-Glyc an Biosynthesis is Initiated in Cis-Golgi Cisternae ........ 271 Complex Polysaccharides are Assembled in Golgi Stacks and the TGN 272 Golgi Membrane Proteins are Targeted by Signals in their Transmembrane Domains, and TGN Proteins by Signals in their Cytoplasmic Tails ........ 274 VESICLE-MEDIATED TRANSPORT MECHANISMS 274 Transport Through the Golgi Stack: A Critical Evaluation of Models 274 The Vesicle Transport Machinery is Highly Conserved . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .... . . .... 276 COP and Clathrin Vesicle Coats are Composed of Many Proteins .... ..... 278 Assembly of Coated Vesicles Involves Sarlp and ARF GTP-Binding Proteins 279 Vesicle Targeting Involves Vesicle-Specific Ligand-Receptor Systems ...... ........ 280 The Vesicle Fusion Machinery is Shared by Different Transport Systems....... 280 Rab GTP-Binding Proteins may be Proofreaders of vlt-SNARE Pair Formation, andlor ActivatorslDeactivators of the Fusion Complex . 281 CONCLUDING REMARKS ... .. 282 The Future? . . .. ........ ........ .... .... .... .... .... .... 282
Novel Cobalt Dichloride Complexes with Hindered Diphenylphosphine Ligands: Synthesis, Characterization, and Behavior in the Polymerization of Butadiene (2019)

Two novel cobalt diphenylphosphine complexes were synthesized by reacting cobalt(II) chloride with <i>tert</i>-butyl(diphenyl)phosphine (P<i><sup>t</sup></i>BuPh<sub>2</sub>) and (<i>S</i>)-(+)neomenthyldiphenylphosphine [(<i>S</i>)-NMDPP]. The crystal structure of the former was determined by single-crystal X-ray diffraction studies. The two complexes were then used in combination with methylaluminoxane (MAO) for the polymerization of 1,3-butadiene: crystalline highly syndiotactic 1,2 poly(1,3-butadiene)s were obtained, with a 1,2 content and a syndiotactic index (percentage of syndiotactic triads [<i>rr</i>]) up to 95% and 85%, respectively. The results obtained further support and confirm what was already observed in the polymerization of 1,3-butadiene with CoCl<sub>2</sub>(PRPh<sub>2</sub>)<sub>2</sub>-MAO (R = methyl, ethyl, <i>normal</i>-propyl, <i>iso</i>-propyl, and cyclohexyl): the nature of the phosphine ligand strongly affects the polymerization stereoselectivity, the polymer syndiotacticity increasing with increasing phosphine ligand steric hindrance.
Vinyl polymerization by carbon black, IV. Some properties of modified carbon black compared with its polymerization initiating activity (1985)

Abstract All grades of carbon black contain large amounts of unpaired electrons and organic functional groups. Polymerization reaction is possibly initiated by the unpaired electrons on the surface; the functional groups have promotional effect on the initiation process. All the properties like texture, geometry, surface area, pH of the aqueous slurry, ash content, and elemental composition have effects on the polymerization reaction. These pertinent physicochemical and surface properties of unmodified and modified N 220 carbon black have been studied in relation to N‐vinylcarbazole polymerization.
Carbon Monoxide Inhibits TLR-Induced Dendritic Cell Immunogenicity (2009)

Heme oxygenase-1 (HO-1) exerts its functions via the catabolism of heme into carbon monoxide (CO), Fe(2+), and biliverdin, as well as by depletion of free heme. We have recently described that overexpression of HO-1 is associated with the tolerogenic capacity to dendritic cells (DCs) stimulated by LPS. In this study, we demonstrate that treatment of human monocyte-derived DCs with CO blocks TLR3 and 4-induced phenotypic maturation, secretion of proinflammatory cytokines, and alloreactive T cell proliferation, while preserving IL-10 production. Treatment of DCs with biliverdin, bilirubin, and deferoxamine or replenishing intracellular heme stores had no effect on DC maturation. HO-1 and CO inhibited LPS-induced activation of the IFN regulatory factor 3 pathway and their effects were independent of p38, ERK, and JNK MAPK. HO-1 and CO treatment also inhibited mouse DC maturation in vitro and mouse DC immunogenic properties in vivo, as shown by adoptive cell transfer in a transgenic model of induced diabetes. Thus, for the first time, our data show that CO treatment inhibits DC immunogenicity induced by TLR ligands and that blockade of IFN regulatory factor 3 is associated with this effect.
Properties of Aged Montmorillonite−Wheat Gluten Composite Films (2006)

The properties of new and aged glycerol-plasticized vital wheat gluten films containing < or =4.5 wt % natural or quaternary ammonium salt modified montmorillonite clay were investigated. The films were cast from pH 4 or pH 11 ethanol/water solutions. The films, aged for < or =120 days, were characterized by tensile testing, X-ray diffraction, and transmission electron microscopy. In addition, water vapor permeability (11% relative humidity) and the content of volatile components were measured. The large reduction in the water vapor permeability with respect to the pristine polymer suggests that the clay platelets were evenly distributed within the films and oriented preferably with the platelet long axis parallel to the film surface. The film prepared from pH 11 solution containing natural clay was, as revealed by transmission electron microscopy and X-ray diffraction, almost completely exfoliated. This film was consequently also the strongest, the stiffest, and the most brittle and, together with the pH 11 film containing modified clay, it also showed the greatest decrease in water vapor permeability. The large blocking effect of the clay had no effect on the aging kinetics of the films. During aging, the pH 4 and pH 11 film strength and the pH 4 film stiffness increased and the pH 4 film ductility decreased at the same rate with or without clay. This suggests that the aging was not diffusion rate limited, that is, that the loss of volatile components or the migration of glycerol or glycerol/wheat gluten phase separation was not limited by diffusion kinetics. The aging rate seemed to be determined by slow structural changes, possibly involving protein denaturation and aggregation processes.
Vitellogenin-like Proteins among Invertebrate Species Diversity: Potential of Proteomic Mass Spectrometry for Biomarker Development (2012)

Cost-effective methodologies along with cross-species applicability constitute key points for biomarker development in ecotoxicology. With the advent of cheaper affordable genomic techniques and high throughput sequencing, omics tools could facilitate the assessment of effects of environmental contaminants for all taxa biodiversity. We assessed the potential of absolute quantification of proteins using mass spectrometry to develop vitellogenin (Vg)-like protein assays for invertebrates. We used available sequences in public databases to rapidly identify Vg-proteotypic peptides in seven species from different main taxa of protostome invertebrates (mollusk bivalves, crustacean amphipods, branchiopods, copepods and isopods, and insect diptera). Functional validation was performed by comparing proteomic signals from reproductive female tissue samples and negative controls (male or juvenile tissues). In a second part, we demonstrate in gammarids, daphnids, drosophilids, and gastropods that the assay validated in Vg-sequenced species can be applied to Vg-unsequenced species thanks to the evolutionary conservation of Vg-proteotypic peptide motifs. Finally, we discuss the relevance of mass spectrometry for biomarker development (specific measurement, rapid development, transferability across species). Our study supplies an illustration of the promising strategy to address the challenge of biodiversity in ecotoxicology, which consists in employing omics tools from comparative and evolutionary perspectives.
Decision Analysis in Orthopaedics (2005)

Orthopaedic surgeons are faced with an ever-growing amount of clinical information from which they are required to make treatment decisions. Many of these decisions can be approached with relative certainty. However, there are many situations where the optimal decision is less clear. These treatment decisions will have competing risks, benefits, or costs. Decision analysis is one method to critically evaluate alternative treatment options with multiple potential outcomes. This method of decision making can be extremely valuable because of the growing number of treatment alternatives, and to the ever-increasing complexity of medical scenarios.
Fast X-Ray Diffraction (XRD) Tomography for Enhanced Identification of Materials (2021)

X-ray computed tomography (CT) can provide 3D images of density, and possibly the atomic number, for large objects like passenger luggage. This information, while generally very useful, is often insufficient to identify threats like explosives and narcotics, which can have a similar average composition as benign everyday materials such as plastics, glass, light metals, etc. A much more specific material signature can be measured with X-ray diffraction (XRD). Unfortunately, XRD signal is very faint compared to the transmitted one, and also challenging to reconstruct for objects larger than a small laboratory sample. In this article we analyze a novel low-cost scanner design which captures CT and XRD signals simultaneously, and uses the least possible collimation to maximize the flux. To simulate a realistic instrument, we derive a formula for the resolution of any diffraction pathway, taking into account the polychromatic spectrum, and the finite size of the source, detector, and each voxel. We then show how to reconstruct XRD patterns from a large phantom with multiple diffracting objects. Our approach includes a reasonable amount of photon counting noise (Poisson statistics), as well as measurement bias, in particular incoherent Compton scattering. The resolution of our reconstruction is sufficient to provide significantly more information than standard CT, thus increasing the accuracy of threat detection. Our theoretical model is implemented in GPU (Graphics Processing Unit) accelerated software which can be used to assess and further optimize scanner designs for specific applications in security, healthcare, and manufacturing quality control.
Ultrabroadband near-infrared pulse generation by noncollinear OPA with angular dispersion compensation (2009)

A telescope-grating-deformable scheme is proposed to compensate the angular dispersion of ultrabroadband spectrum. A simple design consideration is formulated based on the large angular dispersion of the idler from noncollinear optical parametric amplification. A proof of principle experiment is demonstrated. A 3-μJ ultrabroadband near-infrared pulse with spectrum range from 700 to 1400 nm has been generated. The technique has great potential to provide an ultrabroadband seed with negligible angular dispersion for high-power amplification of few-cycle pulses.
Cost of Guessing: Applications to Distributed Data Storage and Repair. (2020)

In this paper, we introduce the notion of the cost of guessing and provide an optimal strategy for guessing a random variable taking values on a finite set whereby each choice may be associated with a positive finite cost value. Moreover, we drive asymptotically tight upper and lower bounds on the moments of cost of guessing problem. Similar to previous studies on the standard guesswork, established bounds on the moments quantify the accumulated cost of guesses required for correctly identifying the unknown choice and are expressed in terms of the Renyi's entropy. A new random variable is introduced to bridge between the cost of guessing and the standard guesswork. Finally, we establish the guessing cost exponent on the moments of the optimal guessing by considering a sequence of random variables. Furthermore, these bounds are shown to serve quite useful for bounding the overall repair latency cost (data repair complexity) for distributed data storage systems in which sparse graph codes may be utilized.
Metallodrug Conjugates with Steroids and Selective Estrogen Receptor Modulators (SERM) (2009)

An overview of conjugates of coordination complexes and organometallic complexes of Pt, Ru, Fe, Re, lanthanoids and other metals with natural and synthetic estrogens and antiestrogens targeting the nuclear estrogen receptors is provided. These conjugates are used as targeted cytotoxic agents or - if radiolabeled - as imaging probes for the detection of estrogen receptor-rich tissues such as hormone-dependent tumours. They are assessed with respect to their estrogen receptor binding affinities, potential synergistic cytotoxic effects in cancer cells and their specificity for tumour over non-malignant cells and tissues. The mechanisms of their modes of action are discussed. Pertinent literature is covered up to 2008.
Next-Generation Sequencing for Diagnosis and Tailored Therapy: A Case Report of Astrovirus-Associated Progressive Encephalitis (2015)

A boy with X-linked agammaglobulinemia experienced progressive global motor decline, cerebellar syndrome, and epilepsy. All standard polymerase chain reactions for neurotropic viruses were negative on cerebrospinal fluid and brain biopsy. Next-generation sequencing allowed fast identification of a new astrovirus strain (HAstV-VA1/HMO-C-PA), which led to tailor the patient's treatment, with encouraging clinical monitoring over 1 year.
Three-dimensional Transfer Function Analysis of a Confocal Fluorescence Microscope With a Finite-sized Source and Detector (1993)

Abstract The influence of a finite source and detector on the three-dimensional imaging of an incident light fluorescent confocal scanning optical microscope is investigated on the basis of its three-dimensional optical-transfer function. It is shown that the optical resolution in such set-ups remains the same as with punctiform pinholes if the source and the detecting pinhole radii are both smaller than the size of the Airy disc.
WWOX and p53 Dysregulation Synergize to Drive the Development of Osteosarcoma (2016)

Osteosarcoma is a highly metastatic form of bone cancer in adolescents and young adults that is resistant to existing treatments. Development of an effective therapy has been hindered by very limited understanding of the mechanisms of osteosarcomagenesis. Here, we used genetically engineered mice to investigate the effects of deleting the tumor suppressor Wwox selectively in either osteoblast progenitors or mature osteoblasts. Mice with conditional deletion of Wwox in preosteoblasts (Wwox<sup>Δosx1</sup>) displayed a severe inhibition of osteogenesis accompanied by p53 upregulation, effects that were not observed in mice lacking Wwox in mature osteoblasts. Deletion of p53 in Wwox<sup>Δosx1</sup> mice rescued the osteogenic defect. In addition, the Wwox;p53<sup>Δosx1</sup> double knockout mice developed poorly differentiated osteosarcomas that resemble human osteosarcoma in histology, location, metastatic behavior, and gene expression. Strikingly, the development of osteosarcomas in these mice was greatly accelerated compared with mice lacking p53 only. In contrast, combined WWOX and p53 inactivation in mature osteoblasts did not accelerate osteosarcomagenesis compared with p53 inactivation alone. These findings provide evidence that a WWOX-p53 network regulates normal bone formation and that disruption of this network in osteoprogenitors results in accelerated osteosarcoma. The Wwox;p53<sup>Δosx1</sup> double knockout establishes a new osteosarcoma model with significant advancement over existing models. Cancer Res; 76(20); 6107-17. ©2016 AACR.
Direct in vivo VH to JH rearrangement violating the 12/23 rule (2005)

V(D)J recombination at the immunoglobulin heavy chain (IgH) locus follows the 12/23 rule to ensure the correct assembly of the variable region gene segments. Here, we report characterization of an in vivo model that allowed us to study recombination violating the 12/23 rule, namely a mouse strain lacking canonical D elements in its IgH locus. We demonstrate that VH to JH joining can support the generation of all B cell subsets. However, the process is inefficient in that B cells and antibodies derived from the DH-less allele are not detectable if the latter is combined with a wild-type IgH allele. There is no preferential usage of any particular VH gene family or JH element in VHJH junctions, indicating that 23/23-guided recombination is possible, but is a low frequency event at the IgH locus in vivo.
Contrasting responses to interferon β‐1b treatment in relapsing‐remitting multiple sclerosis: Does baseline interleukin‐12p35 messenger RNA predict the efficacy of treatment? (2000)

Interferon (IFN)-beta treatment is effective in relapsing-remitting multiple sclerosis (RR-MS) via an as yet unidentified mechanism. In the present study, we investigated whether the expression of messenger RNA (mRNA) encoding the interleukin (IL)-12 subunits p40 and p35, IL-12 receptor chains, IL-18, tumor necrosis factor-alpha (TNFalpha), IFNgamma, IL-10, IL-4, or transforming growth factor-beta in unstimulated whole blood of 26 RR-MS patients changed during 6 months of IFNbeta-1b treatment. In these patients, a significant change was found in TNFalpha mRNA, whereas changes in IL-12 receptor-beta2 and IL-10 mRNA showed a trend. IFNbeta-1b-related changes in cytokine mRNA expression were next evaluated in clinical subgroups of RR-MS patients classified as either clinical responders or nonresponders on the basis of Expanded Disability Status Scale progression and the number of relapses and steroid interventions needed in the 2 years before initiation of treatment compared with the 2 years after initiation of treatment. These subgroups showed different response patterns to IFNbeta-1b treatment with respect to IL-10, TNFalpha, and IL-18 only. Surprisingly, clinical responders displayed no change in these cytokines, whereas nonresponders showed a decrease in TNFalpha and IL-18 mRNA as well as a transient increase in IL-10 mRNA. Baseline levels of IL-12p35 mRNA were lower in the responders compared with the nonresponders: this marker correctly predicted the clinical outcome in 81% of the 26 patients under investigation.