gebhart/patrepeval huggingface dataset:
Aluminophosphate molecular sieves comprised of hydrated triple crankshaft chains (1993)

We report the first synthesis of pure aluminophosphate hydrate H2 (AlPO4-H2) and its structure; AlPO4-H2 is constructed exclusively from a hydrated chain building unit that also builds the 18-ring VPI-5 structure and has one-dimensional channels circumscribed by highly elliptical rings consisting often oxygen atoms, implications from the existence of this building unit for the synthesis of novel aluminophosphate molecular sieves and for the synthesis of aluminosilicate and silicate analogues of AlPO4-H2 and VPI-5 are discussed.
Monitoring the temperature distribution in high-power VECSELs (2011)

Vertical-external-cavity surface-emitting lasers (VECSELs) have received much attention in the scientific community by accessing a broad spectral range, and enabling efficient intra-cavity frequency mixing. They combine the high output power of semiconductor diode lasers with the superior beam quality inherent to surface emitters. The majority of the applications relies on the high output power of the device. Generally, the performance of the VECSEL is limited by overheating. Efficient cooling concepts are therefore inevitable providing distribution and removal of the excess heat. A careful choice of the pump profile is also considered crucial for the optimal output characteristics. Here, the authors study the impact of the size and spatial fluence distribution of the pump spot on the output power. For this purpose the input-output characteristics of the device is monitored while simultaneously tracking the temperature in the active region.
Restructuring Symbolic Programs for Concurrent Execution on (1989)

CURARE, the program restructurer described in this dissertation, automatically transforms a sequential Lisp program into an equivalent concurrent program that executes on a multiprocessor. CURARE first analyzes a program to find its control and data dependences. This analysis is most difficult for references to structures connected by pointers. CURARE uses a new data-dependence algorithm, which finds and classifies these dependencies. The analysis is conservative and may detect conflicts that do not arise in practice. A programmer can temper and refine its results with declarations. Dependences constrain the program''s concurrent execution because, in general, two conflicting statements cannot execute in a different order without affecting the program''s result. A restructerer must know all dependences in order to preserve them. However, not all dependences are essential to produce the program''s result. CURARE attempts to transform the program so it computes its result with fewer conflicts. An optimized program will execute with less synchronization and more concurrency. CURARE then examines loops in a program to find those that are unconstrained or lightly constrained by dependences. By necessity, CURARE treats recursive functions as loops and does not limit itself to explicit program loops. Recursive functions offer Several advantages over explicit loops since they provide a convenient framework for inserting locks and handling the dynamic behavior of symbolic programs. Loops that are suitable for concurrent execution are changed to execute on a set of concurrent serv er processes. These servers execute single loop iterations and therefore need to be extremely inexpensive to invoke. Restructured programs execute significantly faster than the original sequential programs. This improvement is large enough to attract programmers to a multiprocessor, particularly since it requires little effort on their part. Although restructured programs may not make optimal use of a multiprocessor''s parallelism, they make good use of a programmer''s time.
Spectral control of near-field thermal radiation via photonic band engineering of two-dimensional photonic crystal slabs (2018)

In this paper, we numerically investigate a method to obtain narrow-bandwidth near-field thermal radiation spectra by using two-dimensional (2D) photonic crystal (PC) slabs. Our examination reveals that near-field thermal radiation spectra can be artificially controlled via the photonic band engineering of 2D-PC slabs, where the radiation is enhanced in a range of frequencies of the flat bands and suppressed inside the photonic bandgap. By designing a thermal emitter with a 2D-PC slab of appropriate thickness, and by adjusting the gap between the emitter and the absorber, we can implement narrowband near-field thermal radiation that overcomes the far-field blackbody limit in the near-infrared range. Further, its linewidth is as small as Δλ = 0.14 µm.
Isolation and Epitope Mapping of Staphylococcal Enterotoxin B Single-Domain Antibodies (2014)

Single-domain antibodies (sdAbs), derived from the heavy chain only antibodies found in camelids such as llamas have the potential to provide rugged detection reagents with high affinities, and the ability to refold after denaturation. We have isolated and characterized sdAbs specific to staphylococcal enterotoxin B (SEB) which bind to two distinct epitopes and are able to function in a sandwich immunoassay for toxin detection. Characterization of these sdAbs revealed that each exhibited nanomolar binding affinities or better. Melting temperatures for the sdAbs ranged from approximately 60 °C to over 70 °C, with each demonstrating at least partial refolding after denaturation and several were able to completely refold. A first set of sdAbs was isolated by panning the library using adsorbed antigen, all of which recognized the same epitope on SEB. Epitope mapping suggested that these sdAbs bind to a particular fragment of SEB (VKSIDQFLYFDLIYSI) containing position L45 (underlined), which is involved in binding to the major histocompatibility complex (MHC). Differences in the binding affinities of the sdAbs to SEB and a less-toxic vaccine immunogen, SEBv (L45R/Y89A/Y94A) were also consistent with binding to this epitope. A sandwich panning strategy was utilized to isolate sdAbs which bind a second epitope. This epitope differed from the initial one obtained or from that recognized by previously isolated anti-SEB sdAb A3. Using SEB-toxin spiked milk we demonstrated that these newly isolated sdAbs could be utilized in sandwich-assays with each other, A3, and with various monoclonal antibodies.
Heterogeneous dynamics during deformation of a polymer glass (2009)

The origins of molecular mobility in polymer glasses, particularly under deformation, are not well understood. A concerted experimental and computational approach is adopted to examine the segmental motion of a polymeric glass undergoing creep and constant strain rate deformations. Through a combination of molecular dynamics simulations and optical photobleaching experiments we are able to directly probe how dynamic heterogeneity evolves during deformation. Two distinct regimes emerge from our analysis; early in the deformation, the dynamics of the glass are strongly heterogeneous, as evidenced by the spectrum of relaxation times measured experimentally and the participation ratio of the atomic non-affine displacements measured computationally. After the onset of flow, the dynamics become significantly more homogeneous, and the participation ratio increases considerably.
Abstract P2-20-11: Progesterone impacts the growth and immune cell infiltration of murine mammary gland tumors (2023)

Abstract Clinical studies have linked usage of progestins (synthetic progesterone) to breast cancer risk. However, little is understood regarding the role of native progesterone (P4), signaling through the progesterone receptor (PR), in breast tumor formation. Recently, we demonstrated that P4 treatment or PR overexpression can drive changes in immune cell populations in the murine mammary gland and that PR overexpression leads to increased development of mammary gland tumors in mice. Given these findings, we sought to investigate whether P4 impacts tumor growth and immune cell infiltration of mammary gland tumors. We utilized syngeneic mammary gland tumor models to evaluate the effect of P4 on PR+ mammary gland tumor growth, which revealed that P4 promoted tumor growth and impacted immune cell infiltration of PR+ mammary gland tumors. Of note, numbers of tumor-infiltrating dendritic cells were decreased and exhausted T cells and regulatory T cells were increased with P4 treatment in PR+ tumors. To determine if anti-progestin therapies could reverse the growth-promoting effect of P4 on mammary gland tumors, mice bearing PR+ mammary gland tumors were treated with the anti-progestin onapristone. Onapristone treatment led to significantly decreased tumor volumes in two syngeneic mammary gland tumor models and reversed the effect that P4 had on tumor-infiltrating regulatory T cells. To determine if inhibition of tumor growth by onapristone was immunologically mediated, SCID mice bearing PR+ mammary gland tumors were treated with onapristone. Results revealed a decreased ability of onapristone to inhibit tumor growth in SCID mice compared to immunocompetent mice, suggesting that inhibition of tumor growth is, in part, immunologically mediated. These findings offer a novel mechanism of P4-driven mammary gland tumor development and provide rationale in investigating the usage of anti-progestin therapies to promote immune-mediated elimination of mammary gland tumors. Citation Format: Lauryn R Werner, Dominika E. Helm, Julio Tinoco, Eilidh I Chowanec, Sean M Holloran, Richard C Hastings, Junping Wei, Gangjun Lei, Xiao-Yi Yang, Mary A Markiewicz, Prabhakar Chalise, Justin Balko, Zachary C Hartman, Christy R Hagan. Progesterone impacts the growth and immune cell infiltration of murine mammary gland tumors [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-20-11.
Autoradiographic localization of 5HT1 binding sites in the medulla oblongata of the rat (1992)

Serotonin (5HT) binding sites in the medulla oblongata of the rat were localized using autoradiographic techniques with radioactive ligands that express high affinity for the 5HT1 (3H-5HT), 5HT1A (3H-80H-DPAT), or 5HT1B (125I-CYP with isoproterenol) receptor subtypes. 5HT1A sites were concentrated primarily in certain sensory regions of the medulla and in regions that contain serotonergic neurons. 5HT1B sites were diffusely distributed throughout the reticular formation and motor regions as well as being localized to certain sensory regions. A surprising finding was an association of 5HT1B binding sites with the corticospinal tract. 3H-5HT binding generally reflected the combined pattern of 5HT1A and 5HT1B sites but was also extremely dense in the choroid plexus, which exhibited virtually no 5HT1A or 5HT1B ligand binding. Presumably this binding, which was blocked by ketanserin, corresponds to 5HT1C sites. Administration of the serotonergic neurotoxin 5,7-dihydroxytryptamine reduced 5HT1A binding sites in regions of the medulla that contain serotonergic neuronal cell bodies. 5HT1B binding was not significantly altered in any area of the medulla. These studies indicate an important role for 5HT1A ligands in the processing of visceral and somatic sensory information, in regulation of certain cerebellar afferent projections, and in the regulation of serotonergic neuronal activity. 5HT1B ligands would be expected to regulate visceral and somatic efferent activity, as well as sensory information and reticular efferent activity, and might presynaptically regulate cortical inputs to the brain stem and spinal cord.
Inductor Design Methods With Low-Permeability RF Core Materials (2012)

Abstract—This paper presents a design procedure for inductors based on low-permeability magnetic materials, for use in very high frequency (VHF) power conversion. The proposed procedure offers an easy and fast way to compare different magnetic materials based on Steinmetz parameters and quickly select the best among them, to estimate the achievable inductor quality factor and size, and to design the inductor. Approximations used in the proposed methods are discussed. Geometry optimization of magnetic-core inductors is also investigated. The proposed design procedure and methods are verified by experiments. I. BACKGROUND There is a growing interest in switched-mode power elec-tronics capable of efficient operation at very high switching frequencies (e.g., 10-100 MHz) [1]. Power electronics op-erating at such frequencies include resonant inverters [2]–
Semiquantitative Analysis of the Biodistribution of the Combined18F-NaF and18F-FDG Administration for PET/CT Imaging (2015)

The understanding of the biodistribution of radiopharmaceuticals and the lesion uptake of the (18)F(-)/(18)F-FDG scan as well as the variations compared with the uptake on the separate (18)F-FDG PET/CT and (18)F-NaF PET/CT are valuable for more in-depth evaluation of the combined scanning technique.
PM-04 * IN SILICO ANALYSIS OF AVAglio AND RTOG 0825 PHASE III CLINICAL TRIALS SUGGESTS SIGNATURES OF PATIENTS TO RECEIVE BENEFIT FROM COMBINED BEVACIZUMAB AND RADIATION THERAPIES (2014)

Despite the growing interest in anti-angiogenic therapies for glioblastoma (GBM), no statistically significant evidence has been found to indicate that bevacizumab in combination with other therapies increases the overall survival of glioblastoma patients. Most recently two phase III trials, AVAglio and RTOG 0825, were concluded considering bevacizumab in the upfront setting in combination with radiation and chemotherapy. Although the aggregate results of these Phase III studies were disappointing, there remains an open question of the potential benefits of this combination therapy for predictable subpopulations of patients. We utilize a mathematical model of GBM growth which incorporates vascular density, hypoxia and necrosis to investigate differential benefits of combination therapy consisting of surgical resection, radiation and bevacizumab. Proliferation and migration rates of the simulated tumors were varied across known growth dynamics observed in human GBMs. The model assumes that the anti-angiogenic therapy normalizes vasculature and thus decreases hypoxia. We assess the differential hypoxic burden left after a gross total resection along with the change in radiation cell kill from re-normalization of the tissue due to treatment with bevacizumab. We found that hypoxic burden and the resulting change in radiation induced cell kill varied dramatically across a range of tumor growth kinetics. Under the assumption of vasculature renormalization leading to decreased hypoxia, we determined that patients undergoing a gross total resection, which is the case for about 50% of the patients enrolled in the AVAglio and RTOG 0825 Phase III trials, would not likely benefit from combination therapy because the majority of the hypoxic burden would have been surgically removed. For patients not undergoing a gross total resection, our results indicate that there is a sub-population of patients, those with large tumors and high proliferation rates, who would have a dramatic change in the total radiation cell kill when combined with anti-angiogenic therapy.
Search for the rare decay $D^0 \to \mu^+ \mu^-$ (2013)

A search for the rare decay $D^0 \to \mu^+ \mu^-$is performed using a data sample, corresponding to an integrated luminosity of 0.9 fb$^{-1}$, of $pp$ collisions collected at a centre-of-mass energy of 7 TeV by the LHCb experiment. The observed number of events is consistent with the background expectations and corresponds to an upper limit of \mbox{${\cal B}(D^0 \to \mu^+ \mu^-) < 6.2(7.6) \times 10^{-9}$} at \mbox{90%} \mbox{(95%)} confidence level. This result represents an improvement of more than a factor twenty with respect to previous measurements.
Stem Cell Platforms for Regenerative Medicine (2009)

The pandemic of chronic degenerative diseases associated with aging demographics mandates development of effective approaches for tissue repair. As diverse stem cells directly contribute to innate healing, the capacity for de novo tissue reconstruction harbors a promising role for regenerative medicine. Indeed, a spectrum of natural stem cell sources ranging from embryonic to adult progenitors has been recently identified with unique characteristics for regeneration. The accessibility and applicability of the regenerative armamentarium has been further expanded with stem cells engineered by nuclear reprogramming. Through strategies of replacement to implant functional tissues, regeneration to transplant progenitor cells or rejuvenation to activate endogenous self-repair mechanisms, the overarching goal of regenerative medicine is to translate stem cell platforms into practice and achieve cures for diseases limited to palliative interventions. Harnessing the full potential of each platform will optimize matching stem cell-based biologics with the disease-specific niche environment of individual patients to maximize the quality of long-term management, while minimizing the needs for adjunctive therapy. Emerging discovery science with feedback from clinical translation is therefore poised to transform medicine offering safe and effective stem cell biotherapeutics to enable personalized solutions for incurable diseases.
Supplementary Figure Legend from Taxane-Induced Blockade to Nuclear Accumulation of the Androgen Receptor Predicts Clinical Responses in Metastatic Prostate Cancer (2023)

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Cross-Target View to Feature Selection: Identification of Molecular Interaction Features in Ligand−Target Space (2010)

There is growing interest in computational chemogenomics, which aims to identify all possible ligands of all target families using in silico prediction models. In particular, kernel methods provide a means of integrating compounds and proteins in a principled manner and enable the exploration of ligand-target binding on a genomic scale. To better understand the link between ligands and targets, it is of fundamental interest to identify molecular interaction features that contribute to prediction of ligand-target binding. To this end, we describe a feature selection approach based on kernel dimensionality reduction (KDR) that works in a ligand-target space defined by kernels. We further propose an efficient algorithm to overcome a computational bottleneck and thereby provide a useful general approach to feature selection for chemogenomics. Our experiment on cytochrome P450 (CYP) enzymes has shown that the algorithm is capable of identifying predictive features, as well as prioritizing features that are indicative of ligand preference for a given target family. We further illustrate its applicability on the mutation data of HIV protease by identifying influential mutated positions within protease variants. These results suggest that our approach has the potential to uncover the molecular basis for ligand selectivity and off-target effects.
An Alternative Strategy To Determine the Mitochondrial Proteome Using Sucrose Gradient Fractionation and 1D PAGE on Highly Purified Human Heart Mitochondria (2002)

An alternative strategy for mitochondrial proteomics is described that is complementary to previous investigations using 2D PAGE techniques. The strategy involves (a) obtaining highly purified preparations of human heart mitochondria using metrizamide gradients to remove cytosolic and other subcellular contaminant proteins; (b) separation of mitochondrial protein complexes using sucrose density gradients after solubilization with n-dodecyl-beta-D-maltoside; (c) 1D electrophoresis of the sucrose gradient fractions; (d) high-throughput proteomics using robotic gel band excision, in-gel digestion, MALDI target spotting and automated spectral acquisition; and (e) protein identification from mixtures of tryptic peptides by high-precision peptide mass fingerprinting. Using this approach, we rapidly identified 82 bona fide or potential mitochondrial proteins, 40 of which have not been previously reported using 2D PAGE techniques. These proteins include small complex I and complex IV subunits, as well as very basic and hydrophobic transmembrane proteins such as the adenine nucleotide translocase that are not recovered in 2D gels. The technique described here should also be useful for the identification of new protein-protein associations as exemplified by the validation of a recently discovered complex that involves proteins belonging to the prohibitin family.
The N‐terminal cleavage of cellular prion protein in the human brain (2005)

Human brain cellular prion protein (PrP(c)) is cleaved within its highly conserved domain at amino acid 110/111/112. This cleavage generates a highly stable C-terminal fragment (C1). We examined the relative abundance of holo- and truncated PrP(c) in human cerebral cortex and we found important inter-individual variations in the proportion of C1. Neither age nor postmortem interval explain the large variability observed in C1 amount. Interestingly, our results show that high levels of C1 are associated with the presence of the active ADAM 10 suggesting this zinc metalloprotease as a candidate for the cleavage of PrP(c) in the human brain.
Development of a Transformation System for Nitratireductor sp. (2023)

Nitratireductor sp. OM-1 can accumulate butenoic acid, which is a short-chain unsaturated carboxylic acid utilized for chemical products. So far, we have predicted the thioesterase gene, te, as a candidate gene for butenoic acid biosynthesis, based on comparative transcriptome analysis. To confirm the function of te, the gene transfer system in Nitratireductor sp. OM-1 was required. Thus, in this study, we used electroporation as a transformation system and pRK415, a broad host range plasmid, and optimized the conditions. As a result, a maximum transformation efficiency of 7.9 × 10<sup>4</sup> colonies/µg DNA was obtained at 22.5 kV/cm. Moreover, an expression vector, pRK415-te, was constructed by insertion of te, which was successfully transferred into strain OM-1, using electroporation. The recombinant OM-1 strain produced butenoic acid at 26.7 mg/g of dried cell weight, which was a 254% increase compared to transformants harboring an empty vector. This is the first report of a gene transfer system for Nitratireductor sp., which showed that the te gene was responsible for butenoic acid production.
Measurement of quarkonium production in proton–lead and proton–proton collisions at $$5.02~\mathrm {TeV}$$ 5.02 TeV with the ATLAS detector (2018)

The modification of the production of J/, (2S), and (nS) (n = 1, 2, 3) in p+Pb collisions with respect to their production in pp collisions has been studied. The p+Pb and pp datasets used in this paper correspond to integrated luminosities of 28 nb -1 and 25 pb -1 respectively, collected in 2013 and 2015 by the ATLAS detector at the LHC, both at a centre-of-mass energy per nucleon pair of 5.02 TeV. The quarkonium states are reconstructed in the dimuon decay channel. The yields of J/ and (2S) are separated into prompt and non-prompt sources. The measured quarkonium differential cross sections are presented as a function of rapidity and transverse momentum, as is the nuclear modification factor, R pPb for J/ and (nS). No significant modification of the J/ production is observed while (nS) production is found to be suppressed at low transverse momentum in p+Pb collisions relative to pp collisions. The production of excited charmonium and bottomonium states is found to be suppressed relative to that of the ground states in central p+Pb collisions.