gebhart/patrepeval huggingface dataset:
Feasibility of real-time serial comprehensive tumor analytics: Pilot study of olaparib and durvalumab in metastatic triple negative breast cancer (mTNBC). (2020)

e13092 Background: Longitudinal analysis of serial tumor biopsies is an under-utilized approach to studying adaptive mechanisms of resistance. We have established a comprehensive analytic platform to evaluate real-time trial sample analysis to inform precision oncology combinations in mTNBC. The primary endpoint of the study is feasibility of completing all CLIA assays within 28 days of biopsy. Methods: Following a pre-treatment biopsy and 4 weeks of olaparib monotherapy mTNBC patients underwent an on-treatment (tx) biopsy and durvalumab was added to their therapy. Pre- and on-tx biopsies underwent comparative analysis using CLIA assays (immunohistochemistry-IHC, whole exome seq, RNAseq and phospho-proteomics) as well as research assays (multiplex IHC-mIHC, cyclic immunofluorescence-IF, and reverse phase protein array-RPPA). Results: Serial biopsies were obtained from all 3 enrolled patients, and the primary endpoint was achieved for all patients (Table). Treatment was well tolerated, and 2 patients achieved clinical benefit &gt; 6 months. In one patient with a prolonged CR ( &gt; 18 months), the on-tx sample exhibited dramatic changes in protein network rewiring by protein data analysis (RPPA, cyclic-IF), and an increase in immune infiltrate by mIHC. Conclusions: This pilot confirmed the feasibility of rapid real-time analysis to inform treatment decisions. This led to the development and initiation of biomarker driven olaparib combination trials in mTNBC at our institution. Clinical trial information: NCT03544125 . [Table: see text]
Gas Condensate Relative Permeability for Well Calculations (1999)

Abstract This paper addresses several issues related to the modeling and experimental design of relative permeabilities used for simulating gas condensate well deliverability. The key relation defining steady-state flow in gas condensate wells is krg as a function of krg/kro. Strictly speaking, saturations are not important – i.e. the determination of kr(S). Once the krg =f(krg/kro) relationship is experimentally established and correlated with capillary number (Nc), accurate modeling of condensate blockage is possible. Special steady-state experimental procedures have been developed to measure krg as a function of krg/kro and Nc. Saturations, though they can be measured, are not necessary. We have paid particular attention to the effect of hysteresis on the relation krg =f(krg/kro), based on our observation that many repeated cycles of partial/complete imbibition and drainage occur in the near-well region during the life of a gas condensate well. An approach for fitting steady-state gas condensate relative permeability data has been developed and used for modeling relative permeability curves. A generalized relative permeability model is applied, where the "immiscible" or "rock" curves are linked with "miscible" or "straight-line" curves by a transition function dependent on the capillary number. Treatment of "inertial" high velocity flow (HVF) within the condensate blockage region and locally at the wellbore are also treated. The composite effect of condensate blockage is handled using a "Muskat" pseudopressure model, where relative permeabilities are corrected for the positive effect of capillary number dependence and the negative effect of inertial high velocity flow.
Comparison of Prediction Techniques to Compensate Time Delays Caused by Digital Control of a Three-Phase Buck-Type PWM Rectifier System (2008)

The digital control of a three-phase three-switch buck-type rectifier system is analyzed in this paper. Three main sources of time delays in the control loop can be identified for the implementation on a digital signal processor (DSP): 1) the delay time due to the sampling of the control quantities; 2) the one due to the calculation time of the DSP; and 3) the one due to the sample-and-hold function of the pulsewidth modulator. Using the buck-type system as an example, the influence of the time delay on the stability of the inner current control loop is discussed, and two prediction methods for time-delay compensation, i.e., a linear prediction and the Smith prediction, are comparatively evaluated. The control performance and the effect of the delay times and the prediction methods are shown by simulation results and through measurements on a 5-kW prototype.
Modeling blood filtration in hollow fibers dialyzers coupled with patient’s body dynamics (2016)

We develop a mathematical model for cross filtration in a hollow fibers dialyzer, taking into account not only the phenomena occurring within the machine, but also the redistribution of chemicals between intra- and extracellular compartments in the patient’s body. The scheme for the cross flow is derived with reference to a single fiber, starting from the basic laws of fluid dynamics and exploiting the smallness of the ratio between the fiber radius and the fiber length to obtain significant simplifications. We end up with a system of integral and partial di¤erential equations in which the input data are in principle unknown. Indeed, the blood composition is considerably altered while going through the fiber and the body reacts redistributing urea, sodium ions, etc. between intra- and extracellular compartments with its own dynamics, thus updating the various concentrations at the dialyzer inlet. Such a coupling is an essential feature of the model. We present numerical simulations, showing a reasonable agreement with the data for a specific patient taken from the literature.
Activation of phosphorylase kinase from rabbit skeletal muscle by calmodulin and troponin (1979)

TEST 02 - Elsevier's Scopus, the largest abstract and citation database of peer-reviewed literature. Search and access research from the science, technology, medicine, social sciences and arts and humanities fields.
FlexVec: auto-vectorization for irregular loops (2016)

Traditional vectorization techniques build a dependence graph with distance and direction information to determine whether a loop is vectorizable. Since vectorization reorders the execution of instructions across iterations, in general instructions involved in a strongly connected component (SCC) are deemed not vectorizable unless the SCC can be eliminated using techniques such as scalar expansion or privatization. Therefore, traditional vectorization techniques are limited in their ability to efficiently handle loops with dynamic cross-iteration dependencies or complex control flow interweaved within the dependence cycles. When potential dependencies do not occur very often, the end-result is under utilization of the SIMD hardware. In this paper, we propose FlexVec architecture that combines new vector instructions with novel code generation techniques to dynamically adjusts vector length for loop statements affected by cross-iteration dependencies that happen at runtime. We have designed and implemented FlexVec's new ISA as extensions to the recently released AVX-512 ISA. We have evaluated the performance improvements enabled by FlexVec vectorization for 11 C/C++ SPEC 2006 benchmarks and 7 real applications with AVX-512 vectorization as baseline. We show that FlexVec vectorization technique produces a Geomean speedup of 9% for SPEC 2006 and a Geomean speedup of 11% for 7 real applications.
Editorial for the Special Issue on Discontinuous Fiber Composites (2018)

The papers published in this special edition of the Journal of Composites Science will give the polymer engineer and scientist insight into what the existing challenges are in the discontinuous fiber composites field, and how these challenges are being addressed by the research community. [...]
Timing of Lumbar Spinal Fusion Affects Total Hip Arthroplasty Outcomes (2019)

LSF after THA is associated with a reduced dislocation rate compared with THA after LSF. Reasons may include decreasing pelvic mobility in a stable, well-healed THA or early postoperative spine precautions after LSF restricting positions of dislocation.
Transcytosis of IgA Attenuates Salmonella Invasion in Human Enteroids and Intestinal Organoids (2022)

Secretory IgA (SIgA) is the most abundant antibody type in intestinal secretions where it contributes to safeguarding the epithelium from invasive pathogens like the Gram-negative bacterium, Salmonella enterica serovar Typhimurium (STm). For example, we recently reported that passive oral administration of the recombinant monoclonal SIgA antibody, Sal4, to mice promotes STm agglutination in the intestinal lumen and restricts bacterial invasion of Peyer's patch tissues. In this report, we sought to recapitulate Sal4-mediated protection against STm in human Enteroids and human intestinal organoids (HIOs) as models to decipher the molecular mechanisms by which antibodies function in mucosal immunity in the human gastrointestinal tract. We confirm that Enteroids and HIO-derived monolayers are permissive to STm infection, dependent on HilD, the master transcriptional regulator of the SPI-I type three secretion system (T3SS). Stimulation of M-like cells in both Enteroids and HIOs by the addition of RANKL further enhanced STm invasion. The apical addition of Sal4 mouse IgA, as well as recombinant human Sal4 dimeric IgA (dIgA) and SIgA resulted a dose-dependent reduction in bacterial invasion. Moreover, basolateral application of Sal4 dIgA to Enteroid and HIO monolayers gave rise to SIgA in the apical compartment via a pathway dependent on expression of the polymeric immunoglobulin receptor (pIgR). The resulting Sal4 SIgA was sufficient to reduce STm invasion of Enteroid and HIO epithelial cell monolayers by ~20-fold. Recombinant Sal4 IgG was also transported in the Enteroid and HIOs, but to a lesser degree and via a pathway dependent on the neonatal Fc receptor (FCGRT). The models described lay the foundation for future studies into detailed mechanisms of IgA and IgG protection against STm and other pathogens.
Casein Kinase 1 Delta (CK1δ) Regulates Period Length of the Mouse Suprachiasmatic Circadian Clock In Vitro (2010)

The results indicate that CK1delta plays a more prominent role than CK1epsilon in the maintenance of 24-hour rhythms in the master circadian oscillator.
The carbocyanine dye DiD labels in vitro and in vivo neural stem cells of the subventricular zone as well as myelinated structures following in vivo injection in the lateral ventricle (2015)

Carbocyanines are fluorescent lipophilic cationic dyes used since the early 1980s as neuronal tracers. Several applications of these compounds have been developed thanks to their low cell toxicity, lateral diffusion within the cellular membranes, and good photostability. 1,1'-Dioctadecyl-3,3,3',3'-tetramethylindodicarbocyanine 4-chlorobenzenesulfonate (DiD) is an interesting component of this family because, in addition to the classic carbocyanine properties, it has a longer wavelength compared with its analogues. That makes DiD an excellent carbocyanine for labeling cells and tissues with significant intrinsic fluorescence. Drug encapsulation, drug delivery, and cellular transplantation are also fields using DiD-based systems where having detailed knowledge about its behavior as a single entity is important. Recently, promising studies concerned neural stem cells from the subventricular zone of the lateral ventricle in the brain (their natural niche) and their potential therapeutic use. Here, we show that DiD is able to label these stem cells in vitro and present basilar information concerning its pharmacokinetics, concentrations, and microscope protocols. Moreover, when DiD is injected in vivo in the cerebrospinal fluid present in the lateral ventricle of rat, it also labels stem cells as well as myelinated structures of the caudoputamen. This analysis provides a database to consult when planning experiments concerning DiD and neural stem cells from the subventricular zone.
Greater palatine block for V2 trigeminal neuralgia: Case report (2019)

This technique may be an effective treatment for medication-refractory V2 TN. By interrupting the pain cycle, this renders the condition amenable to long-term control using diminished doses of standard antineuralgia pharmaceuticals. The practical implications of the described procedure are that it is simple, safe, and well-tolerated with few or no adverse effects. This novel technique is a diagnostic feature for the dentist to differentiate between sources of facial pain.
Recovery of scandium from leachates of Greek bauxite residue by adsorption on functionalized chitosan–silica hybrid materials (2015)

Scandium recovery from bauxite residue leachates was investigated using ion-exchange adsorption. EGTA–chitosan–silica showed exceptionally high selectivity for scandium. It was used as resin material for column chromatography to isolate pure scandium.
Human in the loop approaches in multi-modal conversational task guidance system development (2022)

Development of task guidance systems for aiding humans in a situated task remains a challenging problem. The role of search (information retrieval) and conversational systems for task guidance has immense potential to help the task performers achieve various goals. However, there are several technical challenges that need to be addressed to deliver such conversational systems, where common supervised approaches fail to deliver the expected results in terms of overall performance, user experience and adaptation to realistic conditions. In this preliminary work we first highlight some of the challenges involved during the development of such systems. We then provide an overview of existing datasets available and highlight their limitations. We finally develop a model-in-the-loop wizard-of-oz based data collection tool and perform a pilot experiment.
Synthesis and evaluation of new Reissert analogs as HIV-1 reverse transcriptase inhibitors. 1. Quinoline and quinoxaline derivatives. (1997)

The synthesis and preliminary evaluation of new quinoline and quinoxaline derivatives (obtained by applying the original Reissert method, conveniently modified) as HIV-1 Reverse Transcriptase (RT) inhibitors are presented in this paper; likewise, the first structure-activity relationships are also proposed. Propyl 2-cyano-1(2H)-quinolin-carboxylate 2e, isopropyl 2-cyano-1 (2H)-quinolincarboxylate 2f, butyl 2-cyano-1 (2H)-quinolincarboxylate 2g and isobutyl 2-cyano-1 (2H)-quinolincarboxylate 2h have been selected as lead compounds. These compounds are active against the HIV-1 RT mutant type P236L (2f, IC50 = 1.2 microM) and present activity as anti-infective agents in HLT41acZ-1IIIB cells, showing no cytotoxicity at the active concentrations.
Steroids. 2. Synthesis of C-18 functionalized steroids via the Smith-Hughes route (1984)

The total synthesis of a series of racemic C-18 functionalized steroids was carried out in a search for novel estrogen-and/or progestin-receptor agonists or antagonists. The target compound 3,18-dihydroxyestra-1,3,5(10)-triene (2), 13-(2-oxopropyl)gona-4-en-3-one (3), 13-(1-hydroxy-1-prop-2-ynyl)gona-4-en-3-one (4a and 4b) and 13-(1-acetoxy-2-oxo-1-propyl)gona-4-en-3-one (5) are position isomers of the highly biologically active estradiol, progesterone, norethindrone, and 17-acetoxyprogesterone, respectively. Nevertheless the synthetic C-18 functionalized steroids 3-5 showed little activity in the Clauberg and anti-Clauberg assays. Compound 2 showed no antagonism in the postcoital assay despite the fact that it exhibited weak but measurable in vitro receptor-binding activity.
ChemInform Abstract: Absolute Configuration of the Polyazamacrolides, Macrocyclic Polyamines Produced by a Ladybird Beetle. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ATP sensitivity of preBötzinger complex neurones in neonatal ratin vitro: mechanism underlying a P2 receptor‐mediated increase in inspiratory frequency (2008)

P2 receptor (R) signalling plays an important role in the central ventilatory response to hypoxia. The frequency increase that results from activation of P2Y(1)Rs in the preBötzinger complex (preBötC; putative site of inspiratory rhythm generation) may contribute, but neither the cellular nor ionic mechanism(s) underlying these effects are known. We applied whole-cell recording to rhythmically-active medullary slices from neonatal rat to define, in preBötC neurones, the candidate cellular and ionic mechanisms through which ATP influences rhythm, and tested the hypothesis that putative rhythmogenic preBötC neurones are uniquely sensitive to ATP. ATP (1 mm) evoked inward currents in all non-respiratory neurones and the majority of respiratory neurons, which included inspiratory, expiratory and putative rhythmogenic inspiratory neurones identified by sensitivity to substance P (1 microM) and DAMGO (50 microM) or by voltage-dependent pacemaker-like activity. ATP current densities were similar in all classes of preBötC respiratory neurone. Reversal potentials and input resistance changes for ATP currents in respiratory neurones suggested they resulted from either inhibition of a K(+) channel or activation of a mixed cationic conductance. The P2YR agonist 2MeSADP (1 mm) evoked only the latter type of current in inspiratory and pacemaker-like neurones. In summary, putative rhythmogenic preBötC neurones were sensitive to ATP. However, this sensitivity was not unique; ATP evoked similar currents in all types of preBötC respiratory neurone. The P2Y(1)R-mediated frequency increase is therefore more likely to reflect activation of a mixed cationic conductance in multiple types of preBötC neurone than excitation of one, highly sensitive group.
Synthesis of Six-Membered Nucleoside Analogs. Part 1: Pyrimidine Nucleosides Based on the 1,3-Dioxane Ring System (1997)

Abstract The synthesis of pyrimidine nucleosides, cis-N-1-[(2-hydroxymethyl)-1,3-dioxan-5-yl]uracil (4) cis-N-1-[(2-hydroxymethyl)-1,3-dioxan-5-yl]thymine (5) and cis-N-1-[(2-hydroxymethyl)-1,3-dioxan-5-yl]cytosine (6) and their corresponding trans isomers is described. Compound 4 showed modest, selective activity against human immunodeficiency virus in acutely infected primary human lymphocytes.
Early Interstitial Lung Disease in Familial Pulmonary Fibrosis (2007)

Asymptomatic ILD in individuals at risk of developing familial IPF can be identified using high-resolution computed tomography scan of the chest, especially in those with a history of smoking. Lung biopsies from individuals in this cohort with early asymptomatic lung disease demonstrate various histologic subtypes of ILD.
Evaluation of bisphenylthiazoles as a promising class for combating multidrug-resistant fungal infections (2021)

To minimize the intrinsic toxicity of the antibacterial agent hydrazinyloxadiazole 1, the hydrazine moiety was replaced with ethylenediamine (compound 7). This replacement generated a potent antifungal agent with no antibacterial activity. Notably, use of a 1,2-diaminocyclohexane moiety, as a conformationally-restricted isostere for ethylenediamine, potentiated the antifungal activity in both the cis and trans forms of N-(5-(2-([1,1'-biphenyl]-4-yl)-4-methylthiazol-5-yl)-1,3,4-oxadiazol-2-yl)cyclohexane-1,2-diamine (compounds 16 and 17). Both compounds 16 and 17 were void of any antibacterial activity; nonetheless, they showed equipotent antifungal activity in vitro to that of the most potent approved antifungal agent, amphotericin B. The promising antifungal effects of compounds 16 and 17 were maintained when assessed against an additional panel of 26 yeast and mold clinical isolates, including the Candida auris and C. krusei. Furthermore, compound 17 showed superior activity to amphotericin B in vitro against Candida glabrata and Cryptococcus gattii. Additionally, neither compound inhibited the normal human microbiota, and both possessed excellent safety profiles and were 16 times more tolerable than amphotericin B.
Effect of Stereogenic Centers on the Self-Sorting, Depolymerization, and Atropisomerization Kinetics of Porphyrin-Based Aggregates (2011)

We present our results on the mixing of different porphyrin molecules in supramolecular assemblies. Herein, chiral amplification experiments reveal the subtle role of the structural (mis)match between these monomers. We show that according to the "sergeant-and-soldiers" principle, a chiral porphyrin "sergeant" efficiently mixes with achiral "soldiers" in the same helical aggregate and strongly biases its handedness. However, when we mix two porphyrin enantiomers in a majority-rules experiment, no chiral amplification is observed at all, which is due to their narcissistic self-sorting into conglomerate-like aggregates. The mixing between two enantiomers in the same stack only occurs in a diluted-majority-rules experiment, in which enantiomeric mixtures of sergeants are diluted with achiral soldiers. The different outcomes of these chiral amplification phenomena are verified by modeling studies that reveal high mismatch penalties, which are ascribed to the high stereocenter loading of 12 methyl groups onto the monomers. Mixed-metal chiral amplification experiments between copper- and zinc-porphyrins show the same distinction in their mixing behavior, which is further supported by fluorescence measurements. The selective removal of chiral Zn-porphyrins from these mixed-metal systems is performed with the Lewis base quinuclidine that depolymerizes the Zn-porphyrins upon axial ligation. This extraction process proceeds at different time scales, depending on the mixed state: slow extraction kinetics for the mixed sergeant-and-soldiers and diluted-majority-rules systems and an instant extraction for the phase-separated majority-rules system. By simultaneously monitoring the supramolecular chirality during extraction, a chiral memory effect is observed for both mixed systems that show slow extraction kinetics. For the sergeant-and-soldiers system, the remaining supramolecular backbone contains achiral monomers only, which give rise to a long lasting chiral memory with slow, entropy-driven atropisomerization. Yet in case of the diluted-majority-rules system, the remaining backbone contains a mixture of achiral and chiral monomers in its unpreferred helicity; giving rise to a short chiral memory, in which the fast atropisomerization is enthalpy-driven due to the high mismatch penalty.
Reconfigurable nanowire assembly enabled field-switchable broadband polarizers (2017)

In this paper, a switchable broadband polarizer based on the electric field directed reconfigurable assembly of gold nanowires (NWs) is presented. Taking advantage of the collective optical properties of the two-dimensional gold NW lattices, we have experimentally demonstrated that transmission of linear polarized light can be purposely controlled using a dual electrode design to reversibly rotate the lattice by 90° on-demand. In addition, our experiments reveal that the transmission control is closely related to the geometrical dimensions of the NWs as well as the applied electric field conditions.
Endocrinologic Control of Men’s Sexual Desire and Arousal/Erection (2016)

Endocrine abnormalities are common in patients with sexual dysfunction. Their identification and treatment is strongly encouraged in disturbances of sexual desire and arousal.