gebhart/patrepeval huggingface dataset:
AB007. SOH22ABS130. The role of routine sentinel lymph node biopsy in elderly patients with breast cancer (2022)

Background: Recent guidelines from the Society of Surgical Oncology recommended against the routine use of sentinel lymph biopsy (SLN) in women over the age of 70 years with pT1 ER-positive breast cancer. The aim of this study was to evaluate the use of axillary staging with SLN in patients aged older than 70 with early-stage breast cancer. Methods: A retrospective review identified all women over 70 years of age with a new diagnosis of invasive breast cancer who proceeded to therapeutic surgery between 2011 and 2020 at St. Vincent’s Hospital, Dublin. All patients proceeded to therapeutic surgery. All patients had an axillary ultrasound at diagnosis. Clinicopathological data was assessed. Final pathological stage for patients who received axillary staging with SLN were assessed. Results: Of 1,360 women aged over 70 at time of diagnosis during the study period, 474 patients (mean age of 80 years) underwent a wide local excision and SLN. Of these, 217 (46%) had a final pathological stage of pT1 and a tumour that was ER positive. Within this group 79% had a negative SLNB (pN0). The rate of SLN positivity was higher in those with pT2 disease at 34% (P=0.005). Conclusions: Axillary staging with SLN is still routinely employed for patients older than age 70 who proceed to surgery for treatment of their breast cancer with a >20% positivity rate, even in those with pT1 disease. Efforts to reduce SLNB use in this cohort should incorporate both assessments of patient frailty and tumour parameters that allow estimates of sentinel node positivity.
Dual Mobility Acetabular Cups in Primary Total Hip Arthroplasty in Patients at High Risk for Dislocation. (2017)

At short-term follow-up, dual-mobility articulations in primary THA offer survivorship, outcomes, and complications comparable to conventional THA designs in patients who are at increased risk for postoperative dislocation. Serious complications, such as polyethylene wear and intraprosthetic dislocations, have occasionally been reported with the use of these components. Therefore, future studies should be prospective, multi-center, and have longer-term follow-up to determine the true benefit of modular dual-mobility articulations in patients who are at high risk for dislocation.
Designing Cyclic Universe Models (2004)

The phenomenological constraints on the scalar field potential in cyclic models of the Universe are presented. We show that cyclic models require a comparable degree of tuning to that needed for inflationary models. The constraints are reduced to a set of simple design rules including "fast-roll" parameters analogous to the "slow-roll" parameters in inflation.
Reactions of Cationic Palladium(II) Methyl and Vinyl Complexes with Alkynes (1998)

[(phen)Pd(CH3)(OEt2)]+[BAr‘4]- (phen = 1,10 phenanthroline, Ar‘ = 3,5-(CF3)2C6H3) reacts with RC⋮CR‘ to form the η2-alkyne complexes [(phen)Pd(CH3)(η2-RC⋮CR‘]+[BAr‘4]- (5a, R = R‘ = SiMe3; 5b, RC6H5, R‘ = H). In contrast, the reaction of the diimine complexes [(ArNC(R)C(R)NAr)Pd(CH3)(NCCH3)]+[BAr‘4]- (1−3) (Ar = 2,6-(CH3)2C6H3, 2,6-(i-Pr)2C6H3; R = H, CH3, 1/2BIAN) with HC⋮CR‘ (R‘ = H, t-Bu) yielded the alkyne insertion products [(ArNC(R)C(R)NAr)Pd(CHC(R)CH3)(NCCH3)]+[BAr‘4]- (3) while the reaction of 1-hexyne with 1a yielded a mixture of the 2,1- and 1,2-insertion products [(N−N)Pd(C(C4H9)CHCH3)(NCCH3)]+[BAr‘4]- and [(N−N)Pd(CHC(C4H9)(CH3)(NCCH3)]+[BAr‘4]-, respectively. The vinyl complexes [(N−N)Pd(CHCRCH3)(NCCH3)]+[BAr‘4]- react with acetylene to form the η1-dienyl complexes [(N−N)Pd(CHCHCHCRCH3)(NCCH3)]+[BAr‘4]-, which then react with acetylene and rearrange to form the novel 5-ethylidene-2-cyclopenten-1-yl complexes [(N−N)Pd(η3-C(CH3)(R)C5H5)]+[X]-. (R = H, t-Bu; X = BAr‘4, O3SCF3) (8).
Interspecies Heterogeneity in the Hepatic Transcriptomic Response to AHR Activation by Dioxin (2011)

This chapter contains sections titled: Motivation and Overview Why Focus on the Liver? Techniques and Approaches Rat Versus Mouse Humans Versus Rodents Unanswered Questions Conclusions References
Electron conducting buffer layers in organic photovoltaics (2011)

It is common to incorporate a cathode-side buffer layer in organic photovoltaic devices (OPVs) to mitigate damage from the evaporation of metal onto the underlying acceptor layer (e.g. C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">60</sub> ), which can lead to exciton quenching and/or a barrier to charge extraction. Additionally, these materials can act as both an optical spacer and an exciton blocking layer. One class of buffer layers consists of a wide bandgap material (e.g. bathocuproine), that transports carriers via damage-induced midgap states. A second class of buffers consists of a material such as tris(acetylacetonato) ruthenium(III) (Ru(acac) <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> ), which has a small highest occupied molecular orbital (HOMO) energy. In that case, electrons from the C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">60</sub> and holes from the cathode recombine at the C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">60</sub> /Ru(acac) <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> interface. In this work, we introduce a third class of buffer that, due to alignment of its lowest unoccupied molecular orbital with that of the acceptor, allows for low resistance transport of electrons between the acceptor and cathode. By utilizing 3,4,9,10 perylenetetracarboxylic bisbenzimidazole (PTCBI) as a buffer layer, we show improved fill factor in squaraine/C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">60</sub> -based devices without a loss in open-circuit voltage or photocurrent, leading to a >;20% increase in power conversion efficiency. Although limited exciton transfer occurs from C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">60</sub> to PTCBI, the short exciton diffusion length of PTCBI, coupled with the lack of loss at the C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">60</sub> /PTCBI interface, suggests that PTCBI also blocks excitons from quenching at metal-induced defects that are present in the absence of a buffer layer.
Connecting the Dots Between MLE and RL for Sequence Prediction (2018)

Sequence prediction models can be learned from example sequences with a variety of training algorithms. Maximum likelihood learning is simple and efficient, yet can suffer from compounding error at test time. Reinforcement learning such as policy gradient addresses the issue but can have prohibitively poor exploration efficiency. A rich set of other algorithms such as RAML, SPG, and data noising, have also been developed from different perspectives. This paper establishes a formal connection between these algorithms. We present a generalized entropy regularized policy optimization formulation, and show that the apparently distinct algorithms can all be reformulated as special instances of the framework, with the only difference being the configurations of a reward function and a couple of hyperparameters. The unified interpretation offers a systematic view of the varying properties of exploration and learning efficiency. Besides, inspired from the framework, we present a new algorithm that dynamically interpolates among the family of algorithms for scheduled sequence model learning. Experiments on machine translation, text summarization, and game imitation learning demonstrate the superiority of the proposed algorithm.
Expression of the human germinal center-associated lymphoma (HGAL) protein, a new marker of germinal center B-cell derivation (2005)

We identified the human germinal center-associated lymphoma (HGAL) in gene-expression profiling studies of diffuse large B-cell lymphoma (DLBCL). The expression of HGAL correlated with survival in patients with DLBCL. The HGAL gene is the human homolog of M17, a mouse gene expressed specifically in normal germinal center (GC) B cells. We generated a monoclonal antibody against the HGAL protein and show that HGAL is expressed in the cytoplasm of GC lymphocytes and in lymphomas of GC derivation. Among 727 lymphomas tested by immunohistochemistry on tissue microarrays, HGAL staining was found in follicular lymphomas (103 of 107), Burkitt lymphomas (40 of 40), mediastinal large B lymphomas (7 of 8), and in DLBCLs (103 of 151). Most marginal zone lymphomas lacked HGAL staining. Lymphocyte-predominant Hodgkin lymphomas (12 of 17) and, surprisingly, classical Hodgkin lymphomas (78 of 107) were found to be positive. Hierarchical clustering of comparative immunohistologic results in DLBCLs demonstrates that the expression of HGAL is similar to 2 other GC-associated proteins, BCL6 and CD10, but different from 2 markers associated with a non-GC phenotype, MUM1/IRF4 and BCL2. The restricted expression and GC specificity of HGAL protein suggest that it may have an important role in the diagnosis of specific lymphomas, and, potentially in the identification of subtypes associated with different prognoses.
Association between asthma, rhinitis, and conjunctivitis multimorbidities with molecular IgE sensitization in adults (2018)

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Contribution of the Global Regulator Gene gacA to Persistence and Dissemination of Pseudomonas fluorescens Biocontrol Strain CHA0 Introduced into Soil Microcosms (1994)

Structural and regulatory genes involved in the synthesis of antimicrobial metabolites are essential for the biocontrol activity of fluorescent pseudomonads and, in principle, amenable to genetic engineering for strain improvement. An eventual large-scale release of such bacteria raises the question of whether such genes also contribute to the persistence and dissemination of the bacteria in soil ecosystems. Pseudomonas fluorescens wild-type strain CHA0 protects plants against a variety of fungal diseases and produces several antimicrobial metabolites. The regulatory gene gacA globally controls antibiotic production and is crucial for disease suppression in CHA0. This gene also regulates the production of extracellular protease and phospholipase. The contribution of gacA to survival and vertical translocation of CHA0 in soil microcosms of increasing complexity was studied in coinoculation experiments with the wild type and a gacA mutant which lacks antibiotics and some exoenzymes. Both strains were marked with spontaneous resistance to rifampin. In a closed system with sterile soil, strain CHA0 and the gacA mutant multiplied for several weeks, whereas these strains declined exponentially in nonsterile soil of different Swiss origins. The gacA mutant was less persistent in nonrhizosphere raw soil than was the wild type, but no competitive disadvantage when colonizing the rhizosphere and roots of wheat was found in the particular soil type and during the period studied. Vertical translocation was assessed after strains had been applied to undisturbed, long (60-cm) or short (20-cm) soil columns, both planted with wheat. A smaller number of cells of the gacA mutant than of the wild type were detected in the percolated water and in different depths of the soil column. Single-strain inoculation gave similar results in all microcosms tested. We conclude that mutation in a single regulatory gene involved in antibiotic and exoenzyme synthesis can affect the survival of P. fluorescens more profoundly in unplanted soil than in the rhizosphere.
Troubleshooting: Interpreting Diagnostic Information to Ensure Appropriate Function (2012)

Pacemakers, defibrillators, and resynchronization devices have become increasingly complex. At times, either due to component malfunction or parameter settings that do not properly match the clinical situation, cardiac electronic devices do not deliver (or withhold) therapy appropriately. The systematic approach to the patient with a potentially malfunctioning device, the acquisition and interpretation of diagnostic information, and the strategies used to correct the malfunction are reviewed in this chapter. Troubleshooting may at times be the most challenging aspect of device management, yet is often the most rewarding, due to the significant clinical impact it offers.
Targeting CCR7-PI3Kγ overcomes resistance to tyrosine kinase inhibitors in ALK-rearranged lymphoma (2023)

Anaplastic lymphoma kinase (ALK) tyrosine kinase inhibitors (TKIs) show potent efficacy in several ALK-driven tumors, but the development of resistance limits their long-term clinical impact. Although resistance mechanisms have been studied extensively in ALK-driven non-small cell lung cancer, they are poorly understood in ALK-driven anaplastic large cell lymphoma (ALCL). Here, we identify a survival pathway supported by the tumor microenvironment that activates phosphatidylinositol 3-kinase γ (PI3K-γ) signaling through the C-C motif chemokine receptor 7 (CCR7). We found increased PI3K signaling in patients and ALCL cell lines resistant to ALK TKIs. PI3Kγ expression was predictive of a lack of response to ALK TKI in patients with ALCL. Expression of CCR7, PI3Kγ, and PI3Kδ were up-regulated during ALK or STAT3 inhibition or degradation and a constitutively active PI3Kγ isoform cooperated with oncogenic ALK to accelerate lymphomagenesis in mice. In a three-dimensional microfluidic chip, endothelial cells that produce the CCR7 ligands CCL19/CCL21 protected ALCL cells from apoptosis induced by crizotinib. The PI3Kγ/δ inhibitor duvelisib potentiated crizotinib activity against ALCL lines and patient-derived xenografts. Furthermore, genetic deletion of CCR7 blocked the central nervous system dissemination and perivascular growth of ALCL in mice treated with crizotinib. Thus, blockade of PI3Kγ or CCR7 signaling together with ALK TKI treatment reduces primary resistance and the survival of persister lymphoma cells in ALCL.
Voxelized Atomic Structure Potentials: Predicting Atomic Forces with the Accuracy of Quantum Mechanics Using Convolutional Neural Networks (2020)

This paper introduces voxelized atomic structure (VASt) potentials as a machine learning (ML) framework for developing interatomic potentials. The VASt framework utilizes a voxelized representation of the atomic structure directly as the input to a convolutional neural network (CNN). This allows for high-fidelity representations of highly complex and diverse spatial arrangements of the atomic environments of interest. The CNN implicitly establishes the low-dimensional features needed to correlate each atomic neighborhood to its net atomic force. The selection of the salient features of the atomic structure (i.e., feature engineering) in the VASt framework is implicit, comprehensive, automated, scalable, and highly efficient. The calibrated convolutional layers learn the complex spatial relationships and multibody interactions that govern the physics of atomic systems with remarkable fidelity. We show that VASt potentials predict highly accurate forces on two phases of silicon carbide and the thermal conductivity of silicon over a range of isotropic strain.
Scanning Laser Vibrometry for Lamb Wave Evaluation of Composite Tubulars (1998)

Abstract This paper is concerned with the development of a technique for long-range ultrasonic nondestructive inspection of composite tubulars. A dry-contact piezoelectric transducer is used to excite Lamb waves in the axial direction. The field scattered by a defect and/or the mode shape distortion caused by the defect is measured by the use of a laser vibrometer. The presence of the defect is indicated by anomalies in the scattered field. The technique was tested on glass/epoxy composite tubes. It is shown that the presence of a defect (for example, a delamination of I ern diameter) can be remotely detected as far away as one meter from the transmitter, and its position can be located with an accuracy of a few centimeters.
A Placebo-Controlled Randomized Trial of Warfarin in Idiopathic Pulmonary Fibrosis (2012)

This study did not show a benefit for warfarin in the treatment of patients with progressive IPF. Treatment with warfarin was associated with an increased risk of mortality in an IPF population who lacked other indications for anticoagulation.
Short-stem anatomical shoulder replacement—a systematic review (2019)

In shoulder arthroplasty, there is a trend for shorter humeral implants to facilitate stem revision and preserve bone stock. This review evaluates the clinical and radiographic outcome of anatomical total shoulder replacement with uncemented humeral short stems. A systematic review was performed using PubMed and Cochrane databases. The search terms “short stem” (all) and “shoulder” (title/abstract) were used. The minimum follow-up was 20 months. The demographic data, clinical outcome (pain, range of motion, outcome scores), radiographic outcome (humeral bone adaptations, humeral loosening, glenoid loosening), risk for high radiographic bone adaptations, complications, and revision were determined. Ten studies comprising 653 shoulder arthroplasties were included in the analysis. At an average follow-up of 20–64 months, the clinical parameters of pain, range of motion, and outcome scores improved significantly in all studies. The most frequent radiographic finding was calcar resorption in 15–71% of patients. High filling ratio, lack of metaphyseal porous coating, and poor bone quality were associated with high bone adaptation. The radiographic changes did not influence the clinical outcome in any study. In 13 of 653 patients (2%), humeral stem loosening was observed leading to stem revision in nine patients, with one study reporting eight of 73 patients with humeral stem loosening. The average weighted complication rate was 6% and the average weighted revision rate was 4%. The short- to medium-term results of uncemented anatomical short-stem shoulder arthroplasty are encouraging and the clinical results are comparable to other 3rd- and 4th-generation shoulder arthroplasties. Further studies with longer follow-up are needed to evaluate and understand why the radiographic changes occur and to prove the theory of bone-sparing revision surgeries.
Optic nerve head sector analysis recognizes glaucoma most effectively around disc poles (1999)

Single sectors located close to the vertical meridian yielded better discrimination than global measurements. When two or more sectors at the superior pole were combined with each other, as well as with their counterparts at the inferior pole, discrimination improved even further. Localized changes concurred frequently, but asymmetrically at both poles of the disc. The depth from reference plane used to define the cup was not critical for separation between normal and glaucomatous eyes.
Tumor FAK orchestrates immunosuppression in ovarian cancer via the CD155/TIGIT axis (2022)

High-grade serous ovarian cancer (HGSOC) is a lethal malignancy characterized by an immunosuppressive tumor microenvironment containing few tumor infiltrating lymphocytes (TILs) and an insensitivity to checkpoint inhibitor immunotherapies. Gains in the PTK2 gene encoding focal adhesion kinase (FAK) at Chr8 q24.3 occur in ∼70% of HGSOC tumors, and elevated FAK messenger RNA (mRNA) levels are associated with poor patient survival. Herein, we show that active FAK, phosphorylated at tyrosine-576 within catalytic domain, is significantly increased in late-stage HGSOC tumors. Active FAK costained with CD155, a checkpoint receptor ligand for TIGIT (T cell immunoreceptor with immunoglobulin and immunoreceptor tyrosine-based inhibitory motif domains), in HGSOC tumors and a selective association between FAK and TIGIT checkpoint ligands were supported by patient transcriptomic database analysis. HGSOC tumors with high FAK expression were associated with low CD3 mRNA levels. Accordingly, late-stage tumors showed elevated active FAK staining and significantly lower levels of CD3+ TILs. Using the KMF (Kras, Myc, FAK) syngeneic ovarian tumor model containing spontaneous PTK2 (FAK) gene gains, the effects of tumor intrinsic genetic or oral small molecule FAK inhibitior (FAKi; VS-4718) were evaluated in vivo. Blocking FAK activity decreased tumor burden, suppressed ascites KMF-associated CD155 levels, and increased peritoneal TILs. The combination of FAKi with blocking TIGIT antibody (1B4) maintained elevated TIL levels and reduced TIGIT+ T regulatory cell levels, prolonged host survival, increased CXCL13 levels, and led to the formation of omental tertiary lymphoid structures. Collectively, our studies support FAK and TIGIT targeting as a rationale immunotherapy combination for HGSOC.
N-Acetyl-glucosamine influences the biofilm formation of Escherichia coli (2018)

This study highlights how catabolism can be involved in biofilm formation of <i>E. coli</i>. Mucus-derived sugars can influence virulence properties of pathogenic <i>E. coli</i> and this study will help us better understand the mechanisms used to prevent colonization of the intestinal mucosa by pathogens.
OmpA influences Escherichia coli biofilm formation by repressing cellulose production through the CpxRA two‐component system (2009)

Previously we discovered that OmpA of Escherichia coli increases biofilm formation on polystyrene surfaces (González Barrios et al., Biotechnol Bioeng, 93:188-200, 2006a). Here we show OmpA influences biofilm formation differently on hydrophobic and hydrophilic surfaces since it represses cellulose production which is hydrophilic. OmpA increased biofilm formation on polystyrene, polypropylene, and polyvinyl surfaces while it decreased biofilm formation on glass surfaces. Sand column assays corroborated that OmpA decreases attachment to hydrophilic surfaces. The ompA mutant formed sticky colonies, and the extracellular polysaccharide that caused stickiness was identified as cellulose. A whole-transcriptome study revealed that OmpA induces the CpxRA two-component signal transduction pathway that responds to membrane stress. CpxA phosphorylates CpxR and results in reduced csgD expression. Reduced CsgD production represses adrA expression and results in reduced cellulose production since CsgD and AdrA are responsible for 3,5-cyclic diguanylic acid and cellulose synthesis. Real-time polymerase chain reaction confirmed csgD and adrA are repressed by OmpA. Biofilm and cellulose assays with double deletion mutants adrA ompA, csgB ompA, and cpxR ompA confirmed OmpA decreased cellulose production and increased biofilm formation on polystyrene surfaces through CpxR and AdrA. Further evidence of the link between OmpA and the CpxRA system was that overproduction of OmpA disrupted the membrane and led to cell lysis. Therefore, OmpA inhibits cellulose production through the CpxRA stress response system, and this reduction in cellulose increases biofilm formation on hydrophobic surfaces.