gebhart/patrepeval huggingface dataset:
Targeted Disruption of Aldh1a1 (Raldh1) Provides Evidence for a Complex Mechanism of Retinoic Acid Synthesis in the Developing Retina (2003)

Genetic studies have shown that retinoic acid (RA) signaling is required for mouse retina development, controlled in part by an RA-generating aldehyde dehydrogenase encoded by Aldh1a2 (Raldh2) expressed transiently in the optic vesicles. We examined the function of a related gene, Aldh1a1 (Raldh1), expressed throughout development in the dorsal retina. Raldh1(-/-) mice are viable and exhibit apparently normal retinal morphology despite a complete absence of Raldh1 protein in the dorsal neural retina. RA signaling in the optic cup, detected by using a RARE-lacZ transgene, is not significantly altered in Raldh1(-/-) embryos at embryonic day 10.5, possibly due to normal expression of Aldh1a3 (Raldh3) in dorsal retinal pigment epithelium and ventral neural retina. However, at E16.5 when Raldh3 is expressed ventrally but not dorsally, Raldh1(-/-) embryos lack RARE-lacZ expression in the dorsal retina and its retinocollicular axonal projections, whereas normal RARE-lacZ expression is detected in the ventral retina and its axonal projections. Retrograde labeling of adult Raldh1(-/-) retinal ganglion cells indicated that dorsal retinal axons project to the superior colliculus, and electroretinography revealed no defect of adult visual function, suggesting that dorsal RA signaling is unnecessary for retinal ganglion cell axonal outgrowth. We observed that RA synthesis in liver of Raldh1(-/-) mice was greatly reduced, thus showing that Raldh1 indeed participates in RA synthesis in vivo. Our findings suggest that RA signaling may be necessary only during early stages of retina development and that if RA synthesis is needed in dorsal retina, it is catalyzed by multiple enzymes, including Raldh1.
Role of the electronic structure on the relationship between the crystallinity of CoFe and its tunneling magnetoresistance (2009)

The influence of the crystallinity of CoFe on tunneling magnetoresistance is investigated in magnetic tunnel junctions with an amorphous Al2O3 tunnel barrier. An enhancement in the tunneling magnetoresistance is found when the CoFe is made amorphous compared to when it is crystalline. Ab initio electronic structure calculations show substantial differences in the band structures of crystalline and amorphous forms of bulk CoFe alloys but a decreased spin polarization at the Fermi energy in the amorphous phase. We speculate that the increased tunneling magnetoresistance is rather due to changes in bonding at the interface between Al2O3 and CoFe.
The association of germline HSD3B1 genotype with outcomes in metastatic hormone-sensitive prostate cancer (mHSPC) treated with androgen deprivation therapy (ADT) with or without enzalutamide (ENZA) [ARCHES]. (2022)

5022 Background: A common missense-encoding germline polymorphism in HSD3B1(1245A→C) stabilizes the 3βHSD1 enzyme and increases the rate-limiting step for metabolic flux from adrenal precursors to potent androgens. This adrenal-permissive HSD3B1(1245C) allele mechanistically drives more rapid progression after ADT in nonmetastatic and low-volume (LV) mHSPC. It is unknown whether upfront treatment with ENZA could improve these poor outcomes. We sought to determine the association between the HSD3B1 genotype and outcomes in ARCHES, a randomized, placebo (PBO)-controlled, phase 3 global study of ADT with ENZA or PBO in mHSPC. Overall, 31.3% of men on placebo crossed over to ENZA prior to progression. Methods: Germline DNA from 660 men (243 LV and 417 high volume [HV]) in ARCHES was genotyped for HSD3B1. Radiographic progression-free survival (rPFS), prostate-specific antigen (PSA) outcomes, and overall survival (OS) were compared between men who inherited 0 (adrenal restrictive) vs. 1–2 copies of the HSD3B1(1245C) allele (adrenal permissive) using log-rank tests, Kaplan-Meier estimates, and Cox proportional hazards models for hazard ratios (HRs). Results: In ARCHES, 340 and 320 men had the adrenal-restrictive and adrenal-permissive HSD3B1 genotype, respectively. The adrenal-permissive genotype was not associated with worse rPFS, time to PSA progression (TTPP), or OS. Cox model HRs for death in the adrenal-permissive compared with adrenal-restrictive men in the ENZA + ADT and PBO + ADT arms were 1.21 (95% confidence interval [CI] 0.84, 1.74) and 1.48 (95% CI 0.98, 2.25), respectively. Three-year OS was 82% and 73% in men treated with ENZA + ADT with restrictive vs. permissive genotypes, respectively, and 68% and 70% in men treated with PBO + ADT. ENZA significantly improved rPFS, TTPP, and OS, irrespective of genotype. HRs for ENZA + ADT vs. PBO + ADT in models adjusted for genotype were: rPFS, 0.64 (p &lt; 0.001); TTPP, 0.27 (p &lt; 0.001), and OS, 0.62 (p &lt; 0.001). Of OS events in the HSD3B1-genotyped men, 48 (23%) and 163 (77%) deaths occurred in the LV and HV groups, respectively. Conclusions: In men with mHSPC, ENZA improved OS, rPFS, and TTPP over PBO + ADT, irrespective of HSD3B1 genotype. Survival analysis of HSD3B1-genotyped men in this study is largely driven by men with HV disease. The analysis of men with LV disease was limited by the small number of events. Clinical trial information: NCT02677896.
Molecular genetic analysis of three AIDS-associated neoplasms of uncertain lineage demonstrates their B-cell derivation and the possible pathogenetic role of the Epstein-Barr virus (1989)

Each of three individuals with acquired immunodeficiency syndrome (AIDS) developed a pleomorphic malignant neoplasm in which a precise histopathologic diagnosis could not be rendered. In each case, the tumor cells expressed leukocyte common antigen and a variable constellation of antigens associated with B- and T-cell activation (HLA- DR, T9, T10, BL2, BL3, Ki-24, BLAST-2). They lacked all B cell, T cell, myeloid, and monocyte lineage-restricted antigens, resulting in their classification as hematopoietic neoplasms of uncertain lineage. However, antigen receptor gene rearrangement analysis demonstrated that each of these three neoplasms exhibited clonal immunoglobulin heavy chain and kappa light chain gene rearrangements and lacked T-cell receptor beta chain gene rearrangements and therefore were B cell- derived non-Hodgkin's lymphomas (NHL) representative of an equivalent, relatively mature stage of B-cell differentiation. In contrast with most AIDS-associated NHLs, each of these three neoplasms lacked c-myc gene rearrangements and contained Epstein-Barr virus (EBV) proteins and/or sequences. These studies demonstrate that these three AIDS- associated neoplasms of uncertain lineage exhibit a strikingly similar constellation of distinctly uncommon morphologic, immunophenotypic, and molecular genetic characteristics that distinguishes them substantially from the vast majority of NHLs that have been reported to occur in association with AIDS. The consistent presence of EBV proteins and/or DNA sequences suggests that the Epstein-Barr virus played a pathogenetic role in the development of these three AIDS-associated neoplasms. Finally, these studies further illustrate the utility of antigen receptor gene rearrangement analysis in the diagnosis and classification of hematopoietic neoplasms of uncertain lineage.
106 Senescence as a therapeutic target for myocardial ageing (2018)

Ageing is the biggest risk factor for impaired cardiovascular health, cardiovascular disease being the leading cause of death in 40% of individuals over 65 years old. Ageing is associated not only with an increased prevalence of cardiovascular disease but also with a poorer prognosis, including increased mortality or incidence of heart failure after myocardial infarction (MI). We have demonstrated that aged (23 month old) mice have an accumulation of cardiomyocyte senescence, reduced regenerative potential and display increased mortality as well as impaired recovery following MI. Cellular senescence is defined not only by the irreversible loss of division potential but also by the production of a senescence-associated secretory phenotype (SASP). This cocktail of pro-inflammatory cytokines, chemokines, matrix proteases and growth factors can impact on tissue function, inducing fibrosis, extracellular matrix degeneration and driving inflammation. We have therefore begun to test if clearance of senescent cardiomyocytes, using the senolytic compound Navitoclax, has the potential to improve cardiac health and post MI outcomes in aged animals. Following treatment with Navitoclax, but prior to MI, aged mice demonstrated a reduction in senescent cardiomyocytes which was associated increased cardiomyocyte generation, a decline in myocardial hypertrophy and a decrease in fibrosis. Following MI, Navitoclax treated mice displayed a tendency towards improved survival and had a significant improvement in cardiac function when compared to vehicle controls. We conclude that clearance of senescent cells is a potential therapeutic strategy for the treatment of age related cardiac dysfunction.
Realize, Analyze, Engage (RAE): A Digital Tool to Support Recovery from Substance Use Disorder (2021)

The RAE platform is a potentially powerful tool to de-escalate stress and craving outside of the clinical milieu, and to connect with a support system needed most. RAE also aims to provide clinicians with actionable insight to understand patients' level of risk, and contextual clues for their triggers in order to provide more personalized recovery support.
Extending the lifetime of blue phosphorescent OLEDs (Conference Presentation) (2017)

Since its first demonstration in 1998, electrophosphorescence has yielded 100% internal quantum efficiency OLEDs (PHOLEDs) across the color gamut. This advance has given birth to a huge global OLED display industry, now estimated to be >$15B, or more than 10% of all displays made. While red and green devices have shown extraordinary operational lifetimes, blue PHOLEDs have had unacceptably short lifetimes. In this talk I discuss the fundamental origins of this deficiency1, and approaches to extending the lifetime of blue PHOLEDs. Indeed, recent results in our laboratory have already yielded a 10 fold improvement in lifetime, the first such major improvement in almost a decade2. The understanding gained from these experiments suggest that much longer lifetimes, even for very deep blue emitting PHOLEDs, is possible. In particular, I will discuss the use of hot excited state managers as a means to greatly extend the lifetime of blues for both displays and lighting. 1. N. C. Giebink, B. W. D’Andrade, M. S. Weaver, P. B. Mackenzie, J. J. Brown, M. E. Thompson and S. R. Forrest, J. Appl. Phys. 103, 044509 (2008). 2. Y. Zhang, J. Lee and S. R. Forrest, Nature Commun. 5, 5008 (2014).
Linear Analysis of Thermo-hydraulic Instabilities of the Advanced Heavy Water Reactor (AHWR) (1998)

Analysis was carried out to predict the threshold of instability for Ledinegg type and density wave oscillations for the Indian Advanced Heavy Water Reactor (AHWR) which is a Natural Circulation Pressure Tube Type Boiling Water Reactor. The mathematical model considers homogeneous two-phase flow and the conservation equations are solved analytically to obtain the steady state thermo-hydraulic characteristics and flow stability map. The model was applied for the AHWR concept after it had been validated with the test data obtained from a simple forced circulation loop with small parallel boiling channels and from the High Temperature Loop (PNC). The results indicate that the proposed design configuration of the AHWR may experience both Ledinegg type (static instability) and Type-I and Type-II density wave oscillations depending on the operating condition. The effects of various geometric and operating parameters on these types of instabilities were studied. It can be seen from the results that the Ledinegg type instability is suppressed with an increase in pressure and disappears when the operating pressure is higher than 0.7MPa. But the density wave instability may occur even at 7 MPa. In addition, it is found that for parallel multiple channels operating under natural circulation condition, the stability of density wave instability is not always enhanced by increasing the throttling coefficients at the inlet of channels.
Multidisciplinary Approach and Outcomes of Pretreatment Small (cT1a) Renal Mass Biopsy: Single-Center Experience (2022)

<b><i>Purpose:</i></b> We evaluated our experience of a multidisciplinary approach to renal mass biopsy (RMB) for small renal masses (SRMs) employing in-office ultrasound (US)-guided biopsy by urology (24%), CT, or US biopsy by interventional radiology (IR) (79%), and endoscopic ultrasound (EUS)-guided biopsy by gastroenterology (GI) (4%). <b><i>Materials and Methods:</i></b> A single-institution retrospective review of patients who underwent RMB for SRM from May 2013 to August 2019 was conducted. Data regarding patient demographics, tumor characteristics, biopsy technique, histopathology, and management were collected. Diagnostic rates, concordance with final pathology, complications, and outcomes were analyzed. <b><i>Results:</i></b> Of the 192 biopsies reviewed, 63% biopsies were malignant, 20% were benign, and 17% were nondiagnostic. Based on biopsy results, 71 patients (37%) elected active surveillance. Thirty-eight (20%) patients underwent cryoablation, 56 (29%) underwent partial nephrectomy, 14 (7%) underwent radical nephrectomy, and the remaining patients were treated elsewhere. The rate of surgery for benign pathology after pretreatment RMB was 3%. The concordance rate between biopsy and final pathology was 99% for malignancy, 96% for specific pathology subtype, and 85% for renal cell carcinoma grade. Median time from diagnosis to definitive treatment was 97 days (urology: 76, IR: 110 and GI: 54, <i>p</i> = 0.002). Three (1.6%) Clavien I complications were reported. <b><i>Conclusion:</i></b> Our multidisciplinary approach to RMB for clinical stage T1a demonstrated favorable safety and diagnostic rates, which effectively directed management strategies and minimized surgery for benign disease. Urologist-performed office biopsies significantly shortened the time from diagnosis to definitive treatment. Our experience with GI EUS biopsy has demonstrated feasibility and safety for tumors that were otherwise not accessible percutaneously.
The Programmable Logic-in-Memory (PLiM) Computer (Invited) (2016)

Realization of logic and storage operations in memristive circuits have opened up a promising research direction of in-memory computing. Elementary digital circuits, e.g., Boolean arithmetic circuits, can be economically realized within memristive circuits with a limited performance overhead as compared to the standard computation paradigms. This paper takes a major step along this direction by proposing a fully-programmable in-memory computing system. In particular, we address, for the first time, the question of controlling the in-memory computation, by proposing a lightweight unit managing the operations performed on a memristive array. Assembly-level programming abstraction is achieved by a natively-implemented majority and complement operator. This platform enables diverse sets of applications to be ported with little effort. As a case study, we present a standardized symmetric-key cipher for lightweight security applications. The detailed system design flow and simulation results with accurate device models are reported validating the approach.
Analysis and Application of a Surface Admittance Operator for Combined Magnetic and Dielectric Contrast in Emerging Interconnect Topologies (2023)

In state-of-the-art interconnect design, topologies including magnetic materials, such as the so-called superlattice conductors, are rapidly emerging as a novel strategy to handle the challenges associated with the evolution toward higher operating frequencies and integration densities. Consequently, it is imperative that the newly developed full-wave electromagnetic solvers rigorously model these innovative materials and still accurately capture phenomena such as the skin and proximity effect in good conductors. In this article, we propose such a method to rigorously characterize this important class of interconnects with arbitrary, possibly frequency-dependent, material properties, including combined dielectric and magnetic contrast. To that end, a 2-D differential surface admittance (DSA) operator is used, which invokes a single-source equivalence theorem to model both nonmagnetic and magnetic conductors efficiently. This operator is combined with the electric field integral equation (EFIE), yielding a comprehensive formalism to extract the pertinent per-unit-of-length (p.u.l.) resistance and inductance parameters of the modeled structures. The numerical properties of our technique are studied in detail, with particular attention to the influence of magnetic materials. Finally, various relevant application examples are considered to establish its correctness and versatility.
A critical examination of submicron optical lithography using simulated projection images (1983)

It may be possible to extend optical lithography well into the submicron regime, given a multilayer resist system that confines imaging to a thin layer, and that eliminates reflection from the substrate. The necessary exposure and focus tolerances are determined by simulating the projection of partially coherent, diffraction-limited images onto an ideal multilayer resist system. Exposure–defocus diagrams are then generated by requiring that critical dimensions satisfy a ±10% tolerance. We investigate the prospects for submicron lithography with 0.75 and 0.5 μm minimum features. Two lens systems are analyzed; a commercially available 0.28 NA lens operating at 436 nm, and an advanced 0.35 NA lens operating at 365 nm. The features studied include contact holes, rectangular lines and spaces, and equal line space gratings, and are representative of many typical IC mask patterns. Linewidth tailoring or biasing allows these features to be printed within tolerance simultaneously if the exposure can be controlled within ±6%. The corresponding depth of focus is about 3 μm for the 0.75 μm features, and 1.5 μm for the 0.5 μm features. More general shape correction may be needed to print objects of arbitrary complexity.
Regulation of skeletal muscle hexokinase II by insulin in nondiabetic and NIDDM subjects. (1998)

Impaired muscle glucose phosphorylation to glucose-6-phosphate by hexokinases (HKs)-I and -II may contribute to insulin resistance in NIDDM and obesity. HK-II expression is regulated by insulin. We tested the hypothesis that basal and insulin-stimulated expression of HK-II is decreased in NIDDM and obese subjects. Skeletal muscle HK-I and HK-II activities were measured in seven lean and six obese normal subjects and eight patients with NIDDM before and at 3 and 5 h of a hyperinsulinemic (80 mU x m(-2) x min(-1)) euglycemic clamp. To assess whether changes in HK-II expression seen during a glucose clamp are likely to be physiologically relevant, we also measured HK-I and HK-II activity in 10 lean normal subjects before and after a high-carbohydrate meal. After an overnight fast, total HK, HK-I, and HK-II activities were similar in lean and obese control subjects; but HK-II was lower in NIDDM patients than in lean subjects (1.42 +/- 0.16 [SE] vs. 2.33 +/- 0.24 nmol x min(-1) x mg(-1) molecular weight, P < 0.05) and accounted for a lower proportion of total HK (33 +/- 3 vs. 47 +/- 3%, P < 0.025). HK-II (but not HK-I) activity increased during the clamp in lean and obese subjects by 34 and 36% after 3 h and by 14 and 22% after 5 h of hyperinsulinemia; no increase was found in the NIDDM patients. In the lean subjects, muscle HK-II activity also increased by 15% 4 h after the meal, from 2.47 +/- 0.19 basally to 2.86 +/- 0.28 nmol x min(-1) x mg(-1) protein (P < 0.05). During the clamps, muscle HK-II activity correlated with muscle citrate synthase activity in the normal subjects (r = 0.58, P < 0.05) but not in the NIDDM patients. A weak relationship was noted between muscle HK-II activity and glucose disposal rate at the end of the clamp when all three groups were combined (r = 0.49, P < 0.05). In summary, NIDDM patients have lower muscle HK-II activity basally and do not increase the activity of this enzyme in response to a 5-h insulin stimulus. This defect may contribute to their insulin resistance. In nondiabetic obese subjects, muscle HK-II expression and its regulation by insulin are normal.
Meat and bone meal as fertilizer for oats - From slaughter house waste to fertilizer (2009)

EU permitted in 2006 the use of meat bone meal(MBM) as fertilizer. MTT Agrifood Research Finland's Kannus conducted a field experiment from 2000 to 2003 with a supplement experiment in 2004. The fertilization effect was 24 % higher after MBM than after chemical fertilizers.
[P4–095]: NILOTINIB REDUCES PHOSPHORYLATED NEUROFILAMENTS AND CORRELATES WITH COGNITIVE IMPROVEMENT IN PARKINSON's DISEASE WITH DEMENTIA AND LEWY BODY DEMENTIA (2017)

Parkinson's disease (PD) is a neurodegenerative disorder that affects motor and non-motor functions. Our pre-clinical data indicate that the tyrosine kinase inhibitor (TKI) Nilotinib improves motor behavior and cognition in several models of neurodegeneration. Nilotinib is FDA-approved for the treatment of chronic myeloid leukemia (CML) at 800mg oral dose twice daily. This is a retrospective biomarker study of an open-label clinical study to examine the safety and efficacy of lower doses (<50% of CML dose) of Nilotinib in human. We randomized 12 participants with mid-late stage PD with dementia (PDD) or Lewy body dementia (LBD) into 150mg (n=5) or 300mg (n=7) groups, who received oral daily doses of Nilotinib for 6 months. We found that most patients who received 150mg Nilotinib were diagnosed with LBD and treatment resulted in cognitive improvement as measured by Mini-Mental Status Exam (MMSE). ELISA measurement of CSF cell death marker (phosphorylated) p-neurofilament was significantly reduced. The change in CSF biomarkers correlated (Pearson's R) with improvement in MMSE (3 points) in LBD patients. Patients who received 300mg Nilotinib were diagnosed with PD or PDD and also showed significant reduction in CSF p-neurofilaments between baseline and 6 months treatment. MMSE was improved (4 points) in these patients. There was a correlation (Pearson's R) between reduction in CSF p-neurofilaments and MMSE (3 points) in PD and PDD. Nilotinib significantly reduces cell death marker p-neurofilaments in CSF in both 150mg (LBD) and 300mg (PDD) groups and this reduction in p-neurofilaments correlates with cognitive improvement, suggesting that p-neurofilaments may be a good biomarker that correlates with clinical cognitive outcomes. These data indicate that further clinical studies are needed to determine the effects of Nilotinib in dementia, including AD and LBD.
Building a Parallel Spatio-Temporal Data-Text Corpus for Summary Generation (2008)

We describe a corpus of naturally occurring road ice weather forecasts and the associated weather prediction data they are based upon. We also show how observations from an analysis of this corpus have been applied to build a prototype Natural Language Generation (NLG) system for producing road ice forecasts. While this corpus occurs in a narrow domain, it has much wider applicability due to the nature of its spatial descriptions, whose primary communicative goal is to describe the interaction between meteorological parameters and geographic features. 1.