gebhart/patrepeval huggingface dataset:
Crystal structure of the eukaryotic translation initiation factor 2A from Schizosaccharomyces pombe (2014)

The eukaryotic translation initiation factor 2A (eIF2A) was identified as a factor that stimulates the binding of methionylated initiator tRNA (Met-tRNA i (Met) ) to the 40S ribosomal subunit, but its physiological role remains poorly defined. Recently, eIF2A was shown to be involved in unconventional translation initiation from CUG codons and in viral protein synthesis under stress conditions where eIF2 is inactivated. We determined the crystal structure of the WD-repeat domain of Schizosaccharomyces pombe eIF2A at 2.5 Å resolution. The structure adopts a novel nine-bladed β-propeller fold. In contrast to the usual β-propeller proteins, the central channel of the molecule has the narrower opening on the bottom of the protein and the wider opening on the top. Highly conserved residues are concentrated in the positively-charged top face, suggesting the importance of this face for interactions with nucleic acids or other initiation factors.
Homogeneity and complexity of avian oncornavirus proviral DNA determined by molecular hybridization (1977)

The homogeneity of DNA complementary to the 35S RNA subunit of avian myeloblastosis virus (AMV) has been demonstrated by single or multistep hybridization. For multistep hybridizations, 35S AMV RNA was preselected for its ability to hybridize either to unfractionated leukemic DNA or to leukemic DNA enriched for unique or for reiterated sequences. These experiments indicate that the viral genome is complementary to DNA sequences with a low reiteration frequency. Competition experiments confirm the absence of fast-hybridizing sequences in viral DNA. Computer analyses of the data reveal that there are two to four copies of viral DNA in infected cells.
Resistance to vanadium inPseudomonas fluorescensATCC 17400 caused by mutations in TCA cycle enzymes (2006)

Vanadium inhibits the growth of Pseudomonas fluorescens ATCC 17400 in the low-iron casamino acids medium and even more when iron is added to the medium. Analysis of transposon mutants allowed the isolation of two mutants with increased resistance to vanadium. One mutant had an insertion in the idh gene coding for the tricarboxylic acid enzyme isocitrate dehydrogenase. The second mutant had the transposon inserted into acnD, one out of three genes coding for a 2-methyl-isocitrate dehydratase (aconitase). In this mutant, there was a higher level of acnB aconitase transcripts while the levels of acnA transcripts were unchanged. A nonpolar idh mutant was obtained, which showed the same level of resistance against vanadium as the original transposon mutant.
The genetic bases of HIV-1 neuropathogenesis (2005)

Abstract Like many retroviruses human immunodeficiency virus type 1 (HIV-1) causes a broad spectrum of neurological diseases. Diverse neurological complications have been described in HIV-1-infected patients ranging from multiple neuropathies involving the peripheral nervous system (PNS) to HIV-1 encephalitis (HIVE) and development of dementia, commonly known as HIV-associated dementia (HAD) in the central nervous system (CNS) (The Dana Consortium 1996; McArthur et al. 1993). The impact of HIV-1-associated neurological disease in the clinical setting is significant. Twenty per cent of untreated AIDS-defined patients will develop HAD, which heralds a worsened survival prognosis (McArthur et al. 1993). HIV-1 infects cells of the CNS soon after primary infection (Davis et al. 1992; Sasseville and Lackner 1997; Poli et al. 1999).
Biosynthesis of Plant-Specific Flavones and Flavonols in Streptomyces venezuelae (2010)

Recently, recombinant Streptomyces venezuelae has been established as a heterologous host for microbial production of flavanones and stilbenes, a class of plant-specific polyketides. In the present work, we expanded the applicability of the S. venezuelae system to the production of more diverse plant polyketides including flavones and flavonols. A plasmid with the synthetic codon-optimized flavone synthase I gene from Petroselium crispum was introduced to S. venezuelae DHS2001 bearing a deletion of the native pikromycin polyketide synthase gene, and the resulting strain generated flavones from exogenously fed flavanones. In addition, a recombinant S. venezuelae mutant expressing a codon-optimized flavanone 3beta-hydroxylase gene from Citrus siensis and a flavonol synthase gene from Citrus unshius also successfully produced flavonols.
Optimization of Rate-Splitting Multiple Access in Beyond Diagonal RIS-Assisted URLLC Systems (2023)

This paper proposes a general optimization framework for rate splitting multiple access (RSMA) in beyond diagonal (BD) reconfigurable intelligent surface (RIS) assisted ultra-reliable low-latency communications (URLLC) systems. This framework can provide a suboptimal solution for a large family of optimization problems in which the objective and/or constraints are linear functions of the rates and/or energy efficiency (EE) of users. Using this framework, we show that RSMA and RIS can be mutually beneficial tools when the system is overloaded, i.e., when the number of users per cell is higher than the number of base station (BS) antennas. Additionally, we show that the benefits of RSMA increase when the packets are shorter and/or the reliability constraint is more stringent. Furthermore, we show that the RSMA benefits increase with the number of users per cell and decrease with the number of BS antennas. Finally, we show that RIS (either diagonal or BD) can highly improve the system performance, and BD-RIS outperforms regular RIS.
XIIIth International Symposium on Supramolecular Chemistry, University of Notre Dame, SouthBend, IN, July 25–30, 2004: Preface (2004)

It is our great pleasure and privilege to introduce the works featured in this special issue of Supramolecular Chemistry. This collection of reviews, communications, and full papers represent some ...
264 Pearl: pathway exploration and analysis in renal disease in the accelerating medicine partnership (amp) lupus network (2017)

<h3>Background and aims</h3> Despite treatments, a substantial proportion of lupus nephritis (LN) patients progress to end stage renal disease and death. Detailed transcriptomic analyses of LN kidneys may identify new therapeutic targets. Our goal is to demonstrate the feasibility of single cell and low-input transcriptomic analyses of LN kidney and urine cells. <h3>Methods</h3> Cells from urine and renal biopsies performed for clinical diagnosis from inform-consented patients (1 class III, 3 class IV+V, 1 class V) and 1 control (healthy part of tumour nephrectomy) were isolated, frozen, sorted and analysed by RNAseq. <h3>Results</h3> Bulk flow sorted cell populations (CD45, epithelial) from kidney samples can separate LN from controls based on gene expression. IFN stimulated genes were differentially expressed in renal CD45 LN cells. Analysis of single cells sorted from 4 LN kidney biopsies revealed major differences in infiltrates composition, with 2 samples demonstrating a high percentage of B cells (average of 18% compared to no B cells in the other 2 samples) and CD4 T cells (18% vs 8%), and low percentage of CD8 T cells (9% vs 23%). A high transcriptomic lupus interferon signature was detected in urine CD45 cells. Distinct infiltrates and distinct expression profiles were detected across patients. <h3>Conclusions</h3> The PEARL-Phase 0 project shows the feasibility of single cell isolation and transcriptomic analysis from LN kidney and urine. Analyses at a bigger scale in the two next phases of the project will accelerate discovery of new therapeutic targets and identification of biomarkers to guide therapeutic decisions in lupus nephritis and integrate the treatment effect.
Preparation and Novel Reduction Reactions of Vinamidinium Salts (2000)

Substituted acetic acids and formamides react in the presence of phosphorus oxychloride to yield the vinamidinium hexafluorophosphate salts 5a-d, 6a-d, and 7 in moderate to good unoptimized recrystallized yields (40-67%) as easily handled nonhygroscopic solids. The 1,3-differentially substituted vinamidinium salts 8 was prepared by amine exchange in 81% yield as are the cyclic diazapinium salts 9 and 10 in > 76% yield. The symmetrical 2-chlorovinamidinium 11 was prepared by displacement of 3 in 71% yield. The 2-chlorovinamidinium salts are cleanly reduced to the parent vinamidinium salts 12-16 using HI or PPh3/pTSA in up to 99% assay yield.
Intratumor Heterogeneity of Homologous Recombination Deficiency in Primary Breast Cancer (2016)

<b>Purpose:</b> The 3-biomarker homologous recombination deficiency (HRD) assay measures the number of telomeric allelic imbalances, loss of heterozygosity, and large-scale state transitions in tumor DNA and combines these metrics into a single score that reflects DNA repair deficiency. The goal of this study is to assess the consistency of these HRD measures in different biopsies from distinct areas of the same cancer.<b>Experimental Design:</b> HRD scores, BRCA mutation status, and <i>BRCA1</i> promoter methylation were assessed in 99 samples from 33 surgically resected, stage I-III breast cancers; each cancer was biopsied in three distinct areas. Homologous recombination repair (HR) deficiency was defined as either high HRD score (≥42) or tumor BRCA mutation.<b>Results:</b> Eighty-one biopsies from 32 cancers were analyzed. Tumor BRCA status was available for all samples, HRD scores for 70, and <i>BRCA1</i> methylation values for 76 samples. The <i>BRCA1/2</i> mutation and promoter methylation status and HR category showed perfect concordance across all biopsies from the same cancer. All tumors with <i>BRCA1/2</i> mutations or promoter methylation had high HRD scores, as did 17% (4/24) of the <i>BRCA1/2</i> wild-type and nonmethylated tumors. The HRD scores were also highly consistent between different biopsies from the same tumor with an intraclass correlation coefficient of 0.977, indicating that only 2.3% of the variance is attributed to within-tumor biopsy-to-biopsy variation.<b>Conclusions:</b> These results indicate that within-tumor spatial heterogeneity for HRD metrics and the technical noise in the assay are small and do not influence HRD scores and HR status. <i>Clin Cancer Res; 23(5); 1193-9. ©2016 AACR</i>.
Acquisition method improvement for Bossa Nova Technologies' full Stokes, passive polarization imaging camera SALSA (2016)

For some applications, the need for fast polarization acquisition is essential (if the scene observed is moving or changing quickly). In this paper, we present a new acquisition method for Bossa Nova Technologies’ full Stokes passive polarization imaging camera, the SALSA. This polarization imaging camera is based on “Division of Time polarimetry” architecture. The use of this technique presents the advantage of preserving the full resolution of the image observed all the while reducing the speed acquisition time. The goal of this new acquisition method is to overcome the limitations associated with Division of Time acquisition technique as well as to obtain high-speed polarization imaging while maintaining the image resolution. The efficiency of this new method is demonstrated in this paper through different experiments.
Spectrofluorometric characterization of dissolved organic matter for indication of precursor organic material and aromaticity (2001)

We studied the fluorescence properties of fulvic acids isolated from streams and rivers receiving predominantly terrestrial sources of organic material and from lakes with microbial sources of organic material. Microbially derived fulvic acids have fluorophores with a more sharply defined emission peak occurring at lower wavelengths than fluorophores in terrestrially derived fulvic acids. We show that the ratio of the emission intensity at a wavelength of 450 nm to that at 500 nm, obtained with an excitation of 370 nm, can serve as a simple index to distinguish sources of isolated aquatic fulvic acids. In our study, this index has a value of ~1.9 for microbially derived fulvic acids and a value of ~1.4 for terrestrially derived fulvic acids. Fulvic acids isolated from four large rivers in the United States have fluorescence index values of 1.4–1.5, consistent with predominantly terrestrial sources. For fulvic acid samples isolated from a river, lakes, and groundwaters in a forested watershed, the fluorescence index varied in a manner suggesting different sources for the seepage and streamfed lakes. Furthermore, we identified these distinctive fluorophores in filtered whole water samples from lakes in a desert oasis in Antarctica and in filtered whole water samples collected during snowmelt from a Rocky Mountain stream. The fluorescence index measurement in filtered whole water samples in field studies may augment the interpretation of dissolved organic carbon sources for understanding carbon cycling in aquatic ecosystems.
Anti-oxidant vitamins reduce normal tissue toxicity induced by radio-immunotherapy (2000)

Our purpose was to determine whether the administration of anti-oxidant vitamins could reduce dose-limiting toxicity from radio-immunotherapy (RAIT) and thereby allow higher escalation of RAIT doses. Lipophilic vitamins A and E were administered i.p. and hydrophilic vitamin C was administered i.m. for 14 days (3 days pre-RAIT through 11 days post-RAIT) alone or with bone marrow transplantation (BMT) to either BALB/c mice for toxicity studies or to nude mice bearing s.c. GW-39 human colonic cancer xenografts for therapy studies. The maximal tolerated dose (MTD) of RAIT (131I-MN14 anti-CEA IgG) that results in no lethality was determined for mice that did not receive vitamins or BMT and those that did receive one or both interventions. Body weight, peripheral white blood cell (pWBC) and platelet (PLT) counts and tumor growth were also measured. Administration of vitamins (equivalent of 3.5 IU/day vitamin A, 0.107 IU/day vitamin E and 4.0 mg/day ascorbic acid) to mice along with BMT increased the MTD by 42% and reduced body weight loss associated with RAIT. Vitamins also reduced the magnitude of RAIT-induced myelosuppression. As early as day 7 after RAIT, vitamins increased WBC counts following both a 400 μCi and a 500 μCi dose. On day 14 after the 400 μCi dose of RAIT (day 7 post-BMT), the additive effect of BMT and vitamin could be detected. Tumor growth was not adversely affected by vitamin administration. Int. J. Cancer 86:276–280, 2000. © 2000 Wiley-Liss, Inc.
Toward a Unified Model Explaining Heterogeneous Ziegler–Natta Catalysis (2015)

We propose a model for MgCl2 supported Ziegler-Natta catalysts capable to reconcile the discrepancies emerged in the last 20 years, when experimental data were tried to be rationalized by molecular models. We show that step defects on the neglected but thermodynamically more stable (104) facet of MgCl2 can lead to sites for strong TiCl4 adsorption. The corresponding Ti-active site is stereoeselective, and its stereoselectivity can be enhanced by coordination of Al-alkyls or Lewis bases in the close proximity. The surface energy of the step defected (104) MgCl2 facet is clearly lower than that of the well accepted (110) facet.
Efficient elimination of cancer cells by deoxyglucose-ABT-263/737 combination therapy (2011)

As single agents, ABT-263 and ABT-737 (ABT), molecular antagonists of the Bcl-2 family, bind tightly to Bcl-2, Bcl-xL and Bcl-w, but not to Mcl-1, and induce apoptosis only in limited cell types. The compound 2-deoxyglucose (2DG), in contrast, partially blocks glycolysis, slowing cell growth but rarely causing cell death. Injected into an animal, 2DG accumulates predominantly in tumors but does not harm other tissues. However, when cells that were highly resistant to ABT were pre-treated with 2DG for 3 hours, ABT became a potent inducer of apoptosis, rapidly releasing cytochrome c from the mitochondria and activating caspases at submicromolar concentrations in a Bak/Bax-dependent manner. Bak is normally sequestered in complexes with Mcl-1 and Bcl-xL. 2DG primes cells by interfering with Bak-Mcl-1 association, making it easier for ABT to dissociate Bak from Bcl-xL, freeing Bak to induce apoptosis. A highly active glucose transporter and Bid, as an agent of the mitochondrial apoptotic signal amplification loop, are necessary for efficient apoptosis induction in this system. This combination treatment of cancer-bearing mice was very effective against tumor xenograft from hormone-independent highly metastasized chemo-resistant human prostate cancer cells, suggesting that the combination treatment may provide a safe and effective alternative to genotoxin-based cancer therapies.
A pilot study of supraphysiologic testosterone (T) and oral etoposide (E) in men with castrate-resistant prostate cancer (CRPC). (2014)

5052 Background: Prostate cancer (PC) cells become resistant to chronic castration via an adaptive increase in androgen receptor (AR) expression, a liability that can be exploited therapeutically. Mechanistically, supraphysiologic androgens can induce PC cell death through topoisomerase 2 (topo2) mediated double-strand DNA breaks and disruption of DNA relicensing due to persistence of AR at origins of replication during the cell cycle. Methods: We evaluated parenteral T in combination with the topo2 inhibitor E in men with CRPC and low metastatic burden (≤5 bone and <10 soft tissue metastases). To rapidly cycle from supraphysiologic (>1500 ng/dL) to near castrate T levels, men received intramuscular T cypionate 400 mg on day (D) 1 and oral E 100 mg D 1-14 of a 28 D cycle. After 3 cycles, men with declining PSA could continue T alone every 28 D. The primary endpoint was PSA response, defined as a PSA below baseline, after cycle 3. Secondary endpoints included objective response rates and safety. Results: Sixteen men enrolled of which 14 completed 3 cycles of T+E and were evaluable for response. 7/14 went on the T-only expansion stage. After 3 cycles, 6/14 men had a PSA response. 7 (50%) had a PSA response at any timepoint [4 (29%) had PSA declines ≥50%] (Table). In men with RECIST-evaluable disease, 2 had progressive and 3 had stable disease (SD), 4 had partial (PR) and 1 had a complete response (CR). Median response duration was 343 D (95% CI, 91 to 434 D). Post T, 12/12 men had a PSA decline to subsequent androgen ablative therapies. Most adverse events (AEs) were ≤grade 2 and considered effects of E. One man died from neutropenic sepsis before completing the 1st cycle. AEs possibly related to T included lower extremity edema (n=1), priapism (n=1) and asymptomatic pulmonary embolism (n=2). No one developed new pain on T. Conclusions: T with or without E demonstrated preliminary efficacy in patients with CRPC as manifested by PSA and objective responses. This regimen is generally safe. Cyclic T-based therapies warrant further study. Clinical trial information: NCT01084759.PSA/radiographic response summary. Subject Cycles (N) Maximum PSA change relative to baseline (%) RECIST response 4 15 -86 PR 6 12 -48 PR 8 3 -46 SD 9 16 -78 NA 13 14 -97 PR 15 8 -18 PR 16 5 -98 CR
Predicting Future Occurrence of Acute Hypotensive Episodes Using Noninvasive and Invasive Features (2021)

We were able to predict AHE with precision and recall above 80% 30 minutes in advance with the large real-world dataset. The prediction of regression model can provide a more fine-grained, interpretable signal to practitioners. Model performance is improved by the inclusion of invasive features in predicting AHE, when compared to predicting the AHE based on only the available, restricted set of noninvasive technologies. This demonstrates the importance of exploring more noninvasive technologies for AHE prediction.
An open-source software package to simulate Cerenkov-based optical measurements in biological media (2013)

This study presents the validation of a tissue-optics software package capable of accurately performing Monte Carlo simulations of Cerenkov-based emission and induced fluorescence by interfacing with the open source radiation-optics transport package Gamos/Geant4.
Interface state density distribution in Au/n-ZnO nanorods Schottky diodes (2012)

Interface states density (NSS) distribution is extracted in Au/ ZnO Schottky diodes. Nanorods of ZnO are grown on silver (Ag) using aqueous chemical growth (ACG) technique. Well aligned hexagonal–shaped vertical nanorods of a mean diameter of 300 - 450 nm and 1.3 -1.9 μm high are revealed in SEM. Gold (Au) Schottky contacts of thickness 60 nm and 1.5mm diameter were evaporated. For electrical characterization of Schottky diodes current-voltage (I-V) and capacitance-Voltage (C-V) measurements are performed. The diodes exhibited a typical non-linear rectifying behavior with a barrier height of 0.62eV and ideality factor of 4.3. Possible reasons for low barrier height and high ideality factor have been addressed. Series resistance (RS) has been calculated from forward I-V characteristics using Chueng's function. The density of interfacial states (NSS) below the conduction band (EC-ESS) is extracted using I-V and C-V measured values. A decrease in interface states density (NSS) is observed from 3.74 × 1011 − 7.98 × 1010 eV−1 cm−2 from 0.30eV - 0.61eV below the conduction band edge.
Asymmetrical Waveform Compensation for Concurrent Dual-Band 1-bit Band-Pass Delta-Sigma Modulator with a Quasi-Elliptic Filter (2017)

The 1-bit band-pass delta-sigma modulator (BP-DSM) achieves high resolution if it uses an oversampling technique. This method can generate concurrent dual-band RF signals from a digitally modulated signal using a 1-bit digital pulse train. It was previously reported that the adjacent channel leakage ratio (ACLR) deteriorates owing to the asymmetrical waveform created by the pulse transition mismatch error of the rising and falling waveforms in the time domain and that the ACLR can be improved by distortion compensation. However, the reported distortion compensation method can only be performed for single-band transmission, and it fails to support multi-band transmission because the asymmetrical waveform compensated signal extends over a wide frequency range and is itself a harmful distortion outside the target band. Unfortunately, the increase of out-of-band power causes the BP-DSM unstable. We therefore propose a distortion compensator for a concurrent dual-band 1-bit BP-DSM that consists of a noise transfer function with a quasi-elliptic filter that can control the out-of-band gain frequency response against out-of-band oscillation. We demonstrate that dual-band LTE signals, each with 40MHz (2×20MHz) bandwidth, at 1.5 and 3.0GHz, can be compensated concurrently for spurious distortion under various combinations of rising and falling times and ACLR of up to 48dB, each with 120MHz bandwidth, including the double sided adjacent channels and next adjacent channels, is achieved.
Manufacturing Yield Improvement for Advanced CMOS Technology Middle-of-Line Interconnect with Cobalt Metallization : YE: YieldEnhancement/Learning (2023)

Middle of Line (MOL) metallization with cobalt has been very promising to reduce the parasitic resistance of advanced CMOS devices. Though significant line resistance reduction has been demonstrated, there are still many challenges in cobalt MOL integration especially for yield improvement. In this study, via resistance and yield are found to be related to the queue time from cobalt CMP to dielectric cap deposition. The failure analysis shows cobalt erosion causing open via resistance. Cobalt erosion is caused by moisture and residual fluorine gas in the FOUP. By using N2 purged FOUP, the via resistance yield is improved.