gebhart/patrepeval huggingface dataset:
Data from Genomic Landscape of Atypical Adenomatous Hyperplasia Reveals Divergent Modes to Lung Adenocarcinoma (2023)

&lt;div&gt;Abstract&lt;p&gt;There is a dearth of knowledge about the pathogenesis of premalignant lung lesions, especially for atypical adenomatous hyperplasia (AAH), the only known precursor for the major lung cancer subtype adenocarcinoma (LUAD). In this study, we performed deep DNA and RNA sequencing analyses of a set of AAH, LUAD, and normal tissues. Somatic &lt;i&gt;BRAF&lt;/i&gt; variants were found in AAHs from 5 of 22 (23%) patients, 4 of 5 of whom had matched LUAD with driver &lt;i&gt;EGFR&lt;/i&gt; mutations. &lt;i&gt;KRAS&lt;/i&gt; mutations were present in AAHs from 4 of 22 (18%) of patients. &lt;i&gt;KRAS&lt;/i&gt; mutations in AAH were only found in ever-smokers and were exclusive to &lt;i&gt;BRAF&lt;/i&gt;-mutant cases. Integrative analysis revealed profiles expressed in &lt;i&gt;KRAS&lt;/i&gt;-mutant cases (&lt;i&gt;UBE2C, REL&lt;/i&gt;) and &lt;i&gt;BRAF&lt;/i&gt;-mutant cases (&lt;i&gt;MAX&lt;/i&gt;) of AAH, or common to both sets of cases (suppressed &lt;i&gt;AXL&lt;/i&gt;). Gene sets associated with suppressed antitumor (Th1; &lt;i&gt;IL12A, GZMB&lt;/i&gt;) and elevated protumor (&lt;i&gt;CCR2, CTLA-4&lt;/i&gt;) immune signaling were enriched in AAH development and progression. Our results reveal potentially divergent &lt;i&gt;BRAF&lt;/i&gt; or &lt;i&gt;KRAS&lt;/i&gt; pathways in AAH as well as immune dysregulation in the pathogenesis of this premalignant lung lesion. &lt;i&gt;Cancer Res; 77(22); 6119–30. ©2017 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Oxadiazole Derivatives for Emitter and Carrier Transport Materials in Organic Electroluminescent Devices. (1991)

10種類のオキサジアゾール誘導体を新しく合成して,有機エレクトロルミネセンス(EL)用材料として評価した。薪規オキサジアゾール誘滋体は,融点が240～365℃ と高く,熱的安定性がよかった。また,置換基を代えることにより,374nmから527nmの蛍光を示した。その中でも,ジメチルアミノ基を有するオキサジアゾール誘導体を発光層に用いて有機EL素子を作製し,1000～2200cd/m2の高輝度な青色および緑色の発光を観察した。また,これらのオキサジアゾール誘導体は電子輪送性とホール輪送性の両方の性質を持った物質であることがわかり,新規の有機EL材料としての使用が期待できる。
Wide-Baseline Relative Camera Pose Estimation with Directional Learning (2021)

Modern deep learning techniques that regress the relative camera pose between two images have difficulty dealing with challenging scenarios, such as large camera motions resulting in occlusions and significant changes in perspective that leave little overlap between images. These models continue to struggle even with the benefit of large supervised training datasets. To address the limitations of these models, we take inspiration from techniques that show regressing keypoint locations in 2D and 3D can be improved by estimating a discrete distribution over keypoint locations. Analogously, in this paper we explore improving camera pose regression by instead predicting a discrete distribution over camera poses. To realize this idea, we introduce DirectionNet, which estimates discrete distributions over the 5D relative pose space using a novel parameterization to make the estimation problem tractable. Specifically, DirectionNet factorizes relative camera pose, specified by a 3D rotation and a translation direction, into a set of 3D direction vectors. Since 3D directions can be identified with points on the sphere, DirectionNet estimates discrete distributions on the sphere as its output. We evaluate our model on challenging synthetic and real pose estimation datasets constructed from Matterport3D and InteriorNet. Promising results show a near 50% reduction in error over direct regression methods.
Safety and immunogenicity of Nanocovax, a SARS-CoV-2 recombinant spike protein vaccine: Interim results of a double-blind, randomised controlled phase 1 and 2 trial (2022)

This work was funded by the Coalition for Epidemic Preparedness Innovations (CEPI), the Ministry of Science and Technology of Vietnam, and Nanogen Pharmaceutical Biotechnology JSC.
TDOA assisted RSSD based localization using UWB and directional antennas (2013)

This paper studies the use of directional antennas for received signal strength difference (RSSD) based localization using ultra-wideband and demonstrates the achievable accuracy with this localization method applied to UWB. As introduced in our previous work the RSSD localization is assisted with one Time Difference of Arrival (TDOA) estimation. The use of directional receiving antennas and an omni-directional transmitting antenna is assumed. Localization is performed in 2D. Two localization approaches are considered: RSSD using statistical channel model and fingerprinting approach. In the case of statistical channel model simulations are performed using Matlab. In the case of fingerprinting approach localization is done based on real indoor-measurements.
Optical bench evaluation of the effect of pupil size in new generation monofocal intraocular lenses (2023)

Optical bench results showed that the ISOPure and RayOne-EMV provide similar performance to a spherical monofocal IOL, with a strong pupil dependency for distance and intermediate vision. The other enhanced monofocal IOL, ICB00, provided a sustained improvement in simulated intermediate VA and maintained distance image quality comparable to that of the standard aspheric monofocal IOLs, even for larger pupils.
ChemInform Abstract: The Intramolecular Stille Reaction (1999)

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.
Analysis of tumor samples from SOLO2: Concordance of BRCA mutation (BRCAm) detection in tumor vs. blood and frequency of BRCA-specific loss of heterozygosity (LOH) and loss of function somatic mutations. (2018)

12017 Background: The PARP inhibitor olaparib is approved for maintenance treatment of platinum-sensitive relapsed ovarian cancer (PSR OC) in the USA based on pivotal studies (Study 19, SOLO2) that demonstrated a progression-free survival benefit of olaparib (Ledermann et al 2012, 2016; Pujade-Lauraine et al 2017). Patients (Pts) with BRCAm benefit most from olaparib, but questions remain on the functional equivalence of germline (g) and somatic BRCAm and the frequency and impact of BRCA-gene-specific LOH (Dougherty et al 2017; Maxwell et al 2017). Methods: Blood and tumor samples from 241 pts with gBRCAm in a Phase III trial of olaparib maintenance monotherapy (300 mg bid tablets; SOLO2; NCT01874353) were analyzed. A concordance analysis of gBRCAm and tumor BRCAm (tBRCAm) status was conducted; gene-specific LOH for BRCA1 and BRCA2 and assessment of homologous recombination deficiency (HRD) using Myriad HRD score (Tumor BRACAnalysis CDxTM test) was also determined. Results: tBRCAm testing was evaluable in 241/289 gBRCAm pts. There was 98% and 100% concordance between pts’ BRCA1m and BRCA2m status, respectively, in tBRCAm vs gBRCAm. 13/241 (5.4%) of gBRCAm were due to large rearrangements (exonic insertions or deletions), of which 4 involving BRCA1 were not detected in the tumor. A further deleterious somatic mutation in BRCA1 was identified in 1/241 pts with gBRCAm tumors. This was a large rearrangement in BRCA1, causing an exon 1–22 deletion that likely constituted the second ‘hit’ in this tumor. Of 210 evaluable LOH samples, 144/144 (100%) gBRCA1m and 65/66 (99%) gBRCA2m tumors had gene-specific LOH. The pt without BRCA2 LOH had an HRD score of 53, was progression-free for 911 days and remained on olaparib at data cut-off. Conclusions: Very high concordance between tBRCA and gBRCA testing is demonstrated, supporting wider implementation of tBRCA testing in addition to availability of gBRCA testing to determine BRCAm status in OC. Deleterious somatic BRCAm almost never arises in gBRCAm tumors, in keeping with BRCA loss being a driver of tumorigenesis in OC. In PSR gBRCAm pts, gene-specific LOH in tumors is almost universal. Clinical trial information: NCT01874353.
A Study of a Digital Manufacturing Procedure for Freeform Optics (2006)

An investigation into a Digital Manufacturing and Testing Procedure (DMTP) for freeform optics is presented in this paper. The paper studies the characteristics of the DMTP which are of special use in ultra-precision machining (UPM) of freeform optics, i.e. the construction of a model of DMTP, the construction of a digital prototype of an optical system, a Digital Testing (DT) system for image quality, digital testing and simulation of the optical image quality.
Nested Genes CDA12 and CDA13 Encode Proteins Associated with Membrane Trafficking in the Ciliate Tetrahymena thermophila (2009)

We describe a novel pair of nested genes, CDA12 and CDA13, from Tetrahymena thermophila. Both are implicated in membrane trafficking associated with cell division and conjugation. Green fluorescent protein localization reveals Cda12p decoration of diverse membrane-bound compartments, including mobile, subcortical tubulovesicular compartments; perinuclear vesicles; and candidates for recycling endosomes. Cda13p decorates intracellular foci located adjacent to cortically aligned mitochondria and their neighboring Golgi networks. The expression of antisense CDA12 RNA in transformants produces defects in cytokinesis, macronuclear segregation, and the processing of pinosomes to downstream compartments. Antisense CDA13 RNA expression produces a conjugation phenotype, resulting in the failure of mating pairs to separate, as well as failures in postconjugation cytokinesis and macronuclear fission. This study offers insight into the membrane trafficking events linking endosome and Golgi network activities, cytokinesis, and karyokinesis and the unique membrane-remodeling events that accompany conjugation in the ciliate T. thermophila. We also highlight an unusual aspect of genome organization in Tetrahymena, namely, the existence of nested, antisense genes.
End-Pumped 895 nm Cs Laser (2004)

A scientific demonstration of a Cs laser is described in which the measured slope efficiency is as high as 0.59 W/W using a Ti:Sapphire laser as a surrogate diode-pump. In addition to presenting experimental data, a laser energetics model that accurately predicts laser performance is described and used to model a power-scaled, diode-pumped system.
Zeosil-Nanoblöcke: Baueinheiten in dernPr4N+-gesteuerten Synthese von Zeolith MFI (2001)

Tetrapropylammonium(TPA)-haltige Vorstufen sind die Bausteine bei der Silicalitkristallisation. In den ersten Schritten entstehen durch geordnete Zusammenlagerung der Vorstufen quaderförmige Silicalitnanopartikel (siehe Bild). Diese Nanoblöcke weisen die Topologie von Zeolith MFI auf und spielen eine Schlüsselrolle bei der TPA-gesteuerten Kristallisation von Zeolithen ausgehend von mono- und polymeren Siliciumquellen.
ChemInform Abstract: MATRIC‐ISOLATION INFRARED AND ELECTRON PARAMAGNETIC RESONANCE SPECTROSCOPIC STUDIES OF THE REACTION OF LITHIUM WITH SILICON TETRAFLUORIDE (1978)

Abstract Li‐Metall wird bei 435°C verdampft und mit SiF 4 gemeinsam in einer Ar‐Matrix (Ar: SiF 4 z lO0:l) kondensiert.
ROS‐ and HIF1α‐dependent IGFBP3 upregulation blocks IGF1 survival signaling and thereby mediates high‐glucose‐induced cardiomyocyte apoptosis (2019)

The prevalence of chronic hyperglycemia and its complications, imposing a critical burden on the worldwide economy and the global healthcare system, is a pressing issue. Mounting evidence indicates that oxidative stress and hypoxia, two noticeable features of hyperglycemia, play a joint crucial role in mediating cellular apoptosis. However, the underlying detailed molecular mechanism remains elusive. Triggered by the observation that insulin-like growth factor (IGF1)-binding protein 3 (IGFBP3) can mediate, in renal cells, high-glucose-induced apoptosis by elevating oxidative stress, we wish to, in this study, know whether or not the similar scenario holds in cardiac cells and, if so, to find its relevant molecular key players, thereby dissecting the underlying molecular pathway. Specifically, we used a combination of three different cellular sources (H9c2 cells, diabetic rats, and neonatal rat ventricular cardiomyocytes) as our model systems of study. We made use of Co-IP assay and western blot analysis in conjunction with loss-of-function reasoning, gain-of-function logic, and inhibitor treatment as our main analytical tools. As a result, briefly, our main findings are that hyperglycemia can induce cardiac IGFBP3 overexpression and secretion, that high levels of IGFBP3 can sequester IGF1 from IGF1 survival pathway, leading to apoptosis, and that IGFBP3 gene upregulation is hypoxia-inducible factor (HIF)1α-dependent and reactive oxygen species dependent. Piecing these findings together allows us to propose the improved molecular regulatory mechanism. In conclusion, we have established the molecular roles of IGFBP3, HIF1, and prolyl hydroxylase domain in connecting oxidative stress with hypoxia and in cellular apoptosis under hyperglycemia.
Treatment of isografted 9L rat brain tumors with beta-5-o-carboranyl-2'-deoxyuridine neutron capture therapy. (2000)

beta-5-o-Carboranyl-2'-deoxyuridine (D-CDU) is a nontoxic pyrimidine nucleoside analogue designed for boron neutron capture therapy of brain tumors. In vitro studies indicated that D-CDU accumulates to levels 92- and 117-fold higher than the extracellular concentration in rat 9L and human U-251 glioma cells, respectively, and persists for several hours at levels 5-fold higher than the extracellular concentration. Furthermore, D-CDU was not toxic to rats injected i.p. with up to 150 mg/kg. On the basis of these studies, D-CDU was evaluated as a neutron capture therapy agent using rats bearing stereotactically implanted intracranial 9L tumors at single i.p. doses of 30 mg/kg and 150 mg/kg of D-CDU (20% 10B enriched), given 2 h before irradiation with thermal neutrons. Boron concentrations in tumors 2 h after dosing were 2.3 +/- 1.6 and 7.4 +/- 1.3 micrograms boron/g tissue (mean +/- SD), corresponding to tumor/brain ratios of 11.5 +/- 3.6 and 6.8 +/- 2.0 micrograms boron/g tissue for the low and high doses, respectively. All untreated animals died within 28 days, whereas half survived at days 32, 55, and 38 for groups receiving neutrons only, 30 mg/kg D-CDU, and 150 mg/kg D-CDU, respectively. Odds ratios of all treatment groups differed significantly from the untreated group (P < 0.002; logrank test). The median survival time for the 30 mg/kg-treated group but not for the 150 mg/kg-treated group was significantly longer than for rats treated with neutrons only (P = 0.036), which may correlate with the decreased tumor selectivity for D-CDU observed at the higher dose. Additional pharmacodynamic studies are warranted to determine optimal dosing strategies for D-CDU.
Antenna/sampling point selection algorithm in fractional sampling-MIMO-OFDM (2008)

MIMO-OFDM systems are expected to realize higher data rates and larger capacity. With more transmit and receive antennas the capacity of MIMO-OFDM systems increases. However, when the number of demodulators is limited, it is essential to select antenna points which achieve selection diversity. On the other hand, through Fractional Sampling (FS), it is possible to separate multipath components and obtain diversity gain. Just like MIMO systems, FS achieves selection diversity by selecting sampling points. This paper presents an antenna/sampling point selection algorithm for MIMO-OFDM systems with Fractional Sampling. Utilizing the characteristics of the correlation among the sampling points in FS, the proposed selection algorithm offers significantly lower computational complexity than conventional algorithms. The proposed algorithm is confirmed through the computational simulations.
A New Receiver Architecture for MIMO Beam-Forming Applications (2017)

Owing to its reduction in hardware complexity and power consumption, hybrid beam-forming has become one of the most promising substitutes for fully digital beam-forming (FDB) in large antenna array systems. In conventional hybrid beam-forming (CHB) architecture, phase shifters are designed to operate at RF band and inaccuracies of the RF phase shifts are unavoidable in practice. Furthermore, these RF phase shifters still consume considerable power if implemented as active devices or a large space/area on dice (form factor) if implemented as passive devices. This issue becomes more critical for massive MIMO systems where lower power consumption and smaller form factor are much desired due to the large number of antenna elements. Aiming at reducing power consumption and form factor of the receiver, we investigate a new method to insert phase shifts via adjusting sampling-offset on sample and hold (S&H) circuit. Based on this method, a new receiver architecture with RF under-sampling technique and adjustable S&H circuit is proposed. We also develop a method to find out the required phase shifts for the beam-forming in the proposed receiver architecture. Performance evaluation at 28 GHz band shows that the proposed technology gives practically the same bit error rate (BER) performance as the CHB architecture but yields advantages in terms of power consumption, chip area, and beam-forming phase errors, which makes it appealing for massive MIMO systems.
Preoperative Risk Factors for Adjacent Segment Degeneration after Two-Level Floating Posterior Fusion at L3-L5 (2019)

RASD was more likely to occur at the adjacent segment on the cephalad side than at the adjacent segment on the caudad side after two-segment floating fusion of L3-L5. A preoperative UIV tilt angle >10° or UIV tilt < -10° was a risk factor for RASD.
Treatment of Acute Myocardial Infarction and Cardiogenic Shock: Outcomes of the RECOVER III Post-Approval Study by SCAI Shock Stage (2023)

Abstract Background The Society for Cardiovascular Angiography and Interventions (SCAI) proposed a staging system (A-E) to predict prognosis in cardiogenic shock. Herein, we report clinical outcomes of the RECOVER III study for the first time, according to SCAI shock classification. Methods RECOVER III is an observational, prospective, multicenter, single-arm, post-approval study of patients with acute myocardial infarction complicated by cardiogenic shock (AMICS) undergoing percutaneous coronary intervention (PCI) with Impella support. Patients enrolled in RECOVER III were assigned a baseline SCAI shock stage. Staging was then repeated within 24 hours after initiation of Impella. Kaplan-Meier survival curve analyses were conducted to assess survival across SCAI shock stages at both timepoints. Results At baseline assessment, 16.5%, 11.4%, and 72.2% were classified as Stage C, D, and E, respectively. At ≤24 hour assessment, 26.4%, 33.2%, and 40.0% were Stage C, D, and E respectively. Thirty-day survival amongst patients with Stage C, D and E shock at baseline was 59.7%, 56.5% and 42.9%, respectively (p=0.003). Survival amongst patients with Stage C, D and E shock at ≤24 hours was 65.7%, 52.1% and 29.5%, respectively (p&lt;0.001). After multivariate analysis of impact of shock stage classifications at baseline and ≤ 24 hours, only Stage E classification at ≤24 hours was a significant predictor of mortality (OR 4.8, p&lt;0.001). Conclusions In a real-world cohort of patients with AMICS undergoing PCI with Impella support, only Stage E classification at ≤ 24 hours was significantly predictive of mortality, suggesting that response to therapy may be more important than clinical severity of shock at presentation. Clinical Perspective Many patients with AMICS treated with Impella present in SCAI Stage E shock, but may improve to a more favorable shock stage within 24 hours of their presentation. In-hospital and 30-day outcomes correlate with SCAI shock stage at presentation, but the correlation is more robust upon repeat assessment within 24 hours after Impella initiation. The SCAI shock staging system may be a useful clinical tool to guide in-hospital management of patients with AMICS, especially within the first 24 hours, and to provide prognostic information to patients and/or their families.
The survival and function of IL-10-producing regulatory B cells are negatively controlled by SLAMF5 (2021)

B cells have essential functions in multiple sclerosis and in its mouse model, experimental autoimmune encephalomyelitis, both as drivers and suppressors of the disease. The suppressive effects are driven by a regulatory B cell (Breg) population that functions, primarily but not exclusively, via the production of IL-10. However, the mechanisms modulating IL-10-producing Breg abundance are poorly understood. Here we identify SLAMF5 for controlling IL-10<sup>+</sup> Breg maintenance and function. In EAE, the deficiency of SLAMF5 in B cells causes accumulation of IL10<sup>+</sup> Bregs in the central nervous system and periphery. Blocking SLAMF5 in vitro induces both human and mouse IL-10-producing Breg cells and increases their survival with a concomitant increase of a transcription factor, c-Maf. Finally, in vivo SLAMF5 blocking in EAE elevates IL-10<sup>+</sup> Breg levels and ameliorates disease severity. Our results suggest that SLAMF5 is a negative moderator of IL-10<sup>+</sup> Breg cells, and may serve as a therapeutic target in MS and other autoimmune diseases.
Activation of BTK by a Phosphorylation Mechanism Initiated by SRC Family Kinases (1996)

Bruton's tyrosine kinase (BTK) is pivotal in B cell activation and development through its participation in the signaling pathways of multiple hematopoietic receptors. The mechanisms controlling BTK activation were studied here by examination of the biochemical consequences of an interaction between BTK and SRC family kinases. This interaction of BTK with SRC kinases transphosphorylated BTK on tyrosine at residue 551, which led to BTK activation. BTK then autophosphorylated at a second site. The same two sites were phosphorylated upon B cell antigen receptor cross-linking. The activated BTK was predominantly membrane-associated, which suggests that BTK integrates distinct receptor signals resulting in SRC kinase activation and BTK membrane targeting.
Complementary structural information of positive‐ and negative‐ion MS n spectra of glycopeptides with neutral and sialylated N‐glycans (2006)

Positive- and negative-ion MSn spectra of chicken egg yolk glycopeptides binding a neutral and a sialylated N-glycan were acquired by using electrospray ionization linear ion trap time-of-flight mass spectrometry (ESI-LIT-TOFMS) and collision-induced dissociation (CID) with helium as collision gas. Several characteristic differences were observed between the positive- and negative-ion CID MSn (n = 2, 3) spectra. In the positive-ion MS2 spectra, the peptide moiety was presumably stable, but the neutral N-glycan moiety caused several B-type fragmentations and the sialylated N-glycan almost lost sialic acid(s). In contrast, in the negative-ion MS2 spectra, the peptide moiety caused several side-chain and N-glycan residue (e.g., N-acetylglucosamine (GlcNAc) residue) fragmentations in addition to backbone cleavages, but the N-glycan moieties were relatively stable. The positive-ion MS3 spectra derived from the protonated peptide ion containing a GlcNAc residue (203.1 Da) provided enough information to determine the peptide amino-acid sequence including the glycosylation site, while the negative-ion MS3 spectra derived from the deprotonated peptide containing a 0,2X1-type cross-ring cleavage (83.1 Da) complicated the peptide sequence analysis due to side-chain and 0,2X1 residue related fragmentations. However, for the structural information of the N-glycan moiety of the glycopeptides, the negative-ion CID MS3 spectra derived from the deprotonated 2,4A6-type cross-ring cleavage ion (neutral N-glycan) or the doubly deprotonated B6-type fragment ion (sialylated N-glycan) are more informative than are those of the corresponding positive-ion CID MS3 spectra. Thus, the positive-ion mode of CID is useful for the analyses of peptide amino-acid sequences including the glycosylation site. The negative-ion mode of CID is especially useful for sialylated N-glycan structural analysis. Therefore, in the structural analysis of N-glycopeptides, their roles are complementary.