gebhart/patrepeval huggingface dataset:
Preliminary genome‐wide association study of bipolar disorder in the Japanese population (2009)

Recent progress in genotyping technology and the development of public databases has enabled large-scale genome-wide association tests with diseases. We performed a two-stage genome-wide association study (GWAS) of bipolar disorder (BD) in Japanese cohorts. First we used Affymetrix 100K GeneChip arrays in the analysis of 107 cases with bipolar I disorder and 107 controls, and selected markers that were nominally significant (P < 0.01) in at least one of the three models (1,577 markers in total). In the follow-up stage, we analyzed these markers using an Illumina platform (1,526 markers; 51 markers were not designable for the platform) and an independent sample set, which consisted of 395 cases (bipolar I + II) and 409 controls. We also assessed the population stratification of current samples using principal components analysis. After the two-stage analysis, 89 markers remained nominally significant (allelic P < 0.05) with the same allele being consistently over-represented in both the first and the follow-up stages. However, none of these were significant after correction for multiple-testing by false discovery rates. Sample stratification was virtually negligible. Collectively, this is the first GWAS of BD in the Japanese population. But given the small sample size and the limited genomic coverage, these results should be taken as preliminary.
Using OpenCL to Enable Software-like Development of an FPGA-Accelerated Biophotonic Cancer Treatment Simulator (2020)

The simulation of light propagation through tissues is important for medical applications, such as photodynamic therapy (PDT) for cancer treatment. To optimize PDT an inverse problem, which works backwards from a desired distribution of light to the parameters that caused it, must be solved. These problems have no closed-form solution and therefore must be solved numerically using an iterative method. This involves running many forward light propagation simulations which is time-consuming and computationally intensive.
Functionalized Carbon Nanoparticles, Blacks and Soots as Electron‐Transfer Building Blocks and Conduits (2014)

Functionalized carbon nanoparticles (or blacks) have promise as novel active high-surface-area electrode materials, as conduits for electrons to enzymes or connections through lipid films, or as nano-building blocks in electroanalysis. With previous applications of bare nanoblacks and composites mainly in electrochemical charge storage and as substrates in fuel cell devices, the full range of benefits of bare and functionalized carbon nanoparticles in assemblies and composite (bio)electrodes is still emerging. Carbon nanoparticles are readily surface-modified, functionalized, embedded, or assembled into nanostructures, employed in bioelectrochemical systems, and incorporated into novel electrochemical sensing devices. This focus review summarizes aspects of a rapidly growing field and some of the recent developments in carbon nanoparticle functionalization with potential applications in (bio)electrochemical, photoelectrochemical, and electroanalytical processes.
Rapid monitoring for transuranic contaminants during buried waste retrieval (1991)

This document reports results of research performed in support of possible future transuranic waste retrieval operations at the Idaho National Engineering Laboratory Radioactive Waste Management Complex. The focus of this research was to evaluate various methods of performing rapid and, as much as possible, on-line'' quantitative measurements of {sup 239}Pu or {sup 241}Am, either as airborne or loose contamination. Four different alpha continuous air monitors were evaluated for lower levels of detection of airborne {sup 239}Pu. All of the continuous air monitors were evaluated by sampling ambient air. In addition, three of the continuous air monitors were evaluated by sampling air synthetically laden with clean dust and dust spiked with {sup 239}Pu. Six methods for making quantitative measurements of loose contamination were investigated. They were: (1) microwave digestion followed by counting in a photon electron rejecting alpha liquid scintillation spectrometer, (2) rapid radiochemical separation followed by alpha spectrometry, (3) measurement of the {sup 241}Am 59 keV gamma ray using a thin window germanium detector, (4) measurement of uranium L-shell x-rays, (5) gross alpha counting using a large-area Ag activated ZnS scintillator, and (6) direct counting of alpha particles using a large-area ionization chamber. 40 refs., 42 figs., 24 tabs.
Self-constructing recurrent fuzzy neural network for DSP-based permanent-magnet linear-synchronous-motor servodrive (2006)

A self-constructing recurrent fuzzy-neural-network (SCRFNN) control system is proposed to control the position of the mover of a field-oriented control permanent-magnet linear-synchronous-motor (PMLSM) servodrive system to track periodic reference trajectories. The proposed SCRFNN combines the merits of self-constructing fuzzy neural network (SCFNN) and the recurrent neural network (RNN). Moreover, the structure and the parameter-learning phases are preformed concurrently and on-line in the SCRFNN. The structure learning is based on the partition of input space, and the parameter learning is based on the supervised gradient-decent method using a delta-adaptation law. Further, all the control algorithms are implemented in a TMS320C32 DSP-based control computer. The simulated and experimental results due to periodic reference trajectories show that the dynamic behaviors of the proposed SCRFNN control system are robust with regard to uncertainties.
c-JUN promotes BCR-ABL–induced lymphoid leukemia by inhibiting methylation of the 5′ region of Cdk6 (2011)

The transcription factor c-JUN and its upstream kinase JNK1 have been implicated in BCR-ABL-induced leukemogenesis. JNK1 has been shown to regulate BCL2 expression, thereby altering leukemogenesis, but the impact of c-JUN remained unclear. In this study, we show that JNK1 and c-JUN promote leukemogenesis via separate pathways, because lack of c-JUN impairs proliferation of p185(BCR-ABL)-transformed cells without affecting their viability. The decreased proliferation of c-Jun(Δ/Δ) cells is associated with the loss of cyclin-dependent kinase 6 (CDK6) expression. In c-Jun(Δ/Δ) cells, CDK6 expression becomes down-regulated upon BCR-ABL-induced transformation, which correlates with CpG island methylation within the 5' region of Cdk6. We verified the impact of Cdk6 deficiency using Cdk6(-/-) mice that developed BCR-ABL-induced B-lymphoid leukemia with significantly increased latency and an attenuated disease phenotype. In addition, we show that reexpression of CDK6 in BCR-ABL-transformed c-Jun(Δ/Δ) cells reconstitutes proliferation and tumor formation in Nu/Nu mice. In summary, our study reveals a novel function for the activating protein 1 (AP-1) transcription factor c-JUN in leukemogenesis by antagonizing promoter methylation. Moreover, we identify CDK6 as relevant and critical target of AP-1-regulated DNA methylation on BCR-ABL-induced transformation, thereby accelerating leukemogenesis.
Hybrid Volatilomics in Healthcare (2022)

Almost 2000 different constituents of the human volatilomehave already been reported from numerous individual studies lookingat volatile organic compounds (VOCs) in specific compartments – skin,breath, blood, urine, feces or cell lines. In most cases, the useof VOCs from a single body fluid is sufficient or even preferred.In this chapter we present and discuss a hybrid volatolomic approachthat can inevitably increase the diagnostic value of the targetedapplication. The hybrid approach reviews the existence of VOCs inseveral body fluids and the usefulness of a “hybrid” approach thatcombines their profiles collected from two or more body fluids. Perspectivesof this approach in developing the field of diagnostics to a new levelwill be presented and discussed.
Antibacterial, Antifungal, Antioxidant, and Docking Studies of Potential Dinaphthodiospyrols from Diospyros lotus Linn Roots (2021)

The main aims of this investigation were the isolation of dimeric naphthoquinones, a new class of dinaphthodiospyrols (<b>1-7</b>), from chloroform fractions and screening them for antibacterial, antifungal, and antioxidant potential. The susceptibility of the isolated compounds, namely, dinaphthodiospyrol A (<b>1</b>), dinaphthodiospyrol B (<b>2</b>), dinaphthodiospyrol C (<b>3</b>), dinaphthodiospyrol D (<b>4</b>), dinaphthodiospyrol E (<b>5</b>), dinaphthodiospyrol F (<b>6</b>), and dinaphthodiospyrol G (<b>7</b>) was assessed for antibacterial potential using well diffusion methods. The isolated compounds showed excellent antibacterial activity against selected bacterial strains, including Gram-positive <i>Bacillus subtilis</i>, <i>Streptococcus epidermis</i>, and <i>Bacillus subtilis</i>, and Gram-negative bacteria <i>Klebsiella pneumonia</i> with the zones of inhibition 6 to 26 nm. The standard drug Imipenem showed a maximum inhibitory zone 30 to 35 nm. Similarly, the isolated compounds were screened for antifungal properties, which showed an excellent reduction in the growth of selected fungal strain including <i>Candida albicans</i>, <i>Aspergillus flavus</i>, <i>Fusarium solani</i>, <i>Trichyton logifusus</i>, <i>Microsporum canis</i> <i>, and</i> <i>Candida glabrata</i>. Among all the screened compounds, <b>7</b> exhibited good activity (30<b>-</b>49 mm), followed by compounds <b>5</b> and <b>6</b>, (35<b>-</b>46 mm), while compounds <b>1-4</b> showed a moderate effect (8<b>-</b>28 mm) against the selected fungal strain against miconazole which showed potent effects (101<b>-</b>110.98 mm). The isolated compounds were also screened for 1, 1-diphenyl-2-picrylhydrazyl (DPPH) activity. In vitro-based free radical was employed using ascorbic acid as a standard antioxidant. The tested compounds (<b>1-7</b>) exhibited significant antioxidant activity in a concentration-dependent manner. The dinaphthodiospyrol <b>7</b> exhibited 97.32% scavenging activity, followed by dinaphthodiospyrol <b>6</b>, 92.01%, and compounds <b>5</b> and <b>4</b> with 89.90 and 88.43% scavenging activity at 100 μg/mL, respectively; ascorbic acid showed 96.45% scavenging effect. Furthermore, docking analysis was performed to know the exact binding mode of the tetra-substituted derivatives of dinaphthodiospyrols to the selected target proteins. From the docking analysis, it was found that the docking results are well correlated with the experimental observations. In conclusion, the dinaphthodiospyrols exhibited excellent antibacterial, antifungal, and free radical scavenging potential.
Hot‐Pressing of Sic with Additions of BaO and C (1985)

Barium oxide and carbon were added to β‐Sic powder as sintering aids. When only BaO or C was added, the Sic powder did not densify. However, densification was promoted by adding both additives together. Transmission electron microscopy of the compact revealed a boundary phase, which was deduced to result from reaction between Sic and barium carbide, the latter being produced by reaction between BaO and C. It is suggested that this reaction product promotes sintering.
Automated segmentation of intraretinal layers from macular optical coherence tomography images (2007)

Commercially-available optical coherence tomography (OCT) systems (e.g., Stratus OCT-3) only segment and provide thickness measurements for the total retina on scans of the macula. Since each intraretinal layer may be affected differently by disease, it is desirable to quantify the properties of each layer separately. Thus, we have developed an automated segmentation approach for the separation of the retina on (anisotropic) 3-D macular OCT scans into five layers. Each macular series consisted of six linear radial scans centered at the fovea. Repeated series (up to six, when available) were acquired for each eye and were first registered and averaged together, resulting in a composite image for each angular location. The six surfaces defining the five layers were then found on each 3-D composite image series by transforming the segmentation task into that of finding a minimum-cost closed set in a geometric graph constructed from edge/regional information and a priori-determined surface smoothness and interaction constraints. The method was applied to the macular OCT scans of 12 patients with unilateral anterior ischemic optic neuropathy (corresponding to 24 3-D composite image series). The boundaries were independently defined by two human experts on one raw scan of each eye. Using the average of the experts' tracings as a reference standard resulted in an overall mean unsigned border positioning error of 6.7 ± 4.0 &mgr;m, with five of the six surfaces showing significantly lower mean errors than those computed between the two observers (p < 0.05, pixel size of 50 × 2 &mgr;m).
A G 1 Cell Cycle Arrest Induced by Ligands of the Reovirus Type 3 Receptor Is Secondary to Inactivation of p21ras and Mitogen-Activated Protein Kinase (1999)

The reovirus type 3 S1 gene product (type 3 hemagglutinin; HA3) is the viral protein responsible for binding to a mammalian cell-surface receptor. It has been shown that HA3 binding to its receptor inhibits cell growth, even in the continuous presence of serum mitogens. Here, receptor-mediated signal transduction leading to growth arrest was studied after binding with synthetic or recombinant ligands in the absence of viral infection. Receptor ligation caused rapid inactivation of p21(ras), a decrease in Raf phosphorylation and in mitogen-activated protein kinase (MAPK) enzymatic activity, and G1 cell cycle arrest. Transfection and expression of constitutively active v-Has-ras prevented the G1 arrest, indicating that inactivation of p21(ras) is causative. Interestingly, v-Has-ras expression also decreased the efficiency of reoviridae replication, suggesting that inactivation of p21(ras) signals is required at some step of the viral cycle. This study may define new mechanisms regulating cell growth and support the approach of using viral proteins to identify and study cellular receptors. Synthetic receptor ligands with antiproliferative properties may be useful in drug development with the aim of blocking mitosis.
Thermoelectric Properties of Electrically Conductive III-Oxynitrides of Al1-xInxOsNt and InOsNt Prepared by Radio-Frequency Reactive Sputtering: Toward a Thermopower Device (2002)

We have studied the thermoelectric properties of Al1-xInxOsNt and InOsNt prepared by radio-frequency sputtering, with the aim of fabricating a thermoelectric power device based on III-nitride semiconductors. For Al0.02In0.98O1.14N0.49 with 0.34 µm thickness, the maximum power factor was 3.24×10-4 W·m-1·K-2 at 973 K, and for InO0.82N0.86 with 0.84 µm thickness, it was 3.75×10-4 W·m-1·K-2 at 973 K.
An Improved Total Synthesis of (+)‐Macroline (I) and Alstonerine (IIa) as well as the Formal Total Synthesis of (‐)‐Talcarpine (III) and (‐)‐Anhydromacrosalhine—methine (IIb). (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
A Pari-Mutuel-Like Mechanism for Information Aggregation: A Field Test inside Intel (2017)

A new information aggregation mechanism (IAM), developed via laboratory experimental methods, is implemented inside Intel Corporation in a long-running field test. The IAM, incorporating features of pari-mutuel betting, is uniquely designed to collect and quantize as probability distributions dispersed, subjectively held information. IAM participants’ incentives support timely information revelation and the emergence of consensus beliefs over future outcomes. Empirical tests demonstrate the robustness of experimental results and the IAM’s practical usefulness in addressing real-world problems. The IAM’s predictive distributions forecasting sales are very accurate, especially for short horizons and direct sales channels, often proving more accurate than Intel’s internal forecast.
Supplementary Table s1 from AQP4 Aggregation State Is a Determinant for Glioma Cell Fate (2023)

&lt;p&gt;Supplementary Table s1. M23-AQP4 mutants. Mutant names, WT and mutated amino acid sequences, position and references are reported. The amino acid positions refer to M1-AQP4.&lt;/p&gt;
A study on the two-dimensional slotline coupling structure for active planar array antennas (2002)

In this paper, a two-dimensional slotline coupling structure combined with E and H-plane slotlines is proposed for the oscillator-type phased array antenna. The proposed structure provides the two-dimensional scanning capability with smaller size and less spurious radiation than the conventional radiation or transmission line coupling structures. These operating characteristics are analyzed and experimentally demonstrated.
A Systematic Study of C-Glucoside Trisphosphates as myo-Inositol Trisphosphate Receptor Ligands. Synthesis of β-C-Glucoside Trisphosphates Based on the Conformational Restriction Strategy (2006)

β-C-Glucoside trisphosphates having a C2 side chain (3,7-anhydro-2-deoxy-d-glycero-d-gulo-octitol 1,5,6-trisphosphate, 11) and a C3 side chain (4,8-anhydro-2,3-dideoxy-d-glycero-d-gulo-nonanitol 1,6,7-trisphosphate, 12) were designed as structurally simplified analogues of a potent d-myo-inositol 1,4,5-trisphosphate (IP3) receptor ligand, adenophostin A. Construction of the β-C-glucosidic structure, which was the key to their synthesis, was achieved by two different methods based on the conformational restriction strategy: (1) radical cyclization with a temporary connecting silicon tether and (2) silane reduction of glyconolactols having an anomeric allyl substituent. Using these methods, the target β-C-glycoside trisphosphates 11 and 12 were successfully synthesized. A structure−activity relationship was established on a series of C-glucoside trisphosphates, including the previously synthesized related compounds, which were a C-glycosidic analogue 3 of adenophostin A, its uracil congener 5, α-C-glucoside trisphosphates 7−9 having a C1, C2, or C3 side chain, and the β-C-glucoside trisphosphates 10−12 having a C1, C2, or C3 side chain. The O-glycosidic linkage of adenophostin A and its analogues proved to be replaced by the chemically and biologically more stable C-glycosidic linkage. The α-C2-glucoside trisphosphate 8 stimulates Ca2+ release with a potency similar to that of IP3 in spite of its simplified structure, indicating a better fit to the receptor than the β-C-glucoside trisphosphates and also the α-congeners having a shorter or longer C1 side chain, which was supported by molecular modeling using the ligand binding domain of the IP3 receptor.
Solar‐Driven Incorporation of Carbon Dioxide into α‐Amino Ketones (2012)

Kraft der Sonne: Ein Prozess, der aus einer Photocyclisierung unter Nutzung von Sonnenenergie und anschließendem CO2-Einbau besteht, ermöglichte die Titelreaktion. Diese Eintopfreaktion lieferte aminosubstituierte cyclische Carbonate und ist ein einfaches Modell für die chemische Nutzung von Sonnenenergie für den CO2-Einbau. R=Sulfonylgruppe. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Gas‐Phase Synthesis of Silicon‐Rich Silicon Nitride Nanoparticles for High Performance Lithium–Ion Batteries (2021)

Abstract The practical application of silicon‐based anodes is severely hindered by continuous capacity fade during cycling. A very promising way to stabilize silicon in lithium–ion battery (LIB) anodes is the utilization of nanostructured silicon‐rich silicon nitride (SiN x ), a conversion‐type anode material. Here, SiN x with structure sizes in the sub‐micrometer range have been synthesized in a hot‐wall reactor by pyrolysis of monosilane and ammonia. This work focusses on understanding process parameter–particle property correlations. Further, a model for the growth of SiN x nanoparticles in this hot–wall–reactor design is proposed. This synthesis concept is of specific interest regarding simplicity, flexibility, and scalability: A way utilizing any mixtures of precursor gases to build multi‐functional nanoparticles that can be directly used for LIBs instead of focusing on modification of nanostructures after they have been formed. Lab‐scale production rates as high as 30 g h −1 can be easily achieved and further scaled. SiN 0.7 nanoparticles provide a first cycle coulombic efficiency of 54%, a specific discharge capacity of 1367 mAh g −1 , and a capacity retention over 80% after 300 cycles at 0.5 C ( j = 0.68 mA cm −2 ). These results imply that silicon‐rich silicon nitrides are promising candidates for high‐performance LIBs with very high durability.
Coded Matrix Computations for D2D-Enabled Linearized Federated Learning (2023)

Federated learning (FL) is a popular technique for training a global model on data distributed across client devices. Like other distributed training techniques, FL is susceptible to straggler (slower or failed) clients. Recent work has proposed to address this through device-to-device (D2D) offloading, which introduces privacy concerns. In this paper, we propose a novel straggler-optimal approach for coded matrix computations which can significantly reduce the communication delay and privacy issues introduced from D2D data transmissions in FL. Moreover, our proposed approach leads to a considerable improvement of the local computation speed when the generated data matrix is sparse. Numerical evaluations confirm the superiority of our proposed method over baseline approaches.
Domain-specific quantification of prion protein in cerebrospinal fluid by targeted mass spectrometry (2019)

Abstract Therapies currently in preclinical development for prion disease seek to lower prion protein (PrP) expression in the brain. Trials of such therapies are likely to rely on quantification of PrP in cerebrospinal fluid (CSF) as a pharmacodynamic biomarker and possibly as a trial endpoint. Studies using PrP ELISA kits have reproducibly shown that CSF PrP is lowered in the symptomatic phase of disease, a potential confounder for reading out the effect of PrP-lowering drugs in symptomatic patients. To date it has been unclear whether the reduced abundance of PrP in CSF results from its incorporation into plaques, retention in intracellular compartments, downregulation as a function of the disease process, or other factors. Because misfolding or proteolytic cleavage could potentially render PrP invisible to ELISA even if its concentration were constant or increasing in disease, we sought to establish an orthogonal method for CSF PrP quantification. We developed a targeted mass spectrometry method based on multiple reaction monitoring (MRM) of nine PrP tryptic peptides quantified relative to known concentrations of isotopically labeled standards. Analytical validation experiments showed process replicate coefficients of variation below 15%, good dilution linearity and recovery, and suitable performance for both CSF and brain homogenate and across humans as well as preclinical species of interest. In N =55 CSF samples from individuals referred to prion surveillance centers with rapidly progressive dementia, all six human PrP peptides, spanning the N- and C-terminal domains of PrP, were uniformly reduced in prion disease cases compared to individuals with non-prion diagnoses. This confirms the findings from ELISA studies, demonstrating that lowered CSF PrP concentration in prion disease is a genuine result of the disease process and not merely an artifact of ELISA-based measurement. We provide a targeted mass spectrometry-based method suitable for preclinical and clinical quantification of CSF PrP as a tool for drug development.