gebhart/patrepeval huggingface dataset:
ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data (2011)

Cellular response to stimuli is typically complex and involves both regulatory and metabolic processes. Large-scale experimental efforts to identify components of these processes often comprise of genetic screening and transcriptomic profiling assays. We previously established that in yeast genetic screens tend to identify response regulators, while transcriptomic profiling assays tend to identify components of metabolic processes. ResponseNet is a network-optimization approach that integrates the results from these assays with data of known molecular interactions. Specifically, ResponseNet identifies a high-probability sub-network, composed of signaling and regulatory molecular interaction paths, through which putative response regulators may lead to the measured transcriptomic changes. Computationally, this is achieved by formulating a minimum-cost flow optimization problem and solving it efficiently using linear programming tools. The ResponseNet web server offers a simple interface for applying ResponseNet. Users can upload weighted lists of proteins and genes and obtain a sparse, weighted, molecular interaction sub-network connecting their data. The predicted sub-network and its gene ontology enrichment analysis are presented graphically or as text. Consequently, the ResponseNet web server enables researchers that were previously limited to separate analysis of their distinct, large-scale experiments, to meaningfully integrate their data and substantially expand their understanding of the underlying cellular response. ResponseNet is available at http://bioinfo.bgu.ac.il/respnet.
Oxyhydrative Scission of trans-2-Butene in the Liquid Phase under Pressure (1978)

Abstract The liquid phase oxidation of trans-2-hutene under pressure using a V2O5–MoO3 catalyst suspended in water has been proved to yield acetic acid and aldehyde selectively at 170 °C. Taking into account the results of the oxidation of intermediate compounds, it is suggested that the reaction follows the same oxyhydrative scission mechanism as has been proposed for the gas phase oxidation.
A hybrid filter bank approach to analog-to-digital conversion (2002)

This paper presents a novel approach to high-speed, high-resolution analog-to-digital (A/D) conversion using a hybrid filter bank with an array of slower speed A/D converters (ADCs). The hybrid filter bank is a new class of filter bank that employs continuous-time analysis filters to allocate a frequency band to each ADC in the array and discrete-time synthesis filters to reconstruct the digitized signal. The filter bank improves the speed and resolution of the A/D conversion by reducing the effects of mismatches between the ADCs in the array. This paper presents a filter design algorithm which minimizes mean-squared reconstruction error for the M-channel hybrid filter bank. A near-perfect-reconstruction, two-channel hybrid filter bank which introduces 0.00095 dB average deviation from 0 dB distortion and -108 dB average aliasing is developed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Radiative engineering of nanoantenna arrays for ultrasensitive vibrational spectroscopy of proteins (2010)

Infrared absorption spectroscopy offers direct access to the vibrational signatures of molecular structure. Although absorption cross sections are nearly 10 orders of magnitude larger than the Raman cross sections, they are small in comparison with those of fluorescent labels. Sensitivity improvements are therefore required in order for the method to be applicable to single molecule/monolayer studies. In this work, we demonstrate a plasmon enhanced vibrational spectroscopy technique which allow for the measurement of molecule specific signatures at the monolayer level. Specifically, we show 4-5 order of magnitude enhancement of the amide-I and II backbone signature of protein monolayers, the signal resulting from only zeptomole quantities of molecules.
Immunity to SOX group B and ZIC2 antigens: novel neuro-ectodermal targets and clinical indicators in small cell lung cancer (2005)

Lung cancer is the most lethal tumor type in the US and Europe, with small cell lung cancer (SCLC) accounting for 15 to 18% of these cases (1, 2). SCLC is one of the most aggressive of all cancers, with up to 70% of patients presenting with distant metastasis at time of diagnosis (3, 4). Despite being initially responsive to therapy, currently the average survival for SCLC cases with limited disease is about 18 months, while patients with extensive disease survive about 9 months from the date of diagnosis (5). New treatment modalities are therefore urgently needed. The search for antigenic targets that could be utilized as part of a vaccine therapy in cancer has been an area of intense research. Identifying the array of antigenic targets in SCLC and understanding whether such responses can result in anti-tumor immunity is critical, and may lead to successful immune vaccination against SCLC. We identified SOX Group B and ZIC2 proteins as highly immunogenic neuro-ectodermal antigens in SCLC by SEREX (6). We recently completed the analysis of 90 SCLC patients, 42 (47%) of whom had antibodies to either SOX1 or ZIC2. None had autoimmune paraneoplastic disease. SOX1, 2 and 3 antibodies were present in 28, 22 and 16% of patients respectively and 28% had ZIC2 antibodies. All patients with SOX2 and/or SOX3 antibodies were SOX1 seropositive. In contrast, only 8 patients (9%) had both SOX and ZIC2 antibodies. 36% of SOX1 seropositive patients had titers equal to or greater than 1:106. Antibody titers against all antigens were highest at time of diagnosis and stable up to 6 months after. Seroreactivity against either SOX1 or ZIC2 showed statistically significant correlations with younger age, female gender, lower LDH levels and better response to initial therapy. Trends towards better overall survival, a larger proportion of limited stage disease and longer times to progression were observed for all seropositive patients when compared to seronegatives. A significant number of neuro-ectodermal antigenic proteins were independently isolated as immune targets in autoimmune paraneoplastic neurological disease (PND) associated with SCLC (7). Despite the infrequent occurrence of autoimmune PND, antibodies to neuro-ectodermal antigens associated with PND, such as Hu or VGCC occur in up to 25% of SCLC patients (8, 9, 10, 11). The presence of anti-neuro-ectodermal antigens in SCLC has been associated with clinical parameters of less aggressive disease (9, 12). Thus, immune responses directed against multiple neuro-endocrine tumor antigens might relate to a better prognosis in SCLC (13). This abstract was published in Cancer Immunity, a Cancer Research Institute journal that ceased publication in 2013 and is now provided online in association with Cancer Immunology Research.
Model based optimization of EMC input filters (2008)

Input filters of power converters for compliance with regulatory electromagnetic compatibility (EMC) standards are often over-dimensioned in practice due to a non-optimal selection of number of filter stages and/or the lack of solid volumetric models of the inductor cores. This paper presents a systematic filter design approach based on a specific filter attenuation requirement and volumetric component parameters. It is shown that a minimal volume can be found for a certain optimal number of filter stages for both the differential mode (DM) and common mode (CM) filter. The considerations are carried out exemplarily for an EMC input filter of a single-phase power converter for the power levels of 100 W, 300 W, and 500 W.
Isolated Familial Somatotropinomas: Does the Disease Map to 11q13 or to 2p16? (2000)

Phenylbutazone Can Spuriously Elevate Unextracted Testosterone Assay Results in Patients withAnkylosing Spondylitis To the editor:Ankylosing spondylitis (AS) is a disease with a strong male preponderance.Reports that AS patients show somewhat elevated serum testosterone/17␤-estradiol ratios have supported the view that testosterone may be relevant in the pathogenesis of AS (1, 2).In a recent study, we have shown, however, that elevations of serum testosterone in both male and female patients with AS are probably spurious (3).In our study levels of serum testosterone, when measured directly in serum by a RIA, as is
Abstract P493: Multiple-ascending-dose Study of IW-1973, a Soluble Guanylate Cyclase Stimulator (2017)

Background: Soluble guanylate cyclase (sGC), an enzyme that catalyzes the formation of cyclic guanosine monophosphate (cGMP) in response to nitric oxide (NO) binding, is a key mediator of local blood flow, inflammation, and fibrosis. IW-1973 is an orally available sGC stimulator that enhances NOsGC-cGMP signaling and reduces blood pressure (BP) in animal models of hypertension, both alone and in combination with other antihypertensive agents. Methods: A Phase 1b placebo-controlled, randomized, multiple-ascending-dose study was conducted to assess safety, tolerability, pharmacokinetics (PK) and pharmacodynamics (BP, heart rate, platelet function, and plasma biomarkers) of IW-1973 in healthy subjects. Four successive cohorts of 11 subjects each (8 active and 3 placebo) were enrolled. Subjects received a starting dose once daily (QD) for 14 days followed by an up-titrated QD dose for 7 days. Results: IW-1973 doses ranging from 15 to 40 mg were tolerated. There were no serious adverse events (AEs), severe AEs, or discontinuations due to AEs. Among the 32 subjects who received IW-1973, the most common AEs (which occurred mainly at doses ≥30 mg) were headache (15 subjects), dizziness/postural dizziness (6) and orthostatic hypotension/BP decreased (4). AEs tended to resolve with continued dosing. The AE profile of higher doses was not clearly improved by up-titration from a lower starting dose. PK was dose proportional, both for C max and AUC, with a T max of 2-4 hours and an effective half-life of 24-37 hours. After 14 days of treatment, least squares mean change from baseline in 24-h ambulatory systolic BP (±SE) was -0.85±1.32 (placebo), -7.29±1.62 (15 mg), -3.27±1.61 (20 mg), -6.75±1.62 (30 mg), and -5.23±1.61 mmHg (≤40 mg, ≤0.5 mg/kg). After 21 days, the change from baseline was -4.81±1.19 (placebo), -8.21±1.46 (15 to 30 mg), -6.29±1.45 (20 to 40 mg), -9.05±1.56 (30 to 40 mg), and -6.58±1.45 mmHg (≤40 to ≥40 mg). IW-1973 produced a dose-related increase in plasma cGMP indicating target engagement. There was no clear effect of IW-1973 administration on platelet function as assessed by the PFA-100 ® system. Conclusion: Further clinical investigation of IW-1973 is ongoing or planned in multiple indications, including resistant hypertension.
Supplementary Methods and Tables from The PSMA-targeting Half-life Extended BiTE Therapy AMG 160 has Potent Antitumor Activity in Preclinical Models of Metastatic Castration-resistant Prostate Cancer (2023)

&lt;p&gt;Supplementary methods, tables, and references.&lt;/p&gt;
Intracellular Survival of Neisseria gonorrhoeae in Male Urethral Epithelial Cells: Importance of a Hexaacyl Lipid A (2002)

Neisseria gonorrhoeae is a strict human pathogen that invades and colonizes the urogenital tracts of males and females. Lipooligosaccharide (LOS) has been shown to play a role in gonococcal pathogenesis. The acyl transferase MsbB is involved in the biosynthesis of the lipid A portion of the LOS. In order to determine the role of an intact lipid A structure on the pathogenesis of N. gonorrhoeae, the msbB gene was cloned and sequenced, a deletion and insertion mutation was introduced into N. gonorrhoeae, and the mutant strain was designated 1291A11K3. Mass spectrometric analyses of 1291A11K3 LOS determined that this mutation resulted in a pentaacyl rather than a hexaacyl lipid A structure. These analyses also demonstrated an increase in the phosphorylation of lipid A and an increase in length of the oligosaccharide of a minor species of the msbB LOS. The interactions of this mutant with male urethral epithelial cells (uec) were examined. Transmission and scanning electron microscopy studies indicated that the msbB mutants formed close associations with and were internalized by the uec at levels similar to those of the parent strain. Gentamicin survival assays performed with 1291A11K3 and 1291 bacteria demonstrated that there was no difference in the abilities of the two strains to adhere to uec; however, significantly fewer 1291A11K3 bacteria than parent strain bacteria were recovered from gentamicin-treated uec. These studies suggest that the lipid A modification in the N. gonorrhoeae msbB mutant may render it more susceptible to innate intracellular killing mechanisms when internalized by uec.
Impedance Based Biosensor for Agricultural Pathogen Detection (2021)

One of the major limitations on food resources worldwide is the deterioration of plant products due to pathogenic infections. Early screening of plants for pathogenic infections can serve as a boon in the Agricultural sector. The standard microbiology techniques have not kept pace with the rapid enumeration and automated methods for bacteria detection. Electrochemical impedance spectroscopy (EIS) serves as a label free bio sensing technique to monitor pathogens in real time. The changes in the electrical impedance of a growing bacterial culture can be monitored to detect activity of microorganisms. In this study, we demonstrate development of a gold interdigitated electrode (gold IDE) based impedance biosensor to detect bacterial cell enrichment in a growth medium. To standardize the impedance measurement protocol, nutrient broth suspended E.coli cells were used as a model system. The changes in the magnitude of impedance is about 1.5MΩ per doubling of E.coli cells. We further extended this strategy to identify the pathogens in real samples using milk as cell growth medium. Distinct difference of about 5MΩ was seen in the impedance recorded for the healthy and infected potato samples. Our results support the potential application of this impedance based biosensor in agricultural pathogen detection
Gangliosidoses (GM1 and GM2) (2016)

GM1 gangliosidosis is due to beta-galactosidase deficiency. The adult-onset form is characterized by progressive generalized dystonia, often associated with akineto-rigid Parkinsonism. Mild skeletal dysplasia and short stature are good diagnostic clues. GM2 gangliosidosis is due to beta-hexosaminidase deficiency. The adult-onset form is characterized by complex neurological disorders, in which features resulting from cerebellar and motor neuron dysfunction are the most frequent. Movement disorders, psychotic symptoms, mild pyramidal signs, axonal polyneuropathy, autonomic dysfunction, and vertical supranuclear palsy can also be observed. Clinical severity and the rate of progression both vary widely from one patient to another. Diagnosis is based on measurements of enzyme activity and molecular analysis. Physiotherapy, speech therapy and management of swallowing are crucial for these patients’ quality of life and prognosis.
A hierarchical Co3O4/CoS microbox heterostructure as a highly efficient bifunctional electrocatalyst for rechargeable Zn–air batteries (2021)

A hierarchical Co 3 O 4 /CoS catalyst derived from a Prussian blue analog (PBA) shows high cell voltage, outstanding power density, and remarkable cycling stability when used in a rechargeable Zn–air battery.
In Situ-Generation of Electrically Conductive Nanoparticles in Bimetallic Phosphate Materials for High Power Lithium Batteries (2012)

Preparation, characterization, and electrochemical evaluation of two promising bimetallic electrochemical displacement materials for energy storage are described herein. The results demonstrate that the material family of silver vanadium phosphorous oxides (AgwVxPyOz) is suitable for high power applications, such as the implantable cardiac defibrillator.
<title>Fourier transform infrared spectrophotometry for thin film monitors: computer and equipment integration for enhanced capabilities</title> (1991)

Fourier transform infrared spectrophotometry (FTIR) is a valuable technique for monitoring thin films used in semiconductor device manufacture. Determinations of the constituent contents in borophosphosilicate (BPSG) phosphosilicate (PSG) silicon oxynitride (SiON:H and spin-on-glass (SOG) thin films are a few applications. Due to the nature of the technique FTIR instrumentation is one of the most extensively computer-dependent pieces of equipment that is likely to be found in a microelectronics plant. In the role of fab monitor or reactor characterization tool FTIR instruments can rapidly generate large amounts of data. Also the drive for greater accuracy and tighter precision is leading to the development of increasingly sophisticated data processing software that tax the computing abilities of most instrument local data stations. By linking a local FTIR data station to a remote minicomputer its capabilities are greatly improved. We discuss three classes of enhancement. First the FTIR in the fab area communicates and interacts in real time with the minicomputer: transferring data segments to it instructing it to perform sophisticated processing and returning the results to the operator in the fab. Characterizations of PSG thin films by this approach are discussed. Second the spectra of large numbers of samples are processed locally. The large database is then transmitted to the minicomputer for study by statistical/graphics software. Results of CVD-reactor spatial profiling experiments for plasma SiON are presented. Third processing of calibration spectra is performed
Cramer-Rao Bound Analysis on RF-Watermark TxID Detection in SFN with Randomly Distributed Co-channel Interferers (2019)

This paper investigates the detection error of RF-watermark type transmitter identification (TxID) signal in a single frequency network (SFN). Based on a Cramer-Rao bound (CRB) of TxID detection, a closed-form outage probability for TxID detection is derived. In order to reflect the practical network condition, the interference from Poisson-distributed out-of-guard interval transmitters are accounted for detection outage probability.
A packet video system using the dynamic time division multiplexing technique (2003)

A packet transmission system carrying a DS-3 rate, NTSC-quality digital video signal has been prototyped and demonstrated successfully. Fixed-bit-rate video signals are transported in packet form using dynamic time division multiplexing (DTDM). A packet assembler integrates the transmit terminals' information into a basic DTDM data stream suitable for application to a broadband ISDN (integrated services digital network). A packet disassembler distributes the incoming data to the proper receive terminals. The flexible and modular architecture of both packet assembler and disassembler allows service equipment to be physically remoted and provides easy expansion or reconfiguration of the service channels in the future. A digital phase-locked loop was designed to null the frequency difference between the receiver clock and that of the transmitter.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Global and dynamic shimming with the scanner’s inbuilt shim system and a custom-made multi-coil setup at 9.4 T (2017)

The homogenization of static magnetic field (B0) is necessary for MR imaging. The unwanted B0 inhomogeneity becomes more pronounced in ultra high field, and the scanner's inbuilt shim setup can not compensate the B0 fluctuation as is needed. Here we propose to use combined setup of the multi-coil approach and the scanner's shim setup to achieve higher homogeneity of B0 field. We employed custom-built multi-coil for slice-wise shimming in combination with the scanner's shim setup for global shimming. The results show improvement about 50 compare to dynamic shimming alone in the most of the slices.
Proceedings of the first ACM conference on Wireless network security (2008)

It is an honor and pleasure to welcome you to the first ACM Wireless Networks Security Conference. I hope that you will find the technical program stimulating, that our meeting venue will facilitate useful discussions, and that this conference will lead to fruitful collaborations in the future.

During the past decade, it became increasingly clear to most researchers in our field that wireless communication technology would pose significant and unique security challenges. Wireless networks represent the underlying technology of what we now call ubiquitous computing. These networks are frequently deployed in environments that are vulnerable to previously unanticipated forms of adversarial attacks. Indeed, several types of wireless networks include components that operate in an unattended manner in potentially hostile settings. This fact and the typical resource constraints that many wireless networks experience has triggered a reassessment of the adversaries' capabilities and modes of attack. New security problems have arisen and along have come new opportunities for fertile research and development. Many of these opportunities are reflected in the program of this conference.

This first WiSec conference is the result of discussions among several researchers who have been active participants in workshops on wireless, mobile, and ad hoc networks for the past few years. In mid' 2006 it became apparent that the three main workshops focusing on security of mobile ad-hoc and sensor networks, namely ACM Wireless Security Workshop (Wise), held in conjunction with ACM Mobicom, ACM Workshop Security in Ad Hoc and Sensor Networks (SASN), held in conjunction with ACM CCS, and the European Workshop on Security and Privacy in Ad hoc and Sensor Networks (ESAS), have outgrown their initial scope. Several members of what later became the Steering Committee of WiSec felt that bringing together participants who traditionally attended these workshops would help consolidate the previously separate efforts in areas of common interest. The Steering Committee agreed that WiSec would alternate holding its technical meetings between the US and Europe, at least for the near future. Of course, we hope that increasing participation from Asia will enable us to extend our meeting venues to include Asia as well.
Effect of Substituents on the Oxidation Potential of Phthalocyanines and Electrocrystallization (1987)

Abstract A series of tetra- or octasubstituted phthalocyaninatocobalt derivatives were prepared and their oxidation behaviors were examined in relation to the nature of substituents. The oxidation potentials of phthalocyanines, especially those of rings were affected by the nature of both substituents and axial ligands. These oxidation potentials were in a linear relation with the Hammett’s constants for substituents or axial ligands. The electrocrystallization proceeded when an oxidation potential higher than that for the phthalocyanine ring was given to the solution. This potential shift was therefore revealed to be an important factor to control the electrocrystallization of these phthalocyanines.
Towards Flexible Inorganic “Mesomaterials”: One‐Pot Low Temperature Synthesis of Mesostructured Nanocrystalline Titania. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Interacting Effects of Geometry and Gravity Upon the Extreme Boiling Heat Fluxes (1968)

Previous studies of the dynamic and thermodynamic similarity of the peak and minimum pool boiling heat fluxes provide a basis for correlating variable-gravity data. This method is explained and applied to existing data. The dependence of the extreme heat fluxes upon g1/4, developed by Zuber for the flat plate geometry, is shown to be inapplicable in other geometries.