gebhart/patrepeval huggingface dataset:
Combined Approach For Analysis And Prediction Of Biologic Time Series With Non-equidistant Observations (2005)

In the modeling of sparse biologic time series, linear least squares (LU) rhythmometry serves, as a first approximation, to identify a previously unknown single period. In a second step, the linearly obtained results can be used as input for a sequential nonlinear least squares (NLLS) analysis. This latter procedure provides interval as well as point estimations for one or several periods characterizing the data and, at each period, for several other parameters. This combined approach was used in the search for circannual variability in the incidence of giardiasis (GD, a common and worldwide distributed gastrointestinal parasitic disease) in Mexico from 1976 to 1985. The linear function thus obtained was then used to predict the incidence of GD for subsequent years (1987-88). A parameter test for comparison of rhythmic characteristics indicates the statistically significant agreement between the predicted and the real incidence for those two years. This predictable variability in the incidence of GD can readily be used in the design of a timespecified health education program for prevention of this infectious disorder. The sequential LLS-NLLS approach allows the detection of multiple periodicities in short, noisy, and nonequidistant data and, as such, can be generally applied in the analysis, modeling and simulation of biologic time series.
Patch-based image Super Resolution using generalized Gaussian mixture\n model (2022)

Single Image Super Resolution (SISR) methods aim to recover the clean images\nin high resolution from low resolution observations.A family of patch-based\napproaches have received considerable attention and development. The minimum\nmean square error (MMSE) methodis a powerful image restoration method that uses\na probability model on the patches of images. This paper proposes an algorithm\nto learn a jointgeneralized Gaussian mixture model (GGMM) from a pair of the\nlow resolution patches and the corresponding high resolution patches fromthe\nreference data. We then reconstruct the high resolution image based on the MMSE\nmethod. Our numerical evaluations indicate that theMMSE-GGMM method competes\nwith other state of the art methods.\n
Formation and regulation of supramolecular chirality in organogel via addition of tartaric acid (2012)

A new 1,8-naphthalimide derivative was prepared in which the C-4 position was substituted by pyridin-4-ol. This derivative shows good gelation property that can gelate most of polar solvents. As an achiral molecule, helical fibre morphology was observed when the compound gelated acetone solvent. When 0.5 eq of D-tartaric acid or L-tartaric acid was added to the gel, the helical morphology was changed from left-handed to right-handed structure. This result was further proved by circular dichroism measurement. FT-IR experiment showed the formation of intermolecular H-bond between the gelator and tartaric acid. The photophysical properties of gelator had no difference before and after addition of tartaric acid; whereas the lamellar structure was varied by addition of tartaric acid.
APLIKASI BASISDATA PERSEWAAN COMPACT DISC CLIENT SERVER (2011)

Penggunaan aplikasi basisdata saat ini berkembang
dengan semakin meningkatnya kebutuhan pengelolaan
basisdata dalam jumlah besar salah satunya adalah
aplikasi persewaan compact disc yang yang
didistribusikan menggunakan jaringan client server.
Sebagai solusi terhadap kebutuhan tersebut digunakan
MySQL untuk membuat suatu basisdata dan Zeos Access
sebagai mesin penghubung antara aplikasi dengan
basisdata tersebut. Beberapa faktor yang melandasi
penggunaan client server adalah kemampuan menangani
jumlah record yang lebih banyak, keamanan data, adanya
pembagian tugas antara client dan server serta
kemampuan untuk pengontrolan transaksi peminjaman
dari pihak client. Metode yang digunakan adalah
pemakaian basisdata persewaan compact disc yang diolah
secara bersamaan baik dari pihak client atau server.
Ketika member melakukan pemesanan melalui aplikasi
yang telah disediakan maka data pemesanan diarahkan
dalam database, aplikasi yang bertindak sebagai adminr
akan mengeksekusi pemesanan koleksi CD tersebut yang
ditujukanpada database server untuk mengubah status
pemesan menjadi peminjam. Akses yang terdapat dalam
aplikasi server adalah proses index, perubahan data,
peminjaman, pengembalian, penukaran dan melihat
laporan pendapatan, sedangkan pada aplikasi client
adalah pencarian dan pemesanan.
Kata-kunci : record, basisdata, index
Detection and Quantification of Botulinum Neurotoxin Type A by a Novel Rapid In Vitro Fluorimetric Assay (2009)

Botulinum neurotoxin type A (BoNT/A), the most poisonous substance known to humans, is a potential bioterrorism agent. The light-chain protein induces a flaccid paralysis through cleavage of the 25-kDa synaptosome-associated protein (SNAP-25), involved in acetylcholine release at the neuromuscular junction. BoNT/A is widely used as a therapeutic agent and to reduce wrinkles. The toxin is used at very low doses, which have to be accurately quantified. With this aim, internally quenched fluorescent substrates containing the fluorophore/repressor pair pyrenylalanine (Pya)/4-nitrophenylalanine (Nop) were developed. Nop and Pya were, respectively, introduced at positions 197 and 200 of the cleavable fragment (amino acids 187 to 203) of SNAP-25 (with norleucine at position 202 [Nle(202)]), which is acetylated at its N terminus and amidated at its C terminus. Cleavage of this peptide occurred between positions 197 and 198, as in SNAP-25, and was easily quantified by the strong fluorescence emission of the metabolite. To increase the assay sensitivity, the peptide sequence of the previous substrate was lengthened to account for exosite binding to BoNT/A. We synthesized the peptide PL50 (SNAP-25-NH(2) acetylated at positions 156 to 203 [Nop(197), Pya(200), Nle(202)]) and its analogue PL51, in which all methionines were replaced by nonoxidizable Nle. Consistent with a large increase in affinity for BoNT/A, PL50 and PL51 exhibit catalytic efficiencies of 2.6 x 10(6) M(-1) s(-1) and 8.85 x 10(6) M(-1) s(-1), respectively, and behave as the best fluorigenic substrates of BoNT/A reported to date. Under optimized assay conditions, they allow simple quantification of as little as 100 and 60 pg of BoNT/A, respectively, within 2 h with a classical fluorimeter. Calibration of the method against the mouse 50% lethal dose assay unequivocally validates the enzymatic assay.
Surface Charge of Nanoparticles Determines Their Endocytic and Transcytotic Pathway in Polarized MDCK Cells (2008)

A major challenge in drug delivery is the internalization through the apical plasma membrane of the polarized epithelial cells lining organs facing the external environment, e.g., lungs and the gastrointestinal tract. The reduced permeation of drugs entering through this pathway is in part due to the mucosal barrier and low rate of endocytosis at these membranes. We investigated the possible role of nanoparticle surface charge on its entry through the apical plasma membrane and its intracellular pathway. We found that both cationic and anionic nanoparticles are targeted mainly to the clathrin endocytic machinery. A fraction of both nanoparticle formulations is suspected to internalize through a macropinocytosis-dependent pathway. A significant amount of nanoparticles transcytose and accumulate at the basolateral membrane. Some anionic but not cationic nanoparticles transited through the degradative lysosomal pathway. Taken together, these observations indicate that cationic nanoparticles, in addition to their potential for drug delivery to epithelia, may be promising carriers for transcytosing drugs to the blood stream.
Chiroptical Properties of Twisted Acenes: Experimental and Computational Study (2019)

Abstract Invited for the cover of this issue is the group of Ori Gidron at The Hebrew University of Jerusalem. The image depicts a twisted anthracene backbone, in right‐ and left‐handed helicities. Read the full text of the article at 10.1002/chem.201805728 .
HF Radar Sea-echo from Shallow Water (2008)

HF radar systems are widely and routinely used for the measurement of ocean surface currents and waves. Analysis methods presently in use are based on the assumption of infinite water depth, and may therefore be inadequate close to shore where the radar echo is strongest. In this paper, we treat the situation when the radar echo is returned from ocean waves that interact with the ocean floor. Simulations are described which demonstrate the effect of shallow water on radar sea-echo. These are used to investigate limits on the existing theory and to define water depths at which shallow-water effects become significant. The second-order spectral energy increases relative to the first-order as the water depth decreases, resulting in spectral saturation when the waveheight exceeds a limit defined by the radar transmit frequency. This effect is particularly marked for lower radar transmit frequencies. The saturation limit on waveheight is less for shallow water. Shallow water affects second-order spectra (which gives wave information) far more than first-order (which gives information on current velocities), the latter being significantly affected only for the lowest radar transmit frequencies for extremely shallow water. We describe analysis of radar echo from shallow water measured by a Rutgers University HF radar system to give ocean wave spectral estimates. Radar-derived wave height, period and direction are compared with simultaneous shallow-water in-situ measurements.
Preliminary analysis of murine cytotoxic T cell responses to the proteins of the flavivirus Kunjin using vaccinia virus expression (1991)

A series of recombinant vaccinia viruses expressing various parts of the entire Kunjin virus (KUN) coding region was used to analyse the cytotoxic T (Tc) cell responses to KUN. CBA/H mice inoculated with KUN or West Nile virus were shown to develop responses to KUN or various vaccinia virus expression constructs in either primary cytotoxic assays, or after secondary stimulation of the Tc cells in vitro with KUN antigens. Tc cells from CBA mice showed the strongest response to target cells infected with recombinant vaccinia viruses expressing parts of the KUN NS3 and NS4A proteins, and only a weak response to the other structural or non-structural proteins. Further analysis of deleted versions of the NS3-NS4A region showed that the main epitope recognized was derived from a sequence of 99 amino acids spanning parts of NS3 and NS4A. No other major epitopes were detected by Tc cells from CBA mice in the remaining 3333 amino acids of the KUN polypeptide.
Sleep Disorders and Sleep Deprivation: An Unmet Public Health Problem (2006)

It is estimated that 50 to 70 million Americans chronically suffer from a disorder of sleep and wakefulness, hindering daily functioning and adversely affecting health and longevity. The cumulative long-term effects of sleep deprivation and sleep disorders have been associated with a wide range of deleterious health consequences including an increased risk of hypertension, diabetes, obesity, depression, heart attack, and stroke. The Institute of Medicine (IOM) Committee on Sleep Medicine and Research concluded that although clinical activities and scientific opportunities in the field are expanding, awareness among the general public and health care professionals is low, given the magnitude of the burden. The available human resources and capacity are insufficient to further develop the science and to diagnose and treat individuals with sleep disorders. Therefore, the current situation necessitates a larger and more interdisciplinary workforce. Traditional scientific and medical disciplines need to be attracted into the somnology and sleep medicine field. Renewed and revitalized commitments to the field from the National Institutes of Health (NIH), academic health centers, private foundations, and professional societies are essential to ensure appropriate public and professional awareness, education and training, basic and clinical research, and patient care. Finally, the fragmentation of research and clinical care currently present in most academic institutions requires the creation of accredited interdisciplinary sleep programs in academic institutions.
Copper-diamond composite substrates for electronic components (2002)

The application of high power density electronic components such as fast microprocessors and power semiconductors is often limited by an inability to maintain the device junctions below their maximum rated operating temperature. The junction temperature rise is determined by the thermal resistance from junction to the ambient thermal environment. Two of the largest contributions to this thermal resistance are the die attach interface and the package base. A decrease in these resistances can allow increased component packing density in MCMs, reduction of heat sink volume in tightly packed systems, enable the use of higher performance circuit components, and improve reliability. The substrate for a multichip module or device package is the primary thermal link between the junctions and the heat sink. Present high power multichip module and single chip package designs use substrate materials such as silicon nitride or copper tungsten that have thermal conductivity in the range of 200 W/m/spl middot/K. We have developed a copper-diamond composite material, named Dymalloy, with a thermal conductivity of 420 W/m/spl middot/K, better than copper, and an adjustable coefficient of thermal expansion, nominally 5.5 ppm//spl deg/C at 25/spl deg/C, compatible with silicon and gallium arsenide. Because of the matched coefficient of thermal expansion it is possible to use low thermal resistance hard die attach methods. Dymalloy is a composite material made using micron size Type I diamond powder that has a published thermal conductivity of 600 to 1000 W/m/spl middot/K in a metal matrix that has a thermal conductivity of 350 W/m/spl middot/K. Besides having exceptional thermal properties, the mechanical properties of this material also make it an attractive candidate as an electronic component substrate material.
Data from MET Tyrosine Kinase Inhibition Enhances the Antitumor Efficacy of an HGF Antibody (2023)

&lt;div&gt;Abstract&lt;p&gt;Receptor tyrosine kinase therapies have proven to be efficacious in specific cancer patient populations; however, a significant limitation of tyrosine kinase inhibitor (TKI) treatment is the emergence of resistance mechanisms leading to a transient, partial, or complete lack of response. Combination therapies using agents with synergistic activity have potential to improve response and reduce acquired resistance. Chemoreagent or TKI treatment can lead to increased expression of hepatocyte growth factor (HGF) and/or MET, and this effect correlates with increased metastasis and poor prognosis. Despite MET's role in resistance and cancer biology, MET TKI monotherapy has yielded disappointing clinical responses. In this study, we describe the biological activity of a selective, oral MET TKI with slow off-rate and its synergistic antitumor effects when combined with an anti-HGF antibody. We evaluated the combined action of simultaneously neutralizing HGF ligand and inhibiting MET kinase activity in two cancer xenograft models that exhibit autocrine HGF/MET activation. The combination therapy results in additive antitumor activity in KP4 pancreatic tumors and synergistic activity in U-87MG glioblastoma tumors. Pharmacodynamic characterization of biomarkers that correlate with combination synergy reveal that monotherapies induce an increase in the total MET protein, whereas combination therapy significantly reduces total MET protein levels and phosphorylation of 4E-BP1. These results hold promise that dual targeting of HGF and MET by combining extracellular ligand inhibitors with intracellular MET TKIs could be an effective intervention strategy for cancer patients who have acquired resistance that is dependent on total MET protein. &lt;i&gt;Mol Cancer Ther; 16(7); 1269–78. ©2017 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Coherent frequency-down-conversion interface for quantum repeaters (2010)

We report a coherence-preserving photon frequency down-conversion experiment based on difference-frequency generation in a periodically poled Lithium niobate waveguide, at the single-photon level. The coherence of the process has been demonstrated by measuring the phase coherence of pseudo single-photon time-bin qubits after frequency conversion with an interference visibility of >96 %. This interface could be of interest for quantum repeater based hybrid networks.
The Complete Set of Thermo-mechanical-Radiation Methods, Simulations and Results for a Swarm of Nanorovers Deployed on the Moon’s Surface (Lunar Zebro Mission) (2022)

Abstract Lunar Zebro’s mission is heading the race for deploying the world’s smallest and lightest swarm of nanorovers on the surface of Moon. The concept validation of a single nanorover is of crucial importance, as it will be the launching pad for deploying a swarm of those nanorovers thereafter. Then, they will get connected in a network, acting as a single device and performing scientific missions analyzing data from remote points on the Moon’s surface. In the current study, the complete set of thermo-mechanical-radiation analyses for Lunar Zebro nanorovers are carried out. These range from the Ground Segment to the Moon environment, taking also into account the extreme mechanical and thermal environment at launch-transit conditions when the nanorover is attached to the lander. An innovative ray tracing method to evaluate the effect of the thermal environment on the Lunar Zebro nanorovers is explained in this paper. Material choices, structural design, and mechanical/thermal strategies for the nanorover to overcome the launch, space and Moon’s conditions are shown. The different analyses methods used, expected loads and results obtained should serve as a baseline for evaluating the behaviour of other small devices attached to a lander when aiming for any space mission. More specifically, for those aiming to go to the Moon, the environmental and mechanical expectations here can also be implemented. The ultimate outcome of the paper is the environmental survivability assurance from an analytical perspective of these nanorovers when being sent to the Moon. The validation of the survivability of a single nanorover will be a breakthrough in the space swarm robotics’ field, resulting in the successful performance of the lightest swarm of nanorovers ever deployed on the Moon’s surface.
Induction of 8-hydroxydeoxyguanosine but not initiation of carcinogenesis by redox enzyme modulations with or without menadione in rat liver (1991)

Inducibility of oxidative stress in rat liver in vivo by menadione-associated redox cycling activation under redox enzyme modulating conditions was examined by monitoring hepatocyte injury and 8-hydroxydeoxyguanosine (8-OHdG) levels of liver DNA. In addition, the treatment-associated liver tumor initiating activity was assessed in terms of development of gamma-glutamyl-transpeptidase (GGT)- and glutathione S-transferase placental form (GST-P)-positive foci and hyperplastic nodules. With or without following menadione treatment (50 mg/kg, i.g.), redox enzyme modulations of increased cytochrome P450 reductase activity induced by phenobarbital (PB)-Na (100 mg/kg, i.p. for 5 days), inhibition of DT-diaphorase by dicumarol (25 mg/kg, i.p.) and depletion of glutathione by phorone (200 mg/kg, i.p.), with or without further supplement of iron EDTA-Na-Fe(III) (70 mg/kg, i.p.), caused both substantial hepatocyte necrosis and 8-OHdG production in Fischer 344 male rats. Subsequent feeding with a 0.05% PB diet for 64 weeks resulted in slightly increased development of GGT-positive foci but not GST-P positive lesions or hyperplastic nodules, suggesting a lack of tumor-initiating activity of the oxidative DNA damage associated with redox enzyme modulations with or without menadione.
WPP-Domain Proteins Mimic the Activity of the HSC70-1 Chaperone in Preventing Mistargeting of RanGAP1-Anchoring Protein WIT1 (2009)

Arabidopsis (Arabidopsis thaliana) tryptophan-proline-proline (WPP)-domain proteins, WPP1 and WPP2, are plant-unique, nuclear envelope-associated proteins of unknown function. They have sequence similarity to the nuclear envelope-targeting domain of plant RanGAP1, the GTPase activating protein of the small GTPase Ran. WPP domain-interacting tail-anchored protein 1 (WIT1) and WIT2 are two Arabidopsis proteins containing a coiled-coil domain and a C-terminal predicted transmembrane domain. They are required for RanGAP1 association with the nuclear envelope in root tips. Here, we show that WIT1 also binds WPP1 and WPP2 in planta, we identify the chaperone heat shock cognate protein 70-1 (HSC70-1) as in vivo interaction partner of WPP1 and WPP2, and we show that HSC70-1 interacts in planta with WIT1. WIT1 and green fluorescent protein (GFP)-WIT1 are targeted to the nuclear envelope in Arabidopsis. In contrast, GFP-WIT1 forms large cytoplasmic aggregates when overexpressed transiently in Nicotiana benthamiana leaf epidermis cells. Coexpression of HSC70-1 significantly reduces GFP-WIT1 aggregation and permits association of most GFP-WIT1 with the nuclear envelope. Significantly, WPP1 and WPP2 show the same activity. A WPP1 mutant with reduced affinity for GFP-WIT1 fails to decrease its aggregation. While the WPP-domain proteins act on a region of WIT1 containing the coiled-coil domain, HSC70-1 additionally acts on the C-terminal transmembrane domain. Taken together, our data suggest that both HSC70-1 and the WPP-domain proteins play a role in facilitating WIT1 nuclear envelope targeting, which is, to our knowledge, the first described in planta activity for the WPP-domain proteins.
Electrode nanogap enhanced and dielectrophoresis-enabled Raman spectroscopy of single biomolecules with simultaneous real-time electronic monitoring (2012)

This work reports a versatile platform for manipulation and sensing of biological molecules based on electrode nanogaps, which function as dielectrophoresis-enabled molecular trapping templates as well as spectroscopic and nanoelectronic detection substrates. On a chip, an array was constructed of Ti/Al nanoelectrode pairs with gap dimensions ranging from few tens of nm to <10 nm. During the molecular trapping process, ionic current measurements across the nanoelectrodes were used to detect trapping of a protein in the gap. Concurrent recording of time-dependent Raman spectra provided evidence of molecule(s) appearing in the nanogap.
Arrhythmia Caused by a Drosophila Tropomyosin Mutation Is Revealed Using a Novel Optical Coherence Tomography Instrument (2010)

These results demonstrate the capability of our OCT instrument to characterize in detail cardiac activity in genetic models for heart disease in Drosophila.