gebhart/patrepeval huggingface dataset:
Phospholipase A2 binding and anti-inflammatory activity (2002)

The functional site of ‘phospholipase A2 inhibitor from python’ (PIP) was predicted based on the hypothesis of proline brackets. Using diAerent sources of secretory phospholipase A2 (sPLA2s) as enzyme, and [ 3 H]arachidonate-labelled Escherichia coli as substrate, short synthetic peptides representing the proposed site were examined for theirsecretoryphospholipase A2(sPLA2)inhibitoryactivity. A decapeptide P-PB.III proved to be the most potent of the tested peptides in inhibiting sPLA2 enzymatic activity in vitro, and exhibited striking anti-inflammatory eAects in vivo in a mouse paw oedema model. P-PB.III inhibited the enzymatic activity of class I, II and III PLA2s, including that of human synovialfluid from arthritis patients. When tested by ELISA, biotinylated P-PB.III interacted positively with various PLA2s, suggesting that the specific region of PIP corresponding to P-PB.III, is likely to be involved in the PLA2‐PLI interaction. The eAect of P-PB.III on the peritoneal inflammatory response after surgical trauma in rats was also examined. P-PB.III eAectively reduced the extent of postsurgical peritoneal adhesions as compared to controls. sPLA2 levels at seventh postoperative day in the peritoneal tissue of P-PB.III-treated rats were also significantly reduced ( P< 0.05)incomparisontothoseoftheuntreatedcontrols. The present results shed additional insight on the essential structural elementsforPLA2binding, andmaybeusefulas a basis for the design of novel therapeutic agents.
Probing the Geometry and Interconnectivity of Pores in Organic Aerogels Using Hyperpolarized <sup>129</sup>Xe NMR Spectroscopy (2004)

Hyperpolarized (HP) 129Xe NMR was used for the first time to probe the geometry and interconnectivity of pores in RF aerogels and to correlate them with the [resorcinol]/[catalyst] (R/C) ratio. We have demonstrated that HP 129Xe NMR is an ideal method for accurately measuring the volume-to-surface-area (Vg/S) ratios for soft mesoporous materials without using any geometric models. The Vg/S parameter, which is related both to the geometry and the interconnectivity of the porous space, has been found to correlate strongly with the R/C ratio and exhibits an unusually large span: an increase in the R/C ratio from 50 to 500 results in about 5-fold rise in Vg/S. Unlike conventional techniques, HP 129Xe NMR spectroscopy probes the geometry and interconnectivity of the nano- or mesopores in soft materials, providing new insights into the pore structure.
Mechanically strong fully biobased anisotropic cellulose aerogels (2016)

A series of mechanically strong and fully biobased carboxymethyl cellulose (CMC)/cellulose nanofibril (CNF) hybrid aerogels were produced <italic>via</italic> an environmentally friendly unidirectional freeze-drying process.
Characterization of a high molecular weight protective antigen of<i>Plasmodium yoelli</i> (1984)

A 230 000 molecular weight Plasmodium yoelii protective antigen was characterized. Two monoclonal antibodies against P. yoelii immunoprecipitated the 230 000 mol. wt protein and a number of lower molecular weight polypeptides. These polypeptides were shown by peptide mapping and specific antibody binding to be fragments of the large protein. Iodination experiments suggested that the lower molecular weight species may be present on the surface of the merozoite. The protein was found not to be glycosylated. By serology, related antigens were shown to be associated with blood-stage schizonts of P. vinckei subspp., P. chabaudi subspp. and P. falciparum.
Exclusion of Linkage Between Bipolar Affective Disorder and Chromosome 16 in 12 Australian Pedigrees (1997)

Several recent reports of possible susceptibility loci for bipolar affective disorder (BAD) have identified sites on a number of chromosomes. Specifically, two Danish studies have suggested the presence of a susceptibility locus for BAD on chromosome 16p13. As the first step of a whole genome scan, we screened 12 Australian families with markers at 16p13 and also a number of markers spanning the entirety of chromosome 16. Linkage analysis was undertaken using both the parametric lod score method (two- and multipoint) with different models and diagnostic thresholds, and the nonparametric affected pedigree member (APM) method. Results of lod score analysis convincingly excluded the 16p13 region from linkage to BAD in these families, while APM provided no support for linkage. Furthermore, using the broad definition of BAD, with individuals affected by bipolar I and II and recurrent unipolar disorders included, the entire chromosome was excluded from linkage to BAD with autosomal-dominant transmission at a maximum age-specific penetrance of 60%, and with autosomal-dominant and recessive modes of transmission at a maximum age-specific penetrance level of 90%. Diagnostic thresholds which did not include unipolar affected individuals were somewhat less informative. However, a majority (between 63-96%, depending upon the model) of the chromosome was clearly excluded using narrow diagnostic thresholds. Moreover, no positive lod scores were obtained at theta = 0.00 for any tested model or diagnostic threshold. Our results indicate that no linkage exists between BAD and chromosome 16 markers in this group of Australian families.
Novel technique of a multifunctional electrosurgical system for minimally invasive surgery (2016)

Bipolar electrosurgery in the minimally invasive endoscopic surgery theater has been traditionally limited to the use of standard bipolar forceps, which are minimally versatile, have a limited range of motion, and are associated with visualization and handling constraints. The authors designed a novel surgical device system in which commonly used surgical instruments (suction, microscissors, micrograspers, and dissectors) co-function as individually insulated and modular electrodes for bipolar electrosurgery. In this feasibility study, the successful use of these prototypes in endonasal endoscopic transsphenoidal surgery was demonstrated on 2 human cadavers, and in an in vivo arterial coagulation model on 2 live rats. This prototype system provided improved bipolar instrument mobility, minimized the requirement to exchange surgical instruments when performing electrosurgery, and allowed for new maneuvers that optimized surgical workflow, such as the ability to suction blood and smoke while cauterizing. This multifunctional bipolar cautery system may improve surgical efficiency and workflow and facilitate surgical microdissection and electrocautery during minimally invasive, endoscopic, robotic or traditional open surgery.
EN2: A Novel Prostate Cancer Biomarker (2013)

Extensive efforts to identify a clinically useful biomarker for the diagnosis of prostate cancer have resulted in important insights into the biology of the disease, but no new test has been approved by regulatory authorities. The unmet need has also shifted to identifying biomarkers that not only diagnose prostate cancer but also indicate whether the patient has 'significant' disease. EN2 is a homeobox-containing transcription factor secreted specifically by prostate cancers into urine, where it can be detected by a simple ELISA assay. A number of studies have demonstrated the enormous potential of EN2 to address this unmet need and provide the urologist with a simple, cheap and efficient prostate cancer biomarker.
Starch-lignin foams (2010)

Although starch foams are well known as biodegradable alternatives to foamed polystyrene, starch-lignin foams have not previously been reported. Lignin is an abundant byproduct of paper manufacture usually burned as fuel for lack of higher-value uses. We have prepared novel starch-kraft lignin foams with a known technique similar to compression molding. Replacing 20% of the starch with lignin has no deleterious effect on density or morphology as indicated by scanning electron microscopy: a thin outer layer of approximately 100 m encloses a region of cellular structure containing 100-200 m voids, with the major internal region of the foam consisting of large voids of up to 1 mm in size. Powder X-ray diffraction shows residual structure in both starch and starch-lignin foams. Differential scanning calorimetry displays endothermic transitions in the starch foam but not in the starch-lignin foam, indicating that lignin stabilizes the residual starch structure. Lignin decreases water absorption; diffusion constants for the starch and starch-lignin foams are 2.6810 -6 and 0.8010 -6 cm 2 /sec, respectively. The flexural strength of the starch-lignin foam is similar to that of foamed polystyrene, the strain at maximum stress is smaller, and the modulus of elasticity is larger.
Three-dimensional continuous particle focusing in a microfluidic channel via standing surface acoustic waves (SSAW) (2011)

Three-dimensional (3D) continuous microparticle focusing has been achieved in a single-layer polydimethylsiloxane (PDMS) microfluidic channel using a standing surface acoustic wave (SSAW). The SSAW was generated by the interference of two identical surface acoustic waves (SAWs) created by two parallel interdigital transducers (IDTs) on a piezoelectric substrate with a microchannel precisely bonded between them. To understand the working principle of the SSAW-based 3D focusing and investigate the position of the focal point, we computed longitudinal waves, generated by the SAWs and radiated into the fluid media from opposite sides of the microchannel, and the resultant pressure and velocity fields due to the interference and reflection of the longitudinal waves. Simulation results predict the existence of a focusing point which is in good agreement with our experimental observations. Compared with other 3D focusing techniques, this method is non-invasive, robust, energy-efficient, easy to implement, and applicable to nearly all types of microparticles.
High-Speed Digital Frequency Scanning Ion Trap Mass Spectrometry (2013)

A novel means of simultaneous ion injection and mass scanning has been studied. Classic injection methods for ion trap mass spectrometry proceed by loading the trap and scanning out in mutually exclusive time segments. This mode implicitly imparts a duty cycle and acquisition rate limit to ion trap mass analysis. Using digital frequency scanning methods without the use of discrete injection phases, we demonstrate continuous injection and acquisition rates up to 1000 Hz (averaging 400,000 Th/s) in a 3D ion trap configuration showing an alternatively faster control of ions over the classic voltage ramping mass-selective instability scanning method. The digital frequency scanning method may accommodate current advances in high-speed separation [e.g., ultraperformance liquid chromatography (UPLC), two-dimensional gas chromatography (GC×GC), ion mobility spectrometry (IMS), and capillary electrophoresis (CE)] and ion transfer efficiency (e.g., ion funnels). These ion sources may comprise high ion currents with compositions that change quickly and require high-speed mass analysis. Though resolution is compromised with higher acquisition rates, the frequency scanning mode permits a more flexible platform to accomplish the optimal trade-off of speed and mass spectral quality.
α-RgIA:  A Novel Conotoxin That Specifically and Potently Blocks the α9α10 nAChR<sup>,</sup> (2006)

The alpha9 and alpha10 nicotinic acetylcholine receptor (nAChR) subunits assemble to form the alpha9alpha10 nAChR subtype. This receptor is believed to mediate cholinergic synaptic transmission between efferent olivocochlear fibers and the hair cells of the cochlea. In addition alpha9 and/or alpha10 expression has been described in dorsal root ganglion neurons, lymphocytes, skin keratinocytes, and the pars tuberalis of the pituitary. Specific antagonists that selectively block the alpha9alpha10 channel could be valuable tools for elucidating its role in these diverse tissues. This study describes a novel alpha-conotoxin from the Western Atlantic species Conus regius, alpha-conotoxin RgIA (alpha-RgIA), that is a subtype specific blocker of the alpha9alpha10 nAChR. alpha-RgIA belongs to the alpha4/3 subfamily of the alpha-conotoxin family; sequence and subtype specificity comparisons between alpha-RgIA and previously characterized alpha4/3 toxins indicate that the amino acids in the C-terminal half of alpha-RgIA are responsible for its preferential inhibition of the alpha9alpha10 nAChR subtype.
Explainable and Scalable Machine-Learning Algorithms for Detection of Autism Spectrum Disorder using fMRI Data (2020)

Diagnosing Autism Spectrum Disorder (ASD) is a challenging problem, and is based purely on behavioral descriptions of symptomology (DSM-5/ICD-10), and requires informants to observe children with disorder across different settings (e.g. home, school). Numerous limitations (e.g., informant discrepancies, lack of adherence to assessment guidelines, informant biases) to current diagnostic practices have the potential to result in over-, under-, or misdiagnosis of the disorder. Advances in neuroimaging technologies are providing a critical step towards a more objective assessment of the disorder. Prior research provides strong evidence that structural and functional magnetic resonance imaging (MRI) data collected from individuals with ASD exhibit distinguishing characteristics that differ in local and global spatial, and temporal neural-patterns of the brain. Our proposed deep-learning model ASD-DiagNet exhibits consistently high accuracy for classification of ASD brain scans from neurotypical scans. We have for the first time integrated traditional machine-learning and deep-learning techniques that allows us to isolate ASD biomarkers from MRI data sets. Our method, called Auto-ASD-Network, uses a combination of deep-learning and Support Vector Machines (SVM) to classify ASD scans from neurotypical scans. Such interpretable models would help explain the decisions made by deep-learning techniques leading to knowledge discovery for neuroscientists, and transparent analysis for clinicians.
Power Minimization in Wireless Network Virtualization with Massive MIMO (2018)

This paper presents a new method of wireless network virtualization to share the downlink of a massive-MIMO base station among multiple Service Providers (SPs). The SPs are allowed to simultaneously utilize all antennas and channel resource of the Infrastructure Provider (InP). This can improve resource utilization but also requires the InP to control the interference between SPs that are oblivious of each other. We develop novel precoding schemes to minimize the InP's transmission power while satisfying certain prescribed maximum deviation between each SP's intended signal to its users and what the InP delivers. This problem is studied for both perfect and imperfect channel state information (CSI). Under perfect CSI, the proposed precoding is optimal and substantially outperforms a time-sharing alternative. Under imperfect CSI, we use a numerical lower bound to show that the proposed precoding is nearly optimal.
Purification and Characterization of a Thermostable Trehalose Synthase from<i>Thermus aquaticus</i> (1996)

Thermostable trehalose synthase, which catalyzes the conversion of maltose into trehalose by intramolecular transglucosylation, was purified from a cell-free extract of the thermophilic bacterium Thermus aquaticus ATCC 33923 to an electrophoretically homogeneity by successive column chromatographies. The purified enzyme had a molecular weight of 105,000 by SDS-polyacrylamide gel electrophoresis and a pI of 4.6 by gel isoelectrofocusing. The N-terminal amino acid of the enzyme was methionine. The optimum pH and temperature were pH 6.5 and 65°C, respectively. The enzyme was stable from pH 5.5 to 9.5 and up to 80°C for 60min. The trehalose synthase from Thermus aquaticus is more thermoactive and thermostable than that from Pimelobacter sp. R48. The yield of trehalose from maltose by the enzyme was independent of the substrate concentration, and tended to increase at lower temperatures. The maximum yield of trehalose from maltose by the enzyme reached 80-82% at 30-40°C. The activity was inhibited by Cu(2+) , Hg(2+), Zn(2+), and Tris.
Human Plasma Proteins from Transgenic Animal Bioreactors (1996)

We have evaluated the transgenic animal bioreactor (TAB) system for the production of human Protein C (HPC), an anticoagulant plasma protein. Mouse whey acidic protein (mWAP) gene regulatory sequences targeted expression of mWAP/HPC hybrid genes to the mammary gland of transgenic mice and pigs. The transgenes were stably transmitted through several generations and expression did not adversely affect the health of animals. We purified recombinant HPC from milk which was structurally and enzymatically similar to the human protein, demonstrating the potential of TABs for the production of plasma proteins. The active fraction was found to be only a part of the total protein secreted. At mg/mL levels of secretion, modifications like proteolytic maturation and γ-carboxylation became limiting factors in the production of functional protein. We have proposed and shown that these limitations may be overcome by engineering the posttranslational protein modification capacity of selected organs of the TAB.
Four-wave mixing and wavelength conversion in coupled-resonator optical waveguides (2008)

The four-wave mixing process in coupled-resonator optical waveguides is considered in detail and an approximate and simple approach allowing one to estimate the conversion efficiency is proposed. The analytical results are verified through a reliable and complete numerical technique taking into account nonlinear induced phase modulations, the large-signal regime, and the pulse shape evolution along the structure. The conversion efficiency is enhanced by the slow down factor to the fourth power and the impact of attenuation and phase mismatch are carefully investigated. The main aim of this study is to provide a technique to design efficient and compact wavelength converters. Two examples of devices operating on signals at 10 and 50 Gbits/s are presented and discussed. Pulse distortions induced by chromatic dispersion, frequency detuning, and slow down factor wavelength dependence are examined and the beneficial role of the nonlinear induced phase modulation on the phase mismatch is pointed out. Numerical examples show that with typical semiconductor characteristics, very high conversion efficiencies with pump powers of only a few tenths of milliwatts are achievable.
Structural requirements for voltage‐dependent block of muscle sodium channels by phenol derivatives (2001)

We have studied the effects of four different phenol derivatives, with methyl and halogen substituents, on heterologously expressed human skeletal muscle sodium channels, in order to find structural determinants of blocking potency. All compounds blocked skeletal muscle sodium channels in a concentration-dependent manner. The methylated phenol 3-methylphenol and the halogenated phenol 4-chlorophenol blocked sodium currents on depolarization from -100 mV to 0 mV with IC(50) values of 2161 and 666 microM respectively. Methylation of the halogenated compound further increased potency, reducing the IC(50) to 268 microM in 2-methyl-4-chlorophenol and to 150 microM in 3,5-dimethyl-4-chlorophenol. Membrane depolarization before the test depolarization increased sodium channel blockade. When depolarizations were started from -70 mV or when a 2.5 s prepulse was introduced before the test pulse inducing slow inactivation, the IC(50) was reduced more than 3 fold in all compounds. The values of K(D) for the fast-inactivated state derived from drug-induced shifts in steady-state availability curves were 14 microM for 3,5-dimethyl-4-chlorophenol, 19 microM for 2-methyl-4-chlorophenol, 26 microM for 4-chlorophenol and 115 microM for 3-methylphenol. All compounds accelerated the current decay during depolarization and slowed recovery from fast inactivation. No relevant frequency-dependent block after depolarizing pulses applied at 10, 50 and 100 Hz was detected for any of the compounds. All the phenol derivatives that we examined are effective blockers of skeletal muscle sodium channels, especially in conditions that are associated with membrane depolarization. Blocking potency is increased by halogenation and by methylation with increasing numbers of methyl groups.
Detection of prostate cancer in multiparametric MRI using random forest with instance weighting (2017)

A prostate computer-aided diagnosis (CAD) based on random forest to detect prostate cancer using a combination of spatial, intensity, and texture features extracted from three sequences, T2W, ADC, and B2000 images, is proposed. The random forest training considers instance-level weighting for equal treatment of small and large cancerous lesions as well as small and large prostate backgrounds. Two other approaches, based on an AutoContext pipeline intended to make better use of sequence-specific patterns, were considered. One pipeline uses random forest on individual sequences while the other uses an image filter described to produce probability map-like images. These were compared to a previously published CAD approach based on support vector machine (SVM) evaluated on the same data. The random forest, features, sampling strategy, and instance-level weighting improve prostate cancer detection performance [area under the curve (AUC) 0.93] in comparison to SVM (AUC 0.86) on the same test data. Using a simple image filtering technique as a first-stage detector to highlight likely regions of prostate cancer helps with learning stability over using a learning-based approach owing to visibility and ambiguity of annotations in each sequence.
Expansive Linguistic Representations to Predict Interpretable Odor Mixture Discriminability (2022)

Abstract Language is often thought as being poorly adapted to precisely describe or quantify smell and olfactory attributes. In this work, we show that semantic descriptors of odors can be implemented in a model to successfully predict odor mixture discriminability, an olfactory attribute. We achieved this by taking advantage of the structure-to-percept model we previously developed for monomolecular odorants, using chemical descriptors to predict pleasantness, intensity and 19 semantic descriptors such as ‘fish’, ‘cold’, ‘burnt’, ‘garlic’, ‘grass’ and ‘sweet’ for odor mixtures, followed by a metric learning to obtain odor mixture discriminability. Through this expansion of the representation of olfactory mixtures, our Semantic model outperforms state of the art methods by taking advantage of the intermediary semantic representations learned from human perception data to enhance and generalize the odor discriminability/similarity predictions. As 10 of the semantic descriptors were selected to predict discriminability/similarity, our approach meets the need of rapidly obtaining interpretable attributes of odor mixtures as illustrated by the difficulty of finding olfactory metamers. More fundamentally, it also shows that language can be used to establish a metric of discriminability in the everyday olfactory space.