gebhart/patrepeval huggingface dataset:
Weak Protein−Protein Interactions Are Sufficient To Drive Assembly of Hepatitis B Virus Capsids (2002)

Hepatitis B virus (HBV) is an enveloped DNA virus with a spherical capsid (or core). The capsid is constructed from 120 copies of the homodimeric capsid protein arranged with T = 4 icosahedral symmetry. We examined in vitro assembly of purified E. coli expressed HBV capsid protein. After equilibration, concentrations of capsid and dimer were evaluated by size exclusion chromatography. The extent of assembly increased as temperature and ionic strength increased. The concentration dependence of capsid assembly conformed to the equilibrium expression: K(capsid) = [capsid]/[dimer](120). Given the known geometry for HBV capsids and dimers, the per capsid assembly energy was partitioned into energy per subunit-subunit contact. We were able to make three major conclusions. (i) Weak interactions (from -2.9 kcal/mol at 21 degrees C in low salt to -4.4 kcal/mol at 37 degrees C in high salt) at each intersubunit contact result in a globally stable capsid; weak intersubunit interactions may be the basis for the phenomenon of capsid breathing. (ii) HBV assembly is characterized by positive enthalpy and entropy. The reaction is entropy-driven, consistent with the largely hydrophobic contacts found in the crystal structure. (iii) Increasing NaCl concentration increases the magnitude of free energy, enthalpy, and entropy, as if ionic strength were increasing the amount of hydrophobic surface buried by assembly. This last point leads us to suggest that salt acts by inducing a conformational change in the dimer from an assembly-inactive form to an assembly-active form. This model of conformational change linked to assembly is consistent with immunological differences between dimer and capsid.
Solvent effects on the polarization transfer between a photo-excited spin-polarized radical pair and a TEMPO radical (2018)

ISIC
Implementation-friendly synchronisation algorithm for DVB-T2 (2010)

To support high-definition television, the revision of DVB-T, the terrestrial digital video broadcasting standard, has recently been developed under the abbreviation DVB-T2. The provision of the anticipated high data rate services requires highly accurate synchronisation and frequency acquisition and tracking. Setting out from the procedure defined by the DVB-T2 implementation guidelines provided by the DVB-T2 standardisation community, a modified, yet implementation-friendly synchronisation algorithm has been developed. Simulation results show a similar performance for synchronisation and frequency offset estimation, as well as the detection of the signalling information contained in the preamble P1 with a significant reduction of the implementation complexity.
Target 2035 – update on the quest for a probe for every protein (2021)

Twenty years after the publication of the first draft of the human genome, our knowledge of the human proteome is still fragmented. The challenge of translating the wealth of new knowledge from genomics into new medicines is that proteins, and not genes, are the primary executers of biological function. Therefore, much of how biology works in health and disease must be understood through the lens of protein function. Accordingly, a subset of human proteins has been at the heart of research interests of scientists over the centuries, and we have accumulated varying degrees of knowledge about approximately 65% of the human proteome. Nevertheless, a large proportion of proteins in the human proteome (∼35%) remains uncharacterized, and less than 5% of the human proteome has been successfully targeted for drug discovery. This highlights the profound disconnect between our abilities to obtain genetic information and subsequent development of effective medicines. Target 2035 is an international federation of biomedical scientists from the public and private sectors, which aims to address this gap by developing and applying new technologies to create by year 2035 chemogenomic libraries, chemical probes, and/or biological probes for the entire human proteome.
Experimental Comparison of Pulse Amplitude Modulation (PAM) and Discrete Multi-tone (DMT) for Short-Reach 400-Gbps Data Communication (2013)

Pulse amplitude modulation (PAM) and discrete multi-tone (DMT) technology are attractive modulation techniques for short-reach applications of the next-generation optical transmission systems. We have simulated and experimentally measured and compared the transmission characteristics of PAM and DMT by using the same simulation model and the same experimental setup. Consequently, we have confirmed that DMT has an advantage over PAM.
Multiparametric, label-free two-photon imaging of metabolic function (Conference Presentation) (2020)

Metabolism plays a critical role in the function of cells and tissues. Changes in metabolic function are hallmarks of numerous conditions, including aging, cancer, obesity and neurodegenerative diseases. Such changes are highly dynamic and heterogeneous at the microscopic scale. Label-free, two-photon microscopic imaging offers opportunities to monitor and characterize such aspects of metabolic function non-destructively. Intensity and lifetime fluorescence measurements from endogenous NAD(P)H and FAD can serve as sensitive indicators of metabolic changes associated with redox state and mitochondrial organization. In fact, a combination of optical metabolic readouts including the redox ratio, NADH bound fraction, and mitochondrial clustering can provide important insights on the specific nature of the metabolic pathway perturbation that yielded the optical changes. Assessment of such information has the potential to improve our understanding, detection, and treatment of numerous diseases. For example, our studies highlight that the use of multiple optical metabolic readouts enables sensitive and specific detection of changes that are associated with adipose tissue type (brown vs beige vs white) and responses to stimuli. In addition, we have discovered that our ability to characterize depth-dependent variations within epithelial tissues, such as the skin and cervix, plays a key role in identifying alterations that occur at the onset of cancer and may be used to develop improved, non-invasive methods for cancer diagnosis. Monitoring of immune system cell activation is another important application area. Such findings pave the way for exploiting label-free, metabolic imaging techniques to understand dynamic cell interaction and their role in the development and treatment of a number of human diseases.
High frequency injection-based stator flux linkage and torque estimation for DB-DTFC implementation on IPMSMs considering cross-saturation effects (2013)

Deadbeat-direct torque and flux control (DB-DTFC) has demonstrated several technical advantages over classical hysteresis DTC and PI regulator based direct torque control (DTC) methods. These include fast torque control, low ripple, easily integrated dynamic loss minimization control, and one control law that uses the inherent Volt-sec. source properties of power electronics to enable operation over all operating conditions including voltage limits. DB-DTFC uses the fundamental machine model to form the inverse solution for Volt-sec selection at each switching period. Therefore, DB-DTFC is a model-based discrete time controller that relies on accurate machine parameter estimation to provide accurate dynamic torque control. In this paper, a new method for high frequency injection-based real-time self- and mutual inductance estimation is proposed and evaluated in both simulations and experiments. In this new method, the estimated inductances including cross-coupling inductance due to cross-saturation are then used to estimate the stator resistance and permanent magnet flux linkage. The stator flux linkage observer using the identified machine parameters, yields improved stator flux linkage estimates that enable precise torque calculation. Experimental evaluation of the HFI-based flux estimates on torque estimation and control accuracy is performed at an IPMSM drive test bench with torque transducer mounted.
Short‐term(S‐T) dietary magnesium(Mg) deficiency(MD) results in generation of cardiovascular risk factors, free radicals & apoptosis, which are inhibited by water‐borne Mg (2008)

It has been suggested that low dietary intake of Mg is an unappreciated risk factor for cardiovascular diseases(CVD), and leads to generation of free radicals and programmed cell death. Can water‐borne Mg overcome these pathological alterations? Using S‐T( 21 days) dietary deficiency of Mg( 10 % normal intake) in Wistar rats, we determined whether S‐T MD would lead to lowering of serum (s)‐Mg,s‐HDL‐cholesterol(HDL‐C),elevation of s‐LDL‐cholesterol ( LDL –C),and s‐calcium(Ca),activation of nitric oxide synthase ( n‐NOS),lipid peroxidation (LP),DNA fragmentations (DNA‐fr.),and activation of caspase‐3( CAS‐3) apoptotic pathways in cardiac ( CA) and aortic smooth muscle ( AOSM) in‐vivo. The MD‐animals were allowed to drink triply‐distilled water containing one of five different levels of Mg while control animals received normal Mg‐containing diets and given triply‐distilled water . On the 22nd day, sera and tissues ( left &amp; right ventricles,atria &amp; abdominal aorta) were analyzed. The data indicate that S‐T MD resulted in reductions in s‐Mg ( ~ 75%),and s‐HDL‐C(~50%) and elevation in s‐Ca and s‐LDL‐C( 3 to 5 times normal),activation of n‐NOS,LP,DNA‐fr and activation of CAS‐3 in CA and AOSM. Intake of water‐borne Mg attenuated, or inhibited the alterations observed in the serum analytes and molecular CVD risk factors. In conclusion, we demonstrate , that S‐T MD results in generation of multiple cardiovascular risk factors and programmed cell death in several CV tissues in rats.
Advances in the Treatment of Plasma Cell Diseases (1996)

Dose-intensive chemotherapy and marrow transplantation in myeloma achieve complete remission in many cases and may significantly prolong patient survival. Use of myeloid growth factors or mobilized blood stem cell preparations decreases morbidity and mortality from treatment. These approaches also show promise in AL amyloidosis.
Tirapazamine: a bioreductive anticancer drug that exploits tumour hypoxia (2000)

Tirapazamine is the second clinical anticancer drug (after porfiromycin) that functions primarily as a hypoxia-selective cytotoxin. Hypoxic cells in tumours are relatively resistant to radiotherapy and to some forms of chemotherapy and are also biologically aggressive, thus representing an important target population in oncology. Tirapazamine undergoes metabolism by reductases to form a transient oxidising radical that can be efficiently scavenged by molecular oxygen in normal tissues to re-form the parent compound. In the absence of oxygen, the oxidising radical abstracts a proton from DNA to form DNA radicals, largely at C4' on the ribose ring. Tirapazamine can also oxidise such DNA radicals to cytotoxic DNA strand breaks. It therefore shows substantial selective cytotoxicity for anoxic cells in culture (typically approximately 100-fold more potent than under oxic conditions) and for the hypoxic subfraction of cells in tumours. Preclinical studies showed enhanced activity of combinations of tirapazamine with radiation (to kill oxygenated cells) and with conventional cytotoxics, especially cisplatin (probably through inhibition of repair of cisplatin DNA cross-links in hypoxic cells). Phase II and III clinical studies of tirapazamine and cisplatin in malignant melanoma and non-small cell lung cancer suggest that the combination is more active than cisplatin alone and preliminary results with advanced squamous cell carcinomas of the head and neck indicate that tirapazamine may enhance the activity of cisplatin with fractionated radiotherapy.
Intrathoracic tumour motion estimation from CT imaging using the 3D optical flow method (2004)

The purpose of this work was to develop and validate an automated method for intrathoracic tumour motion estimation from breath-hold computed tomography (BH CT) imaging using the three-dimensional optical flow method (3D OFM). A modified 3D OFM algorithm provided 3D displacement vectors for each voxel which were used to map tumour voxels on expiration BH CT onto inspiration BH CT images. A thoracic phantom and simulated expiration/inspiration BH CT pairs were used for validation. The 3D OFM was applied to the measured inspiration and expiration BH CT images from one lung cancer and one oesophageal cancer patient. The resulting displacements were plotted in histogram format and analysed to provide insight regarding the tumour motion. The phantom tumour displacement was measured as 1.20 and 2.40 cm with full-width at tenth maximum (FWTM) for the distribution of displacement estimates of 0.008 and 0.006 cm, respectively. The maximum error of any single voxel's motion estimate was 1.1 mm along the z-dimension or approximately one-third of the z-dimension voxel size. The simulated BH CT pairs revealed an rms error of less than 0.25 mm. The displacement of the oesophageal tumours was nonuniform and up to 1.4 cm, this was a new finding. A lung tumour maximum displacement of 2.4 cm was found in the case evaluated. In conclusion, 3D OFM provided an accurate estimation of intrathoracic tumour motion, with estimated errors less than the voxel dimension in a simulated motion phantom study. Surprisingly, oesophageal tumour motion was large and nonuniform, with greatest motion occurring at the gastro-oesophageal junction.
The aerodynamics of flying snake airfoils in tandem configuration (2021)

Flying snakes flatten their body to form a roughly triangular cross-sectional shape, enabling lift production and horizontal acceleration. While gliding, they also assume an S-shaped posture, which could promote aerodynamic interactions between the fore and the aft body. Such interactions have been studied experimentally; however, very coarse models of the snake's cross-sectional shape were used, and the effects were measured only for the downstream model. In this study, the aerodynamic interactions resulting from the snake's posture were approximated using two-dimensional anatomically accurate airfoils positioned in tandem to mimic the snake's geometry during flight. Load cells were used to measure the lift and drag forces, and flow field data were obtained using digital particle image velocimetry (DPIV). The results showed a strong dependence of the aerodynamic performance on the tandem arrangement, with the lift coefficients being generally more influenced than the drag coefficients. Flow field data revealed that the tandem arrangement modified the separated flow and the wake size, and enhanced the lift in cases in which the wake vortices formed closer to the models, producing suction on the dorsal surface. The downforce created by the flow separation from the ventral surface of the models at 0 deg angle of attack was another significant factor contributing to lift production. A number of cases showing large variations of aerodynamic performance included configurations close to the most probable posture of airborne flying snakes, suggesting that small postural variations could be used to control the glide trajectory.
White Matter Signals Reflect Information Transmission Between Brain Regions During Seizures (2021)

White matter supports critical brain functions such as learning and memory, modulates the distribution of action potentials, and transmits neural information between brain regions. Notably, neuronal cell bodies exist in deeper white matter tissue, neurotransmitter vesicles are released directly in white matter, and white matter blood-oxygenation level dependent (BOLD) signals are detectable across a range of different tasks—all appearing to reflect a dynamic, active tissue from which recorded signals can reveal meaningful information about the brain. Yet, the signals within white matter have largely been ignored. Here, we elucidate the properties of white matter signals using intracranial EEG in a bipolar montage. We show that such signals capture the communication between brain regions and differentiate pathophysiologies of epilepsy. In direct contradiction to past assumptions that white matter functional signals provide little value, we show that white matter recordings can elucidate brain function and pathophysiology. Broadly, white matter functional recordings acquired through implantable devices may provide a wealth of currently untapped knowledge about the neurobiology of disease.
Dynamic modeling and simulation of snowplough: normal operation and icepack impact (2000)

Three types of models pertaining to the normal operation and icepack impact of snowploughs are presented. A general method of deriving a dynamic model for multiple blade snowploughs is developed. This model includes all the nonlinear terms against exciting dynamic models, which are derived under the assumption of small pitch motion and roll motion. A force model is developed to estimate the casting forces acting on the blade. An icepack impact model is developed to simulate the dynamic performance of the snowplough under impact caused by an icepack. Simulation shows that if the rear tire cornering stiffness may be increased, the yaw motion and the lateral motion of the snowplough can be remarkably reduced. This may enable a driver to maintain the snowplough heading through use of both steering and braking actions.
Transformation of Size-controlled Platinum Clusters on Surface Ligand-exchange Reactions (2016)

We report the synthesis of dodecanethiolate-protected platinum clusters by atomicity control using a dendrimer reactor followed by ligand-exchange extractions. Spectroscopic investigations suggested that a large cluster (Pt60) partially contains a metallic nature. In contrast, the small one (Pt12) exhibited a fully molecular-like nature with a significant structural rearrangement.
P2P in satellite networks: a tutorial on related problems and some possible solutions (2005)

In the last years, the peer-to-peer (P2P) paradigm, which replaces the client-server one, has experienced a great success. A possible reason is large-scale broadband access deployment. P2P is being used for many different applications: grid computing, telephony, mail, etc. However, P2P is mainly associated to file-sharing applications, due to their popularity. On the other hand, satellite communication systems have been widely adopted to offer broadband Internet access in places where terrestrial access is unfeasible. Due to the special characteristics of satellite networks, P2P protocols are quite inefficient in them if compared to other technologies. In this paper, we describe P2P and how it operates on satellite networks. We focus on the problems that arise from the usage of P2P protocols over TCP connections and how they limit overall system performance. Finally, we comment some possible solutions
Drug Binding Assays do not Reveal Specific Binding of Lacosamide to Collapsin Response Mediator Protein 2 (CRMP‐2) (2012)

The diverse drug binding methods employed here are well suited to detect specific binding of LCM to CRMP-2 in the micromolar range, yet the results obtained were all negative. Results of this study suggest that LCM does not specifically bind to CRMP-2.
Micromachined Heat Sinks (1999)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;A silicon micromachined heat sink is presented. The device uses liquid cooling in microchannels to remove high heat fluxes. Deep reactive ion etching and multiple wafer bonding is employed to fabricate high aspect ratio, enhanced heat transfer surfaces and a flow channel network that enhances cooling efficiency and minimizes the pressure drop across the device. Experimental test results are presented. Tests to date indicate that up to 76.5 W/cm&lt;sup&gt;2&lt;/sup&gt; may be removed by the heat sink based on a 100°C electronic device temperature.&lt;/div&gt;&lt;/div&gt;
Development of a Compact Moving-Sample Magnetometer Using High-Tc Superconducting Quantum Interference Device (2012)

We developed a compact moving-sample magnetometer that uses a high-temperature superconductor–superconducting quantum interference device (high- T c SQUID) to directly measure the flux coupled to a normal detection coil from a sample's magnetic moment in the presence of an external DC magnetic field. The moving-sample method is employed by inserting the sample between the poles of a DC electromagnet and vibrating the sample along the axis perpendicular to the external field axis using an actuator at a frequency of 2.693 Hz. First, the magnetic field of the sample is transferred by a first-order differential normal Cu coil to a SQUID for detection. Then, the SQUID output is fed to a lock-in amplifier for detection. The critical feature of the system design is the use of high- T c SQUID, which enables the realization of a compact system. The basic characteristics of the developed system are presented, and the current system exhibited a detection limit of 1×10 -7 emu.
Deformation Measurement of Plastic Films Using Digital Image Correlation (2002)

Deformations of the surfaces of plastic films (nylon, polyethylene and linear low density polyethylene) used for liquid package gags under tensile loads are measured by a digital image correlation technique. The images, which are necessary for a digital image correlation, are captured by a CCD camera, and digitized by an image-processing devise. Several sets of two images, which are called a reference image and a deformed image, so as to determine deformations between the images are used for obtaining the deformations between the no-load condition and failure of the plastic films. The results show that characteristic deformations, which are probably due to molecular orientation in the plastic films, are measured.
Cover Picture: Linear and Two‐Photon Absorption Properties of Interacting Polar Chromophores: Standard and Unconventional Effects (ChemPhysChem 3/2006) (2006)

The cover picture shows the evolution of two‐photon absorption (TPA) spectra for dimers of polar and polarisable chromophores, as a function of orientation and distance. Strong modulation of nonlinear optical responses can be attained through interchromophoric interactions. Important contributions from interaction terms beyond the standard excitonic model are demonstrated both experimentally and theoretically. Find out more in the Article by Terenziani et al. on page 685.
Neutron Phase Imaging and Tomography (2006)

We report how a setup consisting of three gratings yields quantitative two- and three-dimensional images depicting the quantum-mechanical phase shifts of neutron de Broglie wave packets induced by the influence of macroscopic objects. Since our approach requires only a little spatial and chromatic coherence it provides a more than 2 orders of magnitude higher efficiency than existing techniques. This dramatically reduces the required measurement time for computed phase tomography and opens up the way for three-dimensional investigations of previously inaccessible quantum-mechanical phase interactions of neutrons with matter.