gebhart/patrepeval huggingface dataset:
Advanced Multimedia File Carving (2015)

This chapter discusses the state of the art in multimedia file carving. Combining common file carving approaches with content identification results in advanced multimedia file carving. In this context, ‘advanced’ means that the file carving strategy offers more assistance than the sole collection of evidence data. First, the chapter presents a brief introduction of storage technology aspects relevant for file carving, for example storage devices and file systems. File carving is a general method to enable accessing data lost to the file system. The chapter introduces the more general binary data file carving, and explains file carving designed specifically for multimedia. File carving describes the process of extracting file fragments from a byte stream such as a disk or volume image without file system information. This technique is used to recover data from unallocated space on hard disk storage. The chapter explains consequences of multimedia file characteristics for file carving.
On Closing the Streamwise BiGlobal Stability Problem: The Effect of Boundary Conditions (2015)

The modal streamwise BiGlobal stability approach introduces problems regarding the specification of in- and outflow boundary conditions (BCs). Several conditions linked to lower hierarchical stability frameworks are elaborated and are applied to a freestream and boundary layer flow. The former case is used to demonstrate the odd-even decoupling of the spectrum with the streamwise node number. The latter case illustrates that the spatial growth varies widely with different BCs, while specific Robin BCs yield the largest amplification near a target frequency. Combined, the cases show that the spectra might vary widely while corresponding to very similar spatial growth characteristics and vice versa.
Homogeneous Vector Capsules Enable Adaptive Gradient Descent in Convolutional Neural Networks (2021)

Neural networks traditionally produce a scalar value for an activated neuron. Capsules, on the other hand, produce a vector of values, which has been shown to correspond to a single, composite feature wherein the values of the components of the vectors indicate properties of the feature such as transformation or contrast. We present a new way of parameterizing and training capsules that we refer to as homogeneous vector capsules (HVCs). We demonstrate, experimentally, that altering a convolutional neural network (CNN) to use HVCs can achieve superior classification accuracy without increasing the number of parameters or operations in its architecture as compared to a CNN using a single final fully connected layer. Additionally, the introduction of HVCs enables the use of adaptive gradient descent, reducing the dependence a model's achievable accuracy has on the finely tuned hyperparameters of a non-adaptive optimizer. We demonstrate our method and results using two neural network architectures. For the CNN architecture referred to as Inception v3, replacing the fully connected layers with HVCs increased the test accuracy by an average of 1.32% across all experiments conducted. For a simple monolithic CNN, we show HVCs improve test accuracy by an average of 19.16%.
Conversion of Lavandula distilled straws into high-quality solid fuel: effect of hydrothermal carbonization conditions on fuel characteristics (2022)

Abstract Lavandin hydrochars obtained by hydrothermal carbonization (HTC) of Lavandula distilled straw (LDS) have been studied as an eco-friendly and economical valorization route of residual biomass from cosmetic industry into solid fuels. The critical parameters of the HTC process (temperature and retention time) were normalized to severity factor (SF). Proximate and ultimate analysis, microscopy and thermal analysis were used to characterize hydrochars surface, combustion behavior and kinetics as a function of SF, and to compare them with those of the raw lavandin sample. Results showed that preparation of lavandin hydrochars in temperature and retention time conditions providing SF close to 6 seemed to be the best compromise since under these conditions, the combustion performance of the hydrochar was close to the bituminous coal and lignite.
Disappearance of Anti-Pl7 Correlates with Successful Isolation of Human Immunodeficiency Virus and Deterioration in Clinical Status (1990)

Anti-p17 was examined as a human immunodeficiency virus (HIV) marker predicting the onset of the acquired immunodeficiency syndrome (AIDS). Two different comparisons were done: (1) anti-p17 negativity and successful HIV isolation; and (2) anti-p17 negativity and clinical status, using the Centers for Disease Control classification. Anti-p17 negativity was not only significantly correlated with deterioration in clinical status (P less than 0.01), but also with successful HIV isolation (P less than 0.05). HIV isolation was affected by several drugs, e.g. zidovudine. However, the results of the antibody test were not affected. It is significant that anti-p17 can compensate for the defects of virus isolation.
Exogenous antigen enters the major histocompatibility complex (MHC) class I pathway via multiple endocytic compartments with distinct molecular and proteolytic requirements (78.31) (2009)

Abstract Peptides derived from exogenous proteins are displayed by MHC class I via a pathway termed cross-presentation. Despite extensive study, the endocytic compartment(s) that mediate cross-presentation are poorly understood. Immunization of mice with hen egg-white lysozyme (HEL) protein cross-primes CD8 T cells recognizing HEL 23-31 presented by Db. Here we used liposome-encapsulated HEL to examine the cross-presentation capacity of specific subcellular compartments. Liposome-encapsulated HEL targeted to early endosomes, but not late endosomes/lysosomes, entered the MHC class I pathway. Cross-presentation of early endosomal HEL liposomes apparently required the transporter associated with antigen processing (TAP). However, additional experiments indicated no requirement for proteasome-dependent processing or nascent Db. To test the possibility that early endosomal HEL liposomes were presented by endosomal Db independently of TAP, we incubated TAP-deficient antigen presenting cells (APCs) with early endosomal HEL liposomes and a peptide to promote Db surface-stabilization and eventual entry into the endosomal pathway. Addition of Db surface-stabilizing peptide rescued cross-presentation of early endosomal HEL liposomes by TAP-deficient APCs, implying that Db mis-localization accounted for the cross-presentation defect observed previously. Cross-presentation of early endosomal HEL liposomes was inhibited when endolysosomal acidification was blocked by chloroquine. Surprisingly, chloroquine treatment facilitated cross-presentation of both late endosomal/lysosomal HEL liposomes and soluble HEL. Altogether, these data indicate that exogenous protein antigen can enter the MHC class I pathway through multiple routes within the APC.
Insight into In Situ Amphiphilic Functionalization of Few‐Layered Transition Metal Dichalcogenide Nanosheets (2016)

A facile route toward functionalized amphiphilic layered transition-metal dichalcogenide nanosheets through in situ polymerization of polystyrene-polyacrylamide copolymers is established. The attachment of copolymers greatly affects their dispersibility in different kinds of solvents. Surface-tension components, polarity, and coordination effects of the copolymer are found to be the main factors affecting the dispersibility.
Evaluating the thermal damage resistance of graphene/carbon nanotube hybrid composite coatings (2014)

We study laser irradiation behavior of multiwalled carbon nanotubes (MWCNT) and chemically modified graphene (rGO)-composite spray coatings for use as a thermal absorber material for high-power laser calorimeters. Spray coatings on aluminum test coupon were exposed to increasing laser irradiance for extended exposure times to quantify their damage threshold and optical absorbance. The coatings, prepared at varying mass % of MWCNTs in rGO, demonstrated significantly higher damage threshold values at 2.5 kW laser power at 10.6 μm wavelength than carbon paint or MWCNTs alone. Electron microscopy and Raman spectroscopy of irradiated specimens show that the coating prepared at 50% CNT loading endure at least 2 kW x cm(-2) for 10 seconds without significant damage. The improved damage resistance is attributed to the unique structure of the composite in which the MWCNTs act as an efficient absorber of laser light while the much larger rGO sheets surrounding them, dissipate the heat over a wider area.
Entropy, information and compressive sensing in the quantum domain (2012)

I will discuss our recent efforts with single and double-pixel compressive sensing for applications in ghost imaging, low flux LIDAR, real-time object tracking, precision measurement and entanglement characterization.
Bone Density Variation and Its Effects on Risk of Vertebral Deformity in Men and Women Studied in Thirteen European Centers: The EVOS Study (1997)

In Europe there is a 3-fold variation, according to geographical center, in risk of vertebral deformity in men and women over the age of 50. We investigated the relationship between bone density, as assessed by dual-energy X-ray absorptiometry (DEXA) of the spine and hip and prevalent vertebral deformities in 13 of the 36 centers participating in the European Vertebral Osteoporosis Study (EVOS). Each center recruited an age-stratified sample of men and women aged 50 years and over, and of those who agreed to densitometry, 288/2088 women and 233/1908 men were found to have one or more deformities of the vertebrae between T4 and L4 as assessed by the McCloskey algorithm. DEXA was in each case performed on L2-L4, the proximal femur, or both. Bone densitometry results were cross-calibrated between centers using the European Spine Phantom prototype and results expressed as bone mineral density (BMD, g/cm2). In both genders, subjects with deformities involving loss of anterior vertebral body height alone comprised over 20% of the total with deformities and these related poorly to BMD. Other classes of deformity were found by logistic regression to relate significantly to BMD in one or both genders, with odds ratios for the risk of any of these ranging from 1.67 to 2.11 for a 1 SD reduction in bone density at spine, femoral neck, or trochanter (p < 0.001). Adjusting for anthropometric variables and BMD did not remove the effect of age on risk which rose 1.67- to 1.78-fold per decade according to gender. The greater unadjusted rate of increase in deformity risk with age in women was attributable to their faster rate of bone loss with age; after adjusting for age, body mass index (BMI), and BMD at the trochanter in grams per square centimeter, men had a 2-fold higher risk of deformity than women. Analysis of the relationship between mean bone density and the prevalence of deformity in each center demonstrated no significant differences between centers in either gender, after adjusting for BMD, age, and BMI together with an a posteriori statistical adjustment for imperfect cross-calibration of densitometers. It is concluded that BMD is an important determinant of deformity risk in both genders. Together with age, BMD explains much of the differences in risk both between the sexes and between individual geographical centers in Europe.
Preferential Bonding Orientations of Ferrocene on Surfaces (1997)

We have measured the molecular orientation and bonding of adsorbed ferrocene on Ag(100) and Cu(100) using angle-resolved photoemission spectroscopy (ARPES). The results for molecular adsorption on Ag(100) are complemented by high-resolution electron energy loss spectroscopy (HREELS) measurments and ab initio calculations for the ferrocene vibrational modes. The measurements indicate that ferrocene adsorbs on Ag(100) with the molecular axis perpendicular to the surface. In contrast, as indicated using ARPES and scanning tunneling microscopy, ferrocene adsorbed on the Cu(100) surface is oriented with the molecular axis parallel with the surface. Model calculations allow us to assign all of the observed vibrational modes for the weakly bound molecular ferrocene on Ag(100)−both dipole and impact scattering modes have been observed.
Collagen‐based biomaterials for wound healing (2014)

With its wide distribution in soft and hard connective tissues, collagen is the most abundant of animal proteins. In vitro, natural collagen can be formed into highly organized, three-dimensional scaffolds that are intrinsically biocompatible, biodegradable, nontoxic upon exogenous application, and endowed with high tensile strength. These attributes make collagen the material of choice for wound healing and tissue engineering applications. In this article, we review the structure and molecular interactions of collagen in vivo; the recent use of natural collagen in sponges, injectables, films and membranes, dressings, and skin grafts; and the on-going development of synthetic collagen mimetic peptides as pylons to anchor cytoactive agents in wound beds.
Observation of photoelectric nonvolatile memory and oscillations in VO2 at room temperature (2020)

Vanadium dioxide (VO2) is a phase change material that can reversibly change between high and low resistivity states through electronic and structural phase transitions. Thus far, VO2 memory devices have essentially been volatile at room temperature, and nonvolatile memory has required non-ambient surroundings (e.g., elevated temperatures, electrolytes) and long write times. Here, we report the first observation of optically addressable nonvolatile memory in VO2 at room temperature with a readout by voltage oscillations. The read and write times had to be kept shorter than about 150 μs. The writing of the memory and onset of the voltage oscillations had a minimum optical power threshold. This discovery demonstrates the potential of VO2 for new computing devices and architectures, such as artificial neurons and oscillatory neural networks.
Carbon Smackdown: Smart Windows (LBNL Summer Lecture Series) (2010)

August 3, 2010 Berkeley Lab talk: In the fourth of five Carbon Smackdown matches, Berkeley Lab researchers Delia Milliron of the Materials Sciences Division and Stephen Selkowitz of the Environmental Energy Technologies Division talk about their work on energy-saving smart windows.
Methodology and Applications of Disease Biomarker Identification in Human Serum (2007)

Biomarkers are biomolecules that serve as indicators of biological and pathological processes, or physiological and pharmacological responses to a drug treatment. Because of the high abundance of albumin and heterogeneity of plasma lipoproteins and glycoproteins, biomarkers are difficult to identify in human serum. Due to the clinical significance the identification of disease biomarkers in serum holds great promise for personalized medicine, especially for disease diagnosis and prognosis. This review summarizes some common and emerging proteomics techniques utilized in the separation of serum samples and identification of disease signatures. The practical application of each protein separation or identification technique is analyzed using specific examples. Biomarkers of cancers of prostate, breast, ovary, and lung in human serum have been reviewed, as well as those of heart disease, arthritis, asthma, and cystic fibrosis. Despite the advancement of technology few biomarkers have been approved by the Food and Drug Administration for disease diagnosis and prognosis due to the complexity of structure and function of protein biomarkers and lack of high sensitivity, specificity, and reproducibility for those putative biomarkers. The combination of different types of technologies and statistical analysis may provide more effective methods to identify and validate new disease biomarkers in blood.
300-mW narrow-linewidth deep-ultraviolet light generation at 193 nm by frequency mixing between Yb-hybrid and Er-fiber lasers (2015)

A narrow-linewidth, high average power deep-ultraviolet (DUV) coherent laser emitting at 193 nm is demonstrated by frequency mixing a Yb-hybrid laser with an Er-fiber laser. The Yb-hybrid laser consists of Yb-fiber lasers and an Yb:YAG amplifier. The average output power of the 193 nm laser is 310 mW at 6 kHz, which corresponds to a pulse energy of 51 μJ. To the best of our knowledge, this is the highest average power and pulse energy ever reported for a narrow-linewidth 193 nm light generated by a combination of solid-state and fiber lasers with frequency mixing. We believe this laser will be beneficial for the application of interference lithography by seeding an injection-locking ArF eximer laser.
Efficient precise in vivo base editing in adult dystrophic mice (2020)

ABSTRACT Background Recent advances in the base editing technology have created an exciting opportunity to precisely correct disease-causing mutations. However, the large size of base editors and their inherited off-target activities pose challenges for in vivo base editing. Moreover, the requirement of a protospacer adjacent motif (PAM) sequence within a suitable window near the mutation site further limits the targeting feasibility. In this work, we rationally improved the adenine base editor (ABE) to overcome these challenges and demonstrated the exceptionally high efficiency to precisely edit the Duchenne muscular dystrophy (DMD) mutation in adult mice. Methods We employed a fluorescence reporter assay to assess the feasibility of ABE to correct the dystrophin mutation in mdx 4cv mice. The intein protein trans-splicing (PTS) was used to split the oversized ABE into two halves for efficient packaging into adeno-associated virus 9 (AAV9). The ABE with broadened PAM recognition (ABE-NG) was rationally re-designed for improved off-target RNA editing activity and on-target DNA editing efficiency. The mdx 4cv mice at the 5 weeks of age receiving intramuscular or intravenous injections of AAV9 carrying the improved ABE-NG were analyzed at 10 weeks or 10 months of age. The editing outcomes were analyzed by Sanger and deep sequencing of the amplicons, immunofluorescence staining, Western blot and contractile function measurements. The off-target activities, host immune response and long-term toxicity were analyzed by deep sequencing, ELISA and serological assays, respectively. Results We showed efficient in vitro base correction of the dystrophin mutation carried in mdx 4cv mice using ABE-NG. The super-fast intein-splits of ABE-NG enabled the expression of full-length ABE-NG and efficient AAV9 packaging. We rationally improved ABE-NG with eliminated off-target RNA editing activity and minimal PAM requirement, and packaged into AAV9 (AAV9-iNG). Intramuscular and intravenous administration of AAV9-iNG resulted in dystrophin restoration and functional improvement. At 10 months after AAV9-iNG treatment, a near complete rescue of dystrophin was measured in mdx 4cv mouse hearts. The off-target activities remained low and no obvious toxicity was detected. Conclusions This study highlights the promise of permanent base editing using iABE-NG for the treatment of monogenic diseases, in particular, the genetic cardiomyopathies.
Expansion Microscopy: Toward Nanoscale Imaging of a Diverse Range of Biomolecules (2020)

Expansion microscopy (ExM) has become a powerful imaging tool for visualizing the nanoscale organization of protein and nucleic acid targets in cells and tissues using only a conventional microscope. Until recently, current ExM approaches have had limited applicability to imaging other biomolecules, such as lipids and small molecules. With the new TRITON probes reported by Wen <i>et al.</i> in this issue of <i>ACS Nano</i>, ExM can now be used to perform nanoscale imaging of the cytoskeleton and lipid membranes. In this Perspective, we offer a brief overview of recent developments in ExM, with a focus on biomolecule anchoring and labeling strategies that target a wide range of biomolecules to the water-swellable polymer formed <i>in situ</i>, a key step that ensures biomolecules or labels of interest are separated in space and can be resolved on a conventional microscope. In addition to these new advancements, we discuss challenges and future directions in this exciting field.
Si<SUB>3</SUB>N<SUB>4</SUB>, SiC, Al<SUB>2</SUB>O<SUB>3</SUB>/Cu Bonding with Utilizing Mo Metallization of Ceramics by means of Ion Beam Dynamic Mixing (1992)

Molybdenum metallization of Si3N4 SiC and Al2O3 substrates for metal-ceramic bonding was performed using an ion beam dynamic mixing method. In this method, a cylindrical ceramic substrate 5 mm in diameter and 5 mm in length was irradiated simultaneously with a 8.0×10−15 J (50 keV), 1-2×105 μA/m2 Ti+ ion beam and a Mo molecular beam at a substrate temperature of 573 K. The substrate metallized with a Mo film 2-5 μm in thickness was bonded to a copper pin 2.5 mm in diameter with an amorphous Cu-9Ni-4Sn-7P solder at 973 K in a depressurized Ar gas atmosphere. Tensile strength of the copper/ceramic joint was determined by a universal testing machine. A strong joint of more than 120 MPa for each ceramic could be obtained.Compared to sputtering as a metallization technique, the dynamic mixing resulted in a joint of superior tensile strength and allowed greater versatility in selection of the chemical type of ceramic substrate. With regard to the chemical type of ion beam used for the dynamic mixing, an active metal ion beam such as Ti+ was found to be much more effective in obtaining a strong joint than an inert gas ion beam like Ar+.The ceramic-metal interface region of the Mo-coated Si3N4 or SiC was observed using a high resolution TEM and an XPS. There were differences between the two ceramics in damage and amorphisation of the ceramic crystal grains caused by the high energy Ti+ ion beam. An amorphous layer, composed of the implanted Ti, the evaporated Mo and some of the ceramic’s constituent elements, was observed in both interface regions. In addition, a precipitated TiN crystal was detected in the Si3N4 system.
Enantiospecific Allosteric Modulation of Cannabinoid 1 Receptor (2017)

The cannabinoid 1 receptor (CB1R) is one of the most widely expressed metabotropic G protein-coupled receptors in brain, and its participation in various (patho)physiological processes has made CB1R activation a viable therapeutic modality. Adverse psychotropic effects limit the clinical utility of CB1R orthosteric agonists and have promoted the search for CB1R positive allosteric modulators (PAMs) with the promise of improved drug-like pharmacology and enhanced safety over typical CB1R agonists. In this study, we describe the synthesis and in vitro and ex vivo pharmacology of the novel allosteric CB1R modulator GAT211 (racemic) and its resolved enantiomers, GAT228 (R) and GAT229 (S). GAT211 engages CB1R allosteric site(s), enhances the binding of the orthosteric full agonist [<sup>3</sup>H]CP55,490, and reduces the binding of the orthosteric antagonist/inverse agonist [<sup>3</sup>H]SR141716A. GAT211 displayed both PAM and agonist activity in HEK293A and Neuro2a cells expressing human recombinant CB1R (hCB1R) and in mouse-brain membranes rich in native CB1R. GAT211 also exhibited a strong PAM effect in isolated vas deferens endogenously expressing CB1R. Each resolved and crystallized GAT211 enantiomer showed a markedly distinctive pharmacology as a CB1R allosteric modulator. In all biological systems examined, GAT211's allosteric agonist activity resided with the R-(+)-enantiomer (GAT228), whereas its PAM activity resided with the S-(-)-enantiomer (GAT229), which lacked intrinsic activity. These results constitute the first demonstration of enantiomer-selective CB1R positive allosteric modulation and set a precedent whereby enantiomeric resolution can decisively define the molecular pharmacology of a CB1R allosteric ligand.