gebhart/patrepeval huggingface dataset:
Surface‐Tension‐Driven Gradient Generation in a Fluid Stripe for Bench‐Top and Microwell Applications (2011)

A simple and inexpensive method is presented employing passive mechanisms to generate centimeters-long gradients of molecules and particles in under a second with only a coated glass slide and a micropipette. A drop of solution is pipetted onto a fluid stripe held in place on a glass slide by a hydrophobic boundary. The resulting difference in curvature pressure drives the flow and creates a concentration gradient by convection. Experiments and theoretical models characterize the flows and gradient profiles and their dependence on the fluid volumes, properties, and stripe geometry. A bench-top rapid prototyping method is outlined to allow the user to design and fabricate the coated slides using only tape and hydrophobic spray. The rapid prototyping method is compatible with microwell arrays, allowing soluble gradients to be applied to cells in shear-protected microwells. The method's simplicity makes it accessible to virtually any researcher or student and its use of passive mechanisms makes it ideal for field use and compatible with point-of-care and global health initiatives.
Implementing preinstallation environment media for use in user support (2007)

The creation and usage of a Preinstallation Environment (PE) media for use as a User Services tool for cleaning/repairing security attacks, data recovery and repairing Windows installations. As happens occasionally, a Windows installation is corrupted and a user receives an error indicating the inability to logon to the system. While in some cases a simple Check Disk (ChkDsk /r) at the command prompt is sufficient to fix the error. At times, a Master Boot Record needs to be fixed (FixMBR) or a reconfiguration of the boot settings (BootCFG) is needed. Still other times, the operating system needs to be completely reinstalled. In cases such as these, a user's data needs to be accessed. In our environment the hard drive is usually pulled from the chassis and transported to another office on campus to attach to a secondary system and recovery tools are then run at that location. From a security standpoint, an infected/hacked machine is often also pulled or an expensive Winternals CD must be used to identify the infected files. While this is in theory now, we are building and testing a bootable PE device in which a system can boot from this CD or USB device and then tools can be run or data recovered at the location of the system itself. We then propose to create additional devices for the members of the desktop support staff who are dispatched to identify security breaks or malfunctioning hardware.
Channel monitoring in WDM networks: a systems perspective (1998)

Optical Channel Monitoring in a WDM system implies measurement of wavelength, power, and optical signal-to-noise ratio of all channels. This information can be used for control of network elements, network maintenance, and performance monitoring. I shall discuss a variety of devices applicable to optical monitoring, and useful in the control, maintenance, and provisioning of lightwave systems.
Mathematical handbook for scientists and engineers. Definitions, theorems, and formulas for reference and review (1968)

A reliable source of definitions, theorems, and formulas, this authoritative handbook provides convenient access to information from every area of mathematics. Coverage includes Fourier transforms, Z transforms, linear and nonlinear programming, calculus of variations, random-process theory, special functions, combinatorial analysis, numerical methods, game theory, and much more.
Tumor response to ionizing radiation combined with antiangiogenesis or vascular targeting agents: exploring mechanisms of interaction. (2003)

Recent preclinical studies have suggested that radiotherapy in combination with antiangiogenic/vasculature targeting agents enhances the therapeutic ratio of ionizing radiation alone. Because radiotherapy is one of the most widely used treatments for cancer, it is important to understand how best to use these two modalities to aid in the design of rational patient protocols. The mechanisms of interaction between antiangiogenic/vasculature targeting agents and ionizing radiation are complex and involve interactions between the tumor stroma and vasculature and the tumor cells themselves. Vascular targeting agents are aimed specifically at the existing tumor vasculature. Antiangiogenic agents target angiogenesis or the new growth of tumor vessels. These agents can decrease overall tumor resistance to radiation by affecting both tumor cells and tumor vasculature, thereby breaking the codependent cycle of tumor growth and angiogenesis. The hypoxic microenvironment of the tumor also contributes to the mechanisms of interactions between antiangiogenic/vasculature targeting agents and ionizing radiation. Hypoxia stimulates up-regulation of angiogenic and tumor cell survival factors, giving rise to tumor proliferation, radioresistance, and angiogenesis. Preclinical evidence suggests that antiangiogenic agents reduce tumor hypoxia and provides a rationale for combining these agents with ionizing radiation. Optimal scheduling of combined treatment with these agents and ionizing radiation will ultimately depend on understanding how tumor oxygenation changes as tumors regress and regrow during exposure to these agents. This review article explores the complex interactions between antiangiogenic/vasculature targeting agents and radiation and offers insight into the mechanisms of interaction that may be responsible for improved tumor response to radiation.
FeCl3·6H2Oas a Versatile Catalyst for the Esterification of Steroid Alcohols withFatty Acids (2008)

FeCl3˙6H2O is an active catalyst for the esterification of some steroid alcohols with fatty acids under azeotropic reflux in mesitylene as solvent.
Downstream Processing of Monoclonal Antibodies: Current Practices and Future Opportunities (2008)

This chapter contains sections titled: Introduction A Brief History of cGMP mAb and Intravenous Immunoglobulin (IgIV) Purification Current Approaches in Purification Process Development: Impact of Platform Processes Typical Unit Operations and Processing Alternatives VLS Processes: Ton-Scale Production and Beyond Process Validation Product Life Cycle Management Future Opportunities Conclusions Acknowledgments References
The Short Test of Mental Status (1991)

The Short Test of Mental Status can be administered to patients in inpatient and outpatient settings in approximately 5 minutes, and it contains items that test orientation, attention, immediate recall, arithmetic, abstraction, construction, information, and delayed (approximately 3 minutes) recall. The test was administered to a group of demented community patients and their age- and sex-matched control subjects. Using an age-adjusted approach, sensitivity of the test to identifying dementia is 86.4, with a specificity of 93.5. The test was compared with standardized tests of cognitive function such as the Wechsler Adult Intelligence Scale, Mattis Dementia Scale, and the Auditory Verbal Learning Test, and showed a high degree of correlation. Group means and standard deviations for subtest items and total score are presented for control subjects (n = 138), demented patients (n = 130), and patients with memory impairment only (n = 20). Percentile scores for subtest items in control subjects are also provided.
Chemical and physical interactions at metal/self-assembled organic monolayer interfaces (1994)

Abstract The purpose of research on metals (M) deposited onto self-assembled monolayers (SAMs) is to understand the interactions between metal (M) and eventually metal oxide overlayers on well-ordered organic substrates. Application of M/SAM and inorganic/SAM research results to the understanding of real inorganic/ organic interfaces in vacuum and under environmental conditions can potentially play a key role in the development of advanced devices with stable interfacial properties. The M/SAM approach to interface research is delineated as a new subfield in surface science in the context of other approaches to inorganic/organic interface research. Current issues in M/SAM research are outlined, including chemical compound formation, the morphology (spreading, clustering, or penetration) of the metal species, the kinetics of the metal morphology, the effect of the metal on the degree of order in the SAM, and the rate of metal penetration into the SAM. Probes are recommended that are suitable for M/SAM research. The results of M/SAM studies to date are reviewed, and M/SAM combinations are ranked according to reactivity and penetration. Key probes for addressing gaps in the research results are identified. The effects of defects, disordering, air exposure, and X-ray and electron beam exposure on the experimental results to date are evaluated. Thus far, the results have successfully revealed qualitative relationships of M/SAM chemistry, temperature, and penetration. The chemical interactions that have been found are applicable to real M/polymer interfaces as formed in vacuum. It has yet to be shown that M/SAM research will yield quantitative understanding of interface formation or that M/SAM interfaces are entirely analogous to M/polymer interfaces in the details of interface formation. The future of this subfield of surface science lies in its expansion from M/SAM interfaces in vacuum to other inorganic/SAM interfaces in vacuum and, eventually, under environmental conditions.
Mass spectrometric sequencing of linear peptides by product‐ion analysis in a reflectron time‐of‐flight mass spectrometer using matrix‐assisted laser desorption ionization (1993)

In matrix-assisted laser desorption ionization (MALDI) a large fraction of analyte ions undergo post-source decay (PSD) during flight in the field-free drift path. By means of a modified two-stage reflectron, product ion time-of-flight spectra of medium-sized linear peptides (up to 2800 u) were recorded, containing full sequence information. Precision, accuracy and mass resolution of fragment ions were almost as good as obtained in high-energy collisionally activated dissociation (CAD) studies performed in four-sector instruments. Instrumental sensitivity was better by at least one order of magnitude. In reflectron time-of-flight mass spectrometry (RETOFMS) the cleavage pattern of PSD products is different from that obtained by high-energy and low-energy CAD. Activation mechanisms of PSD were found to be largely determined by collisional events (ion/neutral) occurring in the acceleration field during early plume expansion. Future potentials of PSD analysis after MALDI are discussed.
Molecular Evolution of Adeno-associated Virus for Improved Retinal Gene Therapies (2010)

Current retinal gene therapies using adeno-associated viral (AAV) vectors are limited in their efficacy due to their dependence on an invasive subretinal delivery route to achieve sufficient gene delivery. Additionally, the genetic heterogeneity of inherited retinal degenerative diseases makes gene replacement and antisense therapeutic strategies impractical for treating a broad array of patients. This dissertation sought to address these limitations by creating intravitreally-permissive AAV vectors through directed evolution and examining their therapeutic potential using a mutation-independent approach. \tFirstly, we examined natural barriers to intravitreal vector delivery. We identified the inner limiting membrane (ILM) as the main obstacle to efficient intravitreal gene delivery and found mild digestion with a nonspecific protease, Pronase E, substantially enhanced retinal transduction for several AAV serotypes, most notably for AAV serotype 5 (AAV5). Secondly, we evolved more efficient glial-permissive AAV vectors in the CNS and retina using an in vitro selection methodology. We isolated an AAV variant, ShH10, closely related to AAV6, capable of efficient, selective MÃ¼ller cell infection through intravitreal injection. Thirdly, we utilized this variant to examine the efficacy of intravitreally targeting MÃ¼ller cells to secrete glial-derived neurotrophic factor (GDNF) as a mutation-independent therapy for delaying photoreceptor degeneration in a rat model of retinitis pigmentosa (RP). We achieved functional and histological rescue in treated animals at five months post injection, with an average approximate rescue of 50% in ERG a and b-wave amplitudes. Lastly, we evolved AAV variants to intravitreally transduce photoreceptors using an in vivo selection approach in a transgenic line of mice bearing a rhodopsin-GFP fusion. We isolated an AAV variant, 7M8, derived from an AAV2 peptide display library, capable of significant intravitreal photoreceptor transduction relative to AAV2. The creation of intravitreally-permissive AAV vectors as well as the development of mutation-independent gene therapies will enable safer and more effective therapies for treating inherited retinal degenerative diseases.
Fabrication of a magnetic helical mesostructured silica rod (2008)

We report a one-step synthesis of magnetic helical mesostructured silica (MHMS) by self-assembly of an achiral surfactant, magnetic nanocrystals with stearic acid ligands and silicate. This core-shell structured material consists of an Fe(3)O(4) superparamagnetic nanocrystal core and a highly ordered periodic helical mesoporous silica shell. We propose that the formation of the helical structure is induced by the interaction between the surfactant and dissociated stearic acid ligands. The MHMS obtained possesses superparamagnetism, uniform mesostructure, narrow pore size distribution, high surface area, and large pore volume. Furthermore, the drug release process is demonstrated using aspirin as a drug model and MHMS as a drug carrier in a sodium phosphate buffer solution.
Interaction of the Nck Adapter Protein with p21-activated Kinase (PAK1) (1996)

The p21-activated kinases (PAKs) link G protein-coupled receptors and growth factor receptors (S. Dharmawardhane, R. H. Daniels, and G. M. Bokoch, submitted for publication) to activation of MAP kinase cascades and to cytoskeletal reorganization (M. A. Sells, U. G. Knaus, D. Ambrose, S. Bagrodia, G. M. Bokoch, and J. Chernoff, submitted for publication). The proteins that interact with PAK to mediate its cellular effects and to couple it to upstream receptors are unknown. We describe here a specific interaction of the Nck adapter molecule with PAK1 both in vitro and in vivo. PAK1 and Nck associate in COS-7 and Swiss 3T3 cells constitutively, but this interaction is strengthened upon platelet-derived growth factor receptor stimulation. We show that Nck binds to PAK1 through its second Src homology 3 (SH3) domain, while PAK1 interacts with Nck via the first proline-rich SH3 binding motif at its amino terminus. The interaction of active PAK1 with Nck leads to the phosphorylation of Nck at multiple sites. Association of Nck with PAK1 may serve to link this important regulatory kinase to cell activation by growth factor receptors.
TGF-β activation by bone marrow-derived thrombospondin-1 causes Schistosoma- and hypoxia-induced pulmonary hypertension (2017)

Pulmonary arterial hypertension (PAH) is an obstructive disease of the precapillary pulmonary arteries. Schistosomiasis-associated PAH shares altered vascular TGF-β signalling with idiopathic, heritable and autoimmune-associated etiologies; moreover, TGF-β blockade can prevent experimental pulmonary hypertension (PH) in pre-clinical models. TGF-β is regulated at the level of activation, but how TGF-β is activated in this disease is unknown. Here we show TGF-β activation by thrombospondin-1 (TSP-1) is both required and sufficient for the development of PH in Schistosoma-exposed mice. Following Schistosoma exposure, TSP-1 levels in the lung increase, via recruitment of circulating monocytes, while TSP-1 inhibition or knockout bone marrow prevents TGF-β activation and protects against PH development. TSP-1 blockade also prevents the PH in a second model, chronic hypoxia. Lastly, the plasma concentration of TSP-1 is significantly increased in subjects with scleroderma following PAH development. Targeting TSP-1-dependent activation of TGF-β could thus be a therapeutic approach in TGF-β-dependent vascular diseases.
Raman imaging through a single multimode fibre (2017)

Vibrational spectroscopy is a widespread, powerful method of recording the molecular spectra of constituent molecules within a sample in a label-free manner. As an example, Raman spectroscopy has major applications in materials science, biomedical analysis and clinical studies. The need to access deep tissues and organs in vivo has triggered major advances in fibre Raman probes that are compatible with endoscopic settings. However, imaging in confined geometries still remains out of reach for the current state of art fibre Raman systems without compromising the compactness and flexibility. Here we demonstrate Raman spectroscopic imaging via complex correction in single multimode fibre without using any additional optics and filters in the probe design. Our approach retains the information content typical to traditional fibre bundle imaging, yet within an ultra-thin footprint of diameter 125 μm which is the thinnest Raman imaging probe realised to date. We are able to acquire Raman images, including for bacteria samples, with fields of view exceeding 200 μm in diameter.
Rapid prenatal diagnosis of 14 cases of triploidy using fish with multiple probes (1995)

Fluorescence in situ hybridization (FISH) of chromosome-specific probes to interphase nuclei can rapidly identify aneuploidies in uncultured amniotic fluid cells. Using DNA probe sets specific for chromosomes 13, 18, 21, X, and Y, we have identified 14 fetuses where the hybridization pattern was consistent with a triploid chromosome constitution. In each case, the identification of fetal abnormalities by ultrasound examination initiated a request for rapid determination of ploidy status via prenatal FISH analysis of uncultured amniocytes. FISH produced a three-signal pattern for the three autosomes in combination with signals indicating an XXX or XXY sex chromosome complement. This hybridization pattern was interpreted to be consistent with triploidy. Results were reported to the physician within 2 days of amniocentesis and subsequently confirmed by cytogenetics. These cases demonstrate the utility of FISH for rapid prenatal identification of triploidy, particularly when fetal abnormalities are seen with ultrasonographic examination.
Diode area melting single-layer parametric analysis of 316L stainless steel powder (2017)

Diode area melting (DAM) is a novel additive manufacturing process that utilises customised architectural arrays of low power laser diode emitters for high speed parallel processing of metallic powdered feedstock. The laser diodes operate at shorter laser wavelengths (808 nm) than conventional SLM fibre lasers (1064 nm) theoretically enabling more efficient energy absorption for specific materials. This investigation presents a parametric analysis of the DAM process, identifying the effect of powder characteristics, laser beam profile, laser power and scan speed on the porosity of a single-layer sample. Also presented is the effect of process energy density on melt pool depth (irradiated thermal energy penetration capable of achieving melting) on 316L stainless steel powder. An analysis of the density and the melt depth fraction of single layers is presented in order to identify the conditions that lead to the fabrication of fully dense DAM parts. Energy densities in excess of 86 J/mm3 were theorised as sufficient to enable processing of fully dense layers.
Auto-deleting brain machine interface: Error detection using spiking neural activity in the motor cortex (2015)

Brain machine interfaces (BMIs) aim to assist people with paralysis by increasing their independence and ability to communicate, e.g., by using a cursor-based virtual keyboard. Current BMI clinical trials are hampered by modest performance that causes selection of wrong characters (errors) and thus reduces achieved typing rate. If it were possible to detect these errors without explicit knowledge of the task goal, this could be used to automatically "undo" wrong selections or even prevent upcoming wrong selections. We decoded imminent or recent errors during closed-loop BMI control from intracortical spiking neural activity. In our experiment, a non-human primate controlled a neurally-driven BMI cursor to acquire targets on a grid, which simulates a virtual keyboard. In offline analyses of this closed-loop BMI control data, we identified motor cortical neural signals indicative of task error occurrence. We were able to detect task outcomes (97% accuracy) and even predict upcoming task outcomes (86% accuracy) using neural activity alone. This novel strategy may help increase the performance and clinical viability of BMIs.
NHC–metal complexes based on benzimidazolium moiety for chemical transformation (2012)

N-heterocyclic carbenes (NHC) are now commonly encountered in organometallic and inorganic coordination chemistry because of its environmental friendly nature as solvent and catalyst, high activity, selectivity and easily recovered materials that were used to replace the traditional volatile organic solvents which generally suffered from environmental problems. Benzimidazole based ionic liquids (BILs) offering a new possibility for developing environmentally-friendly basic catalyst with transition metal and non-transition metal (Ag, Au, Ru, Rh, Fe, Co, Cu, Cd and Pd). They are flexible, nonvolatile, noncorrosive and immiscible with many organic solvents. In this review, we wish to present an overview of the preparation and applications in various reactions like alkylation, arylation, etherification, benzoin reaction, aldol condensation and metal mediated catalyst in Suzuki, Suzuki–Miyaura, Heck cross coupling and reduction, also in electrochemical application (electrocatalyst), anion sensor, solar cell, proton conduction, malaria parasite, antimicrobial activity, etc.
A review of high dielectric materials for DRAM capacitors (1997)

Abstract There has been growing interest in the use of materials with the perovskite structure as a dielectric for capacitors in dynamic random access memory chips. The heightened activity in this field is exemplified by the nearly exponential increase in the number of patents issued during the past 5 years. At the present time, a fully functional DRAM with a capacitor incorporating these high-dielectric constant materials has not been demonstrated. All existing DRAMs use silicon dioxide and/or silicon nitride as the capacitor dielectric. This paper will describe the potential advantages of incorporating high-dielectric materials into the storage capacitor of a DRAM and review the requirements of the high-dielectric layer when used in a simple stack capacitor structure suitable for the GBit generation of DRAM. Recent advances in this technology are reviewed and the major issues, which could be potential show-stoppers and still need to be resolved, are described.
‘Perforated patch recording’ allows long‐term monitoring of metabolite‐induced electrical activity and voltage‐dependent Ca2+ currents in pancreatic islet B cells (1989)

We describe the application of 'perforated patch recording' using the pore-forming antibiotic nystatin, to monitor the electrical activity and underlying ionic currents of rat and human pancreatic islet B cells. We demonstrate that glucose-induced electrical activity is seen even in single B cells during current-clamp recordings lasting hours 'L-type' Ca2+-channel currents can also be monitored over this period of time. This technique may prove useful in examining hormone and neurotransmitter modulation of electrical activity in B cells, while minimizing the effects of cytoplasmic 'wash-out'.