gebhart/patrepeval huggingface dataset:
Qualitative and quantitative differentiation of species from Vaccinium by NMR spectroscopy in automation (2013)

The genus Vaccinium contains approximately 450 species including bilberry, blueberry, cranberry, lingonberry, and huckleberry. The fruit of Vaccinium are widely eaten and touted for their health benefits, attributed to antioxidants and micronutrients. Blueberry leaf extract is a traditional medicine of the Cree people, believed to have anti-diabetic properties. Extracts from Vaccinium plants are commonly added to foods, dietary supplements, and cosmetics. Given their widespread use in humans, it is important to have methods to verify the identity and purity of Vaccinium extracts. Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for characterizing mixtures such as plant extracts in full automation. Discrimination of different species, absolute identification & quantification of key compounds and verification if the determined parameters are in the allowed range is the basis for the quality control of a sample. The automation of this process minimizes failures in the analysis. A comprehensive report makes the results easy to interpret. An NMR spectrum, such as a 1D1H spectrum, shows the superposition of the characteristic signals of all of the compounds in the mixture. When enough samples of a specific material are available, chemometric models can be build. Then new samples can be classified against the model to determine whether they represent the same material. The result is represented in different ways, e.g. as quantile plot. Identifying and quantitating of key compounds from a mixture spectrum can be based on spectral analysis or using PLS-1. Both results can be used to verify if the sample is in the allowed range. We will demonstrate the power of these techniques using examples from our ongoing study of Vaccinium.
THE LEWIS SYSTEM AND KIDNEY TRANSPLANTATION (1980)

A significant effect of Lewis antigens on cadaver kidney graft survival was found in 1,300 North American transplants. Lewis-negative recipients had a graft survival rate that was 8% lower than that of Lewis-positive recipients (P = 0.05). This effect of Lewis antigens was enhanced in patients at a high failure risk as determined by age, race, or transplant center. In patients older than 30 years, the effect of Lewis was 14% (P = 0.07), in non-Caucasians 12% (P = 0.07), in all grafts performed at centers with less than 50% overall 1-year graft survival 12% (P = 0.03), and in non-Caucasians that received transplants in centers with less than 50% overall graft survival it was 18% (p = 0.01). These data confirm previous results on the role of Lewis as a histocompatibility system in renal transplantation; furthermore, they demonstrate that the influence of Lewis is larger in patients at high risk.
The Effect of Fluorine Additions to the Oxidation of Silicon (1990)

Experiments were carried out to study the effects of fluorine additions to a dry oxidation ambient. Two distinct classes of fluorine sources, liquid dichlorofluoroethane , and gaseous nitrogen trifluoride , were investigated. We experimentally found that small fluorine additions (up to 0.11% by volume) caused large enhancements in oxidation kinetics. The oxidation kinetics data were analyzed by both the power of time and linear‐parabolic models as a function of fluorine addition, temperature, and the type of fluorine additive. Thermodynamic calculations for these classes of fluorine sources were extensively carried out to determine the active oxidizing species that cause the significant enhancement of the oxidation. According to these calculations, the enhancement of oxidation could be explained by the presence of hydrogen fluoride (HF) and atomic fluorine (F). Secondary ion mass spectrometry (SIMS) was performed to study the incorporation behavior of fluorine into the oxide layer. oxides displayed peaks at the silicon‐oxide interface, while oxides exhibited flat fluorine profiles.
Anthranilic acid-based inhibitors of phosphodiesterase: Design, synthesis, and bioactive evaluation (2011)

Our previous studies identified two 2-benzoylaminobenzoate derivatives 1, which potently inhibited superoxide (O(2)˙(-)) generation induced by formyl-L-methionyl-L-leucyl-L-phenylalanine (FMLP) in human neutrophils. In an attempt to improve their activities, a series of anthranilic acid derivatives were synthesized and their anti-inflammatory effects and underlying mechanisms were investigated in human neutrophils. Of these, compounds 17, 18, 46, 49, and 50 showed the most potent inhibitory effect on FMLP-induced release of O(2)˙(-) in human neutrophils with IC(50) values of 0.20, 0.16, 0.15, 0.06, and 0.29 μM, respectively. SAR analysis showed that the activities of most compounds were dependent on the ester chain length in the A ring. Conversely, a change in the linker between the A and B ring from amide to sulfonamide or N-methyl amide, as well as exchanges in the benzene rings (A or B rings) by isosteric replacements were unfavorable. Further studies indicated that inhibition of O(2)˙(-) production in human neutrophils by these anthranilic acids was associated with an elevation in cellular cAMP levels through the selective inhibition of phosphodiesterase 4. Compound 49 could be approved as a lead for the development of new drugs in the treatment of neutrophilic inflammatory diseases.
New Rotating Dilution Refrigerator for a Study of the Free Surface of Superfluid He (2006)

Mechanical stability is an important requirement of a cryostat for a study of the free surface of liquid He by means of surface state electrons. Hence, we have constructed a new rotating dilution refrigerator using mechanical bearing units. The minimum temperature of the cryostat is 5 mK for rotation speeds up to 0.5 rev/sec, with no significant mechanical vibration. The stability and cooling power are suitable for our free‐surface experiments.
The three extra-cellular zinc metalloproteinases of Streptococcus pneumoniae have a different impact on virulence in mice (2003)

These data suggest Iga, ZmpB and ZmpC as candidate surface proteins responsible for pneumococcal infection and potentially involved in distinct stages of pneumococcal disease.
Novel guanosine derivatives against MERS CoV polymerase: An in silico perspective (2020)

The Middle East Respiratory Syndrome Coronavirus (MERS CoV), also termed camel flu, is a new viral infection that first reported in the year 2012 in the Middle East region and further spread during the last seven years. MERS CoV is characterized by its high mortality rate among different human coronaviruses. MERS CoV polymerase shares more than 20% sequence identity with the Hepatitis C Virus (HCV) Non-structural 5b (NS5b) RNA dependent RNA polymerase (RdRp). Despite the low sequence identity, the active site is conserved between the two proteins, with two consecutive aspartates that are crucial in the nucleotide transfer reaction. In this study, seven nucleotide inhibitors have been tested against MERS CoV RdRp using molecular modeling and docking simulations, from which four are novel compounds. Molecular Dynamics Simulation for 260 nanoseconds is performed on the MERS CoV RdRp model to test the effect of protein dynamics on the binding affinities to the tested nucleotide inhibitors. Results support the hypothesis of using the anti-polymerases (Anti-HCV drugs) against MERS CoV RdRp as a potent candidates. Besides four novel compounds are suggested as a seed for high performance inhibitors against MERS CoV RdRp.Communicated by Ramaswamy H. Sarma.
Accurate Dynamic 3D Sensing With Fourier-Assisted Phase Shifting (2014)

Phase shifting profilometry (PSP) and Fourier transform profilometry (FTP) are two well-known fringe analysis methods for 3D sensing. PSP offers high accuracy but requires multiple images; FTP uses a single image but is limited in its accuracy. In this paper, we propose a novel Fourier-assisted phase shifting (FAPS) method for accurate dynamic 3D sensing. Our key observation is that the motion vulnerability of multi-shot PSP can be overcome through single-shot FTP, while the high accuracy of PSP is preserved. Moreover, to solve the phase ambiguity of complex scenes without additional images, we propose an efficient parallel spatial unwrapping strategy that embeds a sparse set of markers in the fringe patterns. Our dynamic 3D sensing system based on the above principles demonstrates superior performance over previous structured light techniques, including PSP, FTP, and Kinect.
Failure of long-term nerve root stimulation to improve neuropathic pain (2008)

Spinal nerve root stimulation proved to be effective on short-term follow-up in 3 patients with neuropathic pain in a dermatomal distribution. Long-term stimulation, however, was disappointing because of the loss of effectiveness and the occurrence of side effects.
Frequency-Independent Approximate Compensation of Mutual Coupling in a Linear Array Antenna (2009)

The method of the frequency-independent compensation of the strongest mutual coupling (between the neighbor elements only) in a linear array antenna is suggested and studied. It is shown that in the suggested method both the scheme and the parameters of a decoupling multiport network do not depend on properties of the array elements as well as on frequency. An example of a seven-element array is considered.
Fast parallel spiral chemical shift imaging at 3T using iterative SENSE reconstruction (2008)

Spiral chemical shift imaging (CSI) is a fast CSI technique that simultaneously encodes 1D spectral and 2D spatial information. Therefore, it potentially allows one to perform a 2D-CSI experiment in a single shot. However, for most applications, limitations on maximum gradient strength and slew rate make multiple excitations necessary in order to achieve a desired spectral bandwidth. In this work we reduce the number of spatial interleaves and, hence, the minimum total measurement time of spiral CSI by using an iterative sensitivity encoding reconstruction algorithm which utilizes complementary spatial encoding afforded by the spatially inhomogeneous sensitivity profiles of individual receiver coils. The performance of the new method was evaluated in phantom and in vivo experiments. Parallel spiral CSI produced maps of brain metabolites similar to those obtained using conventional gridding reconstruction of the fully sampled data with only a small decrease in time-normalized signal-to-noise ratio and a small increase in noise for higher acceleration factors.
Optimal, reliable estimation of quantum states (2010)

Accurately inferring the state of a quantum device from the results of measurements is a crucial task in building quantum information processing hardware. The predominant state estimation procedure, maximum likelihood estimation (MLE), generally reports an estimate with zero eigenvalues. These cannot be justified. Furthermore, the MLE estimate is incompatible with error bars, so conclusions drawn from it are suspect. I propose an alternative procedure, Bayesian mean estimation (BME). BME never yields zero eigenvalues, its eigenvalues provide a bound on their own uncertainties, and under certain circumstances it is provably the most accurate procedure possible. I show how to implement BME numerically, and how to obtain natural error bars that are compatible with the estimate. Finally, I briefly discuss the differences between Bayesian and frequentist estimation techniques.
Guidelines for Developing an Effective Electrical Safety Program (1979)

This paper describes the steps and key factors involved in preparing an Electrical Safety Program tailored to meet the needs and resources of a patient care facility. The effectiveness of the program depends upon how well the Safety Committee completes the tasks involved. The Electrical Safety Program in use at Boston University Medical Center is described.
Scanning electron microscopy of some endophytic streptomycetes in snakevine-Kennedia nigricans (2005)

Soils of all types and locations have generally served as the major sources of streptomycetous bacteria. These organisms are the source of nearly 80% of the world's antibiotics. Now, it is realized that Streptomyces spp. (within the group of prokaryotic filamentous bacteria known as actinomycetes) can exist as endophytes within the interstices of some higher plants. While it is sometimes possible to isolate one or two different streptomycetes from certain plants, most plants are free of these organisms. However, the snakevine (Kennedia nigricans) of the Northern Territory of Australia has yielded at least 39 different endophytic actinomycetes (95% of them being Streptomyces spp.) Most of these isolates possessed no detectable antibiotic properties, while at least seven had antibacterial and antifungal activities. Examination of eight selected cultures by scanning electron microscopy (SEM) as well as environmental scanning electron microcopy (FEI ESEM FEG) (FEI Company, Hillsobro, Ore., USA) revealed unusual patterns, structures, and features of the spores and hyphae of these microorganisms. For instance, as revealed by ESEM FEG for the first time, it has become obvious that extremely fine hair-like structures (average 25-49 nm with gold-coated specimens) exist on the spores and hyphae of some endophytic streptomycetes. The biological purpose of these hair-like protrusions is unknown. Both SEM and ESEM FEG can be effectively used as tools in identification and elucidation of the biology of these organisms. In addition, unusual colony morphology, observed with the unaided eye can very easily be used to distinguish some of these isolates since characteristic donut and pseudo-horn shaped colonies appeared in culture.
Soliton switching and multi-frequency generation in a nonlinear photonic crystal fiber coupler (2008)

Soliton switching in nonlinear directional couplers implemented in photonic crystal fibers (PCF) examined here. A vector finite element method (FEM) has been developed to precisely calculate the dispersion along with coupling length of the guided modes. The PCF coupler geometry was carefully designed so that it can support soliton pulses. Soliton switching is demonstrated numerically at 1.55 microm for 100 femto-second (fs) pulses. Our theoretical results explain some of the key spectral features previously observed in the experiment.
Acryloylpolystyrene (1968)

Abstract Reactive pendant acryloyl groups can be substituted for hydrogen in the para position on the phenyl groups in polystyrene. Acylation of the polymer with β‐chloropropionyl chloride in solution is followed by dehydrochlorination, yielding acryloylpolystyrene (AP resins). Both the molecular weight of the polymer and the number of acryloyl groups per polymer molecule can be varied over wide limits. AP resins dissolve readily in vinyl aromatic monomers and copolymerize readily with them to yield clear, colorless, infusible polymers with good strength properties. The rate of copolymerization of these mixtures increases with both the number of acryloyl groups and the amount of acryloylpolystyrene in solution. These resins are similar in polymerization behavior and strength properties to the unsaturated polyesters used for production of glass‐reinforced plastics. In addition, the acryloyl groups are available for other reactions in a manner comparable to that of monomeric analogues.
Cross-listing and corporate governance: Bonding or avoiding? (2004)

In their seminal survey of corporate governance, Shleifer and Vishny distill the issue into a blunt question: "How do [the suppliers of finance] make sure that managers do not steal the capital they supply or invest it in bad projects?" The Enron/Arthur Andersen debacle and the ensuing wave’s of scandal vividly proved that American investors may face this question in the most acute form. To the extent that corporate governance issues play a role in the cross-listing decision, it is a negative role. Generally speaking, the foreign issuer regime "cuts corners" exactly on the issues of corporate governance relating to corporate insiders. The notion that issuers may want to improve their corporate governance by subjecting themselves to a better regulatory regime through cross-listing—say, on an American market—is appealingly elegant. If an American firm could use an NYSE listing to bond its insiders to better governance standards, why couldn’t foreign firms do the same? In an oft-cited 1999 article, Jack Coffee argues that they do just that: In other cases, however, the cross-listing may not entail corporate governance improvements. The cross-listing literature refers to differences in investor protection in three separate respects. In practice, however, foreign issuers can easily obtain an exemption from corporate governance listing requirements. The notion that corporations can self-improve their corporate governance by opting into a foreign country’s legal and regulatory regime through cross-listing has made considerable inroads into the legal and finance literature.
Natural Orifice Endoscopic Surgery (NOTES) Techniques for Full Thickness R0 Endoscopic Resection of Deep Seated Subepithelial Tumors (SETs): First U.S. Cases: Presidential Poster (2013)

Purpose: Most UGI SETs are GISTs, potentially malignant tumors. Many guidelines recommend surgery for suspected GISTs ≥2 cm and endoscopic surveillance of those <2 cm. This approach creates a large burden of surgery and endoscopy for small SETs the majority of which are low risk. This situation motivated endoscopists, mostly from Asia, to use ESD to “enucleate” muscularis propria (MP) based SETs. However, such enucleation may leave microscopic residual tumor within the MP. Recently, pioneering Asian centers reported two endoscopic techniques that achieve R0 en bloc resection of MP-based SETs: Submucosal Tunnel Endoscopic Resection (STER)--an offshoot of POEM utilizing the submucosal tunnel method to ensure secure closure of the full-thickness defect in the wall of the GI tract--and endoscopic full-thickness resection (EFTR)-direct full thickness resection with closure of the defect with clips or sutures. We report possibly the first series of EFTR and STER in the U.S. Methods: Procedures were performed from 4/2012-5/2013. Lesion location/size, knives, anesthesia, ASA class, length of procedure, closure technique, histologic diagnosis, adverse events (AEs), and length of stay (LOS) were retrieved from a prospectively maintained database. Results: Fourteen resections (12 EFTRs, 2 STERs) were performed (all procedures but one by one operator, SNS, a gastroenterologist with extensive POEM and ESD experience; one procedure was performed by PZ as part of a live course at our institution). Mean age 61 years (44-83). ASA Class I 14%, II 64%, III 22%. Anesthesia: General 4/14, propofol 10/14. Specialized ESD knives used in all cases (IT2, Hybrid, Hook). SET location: 1 esophagus, 1 GE junction, 10 stomach, 1 sigmoid colon, 1 rectum. 8 GISTs, 4 leiomyomas, 1 schwannoma, 1 leiomyosarcoma. Mean size 25 mm (12-55). Mean resection time 72 minutes (21-170). Closure: endoclips 7/14, endoscopic suturing 4/14, both 3/14. All patients were admitted mainly for observation. Mean LOS 1.8 days (1-3). Complete en bloc resection was achieved in all cases. One minor AE (venting of capnoperitoneum). Conclusion: Unlike traditional ESD, EFTR and STER achieve en bloc R0 resection of moderately sized MP-based SETs. We present the first series of such cases in the U.S. The excellent outcomes probably reflect our extensive experience with POEM, advanced closure techniques, and ESD for SETs. EFTR and STER represent a NOTES alternative to laparoscopic wedge resection. Advantages include: 1. Incisionless approach, 2. “Wedge” resection of SETs at locations where laparoscopic “wedge” resection is challenging or impossible such as the GE junction, esophagus and gastric cardia, and 3. Definitive diagnosis and complete resection obviating any further endoscopic surveillance for low risk lesions. Disclosure - Stavros Stavropoulos ERBE honorarium and Boston Scientific honorarium
Crowdsourcing for Deployable Intelligent Systems (2013)

My work aims to create a scaffold for deployable intelligent systems using crowdsourcing. Current approaches in artificial intelligence (AI) typically focus on solving a narrow subset of problems in a given space - for example: automatic speech recognition as part of a conversational assistant, machine vision as part of a question answering service for blind people, or planning as part of a home assistive robot. This approach is necessary to scope the solution, but often results in a large number of systems that are rarely deployed in real-world setting, but instead operate in toy domains, or in situations where other parts of the problem are assumed to be solved. The framework I have developed aims to use the crowd to help in two ways: (i) make it possible to use human intelligence to power parts of a system that automated approaches cannot or do not yet handle, and (ii) provide a means of enabling more effective deployable systems by people to provide reliable training data on-demand. This summary begins with a brief review of prior work, then outlines a number of different system that I have developed to demonstrate the capabilities of this framework, and concludes with future work to be completed as part of my thesis.
Figure S1 from Bone Marrow Mesenchymal Stem Cells Induce Metabolic Plasticity in Estrogen Receptor–Positive Breast Cancer (2023)

&lt;p&gt;Figure S1. Representative images of NADH lifetimes for various experimental conditions. Cell type of interest is bolded in co-culture comparisons. Top row of images denotes cancer cells marked with nuclear mCherry. Pseudocolor scale depicts high (red) and low (blue) NADH lifetime. Scale bar = 50 µm. A) HS5 and HS27a MSCs in monoculture. B-C) MCF7 (B) or T47D (C) cells in monoculture or with conditioned media (CM) from listed MSCs. D) HCC1428 (HCC) cancer cells in monoculture, CM from MSCs, or direct co-culture with MSCs.&lt;/p&gt;
The role of mesophyll conductance during water stress and recovery in tobacco (Nicotiana sylvestris): acclimation or limitation? (2009)

While the responses of photosynthesis to water stress have been widely studied, acclimation to sustained water stress and recovery after re-watering is poorly understood. In particular, the factors limiting photosynthesis under these conditions, and their possible interactions with other environmental conditions, are unknown. To assess these issues, changes of photosynthetic CO 2 assimilation (A N ) and its underlying limitations were followed during prolonged water stress and subsequent re-watering in tobacco (Nicotiana sylvestris) plants growing under three different climatic conditions: outdoors in summer, outdoors in spring, and indoors in a growth chamber. In particular, the regulation of stomatal conductance (g s ), mesophyll conductance to CO 2 (g m ), leaf photochemistry (chlorophyll fluorescence), and biochemistry (V c,max ) were assessed. Leaf gas exchange and chlorophyll fluorescence data revealed that water stress induced a similar degree of stomatal closure and decreased A N under all three conditions, while V c,max was unaffected. However, the behaviour of g m differed depending on the climatic conditions. In outdoor plants, g m strongly declined with water stress, but it recovered rapidly (1-2 d) after re-watering in spring while it remained low many days after re-watering in summer. In indoor plants, g m initially declined with water stress, but then recovered to control values during the acclimation period. These differences were reflected in different velocities of recovery of A N after re-watering, being the slowest in outdoor summer plants and the fastest in indoor plants. It is suggested that these differences among the experiments are related to the prevailing climatic conditions, i.e. to the fact that stress factors other than water stress have been superimposed (e.g. excessive light and elevated temperature). In conclusion, besides g s , g m contributes greatly to the limitation of photosynthesis during water stress and during recovery from water stress, but its role is strongly dependent on the impact of additional environmental factors.