gebhart/patrepeval huggingface dataset:
A high molecular weight antifertility factor from human seminal plasma (1979)

The presence of a high molecular weight antifertility factor in human seminal plasma was established. The factor can be precipitated by centrifugation at 104 000 g. Its activity is maximal when the protein concentration reaches 150 micrograms/10(5) spermatozoa using the mouse in-vitro fertilization assay as the test system. The factor is heat labile but its activity is not affected by dialysis. It prevents the penetration of the spermatozoa through the layers surrounding the egg but has no effect on the fusion of the spermatozoa with the vitelline membrane. The factor is only partly removed from spermatozoa by washing but is completely dispersed when the spermatozoa are incubated in capacitation medium. The pellet that is precipitated from the seminal plasma does not contain any particles or vesicles. However, it is significantly contaminated with low molecular weight material. This material includes the acrosin inhibitor which is present in large enough quantities to hinder fertilization. Washing the pellet twice with H2O removes these low molecular weight compounds, as indicated by the absence of the acrosin inhibitor, but has no effect on the antifertility properties of the pellet. Therefore, before further study or purification of the factor, it is essential that the pellet is washed such low molecular weight material. The washed pellet consists of at least 7 components as judged by disc gel electrophoresis.
Geometry of a complex formed by double strand break repair proteins at a single DNA end: recruitment of DNA-PKcs induces inward translocation of Ku protein (1999)

Ku protein and the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) are essential components of the double-strand break repair machinery in higher eukaryotic cells. Ku protein binds to broken DNA ends and recruits DNA-PKcs to form an enzymatically active complex. To characterize the arrangement of proteins in this complex, we developed a set of photocross-linking probes, each with a single free end. We have previously used this approach to characterize the contacts in an initial Ku-DNA complex, and we have now applied the same technology to define the events that occur when Ku recruits DNA-PKcs. The new probes allow the binding of one molecule of Ku protein and one molecule of DNA-PKcs in a defined position and orientation. Photocross-linking reveals that DNA-PKcs makes direct contact with the DNA termini, occupying an approximately 10 bp region proximal to the free end. Characterization of the Ku protein cross-linking pattern in the presence and absence of DNA-PKcs suggests that Ku binds to form an initial complex at the DNA ends, and that recruitment of DNA-PKcs induces an inward translocation of this Ku molecule by about one helical turn. The presence of ATP had no effect on protein-DNA contacts, suggesting that neither DNA-PK-mediated phosphorylation nor a putative Ku helicase activity plays a role in modulating protein conformation under the conditions tested.
Purification and Identification of Anti-Oxidant Soybean Peptides by Consecutive Chromatography and Electrospray Ionization-Mass Spectrometry (2013)

Ultrafiltration, ion-exchange chromatography, and gel filtration chromatography were used to purify anti-oxidant peptides from hydrolysates of soybean protein isolates. The <1-kD peptides were found to exhibit much higher anti-oxidant activity as compared to larger ones. Also, the alkaline peptide fractions were shown to have stronger anti-oxidant capacity than acidic and neutral peptides. Interestingly, an anti-oxidant tripeptide, Ser-Phe-Val (352.4 Da), was identified by reversed-phase high-performance liquid chromatography (RP-HPLC) connected online to electrospray ionization mass spectrometry. The tripeptide was further prepared by fluorenylmethoxycarbonyl (Fmoc) solid-phase synthesis and was found to have a dose-dependent protective effect against hydrogen peroxide (H2O2)-induced injuries in rat adrenal pheochromocytoma (PC12) cells.
An Analysis of the SURF Method (2015)

The SURF method (Speeded Up Robust Features) is a fast and robust algorithm for local, similarity invariant representation and comparison of images. Similarly to many other local descriptor-based approaches, interest points of a given image are defined as salient features from a scale-invariant representation. Such a multiple-scale analysis is provided by the convolution of the initial image with discrete kernels at several scales (box filters). The second step consists in building orientation invariant descriptors, by using local gradient statistics (intensity and orientation). The main interest of the SURF approach lies in its fast computation of operators using box filters, thus enabling real-time applications such as tracking and object recognition. The SURF framework described in this paper is based on the PhD thesis of H. Bay [ETH Zurich, 2009], and more specifically on the paper co-written by H. Bay, A. Ess, T. Tuytelaars and L. Van Gool [Computer Vision and Image Understanding, 110 (2008), pp. 346–359]. An implementation is proposed and used to illustrate the approach for image matching. A short comparison with a state-of-the-art approach is also presented, the SIFT algorithm of D. Lowe [International Journal of Computer Vision, 60 (2004), pp. 91–110], with which SURF shares a lot in common.
Thioflavin T as a Molecular Rotor: Fluorescent Properties of Thioflavin T in Solvents with Different Viscosity (2008)

The effect of solvent viscosity on thioflavin T (ThT) fluorescent properties is analyzed to understand the molecular mechanisms of the characteristic increase in ThT fluorescence intensity accompanying its incorporation into the amyloid-like fibrils. To this end, the dependencies of the ThT quantum yield and fluorescence lifetime on temperature and glycerol content in the water-glycerol mixtures are studied. It has been found that fluorescent properties of ThT are typical for the specific class of fluorophores known as molecular rotors. It has been established that the low ThT fluorescence intensity in the solvents with low viscosity is caused by the nonradiative deactivation of the excited state associated with the torsional motion of the ThT benzthiazole and aminobenzene rings relative to each other, which results in the transition of ThT molecule to nonfluorescent twisted internal charge transfer (TICT) state. The rate of this process is determined by the solvent viscosity, whereas the emission does occur from the nonequilibrium locally excited (LE) state. High polarization degree of the ThT fluorescence (P = 0.45) observed for glycerol solutions of different viscosity confirms the nonequilibrium character of the emission from the LE state and testifies that rotational correlation time of the whole molecule is considerably greater than the time required to accomplish transition to the nonfluorescent TICT state. Torsional movements of the ThT fragments take place in the same temporal interval as solvent relaxation, which leads to nonexponential fluorescence decay of the dye in viscous solvents. This photophysical model successfully explains the fluorescent properties of ThT in solvents with different viscosities. The model is confirmed by the results of the quantum-chemical calculations, which showed that energy minimum for the ground state of ThT corresponds to conformation with torsional angle phi = 37 degrees between the benzthiazole and aminobenzene rings and in the excited-state twisted conformation of ThT with phi = 90 degrees has minimal energy. These data support the idea that the reason for the characteristic increase in the ThT fluorescence intensity accompanying its incorporation into the amyloid fibrils is determined by the rigidity of the dye environment, which prevents the rotation of the benzthiazole ring relative to the aminobenzene ring in the excited state.
Retracted: Neuroprotection mediated by glial group‐II metabotropic glutamate receptors requires the activation of the MAP kinase and the phosphatidylinositol‐3‐kinase pathways (2001)

The mGlu2/3 receptor agonists 4-carboxy-3-hydroxyphenylglycine (4C3HPG) and LY379268 attenuated NMDA toxicity in primary cultures containing both neurons and astrocytes. Neuroprotection was abrogated by PD98059 and LY294002, which inhibit the mitogen activated protein kinase (MAPK) and the phosphatidylinositol-3-kinase (PI-3-K) pathways, respectively. Cultured astrocytes lost the ability to produce transforming growth factor-beta1 (TGF-beta1) in response to mGlu2/3 receptor agonists when co-incubated with PD98059 or LY294002. As a result, the glial medium was no longer protective against NMDA toxicity. Activation of the MAPK and PI-3-K pathways in cultured astrocytes treated with 4C3HPG or LY379268 was directly demonstrated by an increase in the phosphorylated forms of ERK-1/2 and Akt. Similarly to that observed in the culture, intracerebral or systemic injections of mGlu2/3 receptor agonists enhanced TGF-beta1 formation in the rat or mouse caudate nucleus, and this effect was reduced by PD98059. PD98059 also reduced the ability of LY379268 to protect striatal neurons against NMDA toxicity. These results suggest that activation of glial mGlu2/3 receptors induces neuroprotection through the activation of the MAPK and PI-3-K pathways leading to the induction of TGF-beta.
Depth profiling of absorbing soft materials using photoacoustic methods (1999)

A Q-switched, frequency doubled, Nd:YAG laser coupled to an optical parametric oscillator generated 4.75-ns laser pulses at 726 nm to create subsurface acoustic waves in India ink solutions, India ink acrylamide gels, and in flat segments of elastin biomaterial stained with India ink. The acoustic waves traveled through the target and were detected by a piezoelectric transducer. The waveforms were converted to measurements of initial laser induced pressure and temperature as functions of depth in the material. An algorithm based on Beer's Law was developed and applied to the acoustic signals to extract information about the absorption coefficient as a function of depth in the samples.
A Boron Alkylidene–Alkene Cycloaddition Reaction: Application to the Synthesis of Aphanamal (2017)

We describe an unusual net [2+2] cycloaddition reaction between boron alkylidenes and unactivated alkenes. This reaction provides a new method for the construction of carbocyclic ring systems bearing versatile organoboronic esters. Aside from surveying the scope of this reaction, we provide details about the mechanistic underpinnings of this process, and examine its application to the synthesis of the natural product aphanamal.
Chemical Control of Cancer (1972)

Improvement of the present mortality from cancer depends upon a means of controlling those cancers that have spread from the original site to distant organs. Killing of tumor cells by means of drugs, whether used by themselves or in combination with surgery or irradiation, provides the strategy most likely to achieve this goal in the near future. There are now 10 disseminated cancers in man wherein drug treatment has resulted in normal life expectancy. The biological pattern of growth of these tumors is different from that of the tumors that have not been so susceptible to drugs. The new knowledge concerning the interdependence of growth pattern and drug susceptibility has led to rational animal models for selection of active drugs, in which more confidence can be placed than upon empiric models. Similarly, the prediction of drug toxicity and pharmacology from animal models has been placed on a firm scientific base. Recent developments in molecular biochemistry hold forth the hope that some day the selection of safe and effective antitumor drugs may be based on a knowledge of in vitro biochemistry.
Carrier Frequency Offset Estimation for OFDMA Uplink Using Multi-Antenna (2010)

In this paper, a novel method is proposed for carrier-frequency offset (CFO) estimation for multi-user in orthogonal frequency division multiple access (OFDMA) uplink. Generalized carrier assignment scheme (GCAS) is supported in order to allow dynamic resource allocation and provide more flexility. The base station is equipped with multi-antenna. Each user's CFO can be estimated by a closed form based on ESPRIT-like method utilizing the rotation invariance of the space-domain snapshot matrix. The method is still effective even in fully loaded system with all subcarriers allocated to users, and the computational complexity can be adjusted dynamically according to the system assignment scheme.
The social challenge of laptops in the learning environment (2006)

This case study is an exploration of the social challenges surrounding laptops in the learning environment. Student engagement, the use of the laptop and professional development are the major components of this study. The ethnographic design methods of interviewing and attendance at a laptop conference all informed this case study. The Eastern Townships School Board began implementing a laptop project in the Fall of 2003, it is the largest laptop integration in Canada and will be in full operation by the Fall of 2005 when grades 3--11 will be using Apple iBook laptops. The new laptop program is known as the Dennis McCullough Enhanced Learning Strategy (Enhanced Learning Strategy). The sample population of this research consisted of grade 5, grade 11 students, and teachers in the elementary and high schools with varying teaching experiences. The use of laptops in the classroom is a new field of research, with very little research data available from a Canadian perspective. In addition to adding to this body of work, the thesis discusses the challenge the teachers were facing when blending instructionist (passive learning) and constructionist (active learning) teaching practices
Submitted) Scalable quantum circuit and control for a superconducting surface code (2016)

We present a scalable scheme for executing the error-correction cycle of a monolithic surface-code fabric composed of fast-flux-tuneable transmon qubits with nearest-neighbor coupling. An eight-qubit unit cell forms the basis for repeating both the quantum hardware and coherent control, enabling spatial multiplexing. This control uses three fixed frequencies for all single-qubit gates and a unique frequency detuning pattern for each qubit in the cell. By pipelining the interaction and readout steps of ancilla-based X- and Z-type stabilizer measurements, we can engineer detuning patterns that avoid all second-order transmon-transmon interactions except those exploited in controlled-phase gates, regardless of fabric size. Our scheme is applicable to defect-based and planar logical qubits, including lattice surgery.
Automatic Data Repair Overwrite Pulse for 3D-TLC NAND Flash Memories with 38x Data-Retention Lifetime Extension (2019)

This paper proposes Automatic Data Repair Overwrite Pulse (ADROP) to improve the reliability of 3D-TLC NAND flash. When ECC cannot correct errors, ADROP overwrites data including errors to failed memory cells and thus adaptively injects electrons to memory cells that were lost during the data-retention by the lateral charge migration and the vertical charge de-trap. As a result, the data-retention lifetime increases by 38.3-times. ADROP is composed of VTH Shift Recovery Pulse (VSRP) and Data Repair Pulse (DRP) that are implemented in the SSD controller without circuit area overhead.
Genetics and Pathogenesis of Feline Infectious Peritonitis Virus (2009)

Feline coronavirus (FCoV) is endemic in feral cat populations and cat colonies, frequently preceding outbreaks of fatal feline infectious peritonitis (FIP). FCoV exhibits 2 biotypes: the pathogenic disease and a benign infection with feline enteric coronavirus (FECV). Uncertainty remains regarding whether genetically distinctive avirulent and virulent forms coexist or whether an avirulent form mutates in vivo, causing FIP. To resolve these alternative hypotheses, we isolated viral sequences from FCoV-infected clinically healthy and sick cats (8 FIP cases and 48 FECV-asymptomatic animals); 735 sequences from 4 gene segments were generated and subjected to phylogenetic analyses. Viral sequences from healthy cats were distinct from sick cats on the basis of genetic distances observed in the membrane and nonstructural protein 7b genes. These data demonstrate distinctive circulating virulent and avirulent strains in natural populations. In addition, 5 membrane protein amino acid residues with functional potential differentiated healthy cats from cats with FIP. These findings may have potential as diagnostic markers for virulent FIP-associated FCoV.
ODE (Object Database and Environment): the language and the data model (1989)

ODE is a database system and environment based on the object paradigm. It offers one integrated data model for both database and general purpose manipulation. The database is defined, queried and manipulated in the database programming language O++ which is based on C++. O++ borrows and extends the object definition facility of C++, called the class. Classes support data encapsulation and multiple inheritance. We provide facilities for creating persistent and versioned objects, defining sets, and iterating over sets and clusters of persistent objects. We also provide facilities to associate constraints and triggers with objects. This paper presents the linguistic facilities provided in O++ and the data model it supports.
Schizochytrium limacinum SR-21 as a source of docosahexaenoic acid: optimal growth and use as a dietary supplement for laying hens (2006)

Culture conditions for the marine fungus Schizochytrium limacinum SR-21 (SR-21) to produce microbial docosahexaenoic acid (DHA) were evaluated, and the practicality of using this fungus product as a dietary supplement for laying Leghorn hens was investigated. The data showed that the cultured fungus produced high biomass and DHA. It generated 584 mg DHA/L of culture at the end of a 6-day culture. The fungus grew better at 25ºC than at 20ºC or 30ºC. With an increase in glucose concentration from 1% to 5% in the culture medium, biomass and DHA production were enhanced. A 6% glucose treatment reduced the biomass production compared with 5% glucose. A bioreactor was used to mass-produce SR-21. The biomass was increased from 1.12 g/L at Day 0 to 12 g/L at Day 4. We established optimal culture conditions of 5% glucose, 2% sea salt, and 1% yeast extract for SR-21. Three concentrations of dried fungal meal (0, 1, or 3% in the diet) were fed to birds over a 3-week period. There were no negative effects of 1 and 3% dietary SR-21 on egg production, egg weight, and egg yolk weight. The DHA content of yolk was increased by the dietary supplementation with the fungal meal both in the 1 and 3% treatments. Dietary fungal meal treatments increased the DHA concentrations of liver and plasma. However, dietary DHA enrichment had no effect on the expression of hepatic lipogenic genes in laying hens.
Characterization of the murine phosphatidylethanolamine N-methyltransferase-2 gene (1996)

Phosphatidylethanolamine N-methyltransferase (PEMT) catalyzes the conversion of phosphatidylethanolamine to phosphatidylcholine in the mammalian liver via three sequential methylations. In the present studies, we cloned and characterized the murine gene for PEMT2, the isoform of the enzyme that localized to the mitochondria-associated membrane. The structure of the gene was determined by analysis of two lambda and three P1 genomic clones, and compared to the known rat PEMT2 cDNA sequence. Southern blotting of mouse genomic DNA indicated that PEMT2 is a single-copy gene. The gene spans at least 35 kb, with seven exons and six introns. Two transcription start sites, 139 and 148 base pairs upstream of the translation start site, were detected by primer extension and reverse transcriptase-polymerase chain reaction. These experiments indicated that the PEMT2 gene is transcribed from a single promoter. Finally, the PEMT2 gene was localized to mouse chromosome 11 by interspecific backcrossing. These experiments represent the first cloning and characterization of a full-length mammalian gene involved in phospholipid biosynthesis.
A Pedagogical Note: Use of Telepractice to Link Student Clinicians to Diverse Populations (2016)

Telepractice is the application of telecommunications technology to the delivery of telehealth services via the online connection of clinicians, clients, and patients for assessment, intervention, or consultation. This article describes a pilot project in which speech-language pathology students in a university training program gained experience in working with culturally diverse preschool students using telepractice technology. The preschool students benefited by making gains in communication skills, while the university students acquired competency in the use of telepractice and in working with children whose cultural and linguistic backgrounds were outside of their experience. To assess the training experience, a Likert-scale survey administered to student clinicians revealed a high degree of satisfaction and improved familiarity with the use of telepractice, and an increased comfort level working with multi-cultural populations.
A Survey of Quantization Methods for Efficient Neural Network Inference (2021)

As soon as abstract mathematical computations were adapted to computation on digital computers, the problem of efficient representation, manipulation, and communication of the numerical values in those computations arose. Strongly related to the problem of numerical representation is the problem of quantization: in what manner should a set of continuous real-valued numbers be distributed over a fixed discrete set of numbers to minimize the number of bits required and also to maximize the accuracy of the attendant computations? This perennial problem of quantization is particularly relevant whenever memory and/or computational resources are severely restricted, and it has come to the forefront in recent years due to the remarkable performance of Neural Network models in computer vision, natural language processing, and related areas. Moving from floating-point representations to low-precision fixed integer values represented in four bits or less holds the potential to reduce the memory footprint and latency by a factor of 16x; and, in fact, reductions of 4x to 8x are often realized in practice in these applications. Thus, it is not surprising that quantization has emerged recently as an important and very active sub-area of research in the efficient implementation of computations associated with Neural Networks. In this article, we survey approaches to the problem of quantizing the numerical values in deep Neural Network computations, covering the advantages/disadvantages of current methods. With this survey and its organization, we hope to have presented a useful snapshot of the current research in quantization for Neural Networks and to have given an intelligent organization to ease the evaluation of future research in this area.