gebhart/patrepeval huggingface dataset:
Single-Molecule Studies of Nucleic Acids and Their Proteins (2018)

This book presents a comprehensive overview of the foundations of single-molecule studies, based on manipulation of the molecules and observation of these with fluorescent probes. It first discusses the forces present at the single-molecule scale, the methods to manipulate them, and their pros and cons. It goes on to present an introduction to single-molecule fluorescent studies based on a quantum description of absorption and emission of radiation due to Einstein. Various considerations in the study of single molecules are introduced (including signal to noise, non-radiative decay, triplet states, etc.) and some novel super-resolution methods are sketched. The elastic and dynamic properties of polymers, their relation to experiments on DNA and RNA, and the structural transitions observed in those molecules upon stretching, twisting, and unzipping are presented. The use of these single-molecule approaches for the investigation of DNA–protein interactions is highlighted via the study of DNA and RNA polymerases, helicases, and topoisomerases. Beyond the confirmation of expected mechanisms (e.g., the relaxation of DNA torsion by topoisomerases in quantized steps) and the discovery of unexpected ones (e.g., strand-switching by helicases, DNA scrunching by RNA polymerases, and chiral discrimination by bacterial topoII), these approaches have also fostered novel (third generation) sequencing technologies.
Cytokine Gene Expression in a Mouse Model: The First Instillations With Viable bacillus Calmette-Guerin Determine the Succeeding Th1 Response (2003)

The model seems an appropriate one in which to investigate changes in Th1 and Th2 cytokine gene expression levels in bladders resulting from modifications in intravesical BCG treatment. It was possible to induce a local Th1 cytokine response with nonviable BCG provided that local sensitization to BCG antigens had occurred during preceding instillations with a viable BCG preparation. Whether such an approach could decrease BCG therapy toxicity, while maintaining antitumor efficacy, remains to be further investigated in patients.
Full-load-range-ZVS hybrid DC-DC converter with two full-bridges for high-power battery charging (1999)

A novel soft switching DC-DC power converter is proposed that is ideal for high-power battery charging applications. Its main advantages are zero-switching under all operating conditions without significant conduction loss penalty, and significantly lower filter requirement compared to conventional power converters. The application of the proposed converter for high-power battery charging is discussed along with simulation and experimental results.
Synthesis and crystal structure of pseudo-sandwich-type heteropolytungstates functionalized by organometallic ruthenium(ii) (2009)

The reaction between [XW(9)O(34)](9-) (X = As, P) and [RuC(6)H(6)Cl(2)](2) in aqueous buffer solution (pH 6.0) leads to the isolation of two pseudo-sandwich-type heteropolytungstates KNa(6)[(RuC(6)H(6))AsW(9)O(34)] x 17 H(2)O (As-1) and Na(7)[(RuC(6)H(6))PW(9)O(34)] x 14 H(2)O (P-2). Single-crystal X-ray diffraction analyses reveal that the two compounds have the following features: (1) in two polyanions [(RuC(6)H(6))XW(9)O(34)](7-) (X = As, 1; P, 2), the (RuC(6)H(6)) unit is linked via three Ru-O(W) bridges to the side of the trilacunary polyanion, while the lacunary site is still free; (2) the units 1 and 2 are connected exclusively by a central Na cation cluster to form the pseudo-sandwich-type heteropolytungstates; and (3) the pseudo-sandwich-type heteropolytungstates are further connected by Na or K cations to construct the 2D and 3D structures. Furthermore, the electrochemical behaviours of As-1 and P-2 in aqueous solution (1.0 M LiCl + HCl, pH 3.0) have been investigated. Two compounds exhibit the expected reduction processes of the W atoms in a negative potential range and the oxidation of the Ru center in a positive potential range. The results of the electrocatalytic experiments reveal that the compound P-2 has electrocatalytic activity towards the reduction of nitrate.
ChemInform Abstract: N,N‐Dibenzyl Formamidine as a New Protective Group for Primary Amines. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
P3‐017: ASSOCIATION ANALYSIS OF RARE VARIANTS NEAR THE APOE REGION WITH CEREBROSPINAL FLUID (CSF) BIOMARKERS OF ALZHEIMER'S DISEASE (2014)

The APOE ε4 allele is the most significant common genetic risk factor for late onset Alzheimer's disease (LOAD). The region surrounding APOE on chromosome 19 has shown consistent association signals with LOAD. However, common variants in the region remain significant after adjusting for APOE ε4 (Jun et al, 2012). We report a rare variant association analysis of genes in the vicinity of APOE with cerebrospinal fluid (CSF) biomarkers of LOAD. A whole genome sequencing (WGS) data set (N=815) from the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort was used in this analysis. 576 non-Hispanic Caucasian participants underwent WGS from a blood sample and had CSF biomarkers at baseline. We extracted all rare variants (MAF < 0.05) within a 300 Kb region in APOE' s vicinity including 9 Genes (Table 1). We assessed CSF biomarkers as LOAD-related quantitative endophenotypes. Gene-based analyses of rare variants were performed using the optimal Sequence Kernel Association Test (SKAT-O). Age, sex, and number of APOE ε4 alleles were used as covariates. A total of 2,608 rare or low frequency variants (MAF < 0.05) were found within a region of ±10Kb from 9 genes near APOE. Among them, 76 rare non-synonymous variants were observed. All 8 genes except APOC4 spanning the entire region were significantly associated with CSF Aβ 1-42 with TOMM40 showing near genome-wide level significance (p < 5 X 10 -7) (Table 1). However, gene-based analysis resulted in greatly diminished associations after adjusting for APOE ε4 allele count. Only 3 genes (CBLC, BCAM, APOE) remained significant after correcting for the number of tests (p < 0.05/9 = 0.0056). Particularly noteworthy were rare variants in APOE that showed significant association independent of ε4 allele count. Rare variants within genes near the APOE region are significantly associated with CSF Aβ 1-42 after adjusting for APOE ε4 allele count. BCAM may meditate intracellular signaling and CBLC plays important roles in cell signaling. These findings warrant further investigation and illustrate the role of next generation sequencing in assessing rare variants which may in turn help explain missing heritability in AD and other complex diseases.
A system to acquire and record physiological and behavioral data remotely from nonhuman primates (1991)

We describe an integrated system to record physiological and behavioral variables from nonhuman primates in social groups. The system records data simultaneously from two animals in family groups of five. It synchronizes behavioral and physiological data within 16 ms, either on-line or from recordings. Behavioral data are entered by trained observers on-line or from videotape. Recordings of physiological data are produced on-line as stripchart records, tape recordings on the audio channels of video cassettes, and magnetic disk files. The physiological data include two arterial blood flows, arterial blood pressure and heart rate. The data are transmitted from freely behaving animals to a central site via radio telemetry. The infrared link controls the radio transmitter and physiological signal processing electronics, as well as two sources of drugs for each animal. All of the electronics are contained in a small, light backpack that can be worn by either male or female baboons.
Tailoring chain structures of l-lactide and ε-caprolactone copolyester macromonomers using rac-binaphthyl-diyl hydrogen phosphate-catalyzed ring-opening copolymerization with monomer addition strategy (2017)

<italic>rac</italic>-BNPH catalyzed ring-opening copolymerization of <sc>l</sc>-lactide and ε-caprolactone with monomer addition strategy effectively tailoring chain structures of macromonomers.
Pulmonary interstitial emphysema: selective bronchial occlusion with a Swan-Ganz catheter. (1988)

A 26 week preterm infant ventilated for hyaline membrane disease developed severe pulmonary interstitial emphysema with extensive right sided bullous formation, mediastinal shift, and subsequent left sided atelectasis. A paediatric Swan-Ganz catheter was used for selective bronchial occlusion with dramatic improvement in the infant9s clinical condition and radiographic findings.
Real-time Photoinduced Waveguides in Sn2P2S6 Bulk Crystals with Visible or Near Infrared Light (2007)

http://www.opticsinfobase.org//abstract.cfm?URI=PR-2007-TuB3
Wafer Test Cavity - Linking Surface Microstructure to RF Performance: a ‘Short-Sample Test Facility’ for characterizing superconducting materials for SRF cavities (2014)

The Wafer Test cavity was designed to create a short sample test system to determine the properties of the superconducting materials and S-I-S hetero-structures. The project, funded by ARRA, was successful in accomplishing several goals to achieving a high gradient test system for SRF research and development. The project led to the design and construction of the two unique cavities that each severed unique purposes: the Wafer test Cavity and the Sapphire Test cavity. The Sapphire Cavity was constructed first to determine the properties of large single crystal sapphires in an SRF environment. The data obtained from the cavity greatly altered the design of the Wafer Cavity and provided the necessary information to ascertain the Wafer Test cavity’s performance.
Using metabolite profiling to construct and validate a metabolite risk score for predicting future weight gain (2019)

We have constructed and validated a generalizable MRS for future weight gain that is an independent predictor distinct from several other known risk factors. The MRS captures a composite biological picture of weight gain, perhaps hinting at the anabolic effects of preserved insulin sensitivity. Future investigation is required to assess the relationships between MRS-predicted weight gain and other obesity-related diseases.
Alpha-fetoprotein Structure and Function: Relevance to Isoforms, Epitopes, and Conformational Variants (2001)

Mammalian alpha-fetoprotein (AFP) is classified as a member of the albuminoid gene superfamily consisting of albumin, AFP, vitamin D (Gc) protein, and alpha-albumin. Molecular variants of AFP have long been reported in the biomedical literature. Early studies identified isoelectric pH isoforms and lectin-binding variants of AFP, which differed in their physicochemical properties, but not in amino acid composition. Genetic variants of AFP, differing in mRNA kilobase length, were later extensively described in rodent models during fetal/perinatal stages, carcinogenesis, and organ regeneration. With the advent of monoclonal antibodies in the early 1980s, multiple antigenic epitopes on native AFP were detected and categorized, culminating in the identification of six to seven major epitopes. During this period, various AFP-binding proteins and receptors were reported to inhibit certain AFP immunoreactions. Concomittantly, human and rodent AFP were cloned and the amino acid sequences of the translated proteins were divulged. Once the amino acid composition of the AFP molecule was known, enzymatic fragments could be identified and synthetic peptide segments synthesized. Following discovery of the molten globule form in 1981, the existence of transitory, intermediate forms of AFP were acknowledged and their physiological significance was realized. In the present review, the various isoforms and variants of AFP are discussed in light of their potential biological relevance.
Intrinsic dechlorination of 1,2-dichloroethane at an industrial site (1998)

Bioremediation strategies for an industrial site located in the Rotterdam Harbor Area, the Netherlands and contaminated with 1,2-dichloroethane (1,2-DCA), are under investigation. The contamination is present in a confined anaerobic aquifer. The objective of the research is to assess the potential of intrinsic (bio )degradation and enhanced biodegradation as effective risk reducing measures. Close to the contaminant source, 1,2-DCA is present at concentrations up to 500 mg per liter. From the possible intrinsic dechlorination products of 1,2-DCA (i.e. 2-chloroethanol, vinylchloride, chloroethane and ethene), vinylchloride (VC) is occuring at relatively high concentrations (up to 2 mg/liter). The type, rate and parameter dependency of the dechlorination processes occurring in this aquifer are currently being investigated by analyzing groundwater concentration profiles of the dechlorination products and by performing laboratory studies with material from the contaminated site. First results indicate that natural attenuation alone, is not sufficient to prevent the plume from further spreading. Therefore a field study at pilot-scale is underway to evaluate remediation strategies which are designed from screening studies at the laboratory scale.
The Role of Temperature on the Degree of End-Closing and Filling of Single-Walled Carbon Nanotubes (2021)

Carbon nanotubes (CNTs), owing to their high surface area-to-volume ratio and hollow core, can be employed as hosts for adsorbed and/or encapsulated molecules. At high temperatures, the ends of CNTs close spontaneously, which is relevant for several applications, including catalysis, gas storage, and biomedical imaging and therapy. This study highlights the influence of the annealing temperature in the range between 400 and 1100 °C on the structure and morphology of single-walled CNTs. The nitrogen adsorption and density functional theory calculations indicate that the fraction of end-closed CNTs increases with temperature. Raman spectroscopy reveals that the thermal treatment does not alter the tubular structure. Insight is also provided into the efficacy of CNTs filling from the molten phase, depending on the annealing temperature. The CNTs are filled with europium (III) chloride and analyzed by using electron microscopy (scanning electron microscopy and high-resolution transmission electron microscopy) and energy-dispersive X-ray spectroscopy, confirming the presence of filling and closed ends. The filling yield increases with temperature, as determined by thermogravimetric analysis. The obtained results show that the apparent surface area of CNTs, fraction of closed ends, and amount of encapsulated payload can be tailored via annealing.
Genomics via Optical Mapping (I): 0-1 Laws for Mapping with Single Molecules (2013)

ABSTRACT The genomic data that can be collected from a single DNA molecule by the best chemical and optical methods (e.g., using technologies from OpGen, BioNanoGenomics, NABSys, PacBio, etc.) are badly corrupted by many poorly understood noise processes. Thus, single molecule technology derives its utility through powerful probabilistic modeling, which can provide precise lower and upper bounds on various experimental parameters to create the correct map or validate sequence assembly. As an example, this analysis shows how as the number of “imaged” single molecules (i.e., coverage) is increased in the optical mapping data, the probability of successful computation of the map jumps from 0 to 1 for fairly small number of molecules.
Operation of a neural network controlled crystal oscillator (2002)

The neural network control of a quartz oscillator has been demonstrated. We have shown that a single neural network can correct an oscillator's output frequency while several environmental sources of frequency shift act on the oscillator. The advantage that a neural network offers over microprocessor controlled oscillators or Kalman filter control techniques is that a neural network does not need an a priori model of the physical system to arrive at the correct control algorithm. The results of this demonstration indicate that a neural network can have beneficial applications in a variety of frequency standard devices. We believe that the neural controller will work best as a control system supervisor, rather than as the main controller of the frequency standard system. Specifically, the neural network would learn the non-linear effects associated with the several servos that control the main physical parameters of a frequency standard (temperature, magnetic field, etc.), and correct the oscillator's frequency based on the state of these servos and any additional sensed environmental parameters. The dominant remaining technical issue is the training of the neural network. During this demonstration program, maintaining a stable, reproducible environment that could be varied quickly and randomly over the whole training parameter space proved to be a significant technological challenge. Future efforts will focus on methods to more efficiently train the neural networks and the identification of specific devices.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Theoretical Study of the UV/Visible Absorption and Emission Solvatochromic Properties of Solvent‐Sensitive Dyes (2003)

Using the density-functional vertical self-consistent reaction field (VSCRF) solvation model, incorporated with the conductor-like screening model (COSMO) and the self-consistent reaction field (SCRF) methods, we have studied the solvatochromic shifts of both the absorption and emission bands of four solvent-sensitive dyes in different solutions. The dye molecules studied here are: S-TBA merocyanine, Abdel-Halim's merocyanine, the rigidified amino-coumarin C153, and Nile red. These dyes were selected because they exemplify different structural features likely to impact the solvent-sensitive fluorescence of "push-pull", or merocyanine, fluorophores. All trends of the blue or red shifts were correctly predicted, comparing with the experimental observations. Explict H-bonding interactions were also considered in several protic solutions like H2O, methanol and ethanol, showing that including explicit H-bonding solvent molecule(s) in the calculations is important to obtain the correct order of the excitation and emission energies. The geometries, electronic structures, dipole moments, and intra- and intermolecular charge transfers of the dyes in different solvents are also discussed.
Protective effects of chronic mild stress during adolescence in the low-novelty responder rat (2015)

Stress-elicited behavioral and physiologic responses vary widely across individuals and depend on a combination of environmental and genetic factors. Adolescence is an important developmental period when neural circuits that guide emotional behavior and stress reactivity are still maturing. A critical question is whether stress exposure elicits contrasting effects when it occurs during adolescence versus adulthood. We previously found that Sprague-Dawley rats selectively bred for low-behavioral response to novelty (bred Low Responders; bLRs) are particularly sensitive to chronic unpredictable mild stress (CMS) exposure in adulthood, which exacerbates their typically high levels of spontaneous depressive- and anxiety-like behavior. Given developmental processes known to occur during adolescence, we sought to determine whether the impact of CMS on bLR rats is equivalent when they are exposed to it during adolescence as compared with adulthood. Young bLR rats were either exposed to CMS or control condition from postnatal days 35-60. As adults, we found that CMS-exposed bLRs maintained high levels of sucrose preference and exhibited increased social exploration along with decreased immobility on the forced swim test compared with bLR controls. These data indicate a protective effect of CMS exposure during adolescence in bLR rats.
The Impact of Premenstrual Symptomatology on Functioning and Treatment-Seeking Behavior: Experience from the United States, United Kingdom, and France (1999)

Up to 80% of women experience mood and physical symptoms associated with the menstrual cycle. This study assessed the impact of premenstrual symptomatology on functioning and treatment-seeking behavior for a community-based sample of women in the United States, United Kingdom, and France. A sample of 1045 menstruating women (aged 18-49) completed a telephone questionnaire that measured, at a point in time, premenstrual symptoms, impact on functioning, and treatment-seeking behavior. Results were generally consistent across the three countries. Irritability/anger, fatigue, and physical swelling/bloating, or weight gain were among the most commonly reported symptoms (approximately 80%). Functional impairment tended to be highest at home, followed by social, school, and occupational situations. Among working women, over 50% reported at least somewhat affected occupational functioning. Of women who ever missed work because of symptoms, 1-7 days were missed in the past year. Almost three fourths of the women had never sought treatment, and symptom severity was an important factor in treatment-seeking behavior. Treatment with selective serotonin reuptake inhibitors (SSRIs), which have demonstrated efficacy in this population, occurred with surprisingly low frequency. The functional impairment of premenstrual symptomatology (home, social, and occupational) and treatment-seeking behavior is consistent across countries. Women who experience more impairment are more likely to have severe symptoms and are more likely to believe, relative to women with less severe symptoms, that no treatment is available. This suggests significant unmet medical need in this more severely affected population. Improved clinical identification of these women and increasing awareness of the efficacy of SSRIs in treating premenstrual symptomatology may be of benefit.
Insights into the capping and structure of MoS2 nanotubes as revealed by aberration-corrected STEM (2010)

Aberration-corrected electron microscopy (STEM-HAADF) has been used for the first time to understand the capping, nature and structure of the MoS(2) nanotubes. The MoS(2) nanotubes that have been obtained have various unusual faceted caps presumably arising from the presence of topological defects. A detailed study of the capping of the nanotubes, along with identification that the MoS(2) nanotubes are of the zigzag type have been carried out using both experimental and simulated STEM images. The presence of 3R-rhombohedral stacking of the MoS(2) nanotubes has been identified.